3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap>
60 <strong><a name="Jalview.2.11">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 a graph or histogram
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-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
182 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
186 <li><strong>Java 11 Support</strong>
189 <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
190 and getdown release channels
193 <!-- -->OSX GUI integrations for App menu's 'About' entry and
198 <em>Deprecations</em>
201 <!-- JAL-3035 -->DAS sequence retrieval and annotation
202 capabilities removed from the Jalview Desktop
205 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
206 unmarshalling has been replaced by JAXB for Jalview projects
207 and XML based data retrieval clients</li>
208 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
209 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
210 </ul> <em>Documentation</em>
213 <!-- JAL-3003 -->Added remarks about transparent rendering effects
214 not supported in EPS figure export
216 </ul> <em>Development and Release Processes</em>
219 <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
220 Installers built with Install4j (licensed to the Jalview open
221 source project) rather than InstallAnywhere
224 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
225 settings, receive over the air updates and launch specific
226 versions via (<a href="https://github.com/threerings/getdown">Three
230 <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
233 <!-- JAL-3225 -->Eclipse project configuration managed with
237 Atlassian Bamboo continuous integration for
238 unattended Test Suite execution</li>
240 <!-- JAL-2864 -->Memory test suite to detect leaks in common
243 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
244 implementation that alows updates) used for Sequence Feature collections</li>
245 <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
248 <td align="left" valign="top">
251 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
254 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
255 superposition in Jmol fail on Windows
258 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
259 structures for sequences with lots of PDB structures
262 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
266 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
267 project involving multiple views
270 <!-- JAL-3164 -->Overview for complementary view in a linked
271 CDS/Protein alignment is not updated when Hide Columns by
272 Annotation dialog hides columns
275 <!-- JAL-3158 -->Selection highlighting in the complement of a
276 CDS/Protein alignment stops working after making a selection in
277 one view, then making another selection in the other view
280 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
284 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
285 Settings and Jalview Preferences panels
288 <!-- JAL-2865 -->Jalview hangs when closing windows or the
289 overview updates with large alignments
292 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
293 region if columns were selected by dragging right-to-left and the
294 mouse moved to the left of the first column
297 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
298 hidden column marker via scale popup menu
301 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
302 doesn't tell users the invalid URL
305 <!-- JAL-3178 -->Nonpositional features lose feature group on
306 export as Jalview features file
309 <!-- JAL-2060 -->'Graduated colour' option not offered for
310 manually created features (where if feature score is Float.NaN)
313 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
314 when columns are hidden
317 <!-- JAL-3082 -->Regular expression error for '(' in Select
318 Columns by Annotation description
321 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
322 out of Scale or Annotation Panel
325 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
329 <!-- JAL-3074 -->Left/right drag in annotation can scroll
333 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
337 <!-- JAL-3002 -->Column display is out by one after Page Down,
338 Page Up in wrapped mode
341 <!-- JAL-2839 -->Finder doesn't skip hidden regions
344 <!-- JAL-2932 -->Finder searches in minimised alignments
347 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
348 on opening an alignment
351 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
355 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
356 different groups in the alignment are selected
359 <!-- JAL-2717 -->Internationalised colour scheme names not shown
363 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
367 <!-- JAL-3125 -->Value input for graduated feature colour
368 threshold gets 'unrounded'
371 <!-- JAL-2982 -->PCA image export doesn't respect background
375 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
378 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
381 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
385 <!-- JAL-2964 -->Associate Tree with All Views not restored from
389 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
390 shown in complementary view
393 <!-- JAL-2898 -->stop_gained variants not shown correctly on
397 <!-- JAL-3021 -->Sequence Details report opens positioned to top
401 <!-- JAL-914 -->Help page can be opened twice
403 </ul> <em>Editing</em>
406 <!-- JAL-2822 -->Start and End should be updated when sequence
407 data at beginning or end of alignment added/removed via 'Edit'
411 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
412 relocate sequence features correctly when start of sequence is
413 removed (Known defect since 2.10)
416 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
417 dialog corrupts dataset sequence
420 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled when
421 shown without normalisation
424 <em>New Known Defects</em>
427 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
428 is restored from a Jalview 2.11 project
431 <!-- JAL-3213 -->Alignment panel height can be too small after
435 <!-- JAL-3240 -->Display is incorrect after removing gapped
436 columns within hidden columns
439 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
440 window after dragging left to select columns to left of visible
444 <!-- JAL-2876 -->Features coloured according to their description
445 string and thresholded by score in earlier versions of Jalview are
446 not shown as thresholded features in 2.11. To workaround please
447 create a Score filter instead.
453 <td width="60" nowrap>
455 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
458 <td><div align="left">
462 <!-- JAL-3101 -->Default memory for Jalview webstart and
463 InstallAnywhere increased to 1G.
466 <!-- JAL-247 -->Hidden sequence markers and representative
467 sequence bolding included when exporting alignment as EPS,
468 SVG, PNG or HTML. <em>Display is configured via the
469 Format menu, or for command-line use via a jalview
470 properties file.</em>
473 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
474 API and sequence data now imported as JSON.
477 <!-- JAL-3065 -->Change in recommended way of starting
478 Jalview via a Java command line: add jars in lib directory
479 to CLASSPATH, rather than via the deprecated java.ext.dirs
486 <!-- JAL-3047 -->Support added to execute test suite
487 instrumented with <a href="http://openclover.org/">Open
492 <td><div align="left">
496 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
497 row shown in Feredoxin Structure alignment view of example
501 <!-- JAL-2854 -->Annotation obscures sequences if lots of
502 annotation displayed.
505 <!-- JAL-3107 -->Group conservation/consensus not shown
506 for newly created group when 'Apply to all groups'
510 <!-- JAL-3087 -->Corrupted display when switching to
511 wrapped mode when sequence panel's vertical scrollbar is
515 <!-- JAL-3003 -->Alignment is black in exported EPS file
516 when sequences are selected in exported view.</em>
519 <!-- JAL-3059 -->Groups with different coloured borders
520 aren't rendered with correct colour.
523 <!-- JAL-3092 -->Jalview could hang when importing certain
524 types of knotted RNA secondary structure.
527 <!-- JAL-3095 -->Sequence highlight and selection in
528 trimmed VARNA 2D structure is incorrect for sequences that
532 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
533 annotation when columns are inserted into an alignment,
534 and when exporting as Stockholm flatfile.
537 <!-- JAL-3053 -->Jalview annotation rows containing upper
538 and lower-case 'E' and 'H' do not automatically get
539 treated as RNA secondary structure.
542 <!-- JAL-3106 -->.jvp should be used as default extension
543 (not .jar) when saving a jalview project file.
546 <!-- JAL-3105 -->Mac Users: closing a window correctly
547 transfers focus to previous window on OSX
550 <em>Java 10 Issues Resolved</em>
553 <!-- JAL-2988 -->OSX - Can't save new files via the File
554 or export menus by typing in a name into the Save dialog
558 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
559 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
560 'look and feel' which has improved compatibility with the
561 latest version of OSX.
568 <td width="60" nowrap>
570 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
571 <em>7/06/2018</em></strong>
574 <td><div align="left">
578 <!-- JAL-2920 -->Use HGVS nomenclature for variant
579 annotation retrieved from Uniprot
582 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
583 onto the Jalview Desktop
587 <td><div align="left">
591 <!-- JAL-3017 -->Cannot import features with multiple
592 variant elements (blocks import of some Uniprot records)
595 <!-- JAL-2997 -->Clustal files with sequence positions in
596 right-hand column parsed correctly
599 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
600 not alignment area in exported graphic
603 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
604 window has input focus
607 <!-- JAL-2992 -->Annotation panel set too high when
608 annotation added to view (Windows)
611 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
612 network connectivity is poor
615 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
616 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
617 the currently open URL and links from a page viewed in
618 Firefox or Chrome on Windows is now fully supported. If
619 you are using Edge, only links in the page can be
620 dragged, and with Internet Explorer, only the currently
621 open URL in the browser can be dropped onto Jalview.</em>
627 <td width="60" nowrap>
629 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
632 <td><div align="left">
636 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
637 for disabling automatic superposition of multiple
638 structures and open structures in existing views
641 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
642 ID and annotation area margins can be click-dragged to
646 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
650 <!-- JAL-2759 -->Improved performance for large alignments
651 and lots of hidden columns
654 <!-- JAL-2593 -->Improved performance when rendering lots
655 of features (particularly when transparency is disabled)
658 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
659 exchange of Jalview features and Chimera attributes made
665 <td><div align="left">
668 <!-- JAL-2899 -->Structure and Overview aren't updated
669 when Colour By Annotation threshold slider is adjusted
672 <!-- JAL-2778 -->Slow redraw when Overview panel shown
673 overlapping alignment panel
676 <!-- JAL-2929 -->Overview doesn't show end of unpadded
680 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
681 improved: CDS not handled correctly if transcript has no
685 <!-- JAL-2321 -->Secondary structure and temperature
686 factor annotation not added to sequence when local PDB
687 file associated with it by drag'n'drop or structure
691 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
692 dialog doesn't import PDB files dropped on an alignment
695 <!-- JAL-2666 -->Linked scrolling via protein horizontal
696 scroll bar doesn't work for some CDS/Protein views
699 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
700 Java 1.8u153 onwards and Java 1.9u4+.
703 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
704 columns in annotation row
707 <!-- JAL-2913 -->Preferences panel's ID Width control is not
708 honored in batch mode
711 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
712 for structures added to existing Jmol view
715 <!-- JAL-2223 -->'View Mappings' includes duplicate
716 entries after importing project with multiple views
719 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
720 protein sequences via SIFTS from associated PDB entries
721 with negative residue numbers or missing residues fails
724 <!-- JAL-2952 -->Exception when shading sequence with negative
725 Temperature Factor values from annotated PDB files (e.g.
726 as generated by CONSURF)
729 <!-- JAL-2920 -->Uniprot 'sequence variant' features
730 tooltip doesn't include a text description of mutation
733 <!-- JAL-2922 -->Invert displayed features very slow when
734 structure and/or overview windows are also shown
737 <!-- JAL-2954 -->Selecting columns from highlighted regions
738 very slow for alignments with large numbers of sequences
741 <!-- JAL-2925 -->Copy Consensus fails for group consensus
742 with 'StringIndexOutOfBounds'
745 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
746 platforms running Java 10
749 <!-- JAL-2960 -->Adding a structure to existing structure
750 view appears to do nothing because the view is hidden behind the alignment view
756 <!-- JAL-2926 -->Copy consensus sequence option in applet
757 should copy the group consensus when popup is opened on it
763 <!-- JAL-2913 -->Fixed ID width preference is not respected
766 <em>New Known Defects</em>
769 <!-- JAL-2973 --> Exceptions occasionally raised when
770 editing a large alignment and overview is displayed
773 <!-- JAL-2974 -->'Overview updating' progress bar is shown
774 repeatedly after a series of edits even when the overview
775 is no longer reflecting updates
778 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
779 structures for protein subsequence (if 'Trim Retrieved
780 Sequences' enabled) or Ensembl isoforms (Workaround in
781 2.10.4 is to fail back to N&W mapping)
788 <td width="60" nowrap>
790 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
793 <td><div align="left">
794 <ul><li>Updated Certum Codesigning Certificate
795 (Valid till 30th November 2018)</li></ul></div></td>
796 <td><div align="left">
799 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
800 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
801 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
802 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
803 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
804 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
805 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
811 <td width="60" nowrap>
813 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
816 <td><div align="left">
820 <!-- JAL-2446 -->Faster and more efficient management and
821 rendering of sequence features
824 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
825 429 rate limit request hander
828 <!-- JAL-2773 -->Structure views don't get updated unless
829 their colours have changed
832 <!-- JAL-2495 -->All linked sequences are highlighted for
833 a structure mousover (Jmol) or selection (Chimera)
836 <!-- JAL-2790 -->'Cancel' button in progress bar for
837 JABAWS AACon, RNAAliFold and Disorder prediction jobs
840 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
841 view from Ensembl locus cross-references
844 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
848 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
849 feature can be disabled
852 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
853 PDB easier retrieval of sequences for lists of IDs
856 <!-- JAL-2758 -->Short names for sequences retrieved from
862 <li>Groovy interpreter updated to 2.4.12</li>
863 <li>Example groovy script for generating a matrix of
864 percent identity scores for current alignment.</li>
866 <em>Testing and Deployment</em>
869 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
873 <td><div align="left">
877 <!-- JAL-2643 -->Pressing tab after updating the colour
878 threshold text field doesn't trigger an update to the
882 <!-- JAL-2682 -->Race condition when parsing sequence ID
886 <!-- JAL-2608 -->Overview windows are also closed when
887 alignment window is closed
890 <!-- JAL-2548 -->Export of features doesn't always respect
894 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
895 takes a long time in Cursor mode
901 <!-- JAL-2777 -->Structures with whitespace chainCode
902 cannot be viewed in Chimera
905 <!-- JAL-2728 -->Protein annotation panel too high in
909 <!-- JAL-2757 -->Can't edit the query after the server
910 error warning icon is shown in Uniprot and PDB Free Text
914 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
917 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
920 <!-- JAL-2739 -->Hidden column marker in last column not
921 rendered when switching back from Wrapped to normal view
924 <!-- JAL-2768 -->Annotation display corrupted when
925 scrolling right in unwapped alignment view
928 <!-- JAL-2542 -->Existing features on subsequence
929 incorrectly relocated when full sequence retrieved from
933 <!-- JAL-2733 -->Last reported memory still shown when
934 Desktop->Show Memory is unticked (OSX only)
937 <!-- JAL-2658 -->Amend Features dialog doesn't allow
938 features of same type and group to be selected for
942 <!-- JAL-2524 -->Jalview becomes sluggish in wide
943 alignments when hidden columns are present
946 <!-- JAL-2392 -->Jalview freezes when loading and
947 displaying several structures
950 <!-- JAL-2732 -->Black outlines left after resizing or
954 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
955 within the Jalview desktop on OSX
958 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
959 when in wrapped alignment mode
962 <!-- JAL-2636 -->Scale mark not shown when close to right
963 hand end of alignment
966 <!-- JAL-2684 -->Pairwise alignment of selected regions of
967 each selected sequence do not have correct start/end
971 <!-- JAL-2793 -->Alignment ruler height set incorrectly
972 after canceling the Alignment Window's Font dialog
975 <!-- JAL-2036 -->Show cross-references not enabled after
976 restoring project until a new view is created
979 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
980 URL links appears when only default EMBL-EBI link is
981 configured (since 2.10.2b2)
984 <!-- JAL-2775 -->Overview redraws whole window when box
988 <!-- JAL-2225 -->Structure viewer doesn't map all chains
989 in a multi-chain structure when viewing alignment
990 involving more than one chain (since 2.10)
993 <!-- JAL-2811 -->Double residue highlights in cursor mode
994 if new selection moves alignment window
997 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
998 arrow key in cursor mode to pass hidden column marker
1001 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1002 that produces correctly annotated transcripts and products
1005 <!-- JAL-2776 -->Toggling a feature group after first time
1006 doesn't update associated structure view
1009 <em>Applet</em><br />
1012 <!-- JAL-2687 -->Concurrent modification exception when
1013 closing alignment panel
1016 <em>BioJSON</em><br />
1019 <!-- JAL-2546 -->BioJSON export does not preserve
1020 non-positional features
1023 <em>New Known Issues</em>
1026 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1027 sequence features correctly (for many previous versions of
1031 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1032 using cursor in wrapped panel other than top
1035 <!-- JAL-2791 -->Select columns containing feature ignores
1036 graduated colour threshold
1039 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1040 always preserve numbering and sequence features
1043 <em>Known Java 9 Issues</em>
1046 <!-- JAL-2902 -->Groovy Console very slow to open and is
1047 not responsive when entering characters (Webstart, Java
1054 <td width="60" nowrap>
1055 <div align="center">
1056 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1057 <em>2/10/2017</em></strong>
1060 <td><div align="left">
1061 <em>New features in Jalview Desktop</em>
1064 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1066 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1070 <td><div align="left">
1074 <td width="60" nowrap>
1075 <div align="center">
1076 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1077 <em>7/9/2017</em></strong>
1080 <td><div align="left">
1084 <!-- JAL-2588 -->Show gaps in overview window by colouring
1085 in grey (sequences used to be coloured grey, and gaps were
1089 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1093 <!-- JAL-2587 -->Overview updates immediately on increase
1094 in size and progress bar shown as higher resolution
1095 overview is recalculated
1100 <td><div align="left">
1104 <!-- JAL-2664 -->Overview window redraws every hidden
1105 column region row by row
1108 <!-- JAL-2681 -->duplicate protein sequences shown after
1109 retrieving Ensembl crossrefs for sequences from Uniprot
1112 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1113 format setting is unticked
1116 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1117 if group has show boxes format setting unticked
1120 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1121 autoscrolling whilst dragging current selection group to
1122 include sequences and columns not currently displayed
1125 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1126 assemblies are imported via CIF file
1129 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1130 displayed when threshold or conservation colouring is also
1134 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1138 <!-- JAL-2673 -->Jalview continues to scroll after
1139 dragging a selected region off the visible region of the
1143 <!-- JAL-2724 -->Cannot apply annotation based
1144 colourscheme to all groups in a view
1147 <!-- JAL-2511 -->IDs don't line up with sequences
1148 initially after font size change using the Font chooser or
1155 <td width="60" nowrap>
1156 <div align="center">
1157 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1160 <td><div align="left">
1161 <em>Calculations</em>
1165 <!-- JAL-1933 -->Occupancy annotation row shows number of
1166 ungapped positions in each column of the alignment.
1169 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1170 a calculation dialog box
1173 <!-- JAL-2379 -->Revised implementation of PCA for speed
1174 and memory efficiency (~30x faster)
1177 <!-- JAL-2403 -->Revised implementation of sequence
1178 similarity scores as used by Tree, PCA, Shading Consensus
1179 and other calculations
1182 <!-- JAL-2416 -->Score matrices are stored as resource
1183 files within the Jalview codebase
1186 <!-- JAL-2500 -->Trees computed on Sequence Feature
1187 Similarity may have different topology due to increased
1194 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1195 model for alignments and groups
1198 <!-- JAL-384 -->Custom shading schemes created via groovy
1205 <!-- JAL-2526 -->Efficiency improvements for interacting
1206 with alignment and overview windows
1209 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1213 <!-- JAL-2388 -->Hidden columns and sequences can be
1217 <!-- JAL-2611 -->Click-drag in visible area allows fine
1218 adjustment of visible position
1222 <em>Data import/export</em>
1225 <!-- JAL-2535 -->Posterior probability annotation from
1226 Stockholm files imported as sequence associated annotation
1229 <!-- JAL-2507 -->More robust per-sequence positional
1230 annotation input/output via stockholm flatfile
1233 <!-- JAL-2533 -->Sequence names don't include file
1234 extension when importing structure files without embedded
1235 names or PDB accessions
1238 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1239 format sequence substitution matrices
1242 <em>User Interface</em>
1245 <!-- JAL-2447 --> Experimental Features Checkbox in
1246 Desktop's Tools menu to hide or show untested features in
1250 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1251 via Overview or sequence motif search operations
1254 <!-- JAL-2547 -->Amend sequence features dialog box can be
1255 opened by double clicking gaps within sequence feature
1259 <!-- JAL-1476 -->Status bar message shown when not enough
1260 aligned positions were available to create a 3D structure
1264 <em>3D Structure</em>
1267 <!-- JAL-2430 -->Hidden regions in alignment views are not
1268 coloured in linked structure views
1271 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1272 file-based command exchange
1275 <!-- JAL-2375 -->Structure chooser automatically shows
1276 Cached Structures rather than querying the PDBe if
1277 structures are already available for sequences
1280 <!-- JAL-2520 -->Structures imported via URL are cached in
1281 the Jalview project rather than downloaded again when the
1282 project is reopened.
1285 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1286 to transfer Chimera's structure attributes as Jalview
1287 features, and vice-versa (<strong>Experimental
1291 <em>Web Services</em>
1294 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1297 <!-- JAL-2335 -->Filter non-standard amino acids and
1298 nucleotides when submitting to AACon and other MSA
1302 <!-- JAL-2316, -->URLs for viewing database
1303 cross-references provided by identifiers.org and the
1304 EMBL-EBI's MIRIAM DB
1311 <!-- JAL-2344 -->FileFormatI interface for describing and
1312 identifying file formats (instead of String constants)
1315 <!-- JAL-2228 -->FeatureCounter script refactored for
1316 efficiency when counting all displayed features (not
1317 backwards compatible with 2.10.1)
1320 <em>Example files</em>
1323 <!-- JAL-2631 -->Graduated feature colour style example
1324 included in the example feature file
1327 <em>Documentation</em>
1330 <!-- JAL-2339 -->Release notes reformatted for readability
1331 with the built-in Java help viewer
1334 <!-- JAL-1644 -->Find documentation updated with 'search
1335 sequence description' option
1341 <!-- JAL-2485, -->External service integration tests for
1342 Uniprot REST Free Text Search Client
1345 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1348 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1353 <td><div align="left">
1354 <em>Calculations</em>
1357 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1358 matrix - C->R should be '-3'<br />Old matrix restored
1359 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1361 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1362 Jalview's treatment of gaps in PCA and substitution matrix
1363 based Tree calculations.<br /> <br />In earlier versions
1364 of Jalview, gaps matching gaps were penalised, and gaps
1365 matching non-gaps penalised even more. In the PCA
1366 calculation, gaps were actually treated as non-gaps - so
1367 different costs were applied, which meant Jalview's PCAs
1368 were different to those produced by SeqSpace.<br />Jalview
1369 now treats gaps in the same way as SeqSpace (ie it scores
1370 them as 0). <br /> <br />Enter the following in the
1371 Groovy console to restore pre-2.10.2 behaviour:<br />
1372 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1373 // for 2.10.1 mode <br />
1374 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1375 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1376 these settings will affect all subsequent tree and PCA
1377 calculations (not recommended)</em></li>
1379 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1380 scaling of branch lengths for trees computed using
1381 Sequence Feature Similarity.
1384 <!-- JAL-2377 -->PCA calculation could hang when
1385 generating output report when working with highly
1386 redundant alignments
1389 <!-- JAL-2544 --> Sort by features includes features to
1390 right of selected region when gaps present on right-hand
1394 <em>User Interface</em>
1397 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1398 doesn't reselect a specific sequence's associated
1399 annotation after it was used for colouring a view
1402 <!-- JAL-2419 -->Current selection lost if popup menu
1403 opened on a region of alignment without groups
1406 <!-- JAL-2374 -->Popup menu not always shown for regions
1407 of an alignment with overlapping groups
1410 <!-- JAL-2310 -->Finder double counts if both a sequence's
1411 name and description match
1414 <!-- JAL-2370 -->Hiding column selection containing two
1415 hidden regions results in incorrect hidden regions
1418 <!-- JAL-2386 -->'Apply to all groups' setting when
1419 changing colour does not apply Conservation slider value
1423 <!-- JAL-2373 -->Percentage identity and conservation menu
1424 items do not show a tick or allow shading to be disabled
1427 <!-- JAL-2385 -->Conservation shading or PID threshold
1428 lost when base colourscheme changed if slider not visible
1431 <!-- JAL-2547 -->Sequence features shown in tooltip for
1432 gaps before start of features
1435 <!-- JAL-2623 -->Graduated feature colour threshold not
1436 restored to UI when feature colour is edited
1439 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1440 a time when scrolling vertically in wrapped mode.
1443 <!-- JAL-2630 -->Structure and alignment overview update
1444 as graduate feature colour settings are modified via the
1448 <!-- JAL-2034 -->Overview window doesn't always update
1449 when a group defined on the alignment is resized
1452 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1453 wrapped view result in positional status updates
1457 <!-- JAL-2563 -->Status bar doesn't show position for
1458 ambiguous amino acid and nucleotide symbols
1461 <!-- JAL-2602 -->Copy consensus sequence failed if
1462 alignment included gapped columns
1465 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1466 widgets don't permanently disappear
1469 <!-- JAL-2503 -->Cannot select or filter quantitative
1470 annotation that are shown only as column labels (e.g.
1471 T-Coffee column reliability scores)
1474 <!-- JAL-2594 -->Exception thrown if trying to create a
1475 sequence feature on gaps only
1478 <!-- JAL-2504 -->Features created with 'New feature'
1479 button from a Find inherit previously defined feature type
1480 rather than the Find query string
1483 <!-- JAL-2423 -->incorrect title in output window when
1484 exporting tree calculated in Jalview
1487 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1488 and then revealing them reorders sequences on the
1492 <!-- JAL-964 -->Group panel in sequence feature settings
1493 doesn't update to reflect available set of groups after
1494 interactively adding or modifying features
1497 <!-- JAL-2225 -->Sequence Database chooser unusable on
1501 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1502 only excluded gaps in current sequence and ignored
1509 <!-- JAL-2421 -->Overview window visible region moves
1510 erratically when hidden rows or columns are present
1513 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1514 Structure Viewer's colour menu don't correspond to
1518 <!-- JAL-2405 -->Protein specific colours only offered in
1519 colour and group colour menu for protein alignments
1522 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1523 reflect currently selected view or group's shading
1527 <!-- JAL-2624 -->Feature colour thresholds not respected
1528 when rendered on overview and structures when opacity at
1532 <!-- JAL-2589 -->User defined gap colour not shown in
1533 overview when features overlaid on alignment
1536 <!-- JAL-2567 -->Feature settings for different views not
1537 recovered correctly from Jalview project file
1540 <!-- JAL-2256 -->Feature colours in overview when first opened
1541 (automatically via preferences) are different to the main
1545 <em>Data import/export</em>
1548 <!-- JAL-2576 -->Very large alignments take a long time to
1552 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1553 added after a sequence was imported are not written to
1557 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1558 when importing RNA secondary structure via Stockholm
1561 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1562 not shown in correct direction for simple pseudoknots
1565 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1566 with lightGray or darkGray via features file (but can
1570 <!-- JAL-2383 -->Above PID colour threshold not recovered
1571 when alignment view imported from project
1574 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1575 structure and sequences extracted from structure files
1576 imported via URL and viewed in Jmol
1579 <!-- JAL-2520 -->Structures loaded via URL are saved in
1580 Jalview Projects rather than fetched via URL again when
1581 the project is loaded and the structure viewed
1584 <em>Web Services</em>
1587 <!-- JAL-2519 -->EnsemblGenomes example failing after
1588 release of Ensembl v.88
1591 <!-- JAL-2366 -->Proxy server address and port always
1592 appear enabled in Preferences->Connections
1595 <!-- JAL-2461 -->DAS registry not found exceptions
1596 removed from console output
1599 <!-- JAL-2582 -->Cannot retrieve protein products from
1600 Ensembl by Peptide ID
1603 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1604 created from SIFTs, and spurious 'Couldn't open structure
1605 in Chimera' errors raised after April 2017 update (problem
1606 due to 'null' string rather than empty string used for
1607 residues with no corresponding PDB mapping).
1610 <em>Application UI</em>
1613 <!-- JAL-2361 -->User Defined Colours not added to Colour
1617 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1618 case' residues (button in colourscheme editor debugged and
1619 new documentation and tooltips added)
1622 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1623 doesn't restore group-specific text colour thresholds
1626 <!-- JAL-2243 -->Feature settings panel does not update as
1627 new features are added to alignment
1630 <!-- JAL-2532 -->Cancel in feature settings reverts
1631 changes to feature colours via the Amend features dialog
1634 <!-- JAL-2506 -->Null pointer exception when attempting to
1635 edit graduated feature colour via amend features dialog
1639 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1640 selection menu changes colours of alignment views
1643 <!-- JAL-2426 -->Spurious exceptions in console raised
1644 from alignment calculation workers after alignment has
1648 <!-- JAL-1608 -->Typo in selection popup menu - Create
1649 groups now 'Create Group'
1652 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1653 Create/Undefine group doesn't always work
1656 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1657 shown again after pressing 'Cancel'
1660 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1661 adjusts start position in wrap mode
1664 <!-- JAL-2563 -->Status bar doesn't show positions for
1665 ambiguous amino acids
1668 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1669 CDS/Protein view after CDS sequences added for aligned
1673 <!-- JAL-2592 -->User defined colourschemes called 'User
1674 Defined' don't appear in Colours menu
1680 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1681 score models doesn't always result in an updated PCA plot
1684 <!-- JAL-2442 -->Features not rendered as transparent on
1685 overview or linked structure view
1688 <!-- JAL-2372 -->Colour group by conservation doesn't
1692 <!-- JAL-2517 -->Hitting Cancel after applying
1693 user-defined colourscheme doesn't restore original
1700 <!-- JAL-2314 -->Unit test failure:
1701 jalview.ws.jabaws.RNAStructExportImport setup fails
1704 <!-- JAL-2307 -->Unit test failure:
1705 jalview.ws.sifts.SiftsClientTest due to compatibility
1706 problems with deep array comparison equality asserts in
1707 successive versions of TestNG
1710 <!-- JAL-2479 -->Relocated StructureChooserTest and
1711 ParameterUtilsTest Unit tests to Network suite
1714 <em>New Known Issues</em>
1717 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1718 phase after a sequence motif find operation
1721 <!-- JAL-2550 -->Importing annotation file with rows
1722 containing just upper and lower case letters are
1723 interpreted as WUSS RNA secondary structure symbols
1726 <!-- JAL-2590 -->Cannot load and display Newick trees
1727 reliably from eggnog Ortholog database
1730 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1731 containing features of type Highlight' when 'B' is pressed
1732 to mark columns containing highlighted regions.
1735 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1736 doesn't always add secondary structure annotation.
1741 <td width="60" nowrap>
1742 <div align="center">
1743 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1746 <td><div align="left">
1750 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1751 for all consensus calculations
1754 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1757 <li>Updated Jalview's Certum code signing certificate
1760 <em>Application</em>
1763 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1764 set of database cross-references, sorted alphabetically
1767 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1768 from database cross references. Users with custom links
1769 will receive a <a href="webServices/urllinks.html#warning">warning
1770 dialog</a> asking them to update their preferences.
1773 <!-- JAL-2287-->Cancel button and escape listener on
1774 dialog warning user about disconnecting Jalview from a
1778 <!-- JAL-2320-->Jalview's Chimera control window closes if
1779 the Chimera it is connected to is shut down
1782 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1783 columns menu item to mark columns containing highlighted
1784 regions (e.g. from structure selections or results of a
1788 <!-- JAL-2284-->Command line option for batch-generation
1789 of HTML pages rendering alignment data with the BioJS
1799 <!-- JAL-2286 -->Columns with more than one modal residue
1800 are not coloured or thresholded according to percent
1801 identity (first observed in Jalview 2.8.2)
1804 <!-- JAL-2301 -->Threonine incorrectly reported as not
1808 <!-- JAL-2318 -->Updates to documentation pages (above PID
1809 threshold, amino acid properties)
1812 <!-- JAL-2292 -->Lower case residues in sequences are not
1813 reported as mapped to residues in a structure file in the
1817 <!--JAL-2324 -->Identical features with non-numeric scores
1818 could be added multiple times to a sequence
1821 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1822 bond features shown as two highlighted residues rather
1823 than a range in linked structure views, and treated
1824 correctly when selecting and computing trees from features
1827 <!-- JAL-2281-->Custom URL links for database
1828 cross-references are matched to database name regardless
1833 <em>Application</em>
1836 <!-- JAL-2282-->Custom URL links for specific database
1837 names without regular expressions also offer links from
1841 <!-- JAL-2315-->Removing a single configured link in the
1842 URL links pane in Connections preferences doesn't actually
1843 update Jalview configuration
1846 <!-- JAL-2272-->CTRL-Click on a selected region to open
1847 the alignment area popup menu doesn't work on El-Capitan
1850 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1851 files with similarly named sequences if dropped onto the
1855 <!-- JAL-2312 -->Additional mappings are shown for PDB
1856 entries where more chains exist in the PDB accession than
1857 are reported in the SIFTS file
1860 <!-- JAL-2317-->Certain structures do not get mapped to
1861 the structure view when displayed with Chimera
1864 <!-- JAL-2317-->No chains shown in the Chimera view
1865 panel's View->Show Chains submenu
1868 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1869 work for wrapped alignment views
1872 <!--JAL-2197 -->Rename UI components for running JPred
1873 predictions from 'JNet' to 'JPred'
1876 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1877 corrupted when annotation panel vertical scroll is not at
1878 first annotation row
1881 <!--JAL-2332 -->Attempting to view structure for Hen
1882 lysozyme results in a PDB Client error dialog box
1885 <!-- JAL-2319 -->Structure View's mapping report switched
1886 ranges for PDB and sequence for SIFTS
1889 SIFTS 'Not_Observed' residues mapped to non-existant
1893 <!-- <em>New Known Issues</em>
1900 <td width="60" nowrap>
1901 <div align="center">
1902 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1903 <em>25/10/2016</em></strong>
1906 <td><em>Application</em>
1908 <li>3D Structure chooser opens with 'Cached structures'
1909 view if structures already loaded</li>
1910 <li>Progress bar reports models as they are loaded to
1911 structure views</li>
1917 <li>Colour by conservation always enabled and no tick
1918 shown in menu when BLOSUM or PID shading applied</li>
1919 <li>FER1_ARATH and FER2_ARATH labels were switched in
1920 example sequences/projects/trees</li>
1922 <em>Application</em>
1924 <li>Jalview projects with views of local PDB structure
1925 files saved on Windows cannot be opened on OSX</li>
1926 <li>Multiple structure views can be opened and superposed
1927 without timeout for structures with multiple models or
1928 multiple sequences in alignment</li>
1929 <li>Cannot import or associated local PDB files without a
1930 PDB ID HEADER line</li>
1931 <li>RMSD is not output in Jmol console when superposition
1933 <li>Drag and drop of URL from Browser fails for Linux and
1934 OSX versions earlier than El Capitan</li>
1935 <li>ENA client ignores invalid content from ENA server</li>
1936 <li>Exceptions are not raised in console when ENA client
1937 attempts to fetch non-existent IDs via Fetch DB Refs UI
1939 <li>Exceptions are not raised in console when a new view
1940 is created on the alignment</li>
1941 <li>OSX right-click fixed for group selections: CMD-click
1942 to insert/remove gaps in groups and CTRL-click to open group
1945 <em>Build and deployment</em>
1947 <li>URL link checker now copes with multi-line anchor
1950 <em>New Known Issues</em>
1952 <li>Drag and drop from URL links in browsers do not work
1959 <td width="60" nowrap>
1960 <div align="center">
1961 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1964 <td><em>General</em>
1967 <!-- JAL-2124 -->Updated Spanish translations.
1970 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1971 for importing structure data to Jalview. Enables mmCIF and
1975 <!-- JAL-192 --->Alignment ruler shows positions relative to
1979 <!-- JAL-2202 -->Position/residue shown in status bar when
1980 mousing over sequence associated annotation
1983 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1987 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1988 '()', canonical '[]' and invalid '{}' base pair populations
1992 <!-- JAL-2092 -->Feature settings popup menu options for
1993 showing or hiding columns containing a feature
1996 <!-- JAL-1557 -->Edit selected group by double clicking on
1997 group and sequence associated annotation labels
2000 <!-- JAL-2236 -->Sequence name added to annotation label in
2001 select/hide columns by annotation and colour by annotation
2005 </ul> <em>Application</em>
2008 <!-- JAL-2050-->Automatically hide introns when opening a
2009 gene/transcript view
2012 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2016 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2017 structure mappings with the EMBL-EBI PDBe SIFTS database
2020 <!-- JAL-2079 -->Updated download sites used for Rfam and
2021 Pfam sources to xfam.org
2024 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2027 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2028 over sequences in Jalview
2031 <!-- JAL-2027-->Support for reverse-complement coding
2032 regions in ENA and EMBL
2035 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2036 for record retrieval via ENA rest API
2039 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2043 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2044 groovy script execution
2047 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2048 alignment window's Calculate menu
2051 <!-- JAL-1812 -->Allow groovy scripts that call
2052 Jalview.getAlignFrames() to run in headless mode
2055 <!-- JAL-2068 -->Support for creating new alignment
2056 calculation workers from groovy scripts
2059 <!-- JAL-1369 --->Store/restore reference sequence in
2063 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2064 associations are now saved/restored from project
2067 <!-- JAL-1993 -->Database selection dialog always shown
2068 before sequence fetcher is opened
2071 <!-- JAL-2183 -->Double click on an entry in Jalview's
2072 database chooser opens a sequence fetcher
2075 <!-- JAL-1563 -->Free-text search client for UniProt using
2076 the UniProt REST API
2079 <!-- JAL-2168 -->-nonews command line parameter to prevent
2080 the news reader opening
2083 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2084 querying stored in preferences
2087 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2091 <!-- JAL-1977-->Tooltips shown on database chooser
2094 <!-- JAL-391 -->Reverse complement function in calculate
2095 menu for nucleotide sequences
2098 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2099 and feature counts preserves alignment ordering (and
2100 debugged for complex feature sets).
2103 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2104 viewing structures with Jalview 2.10
2107 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2108 genome, transcript CCDS and gene ids via the Ensembl and
2109 Ensembl Genomes REST API
2112 <!-- JAL-2049 -->Protein sequence variant annotation
2113 computed for 'sequence_variant' annotation on CDS regions
2117 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2121 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2122 Ref Fetcher fails to match, or otherwise updates sequence
2123 data from external database records.
2126 <!-- JAL-2154 -->Revised Jalview Project format for
2127 efficient recovery of sequence coding and alignment
2128 annotation relationships.
2130 </ul> <!-- <em>Applet</em>
2141 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2145 <!-- JAL-2018-->Export features in Jalview format (again)
2146 includes graduated colourschemes
2149 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2150 working with big alignments and lots of hidden columns
2153 <!-- JAL-2053-->Hidden column markers not always rendered
2154 at right of alignment window
2157 <!-- JAL-2067 -->Tidied up links in help file table of
2161 <!-- JAL-2072 -->Feature based tree calculation not shown
2165 <!-- JAL-2075 -->Hidden columns ignored during feature
2166 based tree calculation
2169 <!-- JAL-2065 -->Alignment view stops updating when show
2170 unconserved enabled for group on alignment
2173 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2177 <!-- JAL-2146 -->Alignment column in status incorrectly
2178 shown as "Sequence position" when mousing over
2182 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2183 hidden columns present
2186 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2187 user created annotation added to alignment
2190 <!-- JAL-1841 -->RNA Structure consensus only computed for
2191 '()' base pair annotation
2194 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2195 in zero scores for all base pairs in RNA Structure
2199 <!-- JAL-2174-->Extend selection with columns containing
2203 <!-- JAL-2275 -->Pfam format writer puts extra space at
2204 beginning of sequence
2207 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2211 <!-- JAL-2238 -->Cannot create groups on an alignment from
2212 from a tree when t-coffee scores are shown
2215 <!-- JAL-1836,1967 -->Cannot import and view PDB
2216 structures with chains containing negative resnums (4q4h)
2219 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2223 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2224 to Clustal, PIR and PileUp output
2227 <!-- JAL-2008 -->Reordering sequence features that are
2228 not visible causes alignment window to repaint
2231 <!-- JAL-2006 -->Threshold sliders don't work in
2232 graduated colour and colour by annotation row for e-value
2233 scores associated with features and annotation rows
2236 <!-- JAL-1797 -->amino acid physicochemical conservation
2237 calculation should be case independent
2240 <!-- JAL-2173 -->Remove annotation also updates hidden
2244 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2245 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2246 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2249 <!-- JAL-2065 -->Null pointer exceptions and redraw
2250 problems when reference sequence defined and 'show
2251 non-conserved' enabled
2254 <!-- JAL-1306 -->Quality and Conservation are now shown on
2255 load even when Consensus calculation is disabled
2258 <!-- JAL-1932 -->Remove right on penultimate column of
2259 alignment does nothing
2262 <em>Application</em>
2265 <!-- JAL-1552-->URLs and links can't be imported by
2266 drag'n'drop on OSX when launched via webstart (note - not
2267 yet fixed for El Capitan)
2270 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2271 output when running on non-gb/us i18n platforms
2274 <!-- JAL-1944 -->Error thrown when exporting a view with
2275 hidden sequences as flat-file alignment
2278 <!-- JAL-2030-->InstallAnywhere distribution fails when
2282 <!-- JAL-2080-->Jalview very slow to launch via webstart
2283 (also hotfix for 2.9.0b2)
2286 <!-- JAL-2085 -->Cannot save project when view has a
2287 reference sequence defined
2290 <!-- JAL-1011 -->Columns are suddenly selected in other
2291 alignments and views when revealing hidden columns
2294 <!-- JAL-1989 -->Hide columns not mirrored in complement
2295 view in a cDNA/Protein splitframe
2298 <!-- JAL-1369 -->Cannot save/restore representative
2299 sequence from project when only one sequence is
2303 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2304 in Structure Chooser
2307 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2308 structure consensus didn't refresh annotation panel
2311 <!-- JAL-1962 -->View mapping in structure view shows
2312 mappings between sequence and all chains in a PDB file
2315 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2316 dialogs format columns correctly, don't display array
2317 data, sort columns according to type
2320 <!-- JAL-1975 -->Export complete shown after destination
2321 file chooser is cancelled during an image export
2324 <!-- JAL-2025 -->Error when querying PDB Service with
2325 sequence name containing special characters
2328 <!-- JAL-2024 -->Manual PDB structure querying should be
2332 <!-- JAL-2104 -->Large tooltips with broken HTML
2333 formatting don't wrap
2336 <!-- JAL-1128 -->Figures exported from wrapped view are
2337 truncated so L looks like I in consensus annotation
2340 <!-- JAL-2003 -->Export features should only export the
2341 currently displayed features for the current selection or
2345 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2346 after fetching cross-references, and restoring from
2350 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2351 followed in the structure viewer
2354 <!-- JAL-2163 -->Titles for individual alignments in
2355 splitframe not restored from project
2358 <!-- JAL-2145 -->missing autocalculated annotation at
2359 trailing end of protein alignment in transcript/product
2360 splitview when pad-gaps not enabled by default
2363 <!-- JAL-1797 -->amino acid physicochemical conservation
2367 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2368 article has been read (reopened issue due to
2369 internationalisation problems)
2372 <!-- JAL-1960 -->Only offer PDB structures in structure
2373 viewer based on sequence name, PDB and UniProt
2378 <!-- JAL-1976 -->No progress bar shown during export of
2382 <!-- JAL-2213 -->Structures not always superimposed after
2383 multiple structures are shown for one or more sequences.
2386 <!-- JAL-1370 -->Reference sequence characters should not
2387 be replaced with '.' when 'Show unconserved' format option
2391 <!-- JAL-1823 -->Cannot specify chain code when entering
2392 specific PDB id for sequence
2395 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2396 'Export hidden sequences' is enabled, but 'export hidden
2397 columns' is disabled.
2400 <!--JAL-2026-->Best Quality option in structure chooser
2401 selects lowest rather than highest resolution structures
2405 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2406 to sequence mapping in 'View Mappings' report
2409 <!-- JAL-2284 -->Unable to read old Jalview projects that
2410 contain non-XML data added after Jalvew wrote project.
2413 <!-- JAL-2118 -->Newly created annotation row reorders
2414 after clicking on it to create new annotation for a
2418 <!-- JAL-1980 -->Null Pointer Exception raised when
2419 pressing Add on an orphaned cut'n'paste window.
2421 <!-- may exclude, this is an external service stability issue JAL-1941
2422 -- > RNA 3D structure not added via DSSR service</li> -->
2427 <!-- JAL-2151 -->Incorrect columns are selected when
2428 hidden columns present before start of sequence
2431 <!-- JAL-1986 -->Missing dependencies on applet pages
2435 <!-- JAL-1947 -->Overview pixel size changes when
2436 sequences are hidden in applet
2439 <!-- JAL-1996 -->Updated instructions for applet
2440 deployment on examples pages.
2447 <td width="60" nowrap>
2448 <div align="center">
2449 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2450 <em>16/10/2015</em></strong>
2453 <td><em>General</em>
2455 <li>Time stamps for signed Jalview application and applet
2460 <em>Application</em>
2462 <li>Duplicate group consensus and conservation rows
2463 shown when tree is partitioned</li>
2464 <li>Erratic behaviour when tree partitions made with
2465 multiple cDNA/Protein split views</li>
2471 <td width="60" nowrap>
2472 <div align="center">
2473 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2474 <em>8/10/2015</em></strong>
2477 <td><em>General</em>
2479 <li>Updated Spanish translations of localized text for
2481 </ul> <em>Application</em>
2483 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2484 <li>Signed OSX InstallAnywhere installer<br></li>
2485 <li>Support for per-sequence based annotations in BioJSON</li>
2486 </ul> <em>Applet</em>
2488 <li>Split frame example added to applet examples page</li>
2489 </ul> <em>Build and Deployment</em>
2492 <!-- JAL-1888 -->New ant target for running Jalview's test
2500 <li>Mapping of cDNA to protein in split frames
2501 incorrect when sequence start > 1</li>
2502 <li>Broken images in filter column by annotation dialog
2504 <li>Feature colours not parsed from features file</li>
2505 <li>Exceptions and incomplete link URLs recovered when
2506 loading a features file containing HTML tags in feature
2510 <em>Application</em>
2512 <li>Annotations corrupted after BioJS export and
2514 <li>Incorrect sequence limits after Fetch DB References
2515 with 'trim retrieved sequences'</li>
2516 <li>Incorrect warning about deleting all data when
2517 deleting selected columns</li>
2518 <li>Patch to build system for shipping properly signed
2519 JNLP templates for webstart launch</li>
2520 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2521 unreleased structures for download or viewing</li>
2522 <li>Tab/space/return keystroke operation of EMBL-PDBe
2523 fetcher/viewer dialogs works correctly</li>
2524 <li>Disabled 'minimise' button on Jalview windows
2525 running on OSX to workaround redraw hang bug</li>
2526 <li>Split cDNA/Protein view position and geometry not
2527 recovered from jalview project</li>
2528 <li>Initial enabled/disabled state of annotation menu
2529 sorter 'show autocalculated first/last' corresponds to
2531 <li>Restoring of Clustal, RNA Helices and T-Coffee
2532 color schemes from BioJSON</li>
2536 <li>Reorder sequences mirrored in cDNA/Protein split
2538 <li>Applet with Jmol examples not loading correctly</li>
2544 <td><div align="center">
2545 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2547 <td><em>General</em>
2549 <li>Linked visualisation and analysis of DNA and Protein
2552 <li>Translated cDNA alignments shown as split protein
2553 and DNA alignment views</li>
2554 <li>Codon consensus annotation for linked protein and
2555 cDNA alignment views</li>
2556 <li>Link cDNA or Protein product sequences by loading
2557 them onto Protein or cDNA alignments</li>
2558 <li>Reconstruct linked cDNA alignment from aligned
2559 protein sequences</li>
2562 <li>Jmol integration updated to Jmol v14.2.14</li>
2563 <li>Import and export of Jalview alignment views as <a
2564 href="features/bioJsonFormat.html">BioJSON</a></li>
2565 <li>New alignment annotation file statements for
2566 reference sequences and marking hidden columns</li>
2567 <li>Reference sequence based alignment shading to
2568 highlight variation</li>
2569 <li>Select or hide columns according to alignment
2571 <li>Find option for locating sequences by description</li>
2572 <li>Conserved physicochemical properties shown in amino
2573 acid conservation row</li>
2574 <li>Alignments can be sorted by number of RNA helices</li>
2575 </ul> <em>Application</em>
2577 <li>New cDNA/Protein analysis capabilities
2579 <li>Get Cross-References should open a Split Frame
2580 view with cDNA/Protein</li>
2581 <li>Detect when nucleotide sequences and protein
2582 sequences are placed in the same alignment</li>
2583 <li>Split cDNA/Protein views are saved in Jalview
2588 <li>Use REST API to talk to Chimera</li>
2589 <li>Selected regions in Chimera are highlighted in linked
2590 Jalview windows</li>
2592 <li>VARNA RNA viewer updated to v3.93</li>
2593 <li>VARNA views are saved in Jalview Projects</li>
2594 <li>Pseudoknots displayed as Jalview RNA annotation can
2595 be shown in VARNA</li>
2597 <li>Make groups for selection uses marked columns as well
2598 as the active selected region</li>
2600 <li>Calculate UPGMA and NJ trees using sequence feature
2602 <li>New Export options
2604 <li>New Export Settings dialog to control hidden
2605 region export in flat file generation</li>
2607 <li>Export alignment views for display with the <a
2608 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2610 <li>Export scrollable SVG in HTML page</li>
2611 <li>Optional embedding of BioJSON data when exporting
2612 alignment figures to HTML</li>
2614 <li>3D structure retrieval and display
2616 <li>Free text and structured queries with the PDBe
2618 <li>PDBe Search API based discovery and selection of
2619 PDB structures for a sequence set</li>
2623 <li>JPred4 employed for protein secondary structure
2625 <li>Hide Insertions menu option to hide unaligned columns
2626 for one or a group of sequences</li>
2627 <li>Automatically hide insertions in alignments imported
2628 from the JPred4 web server</li>
2629 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2630 system on OSX<br />LGPL libraries courtesy of <a
2631 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2633 <li>changed 'View nucleotide structure' submenu to 'View
2634 VARNA 2D Structure'</li>
2635 <li>change "View protein structure" menu option to "3D
2638 </ul> <em>Applet</em>
2640 <li>New layout for applet example pages</li>
2641 <li>New parameters to enable SplitFrame view
2642 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2643 <li>New example demonstrating linked viewing of cDNA and
2644 Protein alignments</li>
2645 </ul> <em>Development and deployment</em>
2647 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2648 <li>Include installation type and git revision in build
2649 properties and console log output</li>
2650 <li>Jalview Github organisation, and new github site for
2651 storing BioJsMSA Templates</li>
2652 <li>Jalview's unit tests now managed with TestNG</li>
2655 <!-- <em>General</em>
2657 </ul> --> <!-- issues resolved --> <em>Application</em>
2659 <li>Escape should close any open find dialogs</li>
2660 <li>Typo in select-by-features status report</li>
2661 <li>Consensus RNA secondary secondary structure
2662 predictions are not highlighted in amber</li>
2663 <li>Missing gap character in v2.7 example file means
2664 alignment appears unaligned when pad-gaps is not enabled</li>
2665 <li>First switch to RNA Helices colouring doesn't colour
2666 associated structure views</li>
2667 <li>ID width preference option is greyed out when auto
2668 width checkbox not enabled</li>
2669 <li>Stopped a warning dialog from being shown when
2670 creating user defined colours</li>
2671 <li>'View Mapping' in structure viewer shows sequence
2672 mappings for just that viewer's sequences</li>
2673 <li>Workaround for superposing PDB files containing
2674 multiple models in Chimera</li>
2675 <li>Report sequence position in status bar when hovering
2676 over Jmol structure</li>
2677 <li>Cannot output gaps as '.' symbols with Selection ->
2678 output to text box</li>
2679 <li>Flat file exports of alignments with hidden columns
2680 have incorrect sequence start/end</li>
2681 <li>'Aligning' a second chain to a Chimera structure from
2683 <li>Colour schemes applied to structure viewers don't
2684 work for nucleotide</li>
2685 <li>Loading/cut'n'pasting an empty or invalid file leads
2686 to a grey/invisible alignment window</li>
2687 <li>Exported Jpred annotation from a sequence region
2688 imports to different position</li>
2689 <li>Space at beginning of sequence feature tooltips shown
2690 on some platforms</li>
2691 <li>Chimera viewer 'View | Show Chain' menu is not
2693 <li>'New View' fails with a Null Pointer Exception in
2694 console if Chimera has been opened</li>
2695 <li>Mouseover to Chimera not working</li>
2696 <li>Miscellaneous ENA XML feature qualifiers not
2698 <li>NPE in annotation renderer after 'Extract Scores'</li>
2699 <li>If two structures in one Chimera window, mouseover of
2700 either sequence shows on first structure</li>
2701 <li>'Show annotations' options should not make
2702 non-positional annotations visible</li>
2703 <li>Subsequence secondary structure annotation not shown
2704 in right place after 'view flanking regions'</li>
2705 <li>File Save As type unset when current file format is
2707 <li>Save as '.jar' option removed for saving Jalview
2709 <li>Colour by Sequence colouring in Chimera more
2711 <li>Cannot 'add reference annotation' for a sequence in
2712 several views on same alignment</li>
2713 <li>Cannot show linked products for EMBL / ENA records</li>
2714 <li>Jalview's tooltip wraps long texts containing no
2716 </ul> <em>Applet</em>
2718 <li>Jmol to JalviewLite mouseover/link not working</li>
2719 <li>JalviewLite can't import sequences with ID
2720 descriptions containing angle brackets</li>
2721 </ul> <em>General</em>
2723 <li>Cannot export and reimport RNA secondary structure
2724 via jalview annotation file</li>
2725 <li>Random helix colour palette for colour by annotation
2726 with RNA secondary structure</li>
2727 <li>Mouseover to cDNA from STOP residue in protein
2728 translation doesn't work.</li>
2729 <li>hints when using the select by annotation dialog box</li>
2730 <li>Jmol alignment incorrect if PDB file has alternate CA
2732 <li>FontChooser message dialog appears to hang after
2733 choosing 1pt font</li>
2734 <li>Peptide secondary structure incorrectly imported from
2735 annotation file when annotation display text includes 'e' or
2737 <li>Cannot set colour of new feature type whilst creating
2739 <li>cDNA translation alignment should not be sequence
2740 order dependent</li>
2741 <li>'Show unconserved' doesn't work for lower case
2743 <li>Nucleotide ambiguity codes involving R not recognised</li>
2744 </ul> <em>Deployment and Documentation</em>
2746 <li>Applet example pages appear different to the rest of
2747 www.jalview.org</li>
2748 </ul> <em>Application Known issues</em>
2750 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2751 <li>Misleading message appears after trying to delete
2753 <li>Jalview icon not shown in dock after InstallAnywhere
2754 version launches</li>
2755 <li>Fetching EMBL reference for an RNA sequence results
2756 fails with a sequence mismatch</li>
2757 <li>Corrupted or unreadable alignment display when
2758 scrolling alignment to right</li>
2759 <li>ArrayIndexOutOfBoundsException thrown when remove
2760 empty columns called on alignment with ragged gapped ends</li>
2761 <li>auto calculated alignment annotation rows do not get
2762 placed above or below non-autocalculated rows</li>
2763 <li>Jalview dekstop becomes sluggish at full screen in
2764 ultra-high resolution</li>
2765 <li>Cannot disable consensus calculation independently of
2766 quality and conservation</li>
2767 <li>Mouseover highlighting between cDNA and protein can
2768 become sluggish with more than one splitframe shown</li>
2769 </ul> <em>Applet Known Issues</em>
2771 <li>Core PDB parsing code requires Jmol</li>
2772 <li>Sequence canvas panel goes white when alignment
2773 window is being resized</li>
2779 <td><div align="center">
2780 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2782 <td><em>General</em>
2784 <li>Updated Java code signing certificate donated by
2786 <li>Features and annotation preserved when performing
2787 pairwise alignment</li>
2788 <li>RNA pseudoknot annotation can be
2789 imported/exported/displayed</li>
2790 <li>'colour by annotation' can colour by RNA and
2791 protein secondary structure</li>
2792 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2793 post-hoc with 2.9 release</em>)
2796 </ul> <em>Application</em>
2798 <li>Extract and display secondary structure for sequences
2799 with 3D structures</li>
2800 <li>Support for parsing RNAML</li>
2801 <li>Annotations menu for layout
2803 <li>sort sequence annotation rows by alignment</li>
2804 <li>place sequence annotation above/below alignment
2807 <li>Output in Stockholm format</li>
2808 <li>Internationalisation: improved Spanish (es)
2810 <li>Structure viewer preferences tab</li>
2811 <li>Disorder and Secondary Structure annotation tracks
2812 shared between alignments</li>
2813 <li>UCSF Chimera launch and linked highlighting from
2815 <li>Show/hide all sequence associated annotation rows for
2816 all or current selection</li>
2817 <li>disorder and secondary structure predictions
2818 available as dataset annotation</li>
2819 <li>Per-sequence rna helices colouring</li>
2822 <li>Sequence database accessions imported when fetching
2823 alignments from Rfam</li>
2824 <li>update VARNA version to 3.91</li>
2826 <li>New groovy scripts for exporting aligned positions,
2827 conservation values, and calculating sum of pairs scores.</li>
2828 <li>Command line argument to set default JABAWS server</li>
2829 <li>include installation type in build properties and
2830 console log output</li>
2831 <li>Updated Jalview project format to preserve dataset
2835 <!-- issues resolved --> <em>Application</em>
2837 <li>Distinguish alignment and sequence associated RNA
2838 structure in structure->view->VARNA</li>
2839 <li>Raise dialog box if user deletes all sequences in an
2841 <li>Pressing F1 results in documentation opening twice</li>
2842 <li>Sequence feature tooltip is wrapped</li>
2843 <li>Double click on sequence associated annotation
2844 selects only first column</li>
2845 <li>Redundancy removal doesn't result in unlinked
2846 leaves shown in tree</li>
2847 <li>Undos after several redundancy removals don't undo
2849 <li>Hide sequence doesn't hide associated annotation</li>
2850 <li>User defined colours dialog box too big to fit on
2851 screen and buttons not visible</li>
2852 <li>author list isn't updated if already written to
2853 Jalview properties</li>
2854 <li>Popup menu won't open after retrieving sequence
2856 <li>File open window for associate PDB doesn't open</li>
2857 <li>Left-then-right click on a sequence id opens a
2858 browser search window</li>
2859 <li>Cannot open sequence feature shading/sort popup menu
2860 in feature settings dialog</li>
2861 <li>better tooltip placement for some areas of Jalview
2863 <li>Allow addition of JABAWS Server which doesn't
2864 pass validation</li>
2865 <li>Web services parameters dialog box is too large to
2867 <li>Muscle nucleotide alignment preset obscured by
2869 <li>JABAWS preset submenus don't contain newly
2870 defined user preset</li>
2871 <li>MSA web services warns user if they were launched
2872 with invalid input</li>
2873 <li>Jalview cannot contact DAS Registy when running on
2876 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2877 'Superpose with' submenu not shown when new view
2881 </ul> <!-- <em>Applet</em>
2883 </ul> <em>General</em>
2885 </ul>--> <em>Deployment and Documentation</em>
2887 <li>2G and 1G options in launchApp have no effect on
2888 memory allocation</li>
2889 <li>launchApp service doesn't automatically open
2890 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2892 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2893 InstallAnywhere reports cannot find valid JVM when Java
2894 1.7_055 is available
2896 </ul> <em>Application Known issues</em>
2899 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2900 corrupted or unreadable alignment display when scrolling
2904 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2905 retrieval fails but progress bar continues for DAS retrieval
2906 with large number of ID
2909 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2910 flatfile output of visible region has incorrect sequence
2914 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2915 rna structure consensus doesn't update when secondary
2916 structure tracks are rearranged
2919 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2920 invalid rna structure positional highlighting does not
2921 highlight position of invalid base pairs
2924 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2925 out of memory errors are not raised when saving Jalview
2926 project from alignment window file menu
2929 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2930 Switching to RNA Helices colouring doesn't propagate to
2934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2935 colour by RNA Helices not enabled when user created
2936 annotation added to alignment
2939 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2940 Jalview icon not shown on dock in Mountain Lion/Webstart
2942 </ul> <em>Applet Known Issues</em>
2945 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2946 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2949 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2950 Jalview and Jmol example not compatible with IE9
2953 <li>Sort by annotation score doesn't reverse order
2959 <td><div align="center">
2960 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2963 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2966 <li>Internationalisation of user interface (usually
2967 called i18n support) and translation for Spanish locale</li>
2968 <li>Define/Undefine group on current selection with
2969 Ctrl-G/Shift Ctrl-G</li>
2970 <li>Improved group creation/removal options in
2971 alignment/sequence Popup menu</li>
2972 <li>Sensible precision for symbol distribution
2973 percentages shown in logo tooltip.</li>
2974 <li>Annotation panel height set according to amount of
2975 annotation when alignment first opened</li>
2976 </ul> <em>Application</em>
2978 <li>Interactive consensus RNA secondary structure
2979 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2980 <li>Select columns containing particular features from
2981 Feature Settings dialog</li>
2982 <li>View all 'representative' PDB structures for selected
2984 <li>Update Jalview project format:
2986 <li>New file extension for Jalview projects '.jvp'</li>
2987 <li>Preserve sequence and annotation dataset (to
2988 store secondary structure annotation,etc)</li>
2989 <li>Per group and alignment annotation and RNA helix
2993 <li>New similarity measures for PCA and Tree calculation
2995 <li>Experimental support for retrieval and viewing of
2996 flanking regions for an alignment</li>
3000 <!-- issues resolved --> <em>Application</em>
3002 <li>logo keeps spinning and status remains at queued or
3003 running after job is cancelled</li>
3004 <li>cannot export features from alignments imported from
3005 Jalview/VAMSAS projects</li>
3006 <li>Buggy slider for web service parameters that take
3008 <li>Newly created RNA secondary structure line doesn't
3009 have 'display all symbols' flag set</li>
3010 <li>T-COFFEE alignment score shading scheme and other
3011 annotation shading not saved in Jalview project</li>
3012 <li>Local file cannot be loaded in freshly downloaded
3014 <li>Jalview icon not shown on dock in Mountain
3016 <li>Load file from desktop file browser fails</li>
3017 <li>Occasional NPE thrown when calculating large trees</li>
3018 <li>Cannot reorder or slide sequences after dragging an
3019 alignment onto desktop</li>
3020 <li>Colour by annotation dialog throws NPE after using
3021 'extract scores' function</li>
3022 <li>Loading/cut'n'pasting an empty file leads to a grey
3023 alignment window</li>
3024 <li>Disorder thresholds rendered incorrectly after
3025 performing IUPred disorder prediction</li>
3026 <li>Multiple group annotated consensus rows shown when
3027 changing 'normalise logo' display setting</li>
3028 <li>Find shows blank dialog after 'finished searching' if
3029 nothing matches query</li>
3030 <li>Null Pointer Exceptions raised when sorting by
3031 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3033 <li>Errors in Jmol console when structures in alignment
3034 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3036 <li>Not all working JABAWS services are shown in
3038 <li>JAVAWS version of Jalview fails to launch with
3039 'invalid literal/length code'</li>
3040 <li>Annotation/RNA Helix colourschemes cannot be applied
3041 to alignment with groups (actually fixed in 2.8.0b1)</li>
3042 <li>RNA Helices and T-Coffee Scores available as default
3045 </ul> <em>Applet</em>
3047 <li>Remove group option is shown even when selection is
3049 <li>Apply to all groups ticked but colourscheme changes
3050 don't affect groups</li>
3051 <li>Documented RNA Helices and T-Coffee Scores as valid
3052 colourscheme name</li>
3053 <li>Annotation labels drawn on sequence IDs when
3054 Annotation panel is not displayed</li>
3055 <li>Increased font size for dropdown menus on OSX and
3056 embedded windows</li>
3057 </ul> <em>Other</em>
3059 <li>Consensus sequence for alignments/groups with a
3060 single sequence were not calculated</li>
3061 <li>annotation files that contain only groups imported as
3062 annotation and junk sequences</li>
3063 <li>Fasta files with sequences containing '*' incorrectly
3064 recognised as PFAM or BLC</li>
3065 <li>conservation/PID slider apply all groups option
3066 doesn't affect background (2.8.0b1)
3068 <li>redundancy highlighting is erratic at 0% and 100%</li>
3069 <li>Remove gapped columns fails for sequences with ragged
3071 <li>AMSA annotation row with leading spaces is not
3072 registered correctly on import</li>
3073 <li>Jalview crashes when selecting PCA analysis for
3074 certain alignments</li>
3075 <li>Opening the colour by annotation dialog for an
3076 existing annotation based 'use original colours'
3077 colourscheme loses original colours setting</li>
3082 <td><div align="center">
3083 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3084 <em>30/1/2014</em></strong>
3088 <li>Trusted certificates for JalviewLite applet and
3089 Jalview Desktop application<br />Certificate was donated by
3090 <a href="https://www.certum.eu">Certum</a> to the Jalview
3091 open source project).
3093 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3094 <li>Output in Stockholm format</li>
3095 <li>Allow import of data from gzipped files</li>
3096 <li>Export/import group and sequence associated line
3097 graph thresholds</li>
3098 <li>Nucleotide substitution matrix that supports RNA and
3099 ambiguity codes</li>
3100 <li>Allow disorder predictions to be made on the current
3101 selection (or visible selection) in the same way that JPred
3103 <li>Groovy scripting for headless Jalview operation</li>
3104 </ul> <em>Other improvements</em>
3106 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3107 <li>COMBINE statement uses current SEQUENCE_REF and
3108 GROUP_REF scope to group annotation rows</li>
3109 <li>Support '' style escaping of quotes in Newick
3111 <li>Group options for JABAWS service by command line name</li>
3112 <li>Empty tooltip shown for JABA service options with a
3113 link but no description</li>
3114 <li>Select primary source when selecting authority in
3115 database fetcher GUI</li>
3116 <li>Add .mfa to FASTA file extensions recognised by
3118 <li>Annotation label tooltip text wrap</li>
3123 <li>Slow scrolling when lots of annotation rows are
3125 <li>Lots of NPE (and slowness) after creating RNA
3126 secondary structure annotation line</li>
3127 <li>Sequence database accessions not imported when
3128 fetching alignments from Rfam</li>
3129 <li>Incorrect SHMR submission for sequences with
3131 <li>View all structures does not always superpose
3133 <li>Option widgets in service parameters not updated to
3134 reflect user or preset settings</li>
3135 <li>Null pointer exceptions for some services without
3136 presets or adjustable parameters</li>
3137 <li>Discover PDB IDs entry in structure menu doesn't
3138 discover PDB xRefs</li>
3139 <li>Exception encountered while trying to retrieve
3140 features with DAS</li>
3141 <li>Lowest value in annotation row isn't coloured
3142 when colour by annotation (per sequence) is coloured</li>
3143 <li>Keyboard mode P jumps to start of gapped region when
3144 residue follows a gap</li>
3145 <li>Jalview appears to hang importing an alignment with
3146 Wrap as default or after enabling Wrap</li>
3147 <li>'Right click to add annotations' message
3148 shown in wrap mode when no annotations present</li>
3149 <li>Disorder predictions fail with NPE if no automatic
3150 annotation already exists on alignment</li>
3151 <li>oninit javascript function should be called after
3152 initialisation completes</li>
3153 <li>Remove redundancy after disorder prediction corrupts
3154 alignment window display</li>
3155 <li>Example annotation file in documentation is invalid</li>
3156 <li>Grouped line graph annotation rows are not exported
3157 to annotation file</li>
3158 <li>Multi-harmony analysis cannot be run when only two
3160 <li>Cannot create multiple groups of line graphs with
3161 several 'combine' statements in annotation file</li>
3162 <li>Pressing return several times causes Number Format
3163 exceptions in keyboard mode</li>
3164 <li>Multi-harmony (SHMMR) method doesn't submit
3165 correct partitions for input data</li>
3166 <li>Translation from DNA to Amino Acids fails</li>
3167 <li>Jalview fail to load newick tree with quoted label</li>
3168 <li>--headless flag isn't understood</li>
3169 <li>ClassCastException when generating EPS in headless
3171 <li>Adjusting sequence-associated shading threshold only
3172 changes one row's threshold</li>
3173 <li>Preferences and Feature settings panel panel
3174 doesn't open</li>
3175 <li>hide consensus histogram also hides conservation and
3176 quality histograms</li>
3181 <td><div align="center">
3182 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3184 <td><em>Application</em>
3186 <li>Support for JABAWS 2.0 Services (AACon alignment
3187 conservation, protein disorder and Clustal Omega)</li>
3188 <li>JABAWS server status indicator in Web Services
3190 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3191 in Jalview alignment window</li>
3192 <li>Updated Jalview build and deploy framework for OSX
3193 mountain lion, windows 7, and 8</li>
3194 <li>Nucleotide substitution matrix for PCA that supports
3195 RNA and ambiguity codes</li>
3197 <li>Improved sequence database retrieval GUI</li>
3198 <li>Support fetching and database reference look up
3199 against multiple DAS sources (Fetch all from in 'fetch db
3201 <li>Jalview project improvements
3203 <li>Store and retrieve the 'belowAlignment'
3204 flag for annotation</li>
3205 <li>calcId attribute to group annotation rows on the
3207 <li>Store AACon calculation settings for a view in
3208 Jalview project</li>
3212 <li>horizontal scrolling gesture support</li>
3213 <li>Visual progress indicator when PCA calculation is
3215 <li>Simpler JABA web services menus</li>
3216 <li>visual indication that web service results are still
3217 being retrieved from server</li>
3218 <li>Serialise the dialogs that are shown when Jalview
3219 starts up for first time</li>
3220 <li>Jalview user agent string for interacting with HTTP
3222 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3224 <li>Examples directory and Groovy library included in
3225 InstallAnywhere distribution</li>
3226 </ul> <em>Applet</em>
3228 <li>RNA alignment and secondary structure annotation
3229 visualization applet example</li>
3230 </ul> <em>General</em>
3232 <li>Normalise option for consensus sequence logo</li>
3233 <li>Reset button in PCA window to return dimensions to
3235 <li>Allow seqspace or Jalview variant of alignment PCA
3237 <li>PCA with either nucleic acid and protein substitution
3239 <li>Allow windows containing HTML reports to be exported
3241 <li>Interactive display and editing of RNA secondary
3242 structure contacts</li>
3243 <li>RNA Helix Alignment Colouring</li>
3244 <li>RNA base pair logo consensus</li>
3245 <li>Parse sequence associated secondary structure
3246 information in Stockholm files</li>
3247 <li>HTML Export database accessions and annotation
3248 information presented in tooltip for sequences</li>
3249 <li>Import secondary structure from LOCARNA clustalw
3250 style RNA alignment files</li>
3251 <li>import and visualise T-COFFEE quality scores for an
3253 <li>'colour by annotation' per sequence option to
3254 shade each sequence according to its associated alignment
3256 <li>New Jalview Logo</li>
3257 </ul> <em>Documentation and Development</em>
3259 <li>documentation for score matrices used in Jalview</li>
3260 <li>New Website!</li>
3262 <td><em>Application</em>
3264 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3265 wsdbfetch REST service</li>
3266 <li>Stop windows being moved outside desktop on OSX</li>
3267 <li>Filetype associations not installed for webstart
3269 <li>Jalview does not always retrieve progress of a JABAWS
3270 job execution in full once it is complete</li>
3271 <li>revise SHMR RSBS definition to ensure alignment is
3272 uploaded via ali_file parameter</li>
3273 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3274 <li>View all structures superposed fails with exception</li>
3275 <li>Jnet job queues forever if a very short sequence is
3276 submitted for prediction</li>
3277 <li>Cut and paste menu not opened when mouse clicked on
3279 <li>Putting fractional value into integer text box in
3280 alignment parameter dialog causes Jalview to hang</li>
3281 <li>Structure view highlighting doesn't work on
3283 <li>View all structures fails with exception shown in
3285 <li>Characters in filename associated with PDBEntry not
3286 escaped in a platform independent way</li>
3287 <li>Jalview desktop fails to launch with exception when
3289 <li>Tree calculation reports 'you must have 2 or more
3290 sequences selected' when selection is empty</li>
3291 <li>Jalview desktop fails to launch with jar signature
3292 failure when java web start temporary file caching is
3294 <li>DAS Sequence retrieval with range qualification
3295 results in sequence xref which includes range qualification</li>
3296 <li>Errors during processing of command line arguments
3297 cause progress bar (JAL-898) to be removed</li>
3298 <li>Replace comma for semi-colon option not disabled for
3299 DAS sources in sequence fetcher</li>
3300 <li>Cannot close news reader when JABAWS server warning
3301 dialog is shown</li>
3302 <li>Option widgets not updated to reflect user settings</li>
3303 <li>Edited sequence not submitted to web service</li>
3304 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3305 <li>InstallAnywhere installer doesn't unpack and run
3306 on OSX Mountain Lion</li>
3307 <li>Annotation panel not given a scroll bar when
3308 sequences with alignment annotation are pasted into the
3310 <li>Sequence associated annotation rows not associated
3311 when loaded from Jalview project</li>
3312 <li>Browser launch fails with NPE on java 1.7</li>
3313 <li>JABAWS alignment marked as finished when job was
3314 cancelled or job failed due to invalid input</li>
3315 <li>NPE with v2.7 example when clicking on Tree
3316 associated with all views</li>
3317 <li>Exceptions when copy/paste sequences with grouped
3318 annotation rows to new window</li>
3319 </ul> <em>Applet</em>
3321 <li>Sequence features are momentarily displayed before
3322 they are hidden using hidefeaturegroups applet parameter</li>
3323 <li>loading features via javascript API automatically
3324 enables feature display</li>
3325 <li>scrollToColumnIn javascript API method doesn't
3327 </ul> <em>General</em>
3329 <li>Redundancy removal fails for rna alignment</li>
3330 <li>PCA calculation fails when sequence has been selected
3331 and then deselected</li>
3332 <li>PCA window shows grey box when first opened on OSX</li>
3333 <li>Letters coloured pink in sequence logo when alignment
3334 coloured with clustalx</li>
3335 <li>Choosing fonts without letter symbols defined causes
3336 exceptions and redraw errors</li>
3337 <li>Initial PCA plot view is not same as manually
3338 reconfigured view</li>
3339 <li>Grouped annotation graph label has incorrect line
3341 <li>Grouped annotation graph label display is corrupted
3342 for lots of labels</li>
3347 <div align="center">
3348 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3351 <td><em>Application</em>
3353 <li>Jalview Desktop News Reader</li>
3354 <li>Tweaked default layout of web services menu</li>
3355 <li>View/alignment association menu to enable user to
3356 easily specify which alignment a multi-structure view takes
3357 its colours/correspondences from</li>
3358 <li>Allow properties file location to be specified as URL</li>
3359 <li>Extend Jalview project to preserve associations
3360 between many alignment views and a single Jmol display</li>
3361 <li>Store annotation row height in Jalview project file</li>
3362 <li>Annotation row column label formatting attributes
3363 stored in project file</li>
3364 <li>Annotation row order for auto-calculated annotation
3365 rows preserved in Jalview project file</li>
3366 <li>Visual progress indication when Jalview state is
3367 saved using Desktop window menu</li>
3368 <li>Visual indication that command line arguments are
3369 still being processed</li>
3370 <li>Groovy script execution from URL</li>
3371 <li>Colour by annotation default min and max colours in
3373 <li>Automatically associate PDB files dragged onto an
3374 alignment with sequences that have high similarity and
3376 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3377 <li>'view structures' option to open many
3378 structures in same window</li>
3379 <li>Sort associated views menu option for tree panel</li>
3380 <li>Group all JABA and non-JABA services for a particular
3381 analysis function in its own submenu</li>
3382 </ul> <em>Applet</em>
3384 <li>Userdefined and autogenerated annotation rows for
3386 <li>Adjustment of alignment annotation pane height</li>
3387 <li>Annotation scrollbar for annotation panel</li>
3388 <li>Drag to reorder annotation rows in annotation panel</li>
3389 <li>'automaticScrolling' parameter</li>
3390 <li>Allow sequences with partial ID string matches to be
3391 annotated from GFF/Jalview features files</li>
3392 <li>Sequence logo annotation row in applet</li>
3393 <li>Absolute paths relative to host server in applet
3394 parameters are treated as such</li>
3395 <li>New in the JalviewLite javascript API:
3397 <li>JalviewLite.js javascript library</li>
3398 <li>Javascript callbacks for
3400 <li>Applet initialisation</li>
3401 <li>Sequence/alignment mouse-overs and selections</li>
3404 <li>scrollTo row and column alignment scrolling
3406 <li>Select sequence/alignment regions from javascript</li>
3407 <li>javascript structure viewer harness to pass
3408 messages between Jmol and Jalview when running as
3409 distinct applets</li>
3410 <li>sortBy method</li>
3411 <li>Set of applet and application examples shipped
3412 with documentation</li>
3413 <li>New example to demonstrate JalviewLite and Jmol
3414 javascript message exchange</li>
3416 </ul> <em>General</em>
3418 <li>Enable Jmol displays to be associated with multiple
3419 multiple alignments</li>
3420 <li>Option to automatically sort alignment with new tree</li>
3421 <li>User configurable link to enable redirects to a
3422 www.Jalview.org mirror</li>
3423 <li>Jmol colours option for Jmol displays</li>
3424 <li>Configurable newline string when writing alignment
3425 and other flat files</li>
3426 <li>Allow alignment annotation description lines to
3427 contain html tags</li>
3428 </ul> <em>Documentation and Development</em>
3430 <li>Add groovy test harness for bulk load testing to
3432 <li>Groovy script to load and align a set of sequences
3433 using a web service before displaying the result in the
3434 Jalview desktop</li>
3435 <li>Restructured javascript and applet api documentation</li>
3436 <li>Ant target to publish example html files with applet
3438 <li>Netbeans project for building Jalview from source</li>
3439 <li>ant task to create online javadoc for Jalview source</li>
3441 <td><em>Application</em>
3443 <li>User defined colourscheme throws exception when
3444 current built in colourscheme is saved as new scheme</li>
3445 <li>AlignFrame->Save in application pops up save
3446 dialog for valid filename/format</li>
3447 <li>Cannot view associated structure for UniProt sequence</li>
3448 <li>PDB file association breaks for UniProt sequence
3450 <li>Associate PDB from file dialog does not tell you
3451 which sequence is to be associated with the file</li>
3452 <li>Find All raises null pointer exception when query
3453 only matches sequence IDs</li>
3454 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3455 <li>Jalview project with Jmol views created with Jalview
3456 2.4 cannot be loaded</li>
3457 <li>Filetype associations not installed for webstart
3459 <li>Two or more chains in a single PDB file associated
3460 with sequences in different alignments do not get coloured
3461 by their associated sequence</li>
3462 <li>Visibility status of autocalculated annotation row
3463 not preserved when project is loaded</li>
3464 <li>Annotation row height and visibility attributes not
3465 stored in Jalview project</li>
3466 <li>Tree bootstraps are not preserved when saved as a
3467 Jalview project</li>
3468 <li>Envision2 workflow tooltips are corrupted</li>
3469 <li>Enabling show group conservation also enables colour
3470 by conservation</li>
3471 <li>Duplicate group associated conservation or consensus
3472 created on new view</li>
3473 <li>Annotation scrollbar not displayed after 'show
3474 all hidden annotation rows' option selected</li>
3475 <li>Alignment quality not updated after alignment
3476 annotation row is hidden then shown</li>
3477 <li>Preserve colouring of structures coloured by
3478 sequences in pre Jalview 2.7 projects</li>
3479 <li>Web service job parameter dialog is not laid out
3481 <li>Web services menu not refreshed after 'reset
3482 services' button is pressed in preferences</li>
3483 <li>Annotation off by one in Jalview v2_3 example project</li>
3484 <li>Structures imported from file and saved in project
3485 get name like jalview_pdb1234.txt when reloaded</li>
3486 <li>Jalview does not always retrieve progress of a JABAWS
3487 job execution in full once it is complete</li>
3488 </ul> <em>Applet</em>
3490 <li>Alignment height set incorrectly when lots of
3491 annotation rows are displayed</li>
3492 <li>Relative URLs in feature HTML text not resolved to
3494 <li>View follows highlighting does not work for positions
3496 <li><= shown as = in tooltip</li>
3497 <li>Export features raises exception when no features
3499 <li>Separator string used for serialising lists of IDs
3500 for javascript api is modified when separator string
3501 provided as parameter</li>
3502 <li>Null pointer exception when selecting tree leaves for
3503 alignment with no existing selection</li>
3504 <li>Relative URLs for datasources assumed to be relative
3505 to applet's codebase</li>
3506 <li>Status bar not updated after finished searching and
3507 search wraps around to first result</li>
3508 <li>StructureSelectionManager instance shared between
3509 several Jalview applets causes race conditions and memory
3511 <li>Hover tooltip and mouseover of position on structure
3512 not sent from Jmol in applet</li>
3513 <li>Certain sequences of javascript method calls to
3514 applet API fatally hang browser</li>
3515 </ul> <em>General</em>
3517 <li>View follows structure mouseover scrolls beyond
3518 position with wrapped view and hidden regions</li>
3519 <li>Find sequence position moves to wrong residue
3520 with/without hidden columns</li>
3521 <li>Sequence length given in alignment properties window
3523 <li>InvalidNumberFormat exceptions thrown when trying to
3524 import PDB like structure files</li>
3525 <li>Positional search results are only highlighted
3526 between user-supplied sequence start/end bounds</li>
3527 <li>End attribute of sequence is not validated</li>
3528 <li>Find dialog only finds first sequence containing a
3529 given sequence position</li>
3530 <li>Sequence numbering not preserved in MSF alignment
3532 <li>Jalview PDB file reader does not extract sequence
3533 from nucleotide chains correctly</li>
3534 <li>Structure colours not updated when tree partition
3535 changed in alignment</li>
3536 <li>Sequence associated secondary structure not correctly
3537 parsed in interleaved stockholm</li>
3538 <li>Colour by annotation dialog does not restore current
3540 <li>Hiding (nearly) all sequences doesn't work
3542 <li>Sequences containing lowercase letters are not
3543 properly associated with their pdb files</li>
3544 </ul> <em>Documentation and Development</em>
3546 <li>schemas/JalviewWsParamSet.xsd corrupted by
3547 ApplyCopyright tool</li>
3552 <div align="center">
3553 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3556 <td><em>Application</em>
3558 <li>New warning dialog when the Jalview Desktop cannot
3559 contact web services</li>
3560 <li>JABA service parameters for a preset are shown in
3561 service job window</li>
3562 <li>JABA Service menu entries reworded</li>
3566 <li>Modeller PIR IO broken - cannot correctly import a
3567 pir file emitted by Jalview</li>
3568 <li>Existing feature settings transferred to new
3569 alignment view created from cut'n'paste</li>
3570 <li>Improved test for mixed amino/nucleotide chains when
3571 parsing PDB files</li>
3572 <li>Consensus and conservation annotation rows
3573 occasionally become blank for all new windows</li>
3574 <li>Exception raised when right clicking above sequences
3575 in wrapped view mode</li>
3576 </ul> <em>Application</em>
3578 <li>multiple multiply aligned structure views cause cpu
3579 usage to hit 100% and computer to hang</li>
3580 <li>Web Service parameter layout breaks for long user
3581 parameter names</li>
3582 <li>Jaba service discovery hangs desktop if Jaba server
3589 <div align="center">
3590 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3593 <td><em>Application</em>
3595 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3596 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3599 <li>Web Services preference tab</li>
3600 <li>Analysis parameters dialog box and user defined
3602 <li>Improved speed and layout of Envision2 service menu</li>
3603 <li>Superpose structures using associated sequence
3605 <li>Export coordinates and projection as CSV from PCA
3607 </ul> <em>Applet</em>
3609 <li>enable javascript: execution by the applet via the
3610 link out mechanism</li>
3611 </ul> <em>Other</em>
3613 <li>Updated the Jmol Jalview interface to work with Jmol
3615 <li>The Jalview Desktop and JalviewLite applet now
3616 require Java 1.5</li>
3617 <li>Allow Jalview feature colour specification for GFF
3618 sequence annotation files</li>
3619 <li>New 'colour by label' keword in Jalview feature file
3620 type colour specification</li>
3621 <li>New Jalview Desktop Groovy API method that allows a
3622 script to check if it being run in an interactive session or
3623 in a batch operation from the Jalview command line</li>
3627 <li>clustalx colourscheme colours Ds preferentially when
3628 both D+E are present in over 50% of the column</li>
3629 </ul> <em>Application</em>
3631 <li>typo in AlignmentFrame->View->Hide->all but
3632 selected Regions menu item</li>
3633 <li>sequence fetcher replaces ',' for ';' when the ',' is
3634 part of a valid accession ID</li>
3635 <li>fatal OOM if object retrieved by sequence fetcher
3636 runs out of memory</li>
3637 <li>unhandled Out of Memory Error when viewing pca
3638 analysis results</li>
3639 <li>InstallAnywhere builds fail to launch on OS X java
3640 10.5 update 4 (due to apple Java 1.6 update)</li>
3641 <li>Installanywhere Jalview silently fails to launch</li>
3642 </ul> <em>Applet</em>
3644 <li>Jalview.getFeatureGroups() raises an
3645 ArrayIndexOutOfBoundsException if no feature groups are
3652 <div align="center">
3653 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3659 <li>Alignment prettyprinter doesn't cope with long
3661 <li>clustalx colourscheme colours Ds preferentially when
3662 both D+E are present in over 50% of the column</li>
3663 <li>nucleic acid structures retrieved from PDB do not
3664 import correctly</li>
3665 <li>More columns get selected than were clicked on when a
3666 number of columns are hidden</li>
3667 <li>annotation label popup menu not providing correct
3668 add/hide/show options when rows are hidden or none are
3670 <li>Stockholm format shown in list of readable formats,
3671 and parser copes better with alignments from RFAM.</li>
3672 <li>CSV output of consensus only includes the percentage
3673 of all symbols if sequence logo display is enabled</li>
3675 </ul> <em>Applet</em>
3677 <li>annotation panel disappears when annotation is
3679 </ul> <em>Application</em>
3681 <li>Alignment view not redrawn properly when new
3682 alignment opened where annotation panel is visible but no
3683 annotations are present on alignment</li>
3684 <li>pasted region containing hidden columns is
3685 incorrectly displayed in new alignment window</li>
3686 <li>Jalview slow to complete operations when stdout is
3687 flooded (fix is to close the Jalview console)</li>
3688 <li>typo in AlignmentFrame->View->Hide->all but
3689 selected Rregions menu item.</li>
3690 <li>inconsistent group submenu and Format submenu entry
3691 'Un' or 'Non'conserved</li>
3692 <li>Sequence feature settings are being shared by
3693 multiple distinct alignments</li>
3694 <li>group annotation not recreated when tree partition is
3696 <li>double click on group annotation to select sequences
3697 does not propagate to associated trees</li>
3698 <li>Mac OSX specific issues:
3700 <li>exception raised when mouse clicked on desktop
3701 window background</li>
3702 <li>Desktop menu placed on menu bar and application
3703 name set correctly</li>
3704 <li>sequence feature settings not wide enough for the
3705 save feature colourscheme button</li>
3714 <div align="center">
3715 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3718 <td><em>New Capabilities</em>
3720 <li>URL links generated from description line for
3721 regular-expression based URL links (applet and application)
3723 <li>Non-positional feature URL links are shown in link
3725 <li>Linked viewing of nucleic acid sequences and
3727 <li>Automatic Scrolling option in View menu to display
3728 the currently highlighted region of an alignment.</li>
3729 <li>Order an alignment by sequence length, or using the
3730 average score or total feature count for each sequence.</li>
3731 <li>Shading features by score or associated description</li>
3732 <li>Subdivide alignment and groups based on identity of
3733 selected subsequence (Make Groups from Selection).</li>
3734 <li>New hide/show options including Shift+Control+H to
3735 hide everything but the currently selected region.</li>
3736 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3737 </ul> <em>Application</em>
3739 <li>Fetch DB References capabilities and UI expanded to
3740 support retrieval from DAS sequence sources</li>
3741 <li>Local DAS Sequence sources can be added via the
3742 command line or via the Add local source dialog box.</li>
3743 <li>DAS Dbref and DbxRef feature types are parsed as
3744 database references and protein_name is parsed as
3745 description line (BioSapiens terms).</li>
3746 <li>Enable or disable non-positional feature and database
3747 references in sequence ID tooltip from View menu in
3749 <!-- <li>New hidden columns and rows and representatives capabilities
3750 in annotations file (in progress - not yet fully implemented)</li> -->
3751 <li>Group-associated consensus, sequence logos and
3752 conservation plots</li>
3753 <li>Symbol distributions for each column can be exported
3754 and visualized as sequence logos</li>
3755 <li>Optionally scale multi-character column labels to fit
3756 within each column of annotation row<!-- todo for applet -->
3758 <li>Optional automatic sort of associated alignment view
3759 when a new tree is opened.</li>
3760 <li>Jalview Java Console</li>
3761 <li>Better placement of desktop window when moving
3762 between different screens.</li>
3763 <li>New preference items for sequence ID tooltip and
3764 consensus annotation</li>
3765 <li>Client to submit sequences and IDs to Envision2
3767 <li><em>Vamsas Capabilities</em>
3769 <li>Improved VAMSAS synchronization (Jalview archive
3770 used to preserve views, structures, and tree display
3772 <li>Import of vamsas documents from disk or URL via
3774 <li>Sharing of selected regions between views and
3775 with other VAMSAS applications (Experimental feature!)</li>
3776 <li>Updated API to VAMSAS version 0.2</li>
3778 </ul> <em>Applet</em>
3780 <li>Middle button resizes annotation row height</li>
3783 <li>sortByTree (true/false) - automatically sort the
3784 associated alignment view by the tree when a new tree is
3786 <li>showTreeBootstraps (true/false) - show or hide
3787 branch bootstraps (default is to show them if available)</li>
3788 <li>showTreeDistances (true/false) - show or hide
3789 branch lengths (default is to show them if available)</li>
3790 <li>showUnlinkedTreeNodes (true/false) - indicate if
3791 unassociated nodes should be highlighted in the tree
3793 <li>heightScale and widthScale (1.0 or more) -
3794 increase the height or width of a cell in the alignment
3795 grid relative to the current font size.</li>
3798 <li>Non-positional features displayed in sequence ID
3800 </ul> <em>Other</em>
3802 <li>Features format: graduated colour definitions and
3803 specification of feature scores</li>
3804 <li>Alignment Annotations format: new keywords for group
3805 associated annotation (GROUP_REF) and annotation row display
3806 properties (ROW_PROPERTIES)</li>
3807 <li>XML formats extended to support graduated feature
3808 colourschemes, group associated annotation, and profile
3809 visualization settings.</li></td>
3812 <li>Source field in GFF files parsed as feature source
3813 rather than description</li>
3814 <li>Non-positional features are now included in sequence
3815 feature and gff files (controlled via non-positional feature
3816 visibility in tooltip).</li>
3817 <li>URL links generated for all feature links (bugfix)</li>
3818 <li>Added URL embedding instructions to features file
3820 <li>Codons containing ambiguous nucleotides translated as
3821 'X' in peptide product</li>
3822 <li>Match case switch in find dialog box works for both
3823 sequence ID and sequence string and query strings do not
3824 have to be in upper case to match case-insensitively.</li>
3825 <li>AMSA files only contain first column of
3826 multi-character column annotation labels</li>
3827 <li>Jalview Annotation File generation/parsing consistent
3828 with documentation (e.g. Stockholm annotation can be
3829 exported and re-imported)</li>
3830 <li>PDB files without embedded PDB IDs given a friendly
3832 <li>Find incrementally searches ID string matches as well
3833 as subsequence matches, and correctly reports total number
3837 <li>Better handling of exceptions during sequence
3839 <li>Dasobert generated non-positional feature URL
3840 link text excludes the start_end suffix</li>
3841 <li>DAS feature and source retrieval buttons disabled
3842 when fetch or registry operations in progress.</li>
3843 <li>PDB files retrieved from URLs are cached properly</li>
3844 <li>Sequence description lines properly shared via
3846 <li>Sequence fetcher fetches multiple records for all
3848 <li>Ensured that command line das feature retrieval
3849 completes before alignment figures are generated.</li>
3850 <li>Reduced time taken when opening file browser for
3852 <li>isAligned check prior to calculating tree, PCA or
3853 submitting an MSA to JNet now excludes hidden sequences.</li>
3854 <li>User defined group colours properly recovered
3855 from Jalview projects.</li>
3864 <div align="center">
3865 <strong>2.4.0.b2</strong><br> 28/10/2009
3870 <li>Experimental support for google analytics usage
3872 <li>Jalview privacy settings (user preferences and docs).</li>
3877 <li>Race condition in applet preventing startup in
3879 <li>Exception when feature created from selection beyond
3880 length of sequence.</li>
3881 <li>Allow synthetic PDB files to be imported gracefully</li>
3882 <li>Sequence associated annotation rows associate with
3883 all sequences with a given id</li>
3884 <li>Find function matches case-insensitively for sequence
3885 ID string searches</li>
3886 <li>Non-standard characters do not cause pairwise
3887 alignment to fail with exception</li>
3888 </ul> <em>Application Issues</em>
3890 <li>Sequences are now validated against EMBL database</li>
3891 <li>Sequence fetcher fetches multiple records for all
3893 </ul> <em>InstallAnywhere Issues</em>
3895 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3896 issue with installAnywhere mechanism)</li>
3897 <li>Command line launching of JARs from InstallAnywhere
3898 version (java class versioning error fixed)</li>
3905 <div align="center">
3906 <strong>2.4</strong><br> 27/8/2008
3909 <td><em>User Interface</em>
3911 <li>Linked highlighting of codon and amino acid from
3912 translation and protein products</li>
3913 <li>Linked highlighting of structure associated with
3914 residue mapping to codon position</li>
3915 <li>Sequence Fetcher provides example accession numbers
3916 and 'clear' button</li>
3917 <li>MemoryMonitor added as an option under Desktop's
3919 <li>Extract score function to parse whitespace separated
3920 numeric data in description line</li>
3921 <li>Column labels in alignment annotation can be centred.</li>
3922 <li>Tooltip for sequence associated annotation give name
3924 </ul> <em>Web Services and URL fetching</em>
3926 <li>JPred3 web service</li>
3927 <li>Prototype sequence search client (no public services
3929 <li>Fetch either seed alignment or full alignment from
3931 <li>URL Links created for matching database cross
3932 references as well as sequence ID</li>
3933 <li>URL Links can be created using regular-expressions</li>
3934 </ul> <em>Sequence Database Connectivity</em>
3936 <li>Retrieval of cross-referenced sequences from other
3938 <li>Generalised database reference retrieval and
3939 validation to all fetchable databases</li>
3940 <li>Fetch sequences from DAS sources supporting the
3941 sequence command</li>
3942 </ul> <em>Import and Export</em>
3943 <li>export annotation rows as CSV for spreadsheet import</li>
3944 <li>Jalview projects record alignment dataset associations,
3945 EMBL products, and cDNA sequence mappings</li>
3946 <li>Sequence Group colour can be specified in Annotation
3948 <li>Ad-hoc colouring of group in Annotation File using RGB
3949 triplet as name of colourscheme</li>
3950 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3952 <li>treenode binding for VAMSAS tree exchange</li>
3953 <li>local editing and update of sequences in VAMSAS
3954 alignments (experimental)</li>
3955 <li>Create new or select existing session to join</li>
3956 <li>load and save of vamsas documents</li>
3957 </ul> <em>Application command line</em>
3959 <li>-tree parameter to open trees (introduced for passing
3961 <li>-fetchfrom command line argument to specify nicknames
3962 of DAS servers to query for alignment features</li>
3963 <li>-dasserver command line argument to add new servers
3964 that are also automatically queried for features</li>
3965 <li>-groovy command line argument executes a given groovy
3966 script after all input data has been loaded and parsed</li>
3967 </ul> <em>Applet-Application data exchange</em>
3969 <li>Trees passed as applet parameters can be passed to
3970 application (when using "View in full
3971 application")</li>
3972 </ul> <em>Applet Parameters</em>
3974 <li>feature group display control parameter</li>
3975 <li>debug parameter</li>
3976 <li>showbutton parameter</li>
3977 </ul> <em>Applet API methods</em>
3979 <li>newView public method</li>
3980 <li>Window (current view) specific get/set public methods</li>
3981 <li>Feature display control methods</li>
3982 <li>get list of currently selected sequences</li>
3983 </ul> <em>New Jalview distribution features</em>
3985 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3986 <li>RELEASE file gives build properties for the latest
3987 Jalview release.</li>
3988 <li>Java 1.1 Applet build made easier and donotobfuscate
3989 property controls execution of obfuscator</li>
3990 <li>Build target for generating source distribution</li>
3991 <li>Debug flag for javacc</li>
3992 <li>.jalview_properties file is documented (slightly) in
3993 jalview.bin.Cache</li>
3994 <li>Continuous Build Integration for stable and
3995 development version of Application, Applet and source
4000 <li>selected region output includes visible annotations
4001 (for certain formats)</li>
4002 <li>edit label/displaychar contains existing label/char
4004 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4005 <li>shorter peptide product names from EMBL records</li>
4006 <li>Newick string generator makes compact representations</li>
4007 <li>bootstrap values parsed correctly for tree files with
4009 <li>pathological filechooser bug avoided by not allowing
4010 filenames containing a ':'</li>
4011 <li>Fixed exception when parsing GFF files containing
4012 global sequence features</li>
4013 <li>Alignment datasets are finalized only when number of
4014 references from alignment sequences goes to zero</li>
4015 <li>Close of tree branch colour box without colour
4016 selection causes cascading exceptions</li>
4017 <li>occasional negative imgwidth exceptions</li>
4018 <li>better reporting of non-fatal warnings to user when
4019 file parsing fails.</li>
4020 <li>Save works when Jalview project is default format</li>
4021 <li>Save as dialog opened if current alignment format is
4022 not a valid output format</li>
4023 <li>UniProt canonical names introduced for both das and
4025 <li>Histidine should be midblue (not pink!) in Zappo</li>
4026 <li>error messages passed up and output when data read
4028 <li>edit undo recovers previous dataset sequence when
4029 sequence is edited</li>
4030 <li>allow PDB files without pdb ID HEADER lines (like
4031 those generated by MODELLER) to be read in properly</li>
4032 <li>allow reading of JPred concise files as a normal
4034 <li>Stockholm annotation parsing and alignment properties
4035 import fixed for PFAM records</li>
4036 <li>Structure view windows have correct name in Desktop
4038 <li>annotation consisting of sequence associated scores
4039 can be read and written correctly to annotation file</li>
4040 <li>Aligned cDNA translation to aligned peptide works
4042 <li>Fixed display of hidden sequence markers and
4043 non-italic font for representatives in Applet</li>
4044 <li>Applet Menus are always embedded in applet window on
4046 <li>Newly shown features appear at top of stack (in
4048 <li>Annotations added via parameter not drawn properly
4049 due to null pointer exceptions</li>
4050 <li>Secondary structure lines are drawn starting from
4051 first column of alignment</li>
4052 <li>UniProt XML import updated for new schema release in
4054 <li>Sequence feature to sequence ID match for Features
4055 file is case-insensitive</li>
4056 <li>Sequence features read from Features file appended to
4057 all sequences with matching IDs</li>
4058 <li>PDB structure coloured correctly for associated views
4059 containing a sub-sequence</li>
4060 <li>PDB files can be retrieved by applet from Jar files</li>
4061 <li>feature and annotation file applet parameters
4062 referring to different directories are retrieved correctly</li>
4063 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4064 <li>Fixed application hang whilst waiting for
4065 splash-screen version check to complete</li>
4066 <li>Applet properly URLencodes input parameter values
4067 when passing them to the launchApp service</li>
4068 <li>display name and local features preserved in results
4069 retrieved from web service</li>
4070 <li>Visual delay indication for sequence retrieval and
4071 sequence fetcher initialisation</li>
4072 <li>updated Application to use DAS 1.53e version of
4073 dasobert DAS client</li>
4074 <li>Re-instated Full AMSA support and .amsa file
4076 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4084 <div align="center">
4085 <strong>2.3</strong><br> 9/5/07
4090 <li>Jmol 11.0.2 integration</li>
4091 <li>PDB views stored in Jalview XML files</li>
4092 <li>Slide sequences</li>
4093 <li>Edit sequence in place</li>
4094 <li>EMBL CDS features</li>
4095 <li>DAS Feature mapping</li>
4096 <li>Feature ordering</li>
4097 <li>Alignment Properties</li>
4098 <li>Annotation Scores</li>
4099 <li>Sort by scores</li>
4100 <li>Feature/annotation editing in applet</li>
4105 <li>Headless state operation in 2.2.1</li>
4106 <li>Incorrect and unstable DNA pairwise alignment</li>
4107 <li>Cut and paste of sequences with annotation</li>
4108 <li>Feature group display state in XML</li>
4109 <li>Feature ordering in XML</li>
4110 <li>blc file iteration selection using filename # suffix</li>
4111 <li>Stockholm alignment properties</li>
4112 <li>Stockhom alignment secondary structure annotation</li>
4113 <li>2.2.1 applet had no feature transparency</li>
4114 <li>Number pad keys can be used in cursor mode</li>
4115 <li>Structure Viewer mirror image resolved</li>
4122 <div align="center">
4123 <strong>2.2.1</strong><br> 12/2/07
4128 <li>Non standard characters can be read and displayed
4129 <li>Annotations/Features can be imported/exported to the
4131 <li>Applet allows editing of sequence/annotation/group
4132 name & description
4133 <li>Preference setting to display sequence name in
4135 <li>Annotation file format extended to allow
4136 Sequence_groups to be defined
4137 <li>Default opening of alignment overview panel can be
4138 specified in preferences
4139 <li>PDB residue numbering annotation added to associated
4145 <li>Applet crash under certain Linux OS with Java 1.6
4147 <li>Annotation file export / import bugs fixed
4148 <li>PNG / EPS image output bugs fixed
4154 <div align="center">
4155 <strong>2.2</strong><br> 27/11/06
4160 <li>Multiple views on alignment
4161 <li>Sequence feature editing
4162 <li>"Reload" alignment
4163 <li>"Save" to current filename
4164 <li>Background dependent text colour
4165 <li>Right align sequence ids
4166 <li>User-defined lower case residue colours
4169 <li>Menu item accelerator keys
4170 <li>Control-V pastes to current alignment
4171 <li>Cancel button for DAS Feature Fetching
4172 <li>PCA and PDB Viewers zoom via mouse roller
4173 <li>User-defined sub-tree colours and sub-tree selection
4175 <li>'New Window' button on the 'Output to Text box'
4180 <li>New memory efficient Undo/Redo System
4181 <li>Optimised symbol lookups and conservation/consensus
4183 <li>Region Conservation/Consensus recalculated after
4185 <li>Fixed Remove Empty Columns Bug (empty columns at end
4187 <li>Slowed DAS Feature Fetching for increased robustness.
4189 <li>Made angle brackets in ASCII feature descriptions
4191 <li>Re-instated Zoom function for PCA
4192 <li>Sequence descriptions conserved in web service
4194 <li>UniProt ID discoverer uses any word separated by
4196 <li>WsDbFetch query/result association resolved
4197 <li>Tree leaf to sequence mapping improved
4198 <li>Smooth fonts switch moved to FontChooser dialog box.
4205 <div align="center">
4206 <strong>2.1.1</strong><br> 12/9/06
4211 <li>Copy consensus sequence to clipboard</li>
4216 <li>Image output - rightmost residues are rendered if
4217 sequence id panel has been resized</li>
4218 <li>Image output - all offscreen group boundaries are
4220 <li>Annotation files with sequence references - all
4221 elements in file are relative to sequence position</li>
4222 <li>Mac Applet users can use Alt key for group editing</li>
4228 <div align="center">
4229 <strong>2.1</strong><br> 22/8/06
4234 <li>MAFFT Multiple Alignment in default Web Service list</li>
4235 <li>DAS Feature fetching</li>
4236 <li>Hide sequences and columns</li>
4237 <li>Export Annotations and Features</li>
4238 <li>GFF file reading / writing</li>
4239 <li>Associate structures with sequences from local PDB
4241 <li>Add sequences to exisiting alignment</li>
4242 <li>Recently opened files / URL lists</li>
4243 <li>Applet can launch the full application</li>
4244 <li>Applet has transparency for features (Java 1.2
4246 <li>Applet has user defined colours parameter</li>
4247 <li>Applet can load sequences from parameter
4248 "sequence<em>x</em>"
4254 <li>Redundancy Panel reinstalled in the Applet</li>
4255 <li>Monospaced font - EPS / rescaling bug fixed</li>
4256 <li>Annotation files with sequence references bug fixed</li>
4262 <div align="center">
4263 <strong>2.08.1</strong><br> 2/5/06
4268 <li>Change case of selected region from Popup menu</li>
4269 <li>Choose to match case when searching</li>
4270 <li>Middle mouse button and mouse movement can compress /
4271 expand the visible width and height of the alignment</li>
4276 <li>Annotation Panel displays complete JNet results</li>
4282 <div align="center">
4283 <strong>2.08b</strong><br> 18/4/06
4289 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4290 <li>Righthand label on wrapped alignments shows correct
4297 <div align="center">
4298 <strong>2.08</strong><br> 10/4/06
4303 <li>Editing can be locked to the selection area</li>
4304 <li>Keyboard editing</li>
4305 <li>Create sequence features from searches</li>
4306 <li>Precalculated annotations can be loaded onto
4308 <li>Features file allows grouping of features</li>
4309 <li>Annotation Colouring scheme added</li>
4310 <li>Smooth fonts off by default - Faster rendering</li>
4311 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4316 <li>Drag & Drop fixed on Linux</li>
4317 <li>Jalview Archive file faster to load/save, sequence
4318 descriptions saved.</li>
4324 <div align="center">
4325 <strong>2.07</strong><br> 12/12/05
4330 <li>PDB Structure Viewer enhanced</li>
4331 <li>Sequence Feature retrieval and display enhanced</li>
4332 <li>Choose to output sequence start-end after sequence
4333 name for file output</li>
4334 <li>Sequence Fetcher WSDBFetch@EBI</li>
4335 <li>Applet can read feature files, PDB files and can be
4336 used for HTML form input</li>
4341 <li>HTML output writes groups and features</li>
4342 <li>Group editing is Control and mouse click</li>
4343 <li>File IO bugs</li>
4349 <div align="center">
4350 <strong>2.06</strong><br> 28/9/05
4355 <li>View annotations in wrapped mode</li>
4356 <li>More options for PCA viewer</li>
4361 <li>GUI bugs resolved</li>
4362 <li>Runs with -nodisplay from command line</li>
4368 <div align="center">
4369 <strong>2.05b</strong><br> 15/9/05
4374 <li>Choose EPS export as lineart or text</li>
4375 <li>Jar files are executable</li>
4376 <li>Can read in Uracil - maps to unknown residue</li>
4381 <li>Known OutOfMemory errors give warning message</li>
4382 <li>Overview window calculated more efficiently</li>
4383 <li>Several GUI bugs resolved</li>
4389 <div align="center">
4390 <strong>2.05</strong><br> 30/8/05
4395 <li>Edit and annotate in "Wrapped" view</li>
4400 <li>Several GUI bugs resolved</li>
4406 <div align="center">
4407 <strong>2.04</strong><br> 24/8/05
4412 <li>Hold down mouse wheel & scroll to change font
4418 <li>Improved JPred client reliability</li>
4419 <li>Improved loading of Jalview files</li>
4425 <div align="center">
4426 <strong>2.03</strong><br> 18/8/05
4431 <li>Set Proxy server name and port in preferences</li>
4432 <li>Multiple URL links from sequence ids</li>
4433 <li>User Defined Colours can have a scheme name and added
4435 <li>Choose to ignore gaps in consensus calculation</li>
4436 <li>Unix users can set default web browser</li>
4437 <li>Runs without GUI for batch processing</li>
4438 <li>Dynamically generated Web Service Menus</li>
4443 <li>InstallAnywhere download for Sparc Solaris</li>
4449 <div align="center">
4450 <strong>2.02</strong><br> 18/7/05
4456 <li>Copy & Paste order of sequences maintains
4457 alignment order.</li>
4463 <div align="center">
4464 <strong>2.01</strong><br> 12/7/05
4469 <li>Use delete key for deleting selection.</li>
4470 <li>Use Mouse wheel to scroll sequences.</li>
4471 <li>Help file updated to describe how to add alignment
4473 <li>Version and build date written to build properties
4475 <li>InstallAnywhere installation will check for updates
4476 at launch of Jalview.</li>
4481 <li>Delete gaps bug fixed.</li>
4482 <li>FileChooser sorts columns.</li>
4483 <li>Can remove groups one by one.</li>
4484 <li>Filechooser icons installed.</li>
4485 <li>Finder ignores return character when searching.
4486 Return key will initiate a search.<br>
4493 <div align="center">
4494 <strong>2.0</strong><br> 20/6/05
4499 <li>New codebase</li>