3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
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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>02/07/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
67 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
68 source project) rather than InstallAnywhere
71 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
72 settings, receive over the air updates and launch specific
73 versions via (<a href="https://github.com/threerings/getdown">Three
77 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
78 formats supported by jalview (including .jvp project files)
81 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
82 arguments and switch between different getdown channels
85 <!-- JAL-3141 -->Backup files created when saving Jalview project
90 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
91 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
93 <!-- JAL-2620 -->Alternative genetic code tables for
94 'Translate as cDNA'</li>
96 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
97 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
100 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
101 implementation that allows updates) used for Sequence Feature collections</li>
104 <!-- JAL-2808,JAL-2069,JAL-2820 -->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,JAL-3330 -->Show synonymous codon variants on peptide
115 sequences (also coloured red by default)
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-2816 -->Tooltips displayed for features filtered by
328 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
329 show cross references or Fetch Database References are shown in
333 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
334 peptide sequence (computed variant shown as p.Res.null)
337 <!-- JAL-2060 -->'Graduated colour' option not offered for
338 manually created features (where if feature score is Float.NaN)
341 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
342 when columns are hidden
345 <!-- JAL-3082 -->Regular expression error for '(' in Select
346 Columns by Annotation description
349 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
350 out of Scale or Annotation Panel
353 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
357 <!-- JAL-3074 -->Left/right drag in annotation can scroll
361 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
365 <!-- JAL-3002 -->Column display is out by one after Page Down,
366 Page Up in wrapped mode
369 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
372 <!-- JAL-2932 -->Finder searches in minimised alignments
375 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
376 on opening an alignment
379 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
383 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
384 different groups in the alignment are selected
387 <!-- JAL-2717 -->Internationalised colour scheme names not shown
391 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
395 <!-- JAL-3125 -->Value input for graduated feature colour
396 threshold gets 'unrounded'
399 <!-- JAL-2982 -->PCA image export doesn't respect background
403 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
406 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
409 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
413 <!-- JAL-2964 -->Associate Tree with All Views not restored from
417 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
418 shown in complementary view
421 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
422 without normalisation
425 <!-- JAL-3021 -->Sequence Details report should open positioned at top
429 <!-- JAL-914 -->Help page can be opened twice
432 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
434 </ul> <em>Editing</em>
437 <!-- JAL-2822 -->Start and End should be updated when sequence
438 data at beginning or end of alignment added/removed via 'Edit'
442 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
443 relocate sequence features correctly when start of sequence is
444 removed (Known defect since 2.10)
447 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
448 dialog corrupts dataset sequence
451 <!-- JAL-868 -->Structure colours not updated when associated tree
452 repartitions the alignment view (Regression in 2.10.5)
458 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
459 sequence's End is greater than its length
461 </ul> <em>New Known Defects</em>
463 <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
466 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
467 regions of protein alignment.
470 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
471 is restored from a Jalview 2.11 project
474 <!-- JAL-3213 -->Alignment panel height can be too small after
478 <!-- JAL-3240 -->Display is incorrect after removing gapped
479 columns within hidden columns
482 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
483 window after dragging left to select columns to left of visible
487 <!-- JAL-2876 -->Features coloured according to their description
488 string and thresholded by score in earlier versions of Jalview are
489 not shown as thresholded features in 2.11. To workaround please
490 create a Score filter instead.
492 <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
494 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
496 <li><strong>Java 11 Specific defects</strong>
499 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
507 <td width="60" nowrap>
509 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
512 <td><div align="left">
516 <!-- JAL-3101 -->Default memory for Jalview webstart and
517 InstallAnywhere increased to 1G.
520 <!-- JAL-247 -->Hidden sequence markers and representative
521 sequence bolding included when exporting alignment as EPS,
522 SVG, PNG or HTML. <em>Display is configured via the
523 Format menu, or for command-line use via a jalview
524 properties file.</em>
527 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
528 API and sequence data now imported as JSON.
531 <!-- JAL-3065 -->Change in recommended way of starting
532 Jalview via a Java command line: add jars in lib directory
533 to CLASSPATH, rather than via the deprecated java.ext.dirs
540 <!-- JAL-3047 -->Support added to execute test suite
541 instrumented with <a href="http://openclover.org/">Open
546 <td><div align="left">
550 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
551 row shown in Feredoxin Structure alignment view of example
555 <!-- JAL-2854 -->Annotation obscures sequences if lots of
556 annotation displayed.
559 <!-- JAL-3107 -->Group conservation/consensus not shown
560 for newly created group when 'Apply to all groups'
564 <!-- JAL-3087 -->Corrupted display when switching to
565 wrapped mode when sequence panel's vertical scrollbar is
569 <!-- JAL-3003 -->Alignment is black in exported EPS file
570 when sequences are selected in exported view.</em>
573 <!-- JAL-3059 -->Groups with different coloured borders
574 aren't rendered with correct colour.
577 <!-- JAL-3092 -->Jalview could hang when importing certain
578 types of knotted RNA secondary structure.
581 <!-- JAL-3095 -->Sequence highlight and selection in
582 trimmed VARNA 2D structure is incorrect for sequences that
586 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
587 annotation when columns are inserted into an alignment,
588 and when exporting as Stockholm flatfile.
591 <!-- JAL-3053 -->Jalview annotation rows containing upper
592 and lower-case 'E' and 'H' do not automatically get
593 treated as RNA secondary structure.
596 <!-- JAL-3106 -->.jvp should be used as default extension
597 (not .jar) when saving a jalview project file.
600 <!-- JAL-3105 -->Mac Users: closing a window correctly
601 transfers focus to previous window on OSX
604 <em>Java 10 Issues Resolved</em>
607 <!-- JAL-2988 -->OSX - Can't save new files via the File
608 or export menus by typing in a name into the Save dialog
612 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
613 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
614 'look and feel' which has improved compatibility with the
615 latest version of OSX.
622 <td width="60" nowrap>
624 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
625 <em>7/06/2018</em></strong>
628 <td><div align="left">
632 <!-- JAL-2920 -->Use HGVS nomenclature for variant
633 annotation retrieved from Uniprot
636 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
637 onto the Jalview Desktop
641 <td><div align="left">
645 <!-- JAL-3017 -->Cannot import features with multiple
646 variant elements (blocks import of some Uniprot records)
649 <!-- JAL-2997 -->Clustal files with sequence positions in
650 right-hand column parsed correctly
653 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
654 not alignment area in exported graphic
657 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
658 window has input focus
661 <!-- JAL-2992 -->Annotation panel set too high when
662 annotation added to view (Windows)
665 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
666 network connectivity is poor
669 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
670 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
671 the currently open URL and links from a page viewed in
672 Firefox or Chrome on Windows is now fully supported. If
673 you are using Edge, only links in the page can be
674 dragged, and with Internet Explorer, only the currently
675 open URL in the browser can be dropped onto Jalview.</em>
678 <em>New Known Defects</em>
680 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
685 <td width="60" nowrap>
687 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
690 <td><div align="left">
694 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
695 for disabling automatic superposition of multiple
696 structures and open structures in existing views
699 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
700 ID and annotation area margins can be click-dragged to
704 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
708 <!-- JAL-2759 -->Improved performance for large alignments
709 and lots of hidden columns
712 <!-- JAL-2593 -->Improved performance when rendering lots
713 of features (particularly when transparency is disabled)
716 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
717 exchange of Jalview features and Chimera attributes made
723 <td><div align="left">
726 <!-- JAL-2899 -->Structure and Overview aren't updated
727 when Colour By Annotation threshold slider is adjusted
730 <!-- JAL-2778 -->Slow redraw when Overview panel shown
731 overlapping alignment panel
734 <!-- JAL-2929 -->Overview doesn't show end of unpadded
738 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
739 improved: CDS not handled correctly if transcript has no
743 <!-- JAL-2321 -->Secondary structure and temperature
744 factor annotation not added to sequence when local PDB
745 file associated with it by drag'n'drop or structure
749 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
750 dialog doesn't import PDB files dropped on an alignment
753 <!-- JAL-2666 -->Linked scrolling via protein horizontal
754 scroll bar doesn't work for some CDS/Protein views
757 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
758 Java 1.8u153 onwards and Java 1.9u4+.
761 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
762 columns in annotation row
765 <!-- JAL-2913 -->Preferences panel's ID Width control is not
766 honored in batch mode
769 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
770 for structures added to existing Jmol view
773 <!-- JAL-2223 -->'View Mappings' includes duplicate
774 entries after importing project with multiple views
777 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
778 protein sequences via SIFTS from associated PDB entries
779 with negative residue numbers or missing residues fails
782 <!-- JAL-2952 -->Exception when shading sequence with negative
783 Temperature Factor values from annotated PDB files (e.g.
784 as generated by CONSURF)
787 <!-- JAL-2920 -->Uniprot 'sequence variant' features
788 tooltip doesn't include a text description of mutation
791 <!-- JAL-2922 -->Invert displayed features very slow when
792 structure and/or overview windows are also shown
795 <!-- JAL-2954 -->Selecting columns from highlighted regions
796 very slow for alignments with large numbers of sequences
799 <!-- JAL-2925 -->Copy Consensus fails for group consensus
800 with 'StringIndexOutOfBounds'
803 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
804 platforms running Java 10
807 <!-- JAL-2960 -->Adding a structure to existing structure
808 view appears to do nothing because the view is hidden behind the alignment view
814 <!-- JAL-2926 -->Copy consensus sequence option in applet
815 should copy the group consensus when popup is opened on it
821 <!-- JAL-2913 -->Fixed ID width preference is not respected
824 <em>New Known Defects</em>
827 <!-- JAL-2973 --> Exceptions occasionally raised when
828 editing a large alignment and overview is displayed
831 <!-- JAL-2974 -->'Overview updating' progress bar is shown
832 repeatedly after a series of edits even when the overview
833 is no longer reflecting updates
836 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
837 structures for protein subsequence (if 'Trim Retrieved
838 Sequences' enabled) or Ensembl isoforms (Workaround in
839 2.10.4 is to fail back to N&W mapping)
842 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
843 option gives blank output
850 <td width="60" nowrap>
852 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
855 <td><div align="left">
856 <ul><li>Updated Certum Codesigning Certificate
857 (Valid till 30th November 2018)</li></ul></div></td>
858 <td><div align="left">
861 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
862 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
863 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
864 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
865 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
866 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
867 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
873 <td width="60" nowrap>
875 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
878 <td><div align="left">
882 <!-- JAL-2446 -->Faster and more efficient management and
883 rendering of sequence features
886 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
887 429 rate limit request hander
890 <!-- JAL-2773 -->Structure views don't get updated unless
891 their colours have changed
894 <!-- JAL-2495 -->All linked sequences are highlighted for
895 a structure mousover (Jmol) or selection (Chimera)
898 <!-- JAL-2790 -->'Cancel' button in progress bar for
899 JABAWS AACon, RNAAliFold and Disorder prediction jobs
902 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
903 view from Ensembl locus cross-references
906 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
910 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
911 feature can be disabled
914 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
915 PDB easier retrieval of sequences for lists of IDs
918 <!-- JAL-2758 -->Short names for sequences retrieved from
924 <li>Groovy interpreter updated to 2.4.12</li>
925 <li>Example groovy script for generating a matrix of
926 percent identity scores for current alignment.</li>
928 <em>Testing and Deployment</em>
931 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
935 <td><div align="left">
939 <!-- JAL-2643 -->Pressing tab after updating the colour
940 threshold text field doesn't trigger an update to the
944 <!-- JAL-2682 -->Race condition when parsing sequence ID
948 <!-- JAL-2608 -->Overview windows are also closed when
949 alignment window is closed
952 <!-- JAL-2548 -->Export of features doesn't always respect
956 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
957 takes a long time in Cursor mode
963 <!-- JAL-2777 -->Structures with whitespace chainCode
964 cannot be viewed in Chimera
967 <!-- JAL-2728 -->Protein annotation panel too high in
971 <!-- JAL-2757 -->Can't edit the query after the server
972 error warning icon is shown in Uniprot and PDB Free Text
976 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
979 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
982 <!-- JAL-2739 -->Hidden column marker in last column not
983 rendered when switching back from Wrapped to normal view
986 <!-- JAL-2768 -->Annotation display corrupted when
987 scrolling right in unwapped alignment view
990 <!-- JAL-2542 -->Existing features on subsequence
991 incorrectly relocated when full sequence retrieved from
995 <!-- JAL-2733 -->Last reported memory still shown when
996 Desktop->Show Memory is unticked (OSX only)
999 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1000 features of same type and group to be selected for
1004 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1005 alignments when hidden columns are present
1008 <!-- JAL-2392 -->Jalview freezes when loading and
1009 displaying several structures
1012 <!-- JAL-2732 -->Black outlines left after resizing or
1016 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1017 within the Jalview desktop on OSX
1020 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1021 when in wrapped alignment mode
1024 <!-- JAL-2636 -->Scale mark not shown when close to right
1025 hand end of alignment
1028 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1029 each selected sequence do not have correct start/end
1033 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1034 after canceling the Alignment Window's Font dialog
1037 <!-- JAL-2036 -->Show cross-references not enabled after
1038 restoring project until a new view is created
1041 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1042 URL links appears when only default EMBL-EBI link is
1043 configured (since 2.10.2b2)
1046 <!-- JAL-2775 -->Overview redraws whole window when box
1047 position is adjusted
1050 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1051 in a multi-chain structure when viewing alignment
1052 involving more than one chain (since 2.10)
1055 <!-- JAL-2811 -->Double residue highlights in cursor mode
1056 if new selection moves alignment window
1059 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1060 arrow key in cursor mode to pass hidden column marker
1063 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1064 that produces correctly annotated transcripts and products
1067 <!-- JAL-2776 -->Toggling a feature group after first time
1068 doesn't update associated structure view
1071 <em>Applet</em><br />
1074 <!-- JAL-2687 -->Concurrent modification exception when
1075 closing alignment panel
1078 <em>BioJSON</em><br />
1081 <!-- JAL-2546 -->BioJSON export does not preserve
1082 non-positional features
1085 <em>New Known Issues</em>
1088 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1089 sequence features correctly (for many previous versions of
1093 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1094 using cursor in wrapped panel other than top
1097 <!-- JAL-2791 -->Select columns containing feature ignores
1098 graduated colour threshold
1101 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1102 always preserve numbering and sequence features
1105 <em>Known Java 9 Issues</em>
1108 <!-- JAL-2902 -->Groovy Console very slow to open and is
1109 not responsive when entering characters (Webstart, Java
1116 <td width="60" nowrap>
1117 <div align="center">
1118 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1119 <em>2/10/2017</em></strong>
1122 <td><div align="left">
1123 <em>New features in Jalview Desktop</em>
1126 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1128 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1132 <td><div align="left">
1136 <td width="60" nowrap>
1137 <div align="center">
1138 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1139 <em>7/9/2017</em></strong>
1142 <td><div align="left">
1146 <!-- JAL-2588 -->Show gaps in overview window by colouring
1147 in grey (sequences used to be coloured grey, and gaps were
1151 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1155 <!-- JAL-2587 -->Overview updates immediately on increase
1156 in size and progress bar shown as higher resolution
1157 overview is recalculated
1162 <td><div align="left">
1166 <!-- JAL-2664 -->Overview window redraws every hidden
1167 column region row by row
1170 <!-- JAL-2681 -->duplicate protein sequences shown after
1171 retrieving Ensembl crossrefs for sequences from Uniprot
1174 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1175 format setting is unticked
1178 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1179 if group has show boxes format setting unticked
1182 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1183 autoscrolling whilst dragging current selection group to
1184 include sequences and columns not currently displayed
1187 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1188 assemblies are imported via CIF file
1191 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1192 displayed when threshold or conservation colouring is also
1196 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1200 <!-- JAL-2673 -->Jalview continues to scroll after
1201 dragging a selected region off the visible region of the
1205 <!-- JAL-2724 -->Cannot apply annotation based
1206 colourscheme to all groups in a view
1209 <!-- JAL-2511 -->IDs don't line up with sequences
1210 initially after font size change using the Font chooser or
1217 <td width="60" nowrap>
1218 <div align="center">
1219 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1222 <td><div align="left">
1223 <em>Calculations</em>
1227 <!-- JAL-1933 -->Occupancy annotation row shows number of
1228 ungapped positions in each column of the alignment.
1231 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1232 a calculation dialog box
1235 <!-- JAL-2379 -->Revised implementation of PCA for speed
1236 and memory efficiency (~30x faster)
1239 <!-- JAL-2403 -->Revised implementation of sequence
1240 similarity scores as used by Tree, PCA, Shading Consensus
1241 and other calculations
1244 <!-- JAL-2416 -->Score matrices are stored as resource
1245 files within the Jalview codebase
1248 <!-- JAL-2500 -->Trees computed on Sequence Feature
1249 Similarity may have different topology due to increased
1256 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1257 model for alignments and groups
1260 <!-- JAL-384 -->Custom shading schemes created via groovy
1267 <!-- JAL-2526 -->Efficiency improvements for interacting
1268 with alignment and overview windows
1271 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1275 <!-- JAL-2388 -->Hidden columns and sequences can be
1279 <!-- JAL-2611 -->Click-drag in visible area allows fine
1280 adjustment of visible position
1284 <em>Data import/export</em>
1287 <!-- JAL-2535 -->Posterior probability annotation from
1288 Stockholm files imported as sequence associated annotation
1291 <!-- JAL-2507 -->More robust per-sequence positional
1292 annotation input/output via stockholm flatfile
1295 <!-- JAL-2533 -->Sequence names don't include file
1296 extension when importing structure files without embedded
1297 names or PDB accessions
1300 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1301 format sequence substitution matrices
1304 <em>User Interface</em>
1307 <!-- JAL-2447 --> Experimental Features Checkbox in
1308 Desktop's Tools menu to hide or show untested features in
1312 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1313 via Overview or sequence motif search operations
1316 <!-- JAL-2547 -->Amend sequence features dialog box can be
1317 opened by double clicking gaps within sequence feature
1321 <!-- JAL-1476 -->Status bar message shown when not enough
1322 aligned positions were available to create a 3D structure
1326 <em>3D Structure</em>
1329 <!-- JAL-2430 -->Hidden regions in alignment views are not
1330 coloured in linked structure views
1333 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1334 file-based command exchange
1337 <!-- JAL-2375 -->Structure chooser automatically shows
1338 Cached Structures rather than querying the PDBe if
1339 structures are already available for sequences
1342 <!-- JAL-2520 -->Structures imported via URL are cached in
1343 the Jalview project rather than downloaded again when the
1344 project is reopened.
1347 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1348 to transfer Chimera's structure attributes as Jalview
1349 features, and vice-versa (<strong>Experimental
1353 <em>Web Services</em>
1356 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1359 <!-- JAL-2335 -->Filter non-standard amino acids and
1360 nucleotides when submitting to AACon and other MSA
1364 <!-- JAL-2316, -->URLs for viewing database
1365 cross-references provided by identifiers.org and the
1366 EMBL-EBI's MIRIAM DB
1373 <!-- JAL-2344 -->FileFormatI interface for describing and
1374 identifying file formats (instead of String constants)
1377 <!-- JAL-2228 -->FeatureCounter script refactored for
1378 efficiency when counting all displayed features (not
1379 backwards compatible with 2.10.1)
1382 <em>Example files</em>
1385 <!-- JAL-2631 -->Graduated feature colour style example
1386 included in the example feature file
1389 <em>Documentation</em>
1392 <!-- JAL-2339 -->Release notes reformatted for readability
1393 with the built-in Java help viewer
1396 <!-- JAL-1644 -->Find documentation updated with 'search
1397 sequence description' option
1403 <!-- JAL-2485, -->External service integration tests for
1404 Uniprot REST Free Text Search Client
1407 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1410 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1415 <td><div align="left">
1416 <em>Calculations</em>
1419 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1420 matrix - C->R should be '-3'<br />Old matrix restored
1421 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1423 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1424 Jalview's treatment of gaps in PCA and substitution matrix
1425 based Tree calculations.<br /> <br />In earlier versions
1426 of Jalview, gaps matching gaps were penalised, and gaps
1427 matching non-gaps penalised even more. In the PCA
1428 calculation, gaps were actually treated as non-gaps - so
1429 different costs were applied, which meant Jalview's PCAs
1430 were different to those produced by SeqSpace.<br />Jalview
1431 now treats gaps in the same way as SeqSpace (ie it scores
1432 them as 0). <br /> <br />Enter the following in the
1433 Groovy console to restore pre-2.10.2 behaviour:<br />
1434 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1435 // for 2.10.1 mode <br />
1436 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1437 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1438 these settings will affect all subsequent tree and PCA
1439 calculations (not recommended)</em></li>
1441 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1442 scaling of branch lengths for trees computed using
1443 Sequence Feature Similarity.
1446 <!-- JAL-2377 -->PCA calculation could hang when
1447 generating output report when working with highly
1448 redundant alignments
1451 <!-- JAL-2544 --> Sort by features includes features to
1452 right of selected region when gaps present on right-hand
1456 <em>User Interface</em>
1459 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1460 doesn't reselect a specific sequence's associated
1461 annotation after it was used for colouring a view
1464 <!-- JAL-2419 -->Current selection lost if popup menu
1465 opened on a region of alignment without groups
1468 <!-- JAL-2374 -->Popup menu not always shown for regions
1469 of an alignment with overlapping groups
1472 <!-- JAL-2310 -->Finder double counts if both a sequence's
1473 name and description match
1476 <!-- JAL-2370 -->Hiding column selection containing two
1477 hidden regions results in incorrect hidden regions
1480 <!-- JAL-2386 -->'Apply to all groups' setting when
1481 changing colour does not apply Conservation slider value
1485 <!-- JAL-2373 -->Percentage identity and conservation menu
1486 items do not show a tick or allow shading to be disabled
1489 <!-- JAL-2385 -->Conservation shading or PID threshold
1490 lost when base colourscheme changed if slider not visible
1493 <!-- JAL-2547 -->Sequence features shown in tooltip for
1494 gaps before start of features
1497 <!-- JAL-2623 -->Graduated feature colour threshold not
1498 restored to UI when feature colour is edited
1501 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1502 a time when scrolling vertically in wrapped mode.
1505 <!-- JAL-2630 -->Structure and alignment overview update
1506 as graduate feature colour settings are modified via the
1510 <!-- JAL-2034 -->Overview window doesn't always update
1511 when a group defined on the alignment is resized
1514 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1515 wrapped view result in positional status updates
1519 <!-- JAL-2563 -->Status bar doesn't show position for
1520 ambiguous amino acid and nucleotide symbols
1523 <!-- JAL-2602 -->Copy consensus sequence failed if
1524 alignment included gapped columns
1527 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1528 widgets don't permanently disappear
1531 <!-- JAL-2503 -->Cannot select or filter quantitative
1532 annotation that are shown only as column labels (e.g.
1533 T-Coffee column reliability scores)
1536 <!-- JAL-2594 -->Exception thrown if trying to create a
1537 sequence feature on gaps only
1540 <!-- JAL-2504 -->Features created with 'New feature'
1541 button from a Find inherit previously defined feature type
1542 rather than the Find query string
1545 <!-- JAL-2423 -->incorrect title in output window when
1546 exporting tree calculated in Jalview
1549 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1550 and then revealing them reorders sequences on the
1554 <!-- JAL-964 -->Group panel in sequence feature settings
1555 doesn't update to reflect available set of groups after
1556 interactively adding or modifying features
1559 <!-- JAL-2225 -->Sequence Database chooser unusable on
1563 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1564 only excluded gaps in current sequence and ignored
1571 <!-- JAL-2421 -->Overview window visible region moves
1572 erratically when hidden rows or columns are present
1575 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1576 Structure Viewer's colour menu don't correspond to
1580 <!-- JAL-2405 -->Protein specific colours only offered in
1581 colour and group colour menu for protein alignments
1584 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1585 reflect currently selected view or group's shading
1589 <!-- JAL-2624 -->Feature colour thresholds not respected
1590 when rendered on overview and structures when opacity at
1594 <!-- JAL-2589 -->User defined gap colour not shown in
1595 overview when features overlaid on alignment
1598 <!-- JAL-2567 -->Feature settings for different views not
1599 recovered correctly from Jalview project file
1602 <!-- JAL-2256 -->Feature colours in overview when first opened
1603 (automatically via preferences) are different to the main
1607 <em>Data import/export</em>
1610 <!-- JAL-2576 -->Very large alignments take a long time to
1614 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1615 added after a sequence was imported are not written to
1619 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1620 when importing RNA secondary structure via Stockholm
1623 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1624 not shown in correct direction for simple pseudoknots
1627 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1628 with lightGray or darkGray via features file (but can
1632 <!-- JAL-2383 -->Above PID colour threshold not recovered
1633 when alignment view imported from project
1636 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1637 structure and sequences extracted from structure files
1638 imported via URL and viewed in Jmol
1641 <!-- JAL-2520 -->Structures loaded via URL are saved in
1642 Jalview Projects rather than fetched via URL again when
1643 the project is loaded and the structure viewed
1646 <em>Web Services</em>
1649 <!-- JAL-2519 -->EnsemblGenomes example failing after
1650 release of Ensembl v.88
1653 <!-- JAL-2366 -->Proxy server address and port always
1654 appear enabled in Preferences->Connections
1657 <!-- JAL-2461 -->DAS registry not found exceptions
1658 removed from console output
1661 <!-- JAL-2582 -->Cannot retrieve protein products from
1662 Ensembl by Peptide ID
1665 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1666 created from SIFTs, and spurious 'Couldn't open structure
1667 in Chimera' errors raised after April 2017 update (problem
1668 due to 'null' string rather than empty string used for
1669 residues with no corresponding PDB mapping).
1672 <em>Application UI</em>
1675 <!-- JAL-2361 -->User Defined Colours not added to Colour
1679 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1680 case' residues (button in colourscheme editor debugged and
1681 new documentation and tooltips added)
1684 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1685 doesn't restore group-specific text colour thresholds
1688 <!-- JAL-2243 -->Feature settings panel does not update as
1689 new features are added to alignment
1692 <!-- JAL-2532 -->Cancel in feature settings reverts
1693 changes to feature colours via the Amend features dialog
1696 <!-- JAL-2506 -->Null pointer exception when attempting to
1697 edit graduated feature colour via amend features dialog
1701 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1702 selection menu changes colours of alignment views
1705 <!-- JAL-2426 -->Spurious exceptions in console raised
1706 from alignment calculation workers after alignment has
1710 <!-- JAL-1608 -->Typo in selection popup menu - Create
1711 groups now 'Create Group'
1714 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1715 Create/Undefine group doesn't always work
1718 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1719 shown again after pressing 'Cancel'
1722 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1723 adjusts start position in wrap mode
1726 <!-- JAL-2563 -->Status bar doesn't show positions for
1727 ambiguous amino acids
1730 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1731 CDS/Protein view after CDS sequences added for aligned
1735 <!-- JAL-2592 -->User defined colourschemes called 'User
1736 Defined' don't appear in Colours menu
1742 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1743 score models doesn't always result in an updated PCA plot
1746 <!-- JAL-2442 -->Features not rendered as transparent on
1747 overview or linked structure view
1750 <!-- JAL-2372 -->Colour group by conservation doesn't
1754 <!-- JAL-2517 -->Hitting Cancel after applying
1755 user-defined colourscheme doesn't restore original
1762 <!-- JAL-2314 -->Unit test failure:
1763 jalview.ws.jabaws.RNAStructExportImport setup fails
1766 <!-- JAL-2307 -->Unit test failure:
1767 jalview.ws.sifts.SiftsClientTest due to compatibility
1768 problems with deep array comparison equality asserts in
1769 successive versions of TestNG
1772 <!-- JAL-2479 -->Relocated StructureChooserTest and
1773 ParameterUtilsTest Unit tests to Network suite
1776 <em>New Known Issues</em>
1779 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1780 phase after a sequence motif find operation
1783 <!-- JAL-2550 -->Importing annotation file with rows
1784 containing just upper and lower case letters are
1785 interpreted as WUSS RNA secondary structure symbols
1788 <!-- JAL-2590 -->Cannot load and display Newick trees
1789 reliably from eggnog Ortholog database
1792 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1793 containing features of type Highlight' when 'B' is pressed
1794 to mark columns containing highlighted regions.
1797 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1798 doesn't always add secondary structure annotation.
1803 <td width="60" nowrap>
1804 <div align="center">
1805 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1808 <td><div align="left">
1812 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1813 for all consensus calculations
1816 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1819 <li>Updated Jalview's Certum code signing certificate
1822 <em>Application</em>
1825 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1826 set of database cross-references, sorted alphabetically
1829 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1830 from database cross references. Users with custom links
1831 will receive a <a href="webServices/urllinks.html#warning">warning
1832 dialog</a> asking them to update their preferences.
1835 <!-- JAL-2287-->Cancel button and escape listener on
1836 dialog warning user about disconnecting Jalview from a
1840 <!-- JAL-2320-->Jalview's Chimera control window closes if
1841 the Chimera it is connected to is shut down
1844 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1845 columns menu item to mark columns containing highlighted
1846 regions (e.g. from structure selections or results of a
1850 <!-- JAL-2284-->Command line option for batch-generation
1851 of HTML pages rendering alignment data with the BioJS
1861 <!-- JAL-2286 -->Columns with more than one modal residue
1862 are not coloured or thresholded according to percent
1863 identity (first observed in Jalview 2.8.2)
1866 <!-- JAL-2301 -->Threonine incorrectly reported as not
1870 <!-- JAL-2318 -->Updates to documentation pages (above PID
1871 threshold, amino acid properties)
1874 <!-- JAL-2292 -->Lower case residues in sequences are not
1875 reported as mapped to residues in a structure file in the
1879 <!--JAL-2324 -->Identical features with non-numeric scores
1880 could be added multiple times to a sequence
1883 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1884 bond features shown as two highlighted residues rather
1885 than a range in linked structure views, and treated
1886 correctly when selecting and computing trees from features
1889 <!-- JAL-2281-->Custom URL links for database
1890 cross-references are matched to database name regardless
1895 <em>Application</em>
1898 <!-- JAL-2282-->Custom URL links for specific database
1899 names without regular expressions also offer links from
1903 <!-- JAL-2315-->Removing a single configured link in the
1904 URL links pane in Connections preferences doesn't actually
1905 update Jalview configuration
1908 <!-- JAL-2272-->CTRL-Click on a selected region to open
1909 the alignment area popup menu doesn't work on El-Capitan
1912 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1913 files with similarly named sequences if dropped onto the
1917 <!-- JAL-2312 -->Additional mappings are shown for PDB
1918 entries where more chains exist in the PDB accession than
1919 are reported in the SIFTS file
1922 <!-- JAL-2317-->Certain structures do not get mapped to
1923 the structure view when displayed with Chimera
1926 <!-- JAL-2317-->No chains shown in the Chimera view
1927 panel's View->Show Chains submenu
1930 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1931 work for wrapped alignment views
1934 <!--JAL-2197 -->Rename UI components for running JPred
1935 predictions from 'JNet' to 'JPred'
1938 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1939 corrupted when annotation panel vertical scroll is not at
1940 first annotation row
1943 <!--JAL-2332 -->Attempting to view structure for Hen
1944 lysozyme results in a PDB Client error dialog box
1947 <!-- JAL-2319 -->Structure View's mapping report switched
1948 ranges for PDB and sequence for SIFTS
1951 SIFTS 'Not_Observed' residues mapped to non-existant
1955 <!-- <em>New Known Issues</em>
1962 <td width="60" nowrap>
1963 <div align="center">
1964 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1965 <em>25/10/2016</em></strong>
1968 <td><em>Application</em>
1970 <li>3D Structure chooser opens with 'Cached structures'
1971 view if structures already loaded</li>
1972 <li>Progress bar reports models as they are loaded to
1973 structure views</li>
1979 <li>Colour by conservation always enabled and no tick
1980 shown in menu when BLOSUM or PID shading applied</li>
1981 <li>FER1_ARATH and FER2_ARATH labels were switched in
1982 example sequences/projects/trees</li>
1984 <em>Application</em>
1986 <li>Jalview projects with views of local PDB structure
1987 files saved on Windows cannot be opened on OSX</li>
1988 <li>Multiple structure views can be opened and superposed
1989 without timeout for structures with multiple models or
1990 multiple sequences in alignment</li>
1991 <li>Cannot import or associated local PDB files without a
1992 PDB ID HEADER line</li>
1993 <li>RMSD is not output in Jmol console when superposition
1995 <li>Drag and drop of URL from Browser fails for Linux and
1996 OSX versions earlier than El Capitan</li>
1997 <li>ENA client ignores invalid content from ENA server</li>
1998 <li>Exceptions are not raised in console when ENA client
1999 attempts to fetch non-existent IDs via Fetch DB Refs UI
2001 <li>Exceptions are not raised in console when a new view
2002 is created on the alignment</li>
2003 <li>OSX right-click fixed for group selections: CMD-click
2004 to insert/remove gaps in groups and CTRL-click to open group
2007 <em>Build and deployment</em>
2009 <li>URL link checker now copes with multi-line anchor
2012 <em>New Known Issues</em>
2014 <li>Drag and drop from URL links in browsers do not work
2021 <td width="60" nowrap>
2022 <div align="center">
2023 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2026 <td><em>General</em>
2029 <!-- JAL-2124 -->Updated Spanish translations.
2032 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2033 for importing structure data to Jalview. Enables mmCIF and
2037 <!-- JAL-192 --->Alignment ruler shows positions relative to
2041 <!-- JAL-2202 -->Position/residue shown in status bar when
2042 mousing over sequence associated annotation
2045 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2049 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2050 '()', canonical '[]' and invalid '{}' base pair populations
2054 <!-- JAL-2092 -->Feature settings popup menu options for
2055 showing or hiding columns containing a feature
2058 <!-- JAL-1557 -->Edit selected group by double clicking on
2059 group and sequence associated annotation labels
2062 <!-- JAL-2236 -->Sequence name added to annotation label in
2063 select/hide columns by annotation and colour by annotation
2067 </ul> <em>Application</em>
2070 <!-- JAL-2050-->Automatically hide introns when opening a
2071 gene/transcript view
2074 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2078 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2079 structure mappings with the EMBL-EBI PDBe SIFTS database
2082 <!-- JAL-2079 -->Updated download sites used for Rfam and
2083 Pfam sources to xfam.org
2086 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2089 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2090 over sequences in Jalview
2093 <!-- JAL-2027-->Support for reverse-complement coding
2094 regions in ENA and EMBL
2097 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2098 for record retrieval via ENA rest API
2101 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2105 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2106 groovy script execution
2109 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2110 alignment window's Calculate menu
2113 <!-- JAL-1812 -->Allow groovy scripts that call
2114 Jalview.getAlignFrames() to run in headless mode
2117 <!-- JAL-2068 -->Support for creating new alignment
2118 calculation workers from groovy scripts
2121 <!-- JAL-1369 --->Store/restore reference sequence in
2125 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2126 associations are now saved/restored from project
2129 <!-- JAL-1993 -->Database selection dialog always shown
2130 before sequence fetcher is opened
2133 <!-- JAL-2183 -->Double click on an entry in Jalview's
2134 database chooser opens a sequence fetcher
2137 <!-- JAL-1563 -->Free-text search client for UniProt using
2138 the UniProt REST API
2141 <!-- JAL-2168 -->-nonews command line parameter to prevent
2142 the news reader opening
2145 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2146 querying stored in preferences
2149 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2153 <!-- JAL-1977-->Tooltips shown on database chooser
2156 <!-- JAL-391 -->Reverse complement function in calculate
2157 menu for nucleotide sequences
2160 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2161 and feature counts preserves alignment ordering (and
2162 debugged for complex feature sets).
2165 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2166 viewing structures with Jalview 2.10
2169 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2170 genome, transcript CCDS and gene ids via the Ensembl and
2171 Ensembl Genomes REST API
2174 <!-- JAL-2049 -->Protein sequence variant annotation
2175 computed for 'sequence_variant' annotation on CDS regions
2179 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2183 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2184 Ref Fetcher fails to match, or otherwise updates sequence
2185 data from external database records.
2188 <!-- JAL-2154 -->Revised Jalview Project format for
2189 efficient recovery of sequence coding and alignment
2190 annotation relationships.
2192 </ul> <!-- <em>Applet</em>
2203 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2207 <!-- JAL-2018-->Export features in Jalview format (again)
2208 includes graduated colourschemes
2211 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2212 working with big alignments and lots of hidden columns
2215 <!-- JAL-2053-->Hidden column markers not always rendered
2216 at right of alignment window
2219 <!-- JAL-2067 -->Tidied up links in help file table of
2223 <!-- JAL-2072 -->Feature based tree calculation not shown
2227 <!-- JAL-2075 -->Hidden columns ignored during feature
2228 based tree calculation
2231 <!-- JAL-2065 -->Alignment view stops updating when show
2232 unconserved enabled for group on alignment
2235 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2239 <!-- JAL-2146 -->Alignment column in status incorrectly
2240 shown as "Sequence position" when mousing over
2244 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2245 hidden columns present
2248 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2249 user created annotation added to alignment
2252 <!-- JAL-1841 -->RNA Structure consensus only computed for
2253 '()' base pair annotation
2256 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2257 in zero scores for all base pairs in RNA Structure
2261 <!-- JAL-2174-->Extend selection with columns containing
2265 <!-- JAL-2275 -->Pfam format writer puts extra space at
2266 beginning of sequence
2269 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2273 <!-- JAL-2238 -->Cannot create groups on an alignment from
2274 from a tree when t-coffee scores are shown
2277 <!-- JAL-1836,1967 -->Cannot import and view PDB
2278 structures with chains containing negative resnums (4q4h)
2281 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2285 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2286 to Clustal, PIR and PileUp output
2289 <!-- JAL-2008 -->Reordering sequence features that are
2290 not visible causes alignment window to repaint
2293 <!-- JAL-2006 -->Threshold sliders don't work in
2294 graduated colour and colour by annotation row for e-value
2295 scores associated with features and annotation rows
2298 <!-- JAL-1797 -->amino acid physicochemical conservation
2299 calculation should be case independent
2302 <!-- JAL-2173 -->Remove annotation also updates hidden
2306 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2307 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2308 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2311 <!-- JAL-2065 -->Null pointer exceptions and redraw
2312 problems when reference sequence defined and 'show
2313 non-conserved' enabled
2316 <!-- JAL-1306 -->Quality and Conservation are now shown on
2317 load even when Consensus calculation is disabled
2320 <!-- JAL-1932 -->Remove right on penultimate column of
2321 alignment does nothing
2324 <em>Application</em>
2327 <!-- JAL-1552-->URLs and links can't be imported by
2328 drag'n'drop on OSX when launched via webstart (note - not
2329 yet fixed for El Capitan)
2332 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2333 output when running on non-gb/us i18n platforms
2336 <!-- JAL-1944 -->Error thrown when exporting a view with
2337 hidden sequences as flat-file alignment
2340 <!-- JAL-2030-->InstallAnywhere distribution fails when
2344 <!-- JAL-2080-->Jalview very slow to launch via webstart
2345 (also hotfix for 2.9.0b2)
2348 <!-- JAL-2085 -->Cannot save project when view has a
2349 reference sequence defined
2352 <!-- JAL-1011 -->Columns are suddenly selected in other
2353 alignments and views when revealing hidden columns
2356 <!-- JAL-1989 -->Hide columns not mirrored in complement
2357 view in a cDNA/Protein splitframe
2360 <!-- JAL-1369 -->Cannot save/restore representative
2361 sequence from project when only one sequence is
2365 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2366 in Structure Chooser
2369 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2370 structure consensus didn't refresh annotation panel
2373 <!-- JAL-1962 -->View mapping in structure view shows
2374 mappings between sequence and all chains in a PDB file
2377 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2378 dialogs format columns correctly, don't display array
2379 data, sort columns according to type
2382 <!-- JAL-1975 -->Export complete shown after destination
2383 file chooser is cancelled during an image export
2386 <!-- JAL-2025 -->Error when querying PDB Service with
2387 sequence name containing special characters
2390 <!-- JAL-2024 -->Manual PDB structure querying should be
2394 <!-- JAL-2104 -->Large tooltips with broken HTML
2395 formatting don't wrap
2398 <!-- JAL-1128 -->Figures exported from wrapped view are
2399 truncated so L looks like I in consensus annotation
2402 <!-- JAL-2003 -->Export features should only export the
2403 currently displayed features for the current selection or
2407 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2408 after fetching cross-references, and restoring from
2412 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2413 followed in the structure viewer
2416 <!-- JAL-2163 -->Titles for individual alignments in
2417 splitframe not restored from project
2420 <!-- JAL-2145 -->missing autocalculated annotation at
2421 trailing end of protein alignment in transcript/product
2422 splitview when pad-gaps not enabled by default
2425 <!-- JAL-1797 -->amino acid physicochemical conservation
2429 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2430 article has been read (reopened issue due to
2431 internationalisation problems)
2434 <!-- JAL-1960 -->Only offer PDB structures in structure
2435 viewer based on sequence name, PDB and UniProt
2440 <!-- JAL-1976 -->No progress bar shown during export of
2444 <!-- JAL-2213 -->Structures not always superimposed after
2445 multiple structures are shown for one or more sequences.
2448 <!-- JAL-1370 -->Reference sequence characters should not
2449 be replaced with '.' when 'Show unconserved' format option
2453 <!-- JAL-1823 -->Cannot specify chain code when entering
2454 specific PDB id for sequence
2457 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2458 'Export hidden sequences' is enabled, but 'export hidden
2459 columns' is disabled.
2462 <!--JAL-2026-->Best Quality option in structure chooser
2463 selects lowest rather than highest resolution structures
2467 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2468 to sequence mapping in 'View Mappings' report
2471 <!-- JAL-2284 -->Unable to read old Jalview projects that
2472 contain non-XML data added after Jalvew wrote project.
2475 <!-- JAL-2118 -->Newly created annotation row reorders
2476 after clicking on it to create new annotation for a
2480 <!-- JAL-1980 -->Null Pointer Exception raised when
2481 pressing Add on an orphaned cut'n'paste window.
2483 <!-- may exclude, this is an external service stability issue JAL-1941
2484 -- > RNA 3D structure not added via DSSR service</li> -->
2489 <!-- JAL-2151 -->Incorrect columns are selected when
2490 hidden columns present before start of sequence
2493 <!-- JAL-1986 -->Missing dependencies on applet pages
2497 <!-- JAL-1947 -->Overview pixel size changes when
2498 sequences are hidden in applet
2501 <!-- JAL-1996 -->Updated instructions for applet
2502 deployment on examples pages.
2509 <td width="60" nowrap>
2510 <div align="center">
2511 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2512 <em>16/10/2015</em></strong>
2515 <td><em>General</em>
2517 <li>Time stamps for signed Jalview application and applet
2522 <em>Application</em>
2524 <li>Duplicate group consensus and conservation rows
2525 shown when tree is partitioned</li>
2526 <li>Erratic behaviour when tree partitions made with
2527 multiple cDNA/Protein split views</li>
2533 <td width="60" nowrap>
2534 <div align="center">
2535 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2536 <em>8/10/2015</em></strong>
2539 <td><em>General</em>
2541 <li>Updated Spanish translations of localized text for
2543 </ul> <em>Application</em>
2545 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2546 <li>Signed OSX InstallAnywhere installer<br></li>
2547 <li>Support for per-sequence based annotations in BioJSON</li>
2548 </ul> <em>Applet</em>
2550 <li>Split frame example added to applet examples page</li>
2551 </ul> <em>Build and Deployment</em>
2554 <!-- JAL-1888 -->New ant target for running Jalview's test
2562 <li>Mapping of cDNA to protein in split frames
2563 incorrect when sequence start > 1</li>
2564 <li>Broken images in filter column by annotation dialog
2566 <li>Feature colours not parsed from features file</li>
2567 <li>Exceptions and incomplete link URLs recovered when
2568 loading a features file containing HTML tags in feature
2572 <em>Application</em>
2574 <li>Annotations corrupted after BioJS export and
2576 <li>Incorrect sequence limits after Fetch DB References
2577 with 'trim retrieved sequences'</li>
2578 <li>Incorrect warning about deleting all data when
2579 deleting selected columns</li>
2580 <li>Patch to build system for shipping properly signed
2581 JNLP templates for webstart launch</li>
2582 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2583 unreleased structures for download or viewing</li>
2584 <li>Tab/space/return keystroke operation of EMBL-PDBe
2585 fetcher/viewer dialogs works correctly</li>
2586 <li>Disabled 'minimise' button on Jalview windows
2587 running on OSX to workaround redraw hang bug</li>
2588 <li>Split cDNA/Protein view position and geometry not
2589 recovered from jalview project</li>
2590 <li>Initial enabled/disabled state of annotation menu
2591 sorter 'show autocalculated first/last' corresponds to
2593 <li>Restoring of Clustal, RNA Helices and T-Coffee
2594 color schemes from BioJSON</li>
2598 <li>Reorder sequences mirrored in cDNA/Protein split
2600 <li>Applet with Jmol examples not loading correctly</li>
2606 <td><div align="center">
2607 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2609 <td><em>General</em>
2611 <li>Linked visualisation and analysis of DNA and Protein
2614 <li>Translated cDNA alignments shown as split protein
2615 and DNA alignment views</li>
2616 <li>Codon consensus annotation for linked protein and
2617 cDNA alignment views</li>
2618 <li>Link cDNA or Protein product sequences by loading
2619 them onto Protein or cDNA alignments</li>
2620 <li>Reconstruct linked cDNA alignment from aligned
2621 protein sequences</li>
2624 <li>Jmol integration updated to Jmol v14.2.14</li>
2625 <li>Import and export of Jalview alignment views as <a
2626 href="features/bioJsonFormat.html">BioJSON</a></li>
2627 <li>New alignment annotation file statements for
2628 reference sequences and marking hidden columns</li>
2629 <li>Reference sequence based alignment shading to
2630 highlight variation</li>
2631 <li>Select or hide columns according to alignment
2633 <li>Find option for locating sequences by description</li>
2634 <li>Conserved physicochemical properties shown in amino
2635 acid conservation row</li>
2636 <li>Alignments can be sorted by number of RNA helices</li>
2637 </ul> <em>Application</em>
2639 <li>New cDNA/Protein analysis capabilities
2641 <li>Get Cross-References should open a Split Frame
2642 view with cDNA/Protein</li>
2643 <li>Detect when nucleotide sequences and protein
2644 sequences are placed in the same alignment</li>
2645 <li>Split cDNA/Protein views are saved in Jalview
2650 <li>Use REST API to talk to Chimera</li>
2651 <li>Selected regions in Chimera are highlighted in linked
2652 Jalview windows</li>
2654 <li>VARNA RNA viewer updated to v3.93</li>
2655 <li>VARNA views are saved in Jalview Projects</li>
2656 <li>Pseudoknots displayed as Jalview RNA annotation can
2657 be shown in VARNA</li>
2659 <li>Make groups for selection uses marked columns as well
2660 as the active selected region</li>
2662 <li>Calculate UPGMA and NJ trees using sequence feature
2664 <li>New Export options
2666 <li>New Export Settings dialog to control hidden
2667 region export in flat file generation</li>
2669 <li>Export alignment views for display with the <a
2670 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2672 <li>Export scrollable SVG in HTML page</li>
2673 <li>Optional embedding of BioJSON data when exporting
2674 alignment figures to HTML</li>
2676 <li>3D structure retrieval and display
2678 <li>Free text and structured queries with the PDBe
2680 <li>PDBe Search API based discovery and selection of
2681 PDB structures for a sequence set</li>
2685 <li>JPred4 employed for protein secondary structure
2687 <li>Hide Insertions menu option to hide unaligned columns
2688 for one or a group of sequences</li>
2689 <li>Automatically hide insertions in alignments imported
2690 from the JPred4 web server</li>
2691 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2692 system on OSX<br />LGPL libraries courtesy of <a
2693 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2695 <li>changed 'View nucleotide structure' submenu to 'View
2696 VARNA 2D Structure'</li>
2697 <li>change "View protein structure" menu option to "3D
2700 </ul> <em>Applet</em>
2702 <li>New layout for applet example pages</li>
2703 <li>New parameters to enable SplitFrame view
2704 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2705 <li>New example demonstrating linked viewing of cDNA and
2706 Protein alignments</li>
2707 </ul> <em>Development and deployment</em>
2709 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2710 <li>Include installation type and git revision in build
2711 properties and console log output</li>
2712 <li>Jalview Github organisation, and new github site for
2713 storing BioJsMSA Templates</li>
2714 <li>Jalview's unit tests now managed with TestNG</li>
2717 <!-- <em>General</em>
2719 </ul> --> <!-- issues resolved --> <em>Application</em>
2721 <li>Escape should close any open find dialogs</li>
2722 <li>Typo in select-by-features status report</li>
2723 <li>Consensus RNA secondary secondary structure
2724 predictions are not highlighted in amber</li>
2725 <li>Missing gap character in v2.7 example file means
2726 alignment appears unaligned when pad-gaps is not enabled</li>
2727 <li>First switch to RNA Helices colouring doesn't colour
2728 associated structure views</li>
2729 <li>ID width preference option is greyed out when auto
2730 width checkbox not enabled</li>
2731 <li>Stopped a warning dialog from being shown when
2732 creating user defined colours</li>
2733 <li>'View Mapping' in structure viewer shows sequence
2734 mappings for just that viewer's sequences</li>
2735 <li>Workaround for superposing PDB files containing
2736 multiple models in Chimera</li>
2737 <li>Report sequence position in status bar when hovering
2738 over Jmol structure</li>
2739 <li>Cannot output gaps as '.' symbols with Selection ->
2740 output to text box</li>
2741 <li>Flat file exports of alignments with hidden columns
2742 have incorrect sequence start/end</li>
2743 <li>'Aligning' a second chain to a Chimera structure from
2745 <li>Colour schemes applied to structure viewers don't
2746 work for nucleotide</li>
2747 <li>Loading/cut'n'pasting an empty or invalid file leads
2748 to a grey/invisible alignment window</li>
2749 <li>Exported Jpred annotation from a sequence region
2750 imports to different position</li>
2751 <li>Space at beginning of sequence feature tooltips shown
2752 on some platforms</li>
2753 <li>Chimera viewer 'View | Show Chain' menu is not
2755 <li>'New View' fails with a Null Pointer Exception in
2756 console if Chimera has been opened</li>
2757 <li>Mouseover to Chimera not working</li>
2758 <li>Miscellaneous ENA XML feature qualifiers not
2760 <li>NPE in annotation renderer after 'Extract Scores'</li>
2761 <li>If two structures in one Chimera window, mouseover of
2762 either sequence shows on first structure</li>
2763 <li>'Show annotations' options should not make
2764 non-positional annotations visible</li>
2765 <li>Subsequence secondary structure annotation not shown
2766 in right place after 'view flanking regions'</li>
2767 <li>File Save As type unset when current file format is
2769 <li>Save as '.jar' option removed for saving Jalview
2771 <li>Colour by Sequence colouring in Chimera more
2773 <li>Cannot 'add reference annotation' for a sequence in
2774 several views on same alignment</li>
2775 <li>Cannot show linked products for EMBL / ENA records</li>
2776 <li>Jalview's tooltip wraps long texts containing no
2778 </ul> <em>Applet</em>
2780 <li>Jmol to JalviewLite mouseover/link not working</li>
2781 <li>JalviewLite can't import sequences with ID
2782 descriptions containing angle brackets</li>
2783 </ul> <em>General</em>
2785 <li>Cannot export and reimport RNA secondary structure
2786 via jalview annotation file</li>
2787 <li>Random helix colour palette for colour by annotation
2788 with RNA secondary structure</li>
2789 <li>Mouseover to cDNA from STOP residue in protein
2790 translation doesn't work.</li>
2791 <li>hints when using the select by annotation dialog box</li>
2792 <li>Jmol alignment incorrect if PDB file has alternate CA
2794 <li>FontChooser message dialog appears to hang after
2795 choosing 1pt font</li>
2796 <li>Peptide secondary structure incorrectly imported from
2797 annotation file when annotation display text includes 'e' or
2799 <li>Cannot set colour of new feature type whilst creating
2801 <li>cDNA translation alignment should not be sequence
2802 order dependent</li>
2803 <li>'Show unconserved' doesn't work for lower case
2805 <li>Nucleotide ambiguity codes involving R not recognised</li>
2806 </ul> <em>Deployment and Documentation</em>
2808 <li>Applet example pages appear different to the rest of
2809 www.jalview.org</li>
2810 </ul> <em>Application Known issues</em>
2812 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2813 <li>Misleading message appears after trying to delete
2815 <li>Jalview icon not shown in dock after InstallAnywhere
2816 version launches</li>
2817 <li>Fetching EMBL reference for an RNA sequence results
2818 fails with a sequence mismatch</li>
2819 <li>Corrupted or unreadable alignment display when
2820 scrolling alignment to right</li>
2821 <li>ArrayIndexOutOfBoundsException thrown when remove
2822 empty columns called on alignment with ragged gapped ends</li>
2823 <li>auto calculated alignment annotation rows do not get
2824 placed above or below non-autocalculated rows</li>
2825 <li>Jalview dekstop becomes sluggish at full screen in
2826 ultra-high resolution</li>
2827 <li>Cannot disable consensus calculation independently of
2828 quality and conservation</li>
2829 <li>Mouseover highlighting between cDNA and protein can
2830 become sluggish with more than one splitframe shown</li>
2831 </ul> <em>Applet Known Issues</em>
2833 <li>Core PDB parsing code requires Jmol</li>
2834 <li>Sequence canvas panel goes white when alignment
2835 window is being resized</li>
2841 <td><div align="center">
2842 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2844 <td><em>General</em>
2846 <li>Updated Java code signing certificate donated by
2848 <li>Features and annotation preserved when performing
2849 pairwise alignment</li>
2850 <li>RNA pseudoknot annotation can be
2851 imported/exported/displayed</li>
2852 <li>'colour by annotation' can colour by RNA and
2853 protein secondary structure</li>
2854 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2855 post-hoc with 2.9 release</em>)
2858 </ul> <em>Application</em>
2860 <li>Extract and display secondary structure for sequences
2861 with 3D structures</li>
2862 <li>Support for parsing RNAML</li>
2863 <li>Annotations menu for layout
2865 <li>sort sequence annotation rows by alignment</li>
2866 <li>place sequence annotation above/below alignment
2869 <li>Output in Stockholm format</li>
2870 <li>Internationalisation: improved Spanish (es)
2872 <li>Structure viewer preferences tab</li>
2873 <li>Disorder and Secondary Structure annotation tracks
2874 shared between alignments</li>
2875 <li>UCSF Chimera launch and linked highlighting from
2877 <li>Show/hide all sequence associated annotation rows for
2878 all or current selection</li>
2879 <li>disorder and secondary structure predictions
2880 available as dataset annotation</li>
2881 <li>Per-sequence rna helices colouring</li>
2884 <li>Sequence database accessions imported when fetching
2885 alignments from Rfam</li>
2886 <li>update VARNA version to 3.91</li>
2888 <li>New groovy scripts for exporting aligned positions,
2889 conservation values, and calculating sum of pairs scores.</li>
2890 <li>Command line argument to set default JABAWS server</li>
2891 <li>include installation type in build properties and
2892 console log output</li>
2893 <li>Updated Jalview project format to preserve dataset
2897 <!-- issues resolved --> <em>Application</em>
2899 <li>Distinguish alignment and sequence associated RNA
2900 structure in structure->view->VARNA</li>
2901 <li>Raise dialog box if user deletes all sequences in an
2903 <li>Pressing F1 results in documentation opening twice</li>
2904 <li>Sequence feature tooltip is wrapped</li>
2905 <li>Double click on sequence associated annotation
2906 selects only first column</li>
2907 <li>Redundancy removal doesn't result in unlinked
2908 leaves shown in tree</li>
2909 <li>Undos after several redundancy removals don't undo
2911 <li>Hide sequence doesn't hide associated annotation</li>
2912 <li>User defined colours dialog box too big to fit on
2913 screen and buttons not visible</li>
2914 <li>author list isn't updated if already written to
2915 Jalview properties</li>
2916 <li>Popup menu won't open after retrieving sequence
2918 <li>File open window for associate PDB doesn't open</li>
2919 <li>Left-then-right click on a sequence id opens a
2920 browser search window</li>
2921 <li>Cannot open sequence feature shading/sort popup menu
2922 in feature settings dialog</li>
2923 <li>better tooltip placement for some areas of Jalview
2925 <li>Allow addition of JABAWS Server which doesn't
2926 pass validation</li>
2927 <li>Web services parameters dialog box is too large to
2929 <li>Muscle nucleotide alignment preset obscured by
2931 <li>JABAWS preset submenus don't contain newly
2932 defined user preset</li>
2933 <li>MSA web services warns user if they were launched
2934 with invalid input</li>
2935 <li>Jalview cannot contact DAS Registy when running on
2938 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2939 'Superpose with' submenu not shown when new view
2943 </ul> <!-- <em>Applet</em>
2945 </ul> <em>General</em>
2947 </ul>--> <em>Deployment and Documentation</em>
2949 <li>2G and 1G options in launchApp have no effect on
2950 memory allocation</li>
2951 <li>launchApp service doesn't automatically open
2952 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2954 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2955 InstallAnywhere reports cannot find valid JVM when Java
2956 1.7_055 is available
2958 </ul> <em>Application Known issues</em>
2961 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2962 corrupted or unreadable alignment display when scrolling
2966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2967 retrieval fails but progress bar continues for DAS retrieval
2968 with large number of ID
2971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2972 flatfile output of visible region has incorrect sequence
2976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2977 rna structure consensus doesn't update when secondary
2978 structure tracks are rearranged
2981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2982 invalid rna structure positional highlighting does not
2983 highlight position of invalid base pairs
2986 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2987 out of memory errors are not raised when saving Jalview
2988 project from alignment window file menu
2991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2992 Switching to RNA Helices colouring doesn't propagate to
2996 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2997 colour by RNA Helices not enabled when user created
2998 annotation added to alignment
3001 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3002 Jalview icon not shown on dock in Mountain Lion/Webstart
3004 </ul> <em>Applet Known Issues</em>
3007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3008 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3011 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3012 Jalview and Jmol example not compatible with IE9
3015 <li>Sort by annotation score doesn't reverse order
3021 <td><div align="center">
3022 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3025 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3028 <li>Internationalisation of user interface (usually
3029 called i18n support) and translation for Spanish locale</li>
3030 <li>Define/Undefine group on current selection with
3031 Ctrl-G/Shift Ctrl-G</li>
3032 <li>Improved group creation/removal options in
3033 alignment/sequence Popup menu</li>
3034 <li>Sensible precision for symbol distribution
3035 percentages shown in logo tooltip.</li>
3036 <li>Annotation panel height set according to amount of
3037 annotation when alignment first opened</li>
3038 </ul> <em>Application</em>
3040 <li>Interactive consensus RNA secondary structure
3041 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3042 <li>Select columns containing particular features from
3043 Feature Settings dialog</li>
3044 <li>View all 'representative' PDB structures for selected
3046 <li>Update Jalview project format:
3048 <li>New file extension for Jalview projects '.jvp'</li>
3049 <li>Preserve sequence and annotation dataset (to
3050 store secondary structure annotation,etc)</li>
3051 <li>Per group and alignment annotation and RNA helix
3055 <li>New similarity measures for PCA and Tree calculation
3057 <li>Experimental support for retrieval and viewing of
3058 flanking regions for an alignment</li>
3062 <!-- issues resolved --> <em>Application</em>
3064 <li>logo keeps spinning and status remains at queued or
3065 running after job is cancelled</li>
3066 <li>cannot export features from alignments imported from
3067 Jalview/VAMSAS projects</li>
3068 <li>Buggy slider for web service parameters that take
3070 <li>Newly created RNA secondary structure line doesn't
3071 have 'display all symbols' flag set</li>
3072 <li>T-COFFEE alignment score shading scheme and other
3073 annotation shading not saved in Jalview project</li>
3074 <li>Local file cannot be loaded in freshly downloaded
3076 <li>Jalview icon not shown on dock in Mountain
3078 <li>Load file from desktop file browser fails</li>
3079 <li>Occasional NPE thrown when calculating large trees</li>
3080 <li>Cannot reorder or slide sequences after dragging an
3081 alignment onto desktop</li>
3082 <li>Colour by annotation dialog throws NPE after using
3083 'extract scores' function</li>
3084 <li>Loading/cut'n'pasting an empty file leads to a grey
3085 alignment window</li>
3086 <li>Disorder thresholds rendered incorrectly after
3087 performing IUPred disorder prediction</li>
3088 <li>Multiple group annotated consensus rows shown when
3089 changing 'normalise logo' display setting</li>
3090 <li>Find shows blank dialog after 'finished searching' if
3091 nothing matches query</li>
3092 <li>Null Pointer Exceptions raised when sorting by
3093 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3095 <li>Errors in Jmol console when structures in alignment
3096 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3098 <li>Not all working JABAWS services are shown in
3100 <li>JAVAWS version of Jalview fails to launch with
3101 'invalid literal/length code'</li>
3102 <li>Annotation/RNA Helix colourschemes cannot be applied
3103 to alignment with groups (actually fixed in 2.8.0b1)</li>
3104 <li>RNA Helices and T-Coffee Scores available as default
3107 </ul> <em>Applet</em>
3109 <li>Remove group option is shown even when selection is
3111 <li>Apply to all groups ticked but colourscheme changes
3112 don't affect groups</li>
3113 <li>Documented RNA Helices and T-Coffee Scores as valid
3114 colourscheme name</li>
3115 <li>Annotation labels drawn on sequence IDs when
3116 Annotation panel is not displayed</li>
3117 <li>Increased font size for dropdown menus on OSX and
3118 embedded windows</li>
3119 </ul> <em>Other</em>
3121 <li>Consensus sequence for alignments/groups with a
3122 single sequence were not calculated</li>
3123 <li>annotation files that contain only groups imported as
3124 annotation and junk sequences</li>
3125 <li>Fasta files with sequences containing '*' incorrectly
3126 recognised as PFAM or BLC</li>
3127 <li>conservation/PID slider apply all groups option
3128 doesn't affect background (2.8.0b1)
3130 <li>redundancy highlighting is erratic at 0% and 100%</li>
3131 <li>Remove gapped columns fails for sequences with ragged
3133 <li>AMSA annotation row with leading spaces is not
3134 registered correctly on import</li>
3135 <li>Jalview crashes when selecting PCA analysis for
3136 certain alignments</li>
3137 <li>Opening the colour by annotation dialog for an
3138 existing annotation based 'use original colours'
3139 colourscheme loses original colours setting</li>
3144 <td><div align="center">
3145 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3146 <em>30/1/2014</em></strong>
3150 <li>Trusted certificates for JalviewLite applet and
3151 Jalview Desktop application<br />Certificate was donated by
3152 <a href="https://www.certum.eu">Certum</a> to the Jalview
3153 open source project).
3155 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3156 <li>Output in Stockholm format</li>
3157 <li>Allow import of data from gzipped files</li>
3158 <li>Export/import group and sequence associated line
3159 graph thresholds</li>
3160 <li>Nucleotide substitution matrix that supports RNA and
3161 ambiguity codes</li>
3162 <li>Allow disorder predictions to be made on the current
3163 selection (or visible selection) in the same way that JPred
3165 <li>Groovy scripting for headless Jalview operation</li>
3166 </ul> <em>Other improvements</em>
3168 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3169 <li>COMBINE statement uses current SEQUENCE_REF and
3170 GROUP_REF scope to group annotation rows</li>
3171 <li>Support '' style escaping of quotes in Newick
3173 <li>Group options for JABAWS service by command line name</li>
3174 <li>Empty tooltip shown for JABA service options with a
3175 link but no description</li>
3176 <li>Select primary source when selecting authority in
3177 database fetcher GUI</li>
3178 <li>Add .mfa to FASTA file extensions recognised by
3180 <li>Annotation label tooltip text wrap</li>
3185 <li>Slow scrolling when lots of annotation rows are
3187 <li>Lots of NPE (and slowness) after creating RNA
3188 secondary structure annotation line</li>
3189 <li>Sequence database accessions not imported when
3190 fetching alignments from Rfam</li>
3191 <li>Incorrect SHMR submission for sequences with
3193 <li>View all structures does not always superpose
3195 <li>Option widgets in service parameters not updated to
3196 reflect user or preset settings</li>
3197 <li>Null pointer exceptions for some services without
3198 presets or adjustable parameters</li>
3199 <li>Discover PDB IDs entry in structure menu doesn't
3200 discover PDB xRefs</li>
3201 <li>Exception encountered while trying to retrieve
3202 features with DAS</li>
3203 <li>Lowest value in annotation row isn't coloured
3204 when colour by annotation (per sequence) is coloured</li>
3205 <li>Keyboard mode P jumps to start of gapped region when
3206 residue follows a gap</li>
3207 <li>Jalview appears to hang importing an alignment with
3208 Wrap as default or after enabling Wrap</li>
3209 <li>'Right click to add annotations' message
3210 shown in wrap mode when no annotations present</li>
3211 <li>Disorder predictions fail with NPE if no automatic
3212 annotation already exists on alignment</li>
3213 <li>oninit javascript function should be called after
3214 initialisation completes</li>
3215 <li>Remove redundancy after disorder prediction corrupts
3216 alignment window display</li>
3217 <li>Example annotation file in documentation is invalid</li>
3218 <li>Grouped line graph annotation rows are not exported
3219 to annotation file</li>
3220 <li>Multi-harmony analysis cannot be run when only two
3222 <li>Cannot create multiple groups of line graphs with
3223 several 'combine' statements in annotation file</li>
3224 <li>Pressing return several times causes Number Format
3225 exceptions in keyboard mode</li>
3226 <li>Multi-harmony (SHMMR) method doesn't submit
3227 correct partitions for input data</li>
3228 <li>Translation from DNA to Amino Acids fails</li>
3229 <li>Jalview fail to load newick tree with quoted label</li>
3230 <li>--headless flag isn't understood</li>
3231 <li>ClassCastException when generating EPS in headless
3233 <li>Adjusting sequence-associated shading threshold only
3234 changes one row's threshold</li>
3235 <li>Preferences and Feature settings panel panel
3236 doesn't open</li>
3237 <li>hide consensus histogram also hides conservation and
3238 quality histograms</li>
3243 <td><div align="center">
3244 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3246 <td><em>Application</em>
3248 <li>Support for JABAWS 2.0 Services (AACon alignment
3249 conservation, protein disorder and Clustal Omega)</li>
3250 <li>JABAWS server status indicator in Web Services
3252 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3253 in Jalview alignment window</li>
3254 <li>Updated Jalview build and deploy framework for OSX
3255 mountain lion, windows 7, and 8</li>
3256 <li>Nucleotide substitution matrix for PCA that supports
3257 RNA and ambiguity codes</li>
3259 <li>Improved sequence database retrieval GUI</li>
3260 <li>Support fetching and database reference look up
3261 against multiple DAS sources (Fetch all from in 'fetch db
3263 <li>Jalview project improvements
3265 <li>Store and retrieve the 'belowAlignment'
3266 flag for annotation</li>
3267 <li>calcId attribute to group annotation rows on the
3269 <li>Store AACon calculation settings for a view in
3270 Jalview project</li>
3274 <li>horizontal scrolling gesture support</li>
3275 <li>Visual progress indicator when PCA calculation is
3277 <li>Simpler JABA web services menus</li>
3278 <li>visual indication that web service results are still
3279 being retrieved from server</li>
3280 <li>Serialise the dialogs that are shown when Jalview
3281 starts up for first time</li>
3282 <li>Jalview user agent string for interacting with HTTP
3284 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3286 <li>Examples directory and Groovy library included in
3287 InstallAnywhere distribution</li>
3288 </ul> <em>Applet</em>
3290 <li>RNA alignment and secondary structure annotation
3291 visualization applet example</li>
3292 </ul> <em>General</em>
3294 <li>Normalise option for consensus sequence logo</li>
3295 <li>Reset button in PCA window to return dimensions to
3297 <li>Allow seqspace or Jalview variant of alignment PCA
3299 <li>PCA with either nucleic acid and protein substitution
3301 <li>Allow windows containing HTML reports to be exported
3303 <li>Interactive display and editing of RNA secondary
3304 structure contacts</li>
3305 <li>RNA Helix Alignment Colouring</li>
3306 <li>RNA base pair logo consensus</li>
3307 <li>Parse sequence associated secondary structure
3308 information in Stockholm files</li>
3309 <li>HTML Export database accessions and annotation
3310 information presented in tooltip for sequences</li>
3311 <li>Import secondary structure from LOCARNA clustalw
3312 style RNA alignment files</li>
3313 <li>import and visualise T-COFFEE quality scores for an
3315 <li>'colour by annotation' per sequence option to
3316 shade each sequence according to its associated alignment
3318 <li>New Jalview Logo</li>
3319 </ul> <em>Documentation and Development</em>
3321 <li>documentation for score matrices used in Jalview</li>
3322 <li>New Website!</li>
3324 <td><em>Application</em>
3326 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3327 wsdbfetch REST service</li>
3328 <li>Stop windows being moved outside desktop on OSX</li>
3329 <li>Filetype associations not installed for webstart
3331 <li>Jalview does not always retrieve progress of a JABAWS
3332 job execution in full once it is complete</li>
3333 <li>revise SHMR RSBS definition to ensure alignment is
3334 uploaded via ali_file parameter</li>
3335 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3336 <li>View all structures superposed fails with exception</li>
3337 <li>Jnet job queues forever if a very short sequence is
3338 submitted for prediction</li>
3339 <li>Cut and paste menu not opened when mouse clicked on
3341 <li>Putting fractional value into integer text box in
3342 alignment parameter dialog causes Jalview to hang</li>
3343 <li>Structure view highlighting doesn't work on
3345 <li>View all structures fails with exception shown in
3347 <li>Characters in filename associated with PDBEntry not
3348 escaped in a platform independent way</li>
3349 <li>Jalview desktop fails to launch with exception when
3351 <li>Tree calculation reports 'you must have 2 or more
3352 sequences selected' when selection is empty</li>
3353 <li>Jalview desktop fails to launch with jar signature
3354 failure when java web start temporary file caching is
3356 <li>DAS Sequence retrieval with range qualification
3357 results in sequence xref which includes range qualification</li>
3358 <li>Errors during processing of command line arguments
3359 cause progress bar (JAL-898) to be removed</li>
3360 <li>Replace comma for semi-colon option not disabled for
3361 DAS sources in sequence fetcher</li>
3362 <li>Cannot close news reader when JABAWS server warning
3363 dialog is shown</li>
3364 <li>Option widgets not updated to reflect user settings</li>
3365 <li>Edited sequence not submitted to web service</li>
3366 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3367 <li>InstallAnywhere installer doesn't unpack and run
3368 on OSX Mountain Lion</li>
3369 <li>Annotation panel not given a scroll bar when
3370 sequences with alignment annotation are pasted into the
3372 <li>Sequence associated annotation rows not associated
3373 when loaded from Jalview project</li>
3374 <li>Browser launch fails with NPE on java 1.7</li>
3375 <li>JABAWS alignment marked as finished when job was
3376 cancelled or job failed due to invalid input</li>
3377 <li>NPE with v2.7 example when clicking on Tree
3378 associated with all views</li>
3379 <li>Exceptions when copy/paste sequences with grouped
3380 annotation rows to new window</li>
3381 </ul> <em>Applet</em>
3383 <li>Sequence features are momentarily displayed before
3384 they are hidden using hidefeaturegroups applet parameter</li>
3385 <li>loading features via javascript API automatically
3386 enables feature display</li>
3387 <li>scrollToColumnIn javascript API method doesn't
3389 </ul> <em>General</em>
3391 <li>Redundancy removal fails for rna alignment</li>
3392 <li>PCA calculation fails when sequence has been selected
3393 and then deselected</li>
3394 <li>PCA window shows grey box when first opened on OSX</li>
3395 <li>Letters coloured pink in sequence logo when alignment
3396 coloured with clustalx</li>
3397 <li>Choosing fonts without letter symbols defined causes
3398 exceptions and redraw errors</li>
3399 <li>Initial PCA plot view is not same as manually
3400 reconfigured view</li>
3401 <li>Grouped annotation graph label has incorrect line
3403 <li>Grouped annotation graph label display is corrupted
3404 for lots of labels</li>
3409 <div align="center">
3410 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3413 <td><em>Application</em>
3415 <li>Jalview Desktop News Reader</li>
3416 <li>Tweaked default layout of web services menu</li>
3417 <li>View/alignment association menu to enable user to
3418 easily specify which alignment a multi-structure view takes
3419 its colours/correspondences from</li>
3420 <li>Allow properties file location to be specified as URL</li>
3421 <li>Extend Jalview project to preserve associations
3422 between many alignment views and a single Jmol display</li>
3423 <li>Store annotation row height in Jalview project file</li>
3424 <li>Annotation row column label formatting attributes
3425 stored in project file</li>
3426 <li>Annotation row order for auto-calculated annotation
3427 rows preserved in Jalview project file</li>
3428 <li>Visual progress indication when Jalview state is
3429 saved using Desktop window menu</li>
3430 <li>Visual indication that command line arguments are
3431 still being processed</li>
3432 <li>Groovy script execution from URL</li>
3433 <li>Colour by annotation default min and max colours in
3435 <li>Automatically associate PDB files dragged onto an
3436 alignment with sequences that have high similarity and
3438 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3439 <li>'view structures' option to open many
3440 structures in same window</li>
3441 <li>Sort associated views menu option for tree panel</li>
3442 <li>Group all JABA and non-JABA services for a particular
3443 analysis function in its own submenu</li>
3444 </ul> <em>Applet</em>
3446 <li>Userdefined and autogenerated annotation rows for
3448 <li>Adjustment of alignment annotation pane height</li>
3449 <li>Annotation scrollbar for annotation panel</li>
3450 <li>Drag to reorder annotation rows in annotation panel</li>
3451 <li>'automaticScrolling' parameter</li>
3452 <li>Allow sequences with partial ID string matches to be
3453 annotated from GFF/Jalview features files</li>
3454 <li>Sequence logo annotation row in applet</li>
3455 <li>Absolute paths relative to host server in applet
3456 parameters are treated as such</li>
3457 <li>New in the JalviewLite javascript API:
3459 <li>JalviewLite.js javascript library</li>
3460 <li>Javascript callbacks for
3462 <li>Applet initialisation</li>
3463 <li>Sequence/alignment mouse-overs and selections</li>
3466 <li>scrollTo row and column alignment scrolling
3468 <li>Select sequence/alignment regions from javascript</li>
3469 <li>javascript structure viewer harness to pass
3470 messages between Jmol and Jalview when running as
3471 distinct applets</li>
3472 <li>sortBy method</li>
3473 <li>Set of applet and application examples shipped
3474 with documentation</li>
3475 <li>New example to demonstrate JalviewLite and Jmol
3476 javascript message exchange</li>
3478 </ul> <em>General</em>
3480 <li>Enable Jmol displays to be associated with multiple
3481 multiple alignments</li>
3482 <li>Option to automatically sort alignment with new tree</li>
3483 <li>User configurable link to enable redirects to a
3484 www.Jalview.org mirror</li>
3485 <li>Jmol colours option for Jmol displays</li>
3486 <li>Configurable newline string when writing alignment
3487 and other flat files</li>
3488 <li>Allow alignment annotation description lines to
3489 contain html tags</li>
3490 </ul> <em>Documentation and Development</em>
3492 <li>Add groovy test harness for bulk load testing to
3494 <li>Groovy script to load and align a set of sequences
3495 using a web service before displaying the result in the
3496 Jalview desktop</li>
3497 <li>Restructured javascript and applet api documentation</li>
3498 <li>Ant target to publish example html files with applet
3500 <li>Netbeans project for building Jalview from source</li>
3501 <li>ant task to create online javadoc for Jalview source</li>
3503 <td><em>Application</em>
3505 <li>User defined colourscheme throws exception when
3506 current built in colourscheme is saved as new scheme</li>
3507 <li>AlignFrame->Save in application pops up save
3508 dialog for valid filename/format</li>
3509 <li>Cannot view associated structure for UniProt sequence</li>
3510 <li>PDB file association breaks for UniProt sequence
3512 <li>Associate PDB from file dialog does not tell you
3513 which sequence is to be associated with the file</li>
3514 <li>Find All raises null pointer exception when query
3515 only matches sequence IDs</li>
3516 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3517 <li>Jalview project with Jmol views created with Jalview
3518 2.4 cannot be loaded</li>
3519 <li>Filetype associations not installed for webstart
3521 <li>Two or more chains in a single PDB file associated
3522 with sequences in different alignments do not get coloured
3523 by their associated sequence</li>
3524 <li>Visibility status of autocalculated annotation row
3525 not preserved when project is loaded</li>
3526 <li>Annotation row height and visibility attributes not
3527 stored in Jalview project</li>
3528 <li>Tree bootstraps are not preserved when saved as a
3529 Jalview project</li>
3530 <li>Envision2 workflow tooltips are corrupted</li>
3531 <li>Enabling show group conservation also enables colour
3532 by conservation</li>
3533 <li>Duplicate group associated conservation or consensus
3534 created on new view</li>
3535 <li>Annotation scrollbar not displayed after 'show
3536 all hidden annotation rows' option selected</li>
3537 <li>Alignment quality not updated after alignment
3538 annotation row is hidden then shown</li>
3539 <li>Preserve colouring of structures coloured by
3540 sequences in pre Jalview 2.7 projects</li>
3541 <li>Web service job parameter dialog is not laid out
3543 <li>Web services menu not refreshed after 'reset
3544 services' button is pressed in preferences</li>
3545 <li>Annotation off by one in Jalview v2_3 example project</li>
3546 <li>Structures imported from file and saved in project
3547 get name like jalview_pdb1234.txt when reloaded</li>
3548 <li>Jalview does not always retrieve progress of a JABAWS
3549 job execution in full once it is complete</li>
3550 </ul> <em>Applet</em>
3552 <li>Alignment height set incorrectly when lots of
3553 annotation rows are displayed</li>
3554 <li>Relative URLs in feature HTML text not resolved to
3556 <li>View follows highlighting does not work for positions
3558 <li><= shown as = in tooltip</li>
3559 <li>Export features raises exception when no features
3561 <li>Separator string used for serialising lists of IDs
3562 for javascript api is modified when separator string
3563 provided as parameter</li>
3564 <li>Null pointer exception when selecting tree leaves for
3565 alignment with no existing selection</li>
3566 <li>Relative URLs for datasources assumed to be relative
3567 to applet's codebase</li>
3568 <li>Status bar not updated after finished searching and
3569 search wraps around to first result</li>
3570 <li>StructureSelectionManager instance shared between
3571 several Jalview applets causes race conditions and memory
3573 <li>Hover tooltip and mouseover of position on structure
3574 not sent from Jmol in applet</li>
3575 <li>Certain sequences of javascript method calls to
3576 applet API fatally hang browser</li>
3577 </ul> <em>General</em>
3579 <li>View follows structure mouseover scrolls beyond
3580 position with wrapped view and hidden regions</li>
3581 <li>Find sequence position moves to wrong residue
3582 with/without hidden columns</li>
3583 <li>Sequence length given in alignment properties window
3585 <li>InvalidNumberFormat exceptions thrown when trying to
3586 import PDB like structure files</li>
3587 <li>Positional search results are only highlighted
3588 between user-supplied sequence start/end bounds</li>
3589 <li>End attribute of sequence is not validated</li>
3590 <li>Find dialog only finds first sequence containing a
3591 given sequence position</li>
3592 <li>Sequence numbering not preserved in MSF alignment
3594 <li>Jalview PDB file reader does not extract sequence
3595 from nucleotide chains correctly</li>
3596 <li>Structure colours not updated when tree partition
3597 changed in alignment</li>
3598 <li>Sequence associated secondary structure not correctly
3599 parsed in interleaved stockholm</li>
3600 <li>Colour by annotation dialog does not restore current
3602 <li>Hiding (nearly) all sequences doesn't work
3604 <li>Sequences containing lowercase letters are not
3605 properly associated with their pdb files</li>
3606 </ul> <em>Documentation and Development</em>
3608 <li>schemas/JalviewWsParamSet.xsd corrupted by
3609 ApplyCopyright tool</li>
3614 <div align="center">
3615 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3618 <td><em>Application</em>
3620 <li>New warning dialog when the Jalview Desktop cannot
3621 contact web services</li>
3622 <li>JABA service parameters for a preset are shown in
3623 service job window</li>
3624 <li>JABA Service menu entries reworded</li>
3628 <li>Modeller PIR IO broken - cannot correctly import a
3629 pir file emitted by Jalview</li>
3630 <li>Existing feature settings transferred to new
3631 alignment view created from cut'n'paste</li>
3632 <li>Improved test for mixed amino/nucleotide chains when
3633 parsing PDB files</li>
3634 <li>Consensus and conservation annotation rows
3635 occasionally become blank for all new windows</li>
3636 <li>Exception raised when right clicking above sequences
3637 in wrapped view mode</li>
3638 </ul> <em>Application</em>
3640 <li>multiple multiply aligned structure views cause cpu
3641 usage to hit 100% and computer to hang</li>
3642 <li>Web Service parameter layout breaks for long user
3643 parameter names</li>
3644 <li>Jaba service discovery hangs desktop if Jaba server
3651 <div align="center">
3652 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3655 <td><em>Application</em>
3657 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3658 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3661 <li>Web Services preference tab</li>
3662 <li>Analysis parameters dialog box and user defined
3664 <li>Improved speed and layout of Envision2 service menu</li>
3665 <li>Superpose structures using associated sequence
3667 <li>Export coordinates and projection as CSV from PCA
3669 </ul> <em>Applet</em>
3671 <li>enable javascript: execution by the applet via the
3672 link out mechanism</li>
3673 </ul> <em>Other</em>
3675 <li>Updated the Jmol Jalview interface to work with Jmol
3677 <li>The Jalview Desktop and JalviewLite applet now
3678 require Java 1.5</li>
3679 <li>Allow Jalview feature colour specification for GFF
3680 sequence annotation files</li>
3681 <li>New 'colour by label' keword in Jalview feature file
3682 type colour specification</li>
3683 <li>New Jalview Desktop Groovy API method that allows a
3684 script to check if it being run in an interactive session or
3685 in a batch operation from the Jalview command line</li>
3689 <li>clustalx colourscheme colours Ds preferentially when
3690 both D+E are present in over 50% of the column</li>
3691 </ul> <em>Application</em>
3693 <li>typo in AlignmentFrame->View->Hide->all but
3694 selected Regions menu item</li>
3695 <li>sequence fetcher replaces ',' for ';' when the ',' is
3696 part of a valid accession ID</li>
3697 <li>fatal OOM if object retrieved by sequence fetcher
3698 runs out of memory</li>
3699 <li>unhandled Out of Memory Error when viewing pca
3700 analysis results</li>
3701 <li>InstallAnywhere builds fail to launch on OS X java
3702 10.5 update 4 (due to apple Java 1.6 update)</li>
3703 <li>Installanywhere Jalview silently fails to launch</li>
3704 </ul> <em>Applet</em>
3706 <li>Jalview.getFeatureGroups() raises an
3707 ArrayIndexOutOfBoundsException if no feature groups are
3714 <div align="center">
3715 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3721 <li>Alignment prettyprinter doesn't cope with long
3723 <li>clustalx colourscheme colours Ds preferentially when
3724 both D+E are present in over 50% of the column</li>
3725 <li>nucleic acid structures retrieved from PDB do not
3726 import correctly</li>
3727 <li>More columns get selected than were clicked on when a
3728 number of columns are hidden</li>
3729 <li>annotation label popup menu not providing correct
3730 add/hide/show options when rows are hidden or none are
3732 <li>Stockholm format shown in list of readable formats,
3733 and parser copes better with alignments from RFAM.</li>
3734 <li>CSV output of consensus only includes the percentage
3735 of all symbols if sequence logo display is enabled</li>
3737 </ul> <em>Applet</em>
3739 <li>annotation panel disappears when annotation is
3741 </ul> <em>Application</em>
3743 <li>Alignment view not redrawn properly when new
3744 alignment opened where annotation panel is visible but no
3745 annotations are present on alignment</li>
3746 <li>pasted region containing hidden columns is
3747 incorrectly displayed in new alignment window</li>
3748 <li>Jalview slow to complete operations when stdout is
3749 flooded (fix is to close the Jalview console)</li>
3750 <li>typo in AlignmentFrame->View->Hide->all but
3751 selected Rregions menu item.</li>
3752 <li>inconsistent group submenu and Format submenu entry
3753 'Un' or 'Non'conserved</li>
3754 <li>Sequence feature settings are being shared by
3755 multiple distinct alignments</li>
3756 <li>group annotation not recreated when tree partition is
3758 <li>double click on group annotation to select sequences
3759 does not propagate to associated trees</li>
3760 <li>Mac OSX specific issues:
3762 <li>exception raised when mouse clicked on desktop
3763 window background</li>
3764 <li>Desktop menu placed on menu bar and application
3765 name set correctly</li>
3766 <li>sequence feature settings not wide enough for the
3767 save feature colourscheme button</li>
3776 <div align="center">
3777 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3780 <td><em>New Capabilities</em>
3782 <li>URL links generated from description line for
3783 regular-expression based URL links (applet and application)
3785 <li>Non-positional feature URL links are shown in link
3787 <li>Linked viewing of nucleic acid sequences and
3789 <li>Automatic Scrolling option in View menu to display
3790 the currently highlighted region of an alignment.</li>
3791 <li>Order an alignment by sequence length, or using the
3792 average score or total feature count for each sequence.</li>
3793 <li>Shading features by score or associated description</li>
3794 <li>Subdivide alignment and groups based on identity of
3795 selected subsequence (Make Groups from Selection).</li>
3796 <li>New hide/show options including Shift+Control+H to
3797 hide everything but the currently selected region.</li>
3798 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3799 </ul> <em>Application</em>
3801 <li>Fetch DB References capabilities and UI expanded to
3802 support retrieval from DAS sequence sources</li>
3803 <li>Local DAS Sequence sources can be added via the
3804 command line or via the Add local source dialog box.</li>
3805 <li>DAS Dbref and DbxRef feature types are parsed as
3806 database references and protein_name is parsed as
3807 description line (BioSapiens terms).</li>
3808 <li>Enable or disable non-positional feature and database
3809 references in sequence ID tooltip from View menu in
3811 <!-- <li>New hidden columns and rows and representatives capabilities
3812 in annotations file (in progress - not yet fully implemented)</li> -->
3813 <li>Group-associated consensus, sequence logos and
3814 conservation plots</li>
3815 <li>Symbol distributions for each column can be exported
3816 and visualized as sequence logos</li>
3817 <li>Optionally scale multi-character column labels to fit
3818 within each column of annotation row<!-- todo for applet -->
3820 <li>Optional automatic sort of associated alignment view
3821 when a new tree is opened.</li>
3822 <li>Jalview Java Console</li>
3823 <li>Better placement of desktop window when moving
3824 between different screens.</li>
3825 <li>New preference items for sequence ID tooltip and
3826 consensus annotation</li>
3827 <li>Client to submit sequences and IDs to Envision2
3829 <li><em>Vamsas Capabilities</em>
3831 <li>Improved VAMSAS synchronization (Jalview archive
3832 used to preserve views, structures, and tree display
3834 <li>Import of vamsas documents from disk or URL via
3836 <li>Sharing of selected regions between views and
3837 with other VAMSAS applications (Experimental feature!)</li>
3838 <li>Updated API to VAMSAS version 0.2</li>
3840 </ul> <em>Applet</em>
3842 <li>Middle button resizes annotation row height</li>
3845 <li>sortByTree (true/false) - automatically sort the
3846 associated alignment view by the tree when a new tree is
3848 <li>showTreeBootstraps (true/false) - show or hide
3849 branch bootstraps (default is to show them if available)</li>
3850 <li>showTreeDistances (true/false) - show or hide
3851 branch lengths (default is to show them if available)</li>
3852 <li>showUnlinkedTreeNodes (true/false) - indicate if
3853 unassociated nodes should be highlighted in the tree
3855 <li>heightScale and widthScale (1.0 or more) -
3856 increase the height or width of a cell in the alignment
3857 grid relative to the current font size.</li>
3860 <li>Non-positional features displayed in sequence ID
3862 </ul> <em>Other</em>
3864 <li>Features format: graduated colour definitions and
3865 specification of feature scores</li>
3866 <li>Alignment Annotations format: new keywords for group
3867 associated annotation (GROUP_REF) and annotation row display
3868 properties (ROW_PROPERTIES)</li>
3869 <li>XML formats extended to support graduated feature
3870 colourschemes, group associated annotation, and profile
3871 visualization settings.</li></td>
3874 <li>Source field in GFF files parsed as feature source
3875 rather than description</li>
3876 <li>Non-positional features are now included in sequence
3877 feature and gff files (controlled via non-positional feature
3878 visibility in tooltip).</li>
3879 <li>URL links generated for all feature links (bugfix)</li>
3880 <li>Added URL embedding instructions to features file
3882 <li>Codons containing ambiguous nucleotides translated as
3883 'X' in peptide product</li>
3884 <li>Match case switch in find dialog box works for both
3885 sequence ID and sequence string and query strings do not
3886 have to be in upper case to match case-insensitively.</li>
3887 <li>AMSA files only contain first column of
3888 multi-character column annotation labels</li>
3889 <li>Jalview Annotation File generation/parsing consistent
3890 with documentation (e.g. Stockholm annotation can be
3891 exported and re-imported)</li>
3892 <li>PDB files without embedded PDB IDs given a friendly
3894 <li>Find incrementally searches ID string matches as well
3895 as subsequence matches, and correctly reports total number
3899 <li>Better handling of exceptions during sequence
3901 <li>Dasobert generated non-positional feature URL
3902 link text excludes the start_end suffix</li>
3903 <li>DAS feature and source retrieval buttons disabled
3904 when fetch or registry operations in progress.</li>
3905 <li>PDB files retrieved from URLs are cached properly</li>
3906 <li>Sequence description lines properly shared via
3908 <li>Sequence fetcher fetches multiple records for all
3910 <li>Ensured that command line das feature retrieval
3911 completes before alignment figures are generated.</li>
3912 <li>Reduced time taken when opening file browser for
3914 <li>isAligned check prior to calculating tree, PCA or
3915 submitting an MSA to JNet now excludes hidden sequences.</li>
3916 <li>User defined group colours properly recovered
3917 from Jalview projects.</li>
3926 <div align="center">
3927 <strong>2.4.0.b2</strong><br> 28/10/2009
3932 <li>Experimental support for google analytics usage
3934 <li>Jalview privacy settings (user preferences and docs).</li>
3939 <li>Race condition in applet preventing startup in
3941 <li>Exception when feature created from selection beyond
3942 length of sequence.</li>
3943 <li>Allow synthetic PDB files to be imported gracefully</li>
3944 <li>Sequence associated annotation rows associate with
3945 all sequences with a given id</li>
3946 <li>Find function matches case-insensitively for sequence
3947 ID string searches</li>
3948 <li>Non-standard characters do not cause pairwise
3949 alignment to fail with exception</li>
3950 </ul> <em>Application Issues</em>
3952 <li>Sequences are now validated against EMBL database</li>
3953 <li>Sequence fetcher fetches multiple records for all
3955 </ul> <em>InstallAnywhere Issues</em>
3957 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3958 issue with installAnywhere mechanism)</li>
3959 <li>Command line launching of JARs from InstallAnywhere
3960 version (java class versioning error fixed)</li>
3967 <div align="center">
3968 <strong>2.4</strong><br> 27/8/2008
3971 <td><em>User Interface</em>
3973 <li>Linked highlighting of codon and amino acid from
3974 translation and protein products</li>
3975 <li>Linked highlighting of structure associated with
3976 residue mapping to codon position</li>
3977 <li>Sequence Fetcher provides example accession numbers
3978 and 'clear' button</li>
3979 <li>MemoryMonitor added as an option under Desktop's
3981 <li>Extract score function to parse whitespace separated
3982 numeric data in description line</li>
3983 <li>Column labels in alignment annotation can be centred.</li>
3984 <li>Tooltip for sequence associated annotation give name
3986 </ul> <em>Web Services and URL fetching</em>
3988 <li>JPred3 web service</li>
3989 <li>Prototype sequence search client (no public services
3991 <li>Fetch either seed alignment or full alignment from
3993 <li>URL Links created for matching database cross
3994 references as well as sequence ID</li>
3995 <li>URL Links can be created using regular-expressions</li>
3996 </ul> <em>Sequence Database Connectivity</em>
3998 <li>Retrieval of cross-referenced sequences from other
4000 <li>Generalised database reference retrieval and
4001 validation to all fetchable databases</li>
4002 <li>Fetch sequences from DAS sources supporting the
4003 sequence command</li>
4004 </ul> <em>Import and Export</em>
4005 <li>export annotation rows as CSV for spreadsheet import</li>
4006 <li>Jalview projects record alignment dataset associations,
4007 EMBL products, and cDNA sequence mappings</li>
4008 <li>Sequence Group colour can be specified in Annotation
4010 <li>Ad-hoc colouring of group in Annotation File using RGB
4011 triplet as name of colourscheme</li>
4012 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4014 <li>treenode binding for VAMSAS tree exchange</li>
4015 <li>local editing and update of sequences in VAMSAS
4016 alignments (experimental)</li>
4017 <li>Create new or select existing session to join</li>
4018 <li>load and save of vamsas documents</li>
4019 </ul> <em>Application command line</em>
4021 <li>-tree parameter to open trees (introduced for passing
4023 <li>-fetchfrom command line argument to specify nicknames
4024 of DAS servers to query for alignment features</li>
4025 <li>-dasserver command line argument to add new servers
4026 that are also automatically queried for features</li>
4027 <li>-groovy command line argument executes a given groovy
4028 script after all input data has been loaded and parsed</li>
4029 </ul> <em>Applet-Application data exchange</em>
4031 <li>Trees passed as applet parameters can be passed to
4032 application (when using "View in full
4033 application")</li>
4034 </ul> <em>Applet Parameters</em>
4036 <li>feature group display control parameter</li>
4037 <li>debug parameter</li>
4038 <li>showbutton parameter</li>
4039 </ul> <em>Applet API methods</em>
4041 <li>newView public method</li>
4042 <li>Window (current view) specific get/set public methods</li>
4043 <li>Feature display control methods</li>
4044 <li>get list of currently selected sequences</li>
4045 </ul> <em>New Jalview distribution features</em>
4047 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4048 <li>RELEASE file gives build properties for the latest
4049 Jalview release.</li>
4050 <li>Java 1.1 Applet build made easier and donotobfuscate
4051 property controls execution of obfuscator</li>
4052 <li>Build target for generating source distribution</li>
4053 <li>Debug flag for javacc</li>
4054 <li>.jalview_properties file is documented (slightly) in
4055 jalview.bin.Cache</li>
4056 <li>Continuous Build Integration for stable and
4057 development version of Application, Applet and source
4062 <li>selected region output includes visible annotations
4063 (for certain formats)</li>
4064 <li>edit label/displaychar contains existing label/char
4066 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4067 <li>shorter peptide product names from EMBL records</li>
4068 <li>Newick string generator makes compact representations</li>
4069 <li>bootstrap values parsed correctly for tree files with
4071 <li>pathological filechooser bug avoided by not allowing
4072 filenames containing a ':'</li>
4073 <li>Fixed exception when parsing GFF files containing
4074 global sequence features</li>
4075 <li>Alignment datasets are finalized only when number of
4076 references from alignment sequences goes to zero</li>
4077 <li>Close of tree branch colour box without colour
4078 selection causes cascading exceptions</li>
4079 <li>occasional negative imgwidth exceptions</li>
4080 <li>better reporting of non-fatal warnings to user when
4081 file parsing fails.</li>
4082 <li>Save works when Jalview project is default format</li>
4083 <li>Save as dialog opened if current alignment format is
4084 not a valid output format</li>
4085 <li>UniProt canonical names introduced for both das and
4087 <li>Histidine should be midblue (not pink!) in Zappo</li>
4088 <li>error messages passed up and output when data read
4090 <li>edit undo recovers previous dataset sequence when
4091 sequence is edited</li>
4092 <li>allow PDB files without pdb ID HEADER lines (like
4093 those generated by MODELLER) to be read in properly</li>
4094 <li>allow reading of JPred concise files as a normal
4096 <li>Stockholm annotation parsing and alignment properties
4097 import fixed for PFAM records</li>
4098 <li>Structure view windows have correct name in Desktop
4100 <li>annotation consisting of sequence associated scores
4101 can be read and written correctly to annotation file</li>
4102 <li>Aligned cDNA translation to aligned peptide works
4104 <li>Fixed display of hidden sequence markers and
4105 non-italic font for representatives in Applet</li>
4106 <li>Applet Menus are always embedded in applet window on
4108 <li>Newly shown features appear at top of stack (in
4110 <li>Annotations added via parameter not drawn properly
4111 due to null pointer exceptions</li>
4112 <li>Secondary structure lines are drawn starting from
4113 first column of alignment</li>
4114 <li>UniProt XML import updated for new schema release in
4116 <li>Sequence feature to sequence ID match for Features
4117 file is case-insensitive</li>
4118 <li>Sequence features read from Features file appended to
4119 all sequences with matching IDs</li>
4120 <li>PDB structure coloured correctly for associated views
4121 containing a sub-sequence</li>
4122 <li>PDB files can be retrieved by applet from Jar files</li>
4123 <li>feature and annotation file applet parameters
4124 referring to different directories are retrieved correctly</li>
4125 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4126 <li>Fixed application hang whilst waiting for
4127 splash-screen version check to complete</li>
4128 <li>Applet properly URLencodes input parameter values
4129 when passing them to the launchApp service</li>
4130 <li>display name and local features preserved in results
4131 retrieved from web service</li>
4132 <li>Visual delay indication for sequence retrieval and
4133 sequence fetcher initialisation</li>
4134 <li>updated Application to use DAS 1.53e version of
4135 dasobert DAS client</li>
4136 <li>Re-instated Full AMSA support and .amsa file
4138 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4146 <div align="center">
4147 <strong>2.3</strong><br> 9/5/07
4152 <li>Jmol 11.0.2 integration</li>
4153 <li>PDB views stored in Jalview XML files</li>
4154 <li>Slide sequences</li>
4155 <li>Edit sequence in place</li>
4156 <li>EMBL CDS features</li>
4157 <li>DAS Feature mapping</li>
4158 <li>Feature ordering</li>
4159 <li>Alignment Properties</li>
4160 <li>Annotation Scores</li>
4161 <li>Sort by scores</li>
4162 <li>Feature/annotation editing in applet</li>
4167 <li>Headless state operation in 2.2.1</li>
4168 <li>Incorrect and unstable DNA pairwise alignment</li>
4169 <li>Cut and paste of sequences with annotation</li>
4170 <li>Feature group display state in XML</li>
4171 <li>Feature ordering in XML</li>
4172 <li>blc file iteration selection using filename # suffix</li>
4173 <li>Stockholm alignment properties</li>
4174 <li>Stockhom alignment secondary structure annotation</li>
4175 <li>2.2.1 applet had no feature transparency</li>
4176 <li>Number pad keys can be used in cursor mode</li>
4177 <li>Structure Viewer mirror image resolved</li>
4184 <div align="center">
4185 <strong>2.2.1</strong><br> 12/2/07
4190 <li>Non standard characters can be read and displayed
4191 <li>Annotations/Features can be imported/exported to the
4193 <li>Applet allows editing of sequence/annotation/group
4194 name & description
4195 <li>Preference setting to display sequence name in
4197 <li>Annotation file format extended to allow
4198 Sequence_groups to be defined
4199 <li>Default opening of alignment overview panel can be
4200 specified in preferences
4201 <li>PDB residue numbering annotation added to associated
4207 <li>Applet crash under certain Linux OS with Java 1.6
4209 <li>Annotation file export / import bugs fixed
4210 <li>PNG / EPS image output bugs fixed
4216 <div align="center">
4217 <strong>2.2</strong><br> 27/11/06
4222 <li>Multiple views on alignment
4223 <li>Sequence feature editing
4224 <li>"Reload" alignment
4225 <li>"Save" to current filename
4226 <li>Background dependent text colour
4227 <li>Right align sequence ids
4228 <li>User-defined lower case residue colours
4231 <li>Menu item accelerator keys
4232 <li>Control-V pastes to current alignment
4233 <li>Cancel button for DAS Feature Fetching
4234 <li>PCA and PDB Viewers zoom via mouse roller
4235 <li>User-defined sub-tree colours and sub-tree selection
4237 <li>'New Window' button on the 'Output to Text box'
4242 <li>New memory efficient Undo/Redo System
4243 <li>Optimised symbol lookups and conservation/consensus
4245 <li>Region Conservation/Consensus recalculated after
4247 <li>Fixed Remove Empty Columns Bug (empty columns at end
4249 <li>Slowed DAS Feature Fetching for increased robustness.
4251 <li>Made angle brackets in ASCII feature descriptions
4253 <li>Re-instated Zoom function for PCA
4254 <li>Sequence descriptions conserved in web service
4256 <li>UniProt ID discoverer uses any word separated by
4258 <li>WsDbFetch query/result association resolved
4259 <li>Tree leaf to sequence mapping improved
4260 <li>Smooth fonts switch moved to FontChooser dialog box.
4267 <div align="center">
4268 <strong>2.1.1</strong><br> 12/9/06
4273 <li>Copy consensus sequence to clipboard</li>
4278 <li>Image output - rightmost residues are rendered if
4279 sequence id panel has been resized</li>
4280 <li>Image output - all offscreen group boundaries are
4282 <li>Annotation files with sequence references - all
4283 elements in file are relative to sequence position</li>
4284 <li>Mac Applet users can use Alt key for group editing</li>
4290 <div align="center">
4291 <strong>2.1</strong><br> 22/8/06
4296 <li>MAFFT Multiple Alignment in default Web Service list</li>
4297 <li>DAS Feature fetching</li>
4298 <li>Hide sequences and columns</li>
4299 <li>Export Annotations and Features</li>
4300 <li>GFF file reading / writing</li>
4301 <li>Associate structures with sequences from local PDB
4303 <li>Add sequences to exisiting alignment</li>
4304 <li>Recently opened files / URL lists</li>
4305 <li>Applet can launch the full application</li>
4306 <li>Applet has transparency for features (Java 1.2
4308 <li>Applet has user defined colours parameter</li>
4309 <li>Applet can load sequences from parameter
4310 "sequence<em>x</em>"
4316 <li>Redundancy Panel reinstalled in the Applet</li>
4317 <li>Monospaced font - EPS / rescaling bug fixed</li>
4318 <li>Annotation files with sequence references bug fixed</li>
4324 <div align="center">
4325 <strong>2.08.1</strong><br> 2/5/06
4330 <li>Change case of selected region from Popup menu</li>
4331 <li>Choose to match case when searching</li>
4332 <li>Middle mouse button and mouse movement can compress /
4333 expand the visible width and height of the alignment</li>
4338 <li>Annotation Panel displays complete JNet results</li>
4344 <div align="center">
4345 <strong>2.08b</strong><br> 18/4/06
4351 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4352 <li>Righthand label on wrapped alignments shows correct
4359 <div align="center">
4360 <strong>2.08</strong><br> 10/4/06
4365 <li>Editing can be locked to the selection area</li>
4366 <li>Keyboard editing</li>
4367 <li>Create sequence features from searches</li>
4368 <li>Precalculated annotations can be loaded onto
4370 <li>Features file allows grouping of features</li>
4371 <li>Annotation Colouring scheme added</li>
4372 <li>Smooth fonts off by default - Faster rendering</li>
4373 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4378 <li>Drag & Drop fixed on Linux</li>
4379 <li>Jalview Archive file faster to load/save, sequence
4380 descriptions saved.</li>
4386 <div align="center">
4387 <strong>2.07</strong><br> 12/12/05
4392 <li>PDB Structure Viewer enhanced</li>
4393 <li>Sequence Feature retrieval and display enhanced</li>
4394 <li>Choose to output sequence start-end after sequence
4395 name for file output</li>
4396 <li>Sequence Fetcher WSDBFetch@EBI</li>
4397 <li>Applet can read feature files, PDB files and can be
4398 used for HTML form input</li>
4403 <li>HTML output writes groups and features</li>
4404 <li>Group editing is Control and mouse click</li>
4405 <li>File IO bugs</li>
4411 <div align="center">
4412 <strong>2.06</strong><br> 28/9/05
4417 <li>View annotations in wrapped mode</li>
4418 <li>More options for PCA viewer</li>
4423 <li>GUI bugs resolved</li>
4424 <li>Runs with -nodisplay from command line</li>
4430 <div align="center">
4431 <strong>2.05b</strong><br> 15/9/05
4436 <li>Choose EPS export as lineart or text</li>
4437 <li>Jar files are executable</li>
4438 <li>Can read in Uracil - maps to unknown residue</li>
4443 <li>Known OutOfMemory errors give warning message</li>
4444 <li>Overview window calculated more efficiently</li>
4445 <li>Several GUI bugs resolved</li>
4451 <div align="center">
4452 <strong>2.05</strong><br> 30/8/05
4457 <li>Edit and annotate in "Wrapped" view</li>
4462 <li>Several GUI bugs resolved</li>
4468 <div align="center">
4469 <strong>2.04</strong><br> 24/8/05
4474 <li>Hold down mouse wheel & scroll to change font
4480 <li>Improved JPred client reliability</li>
4481 <li>Improved loading of Jalview files</li>
4487 <div align="center">
4488 <strong>2.03</strong><br> 18/8/05
4493 <li>Set Proxy server name and port in preferences</li>
4494 <li>Multiple URL links from sequence ids</li>
4495 <li>User Defined Colours can have a scheme name and added
4497 <li>Choose to ignore gaps in consensus calculation</li>
4498 <li>Unix users can set default web browser</li>
4499 <li>Runs without GUI for batch processing</li>
4500 <li>Dynamically generated Web Service Menus</li>
4505 <li>InstallAnywhere download for Sparc Solaris</li>
4511 <div align="center">
4512 <strong>2.02</strong><br> 18/7/05
4518 <li>Copy & Paste order of sequences maintains
4519 alignment order.</li>
4525 <div align="center">
4526 <strong>2.01</strong><br> 12/7/05
4531 <li>Use delete key for deleting selection.</li>
4532 <li>Use Mouse wheel to scroll sequences.</li>
4533 <li>Help file updated to describe how to add alignment
4535 <li>Version and build date written to build properties
4537 <li>InstallAnywhere installation will check for updates
4538 at launch of Jalview.</li>
4543 <li>Delete gaps bug fixed.</li>
4544 <li>FileChooser sorts columns.</li>
4545 <li>Can remove groups one by one.</li>
4546 <li>Filechooser icons installed.</li>
4547 <li>Finder ignores return character when searching.
4548 Return key will initiate a search.<br>
4555 <div align="center">
4556 <strong>2.0</strong><br> 20/6/05
4561 <li>New codebase</li>