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;
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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>27/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
67 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
68 source project) rather than InstallAnywhere
71 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
72 settings, receive over the air updates and launch specific
73 versions via (<a href="https://github.com/threerings/getdown">Three
77 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
78 formats supported by jalview (including .jvp project files)
81 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
82 arguments and switch between different getdown channels
85 <!-- JAL-3141 -->Backup files created when saving Jalview project
90 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
91 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
93 <!-- JAL-2620 -->Alternative genetic code tables for
94 'Translate as cDNA'</li>
96 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
97 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
100 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
101 implementation that allows updates) used for Sequence Feature collections</li>
104 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
105 shaded according to any associated attributes (e.g. variant
106 attributes from VCF file, or key-value pairs imported from
107 column 9 of GFF file)
110 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
111 recognise variant features
114 <!-- JAL-2897 -->Show synonymous codon variants on peptide
118 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
122 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
123 algorithm (Z-sort/transparency and filter aware)
126 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
132 <!-- JAL-3205 -->Symmetric score matrices for faster
133 tree and PCA calculations
135 <li><strong>Principal Components Analysis Viewer</strong>
138 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
139 and Viewer state saved in Jalview Project
141 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
144 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
148 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
153 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
155 <li><strong>Speed and Efficiency</strong>
158 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
159 multiple groups when working with large alignments
162 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
166 <li><strong>User Interface</strong>
169 <!-- JAL-2933 -->Finder panel remembers last position in each
173 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
174 what is shown)<br />Only visible region of alignment is shown by
175 default (can be changed in user preferences)
178 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
179 to the Overwrite Dialog
182 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
186 <!-- JAL-1244 -->Status bar shows bounds when dragging a
187 selection region, and gap count when inserting or deleting gaps
190 <!-- JAL-3132 -->Status bar updates over sequence and annotation
194 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
198 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
202 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
205 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
209 <!-- JAL-3181 -->Consistent ordering of links in sequence id
213 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
215 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
219 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
220 <li><strong>Java 11 Support (not yet on general release)</strong>
223 <!-- -->OSX GUI integrations for App menu's 'About' entry and
228 <em>Deprecations</em>
231 <!-- JAL-3035 -->DAS sequence retrieval and annotation
232 capabilities removed from the Jalview Desktop
235 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
236 unmarshalling has been replaced by JAXB for Jalview projects
237 and XML based data retrieval clients</li>
238 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
239 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
240 </ul> <em>Documentation</em>
243 <!-- JAL-3003 -->Added remarks about transparent rendering effects
244 not supported in EPS figure export
246 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
247 </ul> <em>Development and Release Processes</em>
250 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
252 <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
254 <!-- JAL-3225 -->Eclipse project configuration managed with
257 <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
258 Atlassian Bamboo continuous integration for
259 unattended Test Suite execution</li>
261 <!-- JAL-2864 -->Memory test suite to detect leaks in common
263 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
264 <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
267 <td align="left" valign="top">
270 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
273 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
274 superposition in Jmol fail on Windows
277 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
278 structures for sequences with lots of PDB structures
281 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
285 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
286 project involving multiple views
289 <!-- JAL-3164 -->Overview for complementary view in a linked
290 CDS/Protein alignment is not updated when Hide Columns by
291 Annotation dialog hides columns
294 <!-- JAL-3158 -->Selection highlighting in the complement of a
295 CDS/Protein alignment stops working after making a selection in
296 one view, then making another selection in the other view
299 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
303 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
304 Settings and Jalview Preferences panels
307 <!-- JAL-2865 -->Jalview hangs when closing windows or the
308 overview updates with large alignments
311 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
312 region if columns were selected by dragging right-to-left and the
313 mouse moved to the left of the first column
316 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
317 hidden column marker via scale popup menu
320 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
321 doesn't tell users the invalid URL
324 <!-- JAL-3178 -->Nonpositional features lose feature group on
325 export as Jalview features file
328 <!-- JAL-2816 -->Tooltips displayed for features filtered by
332 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
333 show cross references or Fetch Database References are shown in
337 <!-- JAL-2898 -->stop_gained variants not shown correctly on
341 <!-- JAL-2060 -->'Graduated colour' option not offered for
342 manually created features (where if feature score is Float.NaN)
345 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
346 when columns are hidden
349 <!-- JAL-3082 -->Regular expression error for '(' in Select
350 Columns by Annotation description
353 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
354 out of Scale or Annotation Panel
357 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
361 <!-- JAL-3074 -->Left/right drag in annotation can scroll
365 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
369 <!-- JAL-3002 -->Column display is out by one after Page Down,
370 Page Up in wrapped mode
373 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
376 <!-- JAL-2932 -->Finder searches in minimised alignments
379 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
380 on opening an alignment
383 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
387 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
388 different groups in the alignment are selected
391 <!-- JAL-2717 -->Internationalised colour scheme names not shown
395 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
399 <!-- JAL-3125 -->Value input for graduated feature colour
400 threshold gets 'unrounded'
403 <!-- JAL-2982 -->PCA image export doesn't respect background
407 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
410 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
413 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
417 <!-- JAL-2964 -->Associate Tree with All Views not restored from
421 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
422 shown in complementary view
425 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
426 without normalisation
429 <!-- JAL-3021 -->Sequence Details report opens positioned to top
433 <!-- JAL-914 -->Help page can be opened twice
435 </ul> <em>Editing</em>
438 <!-- JAL-2822 -->Start and End should be updated when sequence
439 data at beginning or end of alignment added/removed via 'Edit'
443 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
444 relocate sequence features correctly when start of sequence is
445 removed (Known defect since 2.10)
448 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
449 dialog corrupts dataset sequence
452 <!-- JAL-868 -->Structure colours not updated when associated tree
453 repartitions the alignment view (Regression in 2.10.5)
459 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
460 sequence's End is greater than its length
462 </ul> <em>New Known Defects</em>
465 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
466 regions of protein alignment.
469 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
470 is restored from a Jalview 2.11 project
473 <!-- JAL-3213 -->Alignment panel height can be too small after
477 <!-- JAL-3240 -->Display is incorrect after removing gapped
478 columns within hidden columns
481 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
482 window after dragging left to select columns to left of visible
486 <!-- JAL-2876 -->Features coloured according to their description
487 string and thresholded by score in earlier versions of Jalview are
488 not shown as thresholded features in 2.11. To workaround please
489 create a Score filter instead.
491 <li><strong>Java 11 Specific defects</strong>
494 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
502 <td width="60" nowrap>
504 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
507 <td><div align="left">
511 <!-- JAL-3101 -->Default memory for Jalview webstart and
512 InstallAnywhere increased to 1G.
515 <!-- JAL-247 -->Hidden sequence markers and representative
516 sequence bolding included when exporting alignment as EPS,
517 SVG, PNG or HTML. <em>Display is configured via the
518 Format menu, or for command-line use via a jalview
519 properties file.</em>
522 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
523 API and sequence data now imported as JSON.
526 <!-- JAL-3065 -->Change in recommended way of starting
527 Jalview via a Java command line: add jars in lib directory
528 to CLASSPATH, rather than via the deprecated java.ext.dirs
535 <!-- JAL-3047 -->Support added to execute test suite
536 instrumented with <a href="http://openclover.org/">Open
541 <td><div align="left">
545 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
546 row shown in Feredoxin Structure alignment view of example
550 <!-- JAL-2854 -->Annotation obscures sequences if lots of
551 annotation displayed.
554 <!-- JAL-3107 -->Group conservation/consensus not shown
555 for newly created group when 'Apply to all groups'
559 <!-- JAL-3087 -->Corrupted display when switching to
560 wrapped mode when sequence panel's vertical scrollbar is
564 <!-- JAL-3003 -->Alignment is black in exported EPS file
565 when sequences are selected in exported view.</em>
568 <!-- JAL-3059 -->Groups with different coloured borders
569 aren't rendered with correct colour.
572 <!-- JAL-3092 -->Jalview could hang when importing certain
573 types of knotted RNA secondary structure.
576 <!-- JAL-3095 -->Sequence highlight and selection in
577 trimmed VARNA 2D structure is incorrect for sequences that
581 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
582 annotation when columns are inserted into an alignment,
583 and when exporting as Stockholm flatfile.
586 <!-- JAL-3053 -->Jalview annotation rows containing upper
587 and lower-case 'E' and 'H' do not automatically get
588 treated as RNA secondary structure.
591 <!-- JAL-3106 -->.jvp should be used as default extension
592 (not .jar) when saving a jalview project file.
595 <!-- JAL-3105 -->Mac Users: closing a window correctly
596 transfers focus to previous window on OSX
599 <em>Java 10 Issues Resolved</em>
602 <!-- JAL-2988 -->OSX - Can't save new files via the File
603 or export menus by typing in a name into the Save dialog
607 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
608 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
609 'look and feel' which has improved compatibility with the
610 latest version of OSX.
617 <td width="60" nowrap>
619 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
620 <em>7/06/2018</em></strong>
623 <td><div align="left">
627 <!-- JAL-2920 -->Use HGVS nomenclature for variant
628 annotation retrieved from Uniprot
631 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
632 onto the Jalview Desktop
636 <td><div align="left">
640 <!-- JAL-3017 -->Cannot import features with multiple
641 variant elements (blocks import of some Uniprot records)
644 <!-- JAL-2997 -->Clustal files with sequence positions in
645 right-hand column parsed correctly
648 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
649 not alignment area in exported graphic
652 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
653 window has input focus
656 <!-- JAL-2992 -->Annotation panel set too high when
657 annotation added to view (Windows)
660 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
661 network connectivity is poor
664 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
665 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
666 the currently open URL and links from a page viewed in
667 Firefox or Chrome on Windows is now fully supported. If
668 you are using Edge, only links in the page can be
669 dragged, and with Internet Explorer, only the currently
670 open URL in the browser can be dropped onto Jalview.</em>
673 <em>New Known Defects</em>
675 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
680 <td width="60" nowrap>
682 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
685 <td><div align="left">
689 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
690 for disabling automatic superposition of multiple
691 structures and open structures in existing views
694 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
695 ID and annotation area margins can be click-dragged to
699 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
703 <!-- JAL-2759 -->Improved performance for large alignments
704 and lots of hidden columns
707 <!-- JAL-2593 -->Improved performance when rendering lots
708 of features (particularly when transparency is disabled)
711 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
712 exchange of Jalview features and Chimera attributes made
718 <td><div align="left">
721 <!-- JAL-2899 -->Structure and Overview aren't updated
722 when Colour By Annotation threshold slider is adjusted
725 <!-- JAL-2778 -->Slow redraw when Overview panel shown
726 overlapping alignment panel
729 <!-- JAL-2929 -->Overview doesn't show end of unpadded
733 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
734 improved: CDS not handled correctly if transcript has no
738 <!-- JAL-2321 -->Secondary structure and temperature
739 factor annotation not added to sequence when local PDB
740 file associated with it by drag'n'drop or structure
744 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
745 dialog doesn't import PDB files dropped on an alignment
748 <!-- JAL-2666 -->Linked scrolling via protein horizontal
749 scroll bar doesn't work for some CDS/Protein views
752 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
753 Java 1.8u153 onwards and Java 1.9u4+.
756 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
757 columns in annotation row
760 <!-- JAL-2913 -->Preferences panel's ID Width control is not
761 honored in batch mode
764 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
765 for structures added to existing Jmol view
768 <!-- JAL-2223 -->'View Mappings' includes duplicate
769 entries after importing project with multiple views
772 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
773 protein sequences via SIFTS from associated PDB entries
774 with negative residue numbers or missing residues fails
777 <!-- JAL-2952 -->Exception when shading sequence with negative
778 Temperature Factor values from annotated PDB files (e.g.
779 as generated by CONSURF)
782 <!-- JAL-2920 -->Uniprot 'sequence variant' features
783 tooltip doesn't include a text description of mutation
786 <!-- JAL-2922 -->Invert displayed features very slow when
787 structure and/or overview windows are also shown
790 <!-- JAL-2954 -->Selecting columns from highlighted regions
791 very slow for alignments with large numbers of sequences
794 <!-- JAL-2925 -->Copy Consensus fails for group consensus
795 with 'StringIndexOutOfBounds'
798 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
799 platforms running Java 10
802 <!-- JAL-2960 -->Adding a structure to existing structure
803 view appears to do nothing because the view is hidden behind the alignment view
809 <!-- JAL-2926 -->Copy consensus sequence option in applet
810 should copy the group consensus when popup is opened on it
816 <!-- JAL-2913 -->Fixed ID width preference is not respected
819 <em>New Known Defects</em>
822 <!-- JAL-2973 --> Exceptions occasionally raised when
823 editing a large alignment and overview is displayed
826 <!-- JAL-2974 -->'Overview updating' progress bar is shown
827 repeatedly after a series of edits even when the overview
828 is no longer reflecting updates
831 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
832 structures for protein subsequence (if 'Trim Retrieved
833 Sequences' enabled) or Ensembl isoforms (Workaround in
834 2.10.4 is to fail back to N&W mapping)
837 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
838 option gives blank output
845 <td width="60" nowrap>
847 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
850 <td><div align="left">
851 <ul><li>Updated Certum Codesigning Certificate
852 (Valid till 30th November 2018)</li></ul></div></td>
853 <td><div align="left">
856 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
857 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
858 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
859 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
860 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
861 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
862 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
868 <td width="60" nowrap>
870 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
873 <td><div align="left">
877 <!-- JAL-2446 -->Faster and more efficient management and
878 rendering of sequence features
881 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
882 429 rate limit request hander
885 <!-- JAL-2773 -->Structure views don't get updated unless
886 their colours have changed
889 <!-- JAL-2495 -->All linked sequences are highlighted for
890 a structure mousover (Jmol) or selection (Chimera)
893 <!-- JAL-2790 -->'Cancel' button in progress bar for
894 JABAWS AACon, RNAAliFold and Disorder prediction jobs
897 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
898 view from Ensembl locus cross-references
901 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
905 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
906 feature can be disabled
909 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
910 PDB easier retrieval of sequences for lists of IDs
913 <!-- JAL-2758 -->Short names for sequences retrieved from
919 <li>Groovy interpreter updated to 2.4.12</li>
920 <li>Example groovy script for generating a matrix of
921 percent identity scores for current alignment.</li>
923 <em>Testing and Deployment</em>
926 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
930 <td><div align="left">
934 <!-- JAL-2643 -->Pressing tab after updating the colour
935 threshold text field doesn't trigger an update to the
939 <!-- JAL-2682 -->Race condition when parsing sequence ID
943 <!-- JAL-2608 -->Overview windows are also closed when
944 alignment window is closed
947 <!-- JAL-2548 -->Export of features doesn't always respect
951 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
952 takes a long time in Cursor mode
958 <!-- JAL-2777 -->Structures with whitespace chainCode
959 cannot be viewed in Chimera
962 <!-- JAL-2728 -->Protein annotation panel too high in
966 <!-- JAL-2757 -->Can't edit the query after the server
967 error warning icon is shown in Uniprot and PDB Free Text
971 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
974 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
977 <!-- JAL-2739 -->Hidden column marker in last column not
978 rendered when switching back from Wrapped to normal view
981 <!-- JAL-2768 -->Annotation display corrupted when
982 scrolling right in unwapped alignment view
985 <!-- JAL-2542 -->Existing features on subsequence
986 incorrectly relocated when full sequence retrieved from
990 <!-- JAL-2733 -->Last reported memory still shown when
991 Desktop->Show Memory is unticked (OSX only)
994 <!-- JAL-2658 -->Amend Features dialog doesn't allow
995 features of same type and group to be selected for
999 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1000 alignments when hidden columns are present
1003 <!-- JAL-2392 -->Jalview freezes when loading and
1004 displaying several structures
1007 <!-- JAL-2732 -->Black outlines left after resizing or
1011 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1012 within the Jalview desktop on OSX
1015 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1016 when in wrapped alignment mode
1019 <!-- JAL-2636 -->Scale mark not shown when close to right
1020 hand end of alignment
1023 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1024 each selected sequence do not have correct start/end
1028 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1029 after canceling the Alignment Window's Font dialog
1032 <!-- JAL-2036 -->Show cross-references not enabled after
1033 restoring project until a new view is created
1036 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1037 URL links appears when only default EMBL-EBI link is
1038 configured (since 2.10.2b2)
1041 <!-- JAL-2775 -->Overview redraws whole window when box
1042 position is adjusted
1045 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1046 in a multi-chain structure when viewing alignment
1047 involving more than one chain (since 2.10)
1050 <!-- JAL-2811 -->Double residue highlights in cursor mode
1051 if new selection moves alignment window
1054 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1055 arrow key in cursor mode to pass hidden column marker
1058 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1059 that produces correctly annotated transcripts and products
1062 <!-- JAL-2776 -->Toggling a feature group after first time
1063 doesn't update associated structure view
1066 <em>Applet</em><br />
1069 <!-- JAL-2687 -->Concurrent modification exception when
1070 closing alignment panel
1073 <em>BioJSON</em><br />
1076 <!-- JAL-2546 -->BioJSON export does not preserve
1077 non-positional features
1080 <em>New Known Issues</em>
1083 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1084 sequence features correctly (for many previous versions of
1088 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1089 using cursor in wrapped panel other than top
1092 <!-- JAL-2791 -->Select columns containing feature ignores
1093 graduated colour threshold
1096 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1097 always preserve numbering and sequence features
1100 <em>Known Java 9 Issues</em>
1103 <!-- JAL-2902 -->Groovy Console very slow to open and is
1104 not responsive when entering characters (Webstart, Java
1111 <td width="60" nowrap>
1112 <div align="center">
1113 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1114 <em>2/10/2017</em></strong>
1117 <td><div align="left">
1118 <em>New features in Jalview Desktop</em>
1121 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1123 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1127 <td><div align="left">
1131 <td width="60" nowrap>
1132 <div align="center">
1133 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1134 <em>7/9/2017</em></strong>
1137 <td><div align="left">
1141 <!-- JAL-2588 -->Show gaps in overview window by colouring
1142 in grey (sequences used to be coloured grey, and gaps were
1146 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1150 <!-- JAL-2587 -->Overview updates immediately on increase
1151 in size and progress bar shown as higher resolution
1152 overview is recalculated
1157 <td><div align="left">
1161 <!-- JAL-2664 -->Overview window redraws every hidden
1162 column region row by row
1165 <!-- JAL-2681 -->duplicate protein sequences shown after
1166 retrieving Ensembl crossrefs for sequences from Uniprot
1169 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1170 format setting is unticked
1173 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1174 if group has show boxes format setting unticked
1177 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1178 autoscrolling whilst dragging current selection group to
1179 include sequences and columns not currently displayed
1182 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1183 assemblies are imported via CIF file
1186 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1187 displayed when threshold or conservation colouring is also
1191 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1195 <!-- JAL-2673 -->Jalview continues to scroll after
1196 dragging a selected region off the visible region of the
1200 <!-- JAL-2724 -->Cannot apply annotation based
1201 colourscheme to all groups in a view
1204 <!-- JAL-2511 -->IDs don't line up with sequences
1205 initially after font size change using the Font chooser or
1212 <td width="60" nowrap>
1213 <div align="center">
1214 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1217 <td><div align="left">
1218 <em>Calculations</em>
1222 <!-- JAL-1933 -->Occupancy annotation row shows number of
1223 ungapped positions in each column of the alignment.
1226 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1227 a calculation dialog box
1230 <!-- JAL-2379 -->Revised implementation of PCA for speed
1231 and memory efficiency (~30x faster)
1234 <!-- JAL-2403 -->Revised implementation of sequence
1235 similarity scores as used by Tree, PCA, Shading Consensus
1236 and other calculations
1239 <!-- JAL-2416 -->Score matrices are stored as resource
1240 files within the Jalview codebase
1243 <!-- JAL-2500 -->Trees computed on Sequence Feature
1244 Similarity may have different topology due to increased
1251 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1252 model for alignments and groups
1255 <!-- JAL-384 -->Custom shading schemes created via groovy
1262 <!-- JAL-2526 -->Efficiency improvements for interacting
1263 with alignment and overview windows
1266 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1270 <!-- JAL-2388 -->Hidden columns and sequences can be
1274 <!-- JAL-2611 -->Click-drag in visible area allows fine
1275 adjustment of visible position
1279 <em>Data import/export</em>
1282 <!-- JAL-2535 -->Posterior probability annotation from
1283 Stockholm files imported as sequence associated annotation
1286 <!-- JAL-2507 -->More robust per-sequence positional
1287 annotation input/output via stockholm flatfile
1290 <!-- JAL-2533 -->Sequence names don't include file
1291 extension when importing structure files without embedded
1292 names or PDB accessions
1295 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1296 format sequence substitution matrices
1299 <em>User Interface</em>
1302 <!-- JAL-2447 --> Experimental Features Checkbox in
1303 Desktop's Tools menu to hide or show untested features in
1307 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1308 via Overview or sequence motif search operations
1311 <!-- JAL-2547 -->Amend sequence features dialog box can be
1312 opened by double clicking gaps within sequence feature
1316 <!-- JAL-1476 -->Status bar message shown when not enough
1317 aligned positions were available to create a 3D structure
1321 <em>3D Structure</em>
1324 <!-- JAL-2430 -->Hidden regions in alignment views are not
1325 coloured in linked structure views
1328 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1329 file-based command exchange
1332 <!-- JAL-2375 -->Structure chooser automatically shows
1333 Cached Structures rather than querying the PDBe if
1334 structures are already available for sequences
1337 <!-- JAL-2520 -->Structures imported via URL are cached in
1338 the Jalview project rather than downloaded again when the
1339 project is reopened.
1342 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1343 to transfer Chimera's structure attributes as Jalview
1344 features, and vice-versa (<strong>Experimental
1348 <em>Web Services</em>
1351 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1354 <!-- JAL-2335 -->Filter non-standard amino acids and
1355 nucleotides when submitting to AACon and other MSA
1359 <!-- JAL-2316, -->URLs for viewing database
1360 cross-references provided by identifiers.org and the
1361 EMBL-EBI's MIRIAM DB
1368 <!-- JAL-2344 -->FileFormatI interface for describing and
1369 identifying file formats (instead of String constants)
1372 <!-- JAL-2228 -->FeatureCounter script refactored for
1373 efficiency when counting all displayed features (not
1374 backwards compatible with 2.10.1)
1377 <em>Example files</em>
1380 <!-- JAL-2631 -->Graduated feature colour style example
1381 included in the example feature file
1384 <em>Documentation</em>
1387 <!-- JAL-2339 -->Release notes reformatted for readability
1388 with the built-in Java help viewer
1391 <!-- JAL-1644 -->Find documentation updated with 'search
1392 sequence description' option
1398 <!-- JAL-2485, -->External service integration tests for
1399 Uniprot REST Free Text Search Client
1402 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1405 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1410 <td><div align="left">
1411 <em>Calculations</em>
1414 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1415 matrix - C->R should be '-3'<br />Old matrix restored
1416 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1418 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1419 Jalview's treatment of gaps in PCA and substitution matrix
1420 based Tree calculations.<br /> <br />In earlier versions
1421 of Jalview, gaps matching gaps were penalised, and gaps
1422 matching non-gaps penalised even more. In the PCA
1423 calculation, gaps were actually treated as non-gaps - so
1424 different costs were applied, which meant Jalview's PCAs
1425 were different to those produced by SeqSpace.<br />Jalview
1426 now treats gaps in the same way as SeqSpace (ie it scores
1427 them as 0). <br /> <br />Enter the following in the
1428 Groovy console to restore pre-2.10.2 behaviour:<br />
1429 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1430 // for 2.10.1 mode <br />
1431 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1432 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1433 these settings will affect all subsequent tree and PCA
1434 calculations (not recommended)</em></li>
1436 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1437 scaling of branch lengths for trees computed using
1438 Sequence Feature Similarity.
1441 <!-- JAL-2377 -->PCA calculation could hang when
1442 generating output report when working with highly
1443 redundant alignments
1446 <!-- JAL-2544 --> Sort by features includes features to
1447 right of selected region when gaps present on right-hand
1451 <em>User Interface</em>
1454 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1455 doesn't reselect a specific sequence's associated
1456 annotation after it was used for colouring a view
1459 <!-- JAL-2419 -->Current selection lost if popup menu
1460 opened on a region of alignment without groups
1463 <!-- JAL-2374 -->Popup menu not always shown for regions
1464 of an alignment with overlapping groups
1467 <!-- JAL-2310 -->Finder double counts if both a sequence's
1468 name and description match
1471 <!-- JAL-2370 -->Hiding column selection containing two
1472 hidden regions results in incorrect hidden regions
1475 <!-- JAL-2386 -->'Apply to all groups' setting when
1476 changing colour does not apply Conservation slider value
1480 <!-- JAL-2373 -->Percentage identity and conservation menu
1481 items do not show a tick or allow shading to be disabled
1484 <!-- JAL-2385 -->Conservation shading or PID threshold
1485 lost when base colourscheme changed if slider not visible
1488 <!-- JAL-2547 -->Sequence features shown in tooltip for
1489 gaps before start of features
1492 <!-- JAL-2623 -->Graduated feature colour threshold not
1493 restored to UI when feature colour is edited
1496 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1497 a time when scrolling vertically in wrapped mode.
1500 <!-- JAL-2630 -->Structure and alignment overview update
1501 as graduate feature colour settings are modified via the
1505 <!-- JAL-2034 -->Overview window doesn't always update
1506 when a group defined on the alignment is resized
1509 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1510 wrapped view result in positional status updates
1514 <!-- JAL-2563 -->Status bar doesn't show position for
1515 ambiguous amino acid and nucleotide symbols
1518 <!-- JAL-2602 -->Copy consensus sequence failed if
1519 alignment included gapped columns
1522 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1523 widgets don't permanently disappear
1526 <!-- JAL-2503 -->Cannot select or filter quantitative
1527 annotation that are shown only as column labels (e.g.
1528 T-Coffee column reliability scores)
1531 <!-- JAL-2594 -->Exception thrown if trying to create a
1532 sequence feature on gaps only
1535 <!-- JAL-2504 -->Features created with 'New feature'
1536 button from a Find inherit previously defined feature type
1537 rather than the Find query string
1540 <!-- JAL-2423 -->incorrect title in output window when
1541 exporting tree calculated in Jalview
1544 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1545 and then revealing them reorders sequences on the
1549 <!-- JAL-964 -->Group panel in sequence feature settings
1550 doesn't update to reflect available set of groups after
1551 interactively adding or modifying features
1554 <!-- JAL-2225 -->Sequence Database chooser unusable on
1558 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1559 only excluded gaps in current sequence and ignored
1566 <!-- JAL-2421 -->Overview window visible region moves
1567 erratically when hidden rows or columns are present
1570 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1571 Structure Viewer's colour menu don't correspond to
1575 <!-- JAL-2405 -->Protein specific colours only offered in
1576 colour and group colour menu for protein alignments
1579 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1580 reflect currently selected view or group's shading
1584 <!-- JAL-2624 -->Feature colour thresholds not respected
1585 when rendered on overview and structures when opacity at
1589 <!-- JAL-2589 -->User defined gap colour not shown in
1590 overview when features overlaid on alignment
1593 <!-- JAL-2567 -->Feature settings for different views not
1594 recovered correctly from Jalview project file
1597 <!-- JAL-2256 -->Feature colours in overview when first opened
1598 (automatically via preferences) are different to the main
1602 <em>Data import/export</em>
1605 <!-- JAL-2576 -->Very large alignments take a long time to
1609 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1610 added after a sequence was imported are not written to
1614 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1615 when importing RNA secondary structure via Stockholm
1618 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1619 not shown in correct direction for simple pseudoknots
1622 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1623 with lightGray or darkGray via features file (but can
1627 <!-- JAL-2383 -->Above PID colour threshold not recovered
1628 when alignment view imported from project
1631 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1632 structure and sequences extracted from structure files
1633 imported via URL and viewed in Jmol
1636 <!-- JAL-2520 -->Structures loaded via URL are saved in
1637 Jalview Projects rather than fetched via URL again when
1638 the project is loaded and the structure viewed
1641 <em>Web Services</em>
1644 <!-- JAL-2519 -->EnsemblGenomes example failing after
1645 release of Ensembl v.88
1648 <!-- JAL-2366 -->Proxy server address and port always
1649 appear enabled in Preferences->Connections
1652 <!-- JAL-2461 -->DAS registry not found exceptions
1653 removed from console output
1656 <!-- JAL-2582 -->Cannot retrieve protein products from
1657 Ensembl by Peptide ID
1660 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1661 created from SIFTs, and spurious 'Couldn't open structure
1662 in Chimera' errors raised after April 2017 update (problem
1663 due to 'null' string rather than empty string used for
1664 residues with no corresponding PDB mapping).
1667 <em>Application UI</em>
1670 <!-- JAL-2361 -->User Defined Colours not added to Colour
1674 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1675 case' residues (button in colourscheme editor debugged and
1676 new documentation and tooltips added)
1679 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1680 doesn't restore group-specific text colour thresholds
1683 <!-- JAL-2243 -->Feature settings panel does not update as
1684 new features are added to alignment
1687 <!-- JAL-2532 -->Cancel in feature settings reverts
1688 changes to feature colours via the Amend features dialog
1691 <!-- JAL-2506 -->Null pointer exception when attempting to
1692 edit graduated feature colour via amend features dialog
1696 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1697 selection menu changes colours of alignment views
1700 <!-- JAL-2426 -->Spurious exceptions in console raised
1701 from alignment calculation workers after alignment has
1705 <!-- JAL-1608 -->Typo in selection popup menu - Create
1706 groups now 'Create Group'
1709 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1710 Create/Undefine group doesn't always work
1713 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1714 shown again after pressing 'Cancel'
1717 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1718 adjusts start position in wrap mode
1721 <!-- JAL-2563 -->Status bar doesn't show positions for
1722 ambiguous amino acids
1725 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1726 CDS/Protein view after CDS sequences added for aligned
1730 <!-- JAL-2592 -->User defined colourschemes called 'User
1731 Defined' don't appear in Colours menu
1737 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1738 score models doesn't always result in an updated PCA plot
1741 <!-- JAL-2442 -->Features not rendered as transparent on
1742 overview or linked structure view
1745 <!-- JAL-2372 -->Colour group by conservation doesn't
1749 <!-- JAL-2517 -->Hitting Cancel after applying
1750 user-defined colourscheme doesn't restore original
1757 <!-- JAL-2314 -->Unit test failure:
1758 jalview.ws.jabaws.RNAStructExportImport setup fails
1761 <!-- JAL-2307 -->Unit test failure:
1762 jalview.ws.sifts.SiftsClientTest due to compatibility
1763 problems with deep array comparison equality asserts in
1764 successive versions of TestNG
1767 <!-- JAL-2479 -->Relocated StructureChooserTest and
1768 ParameterUtilsTest Unit tests to Network suite
1771 <em>New Known Issues</em>
1774 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1775 phase after a sequence motif find operation
1778 <!-- JAL-2550 -->Importing annotation file with rows
1779 containing just upper and lower case letters are
1780 interpreted as WUSS RNA secondary structure symbols
1783 <!-- JAL-2590 -->Cannot load and display Newick trees
1784 reliably from eggnog Ortholog database
1787 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1788 containing features of type Highlight' when 'B' is pressed
1789 to mark columns containing highlighted regions.
1792 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1793 doesn't always add secondary structure annotation.
1798 <td width="60" nowrap>
1799 <div align="center">
1800 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1803 <td><div align="left">
1807 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1808 for all consensus calculations
1811 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1814 <li>Updated Jalview's Certum code signing certificate
1817 <em>Application</em>
1820 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1821 set of database cross-references, sorted alphabetically
1824 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1825 from database cross references. Users with custom links
1826 will receive a <a href="webServices/urllinks.html#warning">warning
1827 dialog</a> asking them to update their preferences.
1830 <!-- JAL-2287-->Cancel button and escape listener on
1831 dialog warning user about disconnecting Jalview from a
1835 <!-- JAL-2320-->Jalview's Chimera control window closes if
1836 the Chimera it is connected to is shut down
1839 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1840 columns menu item to mark columns containing highlighted
1841 regions (e.g. from structure selections or results of a
1845 <!-- JAL-2284-->Command line option for batch-generation
1846 of HTML pages rendering alignment data with the BioJS
1856 <!-- JAL-2286 -->Columns with more than one modal residue
1857 are not coloured or thresholded according to percent
1858 identity (first observed in Jalview 2.8.2)
1861 <!-- JAL-2301 -->Threonine incorrectly reported as not
1865 <!-- JAL-2318 -->Updates to documentation pages (above PID
1866 threshold, amino acid properties)
1869 <!-- JAL-2292 -->Lower case residues in sequences are not
1870 reported as mapped to residues in a structure file in the
1874 <!--JAL-2324 -->Identical features with non-numeric scores
1875 could be added multiple times to a sequence
1878 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1879 bond features shown as two highlighted residues rather
1880 than a range in linked structure views, and treated
1881 correctly when selecting and computing trees from features
1884 <!-- JAL-2281-->Custom URL links for database
1885 cross-references are matched to database name regardless
1890 <em>Application</em>
1893 <!-- JAL-2282-->Custom URL links for specific database
1894 names without regular expressions also offer links from
1898 <!-- JAL-2315-->Removing a single configured link in the
1899 URL links pane in Connections preferences doesn't actually
1900 update Jalview configuration
1903 <!-- JAL-2272-->CTRL-Click on a selected region to open
1904 the alignment area popup menu doesn't work on El-Capitan
1907 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1908 files with similarly named sequences if dropped onto the
1912 <!-- JAL-2312 -->Additional mappings are shown for PDB
1913 entries where more chains exist in the PDB accession than
1914 are reported in the SIFTS file
1917 <!-- JAL-2317-->Certain structures do not get mapped to
1918 the structure view when displayed with Chimera
1921 <!-- JAL-2317-->No chains shown in the Chimera view
1922 panel's View->Show Chains submenu
1925 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1926 work for wrapped alignment views
1929 <!--JAL-2197 -->Rename UI components for running JPred
1930 predictions from 'JNet' to 'JPred'
1933 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1934 corrupted when annotation panel vertical scroll is not at
1935 first annotation row
1938 <!--JAL-2332 -->Attempting to view structure for Hen
1939 lysozyme results in a PDB Client error dialog box
1942 <!-- JAL-2319 -->Structure View's mapping report switched
1943 ranges for PDB and sequence for SIFTS
1946 SIFTS 'Not_Observed' residues mapped to non-existant
1950 <!-- <em>New Known Issues</em>
1957 <td width="60" nowrap>
1958 <div align="center">
1959 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1960 <em>25/10/2016</em></strong>
1963 <td><em>Application</em>
1965 <li>3D Structure chooser opens with 'Cached structures'
1966 view if structures already loaded</li>
1967 <li>Progress bar reports models as they are loaded to
1968 structure views</li>
1974 <li>Colour by conservation always enabled and no tick
1975 shown in menu when BLOSUM or PID shading applied</li>
1976 <li>FER1_ARATH and FER2_ARATH labels were switched in
1977 example sequences/projects/trees</li>
1979 <em>Application</em>
1981 <li>Jalview projects with views of local PDB structure
1982 files saved on Windows cannot be opened on OSX</li>
1983 <li>Multiple structure views can be opened and superposed
1984 without timeout for structures with multiple models or
1985 multiple sequences in alignment</li>
1986 <li>Cannot import or associated local PDB files without a
1987 PDB ID HEADER line</li>
1988 <li>RMSD is not output in Jmol console when superposition
1990 <li>Drag and drop of URL from Browser fails for Linux and
1991 OSX versions earlier than El Capitan</li>
1992 <li>ENA client ignores invalid content from ENA server</li>
1993 <li>Exceptions are not raised in console when ENA client
1994 attempts to fetch non-existent IDs via Fetch DB Refs UI
1996 <li>Exceptions are not raised in console when a new view
1997 is created on the alignment</li>
1998 <li>OSX right-click fixed for group selections: CMD-click
1999 to insert/remove gaps in groups and CTRL-click to open group
2002 <em>Build and deployment</em>
2004 <li>URL link checker now copes with multi-line anchor
2007 <em>New Known Issues</em>
2009 <li>Drag and drop from URL links in browsers do not work
2016 <td width="60" nowrap>
2017 <div align="center">
2018 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2021 <td><em>General</em>
2024 <!-- JAL-2124 -->Updated Spanish translations.
2027 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2028 for importing structure data to Jalview. Enables mmCIF and
2032 <!-- JAL-192 --->Alignment ruler shows positions relative to
2036 <!-- JAL-2202 -->Position/residue shown in status bar when
2037 mousing over sequence associated annotation
2040 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2044 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2045 '()', canonical '[]' and invalid '{}' base pair populations
2049 <!-- JAL-2092 -->Feature settings popup menu options for
2050 showing or hiding columns containing a feature
2053 <!-- JAL-1557 -->Edit selected group by double clicking on
2054 group and sequence associated annotation labels
2057 <!-- JAL-2236 -->Sequence name added to annotation label in
2058 select/hide columns by annotation and colour by annotation
2062 </ul> <em>Application</em>
2065 <!-- JAL-2050-->Automatically hide introns when opening a
2066 gene/transcript view
2069 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2073 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2074 structure mappings with the EMBL-EBI PDBe SIFTS database
2077 <!-- JAL-2079 -->Updated download sites used for Rfam and
2078 Pfam sources to xfam.org
2081 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2084 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2085 over sequences in Jalview
2088 <!-- JAL-2027-->Support for reverse-complement coding
2089 regions in ENA and EMBL
2092 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2093 for record retrieval via ENA rest API
2096 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2100 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2101 groovy script execution
2104 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2105 alignment window's Calculate menu
2108 <!-- JAL-1812 -->Allow groovy scripts that call
2109 Jalview.getAlignFrames() to run in headless mode
2112 <!-- JAL-2068 -->Support for creating new alignment
2113 calculation workers from groovy scripts
2116 <!-- JAL-1369 --->Store/restore reference sequence in
2120 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2121 associations are now saved/restored from project
2124 <!-- JAL-1993 -->Database selection dialog always shown
2125 before sequence fetcher is opened
2128 <!-- JAL-2183 -->Double click on an entry in Jalview's
2129 database chooser opens a sequence fetcher
2132 <!-- JAL-1563 -->Free-text search client for UniProt using
2133 the UniProt REST API
2136 <!-- JAL-2168 -->-nonews command line parameter to prevent
2137 the news reader opening
2140 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2141 querying stored in preferences
2144 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2148 <!-- JAL-1977-->Tooltips shown on database chooser
2151 <!-- JAL-391 -->Reverse complement function in calculate
2152 menu for nucleotide sequences
2155 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2156 and feature counts preserves alignment ordering (and
2157 debugged for complex feature sets).
2160 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2161 viewing structures with Jalview 2.10
2164 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2165 genome, transcript CCDS and gene ids via the Ensembl and
2166 Ensembl Genomes REST API
2169 <!-- JAL-2049 -->Protein sequence variant annotation
2170 computed for 'sequence_variant' annotation on CDS regions
2174 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2178 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2179 Ref Fetcher fails to match, or otherwise updates sequence
2180 data from external database records.
2183 <!-- JAL-2154 -->Revised Jalview Project format for
2184 efficient recovery of sequence coding and alignment
2185 annotation relationships.
2187 </ul> <!-- <em>Applet</em>
2198 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2202 <!-- JAL-2018-->Export features in Jalview format (again)
2203 includes graduated colourschemes
2206 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2207 working with big alignments and lots of hidden columns
2210 <!-- JAL-2053-->Hidden column markers not always rendered
2211 at right of alignment window
2214 <!-- JAL-2067 -->Tidied up links in help file table of
2218 <!-- JAL-2072 -->Feature based tree calculation not shown
2222 <!-- JAL-2075 -->Hidden columns ignored during feature
2223 based tree calculation
2226 <!-- JAL-2065 -->Alignment view stops updating when show
2227 unconserved enabled for group on alignment
2230 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2234 <!-- JAL-2146 -->Alignment column in status incorrectly
2235 shown as "Sequence position" when mousing over
2239 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2240 hidden columns present
2243 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2244 user created annotation added to alignment
2247 <!-- JAL-1841 -->RNA Structure consensus only computed for
2248 '()' base pair annotation
2251 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2252 in zero scores for all base pairs in RNA Structure
2256 <!-- JAL-2174-->Extend selection with columns containing
2260 <!-- JAL-2275 -->Pfam format writer puts extra space at
2261 beginning of sequence
2264 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2268 <!-- JAL-2238 -->Cannot create groups on an alignment from
2269 from a tree when t-coffee scores are shown
2272 <!-- JAL-1836,1967 -->Cannot import and view PDB
2273 structures with chains containing negative resnums (4q4h)
2276 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2280 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2281 to Clustal, PIR and PileUp output
2284 <!-- JAL-2008 -->Reordering sequence features that are
2285 not visible causes alignment window to repaint
2288 <!-- JAL-2006 -->Threshold sliders don't work in
2289 graduated colour and colour by annotation row for e-value
2290 scores associated with features and annotation rows
2293 <!-- JAL-1797 -->amino acid physicochemical conservation
2294 calculation should be case independent
2297 <!-- JAL-2173 -->Remove annotation also updates hidden
2301 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2302 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2303 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2306 <!-- JAL-2065 -->Null pointer exceptions and redraw
2307 problems when reference sequence defined and 'show
2308 non-conserved' enabled
2311 <!-- JAL-1306 -->Quality and Conservation are now shown on
2312 load even when Consensus calculation is disabled
2315 <!-- JAL-1932 -->Remove right on penultimate column of
2316 alignment does nothing
2319 <em>Application</em>
2322 <!-- JAL-1552-->URLs and links can't be imported by
2323 drag'n'drop on OSX when launched via webstart (note - not
2324 yet fixed for El Capitan)
2327 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2328 output when running on non-gb/us i18n platforms
2331 <!-- JAL-1944 -->Error thrown when exporting a view with
2332 hidden sequences as flat-file alignment
2335 <!-- JAL-2030-->InstallAnywhere distribution fails when
2339 <!-- JAL-2080-->Jalview very slow to launch via webstart
2340 (also hotfix for 2.9.0b2)
2343 <!-- JAL-2085 -->Cannot save project when view has a
2344 reference sequence defined
2347 <!-- JAL-1011 -->Columns are suddenly selected in other
2348 alignments and views when revealing hidden columns
2351 <!-- JAL-1989 -->Hide columns not mirrored in complement
2352 view in a cDNA/Protein splitframe
2355 <!-- JAL-1369 -->Cannot save/restore representative
2356 sequence from project when only one sequence is
2360 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2361 in Structure Chooser
2364 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2365 structure consensus didn't refresh annotation panel
2368 <!-- JAL-1962 -->View mapping in structure view shows
2369 mappings between sequence and all chains in a PDB file
2372 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2373 dialogs format columns correctly, don't display array
2374 data, sort columns according to type
2377 <!-- JAL-1975 -->Export complete shown after destination
2378 file chooser is cancelled during an image export
2381 <!-- JAL-2025 -->Error when querying PDB Service with
2382 sequence name containing special characters
2385 <!-- JAL-2024 -->Manual PDB structure querying should be
2389 <!-- JAL-2104 -->Large tooltips with broken HTML
2390 formatting don't wrap
2393 <!-- JAL-1128 -->Figures exported from wrapped view are
2394 truncated so L looks like I in consensus annotation
2397 <!-- JAL-2003 -->Export features should only export the
2398 currently displayed features for the current selection or
2402 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2403 after fetching cross-references, and restoring from
2407 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2408 followed in the structure viewer
2411 <!-- JAL-2163 -->Titles for individual alignments in
2412 splitframe not restored from project
2415 <!-- JAL-2145 -->missing autocalculated annotation at
2416 trailing end of protein alignment in transcript/product
2417 splitview when pad-gaps not enabled by default
2420 <!-- JAL-1797 -->amino acid physicochemical conservation
2424 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2425 article has been read (reopened issue due to
2426 internationalisation problems)
2429 <!-- JAL-1960 -->Only offer PDB structures in structure
2430 viewer based on sequence name, PDB and UniProt
2435 <!-- JAL-1976 -->No progress bar shown during export of
2439 <!-- JAL-2213 -->Structures not always superimposed after
2440 multiple structures are shown for one or more sequences.
2443 <!-- JAL-1370 -->Reference sequence characters should not
2444 be replaced with '.' when 'Show unconserved' format option
2448 <!-- JAL-1823 -->Cannot specify chain code when entering
2449 specific PDB id for sequence
2452 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2453 'Export hidden sequences' is enabled, but 'export hidden
2454 columns' is disabled.
2457 <!--JAL-2026-->Best Quality option in structure chooser
2458 selects lowest rather than highest resolution structures
2462 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2463 to sequence mapping in 'View Mappings' report
2466 <!-- JAL-2284 -->Unable to read old Jalview projects that
2467 contain non-XML data added after Jalvew wrote project.
2470 <!-- JAL-2118 -->Newly created annotation row reorders
2471 after clicking on it to create new annotation for a
2475 <!-- JAL-1980 -->Null Pointer Exception raised when
2476 pressing Add on an orphaned cut'n'paste window.
2478 <!-- may exclude, this is an external service stability issue JAL-1941
2479 -- > RNA 3D structure not added via DSSR service</li> -->
2484 <!-- JAL-2151 -->Incorrect columns are selected when
2485 hidden columns present before start of sequence
2488 <!-- JAL-1986 -->Missing dependencies on applet pages
2492 <!-- JAL-1947 -->Overview pixel size changes when
2493 sequences are hidden in applet
2496 <!-- JAL-1996 -->Updated instructions for applet
2497 deployment on examples pages.
2504 <td width="60" nowrap>
2505 <div align="center">
2506 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2507 <em>16/10/2015</em></strong>
2510 <td><em>General</em>
2512 <li>Time stamps for signed Jalview application and applet
2517 <em>Application</em>
2519 <li>Duplicate group consensus and conservation rows
2520 shown when tree is partitioned</li>
2521 <li>Erratic behaviour when tree partitions made with
2522 multiple cDNA/Protein split views</li>
2528 <td width="60" nowrap>
2529 <div align="center">
2530 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2531 <em>8/10/2015</em></strong>
2534 <td><em>General</em>
2536 <li>Updated Spanish translations of localized text for
2538 </ul> <em>Application</em>
2540 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2541 <li>Signed OSX InstallAnywhere installer<br></li>
2542 <li>Support for per-sequence based annotations in BioJSON</li>
2543 </ul> <em>Applet</em>
2545 <li>Split frame example added to applet examples page</li>
2546 </ul> <em>Build and Deployment</em>
2549 <!-- JAL-1888 -->New ant target for running Jalview's test
2557 <li>Mapping of cDNA to protein in split frames
2558 incorrect when sequence start > 1</li>
2559 <li>Broken images in filter column by annotation dialog
2561 <li>Feature colours not parsed from features file</li>
2562 <li>Exceptions and incomplete link URLs recovered when
2563 loading a features file containing HTML tags in feature
2567 <em>Application</em>
2569 <li>Annotations corrupted after BioJS export and
2571 <li>Incorrect sequence limits after Fetch DB References
2572 with 'trim retrieved sequences'</li>
2573 <li>Incorrect warning about deleting all data when
2574 deleting selected columns</li>
2575 <li>Patch to build system for shipping properly signed
2576 JNLP templates for webstart launch</li>
2577 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2578 unreleased structures for download or viewing</li>
2579 <li>Tab/space/return keystroke operation of EMBL-PDBe
2580 fetcher/viewer dialogs works correctly</li>
2581 <li>Disabled 'minimise' button on Jalview windows
2582 running on OSX to workaround redraw hang bug</li>
2583 <li>Split cDNA/Protein view position and geometry not
2584 recovered from jalview project</li>
2585 <li>Initial enabled/disabled state of annotation menu
2586 sorter 'show autocalculated first/last' corresponds to
2588 <li>Restoring of Clustal, RNA Helices and T-Coffee
2589 color schemes from BioJSON</li>
2593 <li>Reorder sequences mirrored in cDNA/Protein split
2595 <li>Applet with Jmol examples not loading correctly</li>
2601 <td><div align="center">
2602 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2604 <td><em>General</em>
2606 <li>Linked visualisation and analysis of DNA and Protein
2609 <li>Translated cDNA alignments shown as split protein
2610 and DNA alignment views</li>
2611 <li>Codon consensus annotation for linked protein and
2612 cDNA alignment views</li>
2613 <li>Link cDNA or Protein product sequences by loading
2614 them onto Protein or cDNA alignments</li>
2615 <li>Reconstruct linked cDNA alignment from aligned
2616 protein sequences</li>
2619 <li>Jmol integration updated to Jmol v14.2.14</li>
2620 <li>Import and export of Jalview alignment views as <a
2621 href="features/bioJsonFormat.html">BioJSON</a></li>
2622 <li>New alignment annotation file statements for
2623 reference sequences and marking hidden columns</li>
2624 <li>Reference sequence based alignment shading to
2625 highlight variation</li>
2626 <li>Select or hide columns according to alignment
2628 <li>Find option for locating sequences by description</li>
2629 <li>Conserved physicochemical properties shown in amino
2630 acid conservation row</li>
2631 <li>Alignments can be sorted by number of RNA helices</li>
2632 </ul> <em>Application</em>
2634 <li>New cDNA/Protein analysis capabilities
2636 <li>Get Cross-References should open a Split Frame
2637 view with cDNA/Protein</li>
2638 <li>Detect when nucleotide sequences and protein
2639 sequences are placed in the same alignment</li>
2640 <li>Split cDNA/Protein views are saved in Jalview
2645 <li>Use REST API to talk to Chimera</li>
2646 <li>Selected regions in Chimera are highlighted in linked
2647 Jalview windows</li>
2649 <li>VARNA RNA viewer updated to v3.93</li>
2650 <li>VARNA views are saved in Jalview Projects</li>
2651 <li>Pseudoknots displayed as Jalview RNA annotation can
2652 be shown in VARNA</li>
2654 <li>Make groups for selection uses marked columns as well
2655 as the active selected region</li>
2657 <li>Calculate UPGMA and NJ trees using sequence feature
2659 <li>New Export options
2661 <li>New Export Settings dialog to control hidden
2662 region export in flat file generation</li>
2664 <li>Export alignment views for display with the <a
2665 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2667 <li>Export scrollable SVG in HTML page</li>
2668 <li>Optional embedding of BioJSON data when exporting
2669 alignment figures to HTML</li>
2671 <li>3D structure retrieval and display
2673 <li>Free text and structured queries with the PDBe
2675 <li>PDBe Search API based discovery and selection of
2676 PDB structures for a sequence set</li>
2680 <li>JPred4 employed for protein secondary structure
2682 <li>Hide Insertions menu option to hide unaligned columns
2683 for one or a group of sequences</li>
2684 <li>Automatically hide insertions in alignments imported
2685 from the JPred4 web server</li>
2686 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2687 system on OSX<br />LGPL libraries courtesy of <a
2688 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2690 <li>changed 'View nucleotide structure' submenu to 'View
2691 VARNA 2D Structure'</li>
2692 <li>change "View protein structure" menu option to "3D
2695 </ul> <em>Applet</em>
2697 <li>New layout for applet example pages</li>
2698 <li>New parameters to enable SplitFrame view
2699 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2700 <li>New example demonstrating linked viewing of cDNA and
2701 Protein alignments</li>
2702 </ul> <em>Development and deployment</em>
2704 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2705 <li>Include installation type and git revision in build
2706 properties and console log output</li>
2707 <li>Jalview Github organisation, and new github site for
2708 storing BioJsMSA Templates</li>
2709 <li>Jalview's unit tests now managed with TestNG</li>
2712 <!-- <em>General</em>
2714 </ul> --> <!-- issues resolved --> <em>Application</em>
2716 <li>Escape should close any open find dialogs</li>
2717 <li>Typo in select-by-features status report</li>
2718 <li>Consensus RNA secondary secondary structure
2719 predictions are not highlighted in amber</li>
2720 <li>Missing gap character in v2.7 example file means
2721 alignment appears unaligned when pad-gaps is not enabled</li>
2722 <li>First switch to RNA Helices colouring doesn't colour
2723 associated structure views</li>
2724 <li>ID width preference option is greyed out when auto
2725 width checkbox not enabled</li>
2726 <li>Stopped a warning dialog from being shown when
2727 creating user defined colours</li>
2728 <li>'View Mapping' in structure viewer shows sequence
2729 mappings for just that viewer's sequences</li>
2730 <li>Workaround for superposing PDB files containing
2731 multiple models in Chimera</li>
2732 <li>Report sequence position in status bar when hovering
2733 over Jmol structure</li>
2734 <li>Cannot output gaps as '.' symbols with Selection ->
2735 output to text box</li>
2736 <li>Flat file exports of alignments with hidden columns
2737 have incorrect sequence start/end</li>
2738 <li>'Aligning' a second chain to a Chimera structure from
2740 <li>Colour schemes applied to structure viewers don't
2741 work for nucleotide</li>
2742 <li>Loading/cut'n'pasting an empty or invalid file leads
2743 to a grey/invisible alignment window</li>
2744 <li>Exported Jpred annotation from a sequence region
2745 imports to different position</li>
2746 <li>Space at beginning of sequence feature tooltips shown
2747 on some platforms</li>
2748 <li>Chimera viewer 'View | Show Chain' menu is not
2750 <li>'New View' fails with a Null Pointer Exception in
2751 console if Chimera has been opened</li>
2752 <li>Mouseover to Chimera not working</li>
2753 <li>Miscellaneous ENA XML feature qualifiers not
2755 <li>NPE in annotation renderer after 'Extract Scores'</li>
2756 <li>If two structures in one Chimera window, mouseover of
2757 either sequence shows on first structure</li>
2758 <li>'Show annotations' options should not make
2759 non-positional annotations visible</li>
2760 <li>Subsequence secondary structure annotation not shown
2761 in right place after 'view flanking regions'</li>
2762 <li>File Save As type unset when current file format is
2764 <li>Save as '.jar' option removed for saving Jalview
2766 <li>Colour by Sequence colouring in Chimera more
2768 <li>Cannot 'add reference annotation' for a sequence in
2769 several views on same alignment</li>
2770 <li>Cannot show linked products for EMBL / ENA records</li>
2771 <li>Jalview's tooltip wraps long texts containing no
2773 </ul> <em>Applet</em>
2775 <li>Jmol to JalviewLite mouseover/link not working</li>
2776 <li>JalviewLite can't import sequences with ID
2777 descriptions containing angle brackets</li>
2778 </ul> <em>General</em>
2780 <li>Cannot export and reimport RNA secondary structure
2781 via jalview annotation file</li>
2782 <li>Random helix colour palette for colour by annotation
2783 with RNA secondary structure</li>
2784 <li>Mouseover to cDNA from STOP residue in protein
2785 translation doesn't work.</li>
2786 <li>hints when using the select by annotation dialog box</li>
2787 <li>Jmol alignment incorrect if PDB file has alternate CA
2789 <li>FontChooser message dialog appears to hang after
2790 choosing 1pt font</li>
2791 <li>Peptide secondary structure incorrectly imported from
2792 annotation file when annotation display text includes 'e' or
2794 <li>Cannot set colour of new feature type whilst creating
2796 <li>cDNA translation alignment should not be sequence
2797 order dependent</li>
2798 <li>'Show unconserved' doesn't work for lower case
2800 <li>Nucleotide ambiguity codes involving R not recognised</li>
2801 </ul> <em>Deployment and Documentation</em>
2803 <li>Applet example pages appear different to the rest of
2804 www.jalview.org</li>
2805 </ul> <em>Application Known issues</em>
2807 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2808 <li>Misleading message appears after trying to delete
2810 <li>Jalview icon not shown in dock after InstallAnywhere
2811 version launches</li>
2812 <li>Fetching EMBL reference for an RNA sequence results
2813 fails with a sequence mismatch</li>
2814 <li>Corrupted or unreadable alignment display when
2815 scrolling alignment to right</li>
2816 <li>ArrayIndexOutOfBoundsException thrown when remove
2817 empty columns called on alignment with ragged gapped ends</li>
2818 <li>auto calculated alignment annotation rows do not get
2819 placed above or below non-autocalculated rows</li>
2820 <li>Jalview dekstop becomes sluggish at full screen in
2821 ultra-high resolution</li>
2822 <li>Cannot disable consensus calculation independently of
2823 quality and conservation</li>
2824 <li>Mouseover highlighting between cDNA and protein can
2825 become sluggish with more than one splitframe shown</li>
2826 </ul> <em>Applet Known Issues</em>
2828 <li>Core PDB parsing code requires Jmol</li>
2829 <li>Sequence canvas panel goes white when alignment
2830 window is being resized</li>
2836 <td><div align="center">
2837 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2839 <td><em>General</em>
2841 <li>Updated Java code signing certificate donated by
2843 <li>Features and annotation preserved when performing
2844 pairwise alignment</li>
2845 <li>RNA pseudoknot annotation can be
2846 imported/exported/displayed</li>
2847 <li>'colour by annotation' can colour by RNA and
2848 protein secondary structure</li>
2849 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2850 post-hoc with 2.9 release</em>)
2853 </ul> <em>Application</em>
2855 <li>Extract and display secondary structure for sequences
2856 with 3D structures</li>
2857 <li>Support for parsing RNAML</li>
2858 <li>Annotations menu for layout
2860 <li>sort sequence annotation rows by alignment</li>
2861 <li>place sequence annotation above/below alignment
2864 <li>Output in Stockholm format</li>
2865 <li>Internationalisation: improved Spanish (es)
2867 <li>Structure viewer preferences tab</li>
2868 <li>Disorder and Secondary Structure annotation tracks
2869 shared between alignments</li>
2870 <li>UCSF Chimera launch and linked highlighting from
2872 <li>Show/hide all sequence associated annotation rows for
2873 all or current selection</li>
2874 <li>disorder and secondary structure predictions
2875 available as dataset annotation</li>
2876 <li>Per-sequence rna helices colouring</li>
2879 <li>Sequence database accessions imported when fetching
2880 alignments from Rfam</li>
2881 <li>update VARNA version to 3.91</li>
2883 <li>New groovy scripts for exporting aligned positions,
2884 conservation values, and calculating sum of pairs scores.</li>
2885 <li>Command line argument to set default JABAWS server</li>
2886 <li>include installation type in build properties and
2887 console log output</li>
2888 <li>Updated Jalview project format to preserve dataset
2892 <!-- issues resolved --> <em>Application</em>
2894 <li>Distinguish alignment and sequence associated RNA
2895 structure in structure->view->VARNA</li>
2896 <li>Raise dialog box if user deletes all sequences in an
2898 <li>Pressing F1 results in documentation opening twice</li>
2899 <li>Sequence feature tooltip is wrapped</li>
2900 <li>Double click on sequence associated annotation
2901 selects only first column</li>
2902 <li>Redundancy removal doesn't result in unlinked
2903 leaves shown in tree</li>
2904 <li>Undos after several redundancy removals don't undo
2906 <li>Hide sequence doesn't hide associated annotation</li>
2907 <li>User defined colours dialog box too big to fit on
2908 screen and buttons not visible</li>
2909 <li>author list isn't updated if already written to
2910 Jalview properties</li>
2911 <li>Popup menu won't open after retrieving sequence
2913 <li>File open window for associate PDB doesn't open</li>
2914 <li>Left-then-right click on a sequence id opens a
2915 browser search window</li>
2916 <li>Cannot open sequence feature shading/sort popup menu
2917 in feature settings dialog</li>
2918 <li>better tooltip placement for some areas of Jalview
2920 <li>Allow addition of JABAWS Server which doesn't
2921 pass validation</li>
2922 <li>Web services parameters dialog box is too large to
2924 <li>Muscle nucleotide alignment preset obscured by
2926 <li>JABAWS preset submenus don't contain newly
2927 defined user preset</li>
2928 <li>MSA web services warns user if they were launched
2929 with invalid input</li>
2930 <li>Jalview cannot contact DAS Registy when running on
2933 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2934 'Superpose with' submenu not shown when new view
2938 </ul> <!-- <em>Applet</em>
2940 </ul> <em>General</em>
2942 </ul>--> <em>Deployment and Documentation</em>
2944 <li>2G and 1G options in launchApp have no effect on
2945 memory allocation</li>
2946 <li>launchApp service doesn't automatically open
2947 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2949 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2950 InstallAnywhere reports cannot find valid JVM when Java
2951 1.7_055 is available
2953 </ul> <em>Application Known issues</em>
2956 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2957 corrupted or unreadable alignment display when scrolling
2961 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2962 retrieval fails but progress bar continues for DAS retrieval
2963 with large number of ID
2966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2967 flatfile output of visible region has incorrect sequence
2971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2972 rna structure consensus doesn't update when secondary
2973 structure tracks are rearranged
2976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2977 invalid rna structure positional highlighting does not
2978 highlight position of invalid base pairs
2981 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2982 out of memory errors are not raised when saving Jalview
2983 project from alignment window file menu
2986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2987 Switching to RNA Helices colouring doesn't propagate to
2991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2992 colour by RNA Helices not enabled when user created
2993 annotation added to alignment
2996 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2997 Jalview icon not shown on dock in Mountain Lion/Webstart
2999 </ul> <em>Applet Known Issues</em>
3002 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3003 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3006 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3007 Jalview and Jmol example not compatible with IE9
3010 <li>Sort by annotation score doesn't reverse order
3016 <td><div align="center">
3017 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3020 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3023 <li>Internationalisation of user interface (usually
3024 called i18n support) and translation for Spanish locale</li>
3025 <li>Define/Undefine group on current selection with
3026 Ctrl-G/Shift Ctrl-G</li>
3027 <li>Improved group creation/removal options in
3028 alignment/sequence Popup menu</li>
3029 <li>Sensible precision for symbol distribution
3030 percentages shown in logo tooltip.</li>
3031 <li>Annotation panel height set according to amount of
3032 annotation when alignment first opened</li>
3033 </ul> <em>Application</em>
3035 <li>Interactive consensus RNA secondary structure
3036 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3037 <li>Select columns containing particular features from
3038 Feature Settings dialog</li>
3039 <li>View all 'representative' PDB structures for selected
3041 <li>Update Jalview project format:
3043 <li>New file extension for Jalview projects '.jvp'</li>
3044 <li>Preserve sequence and annotation dataset (to
3045 store secondary structure annotation,etc)</li>
3046 <li>Per group and alignment annotation and RNA helix
3050 <li>New similarity measures for PCA and Tree calculation
3052 <li>Experimental support for retrieval and viewing of
3053 flanking regions for an alignment</li>
3057 <!-- issues resolved --> <em>Application</em>
3059 <li>logo keeps spinning and status remains at queued or
3060 running after job is cancelled</li>
3061 <li>cannot export features from alignments imported from
3062 Jalview/VAMSAS projects</li>
3063 <li>Buggy slider for web service parameters that take
3065 <li>Newly created RNA secondary structure line doesn't
3066 have 'display all symbols' flag set</li>
3067 <li>T-COFFEE alignment score shading scheme and other
3068 annotation shading not saved in Jalview project</li>
3069 <li>Local file cannot be loaded in freshly downloaded
3071 <li>Jalview icon not shown on dock in Mountain
3073 <li>Load file from desktop file browser fails</li>
3074 <li>Occasional NPE thrown when calculating large trees</li>
3075 <li>Cannot reorder or slide sequences after dragging an
3076 alignment onto desktop</li>
3077 <li>Colour by annotation dialog throws NPE after using
3078 'extract scores' function</li>
3079 <li>Loading/cut'n'pasting an empty file leads to a grey
3080 alignment window</li>
3081 <li>Disorder thresholds rendered incorrectly after
3082 performing IUPred disorder prediction</li>
3083 <li>Multiple group annotated consensus rows shown when
3084 changing 'normalise logo' display setting</li>
3085 <li>Find shows blank dialog after 'finished searching' if
3086 nothing matches query</li>
3087 <li>Null Pointer Exceptions raised when sorting by
3088 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3090 <li>Errors in Jmol console when structures in alignment
3091 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3093 <li>Not all working JABAWS services are shown in
3095 <li>JAVAWS version of Jalview fails to launch with
3096 'invalid literal/length code'</li>
3097 <li>Annotation/RNA Helix colourschemes cannot be applied
3098 to alignment with groups (actually fixed in 2.8.0b1)</li>
3099 <li>RNA Helices and T-Coffee Scores available as default
3102 </ul> <em>Applet</em>
3104 <li>Remove group option is shown even when selection is
3106 <li>Apply to all groups ticked but colourscheme changes
3107 don't affect groups</li>
3108 <li>Documented RNA Helices and T-Coffee Scores as valid
3109 colourscheme name</li>
3110 <li>Annotation labels drawn on sequence IDs when
3111 Annotation panel is not displayed</li>
3112 <li>Increased font size for dropdown menus on OSX and
3113 embedded windows</li>
3114 </ul> <em>Other</em>
3116 <li>Consensus sequence for alignments/groups with a
3117 single sequence were not calculated</li>
3118 <li>annotation files that contain only groups imported as
3119 annotation and junk sequences</li>
3120 <li>Fasta files with sequences containing '*' incorrectly
3121 recognised as PFAM or BLC</li>
3122 <li>conservation/PID slider apply all groups option
3123 doesn't affect background (2.8.0b1)
3125 <li>redundancy highlighting is erratic at 0% and 100%</li>
3126 <li>Remove gapped columns fails for sequences with ragged
3128 <li>AMSA annotation row with leading spaces is not
3129 registered correctly on import</li>
3130 <li>Jalview crashes when selecting PCA analysis for
3131 certain alignments</li>
3132 <li>Opening the colour by annotation dialog for an
3133 existing annotation based 'use original colours'
3134 colourscheme loses original colours setting</li>
3139 <td><div align="center">
3140 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3141 <em>30/1/2014</em></strong>
3145 <li>Trusted certificates for JalviewLite applet and
3146 Jalview Desktop application<br />Certificate was donated by
3147 <a href="https://www.certum.eu">Certum</a> to the Jalview
3148 open source project).
3150 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3151 <li>Output in Stockholm format</li>
3152 <li>Allow import of data from gzipped files</li>
3153 <li>Export/import group and sequence associated line
3154 graph thresholds</li>
3155 <li>Nucleotide substitution matrix that supports RNA and
3156 ambiguity codes</li>
3157 <li>Allow disorder predictions to be made on the current
3158 selection (or visible selection) in the same way that JPred
3160 <li>Groovy scripting for headless Jalview operation</li>
3161 </ul> <em>Other improvements</em>
3163 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3164 <li>COMBINE statement uses current SEQUENCE_REF and
3165 GROUP_REF scope to group annotation rows</li>
3166 <li>Support '' style escaping of quotes in Newick
3168 <li>Group options for JABAWS service by command line name</li>
3169 <li>Empty tooltip shown for JABA service options with a
3170 link but no description</li>
3171 <li>Select primary source when selecting authority in
3172 database fetcher GUI</li>
3173 <li>Add .mfa to FASTA file extensions recognised by
3175 <li>Annotation label tooltip text wrap</li>
3180 <li>Slow scrolling when lots of annotation rows are
3182 <li>Lots of NPE (and slowness) after creating RNA
3183 secondary structure annotation line</li>
3184 <li>Sequence database accessions not imported when
3185 fetching alignments from Rfam</li>
3186 <li>Incorrect SHMR submission for sequences with
3188 <li>View all structures does not always superpose
3190 <li>Option widgets in service parameters not updated to
3191 reflect user or preset settings</li>
3192 <li>Null pointer exceptions for some services without
3193 presets or adjustable parameters</li>
3194 <li>Discover PDB IDs entry in structure menu doesn't
3195 discover PDB xRefs</li>
3196 <li>Exception encountered while trying to retrieve
3197 features with DAS</li>
3198 <li>Lowest value in annotation row isn't coloured
3199 when colour by annotation (per sequence) is coloured</li>
3200 <li>Keyboard mode P jumps to start of gapped region when
3201 residue follows a gap</li>
3202 <li>Jalview appears to hang importing an alignment with
3203 Wrap as default or after enabling Wrap</li>
3204 <li>'Right click to add annotations' message
3205 shown in wrap mode when no annotations present</li>
3206 <li>Disorder predictions fail with NPE if no automatic
3207 annotation already exists on alignment</li>
3208 <li>oninit javascript function should be called after
3209 initialisation completes</li>
3210 <li>Remove redundancy after disorder prediction corrupts
3211 alignment window display</li>
3212 <li>Example annotation file in documentation is invalid</li>
3213 <li>Grouped line graph annotation rows are not exported
3214 to annotation file</li>
3215 <li>Multi-harmony analysis cannot be run when only two
3217 <li>Cannot create multiple groups of line graphs with
3218 several 'combine' statements in annotation file</li>
3219 <li>Pressing return several times causes Number Format
3220 exceptions in keyboard mode</li>
3221 <li>Multi-harmony (SHMMR) method doesn't submit
3222 correct partitions for input data</li>
3223 <li>Translation from DNA to Amino Acids fails</li>
3224 <li>Jalview fail to load newick tree with quoted label</li>
3225 <li>--headless flag isn't understood</li>
3226 <li>ClassCastException when generating EPS in headless
3228 <li>Adjusting sequence-associated shading threshold only
3229 changes one row's threshold</li>
3230 <li>Preferences and Feature settings panel panel
3231 doesn't open</li>
3232 <li>hide consensus histogram also hides conservation and
3233 quality histograms</li>
3238 <td><div align="center">
3239 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3241 <td><em>Application</em>
3243 <li>Support for JABAWS 2.0 Services (AACon alignment
3244 conservation, protein disorder and Clustal Omega)</li>
3245 <li>JABAWS server status indicator in Web Services
3247 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3248 in Jalview alignment window</li>
3249 <li>Updated Jalview build and deploy framework for OSX
3250 mountain lion, windows 7, and 8</li>
3251 <li>Nucleotide substitution matrix for PCA that supports
3252 RNA and ambiguity codes</li>
3254 <li>Improved sequence database retrieval GUI</li>
3255 <li>Support fetching and database reference look up
3256 against multiple DAS sources (Fetch all from in 'fetch db
3258 <li>Jalview project improvements
3260 <li>Store and retrieve the 'belowAlignment'
3261 flag for annotation</li>
3262 <li>calcId attribute to group annotation rows on the
3264 <li>Store AACon calculation settings for a view in
3265 Jalview project</li>
3269 <li>horizontal scrolling gesture support</li>
3270 <li>Visual progress indicator when PCA calculation is
3272 <li>Simpler JABA web services menus</li>
3273 <li>visual indication that web service results are still
3274 being retrieved from server</li>
3275 <li>Serialise the dialogs that are shown when Jalview
3276 starts up for first time</li>
3277 <li>Jalview user agent string for interacting with HTTP
3279 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3281 <li>Examples directory and Groovy library included in
3282 InstallAnywhere distribution</li>
3283 </ul> <em>Applet</em>
3285 <li>RNA alignment and secondary structure annotation
3286 visualization applet example</li>
3287 </ul> <em>General</em>
3289 <li>Normalise option for consensus sequence logo</li>
3290 <li>Reset button in PCA window to return dimensions to
3292 <li>Allow seqspace or Jalview variant of alignment PCA
3294 <li>PCA with either nucleic acid and protein substitution
3296 <li>Allow windows containing HTML reports to be exported
3298 <li>Interactive display and editing of RNA secondary
3299 structure contacts</li>
3300 <li>RNA Helix Alignment Colouring</li>
3301 <li>RNA base pair logo consensus</li>
3302 <li>Parse sequence associated secondary structure
3303 information in Stockholm files</li>
3304 <li>HTML Export database accessions and annotation
3305 information presented in tooltip for sequences</li>
3306 <li>Import secondary structure from LOCARNA clustalw
3307 style RNA alignment files</li>
3308 <li>import and visualise T-COFFEE quality scores for an
3310 <li>'colour by annotation' per sequence option to
3311 shade each sequence according to its associated alignment
3313 <li>New Jalview Logo</li>
3314 </ul> <em>Documentation and Development</em>
3316 <li>documentation for score matrices used in Jalview</li>
3317 <li>New Website!</li>
3319 <td><em>Application</em>
3321 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3322 wsdbfetch REST service</li>
3323 <li>Stop windows being moved outside desktop on OSX</li>
3324 <li>Filetype associations not installed for webstart
3326 <li>Jalview does not always retrieve progress of a JABAWS
3327 job execution in full once it is complete</li>
3328 <li>revise SHMR RSBS definition to ensure alignment is
3329 uploaded via ali_file parameter</li>
3330 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3331 <li>View all structures superposed fails with exception</li>
3332 <li>Jnet job queues forever if a very short sequence is
3333 submitted for prediction</li>
3334 <li>Cut and paste menu not opened when mouse clicked on
3336 <li>Putting fractional value into integer text box in
3337 alignment parameter dialog causes Jalview to hang</li>
3338 <li>Structure view highlighting doesn't work on
3340 <li>View all structures fails with exception shown in
3342 <li>Characters in filename associated with PDBEntry not
3343 escaped in a platform independent way</li>
3344 <li>Jalview desktop fails to launch with exception when
3346 <li>Tree calculation reports 'you must have 2 or more
3347 sequences selected' when selection is empty</li>
3348 <li>Jalview desktop fails to launch with jar signature
3349 failure when java web start temporary file caching is
3351 <li>DAS Sequence retrieval with range qualification
3352 results in sequence xref which includes range qualification</li>
3353 <li>Errors during processing of command line arguments
3354 cause progress bar (JAL-898) to be removed</li>
3355 <li>Replace comma for semi-colon option not disabled for
3356 DAS sources in sequence fetcher</li>
3357 <li>Cannot close news reader when JABAWS server warning
3358 dialog is shown</li>
3359 <li>Option widgets not updated to reflect user settings</li>
3360 <li>Edited sequence not submitted to web service</li>
3361 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3362 <li>InstallAnywhere installer doesn't unpack and run
3363 on OSX Mountain Lion</li>
3364 <li>Annotation panel not given a scroll bar when
3365 sequences with alignment annotation are pasted into the
3367 <li>Sequence associated annotation rows not associated
3368 when loaded from Jalview project</li>
3369 <li>Browser launch fails with NPE on java 1.7</li>
3370 <li>JABAWS alignment marked as finished when job was
3371 cancelled or job failed due to invalid input</li>
3372 <li>NPE with v2.7 example when clicking on Tree
3373 associated with all views</li>
3374 <li>Exceptions when copy/paste sequences with grouped
3375 annotation rows to new window</li>
3376 </ul> <em>Applet</em>
3378 <li>Sequence features are momentarily displayed before
3379 they are hidden using hidefeaturegroups applet parameter</li>
3380 <li>loading features via javascript API automatically
3381 enables feature display</li>
3382 <li>scrollToColumnIn javascript API method doesn't
3384 </ul> <em>General</em>
3386 <li>Redundancy removal fails for rna alignment</li>
3387 <li>PCA calculation fails when sequence has been selected
3388 and then deselected</li>
3389 <li>PCA window shows grey box when first opened on OSX</li>
3390 <li>Letters coloured pink in sequence logo when alignment
3391 coloured with clustalx</li>
3392 <li>Choosing fonts without letter symbols defined causes
3393 exceptions and redraw errors</li>
3394 <li>Initial PCA plot view is not same as manually
3395 reconfigured view</li>
3396 <li>Grouped annotation graph label has incorrect line
3398 <li>Grouped annotation graph label display is corrupted
3399 for lots of labels</li>
3404 <div align="center">
3405 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3408 <td><em>Application</em>
3410 <li>Jalview Desktop News Reader</li>
3411 <li>Tweaked default layout of web services menu</li>
3412 <li>View/alignment association menu to enable user to
3413 easily specify which alignment a multi-structure view takes
3414 its colours/correspondences from</li>
3415 <li>Allow properties file location to be specified as URL</li>
3416 <li>Extend Jalview project to preserve associations
3417 between many alignment views and a single Jmol display</li>
3418 <li>Store annotation row height in Jalview project file</li>
3419 <li>Annotation row column label formatting attributes
3420 stored in project file</li>
3421 <li>Annotation row order for auto-calculated annotation
3422 rows preserved in Jalview project file</li>
3423 <li>Visual progress indication when Jalview state is
3424 saved using Desktop window menu</li>
3425 <li>Visual indication that command line arguments are
3426 still being processed</li>
3427 <li>Groovy script execution from URL</li>
3428 <li>Colour by annotation default min and max colours in
3430 <li>Automatically associate PDB files dragged onto an
3431 alignment with sequences that have high similarity and
3433 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3434 <li>'view structures' option to open many
3435 structures in same window</li>
3436 <li>Sort associated views menu option for tree panel</li>
3437 <li>Group all JABA and non-JABA services for a particular
3438 analysis function in its own submenu</li>
3439 </ul> <em>Applet</em>
3441 <li>Userdefined and autogenerated annotation rows for
3443 <li>Adjustment of alignment annotation pane height</li>
3444 <li>Annotation scrollbar for annotation panel</li>
3445 <li>Drag to reorder annotation rows in annotation panel</li>
3446 <li>'automaticScrolling' parameter</li>
3447 <li>Allow sequences with partial ID string matches to be
3448 annotated from GFF/Jalview features files</li>
3449 <li>Sequence logo annotation row in applet</li>
3450 <li>Absolute paths relative to host server in applet
3451 parameters are treated as such</li>
3452 <li>New in the JalviewLite javascript API:
3454 <li>JalviewLite.js javascript library</li>
3455 <li>Javascript callbacks for
3457 <li>Applet initialisation</li>
3458 <li>Sequence/alignment mouse-overs and selections</li>
3461 <li>scrollTo row and column alignment scrolling
3463 <li>Select sequence/alignment regions from javascript</li>
3464 <li>javascript structure viewer harness to pass
3465 messages between Jmol and Jalview when running as
3466 distinct applets</li>
3467 <li>sortBy method</li>
3468 <li>Set of applet and application examples shipped
3469 with documentation</li>
3470 <li>New example to demonstrate JalviewLite and Jmol
3471 javascript message exchange</li>
3473 </ul> <em>General</em>
3475 <li>Enable Jmol displays to be associated with multiple
3476 multiple alignments</li>
3477 <li>Option to automatically sort alignment with new tree</li>
3478 <li>User configurable link to enable redirects to a
3479 www.Jalview.org mirror</li>
3480 <li>Jmol colours option for Jmol displays</li>
3481 <li>Configurable newline string when writing alignment
3482 and other flat files</li>
3483 <li>Allow alignment annotation description lines to
3484 contain html tags</li>
3485 </ul> <em>Documentation and Development</em>
3487 <li>Add groovy test harness for bulk load testing to
3489 <li>Groovy script to load and align a set of sequences
3490 using a web service before displaying the result in the
3491 Jalview desktop</li>
3492 <li>Restructured javascript and applet api documentation</li>
3493 <li>Ant target to publish example html files with applet
3495 <li>Netbeans project for building Jalview from source</li>
3496 <li>ant task to create online javadoc for Jalview source</li>
3498 <td><em>Application</em>
3500 <li>User defined colourscheme throws exception when
3501 current built in colourscheme is saved as new scheme</li>
3502 <li>AlignFrame->Save in application pops up save
3503 dialog for valid filename/format</li>
3504 <li>Cannot view associated structure for UniProt sequence</li>
3505 <li>PDB file association breaks for UniProt sequence
3507 <li>Associate PDB from file dialog does not tell you
3508 which sequence is to be associated with the file</li>
3509 <li>Find All raises null pointer exception when query
3510 only matches sequence IDs</li>
3511 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3512 <li>Jalview project with Jmol views created with Jalview
3513 2.4 cannot be loaded</li>
3514 <li>Filetype associations not installed for webstart
3516 <li>Two or more chains in a single PDB file associated
3517 with sequences in different alignments do not get coloured
3518 by their associated sequence</li>
3519 <li>Visibility status of autocalculated annotation row
3520 not preserved when project is loaded</li>
3521 <li>Annotation row height and visibility attributes not
3522 stored in Jalview project</li>
3523 <li>Tree bootstraps are not preserved when saved as a
3524 Jalview project</li>
3525 <li>Envision2 workflow tooltips are corrupted</li>
3526 <li>Enabling show group conservation also enables colour
3527 by conservation</li>
3528 <li>Duplicate group associated conservation or consensus
3529 created on new view</li>
3530 <li>Annotation scrollbar not displayed after 'show
3531 all hidden annotation rows' option selected</li>
3532 <li>Alignment quality not updated after alignment
3533 annotation row is hidden then shown</li>
3534 <li>Preserve colouring of structures coloured by
3535 sequences in pre Jalview 2.7 projects</li>
3536 <li>Web service job parameter dialog is not laid out
3538 <li>Web services menu not refreshed after 'reset
3539 services' button is pressed in preferences</li>
3540 <li>Annotation off by one in Jalview v2_3 example project</li>
3541 <li>Structures imported from file and saved in project
3542 get name like jalview_pdb1234.txt when reloaded</li>
3543 <li>Jalview does not always retrieve progress of a JABAWS
3544 job execution in full once it is complete</li>
3545 </ul> <em>Applet</em>
3547 <li>Alignment height set incorrectly when lots of
3548 annotation rows are displayed</li>
3549 <li>Relative URLs in feature HTML text not resolved to
3551 <li>View follows highlighting does not work for positions
3553 <li><= shown as = in tooltip</li>
3554 <li>Export features raises exception when no features
3556 <li>Separator string used for serialising lists of IDs
3557 for javascript api is modified when separator string
3558 provided as parameter</li>
3559 <li>Null pointer exception when selecting tree leaves for
3560 alignment with no existing selection</li>
3561 <li>Relative URLs for datasources assumed to be relative
3562 to applet's codebase</li>
3563 <li>Status bar not updated after finished searching and
3564 search wraps around to first result</li>
3565 <li>StructureSelectionManager instance shared between
3566 several Jalview applets causes race conditions and memory
3568 <li>Hover tooltip and mouseover of position on structure
3569 not sent from Jmol in applet</li>
3570 <li>Certain sequences of javascript method calls to
3571 applet API fatally hang browser</li>
3572 </ul> <em>General</em>
3574 <li>View follows structure mouseover scrolls beyond
3575 position with wrapped view and hidden regions</li>
3576 <li>Find sequence position moves to wrong residue
3577 with/without hidden columns</li>
3578 <li>Sequence length given in alignment properties window
3580 <li>InvalidNumberFormat exceptions thrown when trying to
3581 import PDB like structure files</li>
3582 <li>Positional search results are only highlighted
3583 between user-supplied sequence start/end bounds</li>
3584 <li>End attribute of sequence is not validated</li>
3585 <li>Find dialog only finds first sequence containing a
3586 given sequence position</li>
3587 <li>Sequence numbering not preserved in MSF alignment
3589 <li>Jalview PDB file reader does not extract sequence
3590 from nucleotide chains correctly</li>
3591 <li>Structure colours not updated when tree partition
3592 changed in alignment</li>
3593 <li>Sequence associated secondary structure not correctly
3594 parsed in interleaved stockholm</li>
3595 <li>Colour by annotation dialog does not restore current
3597 <li>Hiding (nearly) all sequences doesn't work
3599 <li>Sequences containing lowercase letters are not
3600 properly associated with their pdb files</li>
3601 </ul> <em>Documentation and Development</em>
3603 <li>schemas/JalviewWsParamSet.xsd corrupted by
3604 ApplyCopyright tool</li>
3609 <div align="center">
3610 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3613 <td><em>Application</em>
3615 <li>New warning dialog when the Jalview Desktop cannot
3616 contact web services</li>
3617 <li>JABA service parameters for a preset are shown in
3618 service job window</li>
3619 <li>JABA Service menu entries reworded</li>
3623 <li>Modeller PIR IO broken - cannot correctly import a
3624 pir file emitted by Jalview</li>
3625 <li>Existing feature settings transferred to new
3626 alignment view created from cut'n'paste</li>
3627 <li>Improved test for mixed amino/nucleotide chains when
3628 parsing PDB files</li>
3629 <li>Consensus and conservation annotation rows
3630 occasionally become blank for all new windows</li>
3631 <li>Exception raised when right clicking above sequences
3632 in wrapped view mode</li>
3633 </ul> <em>Application</em>
3635 <li>multiple multiply aligned structure views cause cpu
3636 usage to hit 100% and computer to hang</li>
3637 <li>Web Service parameter layout breaks for long user
3638 parameter names</li>
3639 <li>Jaba service discovery hangs desktop if Jaba server
3646 <div align="center">
3647 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3650 <td><em>Application</em>
3652 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3653 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3656 <li>Web Services preference tab</li>
3657 <li>Analysis parameters dialog box and user defined
3659 <li>Improved speed and layout of Envision2 service menu</li>
3660 <li>Superpose structures using associated sequence
3662 <li>Export coordinates and projection as CSV from PCA
3664 </ul> <em>Applet</em>
3666 <li>enable javascript: execution by the applet via the
3667 link out mechanism</li>
3668 </ul> <em>Other</em>
3670 <li>Updated the Jmol Jalview interface to work with Jmol
3672 <li>The Jalview Desktop and JalviewLite applet now
3673 require Java 1.5</li>
3674 <li>Allow Jalview feature colour specification for GFF
3675 sequence annotation files</li>
3676 <li>New 'colour by label' keword in Jalview feature file
3677 type colour specification</li>
3678 <li>New Jalview Desktop Groovy API method that allows a
3679 script to check if it being run in an interactive session or
3680 in a batch operation from the Jalview command line</li>
3684 <li>clustalx colourscheme colours Ds preferentially when
3685 both D+E are present in over 50% of the column</li>
3686 </ul> <em>Application</em>
3688 <li>typo in AlignmentFrame->View->Hide->all but
3689 selected Regions menu item</li>
3690 <li>sequence fetcher replaces ',' for ';' when the ',' is
3691 part of a valid accession ID</li>
3692 <li>fatal OOM if object retrieved by sequence fetcher
3693 runs out of memory</li>
3694 <li>unhandled Out of Memory Error when viewing pca
3695 analysis results</li>
3696 <li>InstallAnywhere builds fail to launch on OS X java
3697 10.5 update 4 (due to apple Java 1.6 update)</li>
3698 <li>Installanywhere Jalview silently fails to launch</li>
3699 </ul> <em>Applet</em>
3701 <li>Jalview.getFeatureGroups() raises an
3702 ArrayIndexOutOfBoundsException if no feature groups are
3709 <div align="center">
3710 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3716 <li>Alignment prettyprinter doesn't cope with long
3718 <li>clustalx colourscheme colours Ds preferentially when
3719 both D+E are present in over 50% of the column</li>
3720 <li>nucleic acid structures retrieved from PDB do not
3721 import correctly</li>
3722 <li>More columns get selected than were clicked on when a
3723 number of columns are hidden</li>
3724 <li>annotation label popup menu not providing correct
3725 add/hide/show options when rows are hidden or none are
3727 <li>Stockholm format shown in list of readable formats,
3728 and parser copes better with alignments from RFAM.</li>
3729 <li>CSV output of consensus only includes the percentage
3730 of all symbols if sequence logo display is enabled</li>
3732 </ul> <em>Applet</em>
3734 <li>annotation panel disappears when annotation is
3736 </ul> <em>Application</em>
3738 <li>Alignment view not redrawn properly when new
3739 alignment opened where annotation panel is visible but no
3740 annotations are present on alignment</li>
3741 <li>pasted region containing hidden columns is
3742 incorrectly displayed in new alignment window</li>
3743 <li>Jalview slow to complete operations when stdout is
3744 flooded (fix is to close the Jalview console)</li>
3745 <li>typo in AlignmentFrame->View->Hide->all but
3746 selected Rregions menu item.</li>
3747 <li>inconsistent group submenu and Format submenu entry
3748 'Un' or 'Non'conserved</li>
3749 <li>Sequence feature settings are being shared by
3750 multiple distinct alignments</li>
3751 <li>group annotation not recreated when tree partition is
3753 <li>double click on group annotation to select sequences
3754 does not propagate to associated trees</li>
3755 <li>Mac OSX specific issues:
3757 <li>exception raised when mouse clicked on desktop
3758 window background</li>
3759 <li>Desktop menu placed on menu bar and application
3760 name set correctly</li>
3761 <li>sequence feature settings not wide enough for the
3762 save feature colourscheme button</li>
3771 <div align="center">
3772 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3775 <td><em>New Capabilities</em>
3777 <li>URL links generated from description line for
3778 regular-expression based URL links (applet and application)
3780 <li>Non-positional feature URL links are shown in link
3782 <li>Linked viewing of nucleic acid sequences and
3784 <li>Automatic Scrolling option in View menu to display
3785 the currently highlighted region of an alignment.</li>
3786 <li>Order an alignment by sequence length, or using the
3787 average score or total feature count for each sequence.</li>
3788 <li>Shading features by score or associated description</li>
3789 <li>Subdivide alignment and groups based on identity of
3790 selected subsequence (Make Groups from Selection).</li>
3791 <li>New hide/show options including Shift+Control+H to
3792 hide everything but the currently selected region.</li>
3793 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3794 </ul> <em>Application</em>
3796 <li>Fetch DB References capabilities and UI expanded to
3797 support retrieval from DAS sequence sources</li>
3798 <li>Local DAS Sequence sources can be added via the
3799 command line or via the Add local source dialog box.</li>
3800 <li>DAS Dbref and DbxRef feature types are parsed as
3801 database references and protein_name is parsed as
3802 description line (BioSapiens terms).</li>
3803 <li>Enable or disable non-positional feature and database
3804 references in sequence ID tooltip from View menu in
3806 <!-- <li>New hidden columns and rows and representatives capabilities
3807 in annotations file (in progress - not yet fully implemented)</li> -->
3808 <li>Group-associated consensus, sequence logos and
3809 conservation plots</li>
3810 <li>Symbol distributions for each column can be exported
3811 and visualized as sequence logos</li>
3812 <li>Optionally scale multi-character column labels to fit
3813 within each column of annotation row<!-- todo for applet -->
3815 <li>Optional automatic sort of associated alignment view
3816 when a new tree is opened.</li>
3817 <li>Jalview Java Console</li>
3818 <li>Better placement of desktop window when moving
3819 between different screens.</li>
3820 <li>New preference items for sequence ID tooltip and
3821 consensus annotation</li>
3822 <li>Client to submit sequences and IDs to Envision2
3824 <li><em>Vamsas Capabilities</em>
3826 <li>Improved VAMSAS synchronization (Jalview archive
3827 used to preserve views, structures, and tree display
3829 <li>Import of vamsas documents from disk or URL via
3831 <li>Sharing of selected regions between views and
3832 with other VAMSAS applications (Experimental feature!)</li>
3833 <li>Updated API to VAMSAS version 0.2</li>
3835 </ul> <em>Applet</em>
3837 <li>Middle button resizes annotation row height</li>
3840 <li>sortByTree (true/false) - automatically sort the
3841 associated alignment view by the tree when a new tree is
3843 <li>showTreeBootstraps (true/false) - show or hide
3844 branch bootstraps (default is to show them if available)</li>
3845 <li>showTreeDistances (true/false) - show or hide
3846 branch lengths (default is to show them if available)</li>
3847 <li>showUnlinkedTreeNodes (true/false) - indicate if
3848 unassociated nodes should be highlighted in the tree
3850 <li>heightScale and widthScale (1.0 or more) -
3851 increase the height or width of a cell in the alignment
3852 grid relative to the current font size.</li>
3855 <li>Non-positional features displayed in sequence ID
3857 </ul> <em>Other</em>
3859 <li>Features format: graduated colour definitions and
3860 specification of feature scores</li>
3861 <li>Alignment Annotations format: new keywords for group
3862 associated annotation (GROUP_REF) and annotation row display
3863 properties (ROW_PROPERTIES)</li>
3864 <li>XML formats extended to support graduated feature
3865 colourschemes, group associated annotation, and profile
3866 visualization settings.</li></td>
3869 <li>Source field in GFF files parsed as feature source
3870 rather than description</li>
3871 <li>Non-positional features are now included in sequence
3872 feature and gff files (controlled via non-positional feature
3873 visibility in tooltip).</li>
3874 <li>URL links generated for all feature links (bugfix)</li>
3875 <li>Added URL embedding instructions to features file
3877 <li>Codons containing ambiguous nucleotides translated as
3878 'X' in peptide product</li>
3879 <li>Match case switch in find dialog box works for both
3880 sequence ID and sequence string and query strings do not
3881 have to be in upper case to match case-insensitively.</li>
3882 <li>AMSA files only contain first column of
3883 multi-character column annotation labels</li>
3884 <li>Jalview Annotation File generation/parsing consistent
3885 with documentation (e.g. Stockholm annotation can be
3886 exported and re-imported)</li>
3887 <li>PDB files without embedded PDB IDs given a friendly
3889 <li>Find incrementally searches ID string matches as well
3890 as subsequence matches, and correctly reports total number
3894 <li>Better handling of exceptions during sequence
3896 <li>Dasobert generated non-positional feature URL
3897 link text excludes the start_end suffix</li>
3898 <li>DAS feature and source retrieval buttons disabled
3899 when fetch or registry operations in progress.</li>
3900 <li>PDB files retrieved from URLs are cached properly</li>
3901 <li>Sequence description lines properly shared via
3903 <li>Sequence fetcher fetches multiple records for all
3905 <li>Ensured that command line das feature retrieval
3906 completes before alignment figures are generated.</li>
3907 <li>Reduced time taken when opening file browser for
3909 <li>isAligned check prior to calculating tree, PCA or
3910 submitting an MSA to JNet now excludes hidden sequences.</li>
3911 <li>User defined group colours properly recovered
3912 from Jalview projects.</li>
3921 <div align="center">
3922 <strong>2.4.0.b2</strong><br> 28/10/2009
3927 <li>Experimental support for google analytics usage
3929 <li>Jalview privacy settings (user preferences and docs).</li>
3934 <li>Race condition in applet preventing startup in
3936 <li>Exception when feature created from selection beyond
3937 length of sequence.</li>
3938 <li>Allow synthetic PDB files to be imported gracefully</li>
3939 <li>Sequence associated annotation rows associate with
3940 all sequences with a given id</li>
3941 <li>Find function matches case-insensitively for sequence
3942 ID string searches</li>
3943 <li>Non-standard characters do not cause pairwise
3944 alignment to fail with exception</li>
3945 </ul> <em>Application Issues</em>
3947 <li>Sequences are now validated against EMBL database</li>
3948 <li>Sequence fetcher fetches multiple records for all
3950 </ul> <em>InstallAnywhere Issues</em>
3952 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3953 issue with installAnywhere mechanism)</li>
3954 <li>Command line launching of JARs from InstallAnywhere
3955 version (java class versioning error fixed)</li>
3962 <div align="center">
3963 <strong>2.4</strong><br> 27/8/2008
3966 <td><em>User Interface</em>
3968 <li>Linked highlighting of codon and amino acid from
3969 translation and protein products</li>
3970 <li>Linked highlighting of structure associated with
3971 residue mapping to codon position</li>
3972 <li>Sequence Fetcher provides example accession numbers
3973 and 'clear' button</li>
3974 <li>MemoryMonitor added as an option under Desktop's
3976 <li>Extract score function to parse whitespace separated
3977 numeric data in description line</li>
3978 <li>Column labels in alignment annotation can be centred.</li>
3979 <li>Tooltip for sequence associated annotation give name
3981 </ul> <em>Web Services and URL fetching</em>
3983 <li>JPred3 web service</li>
3984 <li>Prototype sequence search client (no public services
3986 <li>Fetch either seed alignment or full alignment from
3988 <li>URL Links created for matching database cross
3989 references as well as sequence ID</li>
3990 <li>URL Links can be created using regular-expressions</li>
3991 </ul> <em>Sequence Database Connectivity</em>
3993 <li>Retrieval of cross-referenced sequences from other
3995 <li>Generalised database reference retrieval and
3996 validation to all fetchable databases</li>
3997 <li>Fetch sequences from DAS sources supporting the
3998 sequence command</li>
3999 </ul> <em>Import and Export</em>
4000 <li>export annotation rows as CSV for spreadsheet import</li>
4001 <li>Jalview projects record alignment dataset associations,
4002 EMBL products, and cDNA sequence mappings</li>
4003 <li>Sequence Group colour can be specified in Annotation
4005 <li>Ad-hoc colouring of group in Annotation File using RGB
4006 triplet as name of colourscheme</li>
4007 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4009 <li>treenode binding for VAMSAS tree exchange</li>
4010 <li>local editing and update of sequences in VAMSAS
4011 alignments (experimental)</li>
4012 <li>Create new or select existing session to join</li>
4013 <li>load and save of vamsas documents</li>
4014 </ul> <em>Application command line</em>
4016 <li>-tree parameter to open trees (introduced for passing
4018 <li>-fetchfrom command line argument to specify nicknames
4019 of DAS servers to query for alignment features</li>
4020 <li>-dasserver command line argument to add new servers
4021 that are also automatically queried for features</li>
4022 <li>-groovy command line argument executes a given groovy
4023 script after all input data has been loaded and parsed</li>
4024 </ul> <em>Applet-Application data exchange</em>
4026 <li>Trees passed as applet parameters can be passed to
4027 application (when using "View in full
4028 application")</li>
4029 </ul> <em>Applet Parameters</em>
4031 <li>feature group display control parameter</li>
4032 <li>debug parameter</li>
4033 <li>showbutton parameter</li>
4034 </ul> <em>Applet API methods</em>
4036 <li>newView public method</li>
4037 <li>Window (current view) specific get/set public methods</li>
4038 <li>Feature display control methods</li>
4039 <li>get list of currently selected sequences</li>
4040 </ul> <em>New Jalview distribution features</em>
4042 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4043 <li>RELEASE file gives build properties for the latest
4044 Jalview release.</li>
4045 <li>Java 1.1 Applet build made easier and donotobfuscate
4046 property controls execution of obfuscator</li>
4047 <li>Build target for generating source distribution</li>
4048 <li>Debug flag for javacc</li>
4049 <li>.jalview_properties file is documented (slightly) in
4050 jalview.bin.Cache</li>
4051 <li>Continuous Build Integration for stable and
4052 development version of Application, Applet and source
4057 <li>selected region output includes visible annotations
4058 (for certain formats)</li>
4059 <li>edit label/displaychar contains existing label/char
4061 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4062 <li>shorter peptide product names from EMBL records</li>
4063 <li>Newick string generator makes compact representations</li>
4064 <li>bootstrap values parsed correctly for tree files with
4066 <li>pathological filechooser bug avoided by not allowing
4067 filenames containing a ':'</li>
4068 <li>Fixed exception when parsing GFF files containing
4069 global sequence features</li>
4070 <li>Alignment datasets are finalized only when number of
4071 references from alignment sequences goes to zero</li>
4072 <li>Close of tree branch colour box without colour
4073 selection causes cascading exceptions</li>
4074 <li>occasional negative imgwidth exceptions</li>
4075 <li>better reporting of non-fatal warnings to user when
4076 file parsing fails.</li>
4077 <li>Save works when Jalview project is default format</li>
4078 <li>Save as dialog opened if current alignment format is
4079 not a valid output format</li>
4080 <li>UniProt canonical names introduced for both das and
4082 <li>Histidine should be midblue (not pink!) in Zappo</li>
4083 <li>error messages passed up and output when data read
4085 <li>edit undo recovers previous dataset sequence when
4086 sequence is edited</li>
4087 <li>allow PDB files without pdb ID HEADER lines (like
4088 those generated by MODELLER) to be read in properly</li>
4089 <li>allow reading of JPred concise files as a normal
4091 <li>Stockholm annotation parsing and alignment properties
4092 import fixed for PFAM records</li>
4093 <li>Structure view windows have correct name in Desktop
4095 <li>annotation consisting of sequence associated scores
4096 can be read and written correctly to annotation file</li>
4097 <li>Aligned cDNA translation to aligned peptide works
4099 <li>Fixed display of hidden sequence markers and
4100 non-italic font for representatives in Applet</li>
4101 <li>Applet Menus are always embedded in applet window on
4103 <li>Newly shown features appear at top of stack (in
4105 <li>Annotations added via parameter not drawn properly
4106 due to null pointer exceptions</li>
4107 <li>Secondary structure lines are drawn starting from
4108 first column of alignment</li>
4109 <li>UniProt XML import updated for new schema release in
4111 <li>Sequence feature to sequence ID match for Features
4112 file is case-insensitive</li>
4113 <li>Sequence features read from Features file appended to
4114 all sequences with matching IDs</li>
4115 <li>PDB structure coloured correctly for associated views
4116 containing a sub-sequence</li>
4117 <li>PDB files can be retrieved by applet from Jar files</li>
4118 <li>feature and annotation file applet parameters
4119 referring to different directories are retrieved correctly</li>
4120 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4121 <li>Fixed application hang whilst waiting for
4122 splash-screen version check to complete</li>
4123 <li>Applet properly URLencodes input parameter values
4124 when passing them to the launchApp service</li>
4125 <li>display name and local features preserved in results
4126 retrieved from web service</li>
4127 <li>Visual delay indication for sequence retrieval and
4128 sequence fetcher initialisation</li>
4129 <li>updated Application to use DAS 1.53e version of
4130 dasobert DAS client</li>
4131 <li>Re-instated Full AMSA support and .amsa file
4133 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4141 <div align="center">
4142 <strong>2.3</strong><br> 9/5/07
4147 <li>Jmol 11.0.2 integration</li>
4148 <li>PDB views stored in Jalview XML files</li>
4149 <li>Slide sequences</li>
4150 <li>Edit sequence in place</li>
4151 <li>EMBL CDS features</li>
4152 <li>DAS Feature mapping</li>
4153 <li>Feature ordering</li>
4154 <li>Alignment Properties</li>
4155 <li>Annotation Scores</li>
4156 <li>Sort by scores</li>
4157 <li>Feature/annotation editing in applet</li>
4162 <li>Headless state operation in 2.2.1</li>
4163 <li>Incorrect and unstable DNA pairwise alignment</li>
4164 <li>Cut and paste of sequences with annotation</li>
4165 <li>Feature group display state in XML</li>
4166 <li>Feature ordering in XML</li>
4167 <li>blc file iteration selection using filename # suffix</li>
4168 <li>Stockholm alignment properties</li>
4169 <li>Stockhom alignment secondary structure annotation</li>
4170 <li>2.2.1 applet had no feature transparency</li>
4171 <li>Number pad keys can be used in cursor mode</li>
4172 <li>Structure Viewer mirror image resolved</li>
4179 <div align="center">
4180 <strong>2.2.1</strong><br> 12/2/07
4185 <li>Non standard characters can be read and displayed
4186 <li>Annotations/Features can be imported/exported to the
4188 <li>Applet allows editing of sequence/annotation/group
4189 name & description
4190 <li>Preference setting to display sequence name in
4192 <li>Annotation file format extended to allow
4193 Sequence_groups to be defined
4194 <li>Default opening of alignment overview panel can be
4195 specified in preferences
4196 <li>PDB residue numbering annotation added to associated
4202 <li>Applet crash under certain Linux OS with Java 1.6
4204 <li>Annotation file export / import bugs fixed
4205 <li>PNG / EPS image output bugs fixed
4211 <div align="center">
4212 <strong>2.2</strong><br> 27/11/06
4217 <li>Multiple views on alignment
4218 <li>Sequence feature editing
4219 <li>"Reload" alignment
4220 <li>"Save" to current filename
4221 <li>Background dependent text colour
4222 <li>Right align sequence ids
4223 <li>User-defined lower case residue colours
4226 <li>Menu item accelerator keys
4227 <li>Control-V pastes to current alignment
4228 <li>Cancel button for DAS Feature Fetching
4229 <li>PCA and PDB Viewers zoom via mouse roller
4230 <li>User-defined sub-tree colours and sub-tree selection
4232 <li>'New Window' button on the 'Output to Text box'
4237 <li>New memory efficient Undo/Redo System
4238 <li>Optimised symbol lookups and conservation/consensus
4240 <li>Region Conservation/Consensus recalculated after
4242 <li>Fixed Remove Empty Columns Bug (empty columns at end
4244 <li>Slowed DAS Feature Fetching for increased robustness.
4246 <li>Made angle brackets in ASCII feature descriptions
4248 <li>Re-instated Zoom function for PCA
4249 <li>Sequence descriptions conserved in web service
4251 <li>UniProt ID discoverer uses any word separated by
4253 <li>WsDbFetch query/result association resolved
4254 <li>Tree leaf to sequence mapping improved
4255 <li>Smooth fonts switch moved to FontChooser dialog box.
4262 <div align="center">
4263 <strong>2.1.1</strong><br> 12/9/06
4268 <li>Copy consensus sequence to clipboard</li>
4273 <li>Image output - rightmost residues are rendered if
4274 sequence id panel has been resized</li>
4275 <li>Image output - all offscreen group boundaries are
4277 <li>Annotation files with sequence references - all
4278 elements in file are relative to sequence position</li>
4279 <li>Mac Applet users can use Alt key for group editing</li>
4285 <div align="center">
4286 <strong>2.1</strong><br> 22/8/06
4291 <li>MAFFT Multiple Alignment in default Web Service list</li>
4292 <li>DAS Feature fetching</li>
4293 <li>Hide sequences and columns</li>
4294 <li>Export Annotations and Features</li>
4295 <li>GFF file reading / writing</li>
4296 <li>Associate structures with sequences from local PDB
4298 <li>Add sequences to exisiting alignment</li>
4299 <li>Recently opened files / URL lists</li>
4300 <li>Applet can launch the full application</li>
4301 <li>Applet has transparency for features (Java 1.2
4303 <li>Applet has user defined colours parameter</li>
4304 <li>Applet can load sequences from parameter
4305 "sequence<em>x</em>"
4311 <li>Redundancy Panel reinstalled in the Applet</li>
4312 <li>Monospaced font - EPS / rescaling bug fixed</li>
4313 <li>Annotation files with sequence references bug fixed</li>
4319 <div align="center">
4320 <strong>2.08.1</strong><br> 2/5/06
4325 <li>Change case of selected region from Popup menu</li>
4326 <li>Choose to match case when searching</li>
4327 <li>Middle mouse button and mouse movement can compress /
4328 expand the visible width and height of the alignment</li>
4333 <li>Annotation Panel displays complete JNet results</li>
4339 <div align="center">
4340 <strong>2.08b</strong><br> 18/4/06
4346 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4347 <li>Righthand label on wrapped alignments shows correct
4354 <div align="center">
4355 <strong>2.08</strong><br> 10/4/06
4360 <li>Editing can be locked to the selection area</li>
4361 <li>Keyboard editing</li>
4362 <li>Create sequence features from searches</li>
4363 <li>Precalculated annotations can be loaded onto
4365 <li>Features file allows grouping of features</li>
4366 <li>Annotation Colouring scheme added</li>
4367 <li>Smooth fonts off by default - Faster rendering</li>
4368 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4373 <li>Drag & Drop fixed on Linux</li>
4374 <li>Jalview Archive file faster to load/save, sequence
4375 descriptions saved.</li>
4381 <div align="center">
4382 <strong>2.07</strong><br> 12/12/05
4387 <li>PDB Structure Viewer enhanced</li>
4388 <li>Sequence Feature retrieval and display enhanced</li>
4389 <li>Choose to output sequence start-end after sequence
4390 name for file output</li>
4391 <li>Sequence Fetcher WSDBFetch@EBI</li>
4392 <li>Applet can read feature files, PDB files and can be
4393 used for HTML form input</li>
4398 <li>HTML output writes groups and features</li>
4399 <li>Group editing is Control and mouse click</li>
4400 <li>File IO bugs</li>
4406 <div align="center">
4407 <strong>2.06</strong><br> 28/9/05
4412 <li>View annotations in wrapped mode</li>
4413 <li>More options for PCA viewer</li>
4418 <li>GUI bugs resolved</li>
4419 <li>Runs with -nodisplay from command line</li>
4425 <div align="center">
4426 <strong>2.05b</strong><br> 15/9/05
4431 <li>Choose EPS export as lineart or text</li>
4432 <li>Jar files are executable</li>
4433 <li>Can read in Uracil - maps to unknown residue</li>
4438 <li>Known OutOfMemory errors give warning message</li>
4439 <li>Overview window calculated more efficiently</li>
4440 <li>Several GUI bugs resolved</li>
4446 <div align="center">
4447 <strong>2.05</strong><br> 30/8/05
4452 <li>Edit and annotate in "Wrapped" view</li>
4457 <li>Several GUI bugs resolved</li>
4463 <div align="center">
4464 <strong>2.04</strong><br> 24/8/05
4469 <li>Hold down mouse wheel & scroll to change font
4475 <li>Improved JPred client reliability</li>
4476 <li>Improved loading of Jalview files</li>
4482 <div align="center">
4483 <strong>2.03</strong><br> 18/8/05
4488 <li>Set Proxy server name and port in preferences</li>
4489 <li>Multiple URL links from sequence ids</li>
4490 <li>User Defined Colours can have a scheme name and added
4492 <li>Choose to ignore gaps in consensus calculation</li>
4493 <li>Unix users can set default web browser</li>
4494 <li>Runs without GUI for batch processing</li>
4495 <li>Dynamically generated Web Service Menus</li>
4500 <li>InstallAnywhere download for Sparc Solaris</li>
4506 <div align="center">
4507 <strong>2.02</strong><br> 18/7/05
4513 <li>Copy & Paste order of sequences maintains
4514 alignment order.</li>
4520 <div align="center">
4521 <strong>2.01</strong><br> 12/7/05
4526 <li>Use delete key for deleting selection.</li>
4527 <li>Use Mouse wheel to scroll sequences.</li>
4528 <li>Help file updated to describe how to add alignment
4530 <li>Version and build date written to build properties
4532 <li>InstallAnywhere installation will check for updates
4533 at launch of Jalview.</li>
4538 <li>Delete gaps bug fixed.</li>
4539 <li>FileChooser sorts columns.</li>
4540 <li>Can remove groups one by one.</li>
4541 <li>Filechooser icons installed.</li>
4542 <li>Finder ignores return character when searching.
4543 Return key will initiate a search.<br>
4550 <div align="center">
4551 <strong>2.0</strong><br> 20/6/05
4556 <li>New codebase</li>