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>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">2.11</a><br />
61 <em>14/05/2019 (final due date !)</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
68 <!-- JAL-3141 -->Optional automatic backups when saving
69 Jalview project or alignment files</li>
71 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
72 Viewer state is saved in Jalview Project<br />The 'Change
73 parameters' option has also been removed from the PCA viewer</li>
75 <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
77 <!-- JAL-2620 -->Alternative genetic code tables supported for
78 'Translate as cDNA'</li>
80 <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
82 <!-- JAL-3198 -->More efficient creation of selections and
83 multiple groups when working with large alignments</li>
85 <!-- JAL-3200 -->Speedier import of annotation rows when
86 parsing stockholm files</li>
88 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
90 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
91 shaded according to any associated attributes (e.g. variant
92 attributes from VCF file, or key-value pairs imported from
93 column 9 of GFF file)</li>
95 <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
97 <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
99 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
100 algorithm (Z-sort/transparency and filter aware)</li>
102 <!-- JAL-2527 -->Alignment Overview now by default shows
103 only visible region of alignment (this can be changed in
104 user preferences)</li>
106 <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
108 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
109 all sequences are hidden</li>
111 <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
112 region, and gap count when inserting or deleting gaps</li>
114 <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
116 <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
118 <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
120 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
122 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
124 <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
126 <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
128 <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
130 <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
132 <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
133 to a hidden column marker</li>
135 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
137 <!-- JAL-2965 -->PCA depth queuing with graduated colours</li>
139 <em>Deprecations</em>
142 <!-- JAL-3035 -->DAS sequence retrieval and annotation
143 capabilities removed from the Jalview Desktop
146 <em>Release Processes</em>
149 Atlassian Bamboo continuous integration server for
150 unattended Test Suite execution</li>
152 <!-- JAL-2864 -->Memory test suite to detect leaks in common
155 <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
156 implementation) used for Sequence Feature collections</li>
158 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
159 unmarshalling has been replaced by JAXB for Jalview projects
160 and XML based data retrieval clients</li>
163 <td align="left" valign="top">
166 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
168 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
169 Jalview project involving multiple views</li>
171 <!-- JAL-3164 -->Overview for complementary view in a linked
172 CDS/Protein alignment is not updated when Hide Columns by
173 Annotation dialog hides columns</li>
175 <!-- JAL-3158 -->Selection highlighting in the complement of
176 a CDS/Protein alignment stops working after making a
177 selection in one view, then making another selection in the
180 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
182 <!-- JAL-3154 -->Table Columns could be re-ordered in
183 Feature Settings and Jalview Preferences panels</li>
185 <!-- JAL-2865 -->Jalview hangs when closing windows
186 or the overview updates with large alignments</li>
188 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
189 region if columns were selected by dragging right-to-left
190 and the mouse moved to the left of the first column</li>
192 <!-- JAL-2846 -->Error message for trying to load in invalid
193 URLs doesn't tell users the invalid URL</li>
195 <!-- JAL-3178 -->Nonpositional features lose feature group
196 on export as Jalview features file</li>
198 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
199 printed when columns are hidden</li>
201 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
203 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
204 dragging out of Scale or Annotation Panel</li>
206 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
208 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
210 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
212 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
214 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
216 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
218 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
219 opening an alignment</li>
221 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
223 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
224 different groups in the alignment are selected</li>
226 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
228 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
230 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
232 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
234 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
236 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
238 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
240 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
242 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
244 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
246 <!-- JAL-914 -->Help page can be opened twice</li>
251 <!-- JAL-2822 -->Start and End should be updated when
252 sequence data at beginning or end of alignment added/removed
253 via 'Edit' sequence</li>
255 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
256 sequence features correctly when start of sequence is
257 removed (Known defect since 2.10)</li>
259 <em>New Known Defects</em>
262 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
264 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
269 <td width="60" nowrap>
271 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
274 <td><div align="left">
278 <!-- JAL-3101 -->Default memory for Jalview webstart and
279 InstallAnywhere increased to 1G.
282 <!-- JAL-247 -->Hidden sequence markers and representative
283 sequence bolding included when exporting alignment as EPS,
284 SVG, PNG or HTML. <em>Display is configured via the
285 Format menu, or for command-line use via a jalview
286 properties file.</em>
289 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
290 API and sequence data now imported as JSON.
293 <!-- JAL-3065 -->Change in recommended way of starting
294 Jalview via a Java command line: add jars in lib directory
295 to CLASSPATH, rather than via the deprecated java.ext.dirs
302 <!-- JAL-3047 -->Support added to execute test suite
303 instrumented with <a href="http://openclover.org/">Open
308 <td><div align="left">
312 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
313 row shown in Feredoxin Structure alignment view of example
317 <!-- JAL-2854 -->Annotation obscures sequences if lots of
318 annotation displayed.
321 <!-- JAL-3107 -->Group conservation/consensus not shown
322 for newly created group when 'Apply to all groups'
326 <!-- JAL-3087 -->Corrupted display when switching to
327 wrapped mode when sequence panel's vertical scrollbar is
331 <!-- JAL-3003 -->Alignment is black in exported EPS file
332 when sequences are selected in exported view.</em>
335 <!-- JAL-3059 -->Groups with different coloured borders
336 aren't rendered with correct colour.
339 <!-- JAL-3092 -->Jalview could hang when importing certain
340 types of knotted RNA secondary structure.
343 <!-- JAL-3095 -->Sequence highlight and selection in
344 trimmed VARNA 2D structure is incorrect for sequences that
348 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
349 annotation when columns are inserted into an alignment,
350 and when exporting as Stockholm flatfile.
353 <!-- JAL-3053 -->Jalview annotation rows containing upper
354 and lower-case 'E' and 'H' do not automatically get
355 treated as RNA secondary structure.
358 <!-- JAL-3106 -->.jvp should be used as default extension
359 (not .jar) when saving a jalview project file.
362 <!-- JAL-3105 -->Mac Users: closing a window correctly
363 transfers focus to previous window on OSX
366 <em>Java 10 Issues Resolved</em>
369 <!-- JAL-2988 -->OSX - Can't save new files via the File
370 or export menus by typing in a name into the Save dialog
374 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
375 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
376 'look and feel' which has improved compatibility with the
377 latest version of OSX.
384 <td width="60" nowrap>
386 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
387 <em>7/06/2018</em></strong>
390 <td><div align="left">
394 <!-- JAL-2920 -->Use HGVS nomenclature for variant
395 annotation retrieved from Uniprot
398 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
399 onto the Jalview Desktop
403 <td><div align="left">
407 <!-- JAL-3017 -->Cannot import features with multiple
408 variant elements (blocks import of some Uniprot records)
411 <!-- JAL-2997 -->Clustal files with sequence positions in
412 right-hand column parsed correctly
415 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
416 not alignment area in exported graphic
419 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
420 window has input focus
423 <!-- JAL-2992 -->Annotation panel set too high when
424 annotation added to view (Windows)
427 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
428 network connectivity is poor
431 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
432 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
433 the currently open URL and links from a page viewed in
434 Firefox or Chrome on Windows is now fully supported. If
435 you are using Edge, only links in the page can be
436 dragged, and with Internet Explorer, only the currently
437 open URL in the browser can be dropped onto Jalview.</em>
443 <td width="60" nowrap>
445 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
448 <td><div align="left">
452 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
453 for disabling automatic superposition of multiple
454 structures and open structures in existing views
457 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
458 ID and annotation area margins can be click-dragged to
462 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
466 <!-- JAL-2759 -->Improved performance for large alignments
467 and lots of hidden columns
470 <!-- JAL-2593 -->Improved performance when rendering lots
471 of features (particularly when transparency is disabled)
476 <td><div align="left">
479 <!-- JAL-2899 -->Structure and Overview aren't updated
480 when Colour By Annotation threshold slider is adjusted
483 <!-- JAL-2778 -->Slow redraw when Overview panel shown
484 overlapping alignment panel
487 <!-- JAL-2929 -->Overview doesn't show end of unpadded
491 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
492 improved: CDS not handled correctly if transcript has no
496 <!-- JAL-2321 -->Secondary structure and temperature
497 factor annotation not added to sequence when local PDB
498 file associated with it by drag'n'drop or structure
502 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
503 dialog doesn't import PDB files dropped on an alignment
506 <!-- JAL-2666 -->Linked scrolling via protein horizontal
507 scroll bar doesn't work for some CDS/Protein views
510 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
511 Java 1.8u153 onwards and Java 1.9u4+.
514 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
515 columns in annotation row
518 <!-- JAL-2913 -->Preferences panel's ID Width control is not
519 honored in batch mode
522 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
523 for structures added to existing Jmol view
526 <!-- JAL-2223 -->'View Mappings' includes duplicate
527 entries after importing project with multiple views
530 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
531 protein sequences via SIFTS from associated PDB entries
532 with negative residue numbers or missing residues fails
535 <!-- JAL-2952 -->Exception when shading sequence with negative
536 Temperature Factor values from annotated PDB files (e.g.
537 as generated by CONSURF)
540 <!-- JAL-2920 -->Uniprot 'sequence variant' features
541 tooltip doesn't include a text description of mutation
544 <!-- JAL-2922 -->Invert displayed features very slow when
545 structure and/or overview windows are also shown
548 <!-- JAL-2954 -->Selecting columns from highlighted regions
549 very slow for alignments with large numbers of sequences
552 <!-- JAL-2925 -->Copy Consensus fails for group consensus
553 with 'StringIndexOutOfBounds'
556 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
557 platforms running Java 10
560 <!-- JAL-2960 -->Adding a structure to existing structure
561 view appears to do nothing because the view is hidden behind the alignment view
567 <!-- JAL-2926 -->Copy consensus sequence option in applet
568 should copy the group consensus when popup is opened on it
574 <!-- JAL-2913 -->Fixed ID width preference is not respected
577 <em>New Known Defects</em>
580 <!-- JAL-2973 --> Exceptions occasionally raised when
581 editing a large alignment and overview is displayed
584 <!-- JAL-2974 -->'Overview updating' progress bar is shown
585 repeatedly after a series of edits even when the overview
586 is no longer reflecting updates
589 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
590 structures for protein subsequence (if 'Trim Retrieved
591 Sequences' enabled) or Ensembl isoforms (Workaround in
592 2.10.4 is to fail back to N&W mapping)
599 <td width="60" nowrap>
601 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
604 <td><div align="left">
605 <ul><li>Updated Certum Codesigning Certificate
606 (Valid till 30th November 2018)</li></ul></div></td>
607 <td><div align="left">
610 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
611 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
612 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
613 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
614 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
615 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
616 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
622 <td width="60" nowrap>
624 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
627 <td><div align="left">
631 <!-- JAL-2446 -->Faster and more efficient management and
632 rendering of sequence features
635 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
636 429 rate limit request hander
639 <!-- JAL-2773 -->Structure views don't get updated unless
640 their colours have changed
643 <!-- JAL-2495 -->All linked sequences are highlighted for
644 a structure mousover (Jmol) or selection (Chimera)
647 <!-- JAL-2790 -->'Cancel' button in progress bar for
648 JABAWS AACon, RNAAliFold and Disorder prediction jobs
651 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
652 view from Ensembl locus cross-references
655 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
659 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
660 feature can be disabled
663 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
664 PDB easier retrieval of sequences for lists of IDs
667 <!-- JAL-2758 -->Short names for sequences retrieved from
673 <li>Groovy interpreter updated to 2.4.12</li>
674 <li>Example groovy script for generating a matrix of
675 percent identity scores for current alignment.</li>
677 <em>Testing and Deployment</em>
680 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
684 <td><div align="left">
688 <!-- JAL-2643 -->Pressing tab after updating the colour
689 threshold text field doesn't trigger an update to the
693 <!-- JAL-2682 -->Race condition when parsing sequence ID
697 <!-- JAL-2608 -->Overview windows are also closed when
698 alignment window is closed
701 <!-- JAL-2548 -->Export of features doesn't always respect
705 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
706 takes a long time in Cursor mode
712 <!-- JAL-2777 -->Structures with whitespace chainCode
713 cannot be viewed in Chimera
716 <!-- JAL-2728 -->Protein annotation panel too high in
720 <!-- JAL-2757 -->Can't edit the query after the server
721 error warning icon is shown in Uniprot and PDB Free Text
725 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
728 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
731 <!-- JAL-2739 -->Hidden column marker in last column not
732 rendered when switching back from Wrapped to normal view
735 <!-- JAL-2768 -->Annotation display corrupted when
736 scrolling right in unwapped alignment view
739 <!-- JAL-2542 -->Existing features on subsequence
740 incorrectly relocated when full sequence retrieved from
744 <!-- JAL-2733 -->Last reported memory still shown when
745 Desktop->Show Memory is unticked (OSX only)
748 <!-- JAL-2658 -->Amend Features dialog doesn't allow
749 features of same type and group to be selected for
753 <!-- JAL-2524 -->Jalview becomes sluggish in wide
754 alignments when hidden columns are present
757 <!-- JAL-2392 -->Jalview freezes when loading and
758 displaying several structures
761 <!-- JAL-2732 -->Black outlines left after resizing or
765 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
766 within the Jalview desktop on OSX
769 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
770 when in wrapped alignment mode
773 <!-- JAL-2636 -->Scale mark not shown when close to right
774 hand end of alignment
777 <!-- JAL-2684 -->Pairwise alignment of selected regions of
778 each selected sequence do not have correct start/end
782 <!-- JAL-2793 -->Alignment ruler height set incorrectly
783 after canceling the Alignment Window's Font dialog
786 <!-- JAL-2036 -->Show cross-references not enabled after
787 restoring project until a new view is created
790 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
791 URL links appears when only default EMBL-EBI link is
792 configured (since 2.10.2b2)
795 <!-- JAL-2775 -->Overview redraws whole window when box
799 <!-- JAL-2225 -->Structure viewer doesn't map all chains
800 in a multi-chain structure when viewing alignment
801 involving more than one chain (since 2.10)
804 <!-- JAL-2811 -->Double residue highlights in cursor mode
805 if new selection moves alignment window
808 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
809 arrow key in cursor mode to pass hidden column marker
812 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
813 that produces correctly annotated transcripts and products
816 <!-- JAL-2776 -->Toggling a feature group after first time
817 doesn't update associated structure view
820 <em>Applet</em><br />
823 <!-- JAL-2687 -->Concurrent modification exception when
824 closing alignment panel
827 <em>BioJSON</em><br />
830 <!-- JAL-2546 -->BioJSON export does not preserve
831 non-positional features
834 <em>New Known Issues</em>
837 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
838 sequence features correctly (for many previous versions of
842 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
843 using cursor in wrapped panel other than top
846 <!-- JAL-2791 -->Select columns containing feature ignores
847 graduated colour threshold
850 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
851 always preserve numbering and sequence features
854 <em>Known Java 9 Issues</em>
857 <!-- JAL-2902 -->Groovy Console very slow to open and is
858 not responsive when entering characters (Webstart, Java
865 <td width="60" nowrap>
867 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
868 <em>2/10/2017</em></strong>
871 <td><div align="left">
872 <em>New features in Jalview Desktop</em>
875 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
877 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
881 <td><div align="left">
885 <td width="60" nowrap>
887 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
888 <em>7/9/2017</em></strong>
891 <td><div align="left">
895 <!-- JAL-2588 -->Show gaps in overview window by colouring
896 in grey (sequences used to be coloured grey, and gaps were
900 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
904 <!-- JAL-2587 -->Overview updates immediately on increase
905 in size and progress bar shown as higher resolution
906 overview is recalculated
911 <td><div align="left">
915 <!-- JAL-2664 -->Overview window redraws every hidden
916 column region row by row
919 <!-- JAL-2681 -->duplicate protein sequences shown after
920 retrieving Ensembl crossrefs for sequences from Uniprot
923 <!-- JAL-2603 -->Overview window throws NPE if show boxes
924 format setting is unticked
927 <!-- JAL-2610 -->Groups are coloured wrongly in overview
928 if group has show boxes format setting unticked
931 <!-- JAL-2672,JAL-2665 -->Redraw problems when
932 autoscrolling whilst dragging current selection group to
933 include sequences and columns not currently displayed
936 <!-- JAL-2691 -->Not all chains are mapped when multimeric
937 assemblies are imported via CIF file
940 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
941 displayed when threshold or conservation colouring is also
945 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
949 <!-- JAL-2673 -->Jalview continues to scroll after
950 dragging a selected region off the visible region of the
954 <!-- JAL-2724 -->Cannot apply annotation based
955 colourscheme to all groups in a view
958 <!-- JAL-2511 -->IDs don't line up with sequences
959 initially after font size change using the Font chooser or
966 <td width="60" nowrap>
968 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
971 <td><div align="left">
972 <em>Calculations</em>
976 <!-- JAL-1933 -->Occupancy annotation row shows number of
977 ungapped positions in each column of the alignment.
980 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
981 a calculation dialog box
984 <!-- JAL-2379 -->Revised implementation of PCA for speed
985 and memory efficiency (~30x faster)
988 <!-- JAL-2403 -->Revised implementation of sequence
989 similarity scores as used by Tree, PCA, Shading Consensus
990 and other calculations
993 <!-- JAL-2416 -->Score matrices are stored as resource
994 files within the Jalview codebase
997 <!-- JAL-2500 -->Trees computed on Sequence Feature
998 Similarity may have different topology due to increased
1005 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1006 model for alignments and groups
1009 <!-- JAL-384 -->Custom shading schemes created via groovy
1016 <!-- JAL-2526 -->Efficiency improvements for interacting
1017 with alignment and overview windows
1020 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1024 <!-- JAL-2388 -->Hidden columns and sequences can be
1028 <!-- JAL-2611 -->Click-drag in visible area allows fine
1029 adjustment of visible position
1033 <em>Data import/export</em>
1036 <!-- JAL-2535 -->Posterior probability annotation from
1037 Stockholm files imported as sequence associated annotation
1040 <!-- JAL-2507 -->More robust per-sequence positional
1041 annotation input/output via stockholm flatfile
1044 <!-- JAL-2533 -->Sequence names don't include file
1045 extension when importing structure files without embedded
1046 names or PDB accessions
1049 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1050 format sequence substitution matrices
1053 <em>User Interface</em>
1056 <!-- JAL-2447 --> Experimental Features Checkbox in
1057 Desktop's Tools menu to hide or show untested features in
1061 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1062 via Overview or sequence motif search operations
1065 <!-- JAL-2547 -->Amend sequence features dialog box can be
1066 opened by double clicking gaps within sequence feature
1070 <!-- JAL-1476 -->Status bar message shown when not enough
1071 aligned positions were available to create a 3D structure
1075 <em>3D Structure</em>
1078 <!-- JAL-2430 -->Hidden regions in alignment views are not
1079 coloured in linked structure views
1082 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1083 file-based command exchange
1086 <!-- JAL-2375 -->Structure chooser automatically shows
1087 Cached Structures rather than querying the PDBe if
1088 structures are already available for sequences
1091 <!-- JAL-2520 -->Structures imported via URL are cached in
1092 the Jalview project rather than downloaded again when the
1093 project is reopened.
1096 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1097 to transfer Chimera's structure attributes as Jalview
1098 features, and vice-versa (<strong>Experimental
1102 <em>Web Services</em>
1105 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1108 <!-- JAL-2335 -->Filter non-standard amino acids and
1109 nucleotides when submitting to AACon and other MSA
1113 <!-- JAL-2316, -->URLs for viewing database
1114 cross-references provided by identifiers.org and the
1115 EMBL-EBI's MIRIAM DB
1122 <!-- JAL-2344 -->FileFormatI interface for describing and
1123 identifying file formats (instead of String constants)
1126 <!-- JAL-2228 -->FeatureCounter script refactored for
1127 efficiency when counting all displayed features (not
1128 backwards compatible with 2.10.1)
1131 <em>Example files</em>
1134 <!-- JAL-2631 -->Graduated feature colour style example
1135 included in the example feature file
1138 <em>Documentation</em>
1141 <!-- JAL-2339 -->Release notes reformatted for readability
1142 with the built-in Java help viewer
1145 <!-- JAL-1644 -->Find documentation updated with 'search
1146 sequence description' option
1152 <!-- JAL-2485, -->External service integration tests for
1153 Uniprot REST Free Text Search Client
1156 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1159 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1164 <td><div align="left">
1165 <em>Calculations</em>
1168 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1169 matrix - C->R should be '-3'<br />Old matrix restored
1170 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1172 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1173 Jalview's treatment of gaps in PCA and substitution matrix
1174 based Tree calculations.<br /> <br />In earlier versions
1175 of Jalview, gaps matching gaps were penalised, and gaps
1176 matching non-gaps penalised even more. In the PCA
1177 calculation, gaps were actually treated as non-gaps - so
1178 different costs were applied, which meant Jalview's PCAs
1179 were different to those produced by SeqSpace.<br />Jalview
1180 now treats gaps in the same way as SeqSpace (ie it scores
1181 them as 0). <br /> <br />Enter the following in the
1182 Groovy console to restore pre-2.10.2 behaviour:<br />
1183 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1184 // for 2.10.1 mode <br />
1185 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1186 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1187 these settings will affect all subsequent tree and PCA
1188 calculations (not recommended)</em></li>
1190 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1191 scaling of branch lengths for trees computed using
1192 Sequence Feature Similarity.
1195 <!-- JAL-2377 -->PCA calculation could hang when
1196 generating output report when working with highly
1197 redundant alignments
1200 <!-- JAL-2544 --> Sort by features includes features to
1201 right of selected region when gaps present on right-hand
1205 <em>User Interface</em>
1208 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1209 doesn't reselect a specific sequence's associated
1210 annotation after it was used for colouring a view
1213 <!-- JAL-2419 -->Current selection lost if popup menu
1214 opened on a region of alignment without groups
1217 <!-- JAL-2374 -->Popup menu not always shown for regions
1218 of an alignment with overlapping groups
1221 <!-- JAL-2310 -->Finder double counts if both a sequence's
1222 name and description match
1225 <!-- JAL-2370 -->Hiding column selection containing two
1226 hidden regions results in incorrect hidden regions
1229 <!-- JAL-2386 -->'Apply to all groups' setting when
1230 changing colour does not apply Conservation slider value
1234 <!-- JAL-2373 -->Percentage identity and conservation menu
1235 items do not show a tick or allow shading to be disabled
1238 <!-- JAL-2385 -->Conservation shading or PID threshold
1239 lost when base colourscheme changed if slider not visible
1242 <!-- JAL-2547 -->Sequence features shown in tooltip for
1243 gaps before start of features
1246 <!-- JAL-2623 -->Graduated feature colour threshold not
1247 restored to UI when feature colour is edited
1250 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1251 a time when scrolling vertically in wrapped mode.
1254 <!-- JAL-2630 -->Structure and alignment overview update
1255 as graduate feature colour settings are modified via the
1259 <!-- JAL-2034 -->Overview window doesn't always update
1260 when a group defined on the alignment is resized
1263 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1264 wrapped view result in positional status updates
1268 <!-- JAL-2563 -->Status bar doesn't show position for
1269 ambiguous amino acid and nucleotide symbols
1272 <!-- JAL-2602 -->Copy consensus sequence failed if
1273 alignment included gapped columns
1276 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1277 widgets don't permanently disappear
1280 <!-- JAL-2503 -->Cannot select or filter quantitative
1281 annotation that are shown only as column labels (e.g.
1282 T-Coffee column reliability scores)
1285 <!-- JAL-2594 -->Exception thrown if trying to create a
1286 sequence feature on gaps only
1289 <!-- JAL-2504 -->Features created with 'New feature'
1290 button from a Find inherit previously defined feature type
1291 rather than the Find query string
1294 <!-- JAL-2423 -->incorrect title in output window when
1295 exporting tree calculated in Jalview
1298 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1299 and then revealing them reorders sequences on the
1303 <!-- JAL-964 -->Group panel in sequence feature settings
1304 doesn't update to reflect available set of groups after
1305 interactively adding or modifying features
1308 <!-- JAL-2225 -->Sequence Database chooser unusable on
1312 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1313 only excluded gaps in current sequence and ignored
1320 <!-- JAL-2421 -->Overview window visible region moves
1321 erratically when hidden rows or columns are present
1324 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1325 Structure Viewer's colour menu don't correspond to
1329 <!-- JAL-2405 -->Protein specific colours only offered in
1330 colour and group colour menu for protein alignments
1333 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1334 reflect currently selected view or group's shading
1338 <!-- JAL-2624 -->Feature colour thresholds not respected
1339 when rendered on overview and structures when opacity at
1343 <!-- JAL-2589 -->User defined gap colour not shown in
1344 overview when features overlaid on alignment
1347 <em>Data import/export</em>
1350 <!-- JAL-2576 -->Very large alignments take a long time to
1354 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1355 added after a sequence was imported are not written to
1359 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1360 when importing RNA secondary structure via Stockholm
1363 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1364 not shown in correct direction for simple pseudoknots
1367 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1368 with lightGray or darkGray via features file (but can
1372 <!-- JAL-2383 -->Above PID colour threshold not recovered
1373 when alignment view imported from project
1376 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1377 structure and sequences extracted from structure files
1378 imported via URL and viewed in Jmol
1381 <!-- JAL-2520 -->Structures loaded via URL are saved in
1382 Jalview Projects rather than fetched via URL again when
1383 the project is loaded and the structure viewed
1386 <em>Web Services</em>
1389 <!-- JAL-2519 -->EnsemblGenomes example failing after
1390 release of Ensembl v.88
1393 <!-- JAL-2366 -->Proxy server address and port always
1394 appear enabled in Preferences->Connections
1397 <!-- JAL-2461 -->DAS registry not found exceptions
1398 removed from console output
1401 <!-- JAL-2582 -->Cannot retrieve protein products from
1402 Ensembl by Peptide ID
1405 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1406 created from SIFTs, and spurious 'Couldn't open structure
1407 in Chimera' errors raised after April 2017 update (problem
1408 due to 'null' string rather than empty string used for
1409 residues with no corresponding PDB mapping).
1412 <em>Application UI</em>
1415 <!-- JAL-2361 -->User Defined Colours not added to Colour
1419 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1420 case' residues (button in colourscheme editor debugged and
1421 new documentation and tooltips added)
1424 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1425 doesn't restore group-specific text colour thresholds
1428 <!-- JAL-2243 -->Feature settings panel does not update as
1429 new features are added to alignment
1432 <!-- JAL-2532 -->Cancel in feature settings reverts
1433 changes to feature colours via the Amend features dialog
1436 <!-- JAL-2506 -->Null pointer exception when attempting to
1437 edit graduated feature colour via amend features dialog
1441 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1442 selection menu changes colours of alignment views
1445 <!-- JAL-2426 -->Spurious exceptions in console raised
1446 from alignment calculation workers after alignment has
1450 <!-- JAL-1608 -->Typo in selection popup menu - Create
1451 groups now 'Create Group'
1454 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1455 Create/Undefine group doesn't always work
1458 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1459 shown again after pressing 'Cancel'
1462 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1463 adjusts start position in wrap mode
1466 <!-- JAL-2563 -->Status bar doesn't show positions for
1467 ambiguous amino acids
1470 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1471 CDS/Protein view after CDS sequences added for aligned
1475 <!-- JAL-2592 -->User defined colourschemes called 'User
1476 Defined' don't appear in Colours menu
1482 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1483 score models doesn't always result in an updated PCA plot
1486 <!-- JAL-2442 -->Features not rendered as transparent on
1487 overview or linked structure view
1490 <!-- JAL-2372 -->Colour group by conservation doesn't
1494 <!-- JAL-2517 -->Hitting Cancel after applying
1495 user-defined colourscheme doesn't restore original
1502 <!-- JAL-2314 -->Unit test failure:
1503 jalview.ws.jabaws.RNAStructExportImport setup fails
1506 <!-- JAL-2307 -->Unit test failure:
1507 jalview.ws.sifts.SiftsClientTest due to compatibility
1508 problems with deep array comparison equality asserts in
1509 successive versions of TestNG
1512 <!-- JAL-2479 -->Relocated StructureChooserTest and
1513 ParameterUtilsTest Unit tests to Network suite
1516 <em>New Known Issues</em>
1519 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1520 phase after a sequence motif find operation
1523 <!-- JAL-2550 -->Importing annotation file with rows
1524 containing just upper and lower case letters are
1525 interpreted as WUSS RNA secondary structure symbols
1528 <!-- JAL-2590 -->Cannot load and display Newick trees
1529 reliably from eggnog Ortholog database
1532 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1533 containing features of type Highlight' when 'B' is pressed
1534 to mark columns containing highlighted regions.
1537 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1538 doesn't always add secondary structure annotation.
1543 <td width="60" nowrap>
1544 <div align="center">
1545 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1548 <td><div align="left">
1552 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1553 for all consensus calculations
1556 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1559 <li>Updated Jalview's Certum code signing certificate
1562 <em>Application</em>
1565 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1566 set of database cross-references, sorted alphabetically
1569 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1570 from database cross references. Users with custom links
1571 will receive a <a href="webServices/urllinks.html#warning">warning
1572 dialog</a> asking them to update their preferences.
1575 <!-- JAL-2287-->Cancel button and escape listener on
1576 dialog warning user about disconnecting Jalview from a
1580 <!-- JAL-2320-->Jalview's Chimera control window closes if
1581 the Chimera it is connected to is shut down
1584 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1585 columns menu item to mark columns containing highlighted
1586 regions (e.g. from structure selections or results of a
1590 <!-- JAL-2284-->Command line option for batch-generation
1591 of HTML pages rendering alignment data with the BioJS
1601 <!-- JAL-2286 -->Columns with more than one modal residue
1602 are not coloured or thresholded according to percent
1603 identity (first observed in Jalview 2.8.2)
1606 <!-- JAL-2301 -->Threonine incorrectly reported as not
1610 <!-- JAL-2318 -->Updates to documentation pages (above PID
1611 threshold, amino acid properties)
1614 <!-- JAL-2292 -->Lower case residues in sequences are not
1615 reported as mapped to residues in a structure file in the
1619 <!--JAL-2324 -->Identical features with non-numeric scores
1620 could be added multiple times to a sequence
1623 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1624 bond features shown as two highlighted residues rather
1625 than a range in linked structure views, and treated
1626 correctly when selecting and computing trees from features
1629 <!-- JAL-2281-->Custom URL links for database
1630 cross-references are matched to database name regardless
1635 <em>Application</em>
1638 <!-- JAL-2282-->Custom URL links for specific database
1639 names without regular expressions also offer links from
1643 <!-- JAL-2315-->Removing a single configured link in the
1644 URL links pane in Connections preferences doesn't actually
1645 update Jalview configuration
1648 <!-- JAL-2272-->CTRL-Click on a selected region to open
1649 the alignment area popup menu doesn't work on El-Capitan
1652 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1653 files with similarly named sequences if dropped onto the
1657 <!-- JAL-2312 -->Additional mappings are shown for PDB
1658 entries where more chains exist in the PDB accession than
1659 are reported in the SIFTS file
1662 <!-- JAL-2317-->Certain structures do not get mapped to
1663 the structure view when displayed with Chimera
1666 <!-- JAL-2317-->No chains shown in the Chimera view
1667 panel's View->Show Chains submenu
1670 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1671 work for wrapped alignment views
1674 <!--JAL-2197 -->Rename UI components for running JPred
1675 predictions from 'JNet' to 'JPred'
1678 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1679 corrupted when annotation panel vertical scroll is not at
1680 first annotation row
1683 <!--JAL-2332 -->Attempting to view structure for Hen
1684 lysozyme results in a PDB Client error dialog box
1687 <!-- JAL-2319 -->Structure View's mapping report switched
1688 ranges for PDB and sequence for SIFTS
1691 SIFTS 'Not_Observed' residues mapped to non-existant
1695 <!-- <em>New Known Issues</em>
1702 <td width="60" nowrap>
1703 <div align="center">
1704 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1705 <em>25/10/2016</em></strong>
1708 <td><em>Application</em>
1710 <li>3D Structure chooser opens with 'Cached structures'
1711 view if structures already loaded</li>
1712 <li>Progress bar reports models as they are loaded to
1713 structure views</li>
1719 <li>Colour by conservation always enabled and no tick
1720 shown in menu when BLOSUM or PID shading applied</li>
1721 <li>FER1_ARATH and FER2_ARATH labels were switched in
1722 example sequences/projects/trees</li>
1724 <em>Application</em>
1726 <li>Jalview projects with views of local PDB structure
1727 files saved on Windows cannot be opened on OSX</li>
1728 <li>Multiple structure views can be opened and superposed
1729 without timeout for structures with multiple models or
1730 multiple sequences in alignment</li>
1731 <li>Cannot import or associated local PDB files without a
1732 PDB ID HEADER line</li>
1733 <li>RMSD is not output in Jmol console when superposition
1735 <li>Drag and drop of URL from Browser fails for Linux and
1736 OSX versions earlier than El Capitan</li>
1737 <li>ENA client ignores invalid content from ENA server</li>
1738 <li>Exceptions are not raised in console when ENA client
1739 attempts to fetch non-existent IDs via Fetch DB Refs UI
1741 <li>Exceptions are not raised in console when a new view
1742 is created on the alignment</li>
1743 <li>OSX right-click fixed for group selections: CMD-click
1744 to insert/remove gaps in groups and CTRL-click to open group
1747 <em>Build and deployment</em>
1749 <li>URL link checker now copes with multi-line anchor
1752 <em>New Known Issues</em>
1754 <li>Drag and drop from URL links in browsers do not work
1761 <td width="60" nowrap>
1762 <div align="center">
1763 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1766 <td><em>General</em>
1769 <!-- JAL-2124 -->Updated Spanish translations.
1772 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1773 for importing structure data to Jalview. Enables mmCIF and
1777 <!-- JAL-192 --->Alignment ruler shows positions relative to
1781 <!-- JAL-2202 -->Position/residue shown in status bar when
1782 mousing over sequence associated annotation
1785 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1789 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1790 '()', canonical '[]' and invalid '{}' base pair populations
1794 <!-- JAL-2092 -->Feature settings popup menu options for
1795 showing or hiding columns containing a feature
1798 <!-- JAL-1557 -->Edit selected group by double clicking on
1799 group and sequence associated annotation labels
1802 <!-- JAL-2236 -->Sequence name added to annotation label in
1803 select/hide columns by annotation and colour by annotation
1807 </ul> <em>Application</em>
1810 <!-- JAL-2050-->Automatically hide introns when opening a
1811 gene/transcript view
1814 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1818 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1819 structure mappings with the EMBL-EBI PDBe SIFTS database
1822 <!-- JAL-2079 -->Updated download sites used for Rfam and
1823 Pfam sources to xfam.org
1826 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1829 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1830 over sequences in Jalview
1833 <!-- JAL-2027-->Support for reverse-complement coding
1834 regions in ENA and EMBL
1837 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1838 for record retrieval via ENA rest API
1841 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1845 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1846 groovy script execution
1849 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1850 alignment window's Calculate menu
1853 <!-- JAL-1812 -->Allow groovy scripts that call
1854 Jalview.getAlignFrames() to run in headless mode
1857 <!-- JAL-2068 -->Support for creating new alignment
1858 calculation workers from groovy scripts
1861 <!-- JAL-1369 --->Store/restore reference sequence in
1865 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1866 associations are now saved/restored from project
1869 <!-- JAL-1993 -->Database selection dialog always shown
1870 before sequence fetcher is opened
1873 <!-- JAL-2183 -->Double click on an entry in Jalview's
1874 database chooser opens a sequence fetcher
1877 <!-- JAL-1563 -->Free-text search client for UniProt using
1878 the UniProt REST API
1881 <!-- JAL-2168 -->-nonews command line parameter to prevent
1882 the news reader opening
1885 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1886 querying stored in preferences
1889 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1893 <!-- JAL-1977-->Tooltips shown on database chooser
1896 <!-- JAL-391 -->Reverse complement function in calculate
1897 menu for nucleotide sequences
1900 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1901 and feature counts preserves alignment ordering (and
1902 debugged for complex feature sets).
1905 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1906 viewing structures with Jalview 2.10
1909 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1910 genome, transcript CCDS and gene ids via the Ensembl and
1911 Ensembl Genomes REST API
1914 <!-- JAL-2049 -->Protein sequence variant annotation
1915 computed for 'sequence_variant' annotation on CDS regions
1919 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1923 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1924 Ref Fetcher fails to match, or otherwise updates sequence
1925 data from external database records.
1928 <!-- JAL-2154 -->Revised Jalview Project format for
1929 efficient recovery of sequence coding and alignment
1930 annotation relationships.
1932 </ul> <!-- <em>Applet</em>
1943 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1947 <!-- JAL-2018-->Export features in Jalview format (again)
1948 includes graduated colourschemes
1951 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1952 working with big alignments and lots of hidden columns
1955 <!-- JAL-2053-->Hidden column markers not always rendered
1956 at right of alignment window
1959 <!-- JAL-2067 -->Tidied up links in help file table of
1963 <!-- JAL-2072 -->Feature based tree calculation not shown
1967 <!-- JAL-2075 -->Hidden columns ignored during feature
1968 based tree calculation
1971 <!-- JAL-2065 -->Alignment view stops updating when show
1972 unconserved enabled for group on alignment
1975 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1979 <!-- JAL-2146 -->Alignment column in status incorrectly
1980 shown as "Sequence position" when mousing over
1984 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1985 hidden columns present
1988 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1989 user created annotation added to alignment
1992 <!-- JAL-1841 -->RNA Structure consensus only computed for
1993 '()' base pair annotation
1996 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1997 in zero scores for all base pairs in RNA Structure
2001 <!-- JAL-2174-->Extend selection with columns containing
2005 <!-- JAL-2275 -->Pfam format writer puts extra space at
2006 beginning of sequence
2009 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2013 <!-- JAL-2238 -->Cannot create groups on an alignment from
2014 from a tree when t-coffee scores are shown
2017 <!-- JAL-1836,1967 -->Cannot import and view PDB
2018 structures with chains containing negative resnums (4q4h)
2021 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2025 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2026 to Clustal, PIR and PileUp output
2029 <!-- JAL-2008 -->Reordering sequence features that are
2030 not visible causes alignment window to repaint
2033 <!-- JAL-2006 -->Threshold sliders don't work in
2034 graduated colour and colour by annotation row for e-value
2035 scores associated with features and annotation rows
2038 <!-- JAL-1797 -->amino acid physicochemical conservation
2039 calculation should be case independent
2042 <!-- JAL-2173 -->Remove annotation also updates hidden
2046 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2047 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2048 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2051 <!-- JAL-2065 -->Null pointer exceptions and redraw
2052 problems when reference sequence defined and 'show
2053 non-conserved' enabled
2056 <!-- JAL-1306 -->Quality and Conservation are now shown on
2057 load even when Consensus calculation is disabled
2060 <!-- JAL-1932 -->Remove right on penultimate column of
2061 alignment does nothing
2064 <em>Application</em>
2067 <!-- JAL-1552-->URLs and links can't be imported by
2068 drag'n'drop on OSX when launched via webstart (note - not
2069 yet fixed for El Capitan)
2072 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2073 output when running on non-gb/us i18n platforms
2076 <!-- JAL-1944 -->Error thrown when exporting a view with
2077 hidden sequences as flat-file alignment
2080 <!-- JAL-2030-->InstallAnywhere distribution fails when
2084 <!-- JAL-2080-->Jalview very slow to launch via webstart
2085 (also hotfix for 2.9.0b2)
2088 <!-- JAL-2085 -->Cannot save project when view has a
2089 reference sequence defined
2092 <!-- JAL-1011 -->Columns are suddenly selected in other
2093 alignments and views when revealing hidden columns
2096 <!-- JAL-1989 -->Hide columns not mirrored in complement
2097 view in a cDNA/Protein splitframe
2100 <!-- JAL-1369 -->Cannot save/restore representative
2101 sequence from project when only one sequence is
2105 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2106 in Structure Chooser
2109 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2110 structure consensus didn't refresh annotation panel
2113 <!-- JAL-1962 -->View mapping in structure view shows
2114 mappings between sequence and all chains in a PDB file
2117 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2118 dialogs format columns correctly, don't display array
2119 data, sort columns according to type
2122 <!-- JAL-1975 -->Export complete shown after destination
2123 file chooser is cancelled during an image export
2126 <!-- JAL-2025 -->Error when querying PDB Service with
2127 sequence name containing special characters
2130 <!-- JAL-2024 -->Manual PDB structure querying should be
2134 <!-- JAL-2104 -->Large tooltips with broken HTML
2135 formatting don't wrap
2138 <!-- JAL-1128 -->Figures exported from wrapped view are
2139 truncated so L looks like I in consensus annotation
2142 <!-- JAL-2003 -->Export features should only export the
2143 currently displayed features for the current selection or
2147 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2148 after fetching cross-references, and restoring from
2152 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2153 followed in the structure viewer
2156 <!-- JAL-2163 -->Titles for individual alignments in
2157 splitframe not restored from project
2160 <!-- JAL-2145 -->missing autocalculated annotation at
2161 trailing end of protein alignment in transcript/product
2162 splitview when pad-gaps not enabled by default
2165 <!-- JAL-1797 -->amino acid physicochemical conservation
2169 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2170 article has been read (reopened issue due to
2171 internationalisation problems)
2174 <!-- JAL-1960 -->Only offer PDB structures in structure
2175 viewer based on sequence name, PDB and UniProt
2180 <!-- JAL-1976 -->No progress bar shown during export of
2184 <!-- JAL-2213 -->Structures not always superimposed after
2185 multiple structures are shown for one or more sequences.
2188 <!-- JAL-1370 -->Reference sequence characters should not
2189 be replaced with '.' when 'Show unconserved' format option
2193 <!-- JAL-1823 -->Cannot specify chain code when entering
2194 specific PDB id for sequence
2197 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2198 'Export hidden sequences' is enabled, but 'export hidden
2199 columns' is disabled.
2202 <!--JAL-2026-->Best Quality option in structure chooser
2203 selects lowest rather than highest resolution structures
2207 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2208 to sequence mapping in 'View Mappings' report
2211 <!-- JAL-2284 -->Unable to read old Jalview projects that
2212 contain non-XML data added after Jalvew wrote project.
2215 <!-- JAL-2118 -->Newly created annotation row reorders
2216 after clicking on it to create new annotation for a
2220 <!-- JAL-1980 -->Null Pointer Exception raised when
2221 pressing Add on an orphaned cut'n'paste window.
2223 <!-- may exclude, this is an external service stability issue JAL-1941
2224 -- > RNA 3D structure not added via DSSR service</li> -->
2229 <!-- JAL-2151 -->Incorrect columns are selected when
2230 hidden columns present before start of sequence
2233 <!-- JAL-1986 -->Missing dependencies on applet pages
2237 <!-- JAL-1947 -->Overview pixel size changes when
2238 sequences are hidden in applet
2241 <!-- JAL-1996 -->Updated instructions for applet
2242 deployment on examples pages.
2249 <td width="60" nowrap>
2250 <div align="center">
2251 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2252 <em>16/10/2015</em></strong>
2255 <td><em>General</em>
2257 <li>Time stamps for signed Jalview application and applet
2262 <em>Application</em>
2264 <li>Duplicate group consensus and conservation rows
2265 shown when tree is partitioned</li>
2266 <li>Erratic behaviour when tree partitions made with
2267 multiple cDNA/Protein split views</li>
2273 <td width="60" nowrap>
2274 <div align="center">
2275 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2276 <em>8/10/2015</em></strong>
2279 <td><em>General</em>
2281 <li>Updated Spanish translations of localized text for
2283 </ul> <em>Application</em>
2285 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2286 <li>Signed OSX InstallAnywhere installer<br></li>
2287 <li>Support for per-sequence based annotations in BioJSON</li>
2288 </ul> <em>Applet</em>
2290 <li>Split frame example added to applet examples page</li>
2291 </ul> <em>Build and Deployment</em>
2294 <!-- JAL-1888 -->New ant target for running Jalview's test
2302 <li>Mapping of cDNA to protein in split frames
2303 incorrect when sequence start > 1</li>
2304 <li>Broken images in filter column by annotation dialog
2306 <li>Feature colours not parsed from features file</li>
2307 <li>Exceptions and incomplete link URLs recovered when
2308 loading a features file containing HTML tags in feature
2312 <em>Application</em>
2314 <li>Annotations corrupted after BioJS export and
2316 <li>Incorrect sequence limits after Fetch DB References
2317 with 'trim retrieved sequences'</li>
2318 <li>Incorrect warning about deleting all data when
2319 deleting selected columns</li>
2320 <li>Patch to build system for shipping properly signed
2321 JNLP templates for webstart launch</li>
2322 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2323 unreleased structures for download or viewing</li>
2324 <li>Tab/space/return keystroke operation of EMBL-PDBe
2325 fetcher/viewer dialogs works correctly</li>
2326 <li>Disabled 'minimise' button on Jalview windows
2327 running on OSX to workaround redraw hang bug</li>
2328 <li>Split cDNA/Protein view position and geometry not
2329 recovered from jalview project</li>
2330 <li>Initial enabled/disabled state of annotation menu
2331 sorter 'show autocalculated first/last' corresponds to
2333 <li>Restoring of Clustal, RNA Helices and T-Coffee
2334 color schemes from BioJSON</li>
2338 <li>Reorder sequences mirrored in cDNA/Protein split
2340 <li>Applet with Jmol examples not loading correctly</li>
2346 <td><div align="center">
2347 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2349 <td><em>General</em>
2351 <li>Linked visualisation and analysis of DNA and Protein
2354 <li>Translated cDNA alignments shown as split protein
2355 and DNA alignment views</li>
2356 <li>Codon consensus annotation for linked protein and
2357 cDNA alignment views</li>
2358 <li>Link cDNA or Protein product sequences by loading
2359 them onto Protein or cDNA alignments</li>
2360 <li>Reconstruct linked cDNA alignment from aligned
2361 protein sequences</li>
2364 <li>Jmol integration updated to Jmol v14.2.14</li>
2365 <li>Import and export of Jalview alignment views as <a
2366 href="features/bioJsonFormat.html">BioJSON</a></li>
2367 <li>New alignment annotation file statements for
2368 reference sequences and marking hidden columns</li>
2369 <li>Reference sequence based alignment shading to
2370 highlight variation</li>
2371 <li>Select or hide columns according to alignment
2373 <li>Find option for locating sequences by description</li>
2374 <li>Conserved physicochemical properties shown in amino
2375 acid conservation row</li>
2376 <li>Alignments can be sorted by number of RNA helices</li>
2377 </ul> <em>Application</em>
2379 <li>New cDNA/Protein analysis capabilities
2381 <li>Get Cross-References should open a Split Frame
2382 view with cDNA/Protein</li>
2383 <li>Detect when nucleotide sequences and protein
2384 sequences are placed in the same alignment</li>
2385 <li>Split cDNA/Protein views are saved in Jalview
2390 <li>Use REST API to talk to Chimera</li>
2391 <li>Selected regions in Chimera are highlighted in linked
2392 Jalview windows</li>
2394 <li>VARNA RNA viewer updated to v3.93</li>
2395 <li>VARNA views are saved in Jalview Projects</li>
2396 <li>Pseudoknots displayed as Jalview RNA annotation can
2397 be shown in VARNA</li>
2399 <li>Make groups for selection uses marked columns as well
2400 as the active selected region</li>
2402 <li>Calculate UPGMA and NJ trees using sequence feature
2404 <li>New Export options
2406 <li>New Export Settings dialog to control hidden
2407 region export in flat file generation</li>
2409 <li>Export alignment views for display with the <a
2410 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2412 <li>Export scrollable SVG in HTML page</li>
2413 <li>Optional embedding of BioJSON data when exporting
2414 alignment figures to HTML</li>
2416 <li>3D structure retrieval and display
2418 <li>Free text and structured queries with the PDBe
2420 <li>PDBe Search API based discovery and selection of
2421 PDB structures for a sequence set</li>
2425 <li>JPred4 employed for protein secondary structure
2427 <li>Hide Insertions menu option to hide unaligned columns
2428 for one or a group of sequences</li>
2429 <li>Automatically hide insertions in alignments imported
2430 from the JPred4 web server</li>
2431 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2432 system on OSX<br />LGPL libraries courtesy of <a
2433 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2435 <li>changed 'View nucleotide structure' submenu to 'View
2436 VARNA 2D Structure'</li>
2437 <li>change "View protein structure" menu option to "3D
2440 </ul> <em>Applet</em>
2442 <li>New layout for applet example pages</li>
2443 <li>New parameters to enable SplitFrame view
2444 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2445 <li>New example demonstrating linked viewing of cDNA and
2446 Protein alignments</li>
2447 </ul> <em>Development and deployment</em>
2449 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2450 <li>Include installation type and git revision in build
2451 properties and console log output</li>
2452 <li>Jalview Github organisation, and new github site for
2453 storing BioJsMSA Templates</li>
2454 <li>Jalview's unit tests now managed with TestNG</li>
2457 <!-- <em>General</em>
2459 </ul> --> <!-- issues resolved --> <em>Application</em>
2461 <li>Escape should close any open find dialogs</li>
2462 <li>Typo in select-by-features status report</li>
2463 <li>Consensus RNA secondary secondary structure
2464 predictions are not highlighted in amber</li>
2465 <li>Missing gap character in v2.7 example file means
2466 alignment appears unaligned when pad-gaps is not enabled</li>
2467 <li>First switch to RNA Helices colouring doesn't colour
2468 associated structure views</li>
2469 <li>ID width preference option is greyed out when auto
2470 width checkbox not enabled</li>
2471 <li>Stopped a warning dialog from being shown when
2472 creating user defined colours</li>
2473 <li>'View Mapping' in structure viewer shows sequence
2474 mappings for just that viewer's sequences</li>
2475 <li>Workaround for superposing PDB files containing
2476 multiple models in Chimera</li>
2477 <li>Report sequence position in status bar when hovering
2478 over Jmol structure</li>
2479 <li>Cannot output gaps as '.' symbols with Selection ->
2480 output to text box</li>
2481 <li>Flat file exports of alignments with hidden columns
2482 have incorrect sequence start/end</li>
2483 <li>'Aligning' a second chain to a Chimera structure from
2485 <li>Colour schemes applied to structure viewers don't
2486 work for nucleotide</li>
2487 <li>Loading/cut'n'pasting an empty or invalid file leads
2488 to a grey/invisible alignment window</li>
2489 <li>Exported Jpred annotation from a sequence region
2490 imports to different position</li>
2491 <li>Space at beginning of sequence feature tooltips shown
2492 on some platforms</li>
2493 <li>Chimera viewer 'View | Show Chain' menu is not
2495 <li>'New View' fails with a Null Pointer Exception in
2496 console if Chimera has been opened</li>
2497 <li>Mouseover to Chimera not working</li>
2498 <li>Miscellaneous ENA XML feature qualifiers not
2500 <li>NPE in annotation renderer after 'Extract Scores'</li>
2501 <li>If two structures in one Chimera window, mouseover of
2502 either sequence shows on first structure</li>
2503 <li>'Show annotations' options should not make
2504 non-positional annotations visible</li>
2505 <li>Subsequence secondary structure annotation not shown
2506 in right place after 'view flanking regions'</li>
2507 <li>File Save As type unset when current file format is
2509 <li>Save as '.jar' option removed for saving Jalview
2511 <li>Colour by Sequence colouring in Chimera more
2513 <li>Cannot 'add reference annotation' for a sequence in
2514 several views on same alignment</li>
2515 <li>Cannot show linked products for EMBL / ENA records</li>
2516 <li>Jalview's tooltip wraps long texts containing no
2518 </ul> <em>Applet</em>
2520 <li>Jmol to JalviewLite mouseover/link not working</li>
2521 <li>JalviewLite can't import sequences with ID
2522 descriptions containing angle brackets</li>
2523 </ul> <em>General</em>
2525 <li>Cannot export and reimport RNA secondary structure
2526 via jalview annotation file</li>
2527 <li>Random helix colour palette for colour by annotation
2528 with RNA secondary structure</li>
2529 <li>Mouseover to cDNA from STOP residue in protein
2530 translation doesn't work.</li>
2531 <li>hints when using the select by annotation dialog box</li>
2532 <li>Jmol alignment incorrect if PDB file has alternate CA
2534 <li>FontChooser message dialog appears to hang after
2535 choosing 1pt font</li>
2536 <li>Peptide secondary structure incorrectly imported from
2537 annotation file when annotation display text includes 'e' or
2539 <li>Cannot set colour of new feature type whilst creating
2541 <li>cDNA translation alignment should not be sequence
2542 order dependent</li>
2543 <li>'Show unconserved' doesn't work for lower case
2545 <li>Nucleotide ambiguity codes involving R not recognised</li>
2546 </ul> <em>Deployment and Documentation</em>
2548 <li>Applet example pages appear different to the rest of
2549 www.jalview.org</li>
2550 </ul> <em>Application Known issues</em>
2552 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2553 <li>Misleading message appears after trying to delete
2555 <li>Jalview icon not shown in dock after InstallAnywhere
2556 version launches</li>
2557 <li>Fetching EMBL reference for an RNA sequence results
2558 fails with a sequence mismatch</li>
2559 <li>Corrupted or unreadable alignment display when
2560 scrolling alignment to right</li>
2561 <li>ArrayIndexOutOfBoundsException thrown when remove
2562 empty columns called on alignment with ragged gapped ends</li>
2563 <li>auto calculated alignment annotation rows do not get
2564 placed above or below non-autocalculated rows</li>
2565 <li>Jalview dekstop becomes sluggish at full screen in
2566 ultra-high resolution</li>
2567 <li>Cannot disable consensus calculation independently of
2568 quality and conservation</li>
2569 <li>Mouseover highlighting between cDNA and protein can
2570 become sluggish with more than one splitframe shown</li>
2571 </ul> <em>Applet Known Issues</em>
2573 <li>Core PDB parsing code requires Jmol</li>
2574 <li>Sequence canvas panel goes white when alignment
2575 window is being resized</li>
2581 <td><div align="center">
2582 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2584 <td><em>General</em>
2586 <li>Updated Java code signing certificate donated by
2588 <li>Features and annotation preserved when performing
2589 pairwise alignment</li>
2590 <li>RNA pseudoknot annotation can be
2591 imported/exported/displayed</li>
2592 <li>'colour by annotation' can colour by RNA and
2593 protein secondary structure</li>
2594 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2595 post-hoc with 2.9 release</em>)
2598 </ul> <em>Application</em>
2600 <li>Extract and display secondary structure for sequences
2601 with 3D structures</li>
2602 <li>Support for parsing RNAML</li>
2603 <li>Annotations menu for layout
2605 <li>sort sequence annotation rows by alignment</li>
2606 <li>place sequence annotation above/below alignment
2609 <li>Output in Stockholm format</li>
2610 <li>Internationalisation: improved Spanish (es)
2612 <li>Structure viewer preferences tab</li>
2613 <li>Disorder and Secondary Structure annotation tracks
2614 shared between alignments</li>
2615 <li>UCSF Chimera launch and linked highlighting from
2617 <li>Show/hide all sequence associated annotation rows for
2618 all or current selection</li>
2619 <li>disorder and secondary structure predictions
2620 available as dataset annotation</li>
2621 <li>Per-sequence rna helices colouring</li>
2624 <li>Sequence database accessions imported when fetching
2625 alignments from Rfam</li>
2626 <li>update VARNA version to 3.91</li>
2628 <li>New groovy scripts for exporting aligned positions,
2629 conservation values, and calculating sum of pairs scores.</li>
2630 <li>Command line argument to set default JABAWS server</li>
2631 <li>include installation type in build properties and
2632 console log output</li>
2633 <li>Updated Jalview project format to preserve dataset
2637 <!-- issues resolved --> <em>Application</em>
2639 <li>Distinguish alignment and sequence associated RNA
2640 structure in structure->view->VARNA</li>
2641 <li>Raise dialog box if user deletes all sequences in an
2643 <li>Pressing F1 results in documentation opening twice</li>
2644 <li>Sequence feature tooltip is wrapped</li>
2645 <li>Double click on sequence associated annotation
2646 selects only first column</li>
2647 <li>Redundancy removal doesn't result in unlinked
2648 leaves shown in tree</li>
2649 <li>Undos after several redundancy removals don't undo
2651 <li>Hide sequence doesn't hide associated annotation</li>
2652 <li>User defined colours dialog box too big to fit on
2653 screen and buttons not visible</li>
2654 <li>author list isn't updated if already written to
2655 Jalview properties</li>
2656 <li>Popup menu won't open after retrieving sequence
2658 <li>File open window for associate PDB doesn't open</li>
2659 <li>Left-then-right click on a sequence id opens a
2660 browser search window</li>
2661 <li>Cannot open sequence feature shading/sort popup menu
2662 in feature settings dialog</li>
2663 <li>better tooltip placement for some areas of Jalview
2665 <li>Allow addition of JABAWS Server which doesn't
2666 pass validation</li>
2667 <li>Web services parameters dialog box is too large to
2669 <li>Muscle nucleotide alignment preset obscured by
2671 <li>JABAWS preset submenus don't contain newly
2672 defined user preset</li>
2673 <li>MSA web services warns user if they were launched
2674 with invalid input</li>
2675 <li>Jalview cannot contact DAS Registy when running on
2678 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2679 'Superpose with' submenu not shown when new view
2683 </ul> <!-- <em>Applet</em>
2685 </ul> <em>General</em>
2687 </ul>--> <em>Deployment and Documentation</em>
2689 <li>2G and 1G options in launchApp have no effect on
2690 memory allocation</li>
2691 <li>launchApp service doesn't automatically open
2692 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2694 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2695 InstallAnywhere reports cannot find valid JVM when Java
2696 1.7_055 is available
2698 </ul> <em>Application Known issues</em>
2701 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2702 corrupted or unreadable alignment display when scrolling
2706 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2707 retrieval fails but progress bar continues for DAS retrieval
2708 with large number of ID
2711 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2712 flatfile output of visible region has incorrect sequence
2716 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2717 rna structure consensus doesn't update when secondary
2718 structure tracks are rearranged
2721 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2722 invalid rna structure positional highlighting does not
2723 highlight position of invalid base pairs
2726 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2727 out of memory errors are not raised when saving Jalview
2728 project from alignment window file menu
2731 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2732 Switching to RNA Helices colouring doesn't propagate to
2736 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2737 colour by RNA Helices not enabled when user created
2738 annotation added to alignment
2741 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2742 Jalview icon not shown on dock in Mountain Lion/Webstart
2744 </ul> <em>Applet Known Issues</em>
2747 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2748 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2751 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2752 Jalview and Jmol example not compatible with IE9
2755 <li>Sort by annotation score doesn't reverse order
2761 <td><div align="center">
2762 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2765 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2768 <li>Internationalisation of user interface (usually
2769 called i18n support) and translation for Spanish locale</li>
2770 <li>Define/Undefine group on current selection with
2771 Ctrl-G/Shift Ctrl-G</li>
2772 <li>Improved group creation/removal options in
2773 alignment/sequence Popup menu</li>
2774 <li>Sensible precision for symbol distribution
2775 percentages shown in logo tooltip.</li>
2776 <li>Annotation panel height set according to amount of
2777 annotation when alignment first opened</li>
2778 </ul> <em>Application</em>
2780 <li>Interactive consensus RNA secondary structure
2781 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2782 <li>Select columns containing particular features from
2783 Feature Settings dialog</li>
2784 <li>View all 'representative' PDB structures for selected
2786 <li>Update Jalview project format:
2788 <li>New file extension for Jalview projects '.jvp'</li>
2789 <li>Preserve sequence and annotation dataset (to
2790 store secondary structure annotation,etc)</li>
2791 <li>Per group and alignment annotation and RNA helix
2795 <li>New similarity measures for PCA and Tree calculation
2797 <li>Experimental support for retrieval and viewing of
2798 flanking regions for an alignment</li>
2802 <!-- issues resolved --> <em>Application</em>
2804 <li>logo keeps spinning and status remains at queued or
2805 running after job is cancelled</li>
2806 <li>cannot export features from alignments imported from
2807 Jalview/VAMSAS projects</li>
2808 <li>Buggy slider for web service parameters that take
2810 <li>Newly created RNA secondary structure line doesn't
2811 have 'display all symbols' flag set</li>
2812 <li>T-COFFEE alignment score shading scheme and other
2813 annotation shading not saved in Jalview project</li>
2814 <li>Local file cannot be loaded in freshly downloaded
2816 <li>Jalview icon not shown on dock in Mountain
2818 <li>Load file from desktop file browser fails</li>
2819 <li>Occasional NPE thrown when calculating large trees</li>
2820 <li>Cannot reorder or slide sequences after dragging an
2821 alignment onto desktop</li>
2822 <li>Colour by annotation dialog throws NPE after using
2823 'extract scores' function</li>
2824 <li>Loading/cut'n'pasting an empty file leads to a grey
2825 alignment window</li>
2826 <li>Disorder thresholds rendered incorrectly after
2827 performing IUPred disorder prediction</li>
2828 <li>Multiple group annotated consensus rows shown when
2829 changing 'normalise logo' display setting</li>
2830 <li>Find shows blank dialog after 'finished searching' if
2831 nothing matches query</li>
2832 <li>Null Pointer Exceptions raised when sorting by
2833 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2835 <li>Errors in Jmol console when structures in alignment
2836 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2838 <li>Not all working JABAWS services are shown in
2840 <li>JAVAWS version of Jalview fails to launch with
2841 'invalid literal/length code'</li>
2842 <li>Annotation/RNA Helix colourschemes cannot be applied
2843 to alignment with groups (actually fixed in 2.8.0b1)</li>
2844 <li>RNA Helices and T-Coffee Scores available as default
2847 </ul> <em>Applet</em>
2849 <li>Remove group option is shown even when selection is
2851 <li>Apply to all groups ticked but colourscheme changes
2852 don't affect groups</li>
2853 <li>Documented RNA Helices and T-Coffee Scores as valid
2854 colourscheme name</li>
2855 <li>Annotation labels drawn on sequence IDs when
2856 Annotation panel is not displayed</li>
2857 <li>Increased font size for dropdown menus on OSX and
2858 embedded windows</li>
2859 </ul> <em>Other</em>
2861 <li>Consensus sequence for alignments/groups with a
2862 single sequence were not calculated</li>
2863 <li>annotation files that contain only groups imported as
2864 annotation and junk sequences</li>
2865 <li>Fasta files with sequences containing '*' incorrectly
2866 recognised as PFAM or BLC</li>
2867 <li>conservation/PID slider apply all groups option
2868 doesn't affect background (2.8.0b1)
2870 <li>redundancy highlighting is erratic at 0% and 100%</li>
2871 <li>Remove gapped columns fails for sequences with ragged
2873 <li>AMSA annotation row with leading spaces is not
2874 registered correctly on import</li>
2875 <li>Jalview crashes when selecting PCA analysis for
2876 certain alignments</li>
2877 <li>Opening the colour by annotation dialog for an
2878 existing annotation based 'use original colours'
2879 colourscheme loses original colours setting</li>
2884 <td><div align="center">
2885 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2886 <em>30/1/2014</em></strong>
2890 <li>Trusted certificates for JalviewLite applet and
2891 Jalview Desktop application<br />Certificate was donated by
2892 <a href="https://www.certum.eu">Certum</a> to the Jalview
2893 open source project).
2895 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2896 <li>Output in Stockholm format</li>
2897 <li>Allow import of data from gzipped files</li>
2898 <li>Export/import group and sequence associated line
2899 graph thresholds</li>
2900 <li>Nucleotide substitution matrix that supports RNA and
2901 ambiguity codes</li>
2902 <li>Allow disorder predictions to be made on the current
2903 selection (or visible selection) in the same way that JPred
2905 <li>Groovy scripting for headless Jalview operation</li>
2906 </ul> <em>Other improvements</em>
2908 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2909 <li>COMBINE statement uses current SEQUENCE_REF and
2910 GROUP_REF scope to group annotation rows</li>
2911 <li>Support '' style escaping of quotes in Newick
2913 <li>Group options for JABAWS service by command line name</li>
2914 <li>Empty tooltip shown for JABA service options with a
2915 link but no description</li>
2916 <li>Select primary source when selecting authority in
2917 database fetcher GUI</li>
2918 <li>Add .mfa to FASTA file extensions recognised by
2920 <li>Annotation label tooltip text wrap</li>
2925 <li>Slow scrolling when lots of annotation rows are
2927 <li>Lots of NPE (and slowness) after creating RNA
2928 secondary structure annotation line</li>
2929 <li>Sequence database accessions not imported when
2930 fetching alignments from Rfam</li>
2931 <li>Incorrect SHMR submission for sequences with
2933 <li>View all structures does not always superpose
2935 <li>Option widgets in service parameters not updated to
2936 reflect user or preset settings</li>
2937 <li>Null pointer exceptions for some services without
2938 presets or adjustable parameters</li>
2939 <li>Discover PDB IDs entry in structure menu doesn't
2940 discover PDB xRefs</li>
2941 <li>Exception encountered while trying to retrieve
2942 features with DAS</li>
2943 <li>Lowest value in annotation row isn't coloured
2944 when colour by annotation (per sequence) is coloured</li>
2945 <li>Keyboard mode P jumps to start of gapped region when
2946 residue follows a gap</li>
2947 <li>Jalview appears to hang importing an alignment with
2948 Wrap as default or after enabling Wrap</li>
2949 <li>'Right click to add annotations' message
2950 shown in wrap mode when no annotations present</li>
2951 <li>Disorder predictions fail with NPE if no automatic
2952 annotation already exists on alignment</li>
2953 <li>oninit javascript function should be called after
2954 initialisation completes</li>
2955 <li>Remove redundancy after disorder prediction corrupts
2956 alignment window display</li>
2957 <li>Example annotation file in documentation is invalid</li>
2958 <li>Grouped line graph annotation rows are not exported
2959 to annotation file</li>
2960 <li>Multi-harmony analysis cannot be run when only two
2962 <li>Cannot create multiple groups of line graphs with
2963 several 'combine' statements in annotation file</li>
2964 <li>Pressing return several times causes Number Format
2965 exceptions in keyboard mode</li>
2966 <li>Multi-harmony (SHMMR) method doesn't submit
2967 correct partitions for input data</li>
2968 <li>Translation from DNA to Amino Acids fails</li>
2969 <li>Jalview fail to load newick tree with quoted label</li>
2970 <li>--headless flag isn't understood</li>
2971 <li>ClassCastException when generating EPS in headless
2973 <li>Adjusting sequence-associated shading threshold only
2974 changes one row's threshold</li>
2975 <li>Preferences and Feature settings panel panel
2976 doesn't open</li>
2977 <li>hide consensus histogram also hides conservation and
2978 quality histograms</li>
2983 <td><div align="center">
2984 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2986 <td><em>Application</em>
2988 <li>Support for JABAWS 2.0 Services (AACon alignment
2989 conservation, protein disorder and Clustal Omega)</li>
2990 <li>JABAWS server status indicator in Web Services
2992 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2993 in Jalview alignment window</li>
2994 <li>Updated Jalview build and deploy framework for OSX
2995 mountain lion, windows 7, and 8</li>
2996 <li>Nucleotide substitution matrix for PCA that supports
2997 RNA and ambiguity codes</li>
2999 <li>Improved sequence database retrieval GUI</li>
3000 <li>Support fetching and database reference look up
3001 against multiple DAS sources (Fetch all from in 'fetch db
3003 <li>Jalview project improvements
3005 <li>Store and retrieve the 'belowAlignment'
3006 flag for annotation</li>
3007 <li>calcId attribute to group annotation rows on the
3009 <li>Store AACon calculation settings for a view in
3010 Jalview project</li>
3014 <li>horizontal scrolling gesture support</li>
3015 <li>Visual progress indicator when PCA calculation is
3017 <li>Simpler JABA web services menus</li>
3018 <li>visual indication that web service results are still
3019 being retrieved from server</li>
3020 <li>Serialise the dialogs that are shown when Jalview
3021 starts up for first time</li>
3022 <li>Jalview user agent string for interacting with HTTP
3024 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3026 <li>Examples directory and Groovy library included in
3027 InstallAnywhere distribution</li>
3028 </ul> <em>Applet</em>
3030 <li>RNA alignment and secondary structure annotation
3031 visualization applet example</li>
3032 </ul> <em>General</em>
3034 <li>Normalise option for consensus sequence logo</li>
3035 <li>Reset button in PCA window to return dimensions to
3037 <li>Allow seqspace or Jalview variant of alignment PCA
3039 <li>PCA with either nucleic acid and protein substitution
3041 <li>Allow windows containing HTML reports to be exported
3043 <li>Interactive display and editing of RNA secondary
3044 structure contacts</li>
3045 <li>RNA Helix Alignment Colouring</li>
3046 <li>RNA base pair logo consensus</li>
3047 <li>Parse sequence associated secondary structure
3048 information in Stockholm files</li>
3049 <li>HTML Export database accessions and annotation
3050 information presented in tooltip for sequences</li>
3051 <li>Import secondary structure from LOCARNA clustalw
3052 style RNA alignment files</li>
3053 <li>import and visualise T-COFFEE quality scores for an
3055 <li>'colour by annotation' per sequence option to
3056 shade each sequence according to its associated alignment
3058 <li>New Jalview Logo</li>
3059 </ul> <em>Documentation and Development</em>
3061 <li>documentation for score matrices used in Jalview</li>
3062 <li>New Website!</li>
3064 <td><em>Application</em>
3066 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3067 wsdbfetch REST service</li>
3068 <li>Stop windows being moved outside desktop on OSX</li>
3069 <li>Filetype associations not installed for webstart
3071 <li>Jalview does not always retrieve progress of a JABAWS
3072 job execution in full once it is complete</li>
3073 <li>revise SHMR RSBS definition to ensure alignment is
3074 uploaded via ali_file parameter</li>
3075 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3076 <li>View all structures superposed fails with exception</li>
3077 <li>Jnet job queues forever if a very short sequence is
3078 submitted for prediction</li>
3079 <li>Cut and paste menu not opened when mouse clicked on
3081 <li>Putting fractional value into integer text box in
3082 alignment parameter dialog causes Jalview to hang</li>
3083 <li>Structure view highlighting doesn't work on
3085 <li>View all structures fails with exception shown in
3087 <li>Characters in filename associated with PDBEntry not
3088 escaped in a platform independent way</li>
3089 <li>Jalview desktop fails to launch with exception when
3091 <li>Tree calculation reports 'you must have 2 or more
3092 sequences selected' when selection is empty</li>
3093 <li>Jalview desktop fails to launch with jar signature
3094 failure when java web start temporary file caching is
3096 <li>DAS Sequence retrieval with range qualification
3097 results in sequence xref which includes range qualification</li>
3098 <li>Errors during processing of command line arguments
3099 cause progress bar (JAL-898) to be removed</li>
3100 <li>Replace comma for semi-colon option not disabled for
3101 DAS sources in sequence fetcher</li>
3102 <li>Cannot close news reader when JABAWS server warning
3103 dialog is shown</li>
3104 <li>Option widgets not updated to reflect user settings</li>
3105 <li>Edited sequence not submitted to web service</li>
3106 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3107 <li>InstallAnywhere installer doesn't unpack and run
3108 on OSX Mountain Lion</li>
3109 <li>Annotation panel not given a scroll bar when
3110 sequences with alignment annotation are pasted into the
3112 <li>Sequence associated annotation rows not associated
3113 when loaded from Jalview project</li>
3114 <li>Browser launch fails with NPE on java 1.7</li>
3115 <li>JABAWS alignment marked as finished when job was
3116 cancelled or job failed due to invalid input</li>
3117 <li>NPE with v2.7 example when clicking on Tree
3118 associated with all views</li>
3119 <li>Exceptions when copy/paste sequences with grouped
3120 annotation rows to new window</li>
3121 </ul> <em>Applet</em>
3123 <li>Sequence features are momentarily displayed before
3124 they are hidden using hidefeaturegroups applet parameter</li>
3125 <li>loading features via javascript API automatically
3126 enables feature display</li>
3127 <li>scrollToColumnIn javascript API method doesn't
3129 </ul> <em>General</em>
3131 <li>Redundancy removal fails for rna alignment</li>
3132 <li>PCA calculation fails when sequence has been selected
3133 and then deselected</li>
3134 <li>PCA window shows grey box when first opened on OSX</li>
3135 <li>Letters coloured pink in sequence logo when alignment
3136 coloured with clustalx</li>
3137 <li>Choosing fonts without letter symbols defined causes
3138 exceptions and redraw errors</li>
3139 <li>Initial PCA plot view is not same as manually
3140 reconfigured view</li>
3141 <li>Grouped annotation graph label has incorrect line
3143 <li>Grouped annotation graph label display is corrupted
3144 for lots of labels</li>
3149 <div align="center">
3150 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3153 <td><em>Application</em>
3155 <li>Jalview Desktop News Reader</li>
3156 <li>Tweaked default layout of web services menu</li>
3157 <li>View/alignment association menu to enable user to
3158 easily specify which alignment a multi-structure view takes
3159 its colours/correspondences from</li>
3160 <li>Allow properties file location to be specified as URL</li>
3161 <li>Extend Jalview project to preserve associations
3162 between many alignment views and a single Jmol display</li>
3163 <li>Store annotation row height in Jalview project file</li>
3164 <li>Annotation row column label formatting attributes
3165 stored in project file</li>
3166 <li>Annotation row order for auto-calculated annotation
3167 rows preserved in Jalview project file</li>
3168 <li>Visual progress indication when Jalview state is
3169 saved using Desktop window menu</li>
3170 <li>Visual indication that command line arguments are
3171 still being processed</li>
3172 <li>Groovy script execution from URL</li>
3173 <li>Colour by annotation default min and max colours in
3175 <li>Automatically associate PDB files dragged onto an
3176 alignment with sequences that have high similarity and
3178 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3179 <li>'view structures' option to open many
3180 structures in same window</li>
3181 <li>Sort associated views menu option for tree panel</li>
3182 <li>Group all JABA and non-JABA services for a particular
3183 analysis function in its own submenu</li>
3184 </ul> <em>Applet</em>
3186 <li>Userdefined and autogenerated annotation rows for
3188 <li>Adjustment of alignment annotation pane height</li>
3189 <li>Annotation scrollbar for annotation panel</li>
3190 <li>Drag to reorder annotation rows in annotation panel</li>
3191 <li>'automaticScrolling' parameter</li>
3192 <li>Allow sequences with partial ID string matches to be
3193 annotated from GFF/Jalview features files</li>
3194 <li>Sequence logo annotation row in applet</li>
3195 <li>Absolute paths relative to host server in applet
3196 parameters are treated as such</li>
3197 <li>New in the JalviewLite javascript API:
3199 <li>JalviewLite.js javascript library</li>
3200 <li>Javascript callbacks for
3202 <li>Applet initialisation</li>
3203 <li>Sequence/alignment mouse-overs and selections</li>
3206 <li>scrollTo row and column alignment scrolling
3208 <li>Select sequence/alignment regions from javascript</li>
3209 <li>javascript structure viewer harness to pass
3210 messages between Jmol and Jalview when running as
3211 distinct applets</li>
3212 <li>sortBy method</li>
3213 <li>Set of applet and application examples shipped
3214 with documentation</li>
3215 <li>New example to demonstrate JalviewLite and Jmol
3216 javascript message exchange</li>
3218 </ul> <em>General</em>
3220 <li>Enable Jmol displays to be associated with multiple
3221 multiple alignments</li>
3222 <li>Option to automatically sort alignment with new tree</li>
3223 <li>User configurable link to enable redirects to a
3224 www.Jalview.org mirror</li>
3225 <li>Jmol colours option for Jmol displays</li>
3226 <li>Configurable newline string when writing alignment
3227 and other flat files</li>
3228 <li>Allow alignment annotation description lines to
3229 contain html tags</li>
3230 </ul> <em>Documentation and Development</em>
3232 <li>Add groovy test harness for bulk load testing to
3234 <li>Groovy script to load and align a set of sequences
3235 using a web service before displaying the result in the
3236 Jalview desktop</li>
3237 <li>Restructured javascript and applet api documentation</li>
3238 <li>Ant target to publish example html files with applet
3240 <li>Netbeans project for building Jalview from source</li>
3241 <li>ant task to create online javadoc for Jalview source</li>
3243 <td><em>Application</em>
3245 <li>User defined colourscheme throws exception when
3246 current built in colourscheme is saved as new scheme</li>
3247 <li>AlignFrame->Save in application pops up save
3248 dialog for valid filename/format</li>
3249 <li>Cannot view associated structure for UniProt sequence</li>
3250 <li>PDB file association breaks for UniProt sequence
3252 <li>Associate PDB from file dialog does not tell you
3253 which sequence is to be associated with the file</li>
3254 <li>Find All raises null pointer exception when query
3255 only matches sequence IDs</li>
3256 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3257 <li>Jalview project with Jmol views created with Jalview
3258 2.4 cannot be loaded</li>
3259 <li>Filetype associations not installed for webstart
3261 <li>Two or more chains in a single PDB file associated
3262 with sequences in different alignments do not get coloured
3263 by their associated sequence</li>
3264 <li>Visibility status of autocalculated annotation row
3265 not preserved when project is loaded</li>
3266 <li>Annotation row height and visibility attributes not
3267 stored in Jalview project</li>
3268 <li>Tree bootstraps are not preserved when saved as a
3269 Jalview project</li>
3270 <li>Envision2 workflow tooltips are corrupted</li>
3271 <li>Enabling show group conservation also enables colour
3272 by conservation</li>
3273 <li>Duplicate group associated conservation or consensus
3274 created on new view</li>
3275 <li>Annotation scrollbar not displayed after 'show
3276 all hidden annotation rows' option selected</li>
3277 <li>Alignment quality not updated after alignment
3278 annotation row is hidden then shown</li>
3279 <li>Preserve colouring of structures coloured by
3280 sequences in pre Jalview 2.7 projects</li>
3281 <li>Web service job parameter dialog is not laid out
3283 <li>Web services menu not refreshed after 'reset
3284 services' button is pressed in preferences</li>
3285 <li>Annotation off by one in Jalview v2_3 example project</li>
3286 <li>Structures imported from file and saved in project
3287 get name like jalview_pdb1234.txt when reloaded</li>
3288 <li>Jalview does not always retrieve progress of a JABAWS
3289 job execution in full once it is complete</li>
3290 </ul> <em>Applet</em>
3292 <li>Alignment height set incorrectly when lots of
3293 annotation rows are displayed</li>
3294 <li>Relative URLs in feature HTML text not resolved to
3296 <li>View follows highlighting does not work for positions
3298 <li><= shown as = in tooltip</li>
3299 <li>Export features raises exception when no features
3301 <li>Separator string used for serialising lists of IDs
3302 for javascript api is modified when separator string
3303 provided as parameter</li>
3304 <li>Null pointer exception when selecting tree leaves for
3305 alignment with no existing selection</li>
3306 <li>Relative URLs for datasources assumed to be relative
3307 to applet's codebase</li>
3308 <li>Status bar not updated after finished searching and
3309 search wraps around to first result</li>
3310 <li>StructureSelectionManager instance shared between
3311 several Jalview applets causes race conditions and memory
3313 <li>Hover tooltip and mouseover of position on structure
3314 not sent from Jmol in applet</li>
3315 <li>Certain sequences of javascript method calls to
3316 applet API fatally hang browser</li>
3317 </ul> <em>General</em>
3319 <li>View follows structure mouseover scrolls beyond
3320 position with wrapped view and hidden regions</li>
3321 <li>Find sequence position moves to wrong residue
3322 with/without hidden columns</li>
3323 <li>Sequence length given in alignment properties window
3325 <li>InvalidNumberFormat exceptions thrown when trying to
3326 import PDB like structure files</li>
3327 <li>Positional search results are only highlighted
3328 between user-supplied sequence start/end bounds</li>
3329 <li>End attribute of sequence is not validated</li>
3330 <li>Find dialog only finds first sequence containing a
3331 given sequence position</li>
3332 <li>Sequence numbering not preserved in MSF alignment
3334 <li>Jalview PDB file reader does not extract sequence
3335 from nucleotide chains correctly</li>
3336 <li>Structure colours not updated when tree partition
3337 changed in alignment</li>
3338 <li>Sequence associated secondary structure not correctly
3339 parsed in interleaved stockholm</li>
3340 <li>Colour by annotation dialog does not restore current
3342 <li>Hiding (nearly) all sequences doesn't work
3344 <li>Sequences containing lowercase letters are not
3345 properly associated with their pdb files</li>
3346 </ul> <em>Documentation and Development</em>
3348 <li>schemas/JalviewWsParamSet.xsd corrupted by
3349 ApplyCopyright tool</li>
3354 <div align="center">
3355 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3358 <td><em>Application</em>
3360 <li>New warning dialog when the Jalview Desktop cannot
3361 contact web services</li>
3362 <li>JABA service parameters for a preset are shown in
3363 service job window</li>
3364 <li>JABA Service menu entries reworded</li>
3368 <li>Modeller PIR IO broken - cannot correctly import a
3369 pir file emitted by Jalview</li>
3370 <li>Existing feature settings transferred to new
3371 alignment view created from cut'n'paste</li>
3372 <li>Improved test for mixed amino/nucleotide chains when
3373 parsing PDB files</li>
3374 <li>Consensus and conservation annotation rows
3375 occasionally become blank for all new windows</li>
3376 <li>Exception raised when right clicking above sequences
3377 in wrapped view mode</li>
3378 </ul> <em>Application</em>
3380 <li>multiple multiply aligned structure views cause cpu
3381 usage to hit 100% and computer to hang</li>
3382 <li>Web Service parameter layout breaks for long user
3383 parameter names</li>
3384 <li>Jaba service discovery hangs desktop if Jaba server
3391 <div align="center">
3392 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3395 <td><em>Application</em>
3397 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3398 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3401 <li>Web Services preference tab</li>
3402 <li>Analysis parameters dialog box and user defined
3404 <li>Improved speed and layout of Envision2 service menu</li>
3405 <li>Superpose structures using associated sequence
3407 <li>Export coordinates and projection as CSV from PCA
3409 </ul> <em>Applet</em>
3411 <li>enable javascript: execution by the applet via the
3412 link out mechanism</li>
3413 </ul> <em>Other</em>
3415 <li>Updated the Jmol Jalview interface to work with Jmol
3417 <li>The Jalview Desktop and JalviewLite applet now
3418 require Java 1.5</li>
3419 <li>Allow Jalview feature colour specification for GFF
3420 sequence annotation files</li>
3421 <li>New 'colour by label' keword in Jalview feature file
3422 type colour specification</li>
3423 <li>New Jalview Desktop Groovy API method that allows a
3424 script to check if it being run in an interactive session or
3425 in a batch operation from the Jalview command line</li>
3429 <li>clustalx colourscheme colours Ds preferentially when
3430 both D+E are present in over 50% of the column</li>
3431 </ul> <em>Application</em>
3433 <li>typo in AlignmentFrame->View->Hide->all but
3434 selected Regions menu item</li>
3435 <li>sequence fetcher replaces ',' for ';' when the ',' is
3436 part of a valid accession ID</li>
3437 <li>fatal OOM if object retrieved by sequence fetcher
3438 runs out of memory</li>
3439 <li>unhandled Out of Memory Error when viewing pca
3440 analysis results</li>
3441 <li>InstallAnywhere builds fail to launch on OS X java
3442 10.5 update 4 (due to apple Java 1.6 update)</li>
3443 <li>Installanywhere Jalview silently fails to launch</li>
3444 </ul> <em>Applet</em>
3446 <li>Jalview.getFeatureGroups() raises an
3447 ArrayIndexOutOfBoundsException if no feature groups are
3454 <div align="center">
3455 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3461 <li>Alignment prettyprinter doesn't cope with long
3463 <li>clustalx colourscheme colours Ds preferentially when
3464 both D+E are present in over 50% of the column</li>
3465 <li>nucleic acid structures retrieved from PDB do not
3466 import correctly</li>
3467 <li>More columns get selected than were clicked on when a
3468 number of columns are hidden</li>
3469 <li>annotation label popup menu not providing correct
3470 add/hide/show options when rows are hidden or none are
3472 <li>Stockholm format shown in list of readable formats,
3473 and parser copes better with alignments from RFAM.</li>
3474 <li>CSV output of consensus only includes the percentage
3475 of all symbols if sequence logo display is enabled</li>
3477 </ul> <em>Applet</em>
3479 <li>annotation panel disappears when annotation is
3481 </ul> <em>Application</em>
3483 <li>Alignment view not redrawn properly when new
3484 alignment opened where annotation panel is visible but no
3485 annotations are present on alignment</li>
3486 <li>pasted region containing hidden columns is
3487 incorrectly displayed in new alignment window</li>
3488 <li>Jalview slow to complete operations when stdout is
3489 flooded (fix is to close the Jalview console)</li>
3490 <li>typo in AlignmentFrame->View->Hide->all but
3491 selected Rregions menu item.</li>
3492 <li>inconsistent group submenu and Format submenu entry
3493 'Un' or 'Non'conserved</li>
3494 <li>Sequence feature settings are being shared by
3495 multiple distinct alignments</li>
3496 <li>group annotation not recreated when tree partition is
3498 <li>double click on group annotation to select sequences
3499 does not propagate to associated trees</li>
3500 <li>Mac OSX specific issues:
3502 <li>exception raised when mouse clicked on desktop
3503 window background</li>
3504 <li>Desktop menu placed on menu bar and application
3505 name set correctly</li>
3506 <li>sequence feature settings not wide enough for the
3507 save feature colourscheme button</li>
3516 <div align="center">
3517 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3520 <td><em>New Capabilities</em>
3522 <li>URL links generated from description line for
3523 regular-expression based URL links (applet and application)
3525 <li>Non-positional feature URL links are shown in link
3527 <li>Linked viewing of nucleic acid sequences and
3529 <li>Automatic Scrolling option in View menu to display
3530 the currently highlighted region of an alignment.</li>
3531 <li>Order an alignment by sequence length, or using the
3532 average score or total feature count for each sequence.</li>
3533 <li>Shading features by score or associated description</li>
3534 <li>Subdivide alignment and groups based on identity of
3535 selected subsequence (Make Groups from Selection).</li>
3536 <li>New hide/show options including Shift+Control+H to
3537 hide everything but the currently selected region.</li>
3538 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3539 </ul> <em>Application</em>
3541 <li>Fetch DB References capabilities and UI expanded to
3542 support retrieval from DAS sequence sources</li>
3543 <li>Local DAS Sequence sources can be added via the
3544 command line or via the Add local source dialog box.</li>
3545 <li>DAS Dbref and DbxRef feature types are parsed as
3546 database references and protein_name is parsed as
3547 description line (BioSapiens terms).</li>
3548 <li>Enable or disable non-positional feature and database
3549 references in sequence ID tooltip from View menu in
3551 <!-- <li>New hidden columns and rows and representatives capabilities
3552 in annotations file (in progress - not yet fully implemented)</li> -->
3553 <li>Group-associated consensus, sequence logos and
3554 conservation plots</li>
3555 <li>Symbol distributions for each column can be exported
3556 and visualized as sequence logos</li>
3557 <li>Optionally scale multi-character column labels to fit
3558 within each column of annotation row<!-- todo for applet -->
3560 <li>Optional automatic sort of associated alignment view
3561 when a new tree is opened.</li>
3562 <li>Jalview Java Console</li>
3563 <li>Better placement of desktop window when moving
3564 between different screens.</li>
3565 <li>New preference items for sequence ID tooltip and
3566 consensus annotation</li>
3567 <li>Client to submit sequences and IDs to Envision2
3569 <li><em>Vamsas Capabilities</em>
3571 <li>Improved VAMSAS synchronization (Jalview archive
3572 used to preserve views, structures, and tree display
3574 <li>Import of vamsas documents from disk or URL via
3576 <li>Sharing of selected regions between views and
3577 with other VAMSAS applications (Experimental feature!)</li>
3578 <li>Updated API to VAMSAS version 0.2</li>
3580 </ul> <em>Applet</em>
3582 <li>Middle button resizes annotation row height</li>
3585 <li>sortByTree (true/false) - automatically sort the
3586 associated alignment view by the tree when a new tree is
3588 <li>showTreeBootstraps (true/false) - show or hide
3589 branch bootstraps (default is to show them if available)</li>
3590 <li>showTreeDistances (true/false) - show or hide
3591 branch lengths (default is to show them if available)</li>
3592 <li>showUnlinkedTreeNodes (true/false) - indicate if
3593 unassociated nodes should be highlighted in the tree
3595 <li>heightScale and widthScale (1.0 or more) -
3596 increase the height or width of a cell in the alignment
3597 grid relative to the current font size.</li>
3600 <li>Non-positional features displayed in sequence ID
3602 </ul> <em>Other</em>
3604 <li>Features format: graduated colour definitions and
3605 specification of feature scores</li>
3606 <li>Alignment Annotations format: new keywords for group
3607 associated annotation (GROUP_REF) and annotation row display
3608 properties (ROW_PROPERTIES)</li>
3609 <li>XML formats extended to support graduated feature
3610 colourschemes, group associated annotation, and profile
3611 visualization settings.</li></td>
3614 <li>Source field in GFF files parsed as feature source
3615 rather than description</li>
3616 <li>Non-positional features are now included in sequence
3617 feature and gff files (controlled via non-positional feature
3618 visibility in tooltip).</li>
3619 <li>URL links generated for all feature links (bugfix)</li>
3620 <li>Added URL embedding instructions to features file
3622 <li>Codons containing ambiguous nucleotides translated as
3623 'X' in peptide product</li>
3624 <li>Match case switch in find dialog box works for both
3625 sequence ID and sequence string and query strings do not
3626 have to be in upper case to match case-insensitively.</li>
3627 <li>AMSA files only contain first column of
3628 multi-character column annotation labels</li>
3629 <li>Jalview Annotation File generation/parsing consistent
3630 with documentation (e.g. Stockholm annotation can be
3631 exported and re-imported)</li>
3632 <li>PDB files without embedded PDB IDs given a friendly
3634 <li>Find incrementally searches ID string matches as well
3635 as subsequence matches, and correctly reports total number
3639 <li>Better handling of exceptions during sequence
3641 <li>Dasobert generated non-positional feature URL
3642 link text excludes the start_end suffix</li>
3643 <li>DAS feature and source retrieval buttons disabled
3644 when fetch or registry operations in progress.</li>
3645 <li>PDB files retrieved from URLs are cached properly</li>
3646 <li>Sequence description lines properly shared via
3648 <li>Sequence fetcher fetches multiple records for all
3650 <li>Ensured that command line das feature retrieval
3651 completes before alignment figures are generated.</li>
3652 <li>Reduced time taken when opening file browser for
3654 <li>isAligned check prior to calculating tree, PCA or
3655 submitting an MSA to JNet now excludes hidden sequences.</li>
3656 <li>User defined group colours properly recovered
3657 from Jalview projects.</li>
3666 <div align="center">
3667 <strong>2.4.0.b2</strong><br> 28/10/2009
3672 <li>Experimental support for google analytics usage
3674 <li>Jalview privacy settings (user preferences and docs).</li>
3679 <li>Race condition in applet preventing startup in
3681 <li>Exception when feature created from selection beyond
3682 length of sequence.</li>
3683 <li>Allow synthetic PDB files to be imported gracefully</li>
3684 <li>Sequence associated annotation rows associate with
3685 all sequences with a given id</li>
3686 <li>Find function matches case-insensitively for sequence
3687 ID string searches</li>
3688 <li>Non-standard characters do not cause pairwise
3689 alignment to fail with exception</li>
3690 </ul> <em>Application Issues</em>
3692 <li>Sequences are now validated against EMBL database</li>
3693 <li>Sequence fetcher fetches multiple records for all
3695 </ul> <em>InstallAnywhere Issues</em>
3697 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3698 issue with installAnywhere mechanism)</li>
3699 <li>Command line launching of JARs from InstallAnywhere
3700 version (java class versioning error fixed)</li>
3707 <div align="center">
3708 <strong>2.4</strong><br> 27/8/2008
3711 <td><em>User Interface</em>
3713 <li>Linked highlighting of codon and amino acid from
3714 translation and protein products</li>
3715 <li>Linked highlighting of structure associated with
3716 residue mapping to codon position</li>
3717 <li>Sequence Fetcher provides example accession numbers
3718 and 'clear' button</li>
3719 <li>MemoryMonitor added as an option under Desktop's
3721 <li>Extract score function to parse whitespace separated
3722 numeric data in description line</li>
3723 <li>Column labels in alignment annotation can be centred.</li>
3724 <li>Tooltip for sequence associated annotation give name
3726 </ul> <em>Web Services and URL fetching</em>
3728 <li>JPred3 web service</li>
3729 <li>Prototype sequence search client (no public services
3731 <li>Fetch either seed alignment or full alignment from
3733 <li>URL Links created for matching database cross
3734 references as well as sequence ID</li>
3735 <li>URL Links can be created using regular-expressions</li>
3736 </ul> <em>Sequence Database Connectivity</em>
3738 <li>Retrieval of cross-referenced sequences from other
3740 <li>Generalised database reference retrieval and
3741 validation to all fetchable databases</li>
3742 <li>Fetch sequences from DAS sources supporting the
3743 sequence command</li>
3744 </ul> <em>Import and Export</em>
3745 <li>export annotation rows as CSV for spreadsheet import</li>
3746 <li>Jalview projects record alignment dataset associations,
3747 EMBL products, and cDNA sequence mappings</li>
3748 <li>Sequence Group colour can be specified in Annotation
3750 <li>Ad-hoc colouring of group in Annotation File using RGB
3751 triplet as name of colourscheme</li>
3752 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3754 <li>treenode binding for VAMSAS tree exchange</li>
3755 <li>local editing and update of sequences in VAMSAS
3756 alignments (experimental)</li>
3757 <li>Create new or select existing session to join</li>
3758 <li>load and save of vamsas documents</li>
3759 </ul> <em>Application command line</em>
3761 <li>-tree parameter to open trees (introduced for passing
3763 <li>-fetchfrom command line argument to specify nicknames
3764 of DAS servers to query for alignment features</li>
3765 <li>-dasserver command line argument to add new servers
3766 that are also automatically queried for features</li>
3767 <li>-groovy command line argument executes a given groovy
3768 script after all input data has been loaded and parsed</li>
3769 </ul> <em>Applet-Application data exchange</em>
3771 <li>Trees passed as applet parameters can be passed to
3772 application (when using "View in full
3773 application")</li>
3774 </ul> <em>Applet Parameters</em>
3776 <li>feature group display control parameter</li>
3777 <li>debug parameter</li>
3778 <li>showbutton parameter</li>
3779 </ul> <em>Applet API methods</em>
3781 <li>newView public method</li>
3782 <li>Window (current view) specific get/set public methods</li>
3783 <li>Feature display control methods</li>
3784 <li>get list of currently selected sequences</li>
3785 </ul> <em>New Jalview distribution features</em>
3787 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3788 <li>RELEASE file gives build properties for the latest
3789 Jalview release.</li>
3790 <li>Java 1.1 Applet build made easier and donotobfuscate
3791 property controls execution of obfuscator</li>
3792 <li>Build target for generating source distribution</li>
3793 <li>Debug flag for javacc</li>
3794 <li>.jalview_properties file is documented (slightly) in
3795 jalview.bin.Cache</li>
3796 <li>Continuous Build Integration for stable and
3797 development version of Application, Applet and source
3802 <li>selected region output includes visible annotations
3803 (for certain formats)</li>
3804 <li>edit label/displaychar contains existing label/char
3806 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3807 <li>shorter peptide product names from EMBL records</li>
3808 <li>Newick string generator makes compact representations</li>
3809 <li>bootstrap values parsed correctly for tree files with
3811 <li>pathological filechooser bug avoided by not allowing
3812 filenames containing a ':'</li>
3813 <li>Fixed exception when parsing GFF files containing
3814 global sequence features</li>
3815 <li>Alignment datasets are finalized only when number of
3816 references from alignment sequences goes to zero</li>
3817 <li>Close of tree branch colour box without colour
3818 selection causes cascading exceptions</li>
3819 <li>occasional negative imgwidth exceptions</li>
3820 <li>better reporting of non-fatal warnings to user when
3821 file parsing fails.</li>
3822 <li>Save works when Jalview project is default format</li>
3823 <li>Save as dialog opened if current alignment format is
3824 not a valid output format</li>
3825 <li>UniProt canonical names introduced for both das and
3827 <li>Histidine should be midblue (not pink!) in Zappo</li>
3828 <li>error messages passed up and output when data read
3830 <li>edit undo recovers previous dataset sequence when
3831 sequence is edited</li>
3832 <li>allow PDB files without pdb ID HEADER lines (like
3833 those generated by MODELLER) to be read in properly</li>
3834 <li>allow reading of JPred concise files as a normal
3836 <li>Stockholm annotation parsing and alignment properties
3837 import fixed for PFAM records</li>
3838 <li>Structure view windows have correct name in Desktop
3840 <li>annotation consisting of sequence associated scores
3841 can be read and written correctly to annotation file</li>
3842 <li>Aligned cDNA translation to aligned peptide works
3844 <li>Fixed display of hidden sequence markers and
3845 non-italic font for representatives in Applet</li>
3846 <li>Applet Menus are always embedded in applet window on
3848 <li>Newly shown features appear at top of stack (in
3850 <li>Annotations added via parameter not drawn properly
3851 due to null pointer exceptions</li>
3852 <li>Secondary structure lines are drawn starting from
3853 first column of alignment</li>
3854 <li>UniProt XML import updated for new schema release in
3856 <li>Sequence feature to sequence ID match for Features
3857 file is case-insensitive</li>
3858 <li>Sequence features read from Features file appended to
3859 all sequences with matching IDs</li>
3860 <li>PDB structure coloured correctly for associated views
3861 containing a sub-sequence</li>
3862 <li>PDB files can be retrieved by applet from Jar files</li>
3863 <li>feature and annotation file applet parameters
3864 referring to different directories are retrieved correctly</li>
3865 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3866 <li>Fixed application hang whilst waiting for
3867 splash-screen version check to complete</li>
3868 <li>Applet properly URLencodes input parameter values
3869 when passing them to the launchApp service</li>
3870 <li>display name and local features preserved in results
3871 retrieved from web service</li>
3872 <li>Visual delay indication for sequence retrieval and
3873 sequence fetcher initialisation</li>
3874 <li>updated Application to use DAS 1.53e version of
3875 dasobert DAS client</li>
3876 <li>Re-instated Full AMSA support and .amsa file
3878 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3886 <div align="center">
3887 <strong>2.3</strong><br> 9/5/07
3892 <li>Jmol 11.0.2 integration</li>
3893 <li>PDB views stored in Jalview XML files</li>
3894 <li>Slide sequences</li>
3895 <li>Edit sequence in place</li>
3896 <li>EMBL CDS features</li>
3897 <li>DAS Feature mapping</li>
3898 <li>Feature ordering</li>
3899 <li>Alignment Properties</li>
3900 <li>Annotation Scores</li>
3901 <li>Sort by scores</li>
3902 <li>Feature/annotation editing in applet</li>
3907 <li>Headless state operation in 2.2.1</li>
3908 <li>Incorrect and unstable DNA pairwise alignment</li>
3909 <li>Cut and paste of sequences with annotation</li>
3910 <li>Feature group display state in XML</li>
3911 <li>Feature ordering in XML</li>
3912 <li>blc file iteration selection using filename # suffix</li>
3913 <li>Stockholm alignment properties</li>
3914 <li>Stockhom alignment secondary structure annotation</li>
3915 <li>2.2.1 applet had no feature transparency</li>
3916 <li>Number pad keys can be used in cursor mode</li>
3917 <li>Structure Viewer mirror image resolved</li>
3924 <div align="center">
3925 <strong>2.2.1</strong><br> 12/2/07
3930 <li>Non standard characters can be read and displayed
3931 <li>Annotations/Features can be imported/exported to the
3933 <li>Applet allows editing of sequence/annotation/group
3934 name & description
3935 <li>Preference setting to display sequence name in
3937 <li>Annotation file format extended to allow
3938 Sequence_groups to be defined
3939 <li>Default opening of alignment overview panel can be
3940 specified in preferences
3941 <li>PDB residue numbering annotation added to associated
3947 <li>Applet crash under certain Linux OS with Java 1.6
3949 <li>Annotation file export / import bugs fixed
3950 <li>PNG / EPS image output bugs fixed
3956 <div align="center">
3957 <strong>2.2</strong><br> 27/11/06
3962 <li>Multiple views on alignment
3963 <li>Sequence feature editing
3964 <li>"Reload" alignment
3965 <li>"Save" to current filename
3966 <li>Background dependent text colour
3967 <li>Right align sequence ids
3968 <li>User-defined lower case residue colours
3971 <li>Menu item accelerator keys
3972 <li>Control-V pastes to current alignment
3973 <li>Cancel button for DAS Feature Fetching
3974 <li>PCA and PDB Viewers zoom via mouse roller
3975 <li>User-defined sub-tree colours and sub-tree selection
3977 <li>'New Window' button on the 'Output to Text box'
3982 <li>New memory efficient Undo/Redo System
3983 <li>Optimised symbol lookups and conservation/consensus
3985 <li>Region Conservation/Consensus recalculated after
3987 <li>Fixed Remove Empty Columns Bug (empty columns at end
3989 <li>Slowed DAS Feature Fetching for increased robustness.
3991 <li>Made angle brackets in ASCII feature descriptions
3993 <li>Re-instated Zoom function for PCA
3994 <li>Sequence descriptions conserved in web service
3996 <li>UniProt ID discoverer uses any word separated by
3998 <li>WsDbFetch query/result association resolved
3999 <li>Tree leaf to sequence mapping improved
4000 <li>Smooth fonts switch moved to FontChooser dialog box.
4007 <div align="center">
4008 <strong>2.1.1</strong><br> 12/9/06
4013 <li>Copy consensus sequence to clipboard</li>
4018 <li>Image output - rightmost residues are rendered if
4019 sequence id panel has been resized</li>
4020 <li>Image output - all offscreen group boundaries are
4022 <li>Annotation files with sequence references - all
4023 elements in file are relative to sequence position</li>
4024 <li>Mac Applet users can use Alt key for group editing</li>
4030 <div align="center">
4031 <strong>2.1</strong><br> 22/8/06
4036 <li>MAFFT Multiple Alignment in default Web Service list</li>
4037 <li>DAS Feature fetching</li>
4038 <li>Hide sequences and columns</li>
4039 <li>Export Annotations and Features</li>
4040 <li>GFF file reading / writing</li>
4041 <li>Associate structures with sequences from local PDB
4043 <li>Add sequences to exisiting alignment</li>
4044 <li>Recently opened files / URL lists</li>
4045 <li>Applet can launch the full application</li>
4046 <li>Applet has transparency for features (Java 1.2
4048 <li>Applet has user defined colours parameter</li>
4049 <li>Applet can load sequences from parameter
4050 "sequence<em>x</em>"
4056 <li>Redundancy Panel reinstalled in the Applet</li>
4057 <li>Monospaced font - EPS / rescaling bug fixed</li>
4058 <li>Annotation files with sequence references bug fixed</li>
4064 <div align="center">
4065 <strong>2.08.1</strong><br> 2/5/06
4070 <li>Change case of selected region from Popup menu</li>
4071 <li>Choose to match case when searching</li>
4072 <li>Middle mouse button and mouse movement can compress /
4073 expand the visible width and height of the alignment</li>
4078 <li>Annotation Panel displays complete JNet results</li>
4084 <div align="center">
4085 <strong>2.08b</strong><br> 18/4/06
4091 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4092 <li>Righthand label on wrapped alignments shows correct
4099 <div align="center">
4100 <strong>2.08</strong><br> 10/4/06
4105 <li>Editing can be locked to the selection area</li>
4106 <li>Keyboard editing</li>
4107 <li>Create sequence features from searches</li>
4108 <li>Precalculated annotations can be loaded onto
4110 <li>Features file allows grouping of features</li>
4111 <li>Annotation Colouring scheme added</li>
4112 <li>Smooth fonts off by default - Faster rendering</li>
4113 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4118 <li>Drag & Drop fixed on Linux</li>
4119 <li>Jalview Archive file faster to load/save, sequence
4120 descriptions saved.</li>
4126 <div align="center">
4127 <strong>2.07</strong><br> 12/12/05
4132 <li>PDB Structure Viewer enhanced</li>
4133 <li>Sequence Feature retrieval and display enhanced</li>
4134 <li>Choose to output sequence start-end after sequence
4135 name for file output</li>
4136 <li>Sequence Fetcher WSDBFetch@EBI</li>
4137 <li>Applet can read feature files, PDB files and can be
4138 used for HTML form input</li>
4143 <li>HTML output writes groups and features</li>
4144 <li>Group editing is Control and mouse click</li>
4145 <li>File IO bugs</li>
4151 <div align="center">
4152 <strong>2.06</strong><br> 28/9/05
4157 <li>View annotations in wrapped mode</li>
4158 <li>More options for PCA viewer</li>
4163 <li>GUI bugs resolved</li>
4164 <li>Runs with -nodisplay from command line</li>
4170 <div align="center">
4171 <strong>2.05b</strong><br> 15/9/05
4176 <li>Choose EPS export as lineart or text</li>
4177 <li>Jar files are executable</li>
4178 <li>Can read in Uracil - maps to unknown residue</li>
4183 <li>Known OutOfMemory errors give warning message</li>
4184 <li>Overview window calculated more efficiently</li>
4185 <li>Several GUI bugs resolved</li>
4191 <div align="center">
4192 <strong>2.05</strong><br> 30/8/05
4197 <li>Edit and annotate in "Wrapped" view</li>
4202 <li>Several GUI bugs resolved</li>
4208 <div align="center">
4209 <strong>2.04</strong><br> 24/8/05
4214 <li>Hold down mouse wheel & scroll to change font
4220 <li>Improved JPred client reliability</li>
4221 <li>Improved loading of Jalview files</li>
4227 <div align="center">
4228 <strong>2.03</strong><br> 18/8/05
4233 <li>Set Proxy server name and port in preferences</li>
4234 <li>Multiple URL links from sequence ids</li>
4235 <li>User Defined Colours can have a scheme name and added
4237 <li>Choose to ignore gaps in consensus calculation</li>
4238 <li>Unix users can set default web browser</li>
4239 <li>Runs without GUI for batch processing</li>
4240 <li>Dynamically generated Web Service Menus</li>
4245 <li>InstallAnywhere download for Sparc Solaris</li>
4251 <div align="center">
4252 <strong>2.02</strong><br> 18/7/05
4258 <li>Copy & Paste order of sequences maintains
4259 alignment order.</li>
4265 <div align="center">
4266 <strong>2.01</strong><br> 12/7/05
4271 <li>Use delete key for deleting selection.</li>
4272 <li>Use Mouse wheel to scroll sequences.</li>
4273 <li>Help file updated to describe how to add alignment
4275 <li>Version and build date written to build properties
4277 <li>InstallAnywhere installation will check for updates
4278 at launch of Jalview.</li>
4283 <li>Delete gaps bug fixed.</li>
4284 <li>FileChooser sorts columns.</li>
4285 <li>Can remove groups one by one.</li>
4286 <li>Filechooser icons installed.</li>
4287 <li>Finder ignores return character when searching.
4288 Return key will initiate a search.<br>
4295 <div align="center">
4296 <strong>2.0</strong><br> 20/6/05
4301 <li>New codebase</li>