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 (not yet on general release)</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.
449 <li><strong>Java 11 Specific defects</strong>
452 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
460 <td width="60" nowrap>
462 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
465 <td><div align="left">
469 <!-- JAL-3101 -->Default memory for Jalview webstart and
470 InstallAnywhere increased to 1G.
473 <!-- JAL-247 -->Hidden sequence markers and representative
474 sequence bolding included when exporting alignment as EPS,
475 SVG, PNG or HTML. <em>Display is configured via the
476 Format menu, or for command-line use via a jalview
477 properties file.</em>
480 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
481 API and sequence data now imported as JSON.
484 <!-- JAL-3065 -->Change in recommended way of starting
485 Jalview via a Java command line: add jars in lib directory
486 to CLASSPATH, rather than via the deprecated java.ext.dirs
493 <!-- JAL-3047 -->Support added to execute test suite
494 instrumented with <a href="http://openclover.org/">Open
499 <td><div align="left">
503 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
504 row shown in Feredoxin Structure alignment view of example
508 <!-- JAL-2854 -->Annotation obscures sequences if lots of
509 annotation displayed.
512 <!-- JAL-3107 -->Group conservation/consensus not shown
513 for newly created group when 'Apply to all groups'
517 <!-- JAL-3087 -->Corrupted display when switching to
518 wrapped mode when sequence panel's vertical scrollbar is
522 <!-- JAL-3003 -->Alignment is black in exported EPS file
523 when sequences are selected in exported view.</em>
526 <!-- JAL-3059 -->Groups with different coloured borders
527 aren't rendered with correct colour.
530 <!-- JAL-3092 -->Jalview could hang when importing certain
531 types of knotted RNA secondary structure.
534 <!-- JAL-3095 -->Sequence highlight and selection in
535 trimmed VARNA 2D structure is incorrect for sequences that
539 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
540 annotation when columns are inserted into an alignment,
541 and when exporting as Stockholm flatfile.
544 <!-- JAL-3053 -->Jalview annotation rows containing upper
545 and lower-case 'E' and 'H' do not automatically get
546 treated as RNA secondary structure.
549 <!-- JAL-3106 -->.jvp should be used as default extension
550 (not .jar) when saving a jalview project file.
553 <!-- JAL-3105 -->Mac Users: closing a window correctly
554 transfers focus to previous window on OSX
557 <em>Java 10 Issues Resolved</em>
560 <!-- JAL-2988 -->OSX - Can't save new files via the File
561 or export menus by typing in a name into the Save dialog
565 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
566 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
567 'look and feel' which has improved compatibility with the
568 latest version of OSX.
575 <td width="60" nowrap>
577 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
578 <em>7/06/2018</em></strong>
581 <td><div align="left">
585 <!-- JAL-2920 -->Use HGVS nomenclature for variant
586 annotation retrieved from Uniprot
589 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
590 onto the Jalview Desktop
594 <td><div align="left">
598 <!-- JAL-3017 -->Cannot import features with multiple
599 variant elements (blocks import of some Uniprot records)
602 <!-- JAL-2997 -->Clustal files with sequence positions in
603 right-hand column parsed correctly
606 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
607 not alignment area in exported graphic
610 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
611 window has input focus
614 <!-- JAL-2992 -->Annotation panel set too high when
615 annotation added to view (Windows)
618 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
619 network connectivity is poor
622 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
623 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
624 the currently open URL and links from a page viewed in
625 Firefox or Chrome on Windows is now fully supported. If
626 you are using Edge, only links in the page can be
627 dragged, and with Internet Explorer, only the currently
628 open URL in the browser can be dropped onto Jalview.</em>
634 <td width="60" nowrap>
636 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
639 <td><div align="left">
643 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
644 for disabling automatic superposition of multiple
645 structures and open structures in existing views
648 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
649 ID and annotation area margins can be click-dragged to
653 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
657 <!-- JAL-2759 -->Improved performance for large alignments
658 and lots of hidden columns
661 <!-- JAL-2593 -->Improved performance when rendering lots
662 of features (particularly when transparency is disabled)
665 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
666 exchange of Jalview features and Chimera attributes made
672 <td><div align="left">
675 <!-- JAL-2899 -->Structure and Overview aren't updated
676 when Colour By Annotation threshold slider is adjusted
679 <!-- JAL-2778 -->Slow redraw when Overview panel shown
680 overlapping alignment panel
683 <!-- JAL-2929 -->Overview doesn't show end of unpadded
687 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
688 improved: CDS not handled correctly if transcript has no
692 <!-- JAL-2321 -->Secondary structure and temperature
693 factor annotation not added to sequence when local PDB
694 file associated with it by drag'n'drop or structure
698 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
699 dialog doesn't import PDB files dropped on an alignment
702 <!-- JAL-2666 -->Linked scrolling via protein horizontal
703 scroll bar doesn't work for some CDS/Protein views
706 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
707 Java 1.8u153 onwards and Java 1.9u4+.
710 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
711 columns in annotation row
714 <!-- JAL-2913 -->Preferences panel's ID Width control is not
715 honored in batch mode
718 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
719 for structures added to existing Jmol view
722 <!-- JAL-2223 -->'View Mappings' includes duplicate
723 entries after importing project with multiple views
726 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
727 protein sequences via SIFTS from associated PDB entries
728 with negative residue numbers or missing residues fails
731 <!-- JAL-2952 -->Exception when shading sequence with negative
732 Temperature Factor values from annotated PDB files (e.g.
733 as generated by CONSURF)
736 <!-- JAL-2920 -->Uniprot 'sequence variant' features
737 tooltip doesn't include a text description of mutation
740 <!-- JAL-2922 -->Invert displayed features very slow when
741 structure and/or overview windows are also shown
744 <!-- JAL-2954 -->Selecting columns from highlighted regions
745 very slow for alignments with large numbers of sequences
748 <!-- JAL-2925 -->Copy Consensus fails for group consensus
749 with 'StringIndexOutOfBounds'
752 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
753 platforms running Java 10
756 <!-- JAL-2960 -->Adding a structure to existing structure
757 view appears to do nothing because the view is hidden behind the alignment view
763 <!-- JAL-2926 -->Copy consensus sequence option in applet
764 should copy the group consensus when popup is opened on it
770 <!-- JAL-2913 -->Fixed ID width preference is not respected
773 <em>New Known Defects</em>
776 <!-- JAL-2973 --> Exceptions occasionally raised when
777 editing a large alignment and overview is displayed
780 <!-- JAL-2974 -->'Overview updating' progress bar is shown
781 repeatedly after a series of edits even when the overview
782 is no longer reflecting updates
785 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
786 structures for protein subsequence (if 'Trim Retrieved
787 Sequences' enabled) or Ensembl isoforms (Workaround in
788 2.10.4 is to fail back to N&W mapping)
795 <td width="60" nowrap>
797 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
800 <td><div align="left">
801 <ul><li>Updated Certum Codesigning Certificate
802 (Valid till 30th November 2018)</li></ul></div></td>
803 <td><div align="left">
806 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
807 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
808 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
809 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
810 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
811 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
812 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
818 <td width="60" nowrap>
820 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
823 <td><div align="left">
827 <!-- JAL-2446 -->Faster and more efficient management and
828 rendering of sequence features
831 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
832 429 rate limit request hander
835 <!-- JAL-2773 -->Structure views don't get updated unless
836 their colours have changed
839 <!-- JAL-2495 -->All linked sequences are highlighted for
840 a structure mousover (Jmol) or selection (Chimera)
843 <!-- JAL-2790 -->'Cancel' button in progress bar for
844 JABAWS AACon, RNAAliFold and Disorder prediction jobs
847 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
848 view from Ensembl locus cross-references
851 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
855 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
856 feature can be disabled
859 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
860 PDB easier retrieval of sequences for lists of IDs
863 <!-- JAL-2758 -->Short names for sequences retrieved from
869 <li>Groovy interpreter updated to 2.4.12</li>
870 <li>Example groovy script for generating a matrix of
871 percent identity scores for current alignment.</li>
873 <em>Testing and Deployment</em>
876 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
880 <td><div align="left">
884 <!-- JAL-2643 -->Pressing tab after updating the colour
885 threshold text field doesn't trigger an update to the
889 <!-- JAL-2682 -->Race condition when parsing sequence ID
893 <!-- JAL-2608 -->Overview windows are also closed when
894 alignment window is closed
897 <!-- JAL-2548 -->Export of features doesn't always respect
901 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
902 takes a long time in Cursor mode
908 <!-- JAL-2777 -->Structures with whitespace chainCode
909 cannot be viewed in Chimera
912 <!-- JAL-2728 -->Protein annotation panel too high in
916 <!-- JAL-2757 -->Can't edit the query after the server
917 error warning icon is shown in Uniprot and PDB Free Text
921 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
924 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
927 <!-- JAL-2739 -->Hidden column marker in last column not
928 rendered when switching back from Wrapped to normal view
931 <!-- JAL-2768 -->Annotation display corrupted when
932 scrolling right in unwapped alignment view
935 <!-- JAL-2542 -->Existing features on subsequence
936 incorrectly relocated when full sequence retrieved from
940 <!-- JAL-2733 -->Last reported memory still shown when
941 Desktop->Show Memory is unticked (OSX only)
944 <!-- JAL-2658 -->Amend Features dialog doesn't allow
945 features of same type and group to be selected for
949 <!-- JAL-2524 -->Jalview becomes sluggish in wide
950 alignments when hidden columns are present
953 <!-- JAL-2392 -->Jalview freezes when loading and
954 displaying several structures
957 <!-- JAL-2732 -->Black outlines left after resizing or
961 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
962 within the Jalview desktop on OSX
965 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
966 when in wrapped alignment mode
969 <!-- JAL-2636 -->Scale mark not shown when close to right
970 hand end of alignment
973 <!-- JAL-2684 -->Pairwise alignment of selected regions of
974 each selected sequence do not have correct start/end
978 <!-- JAL-2793 -->Alignment ruler height set incorrectly
979 after canceling the Alignment Window's Font dialog
982 <!-- JAL-2036 -->Show cross-references not enabled after
983 restoring project until a new view is created
986 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
987 URL links appears when only default EMBL-EBI link is
988 configured (since 2.10.2b2)
991 <!-- JAL-2775 -->Overview redraws whole window when box
995 <!-- JAL-2225 -->Structure viewer doesn't map all chains
996 in a multi-chain structure when viewing alignment
997 involving more than one chain (since 2.10)
1000 <!-- JAL-2811 -->Double residue highlights in cursor mode
1001 if new selection moves alignment window
1004 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1005 arrow key in cursor mode to pass hidden column marker
1008 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1009 that produces correctly annotated transcripts and products
1012 <!-- JAL-2776 -->Toggling a feature group after first time
1013 doesn't update associated structure view
1016 <em>Applet</em><br />
1019 <!-- JAL-2687 -->Concurrent modification exception when
1020 closing alignment panel
1023 <em>BioJSON</em><br />
1026 <!-- JAL-2546 -->BioJSON export does not preserve
1027 non-positional features
1030 <em>New Known Issues</em>
1033 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1034 sequence features correctly (for many previous versions of
1038 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1039 using cursor in wrapped panel other than top
1042 <!-- JAL-2791 -->Select columns containing feature ignores
1043 graduated colour threshold
1046 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1047 always preserve numbering and sequence features
1050 <em>Known Java 9 Issues</em>
1053 <!-- JAL-2902 -->Groovy Console very slow to open and is
1054 not responsive when entering characters (Webstart, Java
1061 <td width="60" nowrap>
1062 <div align="center">
1063 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1064 <em>2/10/2017</em></strong>
1067 <td><div align="left">
1068 <em>New features in Jalview Desktop</em>
1071 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1073 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1077 <td><div align="left">
1081 <td width="60" nowrap>
1082 <div align="center">
1083 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1084 <em>7/9/2017</em></strong>
1087 <td><div align="left">
1091 <!-- JAL-2588 -->Show gaps in overview window by colouring
1092 in grey (sequences used to be coloured grey, and gaps were
1096 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1100 <!-- JAL-2587 -->Overview updates immediately on increase
1101 in size and progress bar shown as higher resolution
1102 overview is recalculated
1107 <td><div align="left">
1111 <!-- JAL-2664 -->Overview window redraws every hidden
1112 column region row by row
1115 <!-- JAL-2681 -->duplicate protein sequences shown after
1116 retrieving Ensembl crossrefs for sequences from Uniprot
1119 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1120 format setting is unticked
1123 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1124 if group has show boxes format setting unticked
1127 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1128 autoscrolling whilst dragging current selection group to
1129 include sequences and columns not currently displayed
1132 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1133 assemblies are imported via CIF file
1136 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1137 displayed when threshold or conservation colouring is also
1141 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1145 <!-- JAL-2673 -->Jalview continues to scroll after
1146 dragging a selected region off the visible region of the
1150 <!-- JAL-2724 -->Cannot apply annotation based
1151 colourscheme to all groups in a view
1154 <!-- JAL-2511 -->IDs don't line up with sequences
1155 initially after font size change using the Font chooser or
1162 <td width="60" nowrap>
1163 <div align="center">
1164 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1167 <td><div align="left">
1168 <em>Calculations</em>
1172 <!-- JAL-1933 -->Occupancy annotation row shows number of
1173 ungapped positions in each column of the alignment.
1176 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1177 a calculation dialog box
1180 <!-- JAL-2379 -->Revised implementation of PCA for speed
1181 and memory efficiency (~30x faster)
1184 <!-- JAL-2403 -->Revised implementation of sequence
1185 similarity scores as used by Tree, PCA, Shading Consensus
1186 and other calculations
1189 <!-- JAL-2416 -->Score matrices are stored as resource
1190 files within the Jalview codebase
1193 <!-- JAL-2500 -->Trees computed on Sequence Feature
1194 Similarity may have different topology due to increased
1201 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1202 model for alignments and groups
1205 <!-- JAL-384 -->Custom shading schemes created via groovy
1212 <!-- JAL-2526 -->Efficiency improvements for interacting
1213 with alignment and overview windows
1216 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1220 <!-- JAL-2388 -->Hidden columns and sequences can be
1224 <!-- JAL-2611 -->Click-drag in visible area allows fine
1225 adjustment of visible position
1229 <em>Data import/export</em>
1232 <!-- JAL-2535 -->Posterior probability annotation from
1233 Stockholm files imported as sequence associated annotation
1236 <!-- JAL-2507 -->More robust per-sequence positional
1237 annotation input/output via stockholm flatfile
1240 <!-- JAL-2533 -->Sequence names don't include file
1241 extension when importing structure files without embedded
1242 names or PDB accessions
1245 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1246 format sequence substitution matrices
1249 <em>User Interface</em>
1252 <!-- JAL-2447 --> Experimental Features Checkbox in
1253 Desktop's Tools menu to hide or show untested features in
1257 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1258 via Overview or sequence motif search operations
1261 <!-- JAL-2547 -->Amend sequence features dialog box can be
1262 opened by double clicking gaps within sequence feature
1266 <!-- JAL-1476 -->Status bar message shown when not enough
1267 aligned positions were available to create a 3D structure
1271 <em>3D Structure</em>
1274 <!-- JAL-2430 -->Hidden regions in alignment views are not
1275 coloured in linked structure views
1278 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1279 file-based command exchange
1282 <!-- JAL-2375 -->Structure chooser automatically shows
1283 Cached Structures rather than querying the PDBe if
1284 structures are already available for sequences
1287 <!-- JAL-2520 -->Structures imported via URL are cached in
1288 the Jalview project rather than downloaded again when the
1289 project is reopened.
1292 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1293 to transfer Chimera's structure attributes as Jalview
1294 features, and vice-versa (<strong>Experimental
1298 <em>Web Services</em>
1301 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1304 <!-- JAL-2335 -->Filter non-standard amino acids and
1305 nucleotides when submitting to AACon and other MSA
1309 <!-- JAL-2316, -->URLs for viewing database
1310 cross-references provided by identifiers.org and the
1311 EMBL-EBI's MIRIAM DB
1318 <!-- JAL-2344 -->FileFormatI interface for describing and
1319 identifying file formats (instead of String constants)
1322 <!-- JAL-2228 -->FeatureCounter script refactored for
1323 efficiency when counting all displayed features (not
1324 backwards compatible with 2.10.1)
1327 <em>Example files</em>
1330 <!-- JAL-2631 -->Graduated feature colour style example
1331 included in the example feature file
1334 <em>Documentation</em>
1337 <!-- JAL-2339 -->Release notes reformatted for readability
1338 with the built-in Java help viewer
1341 <!-- JAL-1644 -->Find documentation updated with 'search
1342 sequence description' option
1348 <!-- JAL-2485, -->External service integration tests for
1349 Uniprot REST Free Text Search Client
1352 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1355 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1360 <td><div align="left">
1361 <em>Calculations</em>
1364 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1365 matrix - C->R should be '-3'<br />Old matrix restored
1366 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1368 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1369 Jalview's treatment of gaps in PCA and substitution matrix
1370 based Tree calculations.<br /> <br />In earlier versions
1371 of Jalview, gaps matching gaps were penalised, and gaps
1372 matching non-gaps penalised even more. In the PCA
1373 calculation, gaps were actually treated as non-gaps - so
1374 different costs were applied, which meant Jalview's PCAs
1375 were different to those produced by SeqSpace.<br />Jalview
1376 now treats gaps in the same way as SeqSpace (ie it scores
1377 them as 0). <br /> <br />Enter the following in the
1378 Groovy console to restore pre-2.10.2 behaviour:<br />
1379 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1380 // for 2.10.1 mode <br />
1381 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1382 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1383 these settings will affect all subsequent tree and PCA
1384 calculations (not recommended)</em></li>
1386 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1387 scaling of branch lengths for trees computed using
1388 Sequence Feature Similarity.
1391 <!-- JAL-2377 -->PCA calculation could hang when
1392 generating output report when working with highly
1393 redundant alignments
1396 <!-- JAL-2544 --> Sort by features includes features to
1397 right of selected region when gaps present on right-hand
1401 <em>User Interface</em>
1404 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1405 doesn't reselect a specific sequence's associated
1406 annotation after it was used for colouring a view
1409 <!-- JAL-2419 -->Current selection lost if popup menu
1410 opened on a region of alignment without groups
1413 <!-- JAL-2374 -->Popup menu not always shown for regions
1414 of an alignment with overlapping groups
1417 <!-- JAL-2310 -->Finder double counts if both a sequence's
1418 name and description match
1421 <!-- JAL-2370 -->Hiding column selection containing two
1422 hidden regions results in incorrect hidden regions
1425 <!-- JAL-2386 -->'Apply to all groups' setting when
1426 changing colour does not apply Conservation slider value
1430 <!-- JAL-2373 -->Percentage identity and conservation menu
1431 items do not show a tick or allow shading to be disabled
1434 <!-- JAL-2385 -->Conservation shading or PID threshold
1435 lost when base colourscheme changed if slider not visible
1438 <!-- JAL-2547 -->Sequence features shown in tooltip for
1439 gaps before start of features
1442 <!-- JAL-2623 -->Graduated feature colour threshold not
1443 restored to UI when feature colour is edited
1446 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1447 a time when scrolling vertically in wrapped mode.
1450 <!-- JAL-2630 -->Structure and alignment overview update
1451 as graduate feature colour settings are modified via the
1455 <!-- JAL-2034 -->Overview window doesn't always update
1456 when a group defined on the alignment is resized
1459 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1460 wrapped view result in positional status updates
1464 <!-- JAL-2563 -->Status bar doesn't show position for
1465 ambiguous amino acid and nucleotide symbols
1468 <!-- JAL-2602 -->Copy consensus sequence failed if
1469 alignment included gapped columns
1472 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1473 widgets don't permanently disappear
1476 <!-- JAL-2503 -->Cannot select or filter quantitative
1477 annotation that are shown only as column labels (e.g.
1478 T-Coffee column reliability scores)
1481 <!-- JAL-2594 -->Exception thrown if trying to create a
1482 sequence feature on gaps only
1485 <!-- JAL-2504 -->Features created with 'New feature'
1486 button from a Find inherit previously defined feature type
1487 rather than the Find query string
1490 <!-- JAL-2423 -->incorrect title in output window when
1491 exporting tree calculated in Jalview
1494 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1495 and then revealing them reorders sequences on the
1499 <!-- JAL-964 -->Group panel in sequence feature settings
1500 doesn't update to reflect available set of groups after
1501 interactively adding or modifying features
1504 <!-- JAL-2225 -->Sequence Database chooser unusable on
1508 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1509 only excluded gaps in current sequence and ignored
1516 <!-- JAL-2421 -->Overview window visible region moves
1517 erratically when hidden rows or columns are present
1520 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1521 Structure Viewer's colour menu don't correspond to
1525 <!-- JAL-2405 -->Protein specific colours only offered in
1526 colour and group colour menu for protein alignments
1529 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1530 reflect currently selected view or group's shading
1534 <!-- JAL-2624 -->Feature colour thresholds not respected
1535 when rendered on overview and structures when opacity at
1539 <!-- JAL-2589 -->User defined gap colour not shown in
1540 overview when features overlaid on alignment
1543 <!-- JAL-2567 -->Feature settings for different views not
1544 recovered correctly from Jalview project file
1547 <!-- JAL-2256 -->Feature colours in overview when first opened
1548 (automatically via preferences) are different to the main
1552 <em>Data import/export</em>
1555 <!-- JAL-2576 -->Very large alignments take a long time to
1559 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1560 added after a sequence was imported are not written to
1564 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1565 when importing RNA secondary structure via Stockholm
1568 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1569 not shown in correct direction for simple pseudoknots
1572 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1573 with lightGray or darkGray via features file (but can
1577 <!-- JAL-2383 -->Above PID colour threshold not recovered
1578 when alignment view imported from project
1581 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1582 structure and sequences extracted from structure files
1583 imported via URL and viewed in Jmol
1586 <!-- JAL-2520 -->Structures loaded via URL are saved in
1587 Jalview Projects rather than fetched via URL again when
1588 the project is loaded and the structure viewed
1591 <em>Web Services</em>
1594 <!-- JAL-2519 -->EnsemblGenomes example failing after
1595 release of Ensembl v.88
1598 <!-- JAL-2366 -->Proxy server address and port always
1599 appear enabled in Preferences->Connections
1602 <!-- JAL-2461 -->DAS registry not found exceptions
1603 removed from console output
1606 <!-- JAL-2582 -->Cannot retrieve protein products from
1607 Ensembl by Peptide ID
1610 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1611 created from SIFTs, and spurious 'Couldn't open structure
1612 in Chimera' errors raised after April 2017 update (problem
1613 due to 'null' string rather than empty string used for
1614 residues with no corresponding PDB mapping).
1617 <em>Application UI</em>
1620 <!-- JAL-2361 -->User Defined Colours not added to Colour
1624 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1625 case' residues (button in colourscheme editor debugged and
1626 new documentation and tooltips added)
1629 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1630 doesn't restore group-specific text colour thresholds
1633 <!-- JAL-2243 -->Feature settings panel does not update as
1634 new features are added to alignment
1637 <!-- JAL-2532 -->Cancel in feature settings reverts
1638 changes to feature colours via the Amend features dialog
1641 <!-- JAL-2506 -->Null pointer exception when attempting to
1642 edit graduated feature colour via amend features dialog
1646 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1647 selection menu changes colours of alignment views
1650 <!-- JAL-2426 -->Spurious exceptions in console raised
1651 from alignment calculation workers after alignment has
1655 <!-- JAL-1608 -->Typo in selection popup menu - Create
1656 groups now 'Create Group'
1659 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1660 Create/Undefine group doesn't always work
1663 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1664 shown again after pressing 'Cancel'
1667 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1668 adjusts start position in wrap mode
1671 <!-- JAL-2563 -->Status bar doesn't show positions for
1672 ambiguous amino acids
1675 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1676 CDS/Protein view after CDS sequences added for aligned
1680 <!-- JAL-2592 -->User defined colourschemes called 'User
1681 Defined' don't appear in Colours menu
1687 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1688 score models doesn't always result in an updated PCA plot
1691 <!-- JAL-2442 -->Features not rendered as transparent on
1692 overview or linked structure view
1695 <!-- JAL-2372 -->Colour group by conservation doesn't
1699 <!-- JAL-2517 -->Hitting Cancel after applying
1700 user-defined colourscheme doesn't restore original
1707 <!-- JAL-2314 -->Unit test failure:
1708 jalview.ws.jabaws.RNAStructExportImport setup fails
1711 <!-- JAL-2307 -->Unit test failure:
1712 jalview.ws.sifts.SiftsClientTest due to compatibility
1713 problems with deep array comparison equality asserts in
1714 successive versions of TestNG
1717 <!-- JAL-2479 -->Relocated StructureChooserTest and
1718 ParameterUtilsTest Unit tests to Network suite
1721 <em>New Known Issues</em>
1724 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1725 phase after a sequence motif find operation
1728 <!-- JAL-2550 -->Importing annotation file with rows
1729 containing just upper and lower case letters are
1730 interpreted as WUSS RNA secondary structure symbols
1733 <!-- JAL-2590 -->Cannot load and display Newick trees
1734 reliably from eggnog Ortholog database
1737 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1738 containing features of type Highlight' when 'B' is pressed
1739 to mark columns containing highlighted regions.
1742 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1743 doesn't always add secondary structure annotation.
1748 <td width="60" nowrap>
1749 <div align="center">
1750 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1753 <td><div align="left">
1757 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1758 for all consensus calculations
1761 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1764 <li>Updated Jalview's Certum code signing certificate
1767 <em>Application</em>
1770 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1771 set of database cross-references, sorted alphabetically
1774 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1775 from database cross references. Users with custom links
1776 will receive a <a href="webServices/urllinks.html#warning">warning
1777 dialog</a> asking them to update their preferences.
1780 <!-- JAL-2287-->Cancel button and escape listener on
1781 dialog warning user about disconnecting Jalview from a
1785 <!-- JAL-2320-->Jalview's Chimera control window closes if
1786 the Chimera it is connected to is shut down
1789 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1790 columns menu item to mark columns containing highlighted
1791 regions (e.g. from structure selections or results of a
1795 <!-- JAL-2284-->Command line option for batch-generation
1796 of HTML pages rendering alignment data with the BioJS
1806 <!-- JAL-2286 -->Columns with more than one modal residue
1807 are not coloured or thresholded according to percent
1808 identity (first observed in Jalview 2.8.2)
1811 <!-- JAL-2301 -->Threonine incorrectly reported as not
1815 <!-- JAL-2318 -->Updates to documentation pages (above PID
1816 threshold, amino acid properties)
1819 <!-- JAL-2292 -->Lower case residues in sequences are not
1820 reported as mapped to residues in a structure file in the
1824 <!--JAL-2324 -->Identical features with non-numeric scores
1825 could be added multiple times to a sequence
1828 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1829 bond features shown as two highlighted residues rather
1830 than a range in linked structure views, and treated
1831 correctly when selecting and computing trees from features
1834 <!-- JAL-2281-->Custom URL links for database
1835 cross-references are matched to database name regardless
1840 <em>Application</em>
1843 <!-- JAL-2282-->Custom URL links for specific database
1844 names without regular expressions also offer links from
1848 <!-- JAL-2315-->Removing a single configured link in the
1849 URL links pane in Connections preferences doesn't actually
1850 update Jalview configuration
1853 <!-- JAL-2272-->CTRL-Click on a selected region to open
1854 the alignment area popup menu doesn't work on El-Capitan
1857 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1858 files with similarly named sequences if dropped onto the
1862 <!-- JAL-2312 -->Additional mappings are shown for PDB
1863 entries where more chains exist in the PDB accession than
1864 are reported in the SIFTS file
1867 <!-- JAL-2317-->Certain structures do not get mapped to
1868 the structure view when displayed with Chimera
1871 <!-- JAL-2317-->No chains shown in the Chimera view
1872 panel's View->Show Chains submenu
1875 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1876 work for wrapped alignment views
1879 <!--JAL-2197 -->Rename UI components for running JPred
1880 predictions from 'JNet' to 'JPred'
1883 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1884 corrupted when annotation panel vertical scroll is not at
1885 first annotation row
1888 <!--JAL-2332 -->Attempting to view structure for Hen
1889 lysozyme results in a PDB Client error dialog box
1892 <!-- JAL-2319 -->Structure View's mapping report switched
1893 ranges for PDB and sequence for SIFTS
1896 SIFTS 'Not_Observed' residues mapped to non-existant
1900 <!-- <em>New Known Issues</em>
1907 <td width="60" nowrap>
1908 <div align="center">
1909 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1910 <em>25/10/2016</em></strong>
1913 <td><em>Application</em>
1915 <li>3D Structure chooser opens with 'Cached structures'
1916 view if structures already loaded</li>
1917 <li>Progress bar reports models as they are loaded to
1918 structure views</li>
1924 <li>Colour by conservation always enabled and no tick
1925 shown in menu when BLOSUM or PID shading applied</li>
1926 <li>FER1_ARATH and FER2_ARATH labels were switched in
1927 example sequences/projects/trees</li>
1929 <em>Application</em>
1931 <li>Jalview projects with views of local PDB structure
1932 files saved on Windows cannot be opened on OSX</li>
1933 <li>Multiple structure views can be opened and superposed
1934 without timeout for structures with multiple models or
1935 multiple sequences in alignment</li>
1936 <li>Cannot import or associated local PDB files without a
1937 PDB ID HEADER line</li>
1938 <li>RMSD is not output in Jmol console when superposition
1940 <li>Drag and drop of URL from Browser fails for Linux and
1941 OSX versions earlier than El Capitan</li>
1942 <li>ENA client ignores invalid content from ENA server</li>
1943 <li>Exceptions are not raised in console when ENA client
1944 attempts to fetch non-existent IDs via Fetch DB Refs UI
1946 <li>Exceptions are not raised in console when a new view
1947 is created on the alignment</li>
1948 <li>OSX right-click fixed for group selections: CMD-click
1949 to insert/remove gaps in groups and CTRL-click to open group
1952 <em>Build and deployment</em>
1954 <li>URL link checker now copes with multi-line anchor
1957 <em>New Known Issues</em>
1959 <li>Drag and drop from URL links in browsers do not work
1966 <td width="60" nowrap>
1967 <div align="center">
1968 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1971 <td><em>General</em>
1974 <!-- JAL-2124 -->Updated Spanish translations.
1977 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1978 for importing structure data to Jalview. Enables mmCIF and
1982 <!-- JAL-192 --->Alignment ruler shows positions relative to
1986 <!-- JAL-2202 -->Position/residue shown in status bar when
1987 mousing over sequence associated annotation
1990 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1994 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1995 '()', canonical '[]' and invalid '{}' base pair populations
1999 <!-- JAL-2092 -->Feature settings popup menu options for
2000 showing or hiding columns containing a feature
2003 <!-- JAL-1557 -->Edit selected group by double clicking on
2004 group and sequence associated annotation labels
2007 <!-- JAL-2236 -->Sequence name added to annotation label in
2008 select/hide columns by annotation and colour by annotation
2012 </ul> <em>Application</em>
2015 <!-- JAL-2050-->Automatically hide introns when opening a
2016 gene/transcript view
2019 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2023 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2024 structure mappings with the EMBL-EBI PDBe SIFTS database
2027 <!-- JAL-2079 -->Updated download sites used for Rfam and
2028 Pfam sources to xfam.org
2031 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2034 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2035 over sequences in Jalview
2038 <!-- JAL-2027-->Support for reverse-complement coding
2039 regions in ENA and EMBL
2042 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2043 for record retrieval via ENA rest API
2046 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2050 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2051 groovy script execution
2054 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2055 alignment window's Calculate menu
2058 <!-- JAL-1812 -->Allow groovy scripts that call
2059 Jalview.getAlignFrames() to run in headless mode
2062 <!-- JAL-2068 -->Support for creating new alignment
2063 calculation workers from groovy scripts
2066 <!-- JAL-1369 --->Store/restore reference sequence in
2070 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2071 associations are now saved/restored from project
2074 <!-- JAL-1993 -->Database selection dialog always shown
2075 before sequence fetcher is opened
2078 <!-- JAL-2183 -->Double click on an entry in Jalview's
2079 database chooser opens a sequence fetcher
2082 <!-- JAL-1563 -->Free-text search client for UniProt using
2083 the UniProt REST API
2086 <!-- JAL-2168 -->-nonews command line parameter to prevent
2087 the news reader opening
2090 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2091 querying stored in preferences
2094 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2098 <!-- JAL-1977-->Tooltips shown on database chooser
2101 <!-- JAL-391 -->Reverse complement function in calculate
2102 menu for nucleotide sequences
2105 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2106 and feature counts preserves alignment ordering (and
2107 debugged for complex feature sets).
2110 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2111 viewing structures with Jalview 2.10
2114 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2115 genome, transcript CCDS and gene ids via the Ensembl and
2116 Ensembl Genomes REST API
2119 <!-- JAL-2049 -->Protein sequence variant annotation
2120 computed for 'sequence_variant' annotation on CDS regions
2124 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2128 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2129 Ref Fetcher fails to match, or otherwise updates sequence
2130 data from external database records.
2133 <!-- JAL-2154 -->Revised Jalview Project format for
2134 efficient recovery of sequence coding and alignment
2135 annotation relationships.
2137 </ul> <!-- <em>Applet</em>
2148 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2152 <!-- JAL-2018-->Export features in Jalview format (again)
2153 includes graduated colourschemes
2156 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2157 working with big alignments and lots of hidden columns
2160 <!-- JAL-2053-->Hidden column markers not always rendered
2161 at right of alignment window
2164 <!-- JAL-2067 -->Tidied up links in help file table of
2168 <!-- JAL-2072 -->Feature based tree calculation not shown
2172 <!-- JAL-2075 -->Hidden columns ignored during feature
2173 based tree calculation
2176 <!-- JAL-2065 -->Alignment view stops updating when show
2177 unconserved enabled for group on alignment
2180 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2184 <!-- JAL-2146 -->Alignment column in status incorrectly
2185 shown as "Sequence position" when mousing over
2189 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2190 hidden columns present
2193 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2194 user created annotation added to alignment
2197 <!-- JAL-1841 -->RNA Structure consensus only computed for
2198 '()' base pair annotation
2201 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2202 in zero scores for all base pairs in RNA Structure
2206 <!-- JAL-2174-->Extend selection with columns containing
2210 <!-- JAL-2275 -->Pfam format writer puts extra space at
2211 beginning of sequence
2214 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2218 <!-- JAL-2238 -->Cannot create groups on an alignment from
2219 from a tree when t-coffee scores are shown
2222 <!-- JAL-1836,1967 -->Cannot import and view PDB
2223 structures with chains containing negative resnums (4q4h)
2226 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2230 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2231 to Clustal, PIR and PileUp output
2234 <!-- JAL-2008 -->Reordering sequence features that are
2235 not visible causes alignment window to repaint
2238 <!-- JAL-2006 -->Threshold sliders don't work in
2239 graduated colour and colour by annotation row for e-value
2240 scores associated with features and annotation rows
2243 <!-- JAL-1797 -->amino acid physicochemical conservation
2244 calculation should be case independent
2247 <!-- JAL-2173 -->Remove annotation also updates hidden
2251 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2252 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2253 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2256 <!-- JAL-2065 -->Null pointer exceptions and redraw
2257 problems when reference sequence defined and 'show
2258 non-conserved' enabled
2261 <!-- JAL-1306 -->Quality and Conservation are now shown on
2262 load even when Consensus calculation is disabled
2265 <!-- JAL-1932 -->Remove right on penultimate column of
2266 alignment does nothing
2269 <em>Application</em>
2272 <!-- JAL-1552-->URLs and links can't be imported by
2273 drag'n'drop on OSX when launched via webstart (note - not
2274 yet fixed for El Capitan)
2277 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2278 output when running on non-gb/us i18n platforms
2281 <!-- JAL-1944 -->Error thrown when exporting a view with
2282 hidden sequences as flat-file alignment
2285 <!-- JAL-2030-->InstallAnywhere distribution fails when
2289 <!-- JAL-2080-->Jalview very slow to launch via webstart
2290 (also hotfix for 2.9.0b2)
2293 <!-- JAL-2085 -->Cannot save project when view has a
2294 reference sequence defined
2297 <!-- JAL-1011 -->Columns are suddenly selected in other
2298 alignments and views when revealing hidden columns
2301 <!-- JAL-1989 -->Hide columns not mirrored in complement
2302 view in a cDNA/Protein splitframe
2305 <!-- JAL-1369 -->Cannot save/restore representative
2306 sequence from project when only one sequence is
2310 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2311 in Structure Chooser
2314 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2315 structure consensus didn't refresh annotation panel
2318 <!-- JAL-1962 -->View mapping in structure view shows
2319 mappings between sequence and all chains in a PDB file
2322 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2323 dialogs format columns correctly, don't display array
2324 data, sort columns according to type
2327 <!-- JAL-1975 -->Export complete shown after destination
2328 file chooser is cancelled during an image export
2331 <!-- JAL-2025 -->Error when querying PDB Service with
2332 sequence name containing special characters
2335 <!-- JAL-2024 -->Manual PDB structure querying should be
2339 <!-- JAL-2104 -->Large tooltips with broken HTML
2340 formatting don't wrap
2343 <!-- JAL-1128 -->Figures exported from wrapped view are
2344 truncated so L looks like I in consensus annotation
2347 <!-- JAL-2003 -->Export features should only export the
2348 currently displayed features for the current selection or
2352 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2353 after fetching cross-references, and restoring from
2357 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2358 followed in the structure viewer
2361 <!-- JAL-2163 -->Titles for individual alignments in
2362 splitframe not restored from project
2365 <!-- JAL-2145 -->missing autocalculated annotation at
2366 trailing end of protein alignment in transcript/product
2367 splitview when pad-gaps not enabled by default
2370 <!-- JAL-1797 -->amino acid physicochemical conservation
2374 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2375 article has been read (reopened issue due to
2376 internationalisation problems)
2379 <!-- JAL-1960 -->Only offer PDB structures in structure
2380 viewer based on sequence name, PDB and UniProt
2385 <!-- JAL-1976 -->No progress bar shown during export of
2389 <!-- JAL-2213 -->Structures not always superimposed after
2390 multiple structures are shown for one or more sequences.
2393 <!-- JAL-1370 -->Reference sequence characters should not
2394 be replaced with '.' when 'Show unconserved' format option
2398 <!-- JAL-1823 -->Cannot specify chain code when entering
2399 specific PDB id for sequence
2402 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2403 'Export hidden sequences' is enabled, but 'export hidden
2404 columns' is disabled.
2407 <!--JAL-2026-->Best Quality option in structure chooser
2408 selects lowest rather than highest resolution structures
2412 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2413 to sequence mapping in 'View Mappings' report
2416 <!-- JAL-2284 -->Unable to read old Jalview projects that
2417 contain non-XML data added after Jalvew wrote project.
2420 <!-- JAL-2118 -->Newly created annotation row reorders
2421 after clicking on it to create new annotation for a
2425 <!-- JAL-1980 -->Null Pointer Exception raised when
2426 pressing Add on an orphaned cut'n'paste window.
2428 <!-- may exclude, this is an external service stability issue JAL-1941
2429 -- > RNA 3D structure not added via DSSR service</li> -->
2434 <!-- JAL-2151 -->Incorrect columns are selected when
2435 hidden columns present before start of sequence
2438 <!-- JAL-1986 -->Missing dependencies on applet pages
2442 <!-- JAL-1947 -->Overview pixel size changes when
2443 sequences are hidden in applet
2446 <!-- JAL-1996 -->Updated instructions for applet
2447 deployment on examples pages.
2454 <td width="60" nowrap>
2455 <div align="center">
2456 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2457 <em>16/10/2015</em></strong>
2460 <td><em>General</em>
2462 <li>Time stamps for signed Jalview application and applet
2467 <em>Application</em>
2469 <li>Duplicate group consensus and conservation rows
2470 shown when tree is partitioned</li>
2471 <li>Erratic behaviour when tree partitions made with
2472 multiple cDNA/Protein split views</li>
2478 <td width="60" nowrap>
2479 <div align="center">
2480 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2481 <em>8/10/2015</em></strong>
2484 <td><em>General</em>
2486 <li>Updated Spanish translations of localized text for
2488 </ul> <em>Application</em>
2490 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2491 <li>Signed OSX InstallAnywhere installer<br></li>
2492 <li>Support for per-sequence based annotations in BioJSON</li>
2493 </ul> <em>Applet</em>
2495 <li>Split frame example added to applet examples page</li>
2496 </ul> <em>Build and Deployment</em>
2499 <!-- JAL-1888 -->New ant target for running Jalview's test
2507 <li>Mapping of cDNA to protein in split frames
2508 incorrect when sequence start > 1</li>
2509 <li>Broken images in filter column by annotation dialog
2511 <li>Feature colours not parsed from features file</li>
2512 <li>Exceptions and incomplete link URLs recovered when
2513 loading a features file containing HTML tags in feature
2517 <em>Application</em>
2519 <li>Annotations corrupted after BioJS export and
2521 <li>Incorrect sequence limits after Fetch DB References
2522 with 'trim retrieved sequences'</li>
2523 <li>Incorrect warning about deleting all data when
2524 deleting selected columns</li>
2525 <li>Patch to build system for shipping properly signed
2526 JNLP templates for webstart launch</li>
2527 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2528 unreleased structures for download or viewing</li>
2529 <li>Tab/space/return keystroke operation of EMBL-PDBe
2530 fetcher/viewer dialogs works correctly</li>
2531 <li>Disabled 'minimise' button on Jalview windows
2532 running on OSX to workaround redraw hang bug</li>
2533 <li>Split cDNA/Protein view position and geometry not
2534 recovered from jalview project</li>
2535 <li>Initial enabled/disabled state of annotation menu
2536 sorter 'show autocalculated first/last' corresponds to
2538 <li>Restoring of Clustal, RNA Helices and T-Coffee
2539 color schemes from BioJSON</li>
2543 <li>Reorder sequences mirrored in cDNA/Protein split
2545 <li>Applet with Jmol examples not loading correctly</li>
2551 <td><div align="center">
2552 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2554 <td><em>General</em>
2556 <li>Linked visualisation and analysis of DNA and Protein
2559 <li>Translated cDNA alignments shown as split protein
2560 and DNA alignment views</li>
2561 <li>Codon consensus annotation for linked protein and
2562 cDNA alignment views</li>
2563 <li>Link cDNA or Protein product sequences by loading
2564 them onto Protein or cDNA alignments</li>
2565 <li>Reconstruct linked cDNA alignment from aligned
2566 protein sequences</li>
2569 <li>Jmol integration updated to Jmol v14.2.14</li>
2570 <li>Import and export of Jalview alignment views as <a
2571 href="features/bioJsonFormat.html">BioJSON</a></li>
2572 <li>New alignment annotation file statements for
2573 reference sequences and marking hidden columns</li>
2574 <li>Reference sequence based alignment shading to
2575 highlight variation</li>
2576 <li>Select or hide columns according to alignment
2578 <li>Find option for locating sequences by description</li>
2579 <li>Conserved physicochemical properties shown in amino
2580 acid conservation row</li>
2581 <li>Alignments can be sorted by number of RNA helices</li>
2582 </ul> <em>Application</em>
2584 <li>New cDNA/Protein analysis capabilities
2586 <li>Get Cross-References should open a Split Frame
2587 view with cDNA/Protein</li>
2588 <li>Detect when nucleotide sequences and protein
2589 sequences are placed in the same alignment</li>
2590 <li>Split cDNA/Protein views are saved in Jalview
2595 <li>Use REST API to talk to Chimera</li>
2596 <li>Selected regions in Chimera are highlighted in linked
2597 Jalview windows</li>
2599 <li>VARNA RNA viewer updated to v3.93</li>
2600 <li>VARNA views are saved in Jalview Projects</li>
2601 <li>Pseudoknots displayed as Jalview RNA annotation can
2602 be shown in VARNA</li>
2604 <li>Make groups for selection uses marked columns as well
2605 as the active selected region</li>
2607 <li>Calculate UPGMA and NJ trees using sequence feature
2609 <li>New Export options
2611 <li>New Export Settings dialog to control hidden
2612 region export in flat file generation</li>
2614 <li>Export alignment views for display with the <a
2615 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2617 <li>Export scrollable SVG in HTML page</li>
2618 <li>Optional embedding of BioJSON data when exporting
2619 alignment figures to HTML</li>
2621 <li>3D structure retrieval and display
2623 <li>Free text and structured queries with the PDBe
2625 <li>PDBe Search API based discovery and selection of
2626 PDB structures for a sequence set</li>
2630 <li>JPred4 employed for protein secondary structure
2632 <li>Hide Insertions menu option to hide unaligned columns
2633 for one or a group of sequences</li>
2634 <li>Automatically hide insertions in alignments imported
2635 from the JPred4 web server</li>
2636 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2637 system on OSX<br />LGPL libraries courtesy of <a
2638 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2640 <li>changed 'View nucleotide structure' submenu to 'View
2641 VARNA 2D Structure'</li>
2642 <li>change "View protein structure" menu option to "3D
2645 </ul> <em>Applet</em>
2647 <li>New layout for applet example pages</li>
2648 <li>New parameters to enable SplitFrame view
2649 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2650 <li>New example demonstrating linked viewing of cDNA and
2651 Protein alignments</li>
2652 </ul> <em>Development and deployment</em>
2654 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2655 <li>Include installation type and git revision in build
2656 properties and console log output</li>
2657 <li>Jalview Github organisation, and new github site for
2658 storing BioJsMSA Templates</li>
2659 <li>Jalview's unit tests now managed with TestNG</li>
2662 <!-- <em>General</em>
2664 </ul> --> <!-- issues resolved --> <em>Application</em>
2666 <li>Escape should close any open find dialogs</li>
2667 <li>Typo in select-by-features status report</li>
2668 <li>Consensus RNA secondary secondary structure
2669 predictions are not highlighted in amber</li>
2670 <li>Missing gap character in v2.7 example file means
2671 alignment appears unaligned when pad-gaps is not enabled</li>
2672 <li>First switch to RNA Helices colouring doesn't colour
2673 associated structure views</li>
2674 <li>ID width preference option is greyed out when auto
2675 width checkbox not enabled</li>
2676 <li>Stopped a warning dialog from being shown when
2677 creating user defined colours</li>
2678 <li>'View Mapping' in structure viewer shows sequence
2679 mappings for just that viewer's sequences</li>
2680 <li>Workaround for superposing PDB files containing
2681 multiple models in Chimera</li>
2682 <li>Report sequence position in status bar when hovering
2683 over Jmol structure</li>
2684 <li>Cannot output gaps as '.' symbols with Selection ->
2685 output to text box</li>
2686 <li>Flat file exports of alignments with hidden columns
2687 have incorrect sequence start/end</li>
2688 <li>'Aligning' a second chain to a Chimera structure from
2690 <li>Colour schemes applied to structure viewers don't
2691 work for nucleotide</li>
2692 <li>Loading/cut'n'pasting an empty or invalid file leads
2693 to a grey/invisible alignment window</li>
2694 <li>Exported Jpred annotation from a sequence region
2695 imports to different position</li>
2696 <li>Space at beginning of sequence feature tooltips shown
2697 on some platforms</li>
2698 <li>Chimera viewer 'View | Show Chain' menu is not
2700 <li>'New View' fails with a Null Pointer Exception in
2701 console if Chimera has been opened</li>
2702 <li>Mouseover to Chimera not working</li>
2703 <li>Miscellaneous ENA XML feature qualifiers not
2705 <li>NPE in annotation renderer after 'Extract Scores'</li>
2706 <li>If two structures in one Chimera window, mouseover of
2707 either sequence shows on first structure</li>
2708 <li>'Show annotations' options should not make
2709 non-positional annotations visible</li>
2710 <li>Subsequence secondary structure annotation not shown
2711 in right place after 'view flanking regions'</li>
2712 <li>File Save As type unset when current file format is
2714 <li>Save as '.jar' option removed for saving Jalview
2716 <li>Colour by Sequence colouring in Chimera more
2718 <li>Cannot 'add reference annotation' for a sequence in
2719 several views on same alignment</li>
2720 <li>Cannot show linked products for EMBL / ENA records</li>
2721 <li>Jalview's tooltip wraps long texts containing no
2723 </ul> <em>Applet</em>
2725 <li>Jmol to JalviewLite mouseover/link not working</li>
2726 <li>JalviewLite can't import sequences with ID
2727 descriptions containing angle brackets</li>
2728 </ul> <em>General</em>
2730 <li>Cannot export and reimport RNA secondary structure
2731 via jalview annotation file</li>
2732 <li>Random helix colour palette for colour by annotation
2733 with RNA secondary structure</li>
2734 <li>Mouseover to cDNA from STOP residue in protein
2735 translation doesn't work.</li>
2736 <li>hints when using the select by annotation dialog box</li>
2737 <li>Jmol alignment incorrect if PDB file has alternate CA
2739 <li>FontChooser message dialog appears to hang after
2740 choosing 1pt font</li>
2741 <li>Peptide secondary structure incorrectly imported from
2742 annotation file when annotation display text includes 'e' or
2744 <li>Cannot set colour of new feature type whilst creating
2746 <li>cDNA translation alignment should not be sequence
2747 order dependent</li>
2748 <li>'Show unconserved' doesn't work for lower case
2750 <li>Nucleotide ambiguity codes involving R not recognised</li>
2751 </ul> <em>Deployment and Documentation</em>
2753 <li>Applet example pages appear different to the rest of
2754 www.jalview.org</li>
2755 </ul> <em>Application Known issues</em>
2757 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2758 <li>Misleading message appears after trying to delete
2760 <li>Jalview icon not shown in dock after InstallAnywhere
2761 version launches</li>
2762 <li>Fetching EMBL reference for an RNA sequence results
2763 fails with a sequence mismatch</li>
2764 <li>Corrupted or unreadable alignment display when
2765 scrolling alignment to right</li>
2766 <li>ArrayIndexOutOfBoundsException thrown when remove
2767 empty columns called on alignment with ragged gapped ends</li>
2768 <li>auto calculated alignment annotation rows do not get
2769 placed above or below non-autocalculated rows</li>
2770 <li>Jalview dekstop becomes sluggish at full screen in
2771 ultra-high resolution</li>
2772 <li>Cannot disable consensus calculation independently of
2773 quality and conservation</li>
2774 <li>Mouseover highlighting between cDNA and protein can
2775 become sluggish with more than one splitframe shown</li>
2776 </ul> <em>Applet Known Issues</em>
2778 <li>Core PDB parsing code requires Jmol</li>
2779 <li>Sequence canvas panel goes white when alignment
2780 window is being resized</li>
2786 <td><div align="center">
2787 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2789 <td><em>General</em>
2791 <li>Updated Java code signing certificate donated by
2793 <li>Features and annotation preserved when performing
2794 pairwise alignment</li>
2795 <li>RNA pseudoknot annotation can be
2796 imported/exported/displayed</li>
2797 <li>'colour by annotation' can colour by RNA and
2798 protein secondary structure</li>
2799 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2800 post-hoc with 2.9 release</em>)
2803 </ul> <em>Application</em>
2805 <li>Extract and display secondary structure for sequences
2806 with 3D structures</li>
2807 <li>Support for parsing RNAML</li>
2808 <li>Annotations menu for layout
2810 <li>sort sequence annotation rows by alignment</li>
2811 <li>place sequence annotation above/below alignment
2814 <li>Output in Stockholm format</li>
2815 <li>Internationalisation: improved Spanish (es)
2817 <li>Structure viewer preferences tab</li>
2818 <li>Disorder and Secondary Structure annotation tracks
2819 shared between alignments</li>
2820 <li>UCSF Chimera launch and linked highlighting from
2822 <li>Show/hide all sequence associated annotation rows for
2823 all or current selection</li>
2824 <li>disorder and secondary structure predictions
2825 available as dataset annotation</li>
2826 <li>Per-sequence rna helices colouring</li>
2829 <li>Sequence database accessions imported when fetching
2830 alignments from Rfam</li>
2831 <li>update VARNA version to 3.91</li>
2833 <li>New groovy scripts for exporting aligned positions,
2834 conservation values, and calculating sum of pairs scores.</li>
2835 <li>Command line argument to set default JABAWS server</li>
2836 <li>include installation type in build properties and
2837 console log output</li>
2838 <li>Updated Jalview project format to preserve dataset
2842 <!-- issues resolved --> <em>Application</em>
2844 <li>Distinguish alignment and sequence associated RNA
2845 structure in structure->view->VARNA</li>
2846 <li>Raise dialog box if user deletes all sequences in an
2848 <li>Pressing F1 results in documentation opening twice</li>
2849 <li>Sequence feature tooltip is wrapped</li>
2850 <li>Double click on sequence associated annotation
2851 selects only first column</li>
2852 <li>Redundancy removal doesn't result in unlinked
2853 leaves shown in tree</li>
2854 <li>Undos after several redundancy removals don't undo
2856 <li>Hide sequence doesn't hide associated annotation</li>
2857 <li>User defined colours dialog box too big to fit on
2858 screen and buttons not visible</li>
2859 <li>author list isn't updated if already written to
2860 Jalview properties</li>
2861 <li>Popup menu won't open after retrieving sequence
2863 <li>File open window for associate PDB doesn't open</li>
2864 <li>Left-then-right click on a sequence id opens a
2865 browser search window</li>
2866 <li>Cannot open sequence feature shading/sort popup menu
2867 in feature settings dialog</li>
2868 <li>better tooltip placement for some areas of Jalview
2870 <li>Allow addition of JABAWS Server which doesn't
2871 pass validation</li>
2872 <li>Web services parameters dialog box is too large to
2874 <li>Muscle nucleotide alignment preset obscured by
2876 <li>JABAWS preset submenus don't contain newly
2877 defined user preset</li>
2878 <li>MSA web services warns user if they were launched
2879 with invalid input</li>
2880 <li>Jalview cannot contact DAS Registy when running on
2883 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2884 'Superpose with' submenu not shown when new view
2888 </ul> <!-- <em>Applet</em>
2890 </ul> <em>General</em>
2892 </ul>--> <em>Deployment and Documentation</em>
2894 <li>2G and 1G options in launchApp have no effect on
2895 memory allocation</li>
2896 <li>launchApp service doesn't automatically open
2897 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2899 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2900 InstallAnywhere reports cannot find valid JVM when Java
2901 1.7_055 is available
2903 </ul> <em>Application Known issues</em>
2906 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2907 corrupted or unreadable alignment display when scrolling
2911 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2912 retrieval fails but progress bar continues for DAS retrieval
2913 with large number of ID
2916 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2917 flatfile output of visible region has incorrect sequence
2921 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2922 rna structure consensus doesn't update when secondary
2923 structure tracks are rearranged
2926 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2927 invalid rna structure positional highlighting does not
2928 highlight position of invalid base pairs
2931 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2932 out of memory errors are not raised when saving Jalview
2933 project from alignment window file menu
2936 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2937 Switching to RNA Helices colouring doesn't propagate to
2941 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2942 colour by RNA Helices not enabled when user created
2943 annotation added to alignment
2946 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2947 Jalview icon not shown on dock in Mountain Lion/Webstart
2949 </ul> <em>Applet Known Issues</em>
2952 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2953 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2956 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2957 Jalview and Jmol example not compatible with IE9
2960 <li>Sort by annotation score doesn't reverse order
2966 <td><div align="center">
2967 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2970 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2973 <li>Internationalisation of user interface (usually
2974 called i18n support) and translation for Spanish locale</li>
2975 <li>Define/Undefine group on current selection with
2976 Ctrl-G/Shift Ctrl-G</li>
2977 <li>Improved group creation/removal options in
2978 alignment/sequence Popup menu</li>
2979 <li>Sensible precision for symbol distribution
2980 percentages shown in logo tooltip.</li>
2981 <li>Annotation panel height set according to amount of
2982 annotation when alignment first opened</li>
2983 </ul> <em>Application</em>
2985 <li>Interactive consensus RNA secondary structure
2986 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2987 <li>Select columns containing particular features from
2988 Feature Settings dialog</li>
2989 <li>View all 'representative' PDB structures for selected
2991 <li>Update Jalview project format:
2993 <li>New file extension for Jalview projects '.jvp'</li>
2994 <li>Preserve sequence and annotation dataset (to
2995 store secondary structure annotation,etc)</li>
2996 <li>Per group and alignment annotation and RNA helix
3000 <li>New similarity measures for PCA and Tree calculation
3002 <li>Experimental support for retrieval and viewing of
3003 flanking regions for an alignment</li>
3007 <!-- issues resolved --> <em>Application</em>
3009 <li>logo keeps spinning and status remains at queued or
3010 running after job is cancelled</li>
3011 <li>cannot export features from alignments imported from
3012 Jalview/VAMSAS projects</li>
3013 <li>Buggy slider for web service parameters that take
3015 <li>Newly created RNA secondary structure line doesn't
3016 have 'display all symbols' flag set</li>
3017 <li>T-COFFEE alignment score shading scheme and other
3018 annotation shading not saved in Jalview project</li>
3019 <li>Local file cannot be loaded in freshly downloaded
3021 <li>Jalview icon not shown on dock in Mountain
3023 <li>Load file from desktop file browser fails</li>
3024 <li>Occasional NPE thrown when calculating large trees</li>
3025 <li>Cannot reorder or slide sequences after dragging an
3026 alignment onto desktop</li>
3027 <li>Colour by annotation dialog throws NPE after using
3028 'extract scores' function</li>
3029 <li>Loading/cut'n'pasting an empty file leads to a grey
3030 alignment window</li>
3031 <li>Disorder thresholds rendered incorrectly after
3032 performing IUPred disorder prediction</li>
3033 <li>Multiple group annotated consensus rows shown when
3034 changing 'normalise logo' display setting</li>
3035 <li>Find shows blank dialog after 'finished searching' if
3036 nothing matches query</li>
3037 <li>Null Pointer Exceptions raised when sorting by
3038 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3040 <li>Errors in Jmol console when structures in alignment
3041 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3043 <li>Not all working JABAWS services are shown in
3045 <li>JAVAWS version of Jalview fails to launch with
3046 'invalid literal/length code'</li>
3047 <li>Annotation/RNA Helix colourschemes cannot be applied
3048 to alignment with groups (actually fixed in 2.8.0b1)</li>
3049 <li>RNA Helices and T-Coffee Scores available as default
3052 </ul> <em>Applet</em>
3054 <li>Remove group option is shown even when selection is
3056 <li>Apply to all groups ticked but colourscheme changes
3057 don't affect groups</li>
3058 <li>Documented RNA Helices and T-Coffee Scores as valid
3059 colourscheme name</li>
3060 <li>Annotation labels drawn on sequence IDs when
3061 Annotation panel is not displayed</li>
3062 <li>Increased font size for dropdown menus on OSX and
3063 embedded windows</li>
3064 </ul> <em>Other</em>
3066 <li>Consensus sequence for alignments/groups with a
3067 single sequence were not calculated</li>
3068 <li>annotation files that contain only groups imported as
3069 annotation and junk sequences</li>
3070 <li>Fasta files with sequences containing '*' incorrectly
3071 recognised as PFAM or BLC</li>
3072 <li>conservation/PID slider apply all groups option
3073 doesn't affect background (2.8.0b1)
3075 <li>redundancy highlighting is erratic at 0% and 100%</li>
3076 <li>Remove gapped columns fails for sequences with ragged
3078 <li>AMSA annotation row with leading spaces is not
3079 registered correctly on import</li>
3080 <li>Jalview crashes when selecting PCA analysis for
3081 certain alignments</li>
3082 <li>Opening the colour by annotation dialog for an
3083 existing annotation based 'use original colours'
3084 colourscheme loses original colours setting</li>
3089 <td><div align="center">
3090 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3091 <em>30/1/2014</em></strong>
3095 <li>Trusted certificates for JalviewLite applet and
3096 Jalview Desktop application<br />Certificate was donated by
3097 <a href="https://www.certum.eu">Certum</a> to the Jalview
3098 open source project).
3100 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3101 <li>Output in Stockholm format</li>
3102 <li>Allow import of data from gzipped files</li>
3103 <li>Export/import group and sequence associated line
3104 graph thresholds</li>
3105 <li>Nucleotide substitution matrix that supports RNA and
3106 ambiguity codes</li>
3107 <li>Allow disorder predictions to be made on the current
3108 selection (or visible selection) in the same way that JPred
3110 <li>Groovy scripting for headless Jalview operation</li>
3111 </ul> <em>Other improvements</em>
3113 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3114 <li>COMBINE statement uses current SEQUENCE_REF and
3115 GROUP_REF scope to group annotation rows</li>
3116 <li>Support '' style escaping of quotes in Newick
3118 <li>Group options for JABAWS service by command line name</li>
3119 <li>Empty tooltip shown for JABA service options with a
3120 link but no description</li>
3121 <li>Select primary source when selecting authority in
3122 database fetcher GUI</li>
3123 <li>Add .mfa to FASTA file extensions recognised by
3125 <li>Annotation label tooltip text wrap</li>
3130 <li>Slow scrolling when lots of annotation rows are
3132 <li>Lots of NPE (and slowness) after creating RNA
3133 secondary structure annotation line</li>
3134 <li>Sequence database accessions not imported when
3135 fetching alignments from Rfam</li>
3136 <li>Incorrect SHMR submission for sequences with
3138 <li>View all structures does not always superpose
3140 <li>Option widgets in service parameters not updated to
3141 reflect user or preset settings</li>
3142 <li>Null pointer exceptions for some services without
3143 presets or adjustable parameters</li>
3144 <li>Discover PDB IDs entry in structure menu doesn't
3145 discover PDB xRefs</li>
3146 <li>Exception encountered while trying to retrieve
3147 features with DAS</li>
3148 <li>Lowest value in annotation row isn't coloured
3149 when colour by annotation (per sequence) is coloured</li>
3150 <li>Keyboard mode P jumps to start of gapped region when
3151 residue follows a gap</li>
3152 <li>Jalview appears to hang importing an alignment with
3153 Wrap as default or after enabling Wrap</li>
3154 <li>'Right click to add annotations' message
3155 shown in wrap mode when no annotations present</li>
3156 <li>Disorder predictions fail with NPE if no automatic
3157 annotation already exists on alignment</li>
3158 <li>oninit javascript function should be called after
3159 initialisation completes</li>
3160 <li>Remove redundancy after disorder prediction corrupts
3161 alignment window display</li>
3162 <li>Example annotation file in documentation is invalid</li>
3163 <li>Grouped line graph annotation rows are not exported
3164 to annotation file</li>
3165 <li>Multi-harmony analysis cannot be run when only two
3167 <li>Cannot create multiple groups of line graphs with
3168 several 'combine' statements in annotation file</li>
3169 <li>Pressing return several times causes Number Format
3170 exceptions in keyboard mode</li>
3171 <li>Multi-harmony (SHMMR) method doesn't submit
3172 correct partitions for input data</li>
3173 <li>Translation from DNA to Amino Acids fails</li>
3174 <li>Jalview fail to load newick tree with quoted label</li>
3175 <li>--headless flag isn't understood</li>
3176 <li>ClassCastException when generating EPS in headless
3178 <li>Adjusting sequence-associated shading threshold only
3179 changes one row's threshold</li>
3180 <li>Preferences and Feature settings panel panel
3181 doesn't open</li>
3182 <li>hide consensus histogram also hides conservation and
3183 quality histograms</li>
3188 <td><div align="center">
3189 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3191 <td><em>Application</em>
3193 <li>Support for JABAWS 2.0 Services (AACon alignment
3194 conservation, protein disorder and Clustal Omega)</li>
3195 <li>JABAWS server status indicator in Web Services
3197 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3198 in Jalview alignment window</li>
3199 <li>Updated Jalview build and deploy framework for OSX
3200 mountain lion, windows 7, and 8</li>
3201 <li>Nucleotide substitution matrix for PCA that supports
3202 RNA and ambiguity codes</li>
3204 <li>Improved sequence database retrieval GUI</li>
3205 <li>Support fetching and database reference look up
3206 against multiple DAS sources (Fetch all from in 'fetch db
3208 <li>Jalview project improvements
3210 <li>Store and retrieve the 'belowAlignment'
3211 flag for annotation</li>
3212 <li>calcId attribute to group annotation rows on the
3214 <li>Store AACon calculation settings for a view in
3215 Jalview project</li>
3219 <li>horizontal scrolling gesture support</li>
3220 <li>Visual progress indicator when PCA calculation is
3222 <li>Simpler JABA web services menus</li>
3223 <li>visual indication that web service results are still
3224 being retrieved from server</li>
3225 <li>Serialise the dialogs that are shown when Jalview
3226 starts up for first time</li>
3227 <li>Jalview user agent string for interacting with HTTP
3229 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3231 <li>Examples directory and Groovy library included in
3232 InstallAnywhere distribution</li>
3233 </ul> <em>Applet</em>
3235 <li>RNA alignment and secondary structure annotation
3236 visualization applet example</li>
3237 </ul> <em>General</em>
3239 <li>Normalise option for consensus sequence logo</li>
3240 <li>Reset button in PCA window to return dimensions to
3242 <li>Allow seqspace or Jalview variant of alignment PCA
3244 <li>PCA with either nucleic acid and protein substitution
3246 <li>Allow windows containing HTML reports to be exported
3248 <li>Interactive display and editing of RNA secondary
3249 structure contacts</li>
3250 <li>RNA Helix Alignment Colouring</li>
3251 <li>RNA base pair logo consensus</li>
3252 <li>Parse sequence associated secondary structure
3253 information in Stockholm files</li>
3254 <li>HTML Export database accessions and annotation
3255 information presented in tooltip for sequences</li>
3256 <li>Import secondary structure from LOCARNA clustalw
3257 style RNA alignment files</li>
3258 <li>import and visualise T-COFFEE quality scores for an
3260 <li>'colour by annotation' per sequence option to
3261 shade each sequence according to its associated alignment
3263 <li>New Jalview Logo</li>
3264 </ul> <em>Documentation and Development</em>
3266 <li>documentation for score matrices used in Jalview</li>
3267 <li>New Website!</li>
3269 <td><em>Application</em>
3271 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3272 wsdbfetch REST service</li>
3273 <li>Stop windows being moved outside desktop on OSX</li>
3274 <li>Filetype associations not installed for webstart
3276 <li>Jalview does not always retrieve progress of a JABAWS
3277 job execution in full once it is complete</li>
3278 <li>revise SHMR RSBS definition to ensure alignment is
3279 uploaded via ali_file parameter</li>
3280 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3281 <li>View all structures superposed fails with exception</li>
3282 <li>Jnet job queues forever if a very short sequence is
3283 submitted for prediction</li>
3284 <li>Cut and paste menu not opened when mouse clicked on
3286 <li>Putting fractional value into integer text box in
3287 alignment parameter dialog causes Jalview to hang</li>
3288 <li>Structure view highlighting doesn't work on
3290 <li>View all structures fails with exception shown in
3292 <li>Characters in filename associated with PDBEntry not
3293 escaped in a platform independent way</li>
3294 <li>Jalview desktop fails to launch with exception when
3296 <li>Tree calculation reports 'you must have 2 or more
3297 sequences selected' when selection is empty</li>
3298 <li>Jalview desktop fails to launch with jar signature
3299 failure when java web start temporary file caching is
3301 <li>DAS Sequence retrieval with range qualification
3302 results in sequence xref which includes range qualification</li>
3303 <li>Errors during processing of command line arguments
3304 cause progress bar (JAL-898) to be removed</li>
3305 <li>Replace comma for semi-colon option not disabled for
3306 DAS sources in sequence fetcher</li>
3307 <li>Cannot close news reader when JABAWS server warning
3308 dialog is shown</li>
3309 <li>Option widgets not updated to reflect user settings</li>
3310 <li>Edited sequence not submitted to web service</li>
3311 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3312 <li>InstallAnywhere installer doesn't unpack and run
3313 on OSX Mountain Lion</li>
3314 <li>Annotation panel not given a scroll bar when
3315 sequences with alignment annotation are pasted into the
3317 <li>Sequence associated annotation rows not associated
3318 when loaded from Jalview project</li>
3319 <li>Browser launch fails with NPE on java 1.7</li>
3320 <li>JABAWS alignment marked as finished when job was
3321 cancelled or job failed due to invalid input</li>
3322 <li>NPE with v2.7 example when clicking on Tree
3323 associated with all views</li>
3324 <li>Exceptions when copy/paste sequences with grouped
3325 annotation rows to new window</li>
3326 </ul> <em>Applet</em>
3328 <li>Sequence features are momentarily displayed before
3329 they are hidden using hidefeaturegroups applet parameter</li>
3330 <li>loading features via javascript API automatically
3331 enables feature display</li>
3332 <li>scrollToColumnIn javascript API method doesn't
3334 </ul> <em>General</em>
3336 <li>Redundancy removal fails for rna alignment</li>
3337 <li>PCA calculation fails when sequence has been selected
3338 and then deselected</li>
3339 <li>PCA window shows grey box when first opened on OSX</li>
3340 <li>Letters coloured pink in sequence logo when alignment
3341 coloured with clustalx</li>
3342 <li>Choosing fonts without letter symbols defined causes
3343 exceptions and redraw errors</li>
3344 <li>Initial PCA plot view is not same as manually
3345 reconfigured view</li>
3346 <li>Grouped annotation graph label has incorrect line
3348 <li>Grouped annotation graph label display is corrupted
3349 for lots of labels</li>
3354 <div align="center">
3355 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3358 <td><em>Application</em>
3360 <li>Jalview Desktop News Reader</li>
3361 <li>Tweaked default layout of web services menu</li>
3362 <li>View/alignment association menu to enable user to
3363 easily specify which alignment a multi-structure view takes
3364 its colours/correspondences from</li>
3365 <li>Allow properties file location to be specified as URL</li>
3366 <li>Extend Jalview project to preserve associations
3367 between many alignment views and a single Jmol display</li>
3368 <li>Store annotation row height in Jalview project file</li>
3369 <li>Annotation row column label formatting attributes
3370 stored in project file</li>
3371 <li>Annotation row order for auto-calculated annotation
3372 rows preserved in Jalview project file</li>
3373 <li>Visual progress indication when Jalview state is
3374 saved using Desktop window menu</li>
3375 <li>Visual indication that command line arguments are
3376 still being processed</li>
3377 <li>Groovy script execution from URL</li>
3378 <li>Colour by annotation default min and max colours in
3380 <li>Automatically associate PDB files dragged onto an
3381 alignment with sequences that have high similarity and
3383 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3384 <li>'view structures' option to open many
3385 structures in same window</li>
3386 <li>Sort associated views menu option for tree panel</li>
3387 <li>Group all JABA and non-JABA services for a particular
3388 analysis function in its own submenu</li>
3389 </ul> <em>Applet</em>
3391 <li>Userdefined and autogenerated annotation rows for
3393 <li>Adjustment of alignment annotation pane height</li>
3394 <li>Annotation scrollbar for annotation panel</li>
3395 <li>Drag to reorder annotation rows in annotation panel</li>
3396 <li>'automaticScrolling' parameter</li>
3397 <li>Allow sequences with partial ID string matches to be
3398 annotated from GFF/Jalview features files</li>
3399 <li>Sequence logo annotation row in applet</li>
3400 <li>Absolute paths relative to host server in applet
3401 parameters are treated as such</li>
3402 <li>New in the JalviewLite javascript API:
3404 <li>JalviewLite.js javascript library</li>
3405 <li>Javascript callbacks for
3407 <li>Applet initialisation</li>
3408 <li>Sequence/alignment mouse-overs and selections</li>
3411 <li>scrollTo row and column alignment scrolling
3413 <li>Select sequence/alignment regions from javascript</li>
3414 <li>javascript structure viewer harness to pass
3415 messages between Jmol and Jalview when running as
3416 distinct applets</li>
3417 <li>sortBy method</li>
3418 <li>Set of applet and application examples shipped
3419 with documentation</li>
3420 <li>New example to demonstrate JalviewLite and Jmol
3421 javascript message exchange</li>
3423 </ul> <em>General</em>
3425 <li>Enable Jmol displays to be associated with multiple
3426 multiple alignments</li>
3427 <li>Option to automatically sort alignment with new tree</li>
3428 <li>User configurable link to enable redirects to a
3429 www.Jalview.org mirror</li>
3430 <li>Jmol colours option for Jmol displays</li>
3431 <li>Configurable newline string when writing alignment
3432 and other flat files</li>
3433 <li>Allow alignment annotation description lines to
3434 contain html tags</li>
3435 </ul> <em>Documentation and Development</em>
3437 <li>Add groovy test harness for bulk load testing to
3439 <li>Groovy script to load and align a set of sequences
3440 using a web service before displaying the result in the
3441 Jalview desktop</li>
3442 <li>Restructured javascript and applet api documentation</li>
3443 <li>Ant target to publish example html files with applet
3445 <li>Netbeans project for building Jalview from source</li>
3446 <li>ant task to create online javadoc for Jalview source</li>
3448 <td><em>Application</em>
3450 <li>User defined colourscheme throws exception when
3451 current built in colourscheme is saved as new scheme</li>
3452 <li>AlignFrame->Save in application pops up save
3453 dialog for valid filename/format</li>
3454 <li>Cannot view associated structure for UniProt sequence</li>
3455 <li>PDB file association breaks for UniProt sequence
3457 <li>Associate PDB from file dialog does not tell you
3458 which sequence is to be associated with the file</li>
3459 <li>Find All raises null pointer exception when query
3460 only matches sequence IDs</li>
3461 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3462 <li>Jalview project with Jmol views created with Jalview
3463 2.4 cannot be loaded</li>
3464 <li>Filetype associations not installed for webstart
3466 <li>Two or more chains in a single PDB file associated
3467 with sequences in different alignments do not get coloured
3468 by their associated sequence</li>
3469 <li>Visibility status of autocalculated annotation row
3470 not preserved when project is loaded</li>
3471 <li>Annotation row height and visibility attributes not
3472 stored in Jalview project</li>
3473 <li>Tree bootstraps are not preserved when saved as a
3474 Jalview project</li>
3475 <li>Envision2 workflow tooltips are corrupted</li>
3476 <li>Enabling show group conservation also enables colour
3477 by conservation</li>
3478 <li>Duplicate group associated conservation or consensus
3479 created on new view</li>
3480 <li>Annotation scrollbar not displayed after 'show
3481 all hidden annotation rows' option selected</li>
3482 <li>Alignment quality not updated after alignment
3483 annotation row is hidden then shown</li>
3484 <li>Preserve colouring of structures coloured by
3485 sequences in pre Jalview 2.7 projects</li>
3486 <li>Web service job parameter dialog is not laid out
3488 <li>Web services menu not refreshed after 'reset
3489 services' button is pressed in preferences</li>
3490 <li>Annotation off by one in Jalview v2_3 example project</li>
3491 <li>Structures imported from file and saved in project
3492 get name like jalview_pdb1234.txt when reloaded</li>
3493 <li>Jalview does not always retrieve progress of a JABAWS
3494 job execution in full once it is complete</li>
3495 </ul> <em>Applet</em>
3497 <li>Alignment height set incorrectly when lots of
3498 annotation rows are displayed</li>
3499 <li>Relative URLs in feature HTML text not resolved to
3501 <li>View follows highlighting does not work for positions
3503 <li><= shown as = in tooltip</li>
3504 <li>Export features raises exception when no features
3506 <li>Separator string used for serialising lists of IDs
3507 for javascript api is modified when separator string
3508 provided as parameter</li>
3509 <li>Null pointer exception when selecting tree leaves for
3510 alignment with no existing selection</li>
3511 <li>Relative URLs for datasources assumed to be relative
3512 to applet's codebase</li>
3513 <li>Status bar not updated after finished searching and
3514 search wraps around to first result</li>
3515 <li>StructureSelectionManager instance shared between
3516 several Jalview applets causes race conditions and memory
3518 <li>Hover tooltip and mouseover of position on structure
3519 not sent from Jmol in applet</li>
3520 <li>Certain sequences of javascript method calls to
3521 applet API fatally hang browser</li>
3522 </ul> <em>General</em>
3524 <li>View follows structure mouseover scrolls beyond
3525 position with wrapped view and hidden regions</li>
3526 <li>Find sequence position moves to wrong residue
3527 with/without hidden columns</li>
3528 <li>Sequence length given in alignment properties window
3530 <li>InvalidNumberFormat exceptions thrown when trying to
3531 import PDB like structure files</li>
3532 <li>Positional search results are only highlighted
3533 between user-supplied sequence start/end bounds</li>
3534 <li>End attribute of sequence is not validated</li>
3535 <li>Find dialog only finds first sequence containing a
3536 given sequence position</li>
3537 <li>Sequence numbering not preserved in MSF alignment
3539 <li>Jalview PDB file reader does not extract sequence
3540 from nucleotide chains correctly</li>
3541 <li>Structure colours not updated when tree partition
3542 changed in alignment</li>
3543 <li>Sequence associated secondary structure not correctly
3544 parsed in interleaved stockholm</li>
3545 <li>Colour by annotation dialog does not restore current
3547 <li>Hiding (nearly) all sequences doesn't work
3549 <li>Sequences containing lowercase letters are not
3550 properly associated with their pdb files</li>
3551 </ul> <em>Documentation and Development</em>
3553 <li>schemas/JalviewWsParamSet.xsd corrupted by
3554 ApplyCopyright tool</li>
3559 <div align="center">
3560 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3563 <td><em>Application</em>
3565 <li>New warning dialog when the Jalview Desktop cannot
3566 contact web services</li>
3567 <li>JABA service parameters for a preset are shown in
3568 service job window</li>
3569 <li>JABA Service menu entries reworded</li>
3573 <li>Modeller PIR IO broken - cannot correctly import a
3574 pir file emitted by Jalview</li>
3575 <li>Existing feature settings transferred to new
3576 alignment view created from cut'n'paste</li>
3577 <li>Improved test for mixed amino/nucleotide chains when
3578 parsing PDB files</li>
3579 <li>Consensus and conservation annotation rows
3580 occasionally become blank for all new windows</li>
3581 <li>Exception raised when right clicking above sequences
3582 in wrapped view mode</li>
3583 </ul> <em>Application</em>
3585 <li>multiple multiply aligned structure views cause cpu
3586 usage to hit 100% and computer to hang</li>
3587 <li>Web Service parameter layout breaks for long user
3588 parameter names</li>
3589 <li>Jaba service discovery hangs desktop if Jaba server
3596 <div align="center">
3597 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3600 <td><em>Application</em>
3602 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3603 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3606 <li>Web Services preference tab</li>
3607 <li>Analysis parameters dialog box and user defined
3609 <li>Improved speed and layout of Envision2 service menu</li>
3610 <li>Superpose structures using associated sequence
3612 <li>Export coordinates and projection as CSV from PCA
3614 </ul> <em>Applet</em>
3616 <li>enable javascript: execution by the applet via the
3617 link out mechanism</li>
3618 </ul> <em>Other</em>
3620 <li>Updated the Jmol Jalview interface to work with Jmol
3622 <li>The Jalview Desktop and JalviewLite applet now
3623 require Java 1.5</li>
3624 <li>Allow Jalview feature colour specification for GFF
3625 sequence annotation files</li>
3626 <li>New 'colour by label' keword in Jalview feature file
3627 type colour specification</li>
3628 <li>New Jalview Desktop Groovy API method that allows a
3629 script to check if it being run in an interactive session or
3630 in a batch operation from the Jalview command line</li>
3634 <li>clustalx colourscheme colours Ds preferentially when
3635 both D+E are present in over 50% of the column</li>
3636 </ul> <em>Application</em>
3638 <li>typo in AlignmentFrame->View->Hide->all but
3639 selected Regions menu item</li>
3640 <li>sequence fetcher replaces ',' for ';' when the ',' is
3641 part of a valid accession ID</li>
3642 <li>fatal OOM if object retrieved by sequence fetcher
3643 runs out of memory</li>
3644 <li>unhandled Out of Memory Error when viewing pca
3645 analysis results</li>
3646 <li>InstallAnywhere builds fail to launch on OS X java
3647 10.5 update 4 (due to apple Java 1.6 update)</li>
3648 <li>Installanywhere Jalview silently fails to launch</li>
3649 </ul> <em>Applet</em>
3651 <li>Jalview.getFeatureGroups() raises an
3652 ArrayIndexOutOfBoundsException if no feature groups are
3659 <div align="center">
3660 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3666 <li>Alignment prettyprinter doesn't cope with long
3668 <li>clustalx colourscheme colours Ds preferentially when
3669 both D+E are present in over 50% of the column</li>
3670 <li>nucleic acid structures retrieved from PDB do not
3671 import correctly</li>
3672 <li>More columns get selected than were clicked on when a
3673 number of columns are hidden</li>
3674 <li>annotation label popup menu not providing correct
3675 add/hide/show options when rows are hidden or none are
3677 <li>Stockholm format shown in list of readable formats,
3678 and parser copes better with alignments from RFAM.</li>
3679 <li>CSV output of consensus only includes the percentage
3680 of all symbols if sequence logo display is enabled</li>
3682 </ul> <em>Applet</em>
3684 <li>annotation panel disappears when annotation is
3686 </ul> <em>Application</em>
3688 <li>Alignment view not redrawn properly when new
3689 alignment opened where annotation panel is visible but no
3690 annotations are present on alignment</li>
3691 <li>pasted region containing hidden columns is
3692 incorrectly displayed in new alignment window</li>
3693 <li>Jalview slow to complete operations when stdout is
3694 flooded (fix is to close the Jalview console)</li>
3695 <li>typo in AlignmentFrame->View->Hide->all but
3696 selected Rregions menu item.</li>
3697 <li>inconsistent group submenu and Format submenu entry
3698 'Un' or 'Non'conserved</li>
3699 <li>Sequence feature settings are being shared by
3700 multiple distinct alignments</li>
3701 <li>group annotation not recreated when tree partition is
3703 <li>double click on group annotation to select sequences
3704 does not propagate to associated trees</li>
3705 <li>Mac OSX specific issues:
3707 <li>exception raised when mouse clicked on desktop
3708 window background</li>
3709 <li>Desktop menu placed on menu bar and application
3710 name set correctly</li>
3711 <li>sequence feature settings not wide enough for the
3712 save feature colourscheme button</li>
3721 <div align="center">
3722 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3725 <td><em>New Capabilities</em>
3727 <li>URL links generated from description line for
3728 regular-expression based URL links (applet and application)
3730 <li>Non-positional feature URL links are shown in link
3732 <li>Linked viewing of nucleic acid sequences and
3734 <li>Automatic Scrolling option in View menu to display
3735 the currently highlighted region of an alignment.</li>
3736 <li>Order an alignment by sequence length, or using the
3737 average score or total feature count for each sequence.</li>
3738 <li>Shading features by score or associated description</li>
3739 <li>Subdivide alignment and groups based on identity of
3740 selected subsequence (Make Groups from Selection).</li>
3741 <li>New hide/show options including Shift+Control+H to
3742 hide everything but the currently selected region.</li>
3743 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3744 </ul> <em>Application</em>
3746 <li>Fetch DB References capabilities and UI expanded to
3747 support retrieval from DAS sequence sources</li>
3748 <li>Local DAS Sequence sources can be added via the
3749 command line or via the Add local source dialog box.</li>
3750 <li>DAS Dbref and DbxRef feature types are parsed as
3751 database references and protein_name is parsed as
3752 description line (BioSapiens terms).</li>
3753 <li>Enable or disable non-positional feature and database
3754 references in sequence ID tooltip from View menu in
3756 <!-- <li>New hidden columns and rows and representatives capabilities
3757 in annotations file (in progress - not yet fully implemented)</li> -->
3758 <li>Group-associated consensus, sequence logos and
3759 conservation plots</li>
3760 <li>Symbol distributions for each column can be exported
3761 and visualized as sequence logos</li>
3762 <li>Optionally scale multi-character column labels to fit
3763 within each column of annotation row<!-- todo for applet -->
3765 <li>Optional automatic sort of associated alignment view
3766 when a new tree is opened.</li>
3767 <li>Jalview Java Console</li>
3768 <li>Better placement of desktop window when moving
3769 between different screens.</li>
3770 <li>New preference items for sequence ID tooltip and
3771 consensus annotation</li>
3772 <li>Client to submit sequences and IDs to Envision2
3774 <li><em>Vamsas Capabilities</em>
3776 <li>Improved VAMSAS synchronization (Jalview archive
3777 used to preserve views, structures, and tree display
3779 <li>Import of vamsas documents from disk or URL via
3781 <li>Sharing of selected regions between views and
3782 with other VAMSAS applications (Experimental feature!)</li>
3783 <li>Updated API to VAMSAS version 0.2</li>
3785 </ul> <em>Applet</em>
3787 <li>Middle button resizes annotation row height</li>
3790 <li>sortByTree (true/false) - automatically sort the
3791 associated alignment view by the tree when a new tree is
3793 <li>showTreeBootstraps (true/false) - show or hide
3794 branch bootstraps (default is to show them if available)</li>
3795 <li>showTreeDistances (true/false) - show or hide
3796 branch lengths (default is to show them if available)</li>
3797 <li>showUnlinkedTreeNodes (true/false) - indicate if
3798 unassociated nodes should be highlighted in the tree
3800 <li>heightScale and widthScale (1.0 or more) -
3801 increase the height or width of a cell in the alignment
3802 grid relative to the current font size.</li>
3805 <li>Non-positional features displayed in sequence ID
3807 </ul> <em>Other</em>
3809 <li>Features format: graduated colour definitions and
3810 specification of feature scores</li>
3811 <li>Alignment Annotations format: new keywords for group
3812 associated annotation (GROUP_REF) and annotation row display
3813 properties (ROW_PROPERTIES)</li>
3814 <li>XML formats extended to support graduated feature
3815 colourschemes, group associated annotation, and profile
3816 visualization settings.</li></td>
3819 <li>Source field in GFF files parsed as feature source
3820 rather than description</li>
3821 <li>Non-positional features are now included in sequence
3822 feature and gff files (controlled via non-positional feature
3823 visibility in tooltip).</li>
3824 <li>URL links generated for all feature links (bugfix)</li>
3825 <li>Added URL embedding instructions to features file
3827 <li>Codons containing ambiguous nucleotides translated as
3828 'X' in peptide product</li>
3829 <li>Match case switch in find dialog box works for both
3830 sequence ID and sequence string and query strings do not
3831 have to be in upper case to match case-insensitively.</li>
3832 <li>AMSA files only contain first column of
3833 multi-character column annotation labels</li>
3834 <li>Jalview Annotation File generation/parsing consistent
3835 with documentation (e.g. Stockholm annotation can be
3836 exported and re-imported)</li>
3837 <li>PDB files without embedded PDB IDs given a friendly
3839 <li>Find incrementally searches ID string matches as well
3840 as subsequence matches, and correctly reports total number
3844 <li>Better handling of exceptions during sequence
3846 <li>Dasobert generated non-positional feature URL
3847 link text excludes the start_end suffix</li>
3848 <li>DAS feature and source retrieval buttons disabled
3849 when fetch or registry operations in progress.</li>
3850 <li>PDB files retrieved from URLs are cached properly</li>
3851 <li>Sequence description lines properly shared via
3853 <li>Sequence fetcher fetches multiple records for all
3855 <li>Ensured that command line das feature retrieval
3856 completes before alignment figures are generated.</li>
3857 <li>Reduced time taken when opening file browser for
3859 <li>isAligned check prior to calculating tree, PCA or
3860 submitting an MSA to JNet now excludes hidden sequences.</li>
3861 <li>User defined group colours properly recovered
3862 from Jalview projects.</li>
3871 <div align="center">
3872 <strong>2.4.0.b2</strong><br> 28/10/2009
3877 <li>Experimental support for google analytics usage
3879 <li>Jalview privacy settings (user preferences and docs).</li>
3884 <li>Race condition in applet preventing startup in
3886 <li>Exception when feature created from selection beyond
3887 length of sequence.</li>
3888 <li>Allow synthetic PDB files to be imported gracefully</li>
3889 <li>Sequence associated annotation rows associate with
3890 all sequences with a given id</li>
3891 <li>Find function matches case-insensitively for sequence
3892 ID string searches</li>
3893 <li>Non-standard characters do not cause pairwise
3894 alignment to fail with exception</li>
3895 </ul> <em>Application Issues</em>
3897 <li>Sequences are now validated against EMBL database</li>
3898 <li>Sequence fetcher fetches multiple records for all
3900 </ul> <em>InstallAnywhere Issues</em>
3902 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3903 issue with installAnywhere mechanism)</li>
3904 <li>Command line launching of JARs from InstallAnywhere
3905 version (java class versioning error fixed)</li>
3912 <div align="center">
3913 <strong>2.4</strong><br> 27/8/2008
3916 <td><em>User Interface</em>
3918 <li>Linked highlighting of codon and amino acid from
3919 translation and protein products</li>
3920 <li>Linked highlighting of structure associated with
3921 residue mapping to codon position</li>
3922 <li>Sequence Fetcher provides example accession numbers
3923 and 'clear' button</li>
3924 <li>MemoryMonitor added as an option under Desktop's
3926 <li>Extract score function to parse whitespace separated
3927 numeric data in description line</li>
3928 <li>Column labels in alignment annotation can be centred.</li>
3929 <li>Tooltip for sequence associated annotation give name
3931 </ul> <em>Web Services and URL fetching</em>
3933 <li>JPred3 web service</li>
3934 <li>Prototype sequence search client (no public services
3936 <li>Fetch either seed alignment or full alignment from
3938 <li>URL Links created for matching database cross
3939 references as well as sequence ID</li>
3940 <li>URL Links can be created using regular-expressions</li>
3941 </ul> <em>Sequence Database Connectivity</em>
3943 <li>Retrieval of cross-referenced sequences from other
3945 <li>Generalised database reference retrieval and
3946 validation to all fetchable databases</li>
3947 <li>Fetch sequences from DAS sources supporting the
3948 sequence command</li>
3949 </ul> <em>Import and Export</em>
3950 <li>export annotation rows as CSV for spreadsheet import</li>
3951 <li>Jalview projects record alignment dataset associations,
3952 EMBL products, and cDNA sequence mappings</li>
3953 <li>Sequence Group colour can be specified in Annotation
3955 <li>Ad-hoc colouring of group in Annotation File using RGB
3956 triplet as name of colourscheme</li>
3957 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3959 <li>treenode binding for VAMSAS tree exchange</li>
3960 <li>local editing and update of sequences in VAMSAS
3961 alignments (experimental)</li>
3962 <li>Create new or select existing session to join</li>
3963 <li>load and save of vamsas documents</li>
3964 </ul> <em>Application command line</em>
3966 <li>-tree parameter to open trees (introduced for passing
3968 <li>-fetchfrom command line argument to specify nicknames
3969 of DAS servers to query for alignment features</li>
3970 <li>-dasserver command line argument to add new servers
3971 that are also automatically queried for features</li>
3972 <li>-groovy command line argument executes a given groovy
3973 script after all input data has been loaded and parsed</li>
3974 </ul> <em>Applet-Application data exchange</em>
3976 <li>Trees passed as applet parameters can be passed to
3977 application (when using "View in full
3978 application")</li>
3979 </ul> <em>Applet Parameters</em>
3981 <li>feature group display control parameter</li>
3982 <li>debug parameter</li>
3983 <li>showbutton parameter</li>
3984 </ul> <em>Applet API methods</em>
3986 <li>newView public method</li>
3987 <li>Window (current view) specific get/set public methods</li>
3988 <li>Feature display control methods</li>
3989 <li>get list of currently selected sequences</li>
3990 </ul> <em>New Jalview distribution features</em>
3992 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3993 <li>RELEASE file gives build properties for the latest
3994 Jalview release.</li>
3995 <li>Java 1.1 Applet build made easier and donotobfuscate
3996 property controls execution of obfuscator</li>
3997 <li>Build target for generating source distribution</li>
3998 <li>Debug flag for javacc</li>
3999 <li>.jalview_properties file is documented (slightly) in
4000 jalview.bin.Cache</li>
4001 <li>Continuous Build Integration for stable and
4002 development version of Application, Applet and source
4007 <li>selected region output includes visible annotations
4008 (for certain formats)</li>
4009 <li>edit label/displaychar contains existing label/char
4011 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4012 <li>shorter peptide product names from EMBL records</li>
4013 <li>Newick string generator makes compact representations</li>
4014 <li>bootstrap values parsed correctly for tree files with
4016 <li>pathological filechooser bug avoided by not allowing
4017 filenames containing a ':'</li>
4018 <li>Fixed exception when parsing GFF files containing
4019 global sequence features</li>
4020 <li>Alignment datasets are finalized only when number of
4021 references from alignment sequences goes to zero</li>
4022 <li>Close of tree branch colour box without colour
4023 selection causes cascading exceptions</li>
4024 <li>occasional negative imgwidth exceptions</li>
4025 <li>better reporting of non-fatal warnings to user when
4026 file parsing fails.</li>
4027 <li>Save works when Jalview project is default format</li>
4028 <li>Save as dialog opened if current alignment format is
4029 not a valid output format</li>
4030 <li>UniProt canonical names introduced for both das and
4032 <li>Histidine should be midblue (not pink!) in Zappo</li>
4033 <li>error messages passed up and output when data read
4035 <li>edit undo recovers previous dataset sequence when
4036 sequence is edited</li>
4037 <li>allow PDB files without pdb ID HEADER lines (like
4038 those generated by MODELLER) to be read in properly</li>
4039 <li>allow reading of JPred concise files as a normal
4041 <li>Stockholm annotation parsing and alignment properties
4042 import fixed for PFAM records</li>
4043 <li>Structure view windows have correct name in Desktop
4045 <li>annotation consisting of sequence associated scores
4046 can be read and written correctly to annotation file</li>
4047 <li>Aligned cDNA translation to aligned peptide works
4049 <li>Fixed display of hidden sequence markers and
4050 non-italic font for representatives in Applet</li>
4051 <li>Applet Menus are always embedded in applet window on
4053 <li>Newly shown features appear at top of stack (in
4055 <li>Annotations added via parameter not drawn properly
4056 due to null pointer exceptions</li>
4057 <li>Secondary structure lines are drawn starting from
4058 first column of alignment</li>
4059 <li>UniProt XML import updated for new schema release in
4061 <li>Sequence feature to sequence ID match for Features
4062 file is case-insensitive</li>
4063 <li>Sequence features read from Features file appended to
4064 all sequences with matching IDs</li>
4065 <li>PDB structure coloured correctly for associated views
4066 containing a sub-sequence</li>
4067 <li>PDB files can be retrieved by applet from Jar files</li>
4068 <li>feature and annotation file applet parameters
4069 referring to different directories are retrieved correctly</li>
4070 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4071 <li>Fixed application hang whilst waiting for
4072 splash-screen version check to complete</li>
4073 <li>Applet properly URLencodes input parameter values
4074 when passing them to the launchApp service</li>
4075 <li>display name and local features preserved in results
4076 retrieved from web service</li>
4077 <li>Visual delay indication for sequence retrieval and
4078 sequence fetcher initialisation</li>
4079 <li>updated Application to use DAS 1.53e version of
4080 dasobert DAS client</li>
4081 <li>Re-instated Full AMSA support and .amsa file
4083 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4091 <div align="center">
4092 <strong>2.3</strong><br> 9/5/07
4097 <li>Jmol 11.0.2 integration</li>
4098 <li>PDB views stored in Jalview XML files</li>
4099 <li>Slide sequences</li>
4100 <li>Edit sequence in place</li>
4101 <li>EMBL CDS features</li>
4102 <li>DAS Feature mapping</li>
4103 <li>Feature ordering</li>
4104 <li>Alignment Properties</li>
4105 <li>Annotation Scores</li>
4106 <li>Sort by scores</li>
4107 <li>Feature/annotation editing in applet</li>
4112 <li>Headless state operation in 2.2.1</li>
4113 <li>Incorrect and unstable DNA pairwise alignment</li>
4114 <li>Cut and paste of sequences with annotation</li>
4115 <li>Feature group display state in XML</li>
4116 <li>Feature ordering in XML</li>
4117 <li>blc file iteration selection using filename # suffix</li>
4118 <li>Stockholm alignment properties</li>
4119 <li>Stockhom alignment secondary structure annotation</li>
4120 <li>2.2.1 applet had no feature transparency</li>
4121 <li>Number pad keys can be used in cursor mode</li>
4122 <li>Structure Viewer mirror image resolved</li>
4129 <div align="center">
4130 <strong>2.2.1</strong><br> 12/2/07
4135 <li>Non standard characters can be read and displayed
4136 <li>Annotations/Features can be imported/exported to the
4138 <li>Applet allows editing of sequence/annotation/group
4139 name & description
4140 <li>Preference setting to display sequence name in
4142 <li>Annotation file format extended to allow
4143 Sequence_groups to be defined
4144 <li>Default opening of alignment overview panel can be
4145 specified in preferences
4146 <li>PDB residue numbering annotation added to associated
4152 <li>Applet crash under certain Linux OS with Java 1.6
4154 <li>Annotation file export / import bugs fixed
4155 <li>PNG / EPS image output bugs fixed
4161 <div align="center">
4162 <strong>2.2</strong><br> 27/11/06
4167 <li>Multiple views on alignment
4168 <li>Sequence feature editing
4169 <li>"Reload" alignment
4170 <li>"Save" to current filename
4171 <li>Background dependent text colour
4172 <li>Right align sequence ids
4173 <li>User-defined lower case residue colours
4176 <li>Menu item accelerator keys
4177 <li>Control-V pastes to current alignment
4178 <li>Cancel button for DAS Feature Fetching
4179 <li>PCA and PDB Viewers zoom via mouse roller
4180 <li>User-defined sub-tree colours and sub-tree selection
4182 <li>'New Window' button on the 'Output to Text box'
4187 <li>New memory efficient Undo/Redo System
4188 <li>Optimised symbol lookups and conservation/consensus
4190 <li>Region Conservation/Consensus recalculated after
4192 <li>Fixed Remove Empty Columns Bug (empty columns at end
4194 <li>Slowed DAS Feature Fetching for increased robustness.
4196 <li>Made angle brackets in ASCII feature descriptions
4198 <li>Re-instated Zoom function for PCA
4199 <li>Sequence descriptions conserved in web service
4201 <li>UniProt ID discoverer uses any word separated by
4203 <li>WsDbFetch query/result association resolved
4204 <li>Tree leaf to sequence mapping improved
4205 <li>Smooth fonts switch moved to FontChooser dialog box.
4212 <div align="center">
4213 <strong>2.1.1</strong><br> 12/9/06
4218 <li>Copy consensus sequence to clipboard</li>
4223 <li>Image output - rightmost residues are rendered if
4224 sequence id panel has been resized</li>
4225 <li>Image output - all offscreen group boundaries are
4227 <li>Annotation files with sequence references - all
4228 elements in file are relative to sequence position</li>
4229 <li>Mac Applet users can use Alt key for group editing</li>
4235 <div align="center">
4236 <strong>2.1</strong><br> 22/8/06
4241 <li>MAFFT Multiple Alignment in default Web Service list</li>
4242 <li>DAS Feature fetching</li>
4243 <li>Hide sequences and columns</li>
4244 <li>Export Annotations and Features</li>
4245 <li>GFF file reading / writing</li>
4246 <li>Associate structures with sequences from local PDB
4248 <li>Add sequences to exisiting alignment</li>
4249 <li>Recently opened files / URL lists</li>
4250 <li>Applet can launch the full application</li>
4251 <li>Applet has transparency for features (Java 1.2
4253 <li>Applet has user defined colours parameter</li>
4254 <li>Applet can load sequences from parameter
4255 "sequence<em>x</em>"
4261 <li>Redundancy Panel reinstalled in the Applet</li>
4262 <li>Monospaced font - EPS / rescaling bug fixed</li>
4263 <li>Annotation files with sequence references bug fixed</li>
4269 <div align="center">
4270 <strong>2.08.1</strong><br> 2/5/06
4275 <li>Change case of selected region from Popup menu</li>
4276 <li>Choose to match case when searching</li>
4277 <li>Middle mouse button and mouse movement can compress /
4278 expand the visible width and height of the alignment</li>
4283 <li>Annotation Panel displays complete JNet results</li>
4289 <div align="center">
4290 <strong>2.08b</strong><br> 18/4/06
4296 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4297 <li>Righthand label on wrapped alignments shows correct
4304 <div align="center">
4305 <strong>2.08</strong><br> 10/4/06
4310 <li>Editing can be locked to the selection area</li>
4311 <li>Keyboard editing</li>
4312 <li>Create sequence features from searches</li>
4313 <li>Precalculated annotations can be loaded onto
4315 <li>Features file allows grouping of features</li>
4316 <li>Annotation Colouring scheme added</li>
4317 <li>Smooth fonts off by default - Faster rendering</li>
4318 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4323 <li>Drag & Drop fixed on Linux</li>
4324 <li>Jalview Archive file faster to load/save, sequence
4325 descriptions saved.</li>
4331 <div align="center">
4332 <strong>2.07</strong><br> 12/12/05
4337 <li>PDB Structure Viewer enhanced</li>
4338 <li>Sequence Feature retrieval and display enhanced</li>
4339 <li>Choose to output sequence start-end after sequence
4340 name for file output</li>
4341 <li>Sequence Fetcher WSDBFetch@EBI</li>
4342 <li>Applet can read feature files, PDB files and can be
4343 used for HTML form input</li>
4348 <li>HTML output writes groups and features</li>
4349 <li>Group editing is Control and mouse click</li>
4350 <li>File IO bugs</li>
4356 <div align="center">
4357 <strong>2.06</strong><br> 28/9/05
4362 <li>View annotations in wrapped mode</li>
4363 <li>More options for PCA viewer</li>
4368 <li>GUI bugs resolved</li>
4369 <li>Runs with -nodisplay from command line</li>
4375 <div align="center">
4376 <strong>2.05b</strong><br> 15/9/05
4381 <li>Choose EPS export as lineart or text</li>
4382 <li>Jar files are executable</li>
4383 <li>Can read in Uracil - maps to unknown residue</li>
4388 <li>Known OutOfMemory errors give warning message</li>
4389 <li>Overview window calculated more efficiently</li>
4390 <li>Several GUI bugs resolved</li>
4396 <div align="center">
4397 <strong>2.05</strong><br> 30/8/05
4402 <li>Edit and annotate in "Wrapped" view</li>
4407 <li>Several GUI bugs resolved</li>
4413 <div align="center">
4414 <strong>2.04</strong><br> 24/8/05
4419 <li>Hold down mouse wheel & scroll to change font
4425 <li>Improved JPred client reliability</li>
4426 <li>Improved loading of Jalview files</li>
4432 <div align="center">
4433 <strong>2.03</strong><br> 18/8/05
4438 <li>Set Proxy server name and port in preferences</li>
4439 <li>Multiple URL links from sequence ids</li>
4440 <li>User Defined Colours can have a scheme name and added
4442 <li>Choose to ignore gaps in consensus calculation</li>
4443 <li>Unix users can set default web browser</li>
4444 <li>Runs without GUI for batch processing</li>
4445 <li>Dynamically generated Web Service Menus</li>
4450 <li>InstallAnywhere download for Sparc Solaris</li>
4456 <div align="center">
4457 <strong>2.02</strong><br> 18/7/05
4463 <li>Copy & Paste order of sequences maintains
4464 alignment order.</li>
4470 <div align="center">
4471 <strong>2.01</strong><br> 12/7/05
4476 <li>Use delete key for deleting selection.</li>
4477 <li>Use Mouse wheel to scroll sequences.</li>
4478 <li>Help file updated to describe how to add alignment
4480 <li>Version and build date written to build properties
4482 <li>InstallAnywhere installation will check for updates
4483 at launch of Jalview.</li>
4488 <li>Delete gaps bug fixed.</li>
4489 <li>FileChooser sorts columns.</li>
4490 <li>Can remove groups one by one.</li>
4491 <li>Filechooser icons installed.</li>
4492 <li>Finder ignores return character when searching.
4493 Return key will initiate a search.<br>
4500 <div align="center">
4501 <strong>2.0</strong><br> 20/6/05
4506 <li>New codebase</li>