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>20/06/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
68 <!-- JAL-2620 -->Alternative genetic code tables for
69 'Translate as cDNA'</li>
71 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
72 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
75 <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
76 shaded according to any associated attributes (e.g. variant
77 attributes from VCF file, or key-value pairs imported from
81 <!-- JAL-2897 -->Show synonymous codon variants on peptide
85 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
89 <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
90 algorithm (Z-sort/transparency and filter aware)
93 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
99 <!-- JAL-3141 -->Backup files created when saving Jalview project
102 <li><strong>Principal Components Analysis Viewer</strong>
105 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
106 and Viewer state saved in Jalview Project
108 <li>'Change parameters' option removed from viewer's
111 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
115 <!-- JAL-2965 -->PCA plot is depth cued
120 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
122 <li><strong>Speed and Efficiency</strong>
125 <!-- JAL-3198 -->More efficient creation of selections and
126 multiple groups when working with large alignments
129 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
133 <li><strong>User Interface</strong>
136 <!-- JAL-2933 -->Finder panel remembers last position in each
140 <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
141 what is shown)<br />Only visible region of alignment is shown by
142 default (can be changed in user preferences)
145 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
146 to the Overwrite Dialog
149 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
153 <!-- JAL-1244 -->Status bar shows bounds when dragging a
154 selection region, and gap count when inserting or deleting gaps
157 <!-- JAL-3132 -->Status bar updates over sequence and annotation
161 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
165 <!-- JAL-3073 -->Can select columns by dragging left/right in
169 <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
172 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
176 <!-- JAL-3181 -->Consistent ordering of links in sequence id
180 <!-- JAL-3021 -->Sequence Details report opens positioned to top
184 <li><strong>Java 11 Support</strong>
187 <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
188 and getdown release channels
191 <!-- -->OSX GUI integrations for App menu's 'About' entry and
196 <em>Deprecations</em>
199 <!-- JAL-3035 -->DAS sequence retrieval and annotation
200 capabilities removed from the Jalview Desktop
202 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
204 <em>Development and Release Processes</em>
207 <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
208 Installers built with Install4j (licensed to the Jalview open
209 source project) rather than InstallAnywhere
212 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
213 settings, receive over the air updates and launch specific
214 versions via (<a href="https://github.com/threerings/getdown">Three
218 <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
221 <!-- JAL-3225 -->Eclipse project configuration managed with
225 Atlassian Bamboo continuous integration server for
226 unattended Test Suite execution</li>
228 <!-- JAL-2864 -->Memory test suite to detect leaks in common
231 <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
232 implementation) used for Sequence Feature collections</li>
234 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
235 unmarshalling has been replaced by JAXB for Jalview projects
236 and XML based data retrieval clients</li>
239 <td align="left" valign="top">
242 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
244 <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
246 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
248 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
249 Jalview project involving multiple views</li>
251 <!-- JAL-3164 -->Overview for complementary view in a linked
252 CDS/Protein alignment is not updated when Hide Columns by
253 Annotation dialog hides columns</li>
255 <!-- JAL-3158 -->Selection highlighting in the complement of
256 a CDS/Protein alignment stops working after making a
257 selection in one view, then making another selection in the
260 <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
262 <!-- JAL-3154 -->Table Columns could be re-ordered in
263 Feature Settings and Jalview Preferences panels</li>
265 <!-- JAL-2865 -->Jalview hangs when closing windows
266 or the overview updates with large alignments</li>
268 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
269 region if columns were selected by dragging right-to-left
270 and the mouse moved to the left of the first column</li>
272 <!-- JAL-3218 -->Couldn't hide selected columns adjacent
273 to a hidden column marker via scale popup menu</li>
275 <!-- JAL-2846 -->Error message for trying to load in invalid
276 URLs doesn't tell users the invalid URL</li>
278 <!-- JAL-3178 -->Nonpositional features lose feature group
279 on export as Jalview features file</li>
281 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
282 printed when columns are hidden</li>
284 <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
286 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
287 dragging out of Scale or Annotation Panel</li>
289 <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
291 <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
293 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
295 <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
297 <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
299 <!-- JAL-2932 -->Finder searches in minimised alignments</li>
301 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
302 opening an alignment</li>
304 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
306 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
307 different groups in the alignment are selected</li>
309 <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
311 <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
313 <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
315 <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
317 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
319 <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
321 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
323 <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
325 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
327 <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
329 <!-- JAL-914 -->Help page can be opened twice</li>
334 <!-- JAL-2822 -->Start and End should be updated when
335 sequence data at beginning or end of alignment added/removed
336 via 'Edit' sequence</li>
338 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
339 sequence features correctly when start of sequence is
340 removed (Known defect since 2.10)</li>
342 <em>New Known Defects</em>
345 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
347 <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
349 <!-- JAL-3240 -->Display is incorrect after removing gapped columns within hidden columns</li>
354 <td width="60" nowrap>
356 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
359 <td><div align="left">
363 <!-- JAL-3101 -->Default memory for Jalview webstart and
364 InstallAnywhere increased to 1G.
367 <!-- JAL-247 -->Hidden sequence markers and representative
368 sequence bolding included when exporting alignment as EPS,
369 SVG, PNG or HTML. <em>Display is configured via the
370 Format menu, or for command-line use via a jalview
371 properties file.</em>
374 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
375 API and sequence data now imported as JSON.
378 <!-- JAL-3065 -->Change in recommended way of starting
379 Jalview via a Java command line: add jars in lib directory
380 to CLASSPATH, rather than via the deprecated java.ext.dirs
387 <!-- JAL-3047 -->Support added to execute test suite
388 instrumented with <a href="http://openclover.org/">Open
393 <td><div align="left">
397 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
398 row shown in Feredoxin Structure alignment view of example
402 <!-- JAL-2854 -->Annotation obscures sequences if lots of
403 annotation displayed.
406 <!-- JAL-3107 -->Group conservation/consensus not shown
407 for newly created group when 'Apply to all groups'
411 <!-- JAL-3087 -->Corrupted display when switching to
412 wrapped mode when sequence panel's vertical scrollbar is
416 <!-- JAL-3003 -->Alignment is black in exported EPS file
417 when sequences are selected in exported view.</em>
420 <!-- JAL-3059 -->Groups with different coloured borders
421 aren't rendered with correct colour.
424 <!-- JAL-3092 -->Jalview could hang when importing certain
425 types of knotted RNA secondary structure.
428 <!-- JAL-3095 -->Sequence highlight and selection in
429 trimmed VARNA 2D structure is incorrect for sequences that
433 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
434 annotation when columns are inserted into an alignment,
435 and when exporting as Stockholm flatfile.
438 <!-- JAL-3053 -->Jalview annotation rows containing upper
439 and lower-case 'E' and 'H' do not automatically get
440 treated as RNA secondary structure.
443 <!-- JAL-3106 -->.jvp should be used as default extension
444 (not .jar) when saving a jalview project file.
447 <!-- JAL-3105 -->Mac Users: closing a window correctly
448 transfers focus to previous window on OSX
451 <em>Java 10 Issues Resolved</em>
454 <!-- JAL-2988 -->OSX - Can't save new files via the File
455 or export menus by typing in a name into the Save dialog
459 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
460 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
461 'look and feel' which has improved compatibility with the
462 latest version of OSX.
469 <td width="60" nowrap>
471 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
472 <em>7/06/2018</em></strong>
475 <td><div align="left">
479 <!-- JAL-2920 -->Use HGVS nomenclature for variant
480 annotation retrieved from Uniprot
483 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
484 onto the Jalview Desktop
488 <td><div align="left">
492 <!-- JAL-3017 -->Cannot import features with multiple
493 variant elements (blocks import of some Uniprot records)
496 <!-- JAL-2997 -->Clustal files with sequence positions in
497 right-hand column parsed correctly
500 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
501 not alignment area in exported graphic
504 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
505 window has input focus
508 <!-- JAL-2992 -->Annotation panel set too high when
509 annotation added to view (Windows)
512 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
513 network connectivity is poor
516 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
517 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
518 the currently open URL and links from a page viewed in
519 Firefox or Chrome on Windows is now fully supported. If
520 you are using Edge, only links in the page can be
521 dragged, and with Internet Explorer, only the currently
522 open URL in the browser can be dropped onto Jalview.</em>
528 <td width="60" nowrap>
530 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
533 <td><div align="left">
537 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
538 for disabling automatic superposition of multiple
539 structures and open structures in existing views
542 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
543 ID and annotation area margins can be click-dragged to
547 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
551 <!-- JAL-2759 -->Improved performance for large alignments
552 and lots of hidden columns
555 <!-- JAL-2593 -->Improved performance when rendering lots
556 of features (particularly when transparency is disabled)
561 <td><div align="left">
564 <!-- JAL-2899 -->Structure and Overview aren't updated
565 when Colour By Annotation threshold slider is adjusted
568 <!-- JAL-2778 -->Slow redraw when Overview panel shown
569 overlapping alignment panel
572 <!-- JAL-2929 -->Overview doesn't show end of unpadded
576 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
577 improved: CDS not handled correctly if transcript has no
581 <!-- JAL-2321 -->Secondary structure and temperature
582 factor annotation not added to sequence when local PDB
583 file associated with it by drag'n'drop or structure
587 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
588 dialog doesn't import PDB files dropped on an alignment
591 <!-- JAL-2666 -->Linked scrolling via protein horizontal
592 scroll bar doesn't work for some CDS/Protein views
595 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
596 Java 1.8u153 onwards and Java 1.9u4+.
599 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
600 columns in annotation row
603 <!-- JAL-2913 -->Preferences panel's ID Width control is not
604 honored in batch mode
607 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
608 for structures added to existing Jmol view
611 <!-- JAL-2223 -->'View Mappings' includes duplicate
612 entries after importing project with multiple views
615 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
616 protein sequences via SIFTS from associated PDB entries
617 with negative residue numbers or missing residues fails
620 <!-- JAL-2952 -->Exception when shading sequence with negative
621 Temperature Factor values from annotated PDB files (e.g.
622 as generated by CONSURF)
625 <!-- JAL-2920 -->Uniprot 'sequence variant' features
626 tooltip doesn't include a text description of mutation
629 <!-- JAL-2922 -->Invert displayed features very slow when
630 structure and/or overview windows are also shown
633 <!-- JAL-2954 -->Selecting columns from highlighted regions
634 very slow for alignments with large numbers of sequences
637 <!-- JAL-2925 -->Copy Consensus fails for group consensus
638 with 'StringIndexOutOfBounds'
641 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
642 platforms running Java 10
645 <!-- JAL-2960 -->Adding a structure to existing structure
646 view appears to do nothing because the view is hidden behind the alignment view
652 <!-- JAL-2926 -->Copy consensus sequence option in applet
653 should copy the group consensus when popup is opened on it
659 <!-- JAL-2913 -->Fixed ID width preference is not respected
662 <em>New Known Defects</em>
665 <!-- JAL-2973 --> Exceptions occasionally raised when
666 editing a large alignment and overview is displayed
669 <!-- JAL-2974 -->'Overview updating' progress bar is shown
670 repeatedly after a series of edits even when the overview
671 is no longer reflecting updates
674 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
675 structures for protein subsequence (if 'Trim Retrieved
676 Sequences' enabled) or Ensembl isoforms (Workaround in
677 2.10.4 is to fail back to N&W mapping)
684 <td width="60" nowrap>
686 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
689 <td><div align="left">
690 <ul><li>Updated Certum Codesigning Certificate
691 (Valid till 30th November 2018)</li></ul></div></td>
692 <td><div align="left">
695 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
696 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
697 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
698 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
699 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
700 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
701 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
707 <td width="60" nowrap>
709 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
712 <td><div align="left">
716 <!-- JAL-2446 -->Faster and more efficient management and
717 rendering of sequence features
720 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
721 429 rate limit request hander
724 <!-- JAL-2773 -->Structure views don't get updated unless
725 their colours have changed
728 <!-- JAL-2495 -->All linked sequences are highlighted for
729 a structure mousover (Jmol) or selection (Chimera)
732 <!-- JAL-2790 -->'Cancel' button in progress bar for
733 JABAWS AACon, RNAAliFold and Disorder prediction jobs
736 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
737 view from Ensembl locus cross-references
740 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
744 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
745 feature can be disabled
748 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
749 PDB easier retrieval of sequences for lists of IDs
752 <!-- JAL-2758 -->Short names for sequences retrieved from
758 <li>Groovy interpreter updated to 2.4.12</li>
759 <li>Example groovy script for generating a matrix of
760 percent identity scores for current alignment.</li>
762 <em>Testing and Deployment</em>
765 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
769 <td><div align="left">
773 <!-- JAL-2643 -->Pressing tab after updating the colour
774 threshold text field doesn't trigger an update to the
778 <!-- JAL-2682 -->Race condition when parsing sequence ID
782 <!-- JAL-2608 -->Overview windows are also closed when
783 alignment window is closed
786 <!-- JAL-2548 -->Export of features doesn't always respect
790 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
791 takes a long time in Cursor mode
797 <!-- JAL-2777 -->Structures with whitespace chainCode
798 cannot be viewed in Chimera
801 <!-- JAL-2728 -->Protein annotation panel too high in
805 <!-- JAL-2757 -->Can't edit the query after the server
806 error warning icon is shown in Uniprot and PDB Free Text
810 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
813 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
816 <!-- JAL-2739 -->Hidden column marker in last column not
817 rendered when switching back from Wrapped to normal view
820 <!-- JAL-2768 -->Annotation display corrupted when
821 scrolling right in unwapped alignment view
824 <!-- JAL-2542 -->Existing features on subsequence
825 incorrectly relocated when full sequence retrieved from
829 <!-- JAL-2733 -->Last reported memory still shown when
830 Desktop->Show Memory is unticked (OSX only)
833 <!-- JAL-2658 -->Amend Features dialog doesn't allow
834 features of same type and group to be selected for
838 <!-- JAL-2524 -->Jalview becomes sluggish in wide
839 alignments when hidden columns are present
842 <!-- JAL-2392 -->Jalview freezes when loading and
843 displaying several structures
846 <!-- JAL-2732 -->Black outlines left after resizing or
850 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
851 within the Jalview desktop on OSX
854 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
855 when in wrapped alignment mode
858 <!-- JAL-2636 -->Scale mark not shown when close to right
859 hand end of alignment
862 <!-- JAL-2684 -->Pairwise alignment of selected regions of
863 each selected sequence do not have correct start/end
867 <!-- JAL-2793 -->Alignment ruler height set incorrectly
868 after canceling the Alignment Window's Font dialog
871 <!-- JAL-2036 -->Show cross-references not enabled after
872 restoring project until a new view is created
875 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
876 URL links appears when only default EMBL-EBI link is
877 configured (since 2.10.2b2)
880 <!-- JAL-2775 -->Overview redraws whole window when box
884 <!-- JAL-2225 -->Structure viewer doesn't map all chains
885 in a multi-chain structure when viewing alignment
886 involving more than one chain (since 2.10)
889 <!-- JAL-2811 -->Double residue highlights in cursor mode
890 if new selection moves alignment window
893 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
894 arrow key in cursor mode to pass hidden column marker
897 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
898 that produces correctly annotated transcripts and products
901 <!-- JAL-2776 -->Toggling a feature group after first time
902 doesn't update associated structure view
905 <em>Applet</em><br />
908 <!-- JAL-2687 -->Concurrent modification exception when
909 closing alignment panel
912 <em>BioJSON</em><br />
915 <!-- JAL-2546 -->BioJSON export does not preserve
916 non-positional features
919 <em>New Known Issues</em>
922 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
923 sequence features correctly (for many previous versions of
927 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
928 using cursor in wrapped panel other than top
931 <!-- JAL-2791 -->Select columns containing feature ignores
932 graduated colour threshold
935 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
936 always preserve numbering and sequence features
939 <em>Known Java 9 Issues</em>
942 <!-- JAL-2902 -->Groovy Console very slow to open and is
943 not responsive when entering characters (Webstart, Java
950 <td width="60" nowrap>
952 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
953 <em>2/10/2017</em></strong>
956 <td><div align="left">
957 <em>New features in Jalview Desktop</em>
960 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
962 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
966 <td><div align="left">
970 <td width="60" nowrap>
972 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
973 <em>7/9/2017</em></strong>
976 <td><div align="left">
980 <!-- JAL-2588 -->Show gaps in overview window by colouring
981 in grey (sequences used to be coloured grey, and gaps were
985 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
989 <!-- JAL-2587 -->Overview updates immediately on increase
990 in size and progress bar shown as higher resolution
991 overview is recalculated
996 <td><div align="left">
1000 <!-- JAL-2664 -->Overview window redraws every hidden
1001 column region row by row
1004 <!-- JAL-2681 -->duplicate protein sequences shown after
1005 retrieving Ensembl crossrefs for sequences from Uniprot
1008 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1009 format setting is unticked
1012 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1013 if group has show boxes format setting unticked
1016 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1017 autoscrolling whilst dragging current selection group to
1018 include sequences and columns not currently displayed
1021 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1022 assemblies are imported via CIF file
1025 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1026 displayed when threshold or conservation colouring is also
1030 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1034 <!-- JAL-2673 -->Jalview continues to scroll after
1035 dragging a selected region off the visible region of the
1039 <!-- JAL-2724 -->Cannot apply annotation based
1040 colourscheme to all groups in a view
1043 <!-- JAL-2511 -->IDs don't line up with sequences
1044 initially after font size change using the Font chooser or
1051 <td width="60" nowrap>
1052 <div align="center">
1053 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1056 <td><div align="left">
1057 <em>Calculations</em>
1061 <!-- JAL-1933 -->Occupancy annotation row shows number of
1062 ungapped positions in each column of the alignment.
1065 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1066 a calculation dialog box
1069 <!-- JAL-2379 -->Revised implementation of PCA for speed
1070 and memory efficiency (~30x faster)
1073 <!-- JAL-2403 -->Revised implementation of sequence
1074 similarity scores as used by Tree, PCA, Shading Consensus
1075 and other calculations
1078 <!-- JAL-2416 -->Score matrices are stored as resource
1079 files within the Jalview codebase
1082 <!-- JAL-2500 -->Trees computed on Sequence Feature
1083 Similarity may have different topology due to increased
1090 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1091 model for alignments and groups
1094 <!-- JAL-384 -->Custom shading schemes created via groovy
1101 <!-- JAL-2526 -->Efficiency improvements for interacting
1102 with alignment and overview windows
1105 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1109 <!-- JAL-2388 -->Hidden columns and sequences can be
1113 <!-- JAL-2611 -->Click-drag in visible area allows fine
1114 adjustment of visible position
1118 <em>Data import/export</em>
1121 <!-- JAL-2535 -->Posterior probability annotation from
1122 Stockholm files imported as sequence associated annotation
1125 <!-- JAL-2507 -->More robust per-sequence positional
1126 annotation input/output via stockholm flatfile
1129 <!-- JAL-2533 -->Sequence names don't include file
1130 extension when importing structure files without embedded
1131 names or PDB accessions
1134 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1135 format sequence substitution matrices
1138 <em>User Interface</em>
1141 <!-- JAL-2447 --> Experimental Features Checkbox in
1142 Desktop's Tools menu to hide or show untested features in
1146 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1147 via Overview or sequence motif search operations
1150 <!-- JAL-2547 -->Amend sequence features dialog box can be
1151 opened by double clicking gaps within sequence feature
1155 <!-- JAL-1476 -->Status bar message shown when not enough
1156 aligned positions were available to create a 3D structure
1160 <em>3D Structure</em>
1163 <!-- JAL-2430 -->Hidden regions in alignment views are not
1164 coloured in linked structure views
1167 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1168 file-based command exchange
1171 <!-- JAL-2375 -->Structure chooser automatically shows
1172 Cached Structures rather than querying the PDBe if
1173 structures are already available for sequences
1176 <!-- JAL-2520 -->Structures imported via URL are cached in
1177 the Jalview project rather than downloaded again when the
1178 project is reopened.
1181 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1182 to transfer Chimera's structure attributes as Jalview
1183 features, and vice-versa (<strong>Experimental
1187 <em>Web Services</em>
1190 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1193 <!-- JAL-2335 -->Filter non-standard amino acids and
1194 nucleotides when submitting to AACon and other MSA
1198 <!-- JAL-2316, -->URLs for viewing database
1199 cross-references provided by identifiers.org and the
1200 EMBL-EBI's MIRIAM DB
1207 <!-- JAL-2344 -->FileFormatI interface for describing and
1208 identifying file formats (instead of String constants)
1211 <!-- JAL-2228 -->FeatureCounter script refactored for
1212 efficiency when counting all displayed features (not
1213 backwards compatible with 2.10.1)
1216 <em>Example files</em>
1219 <!-- JAL-2631 -->Graduated feature colour style example
1220 included in the example feature file
1223 <em>Documentation</em>
1226 <!-- JAL-2339 -->Release notes reformatted for readability
1227 with the built-in Java help viewer
1230 <!-- JAL-1644 -->Find documentation updated with 'search
1231 sequence description' option
1237 <!-- JAL-2485, -->External service integration tests for
1238 Uniprot REST Free Text Search Client
1241 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1244 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1249 <td><div align="left">
1250 <em>Calculations</em>
1253 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1254 matrix - C->R should be '-3'<br />Old matrix restored
1255 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1257 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1258 Jalview's treatment of gaps in PCA and substitution matrix
1259 based Tree calculations.<br /> <br />In earlier versions
1260 of Jalview, gaps matching gaps were penalised, and gaps
1261 matching non-gaps penalised even more. In the PCA
1262 calculation, gaps were actually treated as non-gaps - so
1263 different costs were applied, which meant Jalview's PCAs
1264 were different to those produced by SeqSpace.<br />Jalview
1265 now treats gaps in the same way as SeqSpace (ie it scores
1266 them as 0). <br /> <br />Enter the following in the
1267 Groovy console to restore pre-2.10.2 behaviour:<br />
1268 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1269 // for 2.10.1 mode <br />
1270 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1271 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1272 these settings will affect all subsequent tree and PCA
1273 calculations (not recommended)</em></li>
1275 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1276 scaling of branch lengths for trees computed using
1277 Sequence Feature Similarity.
1280 <!-- JAL-2377 -->PCA calculation could hang when
1281 generating output report when working with highly
1282 redundant alignments
1285 <!-- JAL-2544 --> Sort by features includes features to
1286 right of selected region when gaps present on right-hand
1290 <em>User Interface</em>
1293 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1294 doesn't reselect a specific sequence's associated
1295 annotation after it was used for colouring a view
1298 <!-- JAL-2419 -->Current selection lost if popup menu
1299 opened on a region of alignment without groups
1302 <!-- JAL-2374 -->Popup menu not always shown for regions
1303 of an alignment with overlapping groups
1306 <!-- JAL-2310 -->Finder double counts if both a sequence's
1307 name and description match
1310 <!-- JAL-2370 -->Hiding column selection containing two
1311 hidden regions results in incorrect hidden regions
1314 <!-- JAL-2386 -->'Apply to all groups' setting when
1315 changing colour does not apply Conservation slider value
1319 <!-- JAL-2373 -->Percentage identity and conservation menu
1320 items do not show a tick or allow shading to be disabled
1323 <!-- JAL-2385 -->Conservation shading or PID threshold
1324 lost when base colourscheme changed if slider not visible
1327 <!-- JAL-2547 -->Sequence features shown in tooltip for
1328 gaps before start of features
1331 <!-- JAL-2623 -->Graduated feature colour threshold not
1332 restored to UI when feature colour is edited
1335 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1336 a time when scrolling vertically in wrapped mode.
1339 <!-- JAL-2630 -->Structure and alignment overview update
1340 as graduate feature colour settings are modified via the
1344 <!-- JAL-2034 -->Overview window doesn't always update
1345 when a group defined on the alignment is resized
1348 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1349 wrapped view result in positional status updates
1353 <!-- JAL-2563 -->Status bar doesn't show position for
1354 ambiguous amino acid and nucleotide symbols
1357 <!-- JAL-2602 -->Copy consensus sequence failed if
1358 alignment included gapped columns
1361 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1362 widgets don't permanently disappear
1365 <!-- JAL-2503 -->Cannot select or filter quantitative
1366 annotation that are shown only as column labels (e.g.
1367 T-Coffee column reliability scores)
1370 <!-- JAL-2594 -->Exception thrown if trying to create a
1371 sequence feature on gaps only
1374 <!-- JAL-2504 -->Features created with 'New feature'
1375 button from a Find inherit previously defined feature type
1376 rather than the Find query string
1379 <!-- JAL-2423 -->incorrect title in output window when
1380 exporting tree calculated in Jalview
1383 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1384 and then revealing them reorders sequences on the
1388 <!-- JAL-964 -->Group panel in sequence feature settings
1389 doesn't update to reflect available set of groups after
1390 interactively adding or modifying features
1393 <!-- JAL-2225 -->Sequence Database chooser unusable on
1397 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1398 only excluded gaps in current sequence and ignored
1405 <!-- JAL-2421 -->Overview window visible region moves
1406 erratically when hidden rows or columns are present
1409 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1410 Structure Viewer's colour menu don't correspond to
1414 <!-- JAL-2405 -->Protein specific colours only offered in
1415 colour and group colour menu for protein alignments
1418 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1419 reflect currently selected view or group's shading
1423 <!-- JAL-2624 -->Feature colour thresholds not respected
1424 when rendered on overview and structures when opacity at
1428 <!-- JAL-2589 -->User defined gap colour not shown in
1429 overview when features overlaid on alignment
1432 <em>Data import/export</em>
1435 <!-- JAL-2576 -->Very large alignments take a long time to
1439 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1440 added after a sequence was imported are not written to
1444 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1445 when importing RNA secondary structure via Stockholm
1448 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1449 not shown in correct direction for simple pseudoknots
1452 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1453 with lightGray or darkGray via features file (but can
1457 <!-- JAL-2383 -->Above PID colour threshold not recovered
1458 when alignment view imported from project
1461 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1462 structure and sequences extracted from structure files
1463 imported via URL and viewed in Jmol
1466 <!-- JAL-2520 -->Structures loaded via URL are saved in
1467 Jalview Projects rather than fetched via URL again when
1468 the project is loaded and the structure viewed
1471 <em>Web Services</em>
1474 <!-- JAL-2519 -->EnsemblGenomes example failing after
1475 release of Ensembl v.88
1478 <!-- JAL-2366 -->Proxy server address and port always
1479 appear enabled in Preferences->Connections
1482 <!-- JAL-2461 -->DAS registry not found exceptions
1483 removed from console output
1486 <!-- JAL-2582 -->Cannot retrieve protein products from
1487 Ensembl by Peptide ID
1490 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1491 created from SIFTs, and spurious 'Couldn't open structure
1492 in Chimera' errors raised after April 2017 update (problem
1493 due to 'null' string rather than empty string used for
1494 residues with no corresponding PDB mapping).
1497 <em>Application UI</em>
1500 <!-- JAL-2361 -->User Defined Colours not added to Colour
1504 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1505 case' residues (button in colourscheme editor debugged and
1506 new documentation and tooltips added)
1509 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1510 doesn't restore group-specific text colour thresholds
1513 <!-- JAL-2243 -->Feature settings panel does not update as
1514 new features are added to alignment
1517 <!-- JAL-2532 -->Cancel in feature settings reverts
1518 changes to feature colours via the Amend features dialog
1521 <!-- JAL-2506 -->Null pointer exception when attempting to
1522 edit graduated feature colour via amend features dialog
1526 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1527 selection menu changes colours of alignment views
1530 <!-- JAL-2426 -->Spurious exceptions in console raised
1531 from alignment calculation workers after alignment has
1535 <!-- JAL-1608 -->Typo in selection popup menu - Create
1536 groups now 'Create Group'
1539 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1540 Create/Undefine group doesn't always work
1543 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1544 shown again after pressing 'Cancel'
1547 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1548 adjusts start position in wrap mode
1551 <!-- JAL-2563 -->Status bar doesn't show positions for
1552 ambiguous amino acids
1555 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1556 CDS/Protein view after CDS sequences added for aligned
1560 <!-- JAL-2592 -->User defined colourschemes called 'User
1561 Defined' don't appear in Colours menu
1567 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1568 score models doesn't always result in an updated PCA plot
1571 <!-- JAL-2442 -->Features not rendered as transparent on
1572 overview or linked structure view
1575 <!-- JAL-2372 -->Colour group by conservation doesn't
1579 <!-- JAL-2517 -->Hitting Cancel after applying
1580 user-defined colourscheme doesn't restore original
1587 <!-- JAL-2314 -->Unit test failure:
1588 jalview.ws.jabaws.RNAStructExportImport setup fails
1591 <!-- JAL-2307 -->Unit test failure:
1592 jalview.ws.sifts.SiftsClientTest due to compatibility
1593 problems with deep array comparison equality asserts in
1594 successive versions of TestNG
1597 <!-- JAL-2479 -->Relocated StructureChooserTest and
1598 ParameterUtilsTest Unit tests to Network suite
1601 <em>New Known Issues</em>
1604 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1605 phase after a sequence motif find operation
1608 <!-- JAL-2550 -->Importing annotation file with rows
1609 containing just upper and lower case letters are
1610 interpreted as WUSS RNA secondary structure symbols
1613 <!-- JAL-2590 -->Cannot load and display Newick trees
1614 reliably from eggnog Ortholog database
1617 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1618 containing features of type Highlight' when 'B' is pressed
1619 to mark columns containing highlighted regions.
1622 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1623 doesn't always add secondary structure annotation.
1628 <td width="60" nowrap>
1629 <div align="center">
1630 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1633 <td><div align="left">
1637 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1638 for all consensus calculations
1641 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1644 <li>Updated Jalview's Certum code signing certificate
1647 <em>Application</em>
1650 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1651 set of database cross-references, sorted alphabetically
1654 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1655 from database cross references. Users with custom links
1656 will receive a <a href="webServices/urllinks.html#warning">warning
1657 dialog</a> asking them to update their preferences.
1660 <!-- JAL-2287-->Cancel button and escape listener on
1661 dialog warning user about disconnecting Jalview from a
1665 <!-- JAL-2320-->Jalview's Chimera control window closes if
1666 the Chimera it is connected to is shut down
1669 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1670 columns menu item to mark columns containing highlighted
1671 regions (e.g. from structure selections or results of a
1675 <!-- JAL-2284-->Command line option for batch-generation
1676 of HTML pages rendering alignment data with the BioJS
1686 <!-- JAL-2286 -->Columns with more than one modal residue
1687 are not coloured or thresholded according to percent
1688 identity (first observed in Jalview 2.8.2)
1691 <!-- JAL-2301 -->Threonine incorrectly reported as not
1695 <!-- JAL-2318 -->Updates to documentation pages (above PID
1696 threshold, amino acid properties)
1699 <!-- JAL-2292 -->Lower case residues in sequences are not
1700 reported as mapped to residues in a structure file in the
1704 <!--JAL-2324 -->Identical features with non-numeric scores
1705 could be added multiple times to a sequence
1708 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1709 bond features shown as two highlighted residues rather
1710 than a range in linked structure views, and treated
1711 correctly when selecting and computing trees from features
1714 <!-- JAL-2281-->Custom URL links for database
1715 cross-references are matched to database name regardless
1720 <em>Application</em>
1723 <!-- JAL-2282-->Custom URL links for specific database
1724 names without regular expressions also offer links from
1728 <!-- JAL-2315-->Removing a single configured link in the
1729 URL links pane in Connections preferences doesn't actually
1730 update Jalview configuration
1733 <!-- JAL-2272-->CTRL-Click on a selected region to open
1734 the alignment area popup menu doesn't work on El-Capitan
1737 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1738 files with similarly named sequences if dropped onto the
1742 <!-- JAL-2312 -->Additional mappings are shown for PDB
1743 entries where more chains exist in the PDB accession than
1744 are reported in the SIFTS file
1747 <!-- JAL-2317-->Certain structures do not get mapped to
1748 the structure view when displayed with Chimera
1751 <!-- JAL-2317-->No chains shown in the Chimera view
1752 panel's View->Show Chains submenu
1755 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1756 work for wrapped alignment views
1759 <!--JAL-2197 -->Rename UI components for running JPred
1760 predictions from 'JNet' to 'JPred'
1763 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1764 corrupted when annotation panel vertical scroll is not at
1765 first annotation row
1768 <!--JAL-2332 -->Attempting to view structure for Hen
1769 lysozyme results in a PDB Client error dialog box
1772 <!-- JAL-2319 -->Structure View's mapping report switched
1773 ranges for PDB and sequence for SIFTS
1776 SIFTS 'Not_Observed' residues mapped to non-existant
1780 <!-- <em>New Known Issues</em>
1787 <td width="60" nowrap>
1788 <div align="center">
1789 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1790 <em>25/10/2016</em></strong>
1793 <td><em>Application</em>
1795 <li>3D Structure chooser opens with 'Cached structures'
1796 view if structures already loaded</li>
1797 <li>Progress bar reports models as they are loaded to
1798 structure views</li>
1804 <li>Colour by conservation always enabled and no tick
1805 shown in menu when BLOSUM or PID shading applied</li>
1806 <li>FER1_ARATH and FER2_ARATH labels were switched in
1807 example sequences/projects/trees</li>
1809 <em>Application</em>
1811 <li>Jalview projects with views of local PDB structure
1812 files saved on Windows cannot be opened on OSX</li>
1813 <li>Multiple structure views can be opened and superposed
1814 without timeout for structures with multiple models or
1815 multiple sequences in alignment</li>
1816 <li>Cannot import or associated local PDB files without a
1817 PDB ID HEADER line</li>
1818 <li>RMSD is not output in Jmol console when superposition
1820 <li>Drag and drop of URL from Browser fails for Linux and
1821 OSX versions earlier than El Capitan</li>
1822 <li>ENA client ignores invalid content from ENA server</li>
1823 <li>Exceptions are not raised in console when ENA client
1824 attempts to fetch non-existent IDs via Fetch DB Refs UI
1826 <li>Exceptions are not raised in console when a new view
1827 is created on the alignment</li>
1828 <li>OSX right-click fixed for group selections: CMD-click
1829 to insert/remove gaps in groups and CTRL-click to open group
1832 <em>Build and deployment</em>
1834 <li>URL link checker now copes with multi-line anchor
1837 <em>New Known Issues</em>
1839 <li>Drag and drop from URL links in browsers do not work
1846 <td width="60" nowrap>
1847 <div align="center">
1848 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1851 <td><em>General</em>
1854 <!-- JAL-2124 -->Updated Spanish translations.
1857 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1858 for importing structure data to Jalview. Enables mmCIF and
1862 <!-- JAL-192 --->Alignment ruler shows positions relative to
1866 <!-- JAL-2202 -->Position/residue shown in status bar when
1867 mousing over sequence associated annotation
1870 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1874 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1875 '()', canonical '[]' and invalid '{}' base pair populations
1879 <!-- JAL-2092 -->Feature settings popup menu options for
1880 showing or hiding columns containing a feature
1883 <!-- JAL-1557 -->Edit selected group by double clicking on
1884 group and sequence associated annotation labels
1887 <!-- JAL-2236 -->Sequence name added to annotation label in
1888 select/hide columns by annotation and colour by annotation
1892 </ul> <em>Application</em>
1895 <!-- JAL-2050-->Automatically hide introns when opening a
1896 gene/transcript view
1899 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1903 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1904 structure mappings with the EMBL-EBI PDBe SIFTS database
1907 <!-- JAL-2079 -->Updated download sites used for Rfam and
1908 Pfam sources to xfam.org
1911 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1914 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1915 over sequences in Jalview
1918 <!-- JAL-2027-->Support for reverse-complement coding
1919 regions in ENA and EMBL
1922 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1923 for record retrieval via ENA rest API
1926 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1930 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1931 groovy script execution
1934 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1935 alignment window's Calculate menu
1938 <!-- JAL-1812 -->Allow groovy scripts that call
1939 Jalview.getAlignFrames() to run in headless mode
1942 <!-- JAL-2068 -->Support for creating new alignment
1943 calculation workers from groovy scripts
1946 <!-- JAL-1369 --->Store/restore reference sequence in
1950 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1951 associations are now saved/restored from project
1954 <!-- JAL-1993 -->Database selection dialog always shown
1955 before sequence fetcher is opened
1958 <!-- JAL-2183 -->Double click on an entry in Jalview's
1959 database chooser opens a sequence fetcher
1962 <!-- JAL-1563 -->Free-text search client for UniProt using
1963 the UniProt REST API
1966 <!-- JAL-2168 -->-nonews command line parameter to prevent
1967 the news reader opening
1970 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1971 querying stored in preferences
1974 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1978 <!-- JAL-1977-->Tooltips shown on database chooser
1981 <!-- JAL-391 -->Reverse complement function in calculate
1982 menu for nucleotide sequences
1985 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1986 and feature counts preserves alignment ordering (and
1987 debugged for complex feature sets).
1990 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1991 viewing structures with Jalview 2.10
1994 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1995 genome, transcript CCDS and gene ids via the Ensembl and
1996 Ensembl Genomes REST API
1999 <!-- JAL-2049 -->Protein sequence variant annotation
2000 computed for 'sequence_variant' annotation on CDS regions
2004 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2008 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2009 Ref Fetcher fails to match, or otherwise updates sequence
2010 data from external database records.
2013 <!-- JAL-2154 -->Revised Jalview Project format for
2014 efficient recovery of sequence coding and alignment
2015 annotation relationships.
2017 </ul> <!-- <em>Applet</em>
2028 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2032 <!-- JAL-2018-->Export features in Jalview format (again)
2033 includes graduated colourschemes
2036 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2037 working with big alignments and lots of hidden columns
2040 <!-- JAL-2053-->Hidden column markers not always rendered
2041 at right of alignment window
2044 <!-- JAL-2067 -->Tidied up links in help file table of
2048 <!-- JAL-2072 -->Feature based tree calculation not shown
2052 <!-- JAL-2075 -->Hidden columns ignored during feature
2053 based tree calculation
2056 <!-- JAL-2065 -->Alignment view stops updating when show
2057 unconserved enabled for group on alignment
2060 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2064 <!-- JAL-2146 -->Alignment column in status incorrectly
2065 shown as "Sequence position" when mousing over
2069 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2070 hidden columns present
2073 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2074 user created annotation added to alignment
2077 <!-- JAL-1841 -->RNA Structure consensus only computed for
2078 '()' base pair annotation
2081 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2082 in zero scores for all base pairs in RNA Structure
2086 <!-- JAL-2174-->Extend selection with columns containing
2090 <!-- JAL-2275 -->Pfam format writer puts extra space at
2091 beginning of sequence
2094 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2098 <!-- JAL-2238 -->Cannot create groups on an alignment from
2099 from a tree when t-coffee scores are shown
2102 <!-- JAL-1836,1967 -->Cannot import and view PDB
2103 structures with chains containing negative resnums (4q4h)
2106 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2110 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2111 to Clustal, PIR and PileUp output
2114 <!-- JAL-2008 -->Reordering sequence features that are
2115 not visible causes alignment window to repaint
2118 <!-- JAL-2006 -->Threshold sliders don't work in
2119 graduated colour and colour by annotation row for e-value
2120 scores associated with features and annotation rows
2123 <!-- JAL-1797 -->amino acid physicochemical conservation
2124 calculation should be case independent
2127 <!-- JAL-2173 -->Remove annotation also updates hidden
2131 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2132 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2133 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2136 <!-- JAL-2065 -->Null pointer exceptions and redraw
2137 problems when reference sequence defined and 'show
2138 non-conserved' enabled
2141 <!-- JAL-1306 -->Quality and Conservation are now shown on
2142 load even when Consensus calculation is disabled
2145 <!-- JAL-1932 -->Remove right on penultimate column of
2146 alignment does nothing
2149 <em>Application</em>
2152 <!-- JAL-1552-->URLs and links can't be imported by
2153 drag'n'drop on OSX when launched via webstart (note - not
2154 yet fixed for El Capitan)
2157 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2158 output when running on non-gb/us i18n platforms
2161 <!-- JAL-1944 -->Error thrown when exporting a view with
2162 hidden sequences as flat-file alignment
2165 <!-- JAL-2030-->InstallAnywhere distribution fails when
2169 <!-- JAL-2080-->Jalview very slow to launch via webstart
2170 (also hotfix for 2.9.0b2)
2173 <!-- JAL-2085 -->Cannot save project when view has a
2174 reference sequence defined
2177 <!-- JAL-1011 -->Columns are suddenly selected in other
2178 alignments and views when revealing hidden columns
2181 <!-- JAL-1989 -->Hide columns not mirrored in complement
2182 view in a cDNA/Protein splitframe
2185 <!-- JAL-1369 -->Cannot save/restore representative
2186 sequence from project when only one sequence is
2190 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2191 in Structure Chooser
2194 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2195 structure consensus didn't refresh annotation panel
2198 <!-- JAL-1962 -->View mapping in structure view shows
2199 mappings between sequence and all chains in a PDB file
2202 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2203 dialogs format columns correctly, don't display array
2204 data, sort columns according to type
2207 <!-- JAL-1975 -->Export complete shown after destination
2208 file chooser is cancelled during an image export
2211 <!-- JAL-2025 -->Error when querying PDB Service with
2212 sequence name containing special characters
2215 <!-- JAL-2024 -->Manual PDB structure querying should be
2219 <!-- JAL-2104 -->Large tooltips with broken HTML
2220 formatting don't wrap
2223 <!-- JAL-1128 -->Figures exported from wrapped view are
2224 truncated so L looks like I in consensus annotation
2227 <!-- JAL-2003 -->Export features should only export the
2228 currently displayed features for the current selection or
2232 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2233 after fetching cross-references, and restoring from
2237 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2238 followed in the structure viewer
2241 <!-- JAL-2163 -->Titles for individual alignments in
2242 splitframe not restored from project
2245 <!-- JAL-2145 -->missing autocalculated annotation at
2246 trailing end of protein alignment in transcript/product
2247 splitview when pad-gaps not enabled by default
2250 <!-- JAL-1797 -->amino acid physicochemical conservation
2254 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2255 article has been read (reopened issue due to
2256 internationalisation problems)
2259 <!-- JAL-1960 -->Only offer PDB structures in structure
2260 viewer based on sequence name, PDB and UniProt
2265 <!-- JAL-1976 -->No progress bar shown during export of
2269 <!-- JAL-2213 -->Structures not always superimposed after
2270 multiple structures are shown for one or more sequences.
2273 <!-- JAL-1370 -->Reference sequence characters should not
2274 be replaced with '.' when 'Show unconserved' format option
2278 <!-- JAL-1823 -->Cannot specify chain code when entering
2279 specific PDB id for sequence
2282 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2283 'Export hidden sequences' is enabled, but 'export hidden
2284 columns' is disabled.
2287 <!--JAL-2026-->Best Quality option in structure chooser
2288 selects lowest rather than highest resolution structures
2292 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2293 to sequence mapping in 'View Mappings' report
2296 <!-- JAL-2284 -->Unable to read old Jalview projects that
2297 contain non-XML data added after Jalvew wrote project.
2300 <!-- JAL-2118 -->Newly created annotation row reorders
2301 after clicking on it to create new annotation for a
2305 <!-- JAL-1980 -->Null Pointer Exception raised when
2306 pressing Add on an orphaned cut'n'paste window.
2308 <!-- may exclude, this is an external service stability issue JAL-1941
2309 -- > RNA 3D structure not added via DSSR service</li> -->
2314 <!-- JAL-2151 -->Incorrect columns are selected when
2315 hidden columns present before start of sequence
2318 <!-- JAL-1986 -->Missing dependencies on applet pages
2322 <!-- JAL-1947 -->Overview pixel size changes when
2323 sequences are hidden in applet
2326 <!-- JAL-1996 -->Updated instructions for applet
2327 deployment on examples pages.
2334 <td width="60" nowrap>
2335 <div align="center">
2336 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2337 <em>16/10/2015</em></strong>
2340 <td><em>General</em>
2342 <li>Time stamps for signed Jalview application and applet
2347 <em>Application</em>
2349 <li>Duplicate group consensus and conservation rows
2350 shown when tree is partitioned</li>
2351 <li>Erratic behaviour when tree partitions made with
2352 multiple cDNA/Protein split views</li>
2358 <td width="60" nowrap>
2359 <div align="center">
2360 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2361 <em>8/10/2015</em></strong>
2364 <td><em>General</em>
2366 <li>Updated Spanish translations of localized text for
2368 </ul> <em>Application</em>
2370 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2371 <li>Signed OSX InstallAnywhere installer<br></li>
2372 <li>Support for per-sequence based annotations in BioJSON</li>
2373 </ul> <em>Applet</em>
2375 <li>Split frame example added to applet examples page</li>
2376 </ul> <em>Build and Deployment</em>
2379 <!-- JAL-1888 -->New ant target for running Jalview's test
2387 <li>Mapping of cDNA to protein in split frames
2388 incorrect when sequence start > 1</li>
2389 <li>Broken images in filter column by annotation dialog
2391 <li>Feature colours not parsed from features file</li>
2392 <li>Exceptions and incomplete link URLs recovered when
2393 loading a features file containing HTML tags in feature
2397 <em>Application</em>
2399 <li>Annotations corrupted after BioJS export and
2401 <li>Incorrect sequence limits after Fetch DB References
2402 with 'trim retrieved sequences'</li>
2403 <li>Incorrect warning about deleting all data when
2404 deleting selected columns</li>
2405 <li>Patch to build system for shipping properly signed
2406 JNLP templates for webstart launch</li>
2407 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2408 unreleased structures for download or viewing</li>
2409 <li>Tab/space/return keystroke operation of EMBL-PDBe
2410 fetcher/viewer dialogs works correctly</li>
2411 <li>Disabled 'minimise' button on Jalview windows
2412 running on OSX to workaround redraw hang bug</li>
2413 <li>Split cDNA/Protein view position and geometry not
2414 recovered from jalview project</li>
2415 <li>Initial enabled/disabled state of annotation menu
2416 sorter 'show autocalculated first/last' corresponds to
2418 <li>Restoring of Clustal, RNA Helices and T-Coffee
2419 color schemes from BioJSON</li>
2423 <li>Reorder sequences mirrored in cDNA/Protein split
2425 <li>Applet with Jmol examples not loading correctly</li>
2431 <td><div align="center">
2432 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2434 <td><em>General</em>
2436 <li>Linked visualisation and analysis of DNA and Protein
2439 <li>Translated cDNA alignments shown as split protein
2440 and DNA alignment views</li>
2441 <li>Codon consensus annotation for linked protein and
2442 cDNA alignment views</li>
2443 <li>Link cDNA or Protein product sequences by loading
2444 them onto Protein or cDNA alignments</li>
2445 <li>Reconstruct linked cDNA alignment from aligned
2446 protein sequences</li>
2449 <li>Jmol integration updated to Jmol v14.2.14</li>
2450 <li>Import and export of Jalview alignment views as <a
2451 href="features/bioJsonFormat.html">BioJSON</a></li>
2452 <li>New alignment annotation file statements for
2453 reference sequences and marking hidden columns</li>
2454 <li>Reference sequence based alignment shading to
2455 highlight variation</li>
2456 <li>Select or hide columns according to alignment
2458 <li>Find option for locating sequences by description</li>
2459 <li>Conserved physicochemical properties shown in amino
2460 acid conservation row</li>
2461 <li>Alignments can be sorted by number of RNA helices</li>
2462 </ul> <em>Application</em>
2464 <li>New cDNA/Protein analysis capabilities
2466 <li>Get Cross-References should open a Split Frame
2467 view with cDNA/Protein</li>
2468 <li>Detect when nucleotide sequences and protein
2469 sequences are placed in the same alignment</li>
2470 <li>Split cDNA/Protein views are saved in Jalview
2475 <li>Use REST API to talk to Chimera</li>
2476 <li>Selected regions in Chimera are highlighted in linked
2477 Jalview windows</li>
2479 <li>VARNA RNA viewer updated to v3.93</li>
2480 <li>VARNA views are saved in Jalview Projects</li>
2481 <li>Pseudoknots displayed as Jalview RNA annotation can
2482 be shown in VARNA</li>
2484 <li>Make groups for selection uses marked columns as well
2485 as the active selected region</li>
2487 <li>Calculate UPGMA and NJ trees using sequence feature
2489 <li>New Export options
2491 <li>New Export Settings dialog to control hidden
2492 region export in flat file generation</li>
2494 <li>Export alignment views for display with the <a
2495 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2497 <li>Export scrollable SVG in HTML page</li>
2498 <li>Optional embedding of BioJSON data when exporting
2499 alignment figures to HTML</li>
2501 <li>3D structure retrieval and display
2503 <li>Free text and structured queries with the PDBe
2505 <li>PDBe Search API based discovery and selection of
2506 PDB structures for a sequence set</li>
2510 <li>JPred4 employed for protein secondary structure
2512 <li>Hide Insertions menu option to hide unaligned columns
2513 for one or a group of sequences</li>
2514 <li>Automatically hide insertions in alignments imported
2515 from the JPred4 web server</li>
2516 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2517 system on OSX<br />LGPL libraries courtesy of <a
2518 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2520 <li>changed 'View nucleotide structure' submenu to 'View
2521 VARNA 2D Structure'</li>
2522 <li>change "View protein structure" menu option to "3D
2525 </ul> <em>Applet</em>
2527 <li>New layout for applet example pages</li>
2528 <li>New parameters to enable SplitFrame view
2529 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2530 <li>New example demonstrating linked viewing of cDNA and
2531 Protein alignments</li>
2532 </ul> <em>Development and deployment</em>
2534 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2535 <li>Include installation type and git revision in build
2536 properties and console log output</li>
2537 <li>Jalview Github organisation, and new github site for
2538 storing BioJsMSA Templates</li>
2539 <li>Jalview's unit tests now managed with TestNG</li>
2542 <!-- <em>General</em>
2544 </ul> --> <!-- issues resolved --> <em>Application</em>
2546 <li>Escape should close any open find dialogs</li>
2547 <li>Typo in select-by-features status report</li>
2548 <li>Consensus RNA secondary secondary structure
2549 predictions are not highlighted in amber</li>
2550 <li>Missing gap character in v2.7 example file means
2551 alignment appears unaligned when pad-gaps is not enabled</li>
2552 <li>First switch to RNA Helices colouring doesn't colour
2553 associated structure views</li>
2554 <li>ID width preference option is greyed out when auto
2555 width checkbox not enabled</li>
2556 <li>Stopped a warning dialog from being shown when
2557 creating user defined colours</li>
2558 <li>'View Mapping' in structure viewer shows sequence
2559 mappings for just that viewer's sequences</li>
2560 <li>Workaround for superposing PDB files containing
2561 multiple models in Chimera</li>
2562 <li>Report sequence position in status bar when hovering
2563 over Jmol structure</li>
2564 <li>Cannot output gaps as '.' symbols with Selection ->
2565 output to text box</li>
2566 <li>Flat file exports of alignments with hidden columns
2567 have incorrect sequence start/end</li>
2568 <li>'Aligning' a second chain to a Chimera structure from
2570 <li>Colour schemes applied to structure viewers don't
2571 work for nucleotide</li>
2572 <li>Loading/cut'n'pasting an empty or invalid file leads
2573 to a grey/invisible alignment window</li>
2574 <li>Exported Jpred annotation from a sequence region
2575 imports to different position</li>
2576 <li>Space at beginning of sequence feature tooltips shown
2577 on some platforms</li>
2578 <li>Chimera viewer 'View | Show Chain' menu is not
2580 <li>'New View' fails with a Null Pointer Exception in
2581 console if Chimera has been opened</li>
2582 <li>Mouseover to Chimera not working</li>
2583 <li>Miscellaneous ENA XML feature qualifiers not
2585 <li>NPE in annotation renderer after 'Extract Scores'</li>
2586 <li>If two structures in one Chimera window, mouseover of
2587 either sequence shows on first structure</li>
2588 <li>'Show annotations' options should not make
2589 non-positional annotations visible</li>
2590 <li>Subsequence secondary structure annotation not shown
2591 in right place after 'view flanking regions'</li>
2592 <li>File Save As type unset when current file format is
2594 <li>Save as '.jar' option removed for saving Jalview
2596 <li>Colour by Sequence colouring in Chimera more
2598 <li>Cannot 'add reference annotation' for a sequence in
2599 several views on same alignment</li>
2600 <li>Cannot show linked products for EMBL / ENA records</li>
2601 <li>Jalview's tooltip wraps long texts containing no
2603 </ul> <em>Applet</em>
2605 <li>Jmol to JalviewLite mouseover/link not working</li>
2606 <li>JalviewLite can't import sequences with ID
2607 descriptions containing angle brackets</li>
2608 </ul> <em>General</em>
2610 <li>Cannot export and reimport RNA secondary structure
2611 via jalview annotation file</li>
2612 <li>Random helix colour palette for colour by annotation
2613 with RNA secondary structure</li>
2614 <li>Mouseover to cDNA from STOP residue in protein
2615 translation doesn't work.</li>
2616 <li>hints when using the select by annotation dialog box</li>
2617 <li>Jmol alignment incorrect if PDB file has alternate CA
2619 <li>FontChooser message dialog appears to hang after
2620 choosing 1pt font</li>
2621 <li>Peptide secondary structure incorrectly imported from
2622 annotation file when annotation display text includes 'e' or
2624 <li>Cannot set colour of new feature type whilst creating
2626 <li>cDNA translation alignment should not be sequence
2627 order dependent</li>
2628 <li>'Show unconserved' doesn't work for lower case
2630 <li>Nucleotide ambiguity codes involving R not recognised</li>
2631 </ul> <em>Deployment and Documentation</em>
2633 <li>Applet example pages appear different to the rest of
2634 www.jalview.org</li>
2635 </ul> <em>Application Known issues</em>
2637 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2638 <li>Misleading message appears after trying to delete
2640 <li>Jalview icon not shown in dock after InstallAnywhere
2641 version launches</li>
2642 <li>Fetching EMBL reference for an RNA sequence results
2643 fails with a sequence mismatch</li>
2644 <li>Corrupted or unreadable alignment display when
2645 scrolling alignment to right</li>
2646 <li>ArrayIndexOutOfBoundsException thrown when remove
2647 empty columns called on alignment with ragged gapped ends</li>
2648 <li>auto calculated alignment annotation rows do not get
2649 placed above or below non-autocalculated rows</li>
2650 <li>Jalview dekstop becomes sluggish at full screen in
2651 ultra-high resolution</li>
2652 <li>Cannot disable consensus calculation independently of
2653 quality and conservation</li>
2654 <li>Mouseover highlighting between cDNA and protein can
2655 become sluggish with more than one splitframe shown</li>
2656 </ul> <em>Applet Known Issues</em>
2658 <li>Core PDB parsing code requires Jmol</li>
2659 <li>Sequence canvas panel goes white when alignment
2660 window is being resized</li>
2666 <td><div align="center">
2667 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2669 <td><em>General</em>
2671 <li>Updated Java code signing certificate donated by
2673 <li>Features and annotation preserved when performing
2674 pairwise alignment</li>
2675 <li>RNA pseudoknot annotation can be
2676 imported/exported/displayed</li>
2677 <li>'colour by annotation' can colour by RNA and
2678 protein secondary structure</li>
2679 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2680 post-hoc with 2.9 release</em>)
2683 </ul> <em>Application</em>
2685 <li>Extract and display secondary structure for sequences
2686 with 3D structures</li>
2687 <li>Support for parsing RNAML</li>
2688 <li>Annotations menu for layout
2690 <li>sort sequence annotation rows by alignment</li>
2691 <li>place sequence annotation above/below alignment
2694 <li>Output in Stockholm format</li>
2695 <li>Internationalisation: improved Spanish (es)
2697 <li>Structure viewer preferences tab</li>
2698 <li>Disorder and Secondary Structure annotation tracks
2699 shared between alignments</li>
2700 <li>UCSF Chimera launch and linked highlighting from
2702 <li>Show/hide all sequence associated annotation rows for
2703 all or current selection</li>
2704 <li>disorder and secondary structure predictions
2705 available as dataset annotation</li>
2706 <li>Per-sequence rna helices colouring</li>
2709 <li>Sequence database accessions imported when fetching
2710 alignments from Rfam</li>
2711 <li>update VARNA version to 3.91</li>
2713 <li>New groovy scripts for exporting aligned positions,
2714 conservation values, and calculating sum of pairs scores.</li>
2715 <li>Command line argument to set default JABAWS server</li>
2716 <li>include installation type in build properties and
2717 console log output</li>
2718 <li>Updated Jalview project format to preserve dataset
2722 <!-- issues resolved --> <em>Application</em>
2724 <li>Distinguish alignment and sequence associated RNA
2725 structure in structure->view->VARNA</li>
2726 <li>Raise dialog box if user deletes all sequences in an
2728 <li>Pressing F1 results in documentation opening twice</li>
2729 <li>Sequence feature tooltip is wrapped</li>
2730 <li>Double click on sequence associated annotation
2731 selects only first column</li>
2732 <li>Redundancy removal doesn't result in unlinked
2733 leaves shown in tree</li>
2734 <li>Undos after several redundancy removals don't undo
2736 <li>Hide sequence doesn't hide associated annotation</li>
2737 <li>User defined colours dialog box too big to fit on
2738 screen and buttons not visible</li>
2739 <li>author list isn't updated if already written to
2740 Jalview properties</li>
2741 <li>Popup menu won't open after retrieving sequence
2743 <li>File open window for associate PDB doesn't open</li>
2744 <li>Left-then-right click on a sequence id opens a
2745 browser search window</li>
2746 <li>Cannot open sequence feature shading/sort popup menu
2747 in feature settings dialog</li>
2748 <li>better tooltip placement for some areas of Jalview
2750 <li>Allow addition of JABAWS Server which doesn't
2751 pass validation</li>
2752 <li>Web services parameters dialog box is too large to
2754 <li>Muscle nucleotide alignment preset obscured by
2756 <li>JABAWS preset submenus don't contain newly
2757 defined user preset</li>
2758 <li>MSA web services warns user if they were launched
2759 with invalid input</li>
2760 <li>Jalview cannot contact DAS Registy when running on
2763 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2764 'Superpose with' submenu not shown when new view
2768 </ul> <!-- <em>Applet</em>
2770 </ul> <em>General</em>
2772 </ul>--> <em>Deployment and Documentation</em>
2774 <li>2G and 1G options in launchApp have no effect on
2775 memory allocation</li>
2776 <li>launchApp service doesn't automatically open
2777 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2779 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2780 InstallAnywhere reports cannot find valid JVM when Java
2781 1.7_055 is available
2783 </ul> <em>Application Known issues</em>
2786 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2787 corrupted or unreadable alignment display when scrolling
2791 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2792 retrieval fails but progress bar continues for DAS retrieval
2793 with large number of ID
2796 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2797 flatfile output of visible region has incorrect sequence
2801 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2802 rna structure consensus doesn't update when secondary
2803 structure tracks are rearranged
2806 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2807 invalid rna structure positional highlighting does not
2808 highlight position of invalid base pairs
2811 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2812 out of memory errors are not raised when saving Jalview
2813 project from alignment window file menu
2816 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2817 Switching to RNA Helices colouring doesn't propagate to
2821 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2822 colour by RNA Helices not enabled when user created
2823 annotation added to alignment
2826 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2827 Jalview icon not shown on dock in Mountain Lion/Webstart
2829 </ul> <em>Applet Known Issues</em>
2832 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2833 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2836 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2837 Jalview and Jmol example not compatible with IE9
2840 <li>Sort by annotation score doesn't reverse order
2846 <td><div align="center">
2847 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2850 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2853 <li>Internationalisation of user interface (usually
2854 called i18n support) and translation for Spanish locale</li>
2855 <li>Define/Undefine group on current selection with
2856 Ctrl-G/Shift Ctrl-G</li>
2857 <li>Improved group creation/removal options in
2858 alignment/sequence Popup menu</li>
2859 <li>Sensible precision for symbol distribution
2860 percentages shown in logo tooltip.</li>
2861 <li>Annotation panel height set according to amount of
2862 annotation when alignment first opened</li>
2863 </ul> <em>Application</em>
2865 <li>Interactive consensus RNA secondary structure
2866 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2867 <li>Select columns containing particular features from
2868 Feature Settings dialog</li>
2869 <li>View all 'representative' PDB structures for selected
2871 <li>Update Jalview project format:
2873 <li>New file extension for Jalview projects '.jvp'</li>
2874 <li>Preserve sequence and annotation dataset (to
2875 store secondary structure annotation,etc)</li>
2876 <li>Per group and alignment annotation and RNA helix
2880 <li>New similarity measures for PCA and Tree calculation
2882 <li>Experimental support for retrieval and viewing of
2883 flanking regions for an alignment</li>
2887 <!-- issues resolved --> <em>Application</em>
2889 <li>logo keeps spinning and status remains at queued or
2890 running after job is cancelled</li>
2891 <li>cannot export features from alignments imported from
2892 Jalview/VAMSAS projects</li>
2893 <li>Buggy slider for web service parameters that take
2895 <li>Newly created RNA secondary structure line doesn't
2896 have 'display all symbols' flag set</li>
2897 <li>T-COFFEE alignment score shading scheme and other
2898 annotation shading not saved in Jalview project</li>
2899 <li>Local file cannot be loaded in freshly downloaded
2901 <li>Jalview icon not shown on dock in Mountain
2903 <li>Load file from desktop file browser fails</li>
2904 <li>Occasional NPE thrown when calculating large trees</li>
2905 <li>Cannot reorder or slide sequences after dragging an
2906 alignment onto desktop</li>
2907 <li>Colour by annotation dialog throws NPE after using
2908 'extract scores' function</li>
2909 <li>Loading/cut'n'pasting an empty file leads to a grey
2910 alignment window</li>
2911 <li>Disorder thresholds rendered incorrectly after
2912 performing IUPred disorder prediction</li>
2913 <li>Multiple group annotated consensus rows shown when
2914 changing 'normalise logo' display setting</li>
2915 <li>Find shows blank dialog after 'finished searching' if
2916 nothing matches query</li>
2917 <li>Null Pointer Exceptions raised when sorting by
2918 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2920 <li>Errors in Jmol console when structures in alignment
2921 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2923 <li>Not all working JABAWS services are shown in
2925 <li>JAVAWS version of Jalview fails to launch with
2926 'invalid literal/length code'</li>
2927 <li>Annotation/RNA Helix colourschemes cannot be applied
2928 to alignment with groups (actually fixed in 2.8.0b1)</li>
2929 <li>RNA Helices and T-Coffee Scores available as default
2932 </ul> <em>Applet</em>
2934 <li>Remove group option is shown even when selection is
2936 <li>Apply to all groups ticked but colourscheme changes
2937 don't affect groups</li>
2938 <li>Documented RNA Helices and T-Coffee Scores as valid
2939 colourscheme name</li>
2940 <li>Annotation labels drawn on sequence IDs when
2941 Annotation panel is not displayed</li>
2942 <li>Increased font size for dropdown menus on OSX and
2943 embedded windows</li>
2944 </ul> <em>Other</em>
2946 <li>Consensus sequence for alignments/groups with a
2947 single sequence were not calculated</li>
2948 <li>annotation files that contain only groups imported as
2949 annotation and junk sequences</li>
2950 <li>Fasta files with sequences containing '*' incorrectly
2951 recognised as PFAM or BLC</li>
2952 <li>conservation/PID slider apply all groups option
2953 doesn't affect background (2.8.0b1)
2955 <li>redundancy highlighting is erratic at 0% and 100%</li>
2956 <li>Remove gapped columns fails for sequences with ragged
2958 <li>AMSA annotation row with leading spaces is not
2959 registered correctly on import</li>
2960 <li>Jalview crashes when selecting PCA analysis for
2961 certain alignments</li>
2962 <li>Opening the colour by annotation dialog for an
2963 existing annotation based 'use original colours'
2964 colourscheme loses original colours setting</li>
2969 <td><div align="center">
2970 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2971 <em>30/1/2014</em></strong>
2975 <li>Trusted certificates for JalviewLite applet and
2976 Jalview Desktop application<br />Certificate was donated by
2977 <a href="https://www.certum.eu">Certum</a> to the Jalview
2978 open source project).
2980 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2981 <li>Output in Stockholm format</li>
2982 <li>Allow import of data from gzipped files</li>
2983 <li>Export/import group and sequence associated line
2984 graph thresholds</li>
2985 <li>Nucleotide substitution matrix that supports RNA and
2986 ambiguity codes</li>
2987 <li>Allow disorder predictions to be made on the current
2988 selection (or visible selection) in the same way that JPred
2990 <li>Groovy scripting for headless Jalview operation</li>
2991 </ul> <em>Other improvements</em>
2993 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2994 <li>COMBINE statement uses current SEQUENCE_REF and
2995 GROUP_REF scope to group annotation rows</li>
2996 <li>Support '' style escaping of quotes in Newick
2998 <li>Group options for JABAWS service by command line name</li>
2999 <li>Empty tooltip shown for JABA service options with a
3000 link but no description</li>
3001 <li>Select primary source when selecting authority in
3002 database fetcher GUI</li>
3003 <li>Add .mfa to FASTA file extensions recognised by
3005 <li>Annotation label tooltip text wrap</li>
3010 <li>Slow scrolling when lots of annotation rows are
3012 <li>Lots of NPE (and slowness) after creating RNA
3013 secondary structure annotation line</li>
3014 <li>Sequence database accessions not imported when
3015 fetching alignments from Rfam</li>
3016 <li>Incorrect SHMR submission for sequences with
3018 <li>View all structures does not always superpose
3020 <li>Option widgets in service parameters not updated to
3021 reflect user or preset settings</li>
3022 <li>Null pointer exceptions for some services without
3023 presets or adjustable parameters</li>
3024 <li>Discover PDB IDs entry in structure menu doesn't
3025 discover PDB xRefs</li>
3026 <li>Exception encountered while trying to retrieve
3027 features with DAS</li>
3028 <li>Lowest value in annotation row isn't coloured
3029 when colour by annotation (per sequence) is coloured</li>
3030 <li>Keyboard mode P jumps to start of gapped region when
3031 residue follows a gap</li>
3032 <li>Jalview appears to hang importing an alignment with
3033 Wrap as default or after enabling Wrap</li>
3034 <li>'Right click to add annotations' message
3035 shown in wrap mode when no annotations present</li>
3036 <li>Disorder predictions fail with NPE if no automatic
3037 annotation already exists on alignment</li>
3038 <li>oninit javascript function should be called after
3039 initialisation completes</li>
3040 <li>Remove redundancy after disorder prediction corrupts
3041 alignment window display</li>
3042 <li>Example annotation file in documentation is invalid</li>
3043 <li>Grouped line graph annotation rows are not exported
3044 to annotation file</li>
3045 <li>Multi-harmony analysis cannot be run when only two
3047 <li>Cannot create multiple groups of line graphs with
3048 several 'combine' statements in annotation file</li>
3049 <li>Pressing return several times causes Number Format
3050 exceptions in keyboard mode</li>
3051 <li>Multi-harmony (SHMMR) method doesn't submit
3052 correct partitions for input data</li>
3053 <li>Translation from DNA to Amino Acids fails</li>
3054 <li>Jalview fail to load newick tree with quoted label</li>
3055 <li>--headless flag isn't understood</li>
3056 <li>ClassCastException when generating EPS in headless
3058 <li>Adjusting sequence-associated shading threshold only
3059 changes one row's threshold</li>
3060 <li>Preferences and Feature settings panel panel
3061 doesn't open</li>
3062 <li>hide consensus histogram also hides conservation and
3063 quality histograms</li>
3068 <td><div align="center">
3069 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3071 <td><em>Application</em>
3073 <li>Support for JABAWS 2.0 Services (AACon alignment
3074 conservation, protein disorder and Clustal Omega)</li>
3075 <li>JABAWS server status indicator in Web Services
3077 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3078 in Jalview alignment window</li>
3079 <li>Updated Jalview build and deploy framework for OSX
3080 mountain lion, windows 7, and 8</li>
3081 <li>Nucleotide substitution matrix for PCA that supports
3082 RNA and ambiguity codes</li>
3084 <li>Improved sequence database retrieval GUI</li>
3085 <li>Support fetching and database reference look up
3086 against multiple DAS sources (Fetch all from in 'fetch db
3088 <li>Jalview project improvements
3090 <li>Store and retrieve the 'belowAlignment'
3091 flag for annotation</li>
3092 <li>calcId attribute to group annotation rows on the
3094 <li>Store AACon calculation settings for a view in
3095 Jalview project</li>
3099 <li>horizontal scrolling gesture support</li>
3100 <li>Visual progress indicator when PCA calculation is
3102 <li>Simpler JABA web services menus</li>
3103 <li>visual indication that web service results are still
3104 being retrieved from server</li>
3105 <li>Serialise the dialogs that are shown when Jalview
3106 starts up for first time</li>
3107 <li>Jalview user agent string for interacting with HTTP
3109 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3111 <li>Examples directory and Groovy library included in
3112 InstallAnywhere distribution</li>
3113 </ul> <em>Applet</em>
3115 <li>RNA alignment and secondary structure annotation
3116 visualization applet example</li>
3117 </ul> <em>General</em>
3119 <li>Normalise option for consensus sequence logo</li>
3120 <li>Reset button in PCA window to return dimensions to
3122 <li>Allow seqspace or Jalview variant of alignment PCA
3124 <li>PCA with either nucleic acid and protein substitution
3126 <li>Allow windows containing HTML reports to be exported
3128 <li>Interactive display and editing of RNA secondary
3129 structure contacts</li>
3130 <li>RNA Helix Alignment Colouring</li>
3131 <li>RNA base pair logo consensus</li>
3132 <li>Parse sequence associated secondary structure
3133 information in Stockholm files</li>
3134 <li>HTML Export database accessions and annotation
3135 information presented in tooltip for sequences</li>
3136 <li>Import secondary structure from LOCARNA clustalw
3137 style RNA alignment files</li>
3138 <li>import and visualise T-COFFEE quality scores for an
3140 <li>'colour by annotation' per sequence option to
3141 shade each sequence according to its associated alignment
3143 <li>New Jalview Logo</li>
3144 </ul> <em>Documentation and Development</em>
3146 <li>documentation for score matrices used in Jalview</li>
3147 <li>New Website!</li>
3149 <td><em>Application</em>
3151 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3152 wsdbfetch REST service</li>
3153 <li>Stop windows being moved outside desktop on OSX</li>
3154 <li>Filetype associations not installed for webstart
3156 <li>Jalview does not always retrieve progress of a JABAWS
3157 job execution in full once it is complete</li>
3158 <li>revise SHMR RSBS definition to ensure alignment is
3159 uploaded via ali_file parameter</li>
3160 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3161 <li>View all structures superposed fails with exception</li>
3162 <li>Jnet job queues forever if a very short sequence is
3163 submitted for prediction</li>
3164 <li>Cut and paste menu not opened when mouse clicked on
3166 <li>Putting fractional value into integer text box in
3167 alignment parameter dialog causes Jalview to hang</li>
3168 <li>Structure view highlighting doesn't work on
3170 <li>View all structures fails with exception shown in
3172 <li>Characters in filename associated with PDBEntry not
3173 escaped in a platform independent way</li>
3174 <li>Jalview desktop fails to launch with exception when
3176 <li>Tree calculation reports 'you must have 2 or more
3177 sequences selected' when selection is empty</li>
3178 <li>Jalview desktop fails to launch with jar signature
3179 failure when java web start temporary file caching is
3181 <li>DAS Sequence retrieval with range qualification
3182 results in sequence xref which includes range qualification</li>
3183 <li>Errors during processing of command line arguments
3184 cause progress bar (JAL-898) to be removed</li>
3185 <li>Replace comma for semi-colon option not disabled for
3186 DAS sources in sequence fetcher</li>
3187 <li>Cannot close news reader when JABAWS server warning
3188 dialog is shown</li>
3189 <li>Option widgets not updated to reflect user settings</li>
3190 <li>Edited sequence not submitted to web service</li>
3191 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3192 <li>InstallAnywhere installer doesn't unpack and run
3193 on OSX Mountain Lion</li>
3194 <li>Annotation panel not given a scroll bar when
3195 sequences with alignment annotation are pasted into the
3197 <li>Sequence associated annotation rows not associated
3198 when loaded from Jalview project</li>
3199 <li>Browser launch fails with NPE on java 1.7</li>
3200 <li>JABAWS alignment marked as finished when job was
3201 cancelled or job failed due to invalid input</li>
3202 <li>NPE with v2.7 example when clicking on Tree
3203 associated with all views</li>
3204 <li>Exceptions when copy/paste sequences with grouped
3205 annotation rows to new window</li>
3206 </ul> <em>Applet</em>
3208 <li>Sequence features are momentarily displayed before
3209 they are hidden using hidefeaturegroups applet parameter</li>
3210 <li>loading features via javascript API automatically
3211 enables feature display</li>
3212 <li>scrollToColumnIn javascript API method doesn't
3214 </ul> <em>General</em>
3216 <li>Redundancy removal fails for rna alignment</li>
3217 <li>PCA calculation fails when sequence has been selected
3218 and then deselected</li>
3219 <li>PCA window shows grey box when first opened on OSX</li>
3220 <li>Letters coloured pink in sequence logo when alignment
3221 coloured with clustalx</li>
3222 <li>Choosing fonts without letter symbols defined causes
3223 exceptions and redraw errors</li>
3224 <li>Initial PCA plot view is not same as manually
3225 reconfigured view</li>
3226 <li>Grouped annotation graph label has incorrect line
3228 <li>Grouped annotation graph label display is corrupted
3229 for lots of labels</li>
3234 <div align="center">
3235 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3238 <td><em>Application</em>
3240 <li>Jalview Desktop News Reader</li>
3241 <li>Tweaked default layout of web services menu</li>
3242 <li>View/alignment association menu to enable user to
3243 easily specify which alignment a multi-structure view takes
3244 its colours/correspondences from</li>
3245 <li>Allow properties file location to be specified as URL</li>
3246 <li>Extend Jalview project to preserve associations
3247 between many alignment views and a single Jmol display</li>
3248 <li>Store annotation row height in Jalview project file</li>
3249 <li>Annotation row column label formatting attributes
3250 stored in project file</li>
3251 <li>Annotation row order for auto-calculated annotation
3252 rows preserved in Jalview project file</li>
3253 <li>Visual progress indication when Jalview state is
3254 saved using Desktop window menu</li>
3255 <li>Visual indication that command line arguments are
3256 still being processed</li>
3257 <li>Groovy script execution from URL</li>
3258 <li>Colour by annotation default min and max colours in
3260 <li>Automatically associate PDB files dragged onto an
3261 alignment with sequences that have high similarity and
3263 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3264 <li>'view structures' option to open many
3265 structures in same window</li>
3266 <li>Sort associated views menu option for tree panel</li>
3267 <li>Group all JABA and non-JABA services for a particular
3268 analysis function in its own submenu</li>
3269 </ul> <em>Applet</em>
3271 <li>Userdefined and autogenerated annotation rows for
3273 <li>Adjustment of alignment annotation pane height</li>
3274 <li>Annotation scrollbar for annotation panel</li>
3275 <li>Drag to reorder annotation rows in annotation panel</li>
3276 <li>'automaticScrolling' parameter</li>
3277 <li>Allow sequences with partial ID string matches to be
3278 annotated from GFF/Jalview features files</li>
3279 <li>Sequence logo annotation row in applet</li>
3280 <li>Absolute paths relative to host server in applet
3281 parameters are treated as such</li>
3282 <li>New in the JalviewLite javascript API:
3284 <li>JalviewLite.js javascript library</li>
3285 <li>Javascript callbacks for
3287 <li>Applet initialisation</li>
3288 <li>Sequence/alignment mouse-overs and selections</li>
3291 <li>scrollTo row and column alignment scrolling
3293 <li>Select sequence/alignment regions from javascript</li>
3294 <li>javascript structure viewer harness to pass
3295 messages between Jmol and Jalview when running as
3296 distinct applets</li>
3297 <li>sortBy method</li>
3298 <li>Set of applet and application examples shipped
3299 with documentation</li>
3300 <li>New example to demonstrate JalviewLite and Jmol
3301 javascript message exchange</li>
3303 </ul> <em>General</em>
3305 <li>Enable Jmol displays to be associated with multiple
3306 multiple alignments</li>
3307 <li>Option to automatically sort alignment with new tree</li>
3308 <li>User configurable link to enable redirects to a
3309 www.Jalview.org mirror</li>
3310 <li>Jmol colours option for Jmol displays</li>
3311 <li>Configurable newline string when writing alignment
3312 and other flat files</li>
3313 <li>Allow alignment annotation description lines to
3314 contain html tags</li>
3315 </ul> <em>Documentation and Development</em>
3317 <li>Add groovy test harness for bulk load testing to
3319 <li>Groovy script to load and align a set of sequences
3320 using a web service before displaying the result in the
3321 Jalview desktop</li>
3322 <li>Restructured javascript and applet api documentation</li>
3323 <li>Ant target to publish example html files with applet
3325 <li>Netbeans project for building Jalview from source</li>
3326 <li>ant task to create online javadoc for Jalview source</li>
3328 <td><em>Application</em>
3330 <li>User defined colourscheme throws exception when
3331 current built in colourscheme is saved as new scheme</li>
3332 <li>AlignFrame->Save in application pops up save
3333 dialog for valid filename/format</li>
3334 <li>Cannot view associated structure for UniProt sequence</li>
3335 <li>PDB file association breaks for UniProt sequence
3337 <li>Associate PDB from file dialog does not tell you
3338 which sequence is to be associated with the file</li>
3339 <li>Find All raises null pointer exception when query
3340 only matches sequence IDs</li>
3341 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3342 <li>Jalview project with Jmol views created with Jalview
3343 2.4 cannot be loaded</li>
3344 <li>Filetype associations not installed for webstart
3346 <li>Two or more chains in a single PDB file associated
3347 with sequences in different alignments do not get coloured
3348 by their associated sequence</li>
3349 <li>Visibility status of autocalculated annotation row
3350 not preserved when project is loaded</li>
3351 <li>Annotation row height and visibility attributes not
3352 stored in Jalview project</li>
3353 <li>Tree bootstraps are not preserved when saved as a
3354 Jalview project</li>
3355 <li>Envision2 workflow tooltips are corrupted</li>
3356 <li>Enabling show group conservation also enables colour
3357 by conservation</li>
3358 <li>Duplicate group associated conservation or consensus
3359 created on new view</li>
3360 <li>Annotation scrollbar not displayed after 'show
3361 all hidden annotation rows' option selected</li>
3362 <li>Alignment quality not updated after alignment
3363 annotation row is hidden then shown</li>
3364 <li>Preserve colouring of structures coloured by
3365 sequences in pre Jalview 2.7 projects</li>
3366 <li>Web service job parameter dialog is not laid out
3368 <li>Web services menu not refreshed after 'reset
3369 services' button is pressed in preferences</li>
3370 <li>Annotation off by one in Jalview v2_3 example project</li>
3371 <li>Structures imported from file and saved in project
3372 get name like jalview_pdb1234.txt when reloaded</li>
3373 <li>Jalview does not always retrieve progress of a JABAWS
3374 job execution in full once it is complete</li>
3375 </ul> <em>Applet</em>
3377 <li>Alignment height set incorrectly when lots of
3378 annotation rows are displayed</li>
3379 <li>Relative URLs in feature HTML text not resolved to
3381 <li>View follows highlighting does not work for positions
3383 <li><= shown as = in tooltip</li>
3384 <li>Export features raises exception when no features
3386 <li>Separator string used for serialising lists of IDs
3387 for javascript api is modified when separator string
3388 provided as parameter</li>
3389 <li>Null pointer exception when selecting tree leaves for
3390 alignment with no existing selection</li>
3391 <li>Relative URLs for datasources assumed to be relative
3392 to applet's codebase</li>
3393 <li>Status bar not updated after finished searching and
3394 search wraps around to first result</li>
3395 <li>StructureSelectionManager instance shared between
3396 several Jalview applets causes race conditions and memory
3398 <li>Hover tooltip and mouseover of position on structure
3399 not sent from Jmol in applet</li>
3400 <li>Certain sequences of javascript method calls to
3401 applet API fatally hang browser</li>
3402 </ul> <em>General</em>
3404 <li>View follows structure mouseover scrolls beyond
3405 position with wrapped view and hidden regions</li>
3406 <li>Find sequence position moves to wrong residue
3407 with/without hidden columns</li>
3408 <li>Sequence length given in alignment properties window
3410 <li>InvalidNumberFormat exceptions thrown when trying to
3411 import PDB like structure files</li>
3412 <li>Positional search results are only highlighted
3413 between user-supplied sequence start/end bounds</li>
3414 <li>End attribute of sequence is not validated</li>
3415 <li>Find dialog only finds first sequence containing a
3416 given sequence position</li>
3417 <li>Sequence numbering not preserved in MSF alignment
3419 <li>Jalview PDB file reader does not extract sequence
3420 from nucleotide chains correctly</li>
3421 <li>Structure colours not updated when tree partition
3422 changed in alignment</li>
3423 <li>Sequence associated secondary structure not correctly
3424 parsed in interleaved stockholm</li>
3425 <li>Colour by annotation dialog does not restore current
3427 <li>Hiding (nearly) all sequences doesn't work
3429 <li>Sequences containing lowercase letters are not
3430 properly associated with their pdb files</li>
3431 </ul> <em>Documentation and Development</em>
3433 <li>schemas/JalviewWsParamSet.xsd corrupted by
3434 ApplyCopyright tool</li>
3439 <div align="center">
3440 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3443 <td><em>Application</em>
3445 <li>New warning dialog when the Jalview Desktop cannot
3446 contact web services</li>
3447 <li>JABA service parameters for a preset are shown in
3448 service job window</li>
3449 <li>JABA Service menu entries reworded</li>
3453 <li>Modeller PIR IO broken - cannot correctly import a
3454 pir file emitted by Jalview</li>
3455 <li>Existing feature settings transferred to new
3456 alignment view created from cut'n'paste</li>
3457 <li>Improved test for mixed amino/nucleotide chains when
3458 parsing PDB files</li>
3459 <li>Consensus and conservation annotation rows
3460 occasionally become blank for all new windows</li>
3461 <li>Exception raised when right clicking above sequences
3462 in wrapped view mode</li>
3463 </ul> <em>Application</em>
3465 <li>multiple multiply aligned structure views cause cpu
3466 usage to hit 100% and computer to hang</li>
3467 <li>Web Service parameter layout breaks for long user
3468 parameter names</li>
3469 <li>Jaba service discovery hangs desktop if Jaba server
3476 <div align="center">
3477 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3480 <td><em>Application</em>
3482 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3483 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3486 <li>Web Services preference tab</li>
3487 <li>Analysis parameters dialog box and user defined
3489 <li>Improved speed and layout of Envision2 service menu</li>
3490 <li>Superpose structures using associated sequence
3492 <li>Export coordinates and projection as CSV from PCA
3494 </ul> <em>Applet</em>
3496 <li>enable javascript: execution by the applet via the
3497 link out mechanism</li>
3498 </ul> <em>Other</em>
3500 <li>Updated the Jmol Jalview interface to work with Jmol
3502 <li>The Jalview Desktop and JalviewLite applet now
3503 require Java 1.5</li>
3504 <li>Allow Jalview feature colour specification for GFF
3505 sequence annotation files</li>
3506 <li>New 'colour by label' keword in Jalview feature file
3507 type colour specification</li>
3508 <li>New Jalview Desktop Groovy API method that allows a
3509 script to check if it being run in an interactive session or
3510 in a batch operation from the Jalview command line</li>
3514 <li>clustalx colourscheme colours Ds preferentially when
3515 both D+E are present in over 50% of the column</li>
3516 </ul> <em>Application</em>
3518 <li>typo in AlignmentFrame->View->Hide->all but
3519 selected Regions menu item</li>
3520 <li>sequence fetcher replaces ',' for ';' when the ',' is
3521 part of a valid accession ID</li>
3522 <li>fatal OOM if object retrieved by sequence fetcher
3523 runs out of memory</li>
3524 <li>unhandled Out of Memory Error when viewing pca
3525 analysis results</li>
3526 <li>InstallAnywhere builds fail to launch on OS X java
3527 10.5 update 4 (due to apple Java 1.6 update)</li>
3528 <li>Installanywhere Jalview silently fails to launch</li>
3529 </ul> <em>Applet</em>
3531 <li>Jalview.getFeatureGroups() raises an
3532 ArrayIndexOutOfBoundsException if no feature groups are
3539 <div align="center">
3540 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3546 <li>Alignment prettyprinter doesn't cope with long
3548 <li>clustalx colourscheme colours Ds preferentially when
3549 both D+E are present in over 50% of the column</li>
3550 <li>nucleic acid structures retrieved from PDB do not
3551 import correctly</li>
3552 <li>More columns get selected than were clicked on when a
3553 number of columns are hidden</li>
3554 <li>annotation label popup menu not providing correct
3555 add/hide/show options when rows are hidden or none are
3557 <li>Stockholm format shown in list of readable formats,
3558 and parser copes better with alignments from RFAM.</li>
3559 <li>CSV output of consensus only includes the percentage
3560 of all symbols if sequence logo display is enabled</li>
3562 </ul> <em>Applet</em>
3564 <li>annotation panel disappears when annotation is
3566 </ul> <em>Application</em>
3568 <li>Alignment view not redrawn properly when new
3569 alignment opened where annotation panel is visible but no
3570 annotations are present on alignment</li>
3571 <li>pasted region containing hidden columns is
3572 incorrectly displayed in new alignment window</li>
3573 <li>Jalview slow to complete operations when stdout is
3574 flooded (fix is to close the Jalview console)</li>
3575 <li>typo in AlignmentFrame->View->Hide->all but
3576 selected Rregions menu item.</li>
3577 <li>inconsistent group submenu and Format submenu entry
3578 'Un' or 'Non'conserved</li>
3579 <li>Sequence feature settings are being shared by
3580 multiple distinct alignments</li>
3581 <li>group annotation not recreated when tree partition is
3583 <li>double click on group annotation to select sequences
3584 does not propagate to associated trees</li>
3585 <li>Mac OSX specific issues:
3587 <li>exception raised when mouse clicked on desktop
3588 window background</li>
3589 <li>Desktop menu placed on menu bar and application
3590 name set correctly</li>
3591 <li>sequence feature settings not wide enough for the
3592 save feature colourscheme button</li>
3601 <div align="center">
3602 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3605 <td><em>New Capabilities</em>
3607 <li>URL links generated from description line for
3608 regular-expression based URL links (applet and application)
3610 <li>Non-positional feature URL links are shown in link
3612 <li>Linked viewing of nucleic acid sequences and
3614 <li>Automatic Scrolling option in View menu to display
3615 the currently highlighted region of an alignment.</li>
3616 <li>Order an alignment by sequence length, or using the
3617 average score or total feature count for each sequence.</li>
3618 <li>Shading features by score or associated description</li>
3619 <li>Subdivide alignment and groups based on identity of
3620 selected subsequence (Make Groups from Selection).</li>
3621 <li>New hide/show options including Shift+Control+H to
3622 hide everything but the currently selected region.</li>
3623 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3624 </ul> <em>Application</em>
3626 <li>Fetch DB References capabilities and UI expanded to
3627 support retrieval from DAS sequence sources</li>
3628 <li>Local DAS Sequence sources can be added via the
3629 command line or via the Add local source dialog box.</li>
3630 <li>DAS Dbref and DbxRef feature types are parsed as
3631 database references and protein_name is parsed as
3632 description line (BioSapiens terms).</li>
3633 <li>Enable or disable non-positional feature and database
3634 references in sequence ID tooltip from View menu in
3636 <!-- <li>New hidden columns and rows and representatives capabilities
3637 in annotations file (in progress - not yet fully implemented)</li> -->
3638 <li>Group-associated consensus, sequence logos and
3639 conservation plots</li>
3640 <li>Symbol distributions for each column can be exported
3641 and visualized as sequence logos</li>
3642 <li>Optionally scale multi-character column labels to fit
3643 within each column of annotation row<!-- todo for applet -->
3645 <li>Optional automatic sort of associated alignment view
3646 when a new tree is opened.</li>
3647 <li>Jalview Java Console</li>
3648 <li>Better placement of desktop window when moving
3649 between different screens.</li>
3650 <li>New preference items for sequence ID tooltip and
3651 consensus annotation</li>
3652 <li>Client to submit sequences and IDs to Envision2
3654 <li><em>Vamsas Capabilities</em>
3656 <li>Improved VAMSAS synchronization (Jalview archive
3657 used to preserve views, structures, and tree display
3659 <li>Import of vamsas documents from disk or URL via
3661 <li>Sharing of selected regions between views and
3662 with other VAMSAS applications (Experimental feature!)</li>
3663 <li>Updated API to VAMSAS version 0.2</li>
3665 </ul> <em>Applet</em>
3667 <li>Middle button resizes annotation row height</li>
3670 <li>sortByTree (true/false) - automatically sort the
3671 associated alignment view by the tree when a new tree is
3673 <li>showTreeBootstraps (true/false) - show or hide
3674 branch bootstraps (default is to show them if available)</li>
3675 <li>showTreeDistances (true/false) - show or hide
3676 branch lengths (default is to show them if available)</li>
3677 <li>showUnlinkedTreeNodes (true/false) - indicate if
3678 unassociated nodes should be highlighted in the tree
3680 <li>heightScale and widthScale (1.0 or more) -
3681 increase the height or width of a cell in the alignment
3682 grid relative to the current font size.</li>
3685 <li>Non-positional features displayed in sequence ID
3687 </ul> <em>Other</em>
3689 <li>Features format: graduated colour definitions and
3690 specification of feature scores</li>
3691 <li>Alignment Annotations format: new keywords for group
3692 associated annotation (GROUP_REF) and annotation row display
3693 properties (ROW_PROPERTIES)</li>
3694 <li>XML formats extended to support graduated feature
3695 colourschemes, group associated annotation, and profile
3696 visualization settings.</li></td>
3699 <li>Source field in GFF files parsed as feature source
3700 rather than description</li>
3701 <li>Non-positional features are now included in sequence
3702 feature and gff files (controlled via non-positional feature
3703 visibility in tooltip).</li>
3704 <li>URL links generated for all feature links (bugfix)</li>
3705 <li>Added URL embedding instructions to features file
3707 <li>Codons containing ambiguous nucleotides translated as
3708 'X' in peptide product</li>
3709 <li>Match case switch in find dialog box works for both
3710 sequence ID and sequence string and query strings do not
3711 have to be in upper case to match case-insensitively.</li>
3712 <li>AMSA files only contain first column of
3713 multi-character column annotation labels</li>
3714 <li>Jalview Annotation File generation/parsing consistent
3715 with documentation (e.g. Stockholm annotation can be
3716 exported and re-imported)</li>
3717 <li>PDB files without embedded PDB IDs given a friendly
3719 <li>Find incrementally searches ID string matches as well
3720 as subsequence matches, and correctly reports total number
3724 <li>Better handling of exceptions during sequence
3726 <li>Dasobert generated non-positional feature URL
3727 link text excludes the start_end suffix</li>
3728 <li>DAS feature and source retrieval buttons disabled
3729 when fetch or registry operations in progress.</li>
3730 <li>PDB files retrieved from URLs are cached properly</li>
3731 <li>Sequence description lines properly shared via
3733 <li>Sequence fetcher fetches multiple records for all
3735 <li>Ensured that command line das feature retrieval
3736 completes before alignment figures are generated.</li>
3737 <li>Reduced time taken when opening file browser for
3739 <li>isAligned check prior to calculating tree, PCA or
3740 submitting an MSA to JNet now excludes hidden sequences.</li>
3741 <li>User defined group colours properly recovered
3742 from Jalview projects.</li>
3751 <div align="center">
3752 <strong>2.4.0.b2</strong><br> 28/10/2009
3757 <li>Experimental support for google analytics usage
3759 <li>Jalview privacy settings (user preferences and docs).</li>
3764 <li>Race condition in applet preventing startup in
3766 <li>Exception when feature created from selection beyond
3767 length of sequence.</li>
3768 <li>Allow synthetic PDB files to be imported gracefully</li>
3769 <li>Sequence associated annotation rows associate with
3770 all sequences with a given id</li>
3771 <li>Find function matches case-insensitively for sequence
3772 ID string searches</li>
3773 <li>Non-standard characters do not cause pairwise
3774 alignment to fail with exception</li>
3775 </ul> <em>Application Issues</em>
3777 <li>Sequences are now validated against EMBL database</li>
3778 <li>Sequence fetcher fetches multiple records for all
3780 </ul> <em>InstallAnywhere Issues</em>
3782 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3783 issue with installAnywhere mechanism)</li>
3784 <li>Command line launching of JARs from InstallAnywhere
3785 version (java class versioning error fixed)</li>
3792 <div align="center">
3793 <strong>2.4</strong><br> 27/8/2008
3796 <td><em>User Interface</em>
3798 <li>Linked highlighting of codon and amino acid from
3799 translation and protein products</li>
3800 <li>Linked highlighting of structure associated with
3801 residue mapping to codon position</li>
3802 <li>Sequence Fetcher provides example accession numbers
3803 and 'clear' button</li>
3804 <li>MemoryMonitor added as an option under Desktop's
3806 <li>Extract score function to parse whitespace separated
3807 numeric data in description line</li>
3808 <li>Column labels in alignment annotation can be centred.</li>
3809 <li>Tooltip for sequence associated annotation give name
3811 </ul> <em>Web Services and URL fetching</em>
3813 <li>JPred3 web service</li>
3814 <li>Prototype sequence search client (no public services
3816 <li>Fetch either seed alignment or full alignment from
3818 <li>URL Links created for matching database cross
3819 references as well as sequence ID</li>
3820 <li>URL Links can be created using regular-expressions</li>
3821 </ul> <em>Sequence Database Connectivity</em>
3823 <li>Retrieval of cross-referenced sequences from other
3825 <li>Generalised database reference retrieval and
3826 validation to all fetchable databases</li>
3827 <li>Fetch sequences from DAS sources supporting the
3828 sequence command</li>
3829 </ul> <em>Import and Export</em>
3830 <li>export annotation rows as CSV for spreadsheet import</li>
3831 <li>Jalview projects record alignment dataset associations,
3832 EMBL products, and cDNA sequence mappings</li>
3833 <li>Sequence Group colour can be specified in Annotation
3835 <li>Ad-hoc colouring of group in Annotation File using RGB
3836 triplet as name of colourscheme</li>
3837 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3839 <li>treenode binding for VAMSAS tree exchange</li>
3840 <li>local editing and update of sequences in VAMSAS
3841 alignments (experimental)</li>
3842 <li>Create new or select existing session to join</li>
3843 <li>load and save of vamsas documents</li>
3844 </ul> <em>Application command line</em>
3846 <li>-tree parameter to open trees (introduced for passing
3848 <li>-fetchfrom command line argument to specify nicknames
3849 of DAS servers to query for alignment features</li>
3850 <li>-dasserver command line argument to add new servers
3851 that are also automatically queried for features</li>
3852 <li>-groovy command line argument executes a given groovy
3853 script after all input data has been loaded and parsed</li>
3854 </ul> <em>Applet-Application data exchange</em>
3856 <li>Trees passed as applet parameters can be passed to
3857 application (when using "View in full
3858 application")</li>
3859 </ul> <em>Applet Parameters</em>
3861 <li>feature group display control parameter</li>
3862 <li>debug parameter</li>
3863 <li>showbutton parameter</li>
3864 </ul> <em>Applet API methods</em>
3866 <li>newView public method</li>
3867 <li>Window (current view) specific get/set public methods</li>
3868 <li>Feature display control methods</li>
3869 <li>get list of currently selected sequences</li>
3870 </ul> <em>New Jalview distribution features</em>
3872 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3873 <li>RELEASE file gives build properties for the latest
3874 Jalview release.</li>
3875 <li>Java 1.1 Applet build made easier and donotobfuscate
3876 property controls execution of obfuscator</li>
3877 <li>Build target for generating source distribution</li>
3878 <li>Debug flag for javacc</li>
3879 <li>.jalview_properties file is documented (slightly) in
3880 jalview.bin.Cache</li>
3881 <li>Continuous Build Integration for stable and
3882 development version of Application, Applet and source
3887 <li>selected region output includes visible annotations
3888 (for certain formats)</li>
3889 <li>edit label/displaychar contains existing label/char
3891 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3892 <li>shorter peptide product names from EMBL records</li>
3893 <li>Newick string generator makes compact representations</li>
3894 <li>bootstrap values parsed correctly for tree files with
3896 <li>pathological filechooser bug avoided by not allowing
3897 filenames containing a ':'</li>
3898 <li>Fixed exception when parsing GFF files containing
3899 global sequence features</li>
3900 <li>Alignment datasets are finalized only when number of
3901 references from alignment sequences goes to zero</li>
3902 <li>Close of tree branch colour box without colour
3903 selection causes cascading exceptions</li>
3904 <li>occasional negative imgwidth exceptions</li>
3905 <li>better reporting of non-fatal warnings to user when
3906 file parsing fails.</li>
3907 <li>Save works when Jalview project is default format</li>
3908 <li>Save as dialog opened if current alignment format is
3909 not a valid output format</li>
3910 <li>UniProt canonical names introduced for both das and
3912 <li>Histidine should be midblue (not pink!) in Zappo</li>
3913 <li>error messages passed up and output when data read
3915 <li>edit undo recovers previous dataset sequence when
3916 sequence is edited</li>
3917 <li>allow PDB files without pdb ID HEADER lines (like
3918 those generated by MODELLER) to be read in properly</li>
3919 <li>allow reading of JPred concise files as a normal
3921 <li>Stockholm annotation parsing and alignment properties
3922 import fixed for PFAM records</li>
3923 <li>Structure view windows have correct name in Desktop
3925 <li>annotation consisting of sequence associated scores
3926 can be read and written correctly to annotation file</li>
3927 <li>Aligned cDNA translation to aligned peptide works
3929 <li>Fixed display of hidden sequence markers and
3930 non-italic font for representatives in Applet</li>
3931 <li>Applet Menus are always embedded in applet window on
3933 <li>Newly shown features appear at top of stack (in
3935 <li>Annotations added via parameter not drawn properly
3936 due to null pointer exceptions</li>
3937 <li>Secondary structure lines are drawn starting from
3938 first column of alignment</li>
3939 <li>UniProt XML import updated for new schema release in
3941 <li>Sequence feature to sequence ID match for Features
3942 file is case-insensitive</li>
3943 <li>Sequence features read from Features file appended to
3944 all sequences with matching IDs</li>
3945 <li>PDB structure coloured correctly for associated views
3946 containing a sub-sequence</li>
3947 <li>PDB files can be retrieved by applet from Jar files</li>
3948 <li>feature and annotation file applet parameters
3949 referring to different directories are retrieved correctly</li>
3950 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3951 <li>Fixed application hang whilst waiting for
3952 splash-screen version check to complete</li>
3953 <li>Applet properly URLencodes input parameter values
3954 when passing them to the launchApp service</li>
3955 <li>display name and local features preserved in results
3956 retrieved from web service</li>
3957 <li>Visual delay indication for sequence retrieval and
3958 sequence fetcher initialisation</li>
3959 <li>updated Application to use DAS 1.53e version of
3960 dasobert DAS client</li>
3961 <li>Re-instated Full AMSA support and .amsa file
3963 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3971 <div align="center">
3972 <strong>2.3</strong><br> 9/5/07
3977 <li>Jmol 11.0.2 integration</li>
3978 <li>PDB views stored in Jalview XML files</li>
3979 <li>Slide sequences</li>
3980 <li>Edit sequence in place</li>
3981 <li>EMBL CDS features</li>
3982 <li>DAS Feature mapping</li>
3983 <li>Feature ordering</li>
3984 <li>Alignment Properties</li>
3985 <li>Annotation Scores</li>
3986 <li>Sort by scores</li>
3987 <li>Feature/annotation editing in applet</li>
3992 <li>Headless state operation in 2.2.1</li>
3993 <li>Incorrect and unstable DNA pairwise alignment</li>
3994 <li>Cut and paste of sequences with annotation</li>
3995 <li>Feature group display state in XML</li>
3996 <li>Feature ordering in XML</li>
3997 <li>blc file iteration selection using filename # suffix</li>
3998 <li>Stockholm alignment properties</li>
3999 <li>Stockhom alignment secondary structure annotation</li>
4000 <li>2.2.1 applet had no feature transparency</li>
4001 <li>Number pad keys can be used in cursor mode</li>
4002 <li>Structure Viewer mirror image resolved</li>
4009 <div align="center">
4010 <strong>2.2.1</strong><br> 12/2/07
4015 <li>Non standard characters can be read and displayed
4016 <li>Annotations/Features can be imported/exported to the
4018 <li>Applet allows editing of sequence/annotation/group
4019 name & description
4020 <li>Preference setting to display sequence name in
4022 <li>Annotation file format extended to allow
4023 Sequence_groups to be defined
4024 <li>Default opening of alignment overview panel can be
4025 specified in preferences
4026 <li>PDB residue numbering annotation added to associated
4032 <li>Applet crash under certain Linux OS with Java 1.6
4034 <li>Annotation file export / import bugs fixed
4035 <li>PNG / EPS image output bugs fixed
4041 <div align="center">
4042 <strong>2.2</strong><br> 27/11/06
4047 <li>Multiple views on alignment
4048 <li>Sequence feature editing
4049 <li>"Reload" alignment
4050 <li>"Save" to current filename
4051 <li>Background dependent text colour
4052 <li>Right align sequence ids
4053 <li>User-defined lower case residue colours
4056 <li>Menu item accelerator keys
4057 <li>Control-V pastes to current alignment
4058 <li>Cancel button for DAS Feature Fetching
4059 <li>PCA and PDB Viewers zoom via mouse roller
4060 <li>User-defined sub-tree colours and sub-tree selection
4062 <li>'New Window' button on the 'Output to Text box'
4067 <li>New memory efficient Undo/Redo System
4068 <li>Optimised symbol lookups and conservation/consensus
4070 <li>Region Conservation/Consensus recalculated after
4072 <li>Fixed Remove Empty Columns Bug (empty columns at end
4074 <li>Slowed DAS Feature Fetching for increased robustness.
4076 <li>Made angle brackets in ASCII feature descriptions
4078 <li>Re-instated Zoom function for PCA
4079 <li>Sequence descriptions conserved in web service
4081 <li>UniProt ID discoverer uses any word separated by
4083 <li>WsDbFetch query/result association resolved
4084 <li>Tree leaf to sequence mapping improved
4085 <li>Smooth fonts switch moved to FontChooser dialog box.
4092 <div align="center">
4093 <strong>2.1.1</strong><br> 12/9/06
4098 <li>Copy consensus sequence to clipboard</li>
4103 <li>Image output - rightmost residues are rendered if
4104 sequence id panel has been resized</li>
4105 <li>Image output - all offscreen group boundaries are
4107 <li>Annotation files with sequence references - all
4108 elements in file are relative to sequence position</li>
4109 <li>Mac Applet users can use Alt key for group editing</li>
4115 <div align="center">
4116 <strong>2.1</strong><br> 22/8/06
4121 <li>MAFFT Multiple Alignment in default Web Service list</li>
4122 <li>DAS Feature fetching</li>
4123 <li>Hide sequences and columns</li>
4124 <li>Export Annotations and Features</li>
4125 <li>GFF file reading / writing</li>
4126 <li>Associate structures with sequences from local PDB
4128 <li>Add sequences to exisiting alignment</li>
4129 <li>Recently opened files / URL lists</li>
4130 <li>Applet can launch the full application</li>
4131 <li>Applet has transparency for features (Java 1.2
4133 <li>Applet has user defined colours parameter</li>
4134 <li>Applet can load sequences from parameter
4135 "sequence<em>x</em>"
4141 <li>Redundancy Panel reinstalled in the Applet</li>
4142 <li>Monospaced font - EPS / rescaling bug fixed</li>
4143 <li>Annotation files with sequence references bug fixed</li>
4149 <div align="center">
4150 <strong>2.08.1</strong><br> 2/5/06
4155 <li>Change case of selected region from Popup menu</li>
4156 <li>Choose to match case when searching</li>
4157 <li>Middle mouse button and mouse movement can compress /
4158 expand the visible width and height of the alignment</li>
4163 <li>Annotation Panel displays complete JNet results</li>
4169 <div align="center">
4170 <strong>2.08b</strong><br> 18/4/06
4176 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4177 <li>Righthand label on wrapped alignments shows correct
4184 <div align="center">
4185 <strong>2.08</strong><br> 10/4/06
4190 <li>Editing can be locked to the selection area</li>
4191 <li>Keyboard editing</li>
4192 <li>Create sequence features from searches</li>
4193 <li>Precalculated annotations can be loaded onto
4195 <li>Features file allows grouping of features</li>
4196 <li>Annotation Colouring scheme added</li>
4197 <li>Smooth fonts off by default - Faster rendering</li>
4198 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4203 <li>Drag & Drop fixed on Linux</li>
4204 <li>Jalview Archive file faster to load/save, sequence
4205 descriptions saved.</li>
4211 <div align="center">
4212 <strong>2.07</strong><br> 12/12/05
4217 <li>PDB Structure Viewer enhanced</li>
4218 <li>Sequence Feature retrieval and display enhanced</li>
4219 <li>Choose to output sequence start-end after sequence
4220 name for file output</li>
4221 <li>Sequence Fetcher WSDBFetch@EBI</li>
4222 <li>Applet can read feature files, PDB files and can be
4223 used for HTML form input</li>
4228 <li>HTML output writes groups and features</li>
4229 <li>Group editing is Control and mouse click</li>
4230 <li>File IO bugs</li>
4236 <div align="center">
4237 <strong>2.06</strong><br> 28/9/05
4242 <li>View annotations in wrapped mode</li>
4243 <li>More options for PCA viewer</li>
4248 <li>GUI bugs resolved</li>
4249 <li>Runs with -nodisplay from command line</li>
4255 <div align="center">
4256 <strong>2.05b</strong><br> 15/9/05
4261 <li>Choose EPS export as lineart or text</li>
4262 <li>Jar files are executable</li>
4263 <li>Can read in Uracil - maps to unknown residue</li>
4268 <li>Known OutOfMemory errors give warning message</li>
4269 <li>Overview window calculated more efficiently</li>
4270 <li>Several GUI bugs resolved</li>
4276 <div align="center">
4277 <strong>2.05</strong><br> 30/8/05
4282 <li>Edit and annotate in "Wrapped" view</li>
4287 <li>Several GUI bugs resolved</li>
4293 <div align="center">
4294 <strong>2.04</strong><br> 24/8/05
4299 <li>Hold down mouse wheel & scroll to change font
4305 <li>Improved JPred client reliability</li>
4306 <li>Improved loading of Jalview files</li>
4312 <div align="center">
4313 <strong>2.03</strong><br> 18/8/05
4318 <li>Set Proxy server name and port in preferences</li>
4319 <li>Multiple URL links from sequence ids</li>
4320 <li>User Defined Colours can have a scheme name and added
4322 <li>Choose to ignore gaps in consensus calculation</li>
4323 <li>Unix users can set default web browser</li>
4324 <li>Runs without GUI for batch processing</li>
4325 <li>Dynamically generated Web Service Menus</li>
4330 <li>InstallAnywhere download for Sparc Solaris</li>
4336 <div align="center">
4337 <strong>2.02</strong><br> 18/7/05
4343 <li>Copy & Paste order of sequences maintains
4344 alignment order.</li>
4350 <div align="center">
4351 <strong>2.01</strong><br> 12/7/05
4356 <li>Use delete key for deleting selection.</li>
4357 <li>Use Mouse wheel to scroll sequences.</li>
4358 <li>Help file updated to describe how to add alignment
4360 <li>Version and build date written to build properties
4362 <li>InstallAnywhere installation will check for updates
4363 at launch of Jalview.</li>
4368 <li>Delete gaps bug fixed.</li>
4369 <li>FileChooser sorts columns.</li>
4370 <li>Can remove groups one by one.</li>
4371 <li>Filechooser icons installed.</li>
4372 <li>Finder ignores return character when searching.
4373 Return key will initiate a search.<br>
4380 <div align="center">
4381 <strong>2.0</strong><br> 20/6/05
4386 <li>New codebase</li>