3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
61 <em>04/07/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
67 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
68 source project) rather than InstallAnywhere
71 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
72 settings, receive over the air updates and launch specific
73 versions via (<a href="https://github.com/threerings/getdown">Three
77 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
78 formats supported by Jalview (including .jvp project files)
81 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
82 arguments and switch between different getdown channels
85 <!-- JAL-3141 -->Backup files created when saving Jalview project
90 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
91 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
93 <!-- JAL-2620 -->Alternative genetic code tables for
94 'Translate as cDNA'</li>
96 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
97 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
100 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
101 implementation that allows updates) used for Sequence Feature collections</li>
103 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
104 features can be filtered and shaded according to any
105 associated attributes (e.g. variant attributes from VCF
106 file, or key-value pairs imported from column 9 of GFF
110 <!-- JAL-2879 -->Feature Attributes and shading schemes
111 stored and restored from Jalview Projects
114 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
115 recognise variant features
118 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
119 sequences (also coloured red by default)
122 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
126 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
127 algorithm (Z-sort/transparency and filter aware)
130 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
136 <!-- JAL-3205 -->Symmetric score matrices for faster
137 tree and PCA calculations
139 <li><strong>Principal Components Analysis Viewer</strong>
142 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
143 and Viewer state saved in Jalview Project
145 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
148 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
152 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
157 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
159 <li><strong>Speed and Efficiency</strong>
162 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
163 multiple groups when working with large alignments
166 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
170 <li><strong>User Interface</strong>
173 <!-- JAL-2933 -->Finder panel remembers last position in each
177 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
178 what is shown)<br />Only visible regions of alignment are shown by
179 default (can be changed in user preferences)
182 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
183 to the Overwrite Dialog
186 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
190 <!-- JAL-1244 -->Status bar shows bounds when dragging a
191 selection region, and gap count when inserting or deleting gaps
194 <!-- JAL-3132 -->Status bar updates over sequence and annotation
198 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
202 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
206 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
209 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
213 <!-- JAL-3181 -->Consistent ordering of links in sequence id
217 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
219 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
223 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
224 <li><strong>Java 11 Support (not yet on general release)</strong>
227 <!-- -->OSX GUI integrations for App menu's 'About' entry and
232 <em>Deprecations</em>
234 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
235 capabilities removed from the Jalview Desktop
237 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
238 unmarshalling has been replaced by JAXB for Jalview projects
239 and XML based data retrieval clients</li>
240 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
241 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
242 </ul> <em>Documentation</em>
244 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
245 not supported in EPS figure export
247 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
248 </ul> <em>Development and Release Processes</em>
251 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
254 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
256 <!-- JAL-3225 -->Eclipse project configuration managed with
260 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
261 Bamboo continuous integration for unattended Test Suite
265 <!-- JAL-2864 -->Memory test suite to detect leaks in common
269 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
273 <!-- JAL-3248 -->Developer documentation migrated to
274 markdown (with HTML rendering)
277 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
280 <!-- JAL-3289 -->New URLs for publishing development
285 <td align="left" valign="top">
288 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
291 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
292 superposition in Jmol fail on Windows
295 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
296 structures for sequences with lots of PDB structures
299 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
303 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
304 project involving multiple views
307 <!-- JAL-3164 -->Overview for complementary view in a linked
308 CDS/Protein alignment is not updated when Hide Columns by
309 Annotation dialog hides columns
312 <!-- JAL-3158 -->Selection highlighting in the complement of a
313 CDS/Protein alignment stops working after making a selection in
314 one view, then making another selection in the other view
317 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
321 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
322 Settings and Jalview Preferences panels
325 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
326 overview with large alignments
329 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
330 region if columns were selected by dragging right-to-left and the
331 mouse moved to the left of the first column
334 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
335 hidden column marker via scale popup menu
338 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
339 doesn't tell users the invalid URL
342 <!-- JAL-2816 -->Tooltips displayed for features filtered by
346 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
347 show cross references or Fetch Database References are shown in
351 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
352 peptide sequence (computed variant shown as p.Res.null)
355 <!-- JAL-2060 -->'Graduated colour' option not offered for
356 manually created features (where feature score is Float.NaN)
359 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
360 when columns are hidden
363 <!-- JAL-3082 -->Regular expression error for '(' in Select
364 Columns by Annotation description
367 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
368 out of Scale or Annotation Panel
371 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
375 <!-- JAL-3074 -->Left/right drag in annotation can scroll
379 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
383 <!-- JAL-3002 -->Column display is out by one after Page Down,
384 Page Up in wrapped mode
387 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
390 <!-- JAL-2932 -->Finder searches in minimised alignments
393 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
394 on opening an alignment
397 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
401 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
402 different groups in the alignment are selected
405 <!-- JAL-2717 -->Internationalised colour scheme names not shown
409 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
413 <!-- JAL-3125 -->Value input for graduated feature colour
414 threshold gets 'unrounded'
417 <!-- JAL-2982 -->PCA image export doesn't respect background
421 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
424 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
427 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
431 <!-- JAL-2964 -->Associate Tree with All Views not restored from
435 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
436 shown in complementary view
439 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
440 without normalisation
443 <!-- JAL-3021 -->Sequence Details report should open positioned at top
447 <!-- JAL-914 -->Help page can be opened twice
450 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
452 </ul> <em>Editing</em>
455 <!-- JAL-2822 -->Start and End should be updated when sequence
456 data at beginning or end of alignment added/removed via 'Edit'
460 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
461 relocate sequence features correctly when start of sequence is
462 removed (Known defect since 2.10)
465 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
466 dialog corrupts dataset sequence
469 <!-- JAL-868 -->Structure colours not updated when associated tree
470 repartitions the alignment view (Regression in 2.10.5)
472 </ul> <em>Datamodel</em>
475 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
476 sequence's End is greater than its length
478 </ul> <em>Bugs fixed for Java 11 Support (not yet on
479 general release)</em>
482 <!-- JAL-3288 -->Menus work properly in split-screen
484 </ul> <em>New Known Defects</em>
487 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
490 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
491 regions of protein alignment.
494 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
495 is restored from a Jalview 2.11 project
498 <!-- JAL-3213 -->Alignment panel height can be too small after
502 <!-- JAL-3240 -->Display is incorrect after removing gapped
503 columns within hidden columns
506 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
507 window after dragging left to select columns to left of visible
511 <!-- JAL-2876 -->Features coloured according to their description
512 string and thresholded by score in earlier versions of Jalview are
513 not shown as thresholded features in 2.11. To workaround please
514 create a Score filter instead.
517 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
519 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
522 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
523 alignments with multiple views can close views unexpectedly
526 <em>Java 11 Specific defects</em>
529 <!-- JAL-3235 -->Jalview Properties file is not sorted
530 alphabetically when saved
536 <td width="60" nowrap>
538 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
541 <td><div align="left">
545 <!-- JAL-3101 -->Default memory for Jalview webstart and
546 InstallAnywhere increased to 1G.
549 <!-- JAL-247 -->Hidden sequence markers and representative
550 sequence bolding included when exporting alignment as EPS,
551 SVG, PNG or HTML. <em>Display is configured via the
552 Format menu, or for command-line use via a Jalview
553 properties file.</em>
556 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
557 API and sequence data now imported as JSON.
560 <!-- JAL-3065 -->Change in recommended way of starting
561 Jalview via a Java command line: add jars in lib directory
562 to CLASSPATH, rather than via the deprecated java.ext.dirs
569 <!-- JAL-3047 -->Support added to execute test suite
570 instrumented with <a href="http://openclover.org/">Open
575 <td><div align="left">
579 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
580 row shown in Feredoxin Structure alignment view of example
584 <!-- JAL-2854 -->Annotation obscures sequences if lots of
585 annotation displayed.
588 <!-- JAL-3107 -->Group conservation/consensus not shown
589 for newly created group when 'Apply to all groups'
593 <!-- JAL-3087 -->Corrupted display when switching to
594 wrapped mode when sequence panel's vertical scrollbar is
598 <!-- JAL-3003 -->Alignment is black in exported EPS file
599 when sequences are selected in exported view.</em>
602 <!-- JAL-3059 -->Groups with different coloured borders
603 aren't rendered with correct colour.
606 <!-- JAL-3092 -->Jalview could hang when importing certain
607 types of knotted RNA secondary structure.
610 <!-- JAL-3095 -->Sequence highlight and selection in
611 trimmed VARNA 2D structure is incorrect for sequences that
615 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
616 annotation when columns are inserted into an alignment,
617 and when exporting as Stockholm flatfile.
620 <!-- JAL-3053 -->Jalview annotation rows containing upper
621 and lower-case 'E' and 'H' do not automatically get
622 treated as RNA secondary structure.
625 <!-- JAL-3106 -->.jvp should be used as default extension
626 (not .jar) when saving a Jalview project file.
629 <!-- JAL-3105 -->Mac Users: closing a window correctly
630 transfers focus to previous window on OSX
633 <em>Java 10 Issues Resolved</em>
636 <!-- JAL-2988 -->OSX - Can't save new files via the File
637 or export menus by typing in a name into the Save dialog
641 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
642 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
643 'look and feel' which has improved compatibility with the
644 latest version of OSX.
651 <td width="60" nowrap>
653 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
654 <em>7/06/2018</em></strong>
657 <td><div align="left">
661 <!-- JAL-2920 -->Use HGVS nomenclature for variant
662 annotation retrieved from Uniprot
665 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
666 onto the Jalview Desktop
670 <td><div align="left">
674 <!-- JAL-3017 -->Cannot import features with multiple
675 variant elements (blocks import of some Uniprot records)
678 <!-- JAL-2997 -->Clustal files with sequence positions in
679 right-hand column parsed correctly
682 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
683 not alignment area in exported graphic
686 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
687 window has input focus
690 <!-- JAL-2992 -->Annotation panel set too high when
691 annotation added to view (Windows)
694 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
695 network connectivity is poor
698 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
699 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
700 the currently open URL and links from a page viewed in
701 Firefox or Chrome on Windows is now fully supported. If
702 you are using Edge, only links in the page can be
703 dragged, and with Internet Explorer, only the currently
704 open URL in the browser can be dropped onto Jalview.</em>
707 <em>New Known Defects</em>
709 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
714 <td width="60" nowrap>
716 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
719 <td><div align="left">
723 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
724 for disabling automatic superposition of multiple
725 structures and open structures in existing views
728 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
729 ID and annotation area margins can be click-dragged to
733 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
737 <!-- JAL-2759 -->Improved performance for large alignments
738 and lots of hidden columns
741 <!-- JAL-2593 -->Improved performance when rendering lots
742 of features (particularly when transparency is disabled)
745 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
746 exchange of Jalview features and Chimera attributes made
752 <td><div align="left">
755 <!-- JAL-2899 -->Structure and Overview aren't updated
756 when Colour By Annotation threshold slider is adjusted
759 <!-- JAL-2778 -->Slow redraw when Overview panel shown
760 overlapping alignment panel
763 <!-- JAL-2929 -->Overview doesn't show end of unpadded
767 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
768 improved: CDS not handled correctly if transcript has no
772 <!-- JAL-2321 -->Secondary structure and temperature
773 factor annotation not added to sequence when local PDB
774 file associated with it by drag'n'drop or structure
778 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
779 dialog doesn't import PDB files dropped on an alignment
782 <!-- JAL-2666 -->Linked scrolling via protein horizontal
783 scroll bar doesn't work for some CDS/Protein views
786 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
787 Java 1.8u153 onwards and Java 1.9u4+.
790 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
791 columns in annotation row
794 <!-- JAL-2913 -->Preferences panel's ID Width control is not
795 honored in batch mode
798 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
799 for structures added to existing Jmol view
802 <!-- JAL-2223 -->'View Mappings' includes duplicate
803 entries after importing project with multiple views
806 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
807 protein sequences via SIFTS from associated PDB entries
808 with negative residue numbers or missing residues fails
811 <!-- JAL-2952 -->Exception when shading sequence with negative
812 Temperature Factor values from annotated PDB files (e.g.
813 as generated by CONSURF)
816 <!-- JAL-2920 -->Uniprot 'sequence variant' features
817 tooltip doesn't include a text description of mutation
820 <!-- JAL-2922 -->Invert displayed features very slow when
821 structure and/or overview windows are also shown
824 <!-- JAL-2954 -->Selecting columns from highlighted regions
825 very slow for alignments with large numbers of sequences
828 <!-- JAL-2925 -->Copy Consensus fails for group consensus
829 with 'StringIndexOutOfBounds'
832 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
833 platforms running Java 10
836 <!-- JAL-2960 -->Adding a structure to existing structure
837 view appears to do nothing because the view is hidden behind the alignment view
843 <!-- JAL-2926 -->Copy consensus sequence option in applet
844 should copy the group consensus when popup is opened on it
850 <!-- JAL-2913 -->Fixed ID width preference is not respected
853 <em>New Known Defects</em>
856 <!-- JAL-2973 --> Exceptions occasionally raised when
857 editing a large alignment and overview is displayed
860 <!-- JAL-2974 -->'Overview updating' progress bar is shown
861 repeatedly after a series of edits even when the overview
862 is no longer reflecting updates
865 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
866 structures for protein subsequence (if 'Trim Retrieved
867 Sequences' enabled) or Ensembl isoforms (Workaround in
868 2.10.4 is to fail back to N&W mapping)
871 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
872 option gives blank output
879 <td width="60" nowrap>
881 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
884 <td><div align="left">
885 <ul><li>Updated Certum Codesigning Certificate
886 (Valid till 30th November 2018)</li></ul></div></td>
887 <td><div align="left">
890 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
891 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
892 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
893 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
894 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
895 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
896 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
902 <td width="60" nowrap>
904 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
907 <td><div align="left">
911 <!-- JAL-2446 -->Faster and more efficient management and
912 rendering of sequence features
915 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
916 429 rate limit request hander
919 <!-- JAL-2773 -->Structure views don't get updated unless
920 their colours have changed
923 <!-- JAL-2495 -->All linked sequences are highlighted for
924 a structure mousover (Jmol) or selection (Chimera)
927 <!-- JAL-2790 -->'Cancel' button in progress bar for
928 JABAWS AACon, RNAAliFold and Disorder prediction jobs
931 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
932 view from Ensembl locus cross-references
935 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
939 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
940 feature can be disabled
943 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
944 PDB easier retrieval of sequences for lists of IDs
947 <!-- JAL-2758 -->Short names for sequences retrieved from
953 <li>Groovy interpreter updated to 2.4.12</li>
954 <li>Example groovy script for generating a matrix of
955 percent identity scores for current alignment.</li>
957 <em>Testing and Deployment</em>
960 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
964 <td><div align="left">
968 <!-- JAL-2643 -->Pressing tab after updating the colour
969 threshold text field doesn't trigger an update to the
973 <!-- JAL-2682 -->Race condition when parsing sequence ID
977 <!-- JAL-2608 -->Overview windows are also closed when
978 alignment window is closed
981 <!-- JAL-2548 -->Export of features doesn't always respect
985 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
986 takes a long time in Cursor mode
992 <!-- JAL-2777 -->Structures with whitespace chainCode
993 cannot be viewed in Chimera
996 <!-- JAL-2728 -->Protein annotation panel too high in
1000 <!-- JAL-2757 -->Can't edit the query after the server
1001 error warning icon is shown in Uniprot and PDB Free Text
1005 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1008 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1011 <!-- JAL-2739 -->Hidden column marker in last column not
1012 rendered when switching back from Wrapped to normal view
1015 <!-- JAL-2768 -->Annotation display corrupted when
1016 scrolling right in unwapped alignment view
1019 <!-- JAL-2542 -->Existing features on subsequence
1020 incorrectly relocated when full sequence retrieved from
1024 <!-- JAL-2733 -->Last reported memory still shown when
1025 Desktop->Show Memory is unticked (OSX only)
1028 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1029 features of same type and group to be selected for
1033 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1034 alignments when hidden columns are present
1037 <!-- JAL-2392 -->Jalview freezes when loading and
1038 displaying several structures
1041 <!-- JAL-2732 -->Black outlines left after resizing or
1045 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1046 within the Jalview desktop on OSX
1049 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1050 when in wrapped alignment mode
1053 <!-- JAL-2636 -->Scale mark not shown when close to right
1054 hand end of alignment
1057 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1058 each selected sequence do not have correct start/end
1062 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1063 after canceling the Alignment Window's Font dialog
1066 <!-- JAL-2036 -->Show cross-references not enabled after
1067 restoring project until a new view is created
1070 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1071 URL links appears when only default EMBL-EBI link is
1072 configured (since 2.10.2b2)
1075 <!-- JAL-2775 -->Overview redraws whole window when box
1076 position is adjusted
1079 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1080 in a multi-chain structure when viewing alignment
1081 involving more than one chain (since 2.10)
1084 <!-- JAL-2811 -->Double residue highlights in cursor mode
1085 if new selection moves alignment window
1088 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1089 arrow key in cursor mode to pass hidden column marker
1092 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1093 that produces correctly annotated transcripts and products
1096 <!-- JAL-2776 -->Toggling a feature group after first time
1097 doesn't update associated structure view
1100 <em>Applet</em><br />
1103 <!-- JAL-2687 -->Concurrent modification exception when
1104 closing alignment panel
1107 <em>BioJSON</em><br />
1110 <!-- JAL-2546 -->BioJSON export does not preserve
1111 non-positional features
1114 <em>New Known Issues</em>
1117 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1118 sequence features correctly (for many previous versions of
1122 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1123 using cursor in wrapped panel other than top
1126 <!-- JAL-2791 -->Select columns containing feature ignores
1127 graduated colour threshold
1130 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1131 always preserve numbering and sequence features
1134 <em>Known Java 9 Issues</em>
1137 <!-- JAL-2902 -->Groovy Console very slow to open and is
1138 not responsive when entering characters (Webstart, Java
1145 <td width="60" nowrap>
1146 <div align="center">
1147 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1148 <em>2/10/2017</em></strong>
1151 <td><div align="left">
1152 <em>New features in Jalview Desktop</em>
1155 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1157 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1161 <td><div align="left">
1165 <td width="60" nowrap>
1166 <div align="center">
1167 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1168 <em>7/9/2017</em></strong>
1171 <td><div align="left">
1175 <!-- JAL-2588 -->Show gaps in overview window by colouring
1176 in grey (sequences used to be coloured grey, and gaps were
1180 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1184 <!-- JAL-2587 -->Overview updates immediately on increase
1185 in size and progress bar shown as higher resolution
1186 overview is recalculated
1191 <td><div align="left">
1195 <!-- JAL-2664 -->Overview window redraws every hidden
1196 column region row by row
1199 <!-- JAL-2681 -->duplicate protein sequences shown after
1200 retrieving Ensembl crossrefs for sequences from Uniprot
1203 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1204 format setting is unticked
1207 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1208 if group has show boxes format setting unticked
1211 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1212 autoscrolling whilst dragging current selection group to
1213 include sequences and columns not currently displayed
1216 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1217 assemblies are imported via CIF file
1220 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1221 displayed when threshold or conservation colouring is also
1225 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1229 <!-- JAL-2673 -->Jalview continues to scroll after
1230 dragging a selected region off the visible region of the
1234 <!-- JAL-2724 -->Cannot apply annotation based
1235 colourscheme to all groups in a view
1238 <!-- JAL-2511 -->IDs don't line up with sequences
1239 initially after font size change using the Font chooser or
1246 <td width="60" nowrap>
1247 <div align="center">
1248 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1251 <td><div align="left">
1252 <em>Calculations</em>
1256 <!-- JAL-1933 -->Occupancy annotation row shows number of
1257 ungapped positions in each column of the alignment.
1260 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1261 a calculation dialog box
1264 <!-- JAL-2379 -->Revised implementation of PCA for speed
1265 and memory efficiency (~30x faster)
1268 <!-- JAL-2403 -->Revised implementation of sequence
1269 similarity scores as used by Tree, PCA, Shading Consensus
1270 and other calculations
1273 <!-- JAL-2416 -->Score matrices are stored as resource
1274 files within the Jalview codebase
1277 <!-- JAL-2500 -->Trees computed on Sequence Feature
1278 Similarity may have different topology due to increased
1285 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1286 model for alignments and groups
1289 <!-- JAL-384 -->Custom shading schemes created via groovy
1296 <!-- JAL-2526 -->Efficiency improvements for interacting
1297 with alignment and overview windows
1300 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1304 <!-- JAL-2388 -->Hidden columns and sequences can be
1308 <!-- JAL-2611 -->Click-drag in visible area allows fine
1309 adjustment of visible position
1313 <em>Data import/export</em>
1316 <!-- JAL-2535 -->Posterior probability annotation from
1317 Stockholm files imported as sequence associated annotation
1320 <!-- JAL-2507 -->More robust per-sequence positional
1321 annotation input/output via stockholm flatfile
1324 <!-- JAL-2533 -->Sequence names don't include file
1325 extension when importing structure files without embedded
1326 names or PDB accessions
1329 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1330 format sequence substitution matrices
1333 <em>User Interface</em>
1336 <!-- JAL-2447 --> Experimental Features Checkbox in
1337 Desktop's Tools menu to hide or show untested features in
1341 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1342 via Overview or sequence motif search operations
1345 <!-- JAL-2547 -->Amend sequence features dialog box can be
1346 opened by double clicking gaps within sequence feature
1350 <!-- JAL-1476 -->Status bar message shown when not enough
1351 aligned positions were available to create a 3D structure
1355 <em>3D Structure</em>
1358 <!-- JAL-2430 -->Hidden regions in alignment views are not
1359 coloured in linked structure views
1362 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1363 file-based command exchange
1366 <!-- JAL-2375 -->Structure chooser automatically shows
1367 Cached Structures rather than querying the PDBe if
1368 structures are already available for sequences
1371 <!-- JAL-2520 -->Structures imported via URL are cached in
1372 the Jalview project rather than downloaded again when the
1373 project is reopened.
1376 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1377 to transfer Chimera's structure attributes as Jalview
1378 features, and vice-versa (<strong>Experimental
1382 <em>Web Services</em>
1385 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1388 <!-- JAL-2335 -->Filter non-standard amino acids and
1389 nucleotides when submitting to AACon and other MSA
1393 <!-- JAL-2316, -->URLs for viewing database
1394 cross-references provided by identifiers.org and the
1395 EMBL-EBI's MIRIAM DB
1402 <!-- JAL-2344 -->FileFormatI interface for describing and
1403 identifying file formats (instead of String constants)
1406 <!-- JAL-2228 -->FeatureCounter script refactored for
1407 efficiency when counting all displayed features (not
1408 backwards compatible with 2.10.1)
1411 <em>Example files</em>
1414 <!-- JAL-2631 -->Graduated feature colour style example
1415 included in the example feature file
1418 <em>Documentation</em>
1421 <!-- JAL-2339 -->Release notes reformatted for readability
1422 with the built-in Java help viewer
1425 <!-- JAL-1644 -->Find documentation updated with 'search
1426 sequence description' option
1432 <!-- JAL-2485, -->External service integration tests for
1433 Uniprot REST Free Text Search Client
1436 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1439 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1444 <td><div align="left">
1445 <em>Calculations</em>
1448 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1449 matrix - C->R should be '-3'<br />Old matrix restored
1450 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1452 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1453 Jalview's treatment of gaps in PCA and substitution matrix
1454 based Tree calculations.<br /> <br />In earlier versions
1455 of Jalview, gaps matching gaps were penalised, and gaps
1456 matching non-gaps penalised even more. In the PCA
1457 calculation, gaps were actually treated as non-gaps - so
1458 different costs were applied, which meant Jalview's PCAs
1459 were different to those produced by SeqSpace.<br />Jalview
1460 now treats gaps in the same way as SeqSpace (ie it scores
1461 them as 0). <br /> <br />Enter the following in the
1462 Groovy console to restore pre-2.10.2 behaviour:<br />
1463 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1464 // for 2.10.1 mode <br />
1465 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1466 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1467 these settings will affect all subsequent tree and PCA
1468 calculations (not recommended)</em></li>
1470 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1471 scaling of branch lengths for trees computed using
1472 Sequence Feature Similarity.
1475 <!-- JAL-2377 -->PCA calculation could hang when
1476 generating output report when working with highly
1477 redundant alignments
1480 <!-- JAL-2544 --> Sort by features includes features to
1481 right of selected region when gaps present on right-hand
1485 <em>User Interface</em>
1488 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1489 doesn't reselect a specific sequence's associated
1490 annotation after it was used for colouring a view
1493 <!-- JAL-2419 -->Current selection lost if popup menu
1494 opened on a region of alignment without groups
1497 <!-- JAL-2374 -->Popup menu not always shown for regions
1498 of an alignment with overlapping groups
1501 <!-- JAL-2310 -->Finder double counts if both a sequence's
1502 name and description match
1505 <!-- JAL-2370 -->Hiding column selection containing two
1506 hidden regions results in incorrect hidden regions
1509 <!-- JAL-2386 -->'Apply to all groups' setting when
1510 changing colour does not apply Conservation slider value
1514 <!-- JAL-2373 -->Percentage identity and conservation menu
1515 items do not show a tick or allow shading to be disabled
1518 <!-- JAL-2385 -->Conservation shading or PID threshold
1519 lost when base colourscheme changed if slider not visible
1522 <!-- JAL-2547 -->Sequence features shown in tooltip for
1523 gaps before start of features
1526 <!-- JAL-2623 -->Graduated feature colour threshold not
1527 restored to UI when feature colour is edited
1530 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1531 a time when scrolling vertically in wrapped mode.
1534 <!-- JAL-2630 -->Structure and alignment overview update
1535 as graduate feature colour settings are modified via the
1539 <!-- JAL-2034 -->Overview window doesn't always update
1540 when a group defined on the alignment is resized
1543 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1544 wrapped view result in positional status updates
1548 <!-- JAL-2563 -->Status bar doesn't show position for
1549 ambiguous amino acid and nucleotide symbols
1552 <!-- JAL-2602 -->Copy consensus sequence failed if
1553 alignment included gapped columns
1556 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1557 widgets don't permanently disappear
1560 <!-- JAL-2503 -->Cannot select or filter quantitative
1561 annotation that are shown only as column labels (e.g.
1562 T-Coffee column reliability scores)
1565 <!-- JAL-2594 -->Exception thrown if trying to create a
1566 sequence feature on gaps only
1569 <!-- JAL-2504 -->Features created with 'New feature'
1570 button from a Find inherit previously defined feature type
1571 rather than the Find query string
1574 <!-- JAL-2423 -->incorrect title in output window when
1575 exporting tree calculated in Jalview
1578 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1579 and then revealing them reorders sequences on the
1583 <!-- JAL-964 -->Group panel in sequence feature settings
1584 doesn't update to reflect available set of groups after
1585 interactively adding or modifying features
1588 <!-- JAL-2225 -->Sequence Database chooser unusable on
1592 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1593 only excluded gaps in current sequence and ignored
1600 <!-- JAL-2421 -->Overview window visible region moves
1601 erratically when hidden rows or columns are present
1604 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1605 Structure Viewer's colour menu don't correspond to
1609 <!-- JAL-2405 -->Protein specific colours only offered in
1610 colour and group colour menu for protein alignments
1613 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1614 reflect currently selected view or group's shading
1618 <!-- JAL-2624 -->Feature colour thresholds not respected
1619 when rendered on overview and structures when opacity at
1623 <!-- JAL-2589 -->User defined gap colour not shown in
1624 overview when features overlaid on alignment
1627 <!-- JAL-2567 -->Feature settings for different views not
1628 recovered correctly from Jalview project file
1631 <!-- JAL-2256 -->Feature colours in overview when first opened
1632 (automatically via preferences) are different to the main
1636 <em>Data import/export</em>
1639 <!-- JAL-2576 -->Very large alignments take a long time to
1643 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1644 added after a sequence was imported are not written to
1648 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1649 when importing RNA secondary structure via Stockholm
1652 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1653 not shown in correct direction for simple pseudoknots
1656 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1657 with lightGray or darkGray via features file (but can
1661 <!-- JAL-2383 -->Above PID colour threshold not recovered
1662 when alignment view imported from project
1665 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1666 structure and sequences extracted from structure files
1667 imported via URL and viewed in Jmol
1670 <!-- JAL-2520 -->Structures loaded via URL are saved in
1671 Jalview Projects rather than fetched via URL again when
1672 the project is loaded and the structure viewed
1675 <em>Web Services</em>
1678 <!-- JAL-2519 -->EnsemblGenomes example failing after
1679 release of Ensembl v.88
1682 <!-- JAL-2366 -->Proxy server address and port always
1683 appear enabled in Preferences->Connections
1686 <!-- JAL-2461 -->DAS registry not found exceptions
1687 removed from console output
1690 <!-- JAL-2582 -->Cannot retrieve protein products from
1691 Ensembl by Peptide ID
1694 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1695 created from SIFTs, and spurious 'Couldn't open structure
1696 in Chimera' errors raised after April 2017 update (problem
1697 due to 'null' string rather than empty string used for
1698 residues with no corresponding PDB mapping).
1701 <em>Application UI</em>
1704 <!-- JAL-2361 -->User Defined Colours not added to Colour
1708 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1709 case' residues (button in colourscheme editor debugged and
1710 new documentation and tooltips added)
1713 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1714 doesn't restore group-specific text colour thresholds
1717 <!-- JAL-2243 -->Feature settings panel does not update as
1718 new features are added to alignment
1721 <!-- JAL-2532 -->Cancel in feature settings reverts
1722 changes to feature colours via the Amend features dialog
1725 <!-- JAL-2506 -->Null pointer exception when attempting to
1726 edit graduated feature colour via amend features dialog
1730 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1731 selection menu changes colours of alignment views
1734 <!-- JAL-2426 -->Spurious exceptions in console raised
1735 from alignment calculation workers after alignment has
1739 <!-- JAL-1608 -->Typo in selection popup menu - Create
1740 groups now 'Create Group'
1743 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1744 Create/Undefine group doesn't always work
1747 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1748 shown again after pressing 'Cancel'
1751 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1752 adjusts start position in wrap mode
1755 <!-- JAL-2563 -->Status bar doesn't show positions for
1756 ambiguous amino acids
1759 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1760 CDS/Protein view after CDS sequences added for aligned
1764 <!-- JAL-2592 -->User defined colourschemes called 'User
1765 Defined' don't appear in Colours menu
1771 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1772 score models doesn't always result in an updated PCA plot
1775 <!-- JAL-2442 -->Features not rendered as transparent on
1776 overview or linked structure view
1779 <!-- JAL-2372 -->Colour group by conservation doesn't
1783 <!-- JAL-2517 -->Hitting Cancel after applying
1784 user-defined colourscheme doesn't restore original
1791 <!-- JAL-2314 -->Unit test failure:
1792 jalview.ws.jabaws.RNAStructExportImport setup fails
1795 <!-- JAL-2307 -->Unit test failure:
1796 jalview.ws.sifts.SiftsClientTest due to compatibility
1797 problems with deep array comparison equality asserts in
1798 successive versions of TestNG
1801 <!-- JAL-2479 -->Relocated StructureChooserTest and
1802 ParameterUtilsTest Unit tests to Network suite
1805 <em>New Known Issues</em>
1808 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1809 phase after a sequence motif find operation
1812 <!-- JAL-2550 -->Importing annotation file with rows
1813 containing just upper and lower case letters are
1814 interpreted as WUSS RNA secondary structure symbols
1817 <!-- JAL-2590 -->Cannot load and display Newick trees
1818 reliably from eggnog Ortholog database
1821 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1822 containing features of type Highlight' when 'B' is pressed
1823 to mark columns containing highlighted regions.
1826 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1827 doesn't always add secondary structure annotation.
1832 <td width="60" nowrap>
1833 <div align="center">
1834 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1837 <td><div align="left">
1841 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1842 for all consensus calculations
1845 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1848 <li>Updated Jalview's Certum code signing certificate
1851 <em>Application</em>
1854 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1855 set of database cross-references, sorted alphabetically
1858 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1859 from database cross references. Users with custom links
1860 will receive a <a href="webServices/urllinks.html#warning">warning
1861 dialog</a> asking them to update their preferences.
1864 <!-- JAL-2287-->Cancel button and escape listener on
1865 dialog warning user about disconnecting Jalview from a
1869 <!-- JAL-2320-->Jalview's Chimera control window closes if
1870 the Chimera it is connected to is shut down
1873 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1874 columns menu item to mark columns containing highlighted
1875 regions (e.g. from structure selections or results of a
1879 <!-- JAL-2284-->Command line option for batch-generation
1880 of HTML pages rendering alignment data with the BioJS
1890 <!-- JAL-2286 -->Columns with more than one modal residue
1891 are not coloured or thresholded according to percent
1892 identity (first observed in Jalview 2.8.2)
1895 <!-- JAL-2301 -->Threonine incorrectly reported as not
1899 <!-- JAL-2318 -->Updates to documentation pages (above PID
1900 threshold, amino acid properties)
1903 <!-- JAL-2292 -->Lower case residues in sequences are not
1904 reported as mapped to residues in a structure file in the
1908 <!--JAL-2324 -->Identical features with non-numeric scores
1909 could be added multiple times to a sequence
1912 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1913 bond features shown as two highlighted residues rather
1914 than a range in linked structure views, and treated
1915 correctly when selecting and computing trees from features
1918 <!-- JAL-2281-->Custom URL links for database
1919 cross-references are matched to database name regardless
1924 <em>Application</em>
1927 <!-- JAL-2282-->Custom URL links for specific database
1928 names without regular expressions also offer links from
1932 <!-- JAL-2315-->Removing a single configured link in the
1933 URL links pane in Connections preferences doesn't actually
1934 update Jalview configuration
1937 <!-- JAL-2272-->CTRL-Click on a selected region to open
1938 the alignment area popup menu doesn't work on El-Capitan
1941 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1942 files with similarly named sequences if dropped onto the
1946 <!-- JAL-2312 -->Additional mappings are shown for PDB
1947 entries where more chains exist in the PDB accession than
1948 are reported in the SIFTS file
1951 <!-- JAL-2317-->Certain structures do not get mapped to
1952 the structure view when displayed with Chimera
1955 <!-- JAL-2317-->No chains shown in the Chimera view
1956 panel's View->Show Chains submenu
1959 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1960 work for wrapped alignment views
1963 <!--JAL-2197 -->Rename UI components for running JPred
1964 predictions from 'JNet' to 'JPred'
1967 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1968 corrupted when annotation panel vertical scroll is not at
1969 first annotation row
1972 <!--JAL-2332 -->Attempting to view structure for Hen
1973 lysozyme results in a PDB Client error dialog box
1976 <!-- JAL-2319 -->Structure View's mapping report switched
1977 ranges for PDB and sequence for SIFTS
1980 SIFTS 'Not_Observed' residues mapped to non-existant
1984 <!-- <em>New Known Issues</em>
1991 <td width="60" nowrap>
1992 <div align="center">
1993 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1994 <em>25/10/2016</em></strong>
1997 <td><em>Application</em>
1999 <li>3D Structure chooser opens with 'Cached structures'
2000 view if structures already loaded</li>
2001 <li>Progress bar reports models as they are loaded to
2002 structure views</li>
2008 <li>Colour by conservation always enabled and no tick
2009 shown in menu when BLOSUM or PID shading applied</li>
2010 <li>FER1_ARATH and FER2_ARATH labels were switched in
2011 example sequences/projects/trees</li>
2013 <em>Application</em>
2015 <li>Jalview projects with views of local PDB structure
2016 files saved on Windows cannot be opened on OSX</li>
2017 <li>Multiple structure views can be opened and superposed
2018 without timeout for structures with multiple models or
2019 multiple sequences in alignment</li>
2020 <li>Cannot import or associated local PDB files without a
2021 PDB ID HEADER line</li>
2022 <li>RMSD is not output in Jmol console when superposition
2024 <li>Drag and drop of URL from Browser fails for Linux and
2025 OSX versions earlier than El Capitan</li>
2026 <li>ENA client ignores invalid content from ENA server</li>
2027 <li>Exceptions are not raised in console when ENA client
2028 attempts to fetch non-existent IDs via Fetch DB Refs UI
2030 <li>Exceptions are not raised in console when a new view
2031 is created on the alignment</li>
2032 <li>OSX right-click fixed for group selections: CMD-click
2033 to insert/remove gaps in groups and CTRL-click to open group
2036 <em>Build and deployment</em>
2038 <li>URL link checker now copes with multi-line anchor
2041 <em>New Known Issues</em>
2043 <li>Drag and drop from URL links in browsers do not work
2050 <td width="60" nowrap>
2051 <div align="center">
2052 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2055 <td><em>General</em>
2058 <!-- JAL-2124 -->Updated Spanish translations.
2061 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2062 for importing structure data to Jalview. Enables mmCIF and
2066 <!-- JAL-192 --->Alignment ruler shows positions relative to
2070 <!-- JAL-2202 -->Position/residue shown in status bar when
2071 mousing over sequence associated annotation
2074 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2078 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2079 '()', canonical '[]' and invalid '{}' base pair populations
2083 <!-- JAL-2092 -->Feature settings popup menu options for
2084 showing or hiding columns containing a feature
2087 <!-- JAL-1557 -->Edit selected group by double clicking on
2088 group and sequence associated annotation labels
2091 <!-- JAL-2236 -->Sequence name added to annotation label in
2092 select/hide columns by annotation and colour by annotation
2096 </ul> <em>Application</em>
2099 <!-- JAL-2050-->Automatically hide introns when opening a
2100 gene/transcript view
2103 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2107 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2108 structure mappings with the EMBL-EBI PDBe SIFTS database
2111 <!-- JAL-2079 -->Updated download sites used for Rfam and
2112 Pfam sources to xfam.org
2115 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2118 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2119 over sequences in Jalview
2122 <!-- JAL-2027-->Support for reverse-complement coding
2123 regions in ENA and EMBL
2126 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2127 for record retrieval via ENA rest API
2130 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2134 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2135 groovy script execution
2138 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2139 alignment window's Calculate menu
2142 <!-- JAL-1812 -->Allow groovy scripts that call
2143 Jalview.getAlignFrames() to run in headless mode
2146 <!-- JAL-2068 -->Support for creating new alignment
2147 calculation workers from groovy scripts
2150 <!-- JAL-1369 --->Store/restore reference sequence in
2154 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2155 associations are now saved/restored from project
2158 <!-- JAL-1993 -->Database selection dialog always shown
2159 before sequence fetcher is opened
2162 <!-- JAL-2183 -->Double click on an entry in Jalview's
2163 database chooser opens a sequence fetcher
2166 <!-- JAL-1563 -->Free-text search client for UniProt using
2167 the UniProt REST API
2170 <!-- JAL-2168 -->-nonews command line parameter to prevent
2171 the news reader opening
2174 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2175 querying stored in preferences
2178 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2182 <!-- JAL-1977-->Tooltips shown on database chooser
2185 <!-- JAL-391 -->Reverse complement function in calculate
2186 menu for nucleotide sequences
2189 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2190 and feature counts preserves alignment ordering (and
2191 debugged for complex feature sets).
2194 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2195 viewing structures with Jalview 2.10
2198 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2199 genome, transcript CCDS and gene ids via the Ensembl and
2200 Ensembl Genomes REST API
2203 <!-- JAL-2049 -->Protein sequence variant annotation
2204 computed for 'sequence_variant' annotation on CDS regions
2208 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2212 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2213 Ref Fetcher fails to match, or otherwise updates sequence
2214 data from external database records.
2217 <!-- JAL-2154 -->Revised Jalview Project format for
2218 efficient recovery of sequence coding and alignment
2219 annotation relationships.
2221 </ul> <!-- <em>Applet</em>
2232 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2236 <!-- JAL-2018-->Export features in Jalview format (again)
2237 includes graduated colourschemes
2240 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2241 working with big alignments and lots of hidden columns
2244 <!-- JAL-2053-->Hidden column markers not always rendered
2245 at right of alignment window
2248 <!-- JAL-2067 -->Tidied up links in help file table of
2252 <!-- JAL-2072 -->Feature based tree calculation not shown
2256 <!-- JAL-2075 -->Hidden columns ignored during feature
2257 based tree calculation
2260 <!-- JAL-2065 -->Alignment view stops updating when show
2261 unconserved enabled for group on alignment
2264 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2268 <!-- JAL-2146 -->Alignment column in status incorrectly
2269 shown as "Sequence position" when mousing over
2273 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2274 hidden columns present
2277 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2278 user created annotation added to alignment
2281 <!-- JAL-1841 -->RNA Structure consensus only computed for
2282 '()' base pair annotation
2285 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2286 in zero scores for all base pairs in RNA Structure
2290 <!-- JAL-2174-->Extend selection with columns containing
2294 <!-- JAL-2275 -->Pfam format writer puts extra space at
2295 beginning of sequence
2298 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2302 <!-- JAL-2238 -->Cannot create groups on an alignment from
2303 from a tree when t-coffee scores are shown
2306 <!-- JAL-1836,1967 -->Cannot import and view PDB
2307 structures with chains containing negative resnums (4q4h)
2310 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2314 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2315 to Clustal, PIR and PileUp output
2318 <!-- JAL-2008 -->Reordering sequence features that are
2319 not visible causes alignment window to repaint
2322 <!-- JAL-2006 -->Threshold sliders don't work in
2323 graduated colour and colour by annotation row for e-value
2324 scores associated with features and annotation rows
2327 <!-- JAL-1797 -->amino acid physicochemical conservation
2328 calculation should be case independent
2331 <!-- JAL-2173 -->Remove annotation also updates hidden
2335 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2336 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2337 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2340 <!-- JAL-2065 -->Null pointer exceptions and redraw
2341 problems when reference sequence defined and 'show
2342 non-conserved' enabled
2345 <!-- JAL-1306 -->Quality and Conservation are now shown on
2346 load even when Consensus calculation is disabled
2349 <!-- JAL-1932 -->Remove right on penultimate column of
2350 alignment does nothing
2353 <em>Application</em>
2356 <!-- JAL-1552-->URLs and links can't be imported by
2357 drag'n'drop on OSX when launched via webstart (note - not
2358 yet fixed for El Capitan)
2361 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2362 output when running on non-gb/us i18n platforms
2365 <!-- JAL-1944 -->Error thrown when exporting a view with
2366 hidden sequences as flat-file alignment
2369 <!-- JAL-2030-->InstallAnywhere distribution fails when
2373 <!-- JAL-2080-->Jalview very slow to launch via webstart
2374 (also hotfix for 2.9.0b2)
2377 <!-- JAL-2085 -->Cannot save project when view has a
2378 reference sequence defined
2381 <!-- JAL-1011 -->Columns are suddenly selected in other
2382 alignments and views when revealing hidden columns
2385 <!-- JAL-1989 -->Hide columns not mirrored in complement
2386 view in a cDNA/Protein splitframe
2389 <!-- JAL-1369 -->Cannot save/restore representative
2390 sequence from project when only one sequence is
2394 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2395 in Structure Chooser
2398 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2399 structure consensus didn't refresh annotation panel
2402 <!-- JAL-1962 -->View mapping in structure view shows
2403 mappings between sequence and all chains in a PDB file
2406 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2407 dialogs format columns correctly, don't display array
2408 data, sort columns according to type
2411 <!-- JAL-1975 -->Export complete shown after destination
2412 file chooser is cancelled during an image export
2415 <!-- JAL-2025 -->Error when querying PDB Service with
2416 sequence name containing special characters
2419 <!-- JAL-2024 -->Manual PDB structure querying should be
2423 <!-- JAL-2104 -->Large tooltips with broken HTML
2424 formatting don't wrap
2427 <!-- JAL-1128 -->Figures exported from wrapped view are
2428 truncated so L looks like I in consensus annotation
2431 <!-- JAL-2003 -->Export features should only export the
2432 currently displayed features for the current selection or
2436 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2437 after fetching cross-references, and restoring from
2441 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2442 followed in the structure viewer
2445 <!-- JAL-2163 -->Titles for individual alignments in
2446 splitframe not restored from project
2449 <!-- JAL-2145 -->missing autocalculated annotation at
2450 trailing end of protein alignment in transcript/product
2451 splitview when pad-gaps not enabled by default
2454 <!-- JAL-1797 -->amino acid physicochemical conservation
2458 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2459 article has been read (reopened issue due to
2460 internationalisation problems)
2463 <!-- JAL-1960 -->Only offer PDB structures in structure
2464 viewer based on sequence name, PDB and UniProt
2469 <!-- JAL-1976 -->No progress bar shown during export of
2473 <!-- JAL-2213 -->Structures not always superimposed after
2474 multiple structures are shown for one or more sequences.
2477 <!-- JAL-1370 -->Reference sequence characters should not
2478 be replaced with '.' when 'Show unconserved' format option
2482 <!-- JAL-1823 -->Cannot specify chain code when entering
2483 specific PDB id for sequence
2486 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2487 'Export hidden sequences' is enabled, but 'export hidden
2488 columns' is disabled.
2491 <!--JAL-2026-->Best Quality option in structure chooser
2492 selects lowest rather than highest resolution structures
2496 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2497 to sequence mapping in 'View Mappings' report
2500 <!-- JAL-2284 -->Unable to read old Jalview projects that
2501 contain non-XML data added after Jalvew wrote project.
2504 <!-- JAL-2118 -->Newly created annotation row reorders
2505 after clicking on it to create new annotation for a
2509 <!-- JAL-1980 -->Null Pointer Exception raised when
2510 pressing Add on an orphaned cut'n'paste window.
2512 <!-- may exclude, this is an external service stability issue JAL-1941
2513 -- > RNA 3D structure not added via DSSR service</li> -->
2518 <!-- JAL-2151 -->Incorrect columns are selected when
2519 hidden columns present before start of sequence
2522 <!-- JAL-1986 -->Missing dependencies on applet pages
2526 <!-- JAL-1947 -->Overview pixel size changes when
2527 sequences are hidden in applet
2530 <!-- JAL-1996 -->Updated instructions for applet
2531 deployment on examples pages.
2538 <td width="60" nowrap>
2539 <div align="center">
2540 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2541 <em>16/10/2015</em></strong>
2544 <td><em>General</em>
2546 <li>Time stamps for signed Jalview application and applet
2551 <em>Application</em>
2553 <li>Duplicate group consensus and conservation rows
2554 shown when tree is partitioned</li>
2555 <li>Erratic behaviour when tree partitions made with
2556 multiple cDNA/Protein split views</li>
2562 <td width="60" nowrap>
2563 <div align="center">
2564 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2565 <em>8/10/2015</em></strong>
2568 <td><em>General</em>
2570 <li>Updated Spanish translations of localized text for
2572 </ul> <em>Application</em>
2574 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2575 <li>Signed OSX InstallAnywhere installer<br></li>
2576 <li>Support for per-sequence based annotations in BioJSON</li>
2577 </ul> <em>Applet</em>
2579 <li>Split frame example added to applet examples page</li>
2580 </ul> <em>Build and Deployment</em>
2583 <!-- JAL-1888 -->New ant target for running Jalview's test
2591 <li>Mapping of cDNA to protein in split frames
2592 incorrect when sequence start > 1</li>
2593 <li>Broken images in filter column by annotation dialog
2595 <li>Feature colours not parsed from features file</li>
2596 <li>Exceptions and incomplete link URLs recovered when
2597 loading a features file containing HTML tags in feature
2601 <em>Application</em>
2603 <li>Annotations corrupted after BioJS export and
2605 <li>Incorrect sequence limits after Fetch DB References
2606 with 'trim retrieved sequences'</li>
2607 <li>Incorrect warning about deleting all data when
2608 deleting selected columns</li>
2609 <li>Patch to build system for shipping properly signed
2610 JNLP templates for webstart launch</li>
2611 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2612 unreleased structures for download or viewing</li>
2613 <li>Tab/space/return keystroke operation of EMBL-PDBe
2614 fetcher/viewer dialogs works correctly</li>
2615 <li>Disabled 'minimise' button on Jalview windows
2616 running on OSX to workaround redraw hang bug</li>
2617 <li>Split cDNA/Protein view position and geometry not
2618 recovered from jalview project</li>
2619 <li>Initial enabled/disabled state of annotation menu
2620 sorter 'show autocalculated first/last' corresponds to
2622 <li>Restoring of Clustal, RNA Helices and T-Coffee
2623 color schemes from BioJSON</li>
2627 <li>Reorder sequences mirrored in cDNA/Protein split
2629 <li>Applet with Jmol examples not loading correctly</li>
2635 <td><div align="center">
2636 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2638 <td><em>General</em>
2640 <li>Linked visualisation and analysis of DNA and Protein
2643 <li>Translated cDNA alignments shown as split protein
2644 and DNA alignment views</li>
2645 <li>Codon consensus annotation for linked protein and
2646 cDNA alignment views</li>
2647 <li>Link cDNA or Protein product sequences by loading
2648 them onto Protein or cDNA alignments</li>
2649 <li>Reconstruct linked cDNA alignment from aligned
2650 protein sequences</li>
2653 <li>Jmol integration updated to Jmol v14.2.14</li>
2654 <li>Import and export of Jalview alignment views as <a
2655 href="features/bioJsonFormat.html">BioJSON</a></li>
2656 <li>New alignment annotation file statements for
2657 reference sequences and marking hidden columns</li>
2658 <li>Reference sequence based alignment shading to
2659 highlight variation</li>
2660 <li>Select or hide columns according to alignment
2662 <li>Find option for locating sequences by description</li>
2663 <li>Conserved physicochemical properties shown in amino
2664 acid conservation row</li>
2665 <li>Alignments can be sorted by number of RNA helices</li>
2666 </ul> <em>Application</em>
2668 <li>New cDNA/Protein analysis capabilities
2670 <li>Get Cross-References should open a Split Frame
2671 view with cDNA/Protein</li>
2672 <li>Detect when nucleotide sequences and protein
2673 sequences are placed in the same alignment</li>
2674 <li>Split cDNA/Protein views are saved in Jalview
2679 <li>Use REST API to talk to Chimera</li>
2680 <li>Selected regions in Chimera are highlighted in linked
2681 Jalview windows</li>
2683 <li>VARNA RNA viewer updated to v3.93</li>
2684 <li>VARNA views are saved in Jalview Projects</li>
2685 <li>Pseudoknots displayed as Jalview RNA annotation can
2686 be shown in VARNA</li>
2688 <li>Make groups for selection uses marked columns as well
2689 as the active selected region</li>
2691 <li>Calculate UPGMA and NJ trees using sequence feature
2693 <li>New Export options
2695 <li>New Export Settings dialog to control hidden
2696 region export in flat file generation</li>
2698 <li>Export alignment views for display with the <a
2699 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2701 <li>Export scrollable SVG in HTML page</li>
2702 <li>Optional embedding of BioJSON data when exporting
2703 alignment figures to HTML</li>
2705 <li>3D structure retrieval and display
2707 <li>Free text and structured queries with the PDBe
2709 <li>PDBe Search API based discovery and selection of
2710 PDB structures for a sequence set</li>
2714 <li>JPred4 employed for protein secondary structure
2716 <li>Hide Insertions menu option to hide unaligned columns
2717 for one or a group of sequences</li>
2718 <li>Automatically hide insertions in alignments imported
2719 from the JPred4 web server</li>
2720 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2721 system on OSX<br />LGPL libraries courtesy of <a
2722 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2724 <li>changed 'View nucleotide structure' submenu to 'View
2725 VARNA 2D Structure'</li>
2726 <li>change "View protein structure" menu option to "3D
2729 </ul> <em>Applet</em>
2731 <li>New layout for applet example pages</li>
2732 <li>New parameters to enable SplitFrame view
2733 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2734 <li>New example demonstrating linked viewing of cDNA and
2735 Protein alignments</li>
2736 </ul> <em>Development and deployment</em>
2738 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2739 <li>Include installation type and git revision in build
2740 properties and console log output</li>
2741 <li>Jalview Github organisation, and new github site for
2742 storing BioJsMSA Templates</li>
2743 <li>Jalview's unit tests now managed with TestNG</li>
2746 <!-- <em>General</em>
2748 </ul> --> <!-- issues resolved --> <em>Application</em>
2750 <li>Escape should close any open find dialogs</li>
2751 <li>Typo in select-by-features status report</li>
2752 <li>Consensus RNA secondary secondary structure
2753 predictions are not highlighted in amber</li>
2754 <li>Missing gap character in v2.7 example file means
2755 alignment appears unaligned when pad-gaps is not enabled</li>
2756 <li>First switch to RNA Helices colouring doesn't colour
2757 associated structure views</li>
2758 <li>ID width preference option is greyed out when auto
2759 width checkbox not enabled</li>
2760 <li>Stopped a warning dialog from being shown when
2761 creating user defined colours</li>
2762 <li>'View Mapping' in structure viewer shows sequence
2763 mappings for just that viewer's sequences</li>
2764 <li>Workaround for superposing PDB files containing
2765 multiple models in Chimera</li>
2766 <li>Report sequence position in status bar when hovering
2767 over Jmol structure</li>
2768 <li>Cannot output gaps as '.' symbols with Selection ->
2769 output to text box</li>
2770 <li>Flat file exports of alignments with hidden columns
2771 have incorrect sequence start/end</li>
2772 <li>'Aligning' a second chain to a Chimera structure from
2774 <li>Colour schemes applied to structure viewers don't
2775 work for nucleotide</li>
2776 <li>Loading/cut'n'pasting an empty or invalid file leads
2777 to a grey/invisible alignment window</li>
2778 <li>Exported Jpred annotation from a sequence region
2779 imports to different position</li>
2780 <li>Space at beginning of sequence feature tooltips shown
2781 on some platforms</li>
2782 <li>Chimera viewer 'View | Show Chain' menu is not
2784 <li>'New View' fails with a Null Pointer Exception in
2785 console if Chimera has been opened</li>
2786 <li>Mouseover to Chimera not working</li>
2787 <li>Miscellaneous ENA XML feature qualifiers not
2789 <li>NPE in annotation renderer after 'Extract Scores'</li>
2790 <li>If two structures in one Chimera window, mouseover of
2791 either sequence shows on first structure</li>
2792 <li>'Show annotations' options should not make
2793 non-positional annotations visible</li>
2794 <li>Subsequence secondary structure annotation not shown
2795 in right place after 'view flanking regions'</li>
2796 <li>File Save As type unset when current file format is
2798 <li>Save as '.jar' option removed for saving Jalview
2800 <li>Colour by Sequence colouring in Chimera more
2802 <li>Cannot 'add reference annotation' for a sequence in
2803 several views on same alignment</li>
2804 <li>Cannot show linked products for EMBL / ENA records</li>
2805 <li>Jalview's tooltip wraps long texts containing no
2807 </ul> <em>Applet</em>
2809 <li>Jmol to JalviewLite mouseover/link not working</li>
2810 <li>JalviewLite can't import sequences with ID
2811 descriptions containing angle brackets</li>
2812 </ul> <em>General</em>
2814 <li>Cannot export and reimport RNA secondary structure
2815 via jalview annotation file</li>
2816 <li>Random helix colour palette for colour by annotation
2817 with RNA secondary structure</li>
2818 <li>Mouseover to cDNA from STOP residue in protein
2819 translation doesn't work.</li>
2820 <li>hints when using the select by annotation dialog box</li>
2821 <li>Jmol alignment incorrect if PDB file has alternate CA
2823 <li>FontChooser message dialog appears to hang after
2824 choosing 1pt font</li>
2825 <li>Peptide secondary structure incorrectly imported from
2826 annotation file when annotation display text includes 'e' or
2828 <li>Cannot set colour of new feature type whilst creating
2830 <li>cDNA translation alignment should not be sequence
2831 order dependent</li>
2832 <li>'Show unconserved' doesn't work for lower case
2834 <li>Nucleotide ambiguity codes involving R not recognised</li>
2835 </ul> <em>Deployment and Documentation</em>
2837 <li>Applet example pages appear different to the rest of
2838 www.jalview.org</li>
2839 </ul> <em>Application Known issues</em>
2841 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2842 <li>Misleading message appears after trying to delete
2844 <li>Jalview icon not shown in dock after InstallAnywhere
2845 version launches</li>
2846 <li>Fetching EMBL reference for an RNA sequence results
2847 fails with a sequence mismatch</li>
2848 <li>Corrupted or unreadable alignment display when
2849 scrolling alignment to right</li>
2850 <li>ArrayIndexOutOfBoundsException thrown when remove
2851 empty columns called on alignment with ragged gapped ends</li>
2852 <li>auto calculated alignment annotation rows do not get
2853 placed above or below non-autocalculated rows</li>
2854 <li>Jalview dekstop becomes sluggish at full screen in
2855 ultra-high resolution</li>
2856 <li>Cannot disable consensus calculation independently of
2857 quality and conservation</li>
2858 <li>Mouseover highlighting between cDNA and protein can
2859 become sluggish with more than one splitframe shown</li>
2860 </ul> <em>Applet Known Issues</em>
2862 <li>Core PDB parsing code requires Jmol</li>
2863 <li>Sequence canvas panel goes white when alignment
2864 window is being resized</li>
2870 <td><div align="center">
2871 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2873 <td><em>General</em>
2875 <li>Updated Java code signing certificate donated by
2877 <li>Features and annotation preserved when performing
2878 pairwise alignment</li>
2879 <li>RNA pseudoknot annotation can be
2880 imported/exported/displayed</li>
2881 <li>'colour by annotation' can colour by RNA and
2882 protein secondary structure</li>
2883 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2884 post-hoc with 2.9 release</em>)
2887 </ul> <em>Application</em>
2889 <li>Extract and display secondary structure for sequences
2890 with 3D structures</li>
2891 <li>Support for parsing RNAML</li>
2892 <li>Annotations menu for layout
2894 <li>sort sequence annotation rows by alignment</li>
2895 <li>place sequence annotation above/below alignment
2898 <li>Output in Stockholm format</li>
2899 <li>Internationalisation: improved Spanish (es)
2901 <li>Structure viewer preferences tab</li>
2902 <li>Disorder and Secondary Structure annotation tracks
2903 shared between alignments</li>
2904 <li>UCSF Chimera launch and linked highlighting from
2906 <li>Show/hide all sequence associated annotation rows for
2907 all or current selection</li>
2908 <li>disorder and secondary structure predictions
2909 available as dataset annotation</li>
2910 <li>Per-sequence rna helices colouring</li>
2913 <li>Sequence database accessions imported when fetching
2914 alignments from Rfam</li>
2915 <li>update VARNA version to 3.91</li>
2917 <li>New groovy scripts for exporting aligned positions,
2918 conservation values, and calculating sum of pairs scores.</li>
2919 <li>Command line argument to set default JABAWS server</li>
2920 <li>include installation type in build properties and
2921 console log output</li>
2922 <li>Updated Jalview project format to preserve dataset
2926 <!-- issues resolved --> <em>Application</em>
2928 <li>Distinguish alignment and sequence associated RNA
2929 structure in structure->view->VARNA</li>
2930 <li>Raise dialog box if user deletes all sequences in an
2932 <li>Pressing F1 results in documentation opening twice</li>
2933 <li>Sequence feature tooltip is wrapped</li>
2934 <li>Double click on sequence associated annotation
2935 selects only first column</li>
2936 <li>Redundancy removal doesn't result in unlinked
2937 leaves shown in tree</li>
2938 <li>Undos after several redundancy removals don't undo
2940 <li>Hide sequence doesn't hide associated annotation</li>
2941 <li>User defined colours dialog box too big to fit on
2942 screen and buttons not visible</li>
2943 <li>author list isn't updated if already written to
2944 Jalview properties</li>
2945 <li>Popup menu won't open after retrieving sequence
2947 <li>File open window for associate PDB doesn't open</li>
2948 <li>Left-then-right click on a sequence id opens a
2949 browser search window</li>
2950 <li>Cannot open sequence feature shading/sort popup menu
2951 in feature settings dialog</li>
2952 <li>better tooltip placement for some areas of Jalview
2954 <li>Allow addition of JABAWS Server which doesn't
2955 pass validation</li>
2956 <li>Web services parameters dialog box is too large to
2958 <li>Muscle nucleotide alignment preset obscured by
2960 <li>JABAWS preset submenus don't contain newly
2961 defined user preset</li>
2962 <li>MSA web services warns user if they were launched
2963 with invalid input</li>
2964 <li>Jalview cannot contact DAS Registy when running on
2967 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2968 'Superpose with' submenu not shown when new view
2972 </ul> <!-- <em>Applet</em>
2974 </ul> <em>General</em>
2976 </ul>--> <em>Deployment and Documentation</em>
2978 <li>2G and 1G options in launchApp have no effect on
2979 memory allocation</li>
2980 <li>launchApp service doesn't automatically open
2981 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2983 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2984 InstallAnywhere reports cannot find valid JVM when Java
2985 1.7_055 is available
2987 </ul> <em>Application Known issues</em>
2990 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2991 corrupted or unreadable alignment display when scrolling
2995 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2996 retrieval fails but progress bar continues for DAS retrieval
2997 with large number of ID
3000 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3001 flatfile output of visible region has incorrect sequence
3005 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3006 rna structure consensus doesn't update when secondary
3007 structure tracks are rearranged
3010 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3011 invalid rna structure positional highlighting does not
3012 highlight position of invalid base pairs
3015 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3016 out of memory errors are not raised when saving Jalview
3017 project from alignment window file menu
3020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3021 Switching to RNA Helices colouring doesn't propagate to
3025 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3026 colour by RNA Helices not enabled when user created
3027 annotation added to alignment
3030 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3031 Jalview icon not shown on dock in Mountain Lion/Webstart
3033 </ul> <em>Applet Known Issues</em>
3036 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3037 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3040 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3041 Jalview and Jmol example not compatible with IE9
3044 <li>Sort by annotation score doesn't reverse order
3050 <td><div align="center">
3051 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3054 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3057 <li>Internationalisation of user interface (usually
3058 called i18n support) and translation for Spanish locale</li>
3059 <li>Define/Undefine group on current selection with
3060 Ctrl-G/Shift Ctrl-G</li>
3061 <li>Improved group creation/removal options in
3062 alignment/sequence Popup menu</li>
3063 <li>Sensible precision for symbol distribution
3064 percentages shown in logo tooltip.</li>
3065 <li>Annotation panel height set according to amount of
3066 annotation when alignment first opened</li>
3067 </ul> <em>Application</em>
3069 <li>Interactive consensus RNA secondary structure
3070 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3071 <li>Select columns containing particular features from
3072 Feature Settings dialog</li>
3073 <li>View all 'representative' PDB structures for selected
3075 <li>Update Jalview project format:
3077 <li>New file extension for Jalview projects '.jvp'</li>
3078 <li>Preserve sequence and annotation dataset (to
3079 store secondary structure annotation,etc)</li>
3080 <li>Per group and alignment annotation and RNA helix
3084 <li>New similarity measures for PCA and Tree calculation
3086 <li>Experimental support for retrieval and viewing of
3087 flanking regions for an alignment</li>
3091 <!-- issues resolved --> <em>Application</em>
3093 <li>logo keeps spinning and status remains at queued or
3094 running after job is cancelled</li>
3095 <li>cannot export features from alignments imported from
3096 Jalview/VAMSAS projects</li>
3097 <li>Buggy slider for web service parameters that take
3099 <li>Newly created RNA secondary structure line doesn't
3100 have 'display all symbols' flag set</li>
3101 <li>T-COFFEE alignment score shading scheme and other
3102 annotation shading not saved in Jalview project</li>
3103 <li>Local file cannot be loaded in freshly downloaded
3105 <li>Jalview icon not shown on dock in Mountain
3107 <li>Load file from desktop file browser fails</li>
3108 <li>Occasional NPE thrown when calculating large trees</li>
3109 <li>Cannot reorder or slide sequences after dragging an
3110 alignment onto desktop</li>
3111 <li>Colour by annotation dialog throws NPE after using
3112 'extract scores' function</li>
3113 <li>Loading/cut'n'pasting an empty file leads to a grey
3114 alignment window</li>
3115 <li>Disorder thresholds rendered incorrectly after
3116 performing IUPred disorder prediction</li>
3117 <li>Multiple group annotated consensus rows shown when
3118 changing 'normalise logo' display setting</li>
3119 <li>Find shows blank dialog after 'finished searching' if
3120 nothing matches query</li>
3121 <li>Null Pointer Exceptions raised when sorting by
3122 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3124 <li>Errors in Jmol console when structures in alignment
3125 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3127 <li>Not all working JABAWS services are shown in
3129 <li>JAVAWS version of Jalview fails to launch with
3130 'invalid literal/length code'</li>
3131 <li>Annotation/RNA Helix colourschemes cannot be applied
3132 to alignment with groups (actually fixed in 2.8.0b1)</li>
3133 <li>RNA Helices and T-Coffee Scores available as default
3136 </ul> <em>Applet</em>
3138 <li>Remove group option is shown even when selection is
3140 <li>Apply to all groups ticked but colourscheme changes
3141 don't affect groups</li>
3142 <li>Documented RNA Helices and T-Coffee Scores as valid
3143 colourscheme name</li>
3144 <li>Annotation labels drawn on sequence IDs when
3145 Annotation panel is not displayed</li>
3146 <li>Increased font size for dropdown menus on OSX and
3147 embedded windows</li>
3148 </ul> <em>Other</em>
3150 <li>Consensus sequence for alignments/groups with a
3151 single sequence were not calculated</li>
3152 <li>annotation files that contain only groups imported as
3153 annotation and junk sequences</li>
3154 <li>Fasta files with sequences containing '*' incorrectly
3155 recognised as PFAM or BLC</li>
3156 <li>conservation/PID slider apply all groups option
3157 doesn't affect background (2.8.0b1)
3159 <li>redundancy highlighting is erratic at 0% and 100%</li>
3160 <li>Remove gapped columns fails for sequences with ragged
3162 <li>AMSA annotation row with leading spaces is not
3163 registered correctly on import</li>
3164 <li>Jalview crashes when selecting PCA analysis for
3165 certain alignments</li>
3166 <li>Opening the colour by annotation dialog for an
3167 existing annotation based 'use original colours'
3168 colourscheme loses original colours setting</li>
3173 <td><div align="center">
3174 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3175 <em>30/1/2014</em></strong>
3179 <li>Trusted certificates for JalviewLite applet and
3180 Jalview Desktop application<br />Certificate was donated by
3181 <a href="https://www.certum.eu">Certum</a> to the Jalview
3182 open source project).
3184 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3185 <li>Output in Stockholm format</li>
3186 <li>Allow import of data from gzipped files</li>
3187 <li>Export/import group and sequence associated line
3188 graph thresholds</li>
3189 <li>Nucleotide substitution matrix that supports RNA and
3190 ambiguity codes</li>
3191 <li>Allow disorder predictions to be made on the current
3192 selection (or visible selection) in the same way that JPred
3194 <li>Groovy scripting for headless Jalview operation</li>
3195 </ul> <em>Other improvements</em>
3197 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3198 <li>COMBINE statement uses current SEQUENCE_REF and
3199 GROUP_REF scope to group annotation rows</li>
3200 <li>Support '' style escaping of quotes in Newick
3202 <li>Group options for JABAWS service by command line name</li>
3203 <li>Empty tooltip shown for JABA service options with a
3204 link but no description</li>
3205 <li>Select primary source when selecting authority in
3206 database fetcher GUI</li>
3207 <li>Add .mfa to FASTA file extensions recognised by
3209 <li>Annotation label tooltip text wrap</li>
3214 <li>Slow scrolling when lots of annotation rows are
3216 <li>Lots of NPE (and slowness) after creating RNA
3217 secondary structure annotation line</li>
3218 <li>Sequence database accessions not imported when
3219 fetching alignments from Rfam</li>
3220 <li>Incorrect SHMR submission for sequences with
3222 <li>View all structures does not always superpose
3224 <li>Option widgets in service parameters not updated to
3225 reflect user or preset settings</li>
3226 <li>Null pointer exceptions for some services without
3227 presets or adjustable parameters</li>
3228 <li>Discover PDB IDs entry in structure menu doesn't
3229 discover PDB xRefs</li>
3230 <li>Exception encountered while trying to retrieve
3231 features with DAS</li>
3232 <li>Lowest value in annotation row isn't coloured
3233 when colour by annotation (per sequence) is coloured</li>
3234 <li>Keyboard mode P jumps to start of gapped region when
3235 residue follows a gap</li>
3236 <li>Jalview appears to hang importing an alignment with
3237 Wrap as default or after enabling Wrap</li>
3238 <li>'Right click to add annotations' message
3239 shown in wrap mode when no annotations present</li>
3240 <li>Disorder predictions fail with NPE if no automatic
3241 annotation already exists on alignment</li>
3242 <li>oninit javascript function should be called after
3243 initialisation completes</li>
3244 <li>Remove redundancy after disorder prediction corrupts
3245 alignment window display</li>
3246 <li>Example annotation file in documentation is invalid</li>
3247 <li>Grouped line graph annotation rows are not exported
3248 to annotation file</li>
3249 <li>Multi-harmony analysis cannot be run when only two
3251 <li>Cannot create multiple groups of line graphs with
3252 several 'combine' statements in annotation file</li>
3253 <li>Pressing return several times causes Number Format
3254 exceptions in keyboard mode</li>
3255 <li>Multi-harmony (SHMMR) method doesn't submit
3256 correct partitions for input data</li>
3257 <li>Translation from DNA to Amino Acids fails</li>
3258 <li>Jalview fail to load newick tree with quoted label</li>
3259 <li>--headless flag isn't understood</li>
3260 <li>ClassCastException when generating EPS in headless
3262 <li>Adjusting sequence-associated shading threshold only
3263 changes one row's threshold</li>
3264 <li>Preferences and Feature settings panel panel
3265 doesn't open</li>
3266 <li>hide consensus histogram also hides conservation and
3267 quality histograms</li>
3272 <td><div align="center">
3273 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3275 <td><em>Application</em>
3277 <li>Support for JABAWS 2.0 Services (AACon alignment
3278 conservation, protein disorder and Clustal Omega)</li>
3279 <li>JABAWS server status indicator in Web Services
3281 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3282 in Jalview alignment window</li>
3283 <li>Updated Jalview build and deploy framework for OSX
3284 mountain lion, windows 7, and 8</li>
3285 <li>Nucleotide substitution matrix for PCA that supports
3286 RNA and ambiguity codes</li>
3288 <li>Improved sequence database retrieval GUI</li>
3289 <li>Support fetching and database reference look up
3290 against multiple DAS sources (Fetch all from in 'fetch db
3292 <li>Jalview project improvements
3294 <li>Store and retrieve the 'belowAlignment'
3295 flag for annotation</li>
3296 <li>calcId attribute to group annotation rows on the
3298 <li>Store AACon calculation settings for a view in
3299 Jalview project</li>
3303 <li>horizontal scrolling gesture support</li>
3304 <li>Visual progress indicator when PCA calculation is
3306 <li>Simpler JABA web services menus</li>
3307 <li>visual indication that web service results are still
3308 being retrieved from server</li>
3309 <li>Serialise the dialogs that are shown when Jalview
3310 starts up for first time</li>
3311 <li>Jalview user agent string for interacting with HTTP
3313 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3315 <li>Examples directory and Groovy library included in
3316 InstallAnywhere distribution</li>
3317 </ul> <em>Applet</em>
3319 <li>RNA alignment and secondary structure annotation
3320 visualization applet example</li>
3321 </ul> <em>General</em>
3323 <li>Normalise option for consensus sequence logo</li>
3324 <li>Reset button in PCA window to return dimensions to
3326 <li>Allow seqspace or Jalview variant of alignment PCA
3328 <li>PCA with either nucleic acid and protein substitution
3330 <li>Allow windows containing HTML reports to be exported
3332 <li>Interactive display and editing of RNA secondary
3333 structure contacts</li>
3334 <li>RNA Helix Alignment Colouring</li>
3335 <li>RNA base pair logo consensus</li>
3336 <li>Parse sequence associated secondary structure
3337 information in Stockholm files</li>
3338 <li>HTML Export database accessions and annotation
3339 information presented in tooltip for sequences</li>
3340 <li>Import secondary structure from LOCARNA clustalw
3341 style RNA alignment files</li>
3342 <li>import and visualise T-COFFEE quality scores for an
3344 <li>'colour by annotation' per sequence option to
3345 shade each sequence according to its associated alignment
3347 <li>New Jalview Logo</li>
3348 </ul> <em>Documentation and Development</em>
3350 <li>documentation for score matrices used in Jalview</li>
3351 <li>New Website!</li>
3353 <td><em>Application</em>
3355 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3356 wsdbfetch REST service</li>
3357 <li>Stop windows being moved outside desktop on OSX</li>
3358 <li>Filetype associations not installed for webstart
3360 <li>Jalview does not always retrieve progress of a JABAWS
3361 job execution in full once it is complete</li>
3362 <li>revise SHMR RSBS definition to ensure alignment is
3363 uploaded via ali_file parameter</li>
3364 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3365 <li>View all structures superposed fails with exception</li>
3366 <li>Jnet job queues forever if a very short sequence is
3367 submitted for prediction</li>
3368 <li>Cut and paste menu not opened when mouse clicked on
3370 <li>Putting fractional value into integer text box in
3371 alignment parameter dialog causes Jalview to hang</li>
3372 <li>Structure view highlighting doesn't work on
3374 <li>View all structures fails with exception shown in
3376 <li>Characters in filename associated with PDBEntry not
3377 escaped in a platform independent way</li>
3378 <li>Jalview desktop fails to launch with exception when
3380 <li>Tree calculation reports 'you must have 2 or more
3381 sequences selected' when selection is empty</li>
3382 <li>Jalview desktop fails to launch with jar signature
3383 failure when java web start temporary file caching is
3385 <li>DAS Sequence retrieval with range qualification
3386 results in sequence xref which includes range qualification</li>
3387 <li>Errors during processing of command line arguments
3388 cause progress bar (JAL-898) to be removed</li>
3389 <li>Replace comma for semi-colon option not disabled for
3390 DAS sources in sequence fetcher</li>
3391 <li>Cannot close news reader when JABAWS server warning
3392 dialog is shown</li>
3393 <li>Option widgets not updated to reflect user settings</li>
3394 <li>Edited sequence not submitted to web service</li>
3395 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3396 <li>InstallAnywhere installer doesn't unpack and run
3397 on OSX Mountain Lion</li>
3398 <li>Annotation panel not given a scroll bar when
3399 sequences with alignment annotation are pasted into the
3401 <li>Sequence associated annotation rows not associated
3402 when loaded from Jalview project</li>
3403 <li>Browser launch fails with NPE on java 1.7</li>
3404 <li>JABAWS alignment marked as finished when job was
3405 cancelled or job failed due to invalid input</li>
3406 <li>NPE with v2.7 example when clicking on Tree
3407 associated with all views</li>
3408 <li>Exceptions when copy/paste sequences with grouped
3409 annotation rows to new window</li>
3410 </ul> <em>Applet</em>
3412 <li>Sequence features are momentarily displayed before
3413 they are hidden using hidefeaturegroups applet parameter</li>
3414 <li>loading features via javascript API automatically
3415 enables feature display</li>
3416 <li>scrollToColumnIn javascript API method doesn't
3418 </ul> <em>General</em>
3420 <li>Redundancy removal fails for rna alignment</li>
3421 <li>PCA calculation fails when sequence has been selected
3422 and then deselected</li>
3423 <li>PCA window shows grey box when first opened on OSX</li>
3424 <li>Letters coloured pink in sequence logo when alignment
3425 coloured with clustalx</li>
3426 <li>Choosing fonts without letter symbols defined causes
3427 exceptions and redraw errors</li>
3428 <li>Initial PCA plot view is not same as manually
3429 reconfigured view</li>
3430 <li>Grouped annotation graph label has incorrect line
3432 <li>Grouped annotation graph label display is corrupted
3433 for lots of labels</li>
3438 <div align="center">
3439 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3442 <td><em>Application</em>
3444 <li>Jalview Desktop News Reader</li>
3445 <li>Tweaked default layout of web services menu</li>
3446 <li>View/alignment association menu to enable user to
3447 easily specify which alignment a multi-structure view takes
3448 its colours/correspondences from</li>
3449 <li>Allow properties file location to be specified as URL</li>
3450 <li>Extend Jalview project to preserve associations
3451 between many alignment views and a single Jmol display</li>
3452 <li>Store annotation row height in Jalview project file</li>
3453 <li>Annotation row column label formatting attributes
3454 stored in project file</li>
3455 <li>Annotation row order for auto-calculated annotation
3456 rows preserved in Jalview project file</li>
3457 <li>Visual progress indication when Jalview state is
3458 saved using Desktop window menu</li>
3459 <li>Visual indication that command line arguments are
3460 still being processed</li>
3461 <li>Groovy script execution from URL</li>
3462 <li>Colour by annotation default min and max colours in
3464 <li>Automatically associate PDB files dragged onto an
3465 alignment with sequences that have high similarity and
3467 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3468 <li>'view structures' option to open many
3469 structures in same window</li>
3470 <li>Sort associated views menu option for tree panel</li>
3471 <li>Group all JABA and non-JABA services for a particular
3472 analysis function in its own submenu</li>
3473 </ul> <em>Applet</em>
3475 <li>Userdefined and autogenerated annotation rows for
3477 <li>Adjustment of alignment annotation pane height</li>
3478 <li>Annotation scrollbar for annotation panel</li>
3479 <li>Drag to reorder annotation rows in annotation panel</li>
3480 <li>'automaticScrolling' parameter</li>
3481 <li>Allow sequences with partial ID string matches to be
3482 annotated from GFF/Jalview features files</li>
3483 <li>Sequence logo annotation row in applet</li>
3484 <li>Absolute paths relative to host server in applet
3485 parameters are treated as such</li>
3486 <li>New in the JalviewLite javascript API:
3488 <li>JalviewLite.js javascript library</li>
3489 <li>Javascript callbacks for
3491 <li>Applet initialisation</li>
3492 <li>Sequence/alignment mouse-overs and selections</li>
3495 <li>scrollTo row and column alignment scrolling
3497 <li>Select sequence/alignment regions from javascript</li>
3498 <li>javascript structure viewer harness to pass
3499 messages between Jmol and Jalview when running as
3500 distinct applets</li>
3501 <li>sortBy method</li>
3502 <li>Set of applet and application examples shipped
3503 with documentation</li>
3504 <li>New example to demonstrate JalviewLite and Jmol
3505 javascript message exchange</li>
3507 </ul> <em>General</em>
3509 <li>Enable Jmol displays to be associated with multiple
3510 multiple alignments</li>
3511 <li>Option to automatically sort alignment with new tree</li>
3512 <li>User configurable link to enable redirects to a
3513 www.Jalview.org mirror</li>
3514 <li>Jmol colours option for Jmol displays</li>
3515 <li>Configurable newline string when writing alignment
3516 and other flat files</li>
3517 <li>Allow alignment annotation description lines to
3518 contain html tags</li>
3519 </ul> <em>Documentation and Development</em>
3521 <li>Add groovy test harness for bulk load testing to
3523 <li>Groovy script to load and align a set of sequences
3524 using a web service before displaying the result in the
3525 Jalview desktop</li>
3526 <li>Restructured javascript and applet api documentation</li>
3527 <li>Ant target to publish example html files with applet
3529 <li>Netbeans project for building Jalview from source</li>
3530 <li>ant task to create online javadoc for Jalview source</li>
3532 <td><em>Application</em>
3534 <li>User defined colourscheme throws exception when
3535 current built in colourscheme is saved as new scheme</li>
3536 <li>AlignFrame->Save in application pops up save
3537 dialog for valid filename/format</li>
3538 <li>Cannot view associated structure for UniProt sequence</li>
3539 <li>PDB file association breaks for UniProt sequence
3541 <li>Associate PDB from file dialog does not tell you
3542 which sequence is to be associated with the file</li>
3543 <li>Find All raises null pointer exception when query
3544 only matches sequence IDs</li>
3545 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3546 <li>Jalview project with Jmol views created with Jalview
3547 2.4 cannot be loaded</li>
3548 <li>Filetype associations not installed for webstart
3550 <li>Two or more chains in a single PDB file associated
3551 with sequences in different alignments do not get coloured
3552 by their associated sequence</li>
3553 <li>Visibility status of autocalculated annotation row
3554 not preserved when project is loaded</li>
3555 <li>Annotation row height and visibility attributes not
3556 stored in Jalview project</li>
3557 <li>Tree bootstraps are not preserved when saved as a
3558 Jalview project</li>
3559 <li>Envision2 workflow tooltips are corrupted</li>
3560 <li>Enabling show group conservation also enables colour
3561 by conservation</li>
3562 <li>Duplicate group associated conservation or consensus
3563 created on new view</li>
3564 <li>Annotation scrollbar not displayed after 'show
3565 all hidden annotation rows' option selected</li>
3566 <li>Alignment quality not updated after alignment
3567 annotation row is hidden then shown</li>
3568 <li>Preserve colouring of structures coloured by
3569 sequences in pre Jalview 2.7 projects</li>
3570 <li>Web service job parameter dialog is not laid out
3572 <li>Web services menu not refreshed after 'reset
3573 services' button is pressed in preferences</li>
3574 <li>Annotation off by one in Jalview v2_3 example project</li>
3575 <li>Structures imported from file and saved in project
3576 get name like jalview_pdb1234.txt when reloaded</li>
3577 <li>Jalview does not always retrieve progress of a JABAWS
3578 job execution in full once it is complete</li>
3579 </ul> <em>Applet</em>
3581 <li>Alignment height set incorrectly when lots of
3582 annotation rows are displayed</li>
3583 <li>Relative URLs in feature HTML text not resolved to
3585 <li>View follows highlighting does not work for positions
3587 <li><= shown as = in tooltip</li>
3588 <li>Export features raises exception when no features
3590 <li>Separator string used for serialising lists of IDs
3591 for javascript api is modified when separator string
3592 provided as parameter</li>
3593 <li>Null pointer exception when selecting tree leaves for
3594 alignment with no existing selection</li>
3595 <li>Relative URLs for datasources assumed to be relative
3596 to applet's codebase</li>
3597 <li>Status bar not updated after finished searching and
3598 search wraps around to first result</li>
3599 <li>StructureSelectionManager instance shared between
3600 several Jalview applets causes race conditions and memory
3602 <li>Hover tooltip and mouseover of position on structure
3603 not sent from Jmol in applet</li>
3604 <li>Certain sequences of javascript method calls to
3605 applet API fatally hang browser</li>
3606 </ul> <em>General</em>
3608 <li>View follows structure mouseover scrolls beyond
3609 position with wrapped view and hidden regions</li>
3610 <li>Find sequence position moves to wrong residue
3611 with/without hidden columns</li>
3612 <li>Sequence length given in alignment properties window
3614 <li>InvalidNumberFormat exceptions thrown when trying to
3615 import PDB like structure files</li>
3616 <li>Positional search results are only highlighted
3617 between user-supplied sequence start/end bounds</li>
3618 <li>End attribute of sequence is not validated</li>
3619 <li>Find dialog only finds first sequence containing a
3620 given sequence position</li>
3621 <li>Sequence numbering not preserved in MSF alignment
3623 <li>Jalview PDB file reader does not extract sequence
3624 from nucleotide chains correctly</li>
3625 <li>Structure colours not updated when tree partition
3626 changed in alignment</li>
3627 <li>Sequence associated secondary structure not correctly
3628 parsed in interleaved stockholm</li>
3629 <li>Colour by annotation dialog does not restore current
3631 <li>Hiding (nearly) all sequences doesn't work
3633 <li>Sequences containing lowercase letters are not
3634 properly associated with their pdb files</li>
3635 </ul> <em>Documentation and Development</em>
3637 <li>schemas/JalviewWsParamSet.xsd corrupted by
3638 ApplyCopyright tool</li>
3643 <div align="center">
3644 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3647 <td><em>Application</em>
3649 <li>New warning dialog when the Jalview Desktop cannot
3650 contact web services</li>
3651 <li>JABA service parameters for a preset are shown in
3652 service job window</li>
3653 <li>JABA Service menu entries reworded</li>
3657 <li>Modeller PIR IO broken - cannot correctly import a
3658 pir file emitted by Jalview</li>
3659 <li>Existing feature settings transferred to new
3660 alignment view created from cut'n'paste</li>
3661 <li>Improved test for mixed amino/nucleotide chains when
3662 parsing PDB files</li>
3663 <li>Consensus and conservation annotation rows
3664 occasionally become blank for all new windows</li>
3665 <li>Exception raised when right clicking above sequences
3666 in wrapped view mode</li>
3667 </ul> <em>Application</em>
3669 <li>multiple multiply aligned structure views cause cpu
3670 usage to hit 100% and computer to hang</li>
3671 <li>Web Service parameter layout breaks for long user
3672 parameter names</li>
3673 <li>Jaba service discovery hangs desktop if Jaba server
3680 <div align="center">
3681 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3684 <td><em>Application</em>
3686 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3687 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3690 <li>Web Services preference tab</li>
3691 <li>Analysis parameters dialog box and user defined
3693 <li>Improved speed and layout of Envision2 service menu</li>
3694 <li>Superpose structures using associated sequence
3696 <li>Export coordinates and projection as CSV from PCA
3698 </ul> <em>Applet</em>
3700 <li>enable javascript: execution by the applet via the
3701 link out mechanism</li>
3702 </ul> <em>Other</em>
3704 <li>Updated the Jmol Jalview interface to work with Jmol
3706 <li>The Jalview Desktop and JalviewLite applet now
3707 require Java 1.5</li>
3708 <li>Allow Jalview feature colour specification for GFF
3709 sequence annotation files</li>
3710 <li>New 'colour by label' keword in Jalview feature file
3711 type colour specification</li>
3712 <li>New Jalview Desktop Groovy API method that allows a
3713 script to check if it being run in an interactive session or
3714 in a batch operation from the Jalview command line</li>
3718 <li>clustalx colourscheme colours Ds preferentially when
3719 both D+E are present in over 50% of the column</li>
3720 </ul> <em>Application</em>
3722 <li>typo in AlignmentFrame->View->Hide->all but
3723 selected Regions menu item</li>
3724 <li>sequence fetcher replaces ',' for ';' when the ',' is
3725 part of a valid accession ID</li>
3726 <li>fatal OOM if object retrieved by sequence fetcher
3727 runs out of memory</li>
3728 <li>unhandled Out of Memory Error when viewing pca
3729 analysis results</li>
3730 <li>InstallAnywhere builds fail to launch on OS X java
3731 10.5 update 4 (due to apple Java 1.6 update)</li>
3732 <li>Installanywhere Jalview silently fails to launch</li>
3733 </ul> <em>Applet</em>
3735 <li>Jalview.getFeatureGroups() raises an
3736 ArrayIndexOutOfBoundsException if no feature groups are
3743 <div align="center">
3744 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3750 <li>Alignment prettyprinter doesn't cope with long
3752 <li>clustalx colourscheme colours Ds preferentially when
3753 both D+E are present in over 50% of the column</li>
3754 <li>nucleic acid structures retrieved from PDB do not
3755 import correctly</li>
3756 <li>More columns get selected than were clicked on when a
3757 number of columns are hidden</li>
3758 <li>annotation label popup menu not providing correct
3759 add/hide/show options when rows are hidden or none are
3761 <li>Stockholm format shown in list of readable formats,
3762 and parser copes better with alignments from RFAM.</li>
3763 <li>CSV output of consensus only includes the percentage
3764 of all symbols if sequence logo display is enabled</li>
3766 </ul> <em>Applet</em>
3768 <li>annotation panel disappears when annotation is
3770 </ul> <em>Application</em>
3772 <li>Alignment view not redrawn properly when new
3773 alignment opened where annotation panel is visible but no
3774 annotations are present on alignment</li>
3775 <li>pasted region containing hidden columns is
3776 incorrectly displayed in new alignment window</li>
3777 <li>Jalview slow to complete operations when stdout is
3778 flooded (fix is to close the Jalview console)</li>
3779 <li>typo in AlignmentFrame->View->Hide->all but
3780 selected Rregions menu item.</li>
3781 <li>inconsistent group submenu and Format submenu entry
3782 'Un' or 'Non'conserved</li>
3783 <li>Sequence feature settings are being shared by
3784 multiple distinct alignments</li>
3785 <li>group annotation not recreated when tree partition is
3787 <li>double click on group annotation to select sequences
3788 does not propagate to associated trees</li>
3789 <li>Mac OSX specific issues:
3791 <li>exception raised when mouse clicked on desktop
3792 window background</li>
3793 <li>Desktop menu placed on menu bar and application
3794 name set correctly</li>
3795 <li>sequence feature settings not wide enough for the
3796 save feature colourscheme button</li>
3805 <div align="center">
3806 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3809 <td><em>New Capabilities</em>
3811 <li>URL links generated from description line for
3812 regular-expression based URL links (applet and application)
3814 <li>Non-positional feature URL links are shown in link
3816 <li>Linked viewing of nucleic acid sequences and
3818 <li>Automatic Scrolling option in View menu to display
3819 the currently highlighted region of an alignment.</li>
3820 <li>Order an alignment by sequence length, or using the
3821 average score or total feature count for each sequence.</li>
3822 <li>Shading features by score or associated description</li>
3823 <li>Subdivide alignment and groups based on identity of
3824 selected subsequence (Make Groups from Selection).</li>
3825 <li>New hide/show options including Shift+Control+H to
3826 hide everything but the currently selected region.</li>
3827 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3828 </ul> <em>Application</em>
3830 <li>Fetch DB References capabilities and UI expanded to
3831 support retrieval from DAS sequence sources</li>
3832 <li>Local DAS Sequence sources can be added via the
3833 command line or via the Add local source dialog box.</li>
3834 <li>DAS Dbref and DbxRef feature types are parsed as
3835 database references and protein_name is parsed as
3836 description line (BioSapiens terms).</li>
3837 <li>Enable or disable non-positional feature and database
3838 references in sequence ID tooltip from View menu in
3840 <!-- <li>New hidden columns and rows and representatives capabilities
3841 in annotations file (in progress - not yet fully implemented)</li> -->
3842 <li>Group-associated consensus, sequence logos and
3843 conservation plots</li>
3844 <li>Symbol distributions for each column can be exported
3845 and visualized as sequence logos</li>
3846 <li>Optionally scale multi-character column labels to fit
3847 within each column of annotation row<!-- todo for applet -->
3849 <li>Optional automatic sort of associated alignment view
3850 when a new tree is opened.</li>
3851 <li>Jalview Java Console</li>
3852 <li>Better placement of desktop window when moving
3853 between different screens.</li>
3854 <li>New preference items for sequence ID tooltip and
3855 consensus annotation</li>
3856 <li>Client to submit sequences and IDs to Envision2
3858 <li><em>Vamsas Capabilities</em>
3860 <li>Improved VAMSAS synchronization (Jalview archive
3861 used to preserve views, structures, and tree display
3863 <li>Import of vamsas documents from disk or URL via
3865 <li>Sharing of selected regions between views and
3866 with other VAMSAS applications (Experimental feature!)</li>
3867 <li>Updated API to VAMSAS version 0.2</li>
3869 </ul> <em>Applet</em>
3871 <li>Middle button resizes annotation row height</li>
3874 <li>sortByTree (true/false) - automatically sort the
3875 associated alignment view by the tree when a new tree is
3877 <li>showTreeBootstraps (true/false) - show or hide
3878 branch bootstraps (default is to show them if available)</li>
3879 <li>showTreeDistances (true/false) - show or hide
3880 branch lengths (default is to show them if available)</li>
3881 <li>showUnlinkedTreeNodes (true/false) - indicate if
3882 unassociated nodes should be highlighted in the tree
3884 <li>heightScale and widthScale (1.0 or more) -
3885 increase the height or width of a cell in the alignment
3886 grid relative to the current font size.</li>
3889 <li>Non-positional features displayed in sequence ID
3891 </ul> <em>Other</em>
3893 <li>Features format: graduated colour definitions and
3894 specification of feature scores</li>
3895 <li>Alignment Annotations format: new keywords for group
3896 associated annotation (GROUP_REF) and annotation row display
3897 properties (ROW_PROPERTIES)</li>
3898 <li>XML formats extended to support graduated feature
3899 colourschemes, group associated annotation, and profile
3900 visualization settings.</li></td>
3903 <li>Source field in GFF files parsed as feature source
3904 rather than description</li>
3905 <li>Non-positional features are now included in sequence
3906 feature and gff files (controlled via non-positional feature
3907 visibility in tooltip).</li>
3908 <li>URL links generated for all feature links (bugfix)</li>
3909 <li>Added URL embedding instructions to features file
3911 <li>Codons containing ambiguous nucleotides translated as
3912 'X' in peptide product</li>
3913 <li>Match case switch in find dialog box works for both
3914 sequence ID and sequence string and query strings do not
3915 have to be in upper case to match case-insensitively.</li>
3916 <li>AMSA files only contain first column of
3917 multi-character column annotation labels</li>
3918 <li>Jalview Annotation File generation/parsing consistent
3919 with documentation (e.g. Stockholm annotation can be
3920 exported and re-imported)</li>
3921 <li>PDB files without embedded PDB IDs given a friendly
3923 <li>Find incrementally searches ID string matches as well
3924 as subsequence matches, and correctly reports total number
3928 <li>Better handling of exceptions during sequence
3930 <li>Dasobert generated non-positional feature URL
3931 link text excludes the start_end suffix</li>
3932 <li>DAS feature and source retrieval buttons disabled
3933 when fetch or registry operations in progress.</li>
3934 <li>PDB files retrieved from URLs are cached properly</li>
3935 <li>Sequence description lines properly shared via
3937 <li>Sequence fetcher fetches multiple records for all
3939 <li>Ensured that command line das feature retrieval
3940 completes before alignment figures are generated.</li>
3941 <li>Reduced time taken when opening file browser for
3943 <li>isAligned check prior to calculating tree, PCA or
3944 submitting an MSA to JNet now excludes hidden sequences.</li>
3945 <li>User defined group colours properly recovered
3946 from Jalview projects.</li>
3955 <div align="center">
3956 <strong>2.4.0.b2</strong><br> 28/10/2009
3961 <li>Experimental support for google analytics usage
3963 <li>Jalview privacy settings (user preferences and docs).</li>
3968 <li>Race condition in applet preventing startup in
3970 <li>Exception when feature created from selection beyond
3971 length of sequence.</li>
3972 <li>Allow synthetic PDB files to be imported gracefully</li>
3973 <li>Sequence associated annotation rows associate with
3974 all sequences with a given id</li>
3975 <li>Find function matches case-insensitively for sequence
3976 ID string searches</li>
3977 <li>Non-standard characters do not cause pairwise
3978 alignment to fail with exception</li>
3979 </ul> <em>Application Issues</em>
3981 <li>Sequences are now validated against EMBL database</li>
3982 <li>Sequence fetcher fetches multiple records for all
3984 </ul> <em>InstallAnywhere Issues</em>
3986 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3987 issue with installAnywhere mechanism)</li>
3988 <li>Command line launching of JARs from InstallAnywhere
3989 version (java class versioning error fixed)</li>
3996 <div align="center">
3997 <strong>2.4</strong><br> 27/8/2008
4000 <td><em>User Interface</em>
4002 <li>Linked highlighting of codon and amino acid from
4003 translation and protein products</li>
4004 <li>Linked highlighting of structure associated with
4005 residue mapping to codon position</li>
4006 <li>Sequence Fetcher provides example accession numbers
4007 and 'clear' button</li>
4008 <li>MemoryMonitor added as an option under Desktop's
4010 <li>Extract score function to parse whitespace separated
4011 numeric data in description line</li>
4012 <li>Column labels in alignment annotation can be centred.</li>
4013 <li>Tooltip for sequence associated annotation give name
4015 </ul> <em>Web Services and URL fetching</em>
4017 <li>JPred3 web service</li>
4018 <li>Prototype sequence search client (no public services
4020 <li>Fetch either seed alignment or full alignment from
4022 <li>URL Links created for matching database cross
4023 references as well as sequence ID</li>
4024 <li>URL Links can be created using regular-expressions</li>
4025 </ul> <em>Sequence Database Connectivity</em>
4027 <li>Retrieval of cross-referenced sequences from other
4029 <li>Generalised database reference retrieval and
4030 validation to all fetchable databases</li>
4031 <li>Fetch sequences from DAS sources supporting the
4032 sequence command</li>
4033 </ul> <em>Import and Export</em>
4034 <li>export annotation rows as CSV for spreadsheet import</li>
4035 <li>Jalview projects record alignment dataset associations,
4036 EMBL products, and cDNA sequence mappings</li>
4037 <li>Sequence Group colour can be specified in Annotation
4039 <li>Ad-hoc colouring of group in Annotation File using RGB
4040 triplet as name of colourscheme</li>
4041 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4043 <li>treenode binding for VAMSAS tree exchange</li>
4044 <li>local editing and update of sequences in VAMSAS
4045 alignments (experimental)</li>
4046 <li>Create new or select existing session to join</li>
4047 <li>load and save of vamsas documents</li>
4048 </ul> <em>Application command line</em>
4050 <li>-tree parameter to open trees (introduced for passing
4052 <li>-fetchfrom command line argument to specify nicknames
4053 of DAS servers to query for alignment features</li>
4054 <li>-dasserver command line argument to add new servers
4055 that are also automatically queried for features</li>
4056 <li>-groovy command line argument executes a given groovy
4057 script after all input data has been loaded and parsed</li>
4058 </ul> <em>Applet-Application data exchange</em>
4060 <li>Trees passed as applet parameters can be passed to
4061 application (when using "View in full
4062 application")</li>
4063 </ul> <em>Applet Parameters</em>
4065 <li>feature group display control parameter</li>
4066 <li>debug parameter</li>
4067 <li>showbutton parameter</li>
4068 </ul> <em>Applet API methods</em>
4070 <li>newView public method</li>
4071 <li>Window (current view) specific get/set public methods</li>
4072 <li>Feature display control methods</li>
4073 <li>get list of currently selected sequences</li>
4074 </ul> <em>New Jalview distribution features</em>
4076 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4077 <li>RELEASE file gives build properties for the latest
4078 Jalview release.</li>
4079 <li>Java 1.1 Applet build made easier and donotobfuscate
4080 property controls execution of obfuscator</li>
4081 <li>Build target for generating source distribution</li>
4082 <li>Debug flag for javacc</li>
4083 <li>.jalview_properties file is documented (slightly) in
4084 jalview.bin.Cache</li>
4085 <li>Continuous Build Integration for stable and
4086 development version of Application, Applet and source
4091 <li>selected region output includes visible annotations
4092 (for certain formats)</li>
4093 <li>edit label/displaychar contains existing label/char
4095 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4096 <li>shorter peptide product names from EMBL records</li>
4097 <li>Newick string generator makes compact representations</li>
4098 <li>bootstrap values parsed correctly for tree files with
4100 <li>pathological filechooser bug avoided by not allowing
4101 filenames containing a ':'</li>
4102 <li>Fixed exception when parsing GFF files containing
4103 global sequence features</li>
4104 <li>Alignment datasets are finalized only when number of
4105 references from alignment sequences goes to zero</li>
4106 <li>Close of tree branch colour box without colour
4107 selection causes cascading exceptions</li>
4108 <li>occasional negative imgwidth exceptions</li>
4109 <li>better reporting of non-fatal warnings to user when
4110 file parsing fails.</li>
4111 <li>Save works when Jalview project is default format</li>
4112 <li>Save as dialog opened if current alignment format is
4113 not a valid output format</li>
4114 <li>UniProt canonical names introduced for both das and
4116 <li>Histidine should be midblue (not pink!) in Zappo</li>
4117 <li>error messages passed up and output when data read
4119 <li>edit undo recovers previous dataset sequence when
4120 sequence is edited</li>
4121 <li>allow PDB files without pdb ID HEADER lines (like
4122 those generated by MODELLER) to be read in properly</li>
4123 <li>allow reading of JPred concise files as a normal
4125 <li>Stockholm annotation parsing and alignment properties
4126 import fixed for PFAM records</li>
4127 <li>Structure view windows have correct name in Desktop
4129 <li>annotation consisting of sequence associated scores
4130 can be read and written correctly to annotation file</li>
4131 <li>Aligned cDNA translation to aligned peptide works
4133 <li>Fixed display of hidden sequence markers and
4134 non-italic font for representatives in Applet</li>
4135 <li>Applet Menus are always embedded in applet window on
4137 <li>Newly shown features appear at top of stack (in
4139 <li>Annotations added via parameter not drawn properly
4140 due to null pointer exceptions</li>
4141 <li>Secondary structure lines are drawn starting from
4142 first column of alignment</li>
4143 <li>UniProt XML import updated for new schema release in
4145 <li>Sequence feature to sequence ID match for Features
4146 file is case-insensitive</li>
4147 <li>Sequence features read from Features file appended to
4148 all sequences with matching IDs</li>
4149 <li>PDB structure coloured correctly for associated views
4150 containing a sub-sequence</li>
4151 <li>PDB files can be retrieved by applet from Jar files</li>
4152 <li>feature and annotation file applet parameters
4153 referring to different directories are retrieved correctly</li>
4154 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4155 <li>Fixed application hang whilst waiting for
4156 splash-screen version check to complete</li>
4157 <li>Applet properly URLencodes input parameter values
4158 when passing them to the launchApp service</li>
4159 <li>display name and local features preserved in results
4160 retrieved from web service</li>
4161 <li>Visual delay indication for sequence retrieval and
4162 sequence fetcher initialisation</li>
4163 <li>updated Application to use DAS 1.53e version of
4164 dasobert DAS client</li>
4165 <li>Re-instated Full AMSA support and .amsa file
4167 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4175 <div align="center">
4176 <strong>2.3</strong><br> 9/5/07
4181 <li>Jmol 11.0.2 integration</li>
4182 <li>PDB views stored in Jalview XML files</li>
4183 <li>Slide sequences</li>
4184 <li>Edit sequence in place</li>
4185 <li>EMBL CDS features</li>
4186 <li>DAS Feature mapping</li>
4187 <li>Feature ordering</li>
4188 <li>Alignment Properties</li>
4189 <li>Annotation Scores</li>
4190 <li>Sort by scores</li>
4191 <li>Feature/annotation editing in applet</li>
4196 <li>Headless state operation in 2.2.1</li>
4197 <li>Incorrect and unstable DNA pairwise alignment</li>
4198 <li>Cut and paste of sequences with annotation</li>
4199 <li>Feature group display state in XML</li>
4200 <li>Feature ordering in XML</li>
4201 <li>blc file iteration selection using filename # suffix</li>
4202 <li>Stockholm alignment properties</li>
4203 <li>Stockhom alignment secondary structure annotation</li>
4204 <li>2.2.1 applet had no feature transparency</li>
4205 <li>Number pad keys can be used in cursor mode</li>
4206 <li>Structure Viewer mirror image resolved</li>
4213 <div align="center">
4214 <strong>2.2.1</strong><br> 12/2/07
4219 <li>Non standard characters can be read and displayed
4220 <li>Annotations/Features can be imported/exported to the
4222 <li>Applet allows editing of sequence/annotation/group
4223 name & description
4224 <li>Preference setting to display sequence name in
4226 <li>Annotation file format extended to allow
4227 Sequence_groups to be defined
4228 <li>Default opening of alignment overview panel can be
4229 specified in preferences
4230 <li>PDB residue numbering annotation added to associated
4236 <li>Applet crash under certain Linux OS with Java 1.6
4238 <li>Annotation file export / import bugs fixed
4239 <li>PNG / EPS image output bugs fixed
4245 <div align="center">
4246 <strong>2.2</strong><br> 27/11/06
4251 <li>Multiple views on alignment
4252 <li>Sequence feature editing
4253 <li>"Reload" alignment
4254 <li>"Save" to current filename
4255 <li>Background dependent text colour
4256 <li>Right align sequence ids
4257 <li>User-defined lower case residue colours
4260 <li>Menu item accelerator keys
4261 <li>Control-V pastes to current alignment
4262 <li>Cancel button for DAS Feature Fetching
4263 <li>PCA and PDB Viewers zoom via mouse roller
4264 <li>User-defined sub-tree colours and sub-tree selection
4266 <li>'New Window' button on the 'Output to Text box'
4271 <li>New memory efficient Undo/Redo System
4272 <li>Optimised symbol lookups and conservation/consensus
4274 <li>Region Conservation/Consensus recalculated after
4276 <li>Fixed Remove Empty Columns Bug (empty columns at end
4278 <li>Slowed DAS Feature Fetching for increased robustness.
4280 <li>Made angle brackets in ASCII feature descriptions
4282 <li>Re-instated Zoom function for PCA
4283 <li>Sequence descriptions conserved in web service
4285 <li>UniProt ID discoverer uses any word separated by
4287 <li>WsDbFetch query/result association resolved
4288 <li>Tree leaf to sequence mapping improved
4289 <li>Smooth fonts switch moved to FontChooser dialog box.
4296 <div align="center">
4297 <strong>2.1.1</strong><br> 12/9/06
4302 <li>Copy consensus sequence to clipboard</li>
4307 <li>Image output - rightmost residues are rendered if
4308 sequence id panel has been resized</li>
4309 <li>Image output - all offscreen group boundaries are
4311 <li>Annotation files with sequence references - all
4312 elements in file are relative to sequence position</li>
4313 <li>Mac Applet users can use Alt key for group editing</li>
4319 <div align="center">
4320 <strong>2.1</strong><br> 22/8/06
4325 <li>MAFFT Multiple Alignment in default Web Service list</li>
4326 <li>DAS Feature fetching</li>
4327 <li>Hide sequences and columns</li>
4328 <li>Export Annotations and Features</li>
4329 <li>GFF file reading / writing</li>
4330 <li>Associate structures with sequences from local PDB
4332 <li>Add sequences to exisiting alignment</li>
4333 <li>Recently opened files / URL lists</li>
4334 <li>Applet can launch the full application</li>
4335 <li>Applet has transparency for features (Java 1.2
4337 <li>Applet has user defined colours parameter</li>
4338 <li>Applet can load sequences from parameter
4339 "sequence<em>x</em>"
4345 <li>Redundancy Panel reinstalled in the Applet</li>
4346 <li>Monospaced font - EPS / rescaling bug fixed</li>
4347 <li>Annotation files with sequence references bug fixed</li>
4353 <div align="center">
4354 <strong>2.08.1</strong><br> 2/5/06
4359 <li>Change case of selected region from Popup menu</li>
4360 <li>Choose to match case when searching</li>
4361 <li>Middle mouse button and mouse movement can compress /
4362 expand the visible width and height of the alignment</li>
4367 <li>Annotation Panel displays complete JNet results</li>
4373 <div align="center">
4374 <strong>2.08b</strong><br> 18/4/06
4380 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4381 <li>Righthand label on wrapped alignments shows correct
4388 <div align="center">
4389 <strong>2.08</strong><br> 10/4/06
4394 <li>Editing can be locked to the selection area</li>
4395 <li>Keyboard editing</li>
4396 <li>Create sequence features from searches</li>
4397 <li>Precalculated annotations can be loaded onto
4399 <li>Features file allows grouping of features</li>
4400 <li>Annotation Colouring scheme added</li>
4401 <li>Smooth fonts off by default - Faster rendering</li>
4402 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4407 <li>Drag & Drop fixed on Linux</li>
4408 <li>Jalview Archive file faster to load/save, sequence
4409 descriptions saved.</li>
4415 <div align="center">
4416 <strong>2.07</strong><br> 12/12/05
4421 <li>PDB Structure Viewer enhanced</li>
4422 <li>Sequence Feature retrieval and display enhanced</li>
4423 <li>Choose to output sequence start-end after sequence
4424 name for file output</li>
4425 <li>Sequence Fetcher WSDBFetch@EBI</li>
4426 <li>Applet can read feature files, PDB files and can be
4427 used for HTML form input</li>
4432 <li>HTML output writes groups and features</li>
4433 <li>Group editing is Control and mouse click</li>
4434 <li>File IO bugs</li>
4440 <div align="center">
4441 <strong>2.06</strong><br> 28/9/05
4446 <li>View annotations in wrapped mode</li>
4447 <li>More options for PCA viewer</li>
4452 <li>GUI bugs resolved</li>
4453 <li>Runs with -nodisplay from command line</li>
4459 <div align="center">
4460 <strong>2.05b</strong><br> 15/9/05
4465 <li>Choose EPS export as lineart or text</li>
4466 <li>Jar files are executable</li>
4467 <li>Can read in Uracil - maps to unknown residue</li>
4472 <li>Known OutOfMemory errors give warning message</li>
4473 <li>Overview window calculated more efficiently</li>
4474 <li>Several GUI bugs resolved</li>
4480 <div align="center">
4481 <strong>2.05</strong><br> 30/8/05
4486 <li>Edit and annotate in "Wrapped" view</li>
4491 <li>Several GUI bugs resolved</li>
4497 <div align="center">
4498 <strong>2.04</strong><br> 24/8/05
4503 <li>Hold down mouse wheel & scroll to change font
4509 <li>Improved JPred client reliability</li>
4510 <li>Improved loading of Jalview files</li>
4516 <div align="center">
4517 <strong>2.03</strong><br> 18/8/05
4522 <li>Set Proxy server name and port in preferences</li>
4523 <li>Multiple URL links from sequence ids</li>
4524 <li>User Defined Colours can have a scheme name and added
4526 <li>Choose to ignore gaps in consensus calculation</li>
4527 <li>Unix users can set default web browser</li>
4528 <li>Runs without GUI for batch processing</li>
4529 <li>Dynamically generated Web Service Menus</li>
4534 <li>InstallAnywhere download for Sparc Solaris</li>
4540 <div align="center">
4541 <strong>2.02</strong><br> 18/7/05
4547 <li>Copy & Paste order of sequences maintains
4548 alignment order.</li>
4554 <div align="center">
4555 <strong>2.01</strong><br> 12/7/05
4560 <li>Use delete key for deleting selection.</li>
4561 <li>Use Mouse wheel to scroll sequences.</li>
4562 <li>Help file updated to describe how to add alignment
4564 <li>Version and build date written to build properties
4566 <li>InstallAnywhere installation will check for updates
4567 at launch of Jalview.</li>
4572 <li>Delete gaps bug fixed.</li>
4573 <li>FileChooser sorts columns.</li>
4574 <li>Can remove groups one by one.</li>
4575 <li>Filechooser icons installed.</li>
4576 <li>Finder ignores return character when searching.
4577 Return key will initiate a search.<br>
4584 <div align="center">
4585 <strong>2.0</strong><br> 20/6/05
4590 <li>New codebase</li>