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.2.11.0">2.11.0</a><br />
61 <em>04/07/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
67 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
68 source project) rather than InstallAnywhere
71 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
72 settings, receive over the air updates and launch specific
73 versions via (<a href="https://github.com/threerings/getdown">Three
77 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
78 formats supported by jalview (including .jvp project files)
81 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
82 arguments and switch between different getdown channels
85 <!-- JAL-3141 -->Backup files created when saving Jalview project
90 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
91 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
93 <!-- JAL-2620 -->Alternative genetic code tables for
94 'Translate as cDNA'</li>
96 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
97 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
100 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
101 implementation that allows updates) used for Sequence Feature collections</li>
104 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
105 features can be filtered and shaded according to any
106 associated attributes (e.g. variant attributes from VCF
107 file, or key-value pairs imported from column 9 of GFF
111 <!-- JAL-2879 -->Feature Attributes and shading schemes
112 stored and restored from Jalview Projects
115 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
116 recognise variant features
119 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
120 sequences (also coloured red by default)
123 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
127 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
128 algorithm (Z-sort/transparency and filter aware)
131 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
137 <!-- JAL-3205 -->Symmetric score matrices for faster
138 tree and PCA calculations
140 <li><strong>Principal Components Analysis Viewer</strong>
143 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
144 and Viewer state saved in Jalview Project
146 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
149 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
153 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
158 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
160 <li><strong>Speed and Efficiency</strong>
163 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
164 multiple groups when working with large alignments
167 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
171 <li><strong>User Interface</strong>
174 <!-- JAL-2933 -->Finder panel remembers last position in each
178 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
179 what is shown)<br />Only visible region of alignment is shown by
180 default (can be changed in user preferences)
183 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
184 to the Overwrite Dialog
187 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
191 <!-- JAL-1244 -->Status bar shows bounds when dragging a
192 selection region, and gap count when inserting or deleting gaps
195 <!-- JAL-3132 -->Status bar updates over sequence and annotation
199 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
203 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
207 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
210 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
214 <!-- JAL-3181 -->Consistent ordering of links in sequence id
218 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
220 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
224 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
225 <li><strong>Java 11 Support (not yet on general release)</strong>
228 <!-- -->OSX GUI integrations for App menu's 'About' entry and
233 <em>Deprecations</em>
236 <!-- JAL-3035 -->DAS sequence retrieval and annotation
237 capabilities removed from the Jalview Desktop
240 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
241 unmarshalling has been replaced by JAXB for Jalview projects
242 and XML based data retrieval clients</li>
243 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
244 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
245 </ul> <em>Documentation</em>
248 <!-- JAL-3003 -->Added remarks about transparent rendering effects
249 not supported in EPS figure export
251 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
252 </ul> <em>Development and Release Processes</em>
255 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
257 <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
259 <!-- JAL-3225 -->Eclipse project configuration managed with
263 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian
264 Bamboo continuous integration for unattended Test Suite
268 <!-- JAL-2864 -->Memory test suite to detect leaks in common
272 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
276 <!-- JAL-3248 -->Developer documentation migrated to
277 markdown (with HTML rendering)
280 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
283 <!-- JAL-3289 -->New URLs for publishing development
290 <td align="left" valign="top">
293 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
296 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
297 superposition in Jmol fail on Windows
300 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
301 structures for sequences with lots of PDB structures
304 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
308 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
309 project involving multiple views
312 <!-- JAL-3164 -->Overview for complementary view in a linked
313 CDS/Protein alignment is not updated when Hide Columns by
314 Annotation dialog hides columns
317 <!-- JAL-3158 -->Selection highlighting in the complement of a
318 CDS/Protein alignment stops working after making a selection in
319 one view, then making another selection in the other view
322 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
326 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
327 Settings and Jalview Preferences panels
330 <!-- JAL-2865 -->Jalview hangs when closing windows or the
331 overview updates with large alignments
334 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
335 region if columns were selected by dragging right-to-left and the
336 mouse moved to the left of the first column
339 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
340 hidden column marker via scale popup menu
343 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
344 doesn't tell users the invalid URL
347 <!-- JAL-2816 -->Tooltips displayed for features filtered by
351 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
352 show cross references or Fetch Database References are shown in
356 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
357 peptide sequence (computed variant shown as p.Res.null)
360 <!-- JAL-2060 -->'Graduated colour' option not offered for
361 manually created features (where if feature score is Float.NaN)
364 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
365 when columns are hidden
368 <!-- JAL-3082 -->Regular expression error for '(' in Select
369 Columns by Annotation description
372 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
373 out of Scale or Annotation Panel
376 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
380 <!-- JAL-3074 -->Left/right drag in annotation can scroll
384 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
388 <!-- JAL-3002 -->Column display is out by one after Page Down,
389 Page Up in wrapped mode
392 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
395 <!-- JAL-2932 -->Finder searches in minimised alignments
398 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
399 on opening an alignment
402 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
406 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
407 different groups in the alignment are selected
410 <!-- JAL-2717 -->Internationalised colour scheme names not shown
414 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
418 <!-- JAL-3125 -->Value input for graduated feature colour
419 threshold gets 'unrounded'
422 <!-- JAL-2982 -->PCA image export doesn't respect background
426 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
429 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
432 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
436 <!-- JAL-2964 -->Associate Tree with All Views not restored from
440 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
441 shown in complementary view
444 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
445 without normalisation
448 <!-- JAL-3021 -->Sequence Details report should open positioned at top
452 <!-- JAL-914 -->Help page can be opened twice
455 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
457 </ul> <em>Editing</em>
460 <!-- JAL-2822 -->Start and End should be updated when sequence
461 data at beginning or end of alignment added/removed via 'Edit'
465 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
466 relocate sequence features correctly when start of sequence is
467 removed (Known defect since 2.10)
470 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
471 dialog corrupts dataset sequence
474 <!-- JAL-868 -->Structure colours not updated when associated tree
475 repartitions the alignment view (Regression in 2.10.5)
481 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
482 sequence's End is greater than its length
484 <li><strong>Bugs fixed for Java 11 Support (not
485 yet on general release)</strong>
488 <!-- JAL-3288 -->Menus work properly in split-screen
491 </ul> <em>New Known Defects</em>
493 <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
496 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
497 regions of protein alignment.
500 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
501 is restored from a Jalview 2.11 project
504 <!-- JAL-3213 -->Alignment panel height can be too small after
508 <!-- JAL-3240 -->Display is incorrect after removing gapped
509 columns within hidden columns
512 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
513 window after dragging left to select columns to left of visible
517 <!-- JAL-2876 -->Features coloured according to their description
518 string and thresholded by score in earlier versions of Jalview are
519 not shown as thresholded features in 2.11. To workaround please
520 create a Score filter instead.
522 <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
524 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
527 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
528 alignments with multiple views can close views unexpectedly
530 <li><strong>Java 11 Specific defects</strong>
533 <!-- JAL-3235 -->Jalview Properties file is not sorted
534 alphabetically when saved
542 <td width="60" nowrap>
544 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
547 <td><div align="left">
551 <!-- JAL-3101 -->Default memory for Jalview webstart and
552 InstallAnywhere increased to 1G.
555 <!-- JAL-247 -->Hidden sequence markers and representative
556 sequence bolding included when exporting alignment as EPS,
557 SVG, PNG or HTML. <em>Display is configured via the
558 Format menu, or for command-line use via a jalview
559 properties file.</em>
562 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
563 API and sequence data now imported as JSON.
566 <!-- JAL-3065 -->Change in recommended way of starting
567 Jalview via a Java command line: add jars in lib directory
568 to CLASSPATH, rather than via the deprecated java.ext.dirs
575 <!-- JAL-3047 -->Support added to execute test suite
576 instrumented with <a href="http://openclover.org/">Open
581 <td><div align="left">
585 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
586 row shown in Feredoxin Structure alignment view of example
590 <!-- JAL-2854 -->Annotation obscures sequences if lots of
591 annotation displayed.
594 <!-- JAL-3107 -->Group conservation/consensus not shown
595 for newly created group when 'Apply to all groups'
599 <!-- JAL-3087 -->Corrupted display when switching to
600 wrapped mode when sequence panel's vertical scrollbar is
604 <!-- JAL-3003 -->Alignment is black in exported EPS file
605 when sequences are selected in exported view.</em>
608 <!-- JAL-3059 -->Groups with different coloured borders
609 aren't rendered with correct colour.
612 <!-- JAL-3092 -->Jalview could hang when importing certain
613 types of knotted RNA secondary structure.
616 <!-- JAL-3095 -->Sequence highlight and selection in
617 trimmed VARNA 2D structure is incorrect for sequences that
621 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
622 annotation when columns are inserted into an alignment,
623 and when exporting as Stockholm flatfile.
626 <!-- JAL-3053 -->Jalview annotation rows containing upper
627 and lower-case 'E' and 'H' do not automatically get
628 treated as RNA secondary structure.
631 <!-- JAL-3106 -->.jvp should be used as default extension
632 (not .jar) when saving a jalview project file.
635 <!-- JAL-3105 -->Mac Users: closing a window correctly
636 transfers focus to previous window on OSX
639 <em>Java 10 Issues Resolved</em>
642 <!-- JAL-2988 -->OSX - Can't save new files via the File
643 or export menus by typing in a name into the Save dialog
647 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
648 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
649 'look and feel' which has improved compatibility with the
650 latest version of OSX.
657 <td width="60" nowrap>
659 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
660 <em>7/06/2018</em></strong>
663 <td><div align="left">
667 <!-- JAL-2920 -->Use HGVS nomenclature for variant
668 annotation retrieved from Uniprot
671 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
672 onto the Jalview Desktop
676 <td><div align="left">
680 <!-- JAL-3017 -->Cannot import features with multiple
681 variant elements (blocks import of some Uniprot records)
684 <!-- JAL-2997 -->Clustal files with sequence positions in
685 right-hand column parsed correctly
688 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
689 not alignment area in exported graphic
692 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
693 window has input focus
696 <!-- JAL-2992 -->Annotation panel set too high when
697 annotation added to view (Windows)
700 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
701 network connectivity is poor
704 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
705 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
706 the currently open URL and links from a page viewed in
707 Firefox or Chrome on Windows is now fully supported. If
708 you are using Edge, only links in the page can be
709 dragged, and with Internet Explorer, only the currently
710 open URL in the browser can be dropped onto Jalview.</em>
713 <em>New Known Defects</em>
715 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
720 <td width="60" nowrap>
722 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
725 <td><div align="left">
729 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
730 for disabling automatic superposition of multiple
731 structures and open structures in existing views
734 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
735 ID and annotation area margins can be click-dragged to
739 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
743 <!-- JAL-2759 -->Improved performance for large alignments
744 and lots of hidden columns
747 <!-- JAL-2593 -->Improved performance when rendering lots
748 of features (particularly when transparency is disabled)
751 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
752 exchange of Jalview features and Chimera attributes made
758 <td><div align="left">
761 <!-- JAL-2899 -->Structure and Overview aren't updated
762 when Colour By Annotation threshold slider is adjusted
765 <!-- JAL-2778 -->Slow redraw when Overview panel shown
766 overlapping alignment panel
769 <!-- JAL-2929 -->Overview doesn't show end of unpadded
773 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
774 improved: CDS not handled correctly if transcript has no
778 <!-- JAL-2321 -->Secondary structure and temperature
779 factor annotation not added to sequence when local PDB
780 file associated with it by drag'n'drop or structure
784 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
785 dialog doesn't import PDB files dropped on an alignment
788 <!-- JAL-2666 -->Linked scrolling via protein horizontal
789 scroll bar doesn't work for some CDS/Protein views
792 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
793 Java 1.8u153 onwards and Java 1.9u4+.
796 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
797 columns in annotation row
800 <!-- JAL-2913 -->Preferences panel's ID Width control is not
801 honored in batch mode
804 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
805 for structures added to existing Jmol view
808 <!-- JAL-2223 -->'View Mappings' includes duplicate
809 entries after importing project with multiple views
812 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
813 protein sequences via SIFTS from associated PDB entries
814 with negative residue numbers or missing residues fails
817 <!-- JAL-2952 -->Exception when shading sequence with negative
818 Temperature Factor values from annotated PDB files (e.g.
819 as generated by CONSURF)
822 <!-- JAL-2920 -->Uniprot 'sequence variant' features
823 tooltip doesn't include a text description of mutation
826 <!-- JAL-2922 -->Invert displayed features very slow when
827 structure and/or overview windows are also shown
830 <!-- JAL-2954 -->Selecting columns from highlighted regions
831 very slow for alignments with large numbers of sequences
834 <!-- JAL-2925 -->Copy Consensus fails for group consensus
835 with 'StringIndexOutOfBounds'
838 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
839 platforms running Java 10
842 <!-- JAL-2960 -->Adding a structure to existing structure
843 view appears to do nothing because the view is hidden behind the alignment view
849 <!-- JAL-2926 -->Copy consensus sequence option in applet
850 should copy the group consensus when popup is opened on it
856 <!-- JAL-2913 -->Fixed ID width preference is not respected
859 <em>New Known Defects</em>
862 <!-- JAL-2973 --> Exceptions occasionally raised when
863 editing a large alignment and overview is displayed
866 <!-- JAL-2974 -->'Overview updating' progress bar is shown
867 repeatedly after a series of edits even when the overview
868 is no longer reflecting updates
871 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
872 structures for protein subsequence (if 'Trim Retrieved
873 Sequences' enabled) or Ensembl isoforms (Workaround in
874 2.10.4 is to fail back to N&W mapping)
877 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
878 option gives blank output
885 <td width="60" nowrap>
887 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
890 <td><div align="left">
891 <ul><li>Updated Certum Codesigning Certificate
892 (Valid till 30th November 2018)</li></ul></div></td>
893 <td><div align="left">
896 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
897 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
898 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
899 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
900 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
901 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
902 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
908 <td width="60" nowrap>
910 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
913 <td><div align="left">
917 <!-- JAL-2446 -->Faster and more efficient management and
918 rendering of sequence features
921 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
922 429 rate limit request hander
925 <!-- JAL-2773 -->Structure views don't get updated unless
926 their colours have changed
929 <!-- JAL-2495 -->All linked sequences are highlighted for
930 a structure mousover (Jmol) or selection (Chimera)
933 <!-- JAL-2790 -->'Cancel' button in progress bar for
934 JABAWS AACon, RNAAliFold and Disorder prediction jobs
937 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
938 view from Ensembl locus cross-references
941 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
945 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
946 feature can be disabled
949 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
950 PDB easier retrieval of sequences for lists of IDs
953 <!-- JAL-2758 -->Short names for sequences retrieved from
959 <li>Groovy interpreter updated to 2.4.12</li>
960 <li>Example groovy script for generating a matrix of
961 percent identity scores for current alignment.</li>
963 <em>Testing and Deployment</em>
966 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
970 <td><div align="left">
974 <!-- JAL-2643 -->Pressing tab after updating the colour
975 threshold text field doesn't trigger an update to the
979 <!-- JAL-2682 -->Race condition when parsing sequence ID
983 <!-- JAL-2608 -->Overview windows are also closed when
984 alignment window is closed
987 <!-- JAL-2548 -->Export of features doesn't always respect
991 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
992 takes a long time in Cursor mode
998 <!-- JAL-2777 -->Structures with whitespace chainCode
999 cannot be viewed in Chimera
1002 <!-- JAL-2728 -->Protein annotation panel too high in
1006 <!-- JAL-2757 -->Can't edit the query after the server
1007 error warning icon is shown in Uniprot and PDB Free Text
1011 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1014 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1017 <!-- JAL-2739 -->Hidden column marker in last column not
1018 rendered when switching back from Wrapped to normal view
1021 <!-- JAL-2768 -->Annotation display corrupted when
1022 scrolling right in unwapped alignment view
1025 <!-- JAL-2542 -->Existing features on subsequence
1026 incorrectly relocated when full sequence retrieved from
1030 <!-- JAL-2733 -->Last reported memory still shown when
1031 Desktop->Show Memory is unticked (OSX only)
1034 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1035 features of same type and group to be selected for
1039 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1040 alignments when hidden columns are present
1043 <!-- JAL-2392 -->Jalview freezes when loading and
1044 displaying several structures
1047 <!-- JAL-2732 -->Black outlines left after resizing or
1051 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1052 within the Jalview desktop on OSX
1055 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1056 when in wrapped alignment mode
1059 <!-- JAL-2636 -->Scale mark not shown when close to right
1060 hand end of alignment
1063 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1064 each selected sequence do not have correct start/end
1068 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1069 after canceling the Alignment Window's Font dialog
1072 <!-- JAL-2036 -->Show cross-references not enabled after
1073 restoring project until a new view is created
1076 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1077 URL links appears when only default EMBL-EBI link is
1078 configured (since 2.10.2b2)
1081 <!-- JAL-2775 -->Overview redraws whole window when box
1082 position is adjusted
1085 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1086 in a multi-chain structure when viewing alignment
1087 involving more than one chain (since 2.10)
1090 <!-- JAL-2811 -->Double residue highlights in cursor mode
1091 if new selection moves alignment window
1094 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1095 arrow key in cursor mode to pass hidden column marker
1098 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1099 that produces correctly annotated transcripts and products
1102 <!-- JAL-2776 -->Toggling a feature group after first time
1103 doesn't update associated structure view
1106 <em>Applet</em><br />
1109 <!-- JAL-2687 -->Concurrent modification exception when
1110 closing alignment panel
1113 <em>BioJSON</em><br />
1116 <!-- JAL-2546 -->BioJSON export does not preserve
1117 non-positional features
1120 <em>New Known Issues</em>
1123 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1124 sequence features correctly (for many previous versions of
1128 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1129 using cursor in wrapped panel other than top
1132 <!-- JAL-2791 -->Select columns containing feature ignores
1133 graduated colour threshold
1136 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1137 always preserve numbering and sequence features
1140 <em>Known Java 9 Issues</em>
1143 <!-- JAL-2902 -->Groovy Console very slow to open and is
1144 not responsive when entering characters (Webstart, Java
1151 <td width="60" nowrap>
1152 <div align="center">
1153 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1154 <em>2/10/2017</em></strong>
1157 <td><div align="left">
1158 <em>New features in Jalview Desktop</em>
1161 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1163 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1167 <td><div align="left">
1171 <td width="60" nowrap>
1172 <div align="center">
1173 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1174 <em>7/9/2017</em></strong>
1177 <td><div align="left">
1181 <!-- JAL-2588 -->Show gaps in overview window by colouring
1182 in grey (sequences used to be coloured grey, and gaps were
1186 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1190 <!-- JAL-2587 -->Overview updates immediately on increase
1191 in size and progress bar shown as higher resolution
1192 overview is recalculated
1197 <td><div align="left">
1201 <!-- JAL-2664 -->Overview window redraws every hidden
1202 column region row by row
1205 <!-- JAL-2681 -->duplicate protein sequences shown after
1206 retrieving Ensembl crossrefs for sequences from Uniprot
1209 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1210 format setting is unticked
1213 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1214 if group has show boxes format setting unticked
1217 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1218 autoscrolling whilst dragging current selection group to
1219 include sequences and columns not currently displayed
1222 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1223 assemblies are imported via CIF file
1226 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1227 displayed when threshold or conservation colouring is also
1231 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1235 <!-- JAL-2673 -->Jalview continues to scroll after
1236 dragging a selected region off the visible region of the
1240 <!-- JAL-2724 -->Cannot apply annotation based
1241 colourscheme to all groups in a view
1244 <!-- JAL-2511 -->IDs don't line up with sequences
1245 initially after font size change using the Font chooser or
1252 <td width="60" nowrap>
1253 <div align="center">
1254 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1257 <td><div align="left">
1258 <em>Calculations</em>
1262 <!-- JAL-1933 -->Occupancy annotation row shows number of
1263 ungapped positions in each column of the alignment.
1266 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1267 a calculation dialog box
1270 <!-- JAL-2379 -->Revised implementation of PCA for speed
1271 and memory efficiency (~30x faster)
1274 <!-- JAL-2403 -->Revised implementation of sequence
1275 similarity scores as used by Tree, PCA, Shading Consensus
1276 and other calculations
1279 <!-- JAL-2416 -->Score matrices are stored as resource
1280 files within the Jalview codebase
1283 <!-- JAL-2500 -->Trees computed on Sequence Feature
1284 Similarity may have different topology due to increased
1291 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1292 model for alignments and groups
1295 <!-- JAL-384 -->Custom shading schemes created via groovy
1302 <!-- JAL-2526 -->Efficiency improvements for interacting
1303 with alignment and overview windows
1306 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1310 <!-- JAL-2388 -->Hidden columns and sequences can be
1314 <!-- JAL-2611 -->Click-drag in visible area allows fine
1315 adjustment of visible position
1319 <em>Data import/export</em>
1322 <!-- JAL-2535 -->Posterior probability annotation from
1323 Stockholm files imported as sequence associated annotation
1326 <!-- JAL-2507 -->More robust per-sequence positional
1327 annotation input/output via stockholm flatfile
1330 <!-- JAL-2533 -->Sequence names don't include file
1331 extension when importing structure files without embedded
1332 names or PDB accessions
1335 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1336 format sequence substitution matrices
1339 <em>User Interface</em>
1342 <!-- JAL-2447 --> Experimental Features Checkbox in
1343 Desktop's Tools menu to hide or show untested features in
1347 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1348 via Overview or sequence motif search operations
1351 <!-- JAL-2547 -->Amend sequence features dialog box can be
1352 opened by double clicking gaps within sequence feature
1356 <!-- JAL-1476 -->Status bar message shown when not enough
1357 aligned positions were available to create a 3D structure
1361 <em>3D Structure</em>
1364 <!-- JAL-2430 -->Hidden regions in alignment views are not
1365 coloured in linked structure views
1368 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1369 file-based command exchange
1372 <!-- JAL-2375 -->Structure chooser automatically shows
1373 Cached Structures rather than querying the PDBe if
1374 structures are already available for sequences
1377 <!-- JAL-2520 -->Structures imported via URL are cached in
1378 the Jalview project rather than downloaded again when the
1379 project is reopened.
1382 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1383 to transfer Chimera's structure attributes as Jalview
1384 features, and vice-versa (<strong>Experimental
1388 <em>Web Services</em>
1391 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1394 <!-- JAL-2335 -->Filter non-standard amino acids and
1395 nucleotides when submitting to AACon and other MSA
1399 <!-- JAL-2316, -->URLs for viewing database
1400 cross-references provided by identifiers.org and the
1401 EMBL-EBI's MIRIAM DB
1408 <!-- JAL-2344 -->FileFormatI interface for describing and
1409 identifying file formats (instead of String constants)
1412 <!-- JAL-2228 -->FeatureCounter script refactored for
1413 efficiency when counting all displayed features (not
1414 backwards compatible with 2.10.1)
1417 <em>Example files</em>
1420 <!-- JAL-2631 -->Graduated feature colour style example
1421 included in the example feature file
1424 <em>Documentation</em>
1427 <!-- JAL-2339 -->Release notes reformatted for readability
1428 with the built-in Java help viewer
1431 <!-- JAL-1644 -->Find documentation updated with 'search
1432 sequence description' option
1438 <!-- JAL-2485, -->External service integration tests for
1439 Uniprot REST Free Text Search Client
1442 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1445 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1450 <td><div align="left">
1451 <em>Calculations</em>
1454 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1455 matrix - C->R should be '-3'<br />Old matrix restored
1456 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1458 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1459 Jalview's treatment of gaps in PCA and substitution matrix
1460 based Tree calculations.<br /> <br />In earlier versions
1461 of Jalview, gaps matching gaps were penalised, and gaps
1462 matching non-gaps penalised even more. In the PCA
1463 calculation, gaps were actually treated as non-gaps - so
1464 different costs were applied, which meant Jalview's PCAs
1465 were different to those produced by SeqSpace.<br />Jalview
1466 now treats gaps in the same way as SeqSpace (ie it scores
1467 them as 0). <br /> <br />Enter the following in the
1468 Groovy console to restore pre-2.10.2 behaviour:<br />
1469 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1470 // for 2.10.1 mode <br />
1471 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1472 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1473 these settings will affect all subsequent tree and PCA
1474 calculations (not recommended)</em></li>
1476 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1477 scaling of branch lengths for trees computed using
1478 Sequence Feature Similarity.
1481 <!-- JAL-2377 -->PCA calculation could hang when
1482 generating output report when working with highly
1483 redundant alignments
1486 <!-- JAL-2544 --> Sort by features includes features to
1487 right of selected region when gaps present on right-hand
1491 <em>User Interface</em>
1494 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1495 doesn't reselect a specific sequence's associated
1496 annotation after it was used for colouring a view
1499 <!-- JAL-2419 -->Current selection lost if popup menu
1500 opened on a region of alignment without groups
1503 <!-- JAL-2374 -->Popup menu not always shown for regions
1504 of an alignment with overlapping groups
1507 <!-- JAL-2310 -->Finder double counts if both a sequence's
1508 name and description match
1511 <!-- JAL-2370 -->Hiding column selection containing two
1512 hidden regions results in incorrect hidden regions
1515 <!-- JAL-2386 -->'Apply to all groups' setting when
1516 changing colour does not apply Conservation slider value
1520 <!-- JAL-2373 -->Percentage identity and conservation menu
1521 items do not show a tick or allow shading to be disabled
1524 <!-- JAL-2385 -->Conservation shading or PID threshold
1525 lost when base colourscheme changed if slider not visible
1528 <!-- JAL-2547 -->Sequence features shown in tooltip for
1529 gaps before start of features
1532 <!-- JAL-2623 -->Graduated feature colour threshold not
1533 restored to UI when feature colour is edited
1536 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1537 a time when scrolling vertically in wrapped mode.
1540 <!-- JAL-2630 -->Structure and alignment overview update
1541 as graduate feature colour settings are modified via the
1545 <!-- JAL-2034 -->Overview window doesn't always update
1546 when a group defined on the alignment is resized
1549 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1550 wrapped view result in positional status updates
1554 <!-- JAL-2563 -->Status bar doesn't show position for
1555 ambiguous amino acid and nucleotide symbols
1558 <!-- JAL-2602 -->Copy consensus sequence failed if
1559 alignment included gapped columns
1562 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1563 widgets don't permanently disappear
1566 <!-- JAL-2503 -->Cannot select or filter quantitative
1567 annotation that are shown only as column labels (e.g.
1568 T-Coffee column reliability scores)
1571 <!-- JAL-2594 -->Exception thrown if trying to create a
1572 sequence feature on gaps only
1575 <!-- JAL-2504 -->Features created with 'New feature'
1576 button from a Find inherit previously defined feature type
1577 rather than the Find query string
1580 <!-- JAL-2423 -->incorrect title in output window when
1581 exporting tree calculated in Jalview
1584 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1585 and then revealing them reorders sequences on the
1589 <!-- JAL-964 -->Group panel in sequence feature settings
1590 doesn't update to reflect available set of groups after
1591 interactively adding or modifying features
1594 <!-- JAL-2225 -->Sequence Database chooser unusable on
1598 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1599 only excluded gaps in current sequence and ignored
1606 <!-- JAL-2421 -->Overview window visible region moves
1607 erratically when hidden rows or columns are present
1610 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1611 Structure Viewer's colour menu don't correspond to
1615 <!-- JAL-2405 -->Protein specific colours only offered in
1616 colour and group colour menu for protein alignments
1619 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1620 reflect currently selected view or group's shading
1624 <!-- JAL-2624 -->Feature colour thresholds not respected
1625 when rendered on overview and structures when opacity at
1629 <!-- JAL-2589 -->User defined gap colour not shown in
1630 overview when features overlaid on alignment
1633 <!-- JAL-2567 -->Feature settings for different views not
1634 recovered correctly from Jalview project file
1637 <!-- JAL-2256 -->Feature colours in overview when first opened
1638 (automatically via preferences) are different to the main
1642 <em>Data import/export</em>
1645 <!-- JAL-2576 -->Very large alignments take a long time to
1649 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1650 added after a sequence was imported are not written to
1654 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1655 when importing RNA secondary structure via Stockholm
1658 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1659 not shown in correct direction for simple pseudoknots
1662 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1663 with lightGray or darkGray via features file (but can
1667 <!-- JAL-2383 -->Above PID colour threshold not recovered
1668 when alignment view imported from project
1671 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1672 structure and sequences extracted from structure files
1673 imported via URL and viewed in Jmol
1676 <!-- JAL-2520 -->Structures loaded via URL are saved in
1677 Jalview Projects rather than fetched via URL again when
1678 the project is loaded and the structure viewed
1681 <em>Web Services</em>
1684 <!-- JAL-2519 -->EnsemblGenomes example failing after
1685 release of Ensembl v.88
1688 <!-- JAL-2366 -->Proxy server address and port always
1689 appear enabled in Preferences->Connections
1692 <!-- JAL-2461 -->DAS registry not found exceptions
1693 removed from console output
1696 <!-- JAL-2582 -->Cannot retrieve protein products from
1697 Ensembl by Peptide ID
1700 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1701 created from SIFTs, and spurious 'Couldn't open structure
1702 in Chimera' errors raised after April 2017 update (problem
1703 due to 'null' string rather than empty string used for
1704 residues with no corresponding PDB mapping).
1707 <em>Application UI</em>
1710 <!-- JAL-2361 -->User Defined Colours not added to Colour
1714 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1715 case' residues (button in colourscheme editor debugged and
1716 new documentation and tooltips added)
1719 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1720 doesn't restore group-specific text colour thresholds
1723 <!-- JAL-2243 -->Feature settings panel does not update as
1724 new features are added to alignment
1727 <!-- JAL-2532 -->Cancel in feature settings reverts
1728 changes to feature colours via the Amend features dialog
1731 <!-- JAL-2506 -->Null pointer exception when attempting to
1732 edit graduated feature colour via amend features dialog
1736 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1737 selection menu changes colours of alignment views
1740 <!-- JAL-2426 -->Spurious exceptions in console raised
1741 from alignment calculation workers after alignment has
1745 <!-- JAL-1608 -->Typo in selection popup menu - Create
1746 groups now 'Create Group'
1749 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1750 Create/Undefine group doesn't always work
1753 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1754 shown again after pressing 'Cancel'
1757 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1758 adjusts start position in wrap mode
1761 <!-- JAL-2563 -->Status bar doesn't show positions for
1762 ambiguous amino acids
1765 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1766 CDS/Protein view after CDS sequences added for aligned
1770 <!-- JAL-2592 -->User defined colourschemes called 'User
1771 Defined' don't appear in Colours menu
1777 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1778 score models doesn't always result in an updated PCA plot
1781 <!-- JAL-2442 -->Features not rendered as transparent on
1782 overview or linked structure view
1785 <!-- JAL-2372 -->Colour group by conservation doesn't
1789 <!-- JAL-2517 -->Hitting Cancel after applying
1790 user-defined colourscheme doesn't restore original
1797 <!-- JAL-2314 -->Unit test failure:
1798 jalview.ws.jabaws.RNAStructExportImport setup fails
1801 <!-- JAL-2307 -->Unit test failure:
1802 jalview.ws.sifts.SiftsClientTest due to compatibility
1803 problems with deep array comparison equality asserts in
1804 successive versions of TestNG
1807 <!-- JAL-2479 -->Relocated StructureChooserTest and
1808 ParameterUtilsTest Unit tests to Network suite
1811 <em>New Known Issues</em>
1814 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1815 phase after a sequence motif find operation
1818 <!-- JAL-2550 -->Importing annotation file with rows
1819 containing just upper and lower case letters are
1820 interpreted as WUSS RNA secondary structure symbols
1823 <!-- JAL-2590 -->Cannot load and display Newick trees
1824 reliably from eggnog Ortholog database
1827 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1828 containing features of type Highlight' when 'B' is pressed
1829 to mark columns containing highlighted regions.
1832 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1833 doesn't always add secondary structure annotation.
1838 <td width="60" nowrap>
1839 <div align="center">
1840 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1843 <td><div align="left">
1847 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1848 for all consensus calculations
1851 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1854 <li>Updated Jalview's Certum code signing certificate
1857 <em>Application</em>
1860 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1861 set of database cross-references, sorted alphabetically
1864 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1865 from database cross references. Users with custom links
1866 will receive a <a href="webServices/urllinks.html#warning">warning
1867 dialog</a> asking them to update their preferences.
1870 <!-- JAL-2287-->Cancel button and escape listener on
1871 dialog warning user about disconnecting Jalview from a
1875 <!-- JAL-2320-->Jalview's Chimera control window closes if
1876 the Chimera it is connected to is shut down
1879 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1880 columns menu item to mark columns containing highlighted
1881 regions (e.g. from structure selections or results of a
1885 <!-- JAL-2284-->Command line option for batch-generation
1886 of HTML pages rendering alignment data with the BioJS
1896 <!-- JAL-2286 -->Columns with more than one modal residue
1897 are not coloured or thresholded according to percent
1898 identity (first observed in Jalview 2.8.2)
1901 <!-- JAL-2301 -->Threonine incorrectly reported as not
1905 <!-- JAL-2318 -->Updates to documentation pages (above PID
1906 threshold, amino acid properties)
1909 <!-- JAL-2292 -->Lower case residues in sequences are not
1910 reported as mapped to residues in a structure file in the
1914 <!--JAL-2324 -->Identical features with non-numeric scores
1915 could be added multiple times to a sequence
1918 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1919 bond features shown as two highlighted residues rather
1920 than a range in linked structure views, and treated
1921 correctly when selecting and computing trees from features
1924 <!-- JAL-2281-->Custom URL links for database
1925 cross-references are matched to database name regardless
1930 <em>Application</em>
1933 <!-- JAL-2282-->Custom URL links for specific database
1934 names without regular expressions also offer links from
1938 <!-- JAL-2315-->Removing a single configured link in the
1939 URL links pane in Connections preferences doesn't actually
1940 update Jalview configuration
1943 <!-- JAL-2272-->CTRL-Click on a selected region to open
1944 the alignment area popup menu doesn't work on El-Capitan
1947 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1948 files with similarly named sequences if dropped onto the
1952 <!-- JAL-2312 -->Additional mappings are shown for PDB
1953 entries where more chains exist in the PDB accession than
1954 are reported in the SIFTS file
1957 <!-- JAL-2317-->Certain structures do not get mapped to
1958 the structure view when displayed with Chimera
1961 <!-- JAL-2317-->No chains shown in the Chimera view
1962 panel's View->Show Chains submenu
1965 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1966 work for wrapped alignment views
1969 <!--JAL-2197 -->Rename UI components for running JPred
1970 predictions from 'JNet' to 'JPred'
1973 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1974 corrupted when annotation panel vertical scroll is not at
1975 first annotation row
1978 <!--JAL-2332 -->Attempting to view structure for Hen
1979 lysozyme results in a PDB Client error dialog box
1982 <!-- JAL-2319 -->Structure View's mapping report switched
1983 ranges for PDB and sequence for SIFTS
1986 SIFTS 'Not_Observed' residues mapped to non-existant
1990 <!-- <em>New Known Issues</em>
1997 <td width="60" nowrap>
1998 <div align="center">
1999 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2000 <em>25/10/2016</em></strong>
2003 <td><em>Application</em>
2005 <li>3D Structure chooser opens with 'Cached structures'
2006 view if structures already loaded</li>
2007 <li>Progress bar reports models as they are loaded to
2008 structure views</li>
2014 <li>Colour by conservation always enabled and no tick
2015 shown in menu when BLOSUM or PID shading applied</li>
2016 <li>FER1_ARATH and FER2_ARATH labels were switched in
2017 example sequences/projects/trees</li>
2019 <em>Application</em>
2021 <li>Jalview projects with views of local PDB structure
2022 files saved on Windows cannot be opened on OSX</li>
2023 <li>Multiple structure views can be opened and superposed
2024 without timeout for structures with multiple models or
2025 multiple sequences in alignment</li>
2026 <li>Cannot import or associated local PDB files without a
2027 PDB ID HEADER line</li>
2028 <li>RMSD is not output in Jmol console when superposition
2030 <li>Drag and drop of URL from Browser fails for Linux and
2031 OSX versions earlier than El Capitan</li>
2032 <li>ENA client ignores invalid content from ENA server</li>
2033 <li>Exceptions are not raised in console when ENA client
2034 attempts to fetch non-existent IDs via Fetch DB Refs UI
2036 <li>Exceptions are not raised in console when a new view
2037 is created on the alignment</li>
2038 <li>OSX right-click fixed for group selections: CMD-click
2039 to insert/remove gaps in groups and CTRL-click to open group
2042 <em>Build and deployment</em>
2044 <li>URL link checker now copes with multi-line anchor
2047 <em>New Known Issues</em>
2049 <li>Drag and drop from URL links in browsers do not work
2056 <td width="60" nowrap>
2057 <div align="center">
2058 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2061 <td><em>General</em>
2064 <!-- JAL-2124 -->Updated Spanish translations.
2067 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2068 for importing structure data to Jalview. Enables mmCIF and
2072 <!-- JAL-192 --->Alignment ruler shows positions relative to
2076 <!-- JAL-2202 -->Position/residue shown in status bar when
2077 mousing over sequence associated annotation
2080 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2084 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2085 '()', canonical '[]' and invalid '{}' base pair populations
2089 <!-- JAL-2092 -->Feature settings popup menu options for
2090 showing or hiding columns containing a feature
2093 <!-- JAL-1557 -->Edit selected group by double clicking on
2094 group and sequence associated annotation labels
2097 <!-- JAL-2236 -->Sequence name added to annotation label in
2098 select/hide columns by annotation and colour by annotation
2102 </ul> <em>Application</em>
2105 <!-- JAL-2050-->Automatically hide introns when opening a
2106 gene/transcript view
2109 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2113 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2114 structure mappings with the EMBL-EBI PDBe SIFTS database
2117 <!-- JAL-2079 -->Updated download sites used for Rfam and
2118 Pfam sources to xfam.org
2121 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2124 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2125 over sequences in Jalview
2128 <!-- JAL-2027-->Support for reverse-complement coding
2129 regions in ENA and EMBL
2132 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2133 for record retrieval via ENA rest API
2136 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2140 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2141 groovy script execution
2144 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2145 alignment window's Calculate menu
2148 <!-- JAL-1812 -->Allow groovy scripts that call
2149 Jalview.getAlignFrames() to run in headless mode
2152 <!-- JAL-2068 -->Support for creating new alignment
2153 calculation workers from groovy scripts
2156 <!-- JAL-1369 --->Store/restore reference sequence in
2160 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2161 associations are now saved/restored from project
2164 <!-- JAL-1993 -->Database selection dialog always shown
2165 before sequence fetcher is opened
2168 <!-- JAL-2183 -->Double click on an entry in Jalview's
2169 database chooser opens a sequence fetcher
2172 <!-- JAL-1563 -->Free-text search client for UniProt using
2173 the UniProt REST API
2176 <!-- JAL-2168 -->-nonews command line parameter to prevent
2177 the news reader opening
2180 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2181 querying stored in preferences
2184 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2188 <!-- JAL-1977-->Tooltips shown on database chooser
2191 <!-- JAL-391 -->Reverse complement function in calculate
2192 menu for nucleotide sequences
2195 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2196 and feature counts preserves alignment ordering (and
2197 debugged for complex feature sets).
2200 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2201 viewing structures with Jalview 2.10
2204 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2205 genome, transcript CCDS and gene ids via the Ensembl and
2206 Ensembl Genomes REST API
2209 <!-- JAL-2049 -->Protein sequence variant annotation
2210 computed for 'sequence_variant' annotation on CDS regions
2214 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2218 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2219 Ref Fetcher fails to match, or otherwise updates sequence
2220 data from external database records.
2223 <!-- JAL-2154 -->Revised Jalview Project format for
2224 efficient recovery of sequence coding and alignment
2225 annotation relationships.
2227 </ul> <!-- <em>Applet</em>
2238 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2242 <!-- JAL-2018-->Export features in Jalview format (again)
2243 includes graduated colourschemes
2246 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2247 working with big alignments and lots of hidden columns
2250 <!-- JAL-2053-->Hidden column markers not always rendered
2251 at right of alignment window
2254 <!-- JAL-2067 -->Tidied up links in help file table of
2258 <!-- JAL-2072 -->Feature based tree calculation not shown
2262 <!-- JAL-2075 -->Hidden columns ignored during feature
2263 based tree calculation
2266 <!-- JAL-2065 -->Alignment view stops updating when show
2267 unconserved enabled for group on alignment
2270 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2274 <!-- JAL-2146 -->Alignment column in status incorrectly
2275 shown as "Sequence position" when mousing over
2279 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2280 hidden columns present
2283 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2284 user created annotation added to alignment
2287 <!-- JAL-1841 -->RNA Structure consensus only computed for
2288 '()' base pair annotation
2291 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2292 in zero scores for all base pairs in RNA Structure
2296 <!-- JAL-2174-->Extend selection with columns containing
2300 <!-- JAL-2275 -->Pfam format writer puts extra space at
2301 beginning of sequence
2304 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2308 <!-- JAL-2238 -->Cannot create groups on an alignment from
2309 from a tree when t-coffee scores are shown
2312 <!-- JAL-1836,1967 -->Cannot import and view PDB
2313 structures with chains containing negative resnums (4q4h)
2316 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2320 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2321 to Clustal, PIR and PileUp output
2324 <!-- JAL-2008 -->Reordering sequence features that are
2325 not visible causes alignment window to repaint
2328 <!-- JAL-2006 -->Threshold sliders don't work in
2329 graduated colour and colour by annotation row for e-value
2330 scores associated with features and annotation rows
2333 <!-- JAL-1797 -->amino acid physicochemical conservation
2334 calculation should be case independent
2337 <!-- JAL-2173 -->Remove annotation also updates hidden
2341 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2342 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2343 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2346 <!-- JAL-2065 -->Null pointer exceptions and redraw
2347 problems when reference sequence defined and 'show
2348 non-conserved' enabled
2351 <!-- JAL-1306 -->Quality and Conservation are now shown on
2352 load even when Consensus calculation is disabled
2355 <!-- JAL-1932 -->Remove right on penultimate column of
2356 alignment does nothing
2359 <em>Application</em>
2362 <!-- JAL-1552-->URLs and links can't be imported by
2363 drag'n'drop on OSX when launched via webstart (note - not
2364 yet fixed for El Capitan)
2367 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2368 output when running on non-gb/us i18n platforms
2371 <!-- JAL-1944 -->Error thrown when exporting a view with
2372 hidden sequences as flat-file alignment
2375 <!-- JAL-2030-->InstallAnywhere distribution fails when
2379 <!-- JAL-2080-->Jalview very slow to launch via webstart
2380 (also hotfix for 2.9.0b2)
2383 <!-- JAL-2085 -->Cannot save project when view has a
2384 reference sequence defined
2387 <!-- JAL-1011 -->Columns are suddenly selected in other
2388 alignments and views when revealing hidden columns
2391 <!-- JAL-1989 -->Hide columns not mirrored in complement
2392 view in a cDNA/Protein splitframe
2395 <!-- JAL-1369 -->Cannot save/restore representative
2396 sequence from project when only one sequence is
2400 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2401 in Structure Chooser
2404 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2405 structure consensus didn't refresh annotation panel
2408 <!-- JAL-1962 -->View mapping in structure view shows
2409 mappings between sequence and all chains in a PDB file
2412 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2413 dialogs format columns correctly, don't display array
2414 data, sort columns according to type
2417 <!-- JAL-1975 -->Export complete shown after destination
2418 file chooser is cancelled during an image export
2421 <!-- JAL-2025 -->Error when querying PDB Service with
2422 sequence name containing special characters
2425 <!-- JAL-2024 -->Manual PDB structure querying should be
2429 <!-- JAL-2104 -->Large tooltips with broken HTML
2430 formatting don't wrap
2433 <!-- JAL-1128 -->Figures exported from wrapped view are
2434 truncated so L looks like I in consensus annotation
2437 <!-- JAL-2003 -->Export features should only export the
2438 currently displayed features for the current selection or
2442 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2443 after fetching cross-references, and restoring from
2447 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2448 followed in the structure viewer
2451 <!-- JAL-2163 -->Titles for individual alignments in
2452 splitframe not restored from project
2455 <!-- JAL-2145 -->missing autocalculated annotation at
2456 trailing end of protein alignment in transcript/product
2457 splitview when pad-gaps not enabled by default
2460 <!-- JAL-1797 -->amino acid physicochemical conservation
2464 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2465 article has been read (reopened issue due to
2466 internationalisation problems)
2469 <!-- JAL-1960 -->Only offer PDB structures in structure
2470 viewer based on sequence name, PDB and UniProt
2475 <!-- JAL-1976 -->No progress bar shown during export of
2479 <!-- JAL-2213 -->Structures not always superimposed after
2480 multiple structures are shown for one or more sequences.
2483 <!-- JAL-1370 -->Reference sequence characters should not
2484 be replaced with '.' when 'Show unconserved' format option
2488 <!-- JAL-1823 -->Cannot specify chain code when entering
2489 specific PDB id for sequence
2492 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2493 'Export hidden sequences' is enabled, but 'export hidden
2494 columns' is disabled.
2497 <!--JAL-2026-->Best Quality option in structure chooser
2498 selects lowest rather than highest resolution structures
2502 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2503 to sequence mapping in 'View Mappings' report
2506 <!-- JAL-2284 -->Unable to read old Jalview projects that
2507 contain non-XML data added after Jalvew wrote project.
2510 <!-- JAL-2118 -->Newly created annotation row reorders
2511 after clicking on it to create new annotation for a
2515 <!-- JAL-1980 -->Null Pointer Exception raised when
2516 pressing Add on an orphaned cut'n'paste window.
2518 <!-- may exclude, this is an external service stability issue JAL-1941
2519 -- > RNA 3D structure not added via DSSR service</li> -->
2524 <!-- JAL-2151 -->Incorrect columns are selected when
2525 hidden columns present before start of sequence
2528 <!-- JAL-1986 -->Missing dependencies on applet pages
2532 <!-- JAL-1947 -->Overview pixel size changes when
2533 sequences are hidden in applet
2536 <!-- JAL-1996 -->Updated instructions for applet
2537 deployment on examples pages.
2544 <td width="60" nowrap>
2545 <div align="center">
2546 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2547 <em>16/10/2015</em></strong>
2550 <td><em>General</em>
2552 <li>Time stamps for signed Jalview application and applet
2557 <em>Application</em>
2559 <li>Duplicate group consensus and conservation rows
2560 shown when tree is partitioned</li>
2561 <li>Erratic behaviour when tree partitions made with
2562 multiple cDNA/Protein split views</li>
2568 <td width="60" nowrap>
2569 <div align="center">
2570 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2571 <em>8/10/2015</em></strong>
2574 <td><em>General</em>
2576 <li>Updated Spanish translations of localized text for
2578 </ul> <em>Application</em>
2580 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2581 <li>Signed OSX InstallAnywhere installer<br></li>
2582 <li>Support for per-sequence based annotations in BioJSON</li>
2583 </ul> <em>Applet</em>
2585 <li>Split frame example added to applet examples page</li>
2586 </ul> <em>Build and Deployment</em>
2589 <!-- JAL-1888 -->New ant target for running Jalview's test
2597 <li>Mapping of cDNA to protein in split frames
2598 incorrect when sequence start > 1</li>
2599 <li>Broken images in filter column by annotation dialog
2601 <li>Feature colours not parsed from features file</li>
2602 <li>Exceptions and incomplete link URLs recovered when
2603 loading a features file containing HTML tags in feature
2607 <em>Application</em>
2609 <li>Annotations corrupted after BioJS export and
2611 <li>Incorrect sequence limits after Fetch DB References
2612 with 'trim retrieved sequences'</li>
2613 <li>Incorrect warning about deleting all data when
2614 deleting selected columns</li>
2615 <li>Patch to build system for shipping properly signed
2616 JNLP templates for webstart launch</li>
2617 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2618 unreleased structures for download or viewing</li>
2619 <li>Tab/space/return keystroke operation of EMBL-PDBe
2620 fetcher/viewer dialogs works correctly</li>
2621 <li>Disabled 'minimise' button on Jalview windows
2622 running on OSX to workaround redraw hang bug</li>
2623 <li>Split cDNA/Protein view position and geometry not
2624 recovered from jalview project</li>
2625 <li>Initial enabled/disabled state of annotation menu
2626 sorter 'show autocalculated first/last' corresponds to
2628 <li>Restoring of Clustal, RNA Helices and T-Coffee
2629 color schemes from BioJSON</li>
2633 <li>Reorder sequences mirrored in cDNA/Protein split
2635 <li>Applet with Jmol examples not loading correctly</li>
2641 <td><div align="center">
2642 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2644 <td><em>General</em>
2646 <li>Linked visualisation and analysis of DNA and Protein
2649 <li>Translated cDNA alignments shown as split protein
2650 and DNA alignment views</li>
2651 <li>Codon consensus annotation for linked protein and
2652 cDNA alignment views</li>
2653 <li>Link cDNA or Protein product sequences by loading
2654 them onto Protein or cDNA alignments</li>
2655 <li>Reconstruct linked cDNA alignment from aligned
2656 protein sequences</li>
2659 <li>Jmol integration updated to Jmol v14.2.14</li>
2660 <li>Import and export of Jalview alignment views as <a
2661 href="features/bioJsonFormat.html">BioJSON</a></li>
2662 <li>New alignment annotation file statements for
2663 reference sequences and marking hidden columns</li>
2664 <li>Reference sequence based alignment shading to
2665 highlight variation</li>
2666 <li>Select or hide columns according to alignment
2668 <li>Find option for locating sequences by description</li>
2669 <li>Conserved physicochemical properties shown in amino
2670 acid conservation row</li>
2671 <li>Alignments can be sorted by number of RNA helices</li>
2672 </ul> <em>Application</em>
2674 <li>New cDNA/Protein analysis capabilities
2676 <li>Get Cross-References should open a Split Frame
2677 view with cDNA/Protein</li>
2678 <li>Detect when nucleotide sequences and protein
2679 sequences are placed in the same alignment</li>
2680 <li>Split cDNA/Protein views are saved in Jalview
2685 <li>Use REST API to talk to Chimera</li>
2686 <li>Selected regions in Chimera are highlighted in linked
2687 Jalview windows</li>
2689 <li>VARNA RNA viewer updated to v3.93</li>
2690 <li>VARNA views are saved in Jalview Projects</li>
2691 <li>Pseudoknots displayed as Jalview RNA annotation can
2692 be shown in VARNA</li>
2694 <li>Make groups for selection uses marked columns as well
2695 as the active selected region</li>
2697 <li>Calculate UPGMA and NJ trees using sequence feature
2699 <li>New Export options
2701 <li>New Export Settings dialog to control hidden
2702 region export in flat file generation</li>
2704 <li>Export alignment views for display with the <a
2705 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2707 <li>Export scrollable SVG in HTML page</li>
2708 <li>Optional embedding of BioJSON data when exporting
2709 alignment figures to HTML</li>
2711 <li>3D structure retrieval and display
2713 <li>Free text and structured queries with the PDBe
2715 <li>PDBe Search API based discovery and selection of
2716 PDB structures for a sequence set</li>
2720 <li>JPred4 employed for protein secondary structure
2722 <li>Hide Insertions menu option to hide unaligned columns
2723 for one or a group of sequences</li>
2724 <li>Automatically hide insertions in alignments imported
2725 from the JPred4 web server</li>
2726 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2727 system on OSX<br />LGPL libraries courtesy of <a
2728 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2730 <li>changed 'View nucleotide structure' submenu to 'View
2731 VARNA 2D Structure'</li>
2732 <li>change "View protein structure" menu option to "3D
2735 </ul> <em>Applet</em>
2737 <li>New layout for applet example pages</li>
2738 <li>New parameters to enable SplitFrame view
2739 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2740 <li>New example demonstrating linked viewing of cDNA and
2741 Protein alignments</li>
2742 </ul> <em>Development and deployment</em>
2744 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2745 <li>Include installation type and git revision in build
2746 properties and console log output</li>
2747 <li>Jalview Github organisation, and new github site for
2748 storing BioJsMSA Templates</li>
2749 <li>Jalview's unit tests now managed with TestNG</li>
2752 <!-- <em>General</em>
2754 </ul> --> <!-- issues resolved --> <em>Application</em>
2756 <li>Escape should close any open find dialogs</li>
2757 <li>Typo in select-by-features status report</li>
2758 <li>Consensus RNA secondary secondary structure
2759 predictions are not highlighted in amber</li>
2760 <li>Missing gap character in v2.7 example file means
2761 alignment appears unaligned when pad-gaps is not enabled</li>
2762 <li>First switch to RNA Helices colouring doesn't colour
2763 associated structure views</li>
2764 <li>ID width preference option is greyed out when auto
2765 width checkbox not enabled</li>
2766 <li>Stopped a warning dialog from being shown when
2767 creating user defined colours</li>
2768 <li>'View Mapping' in structure viewer shows sequence
2769 mappings for just that viewer's sequences</li>
2770 <li>Workaround for superposing PDB files containing
2771 multiple models in Chimera</li>
2772 <li>Report sequence position in status bar when hovering
2773 over Jmol structure</li>
2774 <li>Cannot output gaps as '.' symbols with Selection ->
2775 output to text box</li>
2776 <li>Flat file exports of alignments with hidden columns
2777 have incorrect sequence start/end</li>
2778 <li>'Aligning' a second chain to a Chimera structure from
2780 <li>Colour schemes applied to structure viewers don't
2781 work for nucleotide</li>
2782 <li>Loading/cut'n'pasting an empty or invalid file leads
2783 to a grey/invisible alignment window</li>
2784 <li>Exported Jpred annotation from a sequence region
2785 imports to different position</li>
2786 <li>Space at beginning of sequence feature tooltips shown
2787 on some platforms</li>
2788 <li>Chimera viewer 'View | Show Chain' menu is not
2790 <li>'New View' fails with a Null Pointer Exception in
2791 console if Chimera has been opened</li>
2792 <li>Mouseover to Chimera not working</li>
2793 <li>Miscellaneous ENA XML feature qualifiers not
2795 <li>NPE in annotation renderer after 'Extract Scores'</li>
2796 <li>If two structures in one Chimera window, mouseover of
2797 either sequence shows on first structure</li>
2798 <li>'Show annotations' options should not make
2799 non-positional annotations visible</li>
2800 <li>Subsequence secondary structure annotation not shown
2801 in right place after 'view flanking regions'</li>
2802 <li>File Save As type unset when current file format is
2804 <li>Save as '.jar' option removed for saving Jalview
2806 <li>Colour by Sequence colouring in Chimera more
2808 <li>Cannot 'add reference annotation' for a sequence in
2809 several views on same alignment</li>
2810 <li>Cannot show linked products for EMBL / ENA records</li>
2811 <li>Jalview's tooltip wraps long texts containing no
2813 </ul> <em>Applet</em>
2815 <li>Jmol to JalviewLite mouseover/link not working</li>
2816 <li>JalviewLite can't import sequences with ID
2817 descriptions containing angle brackets</li>
2818 </ul> <em>General</em>
2820 <li>Cannot export and reimport RNA secondary structure
2821 via jalview annotation file</li>
2822 <li>Random helix colour palette for colour by annotation
2823 with RNA secondary structure</li>
2824 <li>Mouseover to cDNA from STOP residue in protein
2825 translation doesn't work.</li>
2826 <li>hints when using the select by annotation dialog box</li>
2827 <li>Jmol alignment incorrect if PDB file has alternate CA
2829 <li>FontChooser message dialog appears to hang after
2830 choosing 1pt font</li>
2831 <li>Peptide secondary structure incorrectly imported from
2832 annotation file when annotation display text includes 'e' or
2834 <li>Cannot set colour of new feature type whilst creating
2836 <li>cDNA translation alignment should not be sequence
2837 order dependent</li>
2838 <li>'Show unconserved' doesn't work for lower case
2840 <li>Nucleotide ambiguity codes involving R not recognised</li>
2841 </ul> <em>Deployment and Documentation</em>
2843 <li>Applet example pages appear different to the rest of
2844 www.jalview.org</li>
2845 </ul> <em>Application Known issues</em>
2847 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2848 <li>Misleading message appears after trying to delete
2850 <li>Jalview icon not shown in dock after InstallAnywhere
2851 version launches</li>
2852 <li>Fetching EMBL reference for an RNA sequence results
2853 fails with a sequence mismatch</li>
2854 <li>Corrupted or unreadable alignment display when
2855 scrolling alignment to right</li>
2856 <li>ArrayIndexOutOfBoundsException thrown when remove
2857 empty columns called on alignment with ragged gapped ends</li>
2858 <li>auto calculated alignment annotation rows do not get
2859 placed above or below non-autocalculated rows</li>
2860 <li>Jalview dekstop becomes sluggish at full screen in
2861 ultra-high resolution</li>
2862 <li>Cannot disable consensus calculation independently of
2863 quality and conservation</li>
2864 <li>Mouseover highlighting between cDNA and protein can
2865 become sluggish with more than one splitframe shown</li>
2866 </ul> <em>Applet Known Issues</em>
2868 <li>Core PDB parsing code requires Jmol</li>
2869 <li>Sequence canvas panel goes white when alignment
2870 window is being resized</li>
2876 <td><div align="center">
2877 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2879 <td><em>General</em>
2881 <li>Updated Java code signing certificate donated by
2883 <li>Features and annotation preserved when performing
2884 pairwise alignment</li>
2885 <li>RNA pseudoknot annotation can be
2886 imported/exported/displayed</li>
2887 <li>'colour by annotation' can colour by RNA and
2888 protein secondary structure</li>
2889 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2890 post-hoc with 2.9 release</em>)
2893 </ul> <em>Application</em>
2895 <li>Extract and display secondary structure for sequences
2896 with 3D structures</li>
2897 <li>Support for parsing RNAML</li>
2898 <li>Annotations menu for layout
2900 <li>sort sequence annotation rows by alignment</li>
2901 <li>place sequence annotation above/below alignment
2904 <li>Output in Stockholm format</li>
2905 <li>Internationalisation: improved Spanish (es)
2907 <li>Structure viewer preferences tab</li>
2908 <li>Disorder and Secondary Structure annotation tracks
2909 shared between alignments</li>
2910 <li>UCSF Chimera launch and linked highlighting from
2912 <li>Show/hide all sequence associated annotation rows for
2913 all or current selection</li>
2914 <li>disorder and secondary structure predictions
2915 available as dataset annotation</li>
2916 <li>Per-sequence rna helices colouring</li>
2919 <li>Sequence database accessions imported when fetching
2920 alignments from Rfam</li>
2921 <li>update VARNA version to 3.91</li>
2923 <li>New groovy scripts for exporting aligned positions,
2924 conservation values, and calculating sum of pairs scores.</li>
2925 <li>Command line argument to set default JABAWS server</li>
2926 <li>include installation type in build properties and
2927 console log output</li>
2928 <li>Updated Jalview project format to preserve dataset
2932 <!-- issues resolved --> <em>Application</em>
2934 <li>Distinguish alignment and sequence associated RNA
2935 structure in structure->view->VARNA</li>
2936 <li>Raise dialog box if user deletes all sequences in an
2938 <li>Pressing F1 results in documentation opening twice</li>
2939 <li>Sequence feature tooltip is wrapped</li>
2940 <li>Double click on sequence associated annotation
2941 selects only first column</li>
2942 <li>Redundancy removal doesn't result in unlinked
2943 leaves shown in tree</li>
2944 <li>Undos after several redundancy removals don't undo
2946 <li>Hide sequence doesn't hide associated annotation</li>
2947 <li>User defined colours dialog box too big to fit on
2948 screen and buttons not visible</li>
2949 <li>author list isn't updated if already written to
2950 Jalview properties</li>
2951 <li>Popup menu won't open after retrieving sequence
2953 <li>File open window for associate PDB doesn't open</li>
2954 <li>Left-then-right click on a sequence id opens a
2955 browser search window</li>
2956 <li>Cannot open sequence feature shading/sort popup menu
2957 in feature settings dialog</li>
2958 <li>better tooltip placement for some areas of Jalview
2960 <li>Allow addition of JABAWS Server which doesn't
2961 pass validation</li>
2962 <li>Web services parameters dialog box is too large to
2964 <li>Muscle nucleotide alignment preset obscured by
2966 <li>JABAWS preset submenus don't contain newly
2967 defined user preset</li>
2968 <li>MSA web services warns user if they were launched
2969 with invalid input</li>
2970 <li>Jalview cannot contact DAS Registy when running on
2973 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2974 'Superpose with' submenu not shown when new view
2978 </ul> <!-- <em>Applet</em>
2980 </ul> <em>General</em>
2982 </ul>--> <em>Deployment and Documentation</em>
2984 <li>2G and 1G options in launchApp have no effect on
2985 memory allocation</li>
2986 <li>launchApp service doesn't automatically open
2987 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2989 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2990 InstallAnywhere reports cannot find valid JVM when Java
2991 1.7_055 is available
2993 </ul> <em>Application Known issues</em>
2996 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2997 corrupted or unreadable alignment display when scrolling
3001 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3002 retrieval fails but progress bar continues for DAS retrieval
3003 with large number of ID
3006 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3007 flatfile output of visible region has incorrect sequence
3011 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3012 rna structure consensus doesn't update when secondary
3013 structure tracks are rearranged
3016 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3017 invalid rna structure positional highlighting does not
3018 highlight position of invalid base pairs
3021 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3022 out of memory errors are not raised when saving Jalview
3023 project from alignment window file menu
3026 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3027 Switching to RNA Helices colouring doesn't propagate to
3031 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3032 colour by RNA Helices not enabled when user created
3033 annotation added to alignment
3036 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3037 Jalview icon not shown on dock in Mountain Lion/Webstart
3039 </ul> <em>Applet Known Issues</em>
3042 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3043 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3046 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3047 Jalview and Jmol example not compatible with IE9
3050 <li>Sort by annotation score doesn't reverse order
3056 <td><div align="center">
3057 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3060 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3063 <li>Internationalisation of user interface (usually
3064 called i18n support) and translation for Spanish locale</li>
3065 <li>Define/Undefine group on current selection with
3066 Ctrl-G/Shift Ctrl-G</li>
3067 <li>Improved group creation/removal options in
3068 alignment/sequence Popup menu</li>
3069 <li>Sensible precision for symbol distribution
3070 percentages shown in logo tooltip.</li>
3071 <li>Annotation panel height set according to amount of
3072 annotation when alignment first opened</li>
3073 </ul> <em>Application</em>
3075 <li>Interactive consensus RNA secondary structure
3076 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3077 <li>Select columns containing particular features from
3078 Feature Settings dialog</li>
3079 <li>View all 'representative' PDB structures for selected
3081 <li>Update Jalview project format:
3083 <li>New file extension for Jalview projects '.jvp'</li>
3084 <li>Preserve sequence and annotation dataset (to
3085 store secondary structure annotation,etc)</li>
3086 <li>Per group and alignment annotation and RNA helix
3090 <li>New similarity measures for PCA and Tree calculation
3092 <li>Experimental support for retrieval and viewing of
3093 flanking regions for an alignment</li>
3097 <!-- issues resolved --> <em>Application</em>
3099 <li>logo keeps spinning and status remains at queued or
3100 running after job is cancelled</li>
3101 <li>cannot export features from alignments imported from
3102 Jalview/VAMSAS projects</li>
3103 <li>Buggy slider for web service parameters that take
3105 <li>Newly created RNA secondary structure line doesn't
3106 have 'display all symbols' flag set</li>
3107 <li>T-COFFEE alignment score shading scheme and other
3108 annotation shading not saved in Jalview project</li>
3109 <li>Local file cannot be loaded in freshly downloaded
3111 <li>Jalview icon not shown on dock in Mountain
3113 <li>Load file from desktop file browser fails</li>
3114 <li>Occasional NPE thrown when calculating large trees</li>
3115 <li>Cannot reorder or slide sequences after dragging an
3116 alignment onto desktop</li>
3117 <li>Colour by annotation dialog throws NPE after using
3118 'extract scores' function</li>
3119 <li>Loading/cut'n'pasting an empty file leads to a grey
3120 alignment window</li>
3121 <li>Disorder thresholds rendered incorrectly after
3122 performing IUPred disorder prediction</li>
3123 <li>Multiple group annotated consensus rows shown when
3124 changing 'normalise logo' display setting</li>
3125 <li>Find shows blank dialog after 'finished searching' if
3126 nothing matches query</li>
3127 <li>Null Pointer Exceptions raised when sorting by
3128 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3130 <li>Errors in Jmol console when structures in alignment
3131 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3133 <li>Not all working JABAWS services are shown in
3135 <li>JAVAWS version of Jalview fails to launch with
3136 'invalid literal/length code'</li>
3137 <li>Annotation/RNA Helix colourschemes cannot be applied
3138 to alignment with groups (actually fixed in 2.8.0b1)</li>
3139 <li>RNA Helices and T-Coffee Scores available as default
3142 </ul> <em>Applet</em>
3144 <li>Remove group option is shown even when selection is
3146 <li>Apply to all groups ticked but colourscheme changes
3147 don't affect groups</li>
3148 <li>Documented RNA Helices and T-Coffee Scores as valid
3149 colourscheme name</li>
3150 <li>Annotation labels drawn on sequence IDs when
3151 Annotation panel is not displayed</li>
3152 <li>Increased font size for dropdown menus on OSX and
3153 embedded windows</li>
3154 </ul> <em>Other</em>
3156 <li>Consensus sequence for alignments/groups with a
3157 single sequence were not calculated</li>
3158 <li>annotation files that contain only groups imported as
3159 annotation and junk sequences</li>
3160 <li>Fasta files with sequences containing '*' incorrectly
3161 recognised as PFAM or BLC</li>
3162 <li>conservation/PID slider apply all groups option
3163 doesn't affect background (2.8.0b1)
3165 <li>redundancy highlighting is erratic at 0% and 100%</li>
3166 <li>Remove gapped columns fails for sequences with ragged
3168 <li>AMSA annotation row with leading spaces is not
3169 registered correctly on import</li>
3170 <li>Jalview crashes when selecting PCA analysis for
3171 certain alignments</li>
3172 <li>Opening the colour by annotation dialog for an
3173 existing annotation based 'use original colours'
3174 colourscheme loses original colours setting</li>
3179 <td><div align="center">
3180 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3181 <em>30/1/2014</em></strong>
3185 <li>Trusted certificates for JalviewLite applet and
3186 Jalview Desktop application<br />Certificate was donated by
3187 <a href="https://www.certum.eu">Certum</a> to the Jalview
3188 open source project).
3190 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3191 <li>Output in Stockholm format</li>
3192 <li>Allow import of data from gzipped files</li>
3193 <li>Export/import group and sequence associated line
3194 graph thresholds</li>
3195 <li>Nucleotide substitution matrix that supports RNA and
3196 ambiguity codes</li>
3197 <li>Allow disorder predictions to be made on the current
3198 selection (or visible selection) in the same way that JPred
3200 <li>Groovy scripting for headless Jalview operation</li>
3201 </ul> <em>Other improvements</em>
3203 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3204 <li>COMBINE statement uses current SEQUENCE_REF and
3205 GROUP_REF scope to group annotation rows</li>
3206 <li>Support '' style escaping of quotes in Newick
3208 <li>Group options for JABAWS service by command line name</li>
3209 <li>Empty tooltip shown for JABA service options with a
3210 link but no description</li>
3211 <li>Select primary source when selecting authority in
3212 database fetcher GUI</li>
3213 <li>Add .mfa to FASTA file extensions recognised by
3215 <li>Annotation label tooltip text wrap</li>
3220 <li>Slow scrolling when lots of annotation rows are
3222 <li>Lots of NPE (and slowness) after creating RNA
3223 secondary structure annotation line</li>
3224 <li>Sequence database accessions not imported when
3225 fetching alignments from Rfam</li>
3226 <li>Incorrect SHMR submission for sequences with
3228 <li>View all structures does not always superpose
3230 <li>Option widgets in service parameters not updated to
3231 reflect user or preset settings</li>
3232 <li>Null pointer exceptions for some services without
3233 presets or adjustable parameters</li>
3234 <li>Discover PDB IDs entry in structure menu doesn't
3235 discover PDB xRefs</li>
3236 <li>Exception encountered while trying to retrieve
3237 features with DAS</li>
3238 <li>Lowest value in annotation row isn't coloured
3239 when colour by annotation (per sequence) is coloured</li>
3240 <li>Keyboard mode P jumps to start of gapped region when
3241 residue follows a gap</li>
3242 <li>Jalview appears to hang importing an alignment with
3243 Wrap as default or after enabling Wrap</li>
3244 <li>'Right click to add annotations' message
3245 shown in wrap mode when no annotations present</li>
3246 <li>Disorder predictions fail with NPE if no automatic
3247 annotation already exists on alignment</li>
3248 <li>oninit javascript function should be called after
3249 initialisation completes</li>
3250 <li>Remove redundancy after disorder prediction corrupts
3251 alignment window display</li>
3252 <li>Example annotation file in documentation is invalid</li>
3253 <li>Grouped line graph annotation rows are not exported
3254 to annotation file</li>
3255 <li>Multi-harmony analysis cannot be run when only two
3257 <li>Cannot create multiple groups of line graphs with
3258 several 'combine' statements in annotation file</li>
3259 <li>Pressing return several times causes Number Format
3260 exceptions in keyboard mode</li>
3261 <li>Multi-harmony (SHMMR) method doesn't submit
3262 correct partitions for input data</li>
3263 <li>Translation from DNA to Amino Acids fails</li>
3264 <li>Jalview fail to load newick tree with quoted label</li>
3265 <li>--headless flag isn't understood</li>
3266 <li>ClassCastException when generating EPS in headless
3268 <li>Adjusting sequence-associated shading threshold only
3269 changes one row's threshold</li>
3270 <li>Preferences and Feature settings panel panel
3271 doesn't open</li>
3272 <li>hide consensus histogram also hides conservation and
3273 quality histograms</li>
3278 <td><div align="center">
3279 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3281 <td><em>Application</em>
3283 <li>Support for JABAWS 2.0 Services (AACon alignment
3284 conservation, protein disorder and Clustal Omega)</li>
3285 <li>JABAWS server status indicator in Web Services
3287 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3288 in Jalview alignment window</li>
3289 <li>Updated Jalview build and deploy framework for OSX
3290 mountain lion, windows 7, and 8</li>
3291 <li>Nucleotide substitution matrix for PCA that supports
3292 RNA and ambiguity codes</li>
3294 <li>Improved sequence database retrieval GUI</li>
3295 <li>Support fetching and database reference look up
3296 against multiple DAS sources (Fetch all from in 'fetch db
3298 <li>Jalview project improvements
3300 <li>Store and retrieve the 'belowAlignment'
3301 flag for annotation</li>
3302 <li>calcId attribute to group annotation rows on the
3304 <li>Store AACon calculation settings for a view in
3305 Jalview project</li>
3309 <li>horizontal scrolling gesture support</li>
3310 <li>Visual progress indicator when PCA calculation is
3312 <li>Simpler JABA web services menus</li>
3313 <li>visual indication that web service results are still
3314 being retrieved from server</li>
3315 <li>Serialise the dialogs that are shown when Jalview
3316 starts up for first time</li>
3317 <li>Jalview user agent string for interacting with HTTP
3319 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3321 <li>Examples directory and Groovy library included in
3322 InstallAnywhere distribution</li>
3323 </ul> <em>Applet</em>
3325 <li>RNA alignment and secondary structure annotation
3326 visualization applet example</li>
3327 </ul> <em>General</em>
3329 <li>Normalise option for consensus sequence logo</li>
3330 <li>Reset button in PCA window to return dimensions to
3332 <li>Allow seqspace or Jalview variant of alignment PCA
3334 <li>PCA with either nucleic acid and protein substitution
3336 <li>Allow windows containing HTML reports to be exported
3338 <li>Interactive display and editing of RNA secondary
3339 structure contacts</li>
3340 <li>RNA Helix Alignment Colouring</li>
3341 <li>RNA base pair logo consensus</li>
3342 <li>Parse sequence associated secondary structure
3343 information in Stockholm files</li>
3344 <li>HTML Export database accessions and annotation
3345 information presented in tooltip for sequences</li>
3346 <li>Import secondary structure from LOCARNA clustalw
3347 style RNA alignment files</li>
3348 <li>import and visualise T-COFFEE quality scores for an
3350 <li>'colour by annotation' per sequence option to
3351 shade each sequence according to its associated alignment
3353 <li>New Jalview Logo</li>
3354 </ul> <em>Documentation and Development</em>
3356 <li>documentation for score matrices used in Jalview</li>
3357 <li>New Website!</li>
3359 <td><em>Application</em>
3361 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3362 wsdbfetch REST service</li>
3363 <li>Stop windows being moved outside desktop on OSX</li>
3364 <li>Filetype associations not installed for webstart
3366 <li>Jalview does not always retrieve progress of a JABAWS
3367 job execution in full once it is complete</li>
3368 <li>revise SHMR RSBS definition to ensure alignment is
3369 uploaded via ali_file parameter</li>
3370 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3371 <li>View all structures superposed fails with exception</li>
3372 <li>Jnet job queues forever if a very short sequence is
3373 submitted for prediction</li>
3374 <li>Cut and paste menu not opened when mouse clicked on
3376 <li>Putting fractional value into integer text box in
3377 alignment parameter dialog causes Jalview to hang</li>
3378 <li>Structure view highlighting doesn't work on
3380 <li>View all structures fails with exception shown in
3382 <li>Characters in filename associated with PDBEntry not
3383 escaped in a platform independent way</li>
3384 <li>Jalview desktop fails to launch with exception when
3386 <li>Tree calculation reports 'you must have 2 or more
3387 sequences selected' when selection is empty</li>
3388 <li>Jalview desktop fails to launch with jar signature
3389 failure when java web start temporary file caching is
3391 <li>DAS Sequence retrieval with range qualification
3392 results in sequence xref which includes range qualification</li>
3393 <li>Errors during processing of command line arguments
3394 cause progress bar (JAL-898) to be removed</li>
3395 <li>Replace comma for semi-colon option not disabled for
3396 DAS sources in sequence fetcher</li>
3397 <li>Cannot close news reader when JABAWS server warning
3398 dialog is shown</li>
3399 <li>Option widgets not updated to reflect user settings</li>
3400 <li>Edited sequence not submitted to web service</li>
3401 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3402 <li>InstallAnywhere installer doesn't unpack and run
3403 on OSX Mountain Lion</li>
3404 <li>Annotation panel not given a scroll bar when
3405 sequences with alignment annotation are pasted into the
3407 <li>Sequence associated annotation rows not associated
3408 when loaded from Jalview project</li>
3409 <li>Browser launch fails with NPE on java 1.7</li>
3410 <li>JABAWS alignment marked as finished when job was
3411 cancelled or job failed due to invalid input</li>
3412 <li>NPE with v2.7 example when clicking on Tree
3413 associated with all views</li>
3414 <li>Exceptions when copy/paste sequences with grouped
3415 annotation rows to new window</li>
3416 </ul> <em>Applet</em>
3418 <li>Sequence features are momentarily displayed before
3419 they are hidden using hidefeaturegroups applet parameter</li>
3420 <li>loading features via javascript API automatically
3421 enables feature display</li>
3422 <li>scrollToColumnIn javascript API method doesn't
3424 </ul> <em>General</em>
3426 <li>Redundancy removal fails for rna alignment</li>
3427 <li>PCA calculation fails when sequence has been selected
3428 and then deselected</li>
3429 <li>PCA window shows grey box when first opened on OSX</li>
3430 <li>Letters coloured pink in sequence logo when alignment
3431 coloured with clustalx</li>
3432 <li>Choosing fonts without letter symbols defined causes
3433 exceptions and redraw errors</li>
3434 <li>Initial PCA plot view is not same as manually
3435 reconfigured view</li>
3436 <li>Grouped annotation graph label has incorrect line
3438 <li>Grouped annotation graph label display is corrupted
3439 for lots of labels</li>
3444 <div align="center">
3445 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3448 <td><em>Application</em>
3450 <li>Jalview Desktop News Reader</li>
3451 <li>Tweaked default layout of web services menu</li>
3452 <li>View/alignment association menu to enable user to
3453 easily specify which alignment a multi-structure view takes
3454 its colours/correspondences from</li>
3455 <li>Allow properties file location to be specified as URL</li>
3456 <li>Extend Jalview project to preserve associations
3457 between many alignment views and a single Jmol display</li>
3458 <li>Store annotation row height in Jalview project file</li>
3459 <li>Annotation row column label formatting attributes
3460 stored in project file</li>
3461 <li>Annotation row order for auto-calculated annotation
3462 rows preserved in Jalview project file</li>
3463 <li>Visual progress indication when Jalview state is
3464 saved using Desktop window menu</li>
3465 <li>Visual indication that command line arguments are
3466 still being processed</li>
3467 <li>Groovy script execution from URL</li>
3468 <li>Colour by annotation default min and max colours in
3470 <li>Automatically associate PDB files dragged onto an
3471 alignment with sequences that have high similarity and
3473 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3474 <li>'view structures' option to open many
3475 structures in same window</li>
3476 <li>Sort associated views menu option for tree panel</li>
3477 <li>Group all JABA and non-JABA services for a particular
3478 analysis function in its own submenu</li>
3479 </ul> <em>Applet</em>
3481 <li>Userdefined and autogenerated annotation rows for
3483 <li>Adjustment of alignment annotation pane height</li>
3484 <li>Annotation scrollbar for annotation panel</li>
3485 <li>Drag to reorder annotation rows in annotation panel</li>
3486 <li>'automaticScrolling' parameter</li>
3487 <li>Allow sequences with partial ID string matches to be
3488 annotated from GFF/Jalview features files</li>
3489 <li>Sequence logo annotation row in applet</li>
3490 <li>Absolute paths relative to host server in applet
3491 parameters are treated as such</li>
3492 <li>New in the JalviewLite javascript API:
3494 <li>JalviewLite.js javascript library</li>
3495 <li>Javascript callbacks for
3497 <li>Applet initialisation</li>
3498 <li>Sequence/alignment mouse-overs and selections</li>
3501 <li>scrollTo row and column alignment scrolling
3503 <li>Select sequence/alignment regions from javascript</li>
3504 <li>javascript structure viewer harness to pass
3505 messages between Jmol and Jalview when running as
3506 distinct applets</li>
3507 <li>sortBy method</li>
3508 <li>Set of applet and application examples shipped
3509 with documentation</li>
3510 <li>New example to demonstrate JalviewLite and Jmol
3511 javascript message exchange</li>
3513 </ul> <em>General</em>
3515 <li>Enable Jmol displays to be associated with multiple
3516 multiple alignments</li>
3517 <li>Option to automatically sort alignment with new tree</li>
3518 <li>User configurable link to enable redirects to a
3519 www.Jalview.org mirror</li>
3520 <li>Jmol colours option for Jmol displays</li>
3521 <li>Configurable newline string when writing alignment
3522 and other flat files</li>
3523 <li>Allow alignment annotation description lines to
3524 contain html tags</li>
3525 </ul> <em>Documentation and Development</em>
3527 <li>Add groovy test harness for bulk load testing to
3529 <li>Groovy script to load and align a set of sequences
3530 using a web service before displaying the result in the
3531 Jalview desktop</li>
3532 <li>Restructured javascript and applet api documentation</li>
3533 <li>Ant target to publish example html files with applet
3535 <li>Netbeans project for building Jalview from source</li>
3536 <li>ant task to create online javadoc for Jalview source</li>
3538 <td><em>Application</em>
3540 <li>User defined colourscheme throws exception when
3541 current built in colourscheme is saved as new scheme</li>
3542 <li>AlignFrame->Save in application pops up save
3543 dialog for valid filename/format</li>
3544 <li>Cannot view associated structure for UniProt sequence</li>
3545 <li>PDB file association breaks for UniProt sequence
3547 <li>Associate PDB from file dialog does not tell you
3548 which sequence is to be associated with the file</li>
3549 <li>Find All raises null pointer exception when query
3550 only matches sequence IDs</li>
3551 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3552 <li>Jalview project with Jmol views created with Jalview
3553 2.4 cannot be loaded</li>
3554 <li>Filetype associations not installed for webstart
3556 <li>Two or more chains in a single PDB file associated
3557 with sequences in different alignments do not get coloured
3558 by their associated sequence</li>
3559 <li>Visibility status of autocalculated annotation row
3560 not preserved when project is loaded</li>
3561 <li>Annotation row height and visibility attributes not
3562 stored in Jalview project</li>
3563 <li>Tree bootstraps are not preserved when saved as a
3564 Jalview project</li>
3565 <li>Envision2 workflow tooltips are corrupted</li>
3566 <li>Enabling show group conservation also enables colour
3567 by conservation</li>
3568 <li>Duplicate group associated conservation or consensus
3569 created on new view</li>
3570 <li>Annotation scrollbar not displayed after 'show
3571 all hidden annotation rows' option selected</li>
3572 <li>Alignment quality not updated after alignment
3573 annotation row is hidden then shown</li>
3574 <li>Preserve colouring of structures coloured by
3575 sequences in pre Jalview 2.7 projects</li>
3576 <li>Web service job parameter dialog is not laid out
3578 <li>Web services menu not refreshed after 'reset
3579 services' button is pressed in preferences</li>
3580 <li>Annotation off by one in Jalview v2_3 example project</li>
3581 <li>Structures imported from file and saved in project
3582 get name like jalview_pdb1234.txt when reloaded</li>
3583 <li>Jalview does not always retrieve progress of a JABAWS
3584 job execution in full once it is complete</li>
3585 </ul> <em>Applet</em>
3587 <li>Alignment height set incorrectly when lots of
3588 annotation rows are displayed</li>
3589 <li>Relative URLs in feature HTML text not resolved to
3591 <li>View follows highlighting does not work for positions
3593 <li><= shown as = in tooltip</li>
3594 <li>Export features raises exception when no features
3596 <li>Separator string used for serialising lists of IDs
3597 for javascript api is modified when separator string
3598 provided as parameter</li>
3599 <li>Null pointer exception when selecting tree leaves for
3600 alignment with no existing selection</li>
3601 <li>Relative URLs for datasources assumed to be relative
3602 to applet's codebase</li>
3603 <li>Status bar not updated after finished searching and
3604 search wraps around to first result</li>
3605 <li>StructureSelectionManager instance shared between
3606 several Jalview applets causes race conditions and memory
3608 <li>Hover tooltip and mouseover of position on structure
3609 not sent from Jmol in applet</li>
3610 <li>Certain sequences of javascript method calls to
3611 applet API fatally hang browser</li>
3612 </ul> <em>General</em>
3614 <li>View follows structure mouseover scrolls beyond
3615 position with wrapped view and hidden regions</li>
3616 <li>Find sequence position moves to wrong residue
3617 with/without hidden columns</li>
3618 <li>Sequence length given in alignment properties window
3620 <li>InvalidNumberFormat exceptions thrown when trying to
3621 import PDB like structure files</li>
3622 <li>Positional search results are only highlighted
3623 between user-supplied sequence start/end bounds</li>
3624 <li>End attribute of sequence is not validated</li>
3625 <li>Find dialog only finds first sequence containing a
3626 given sequence position</li>
3627 <li>Sequence numbering not preserved in MSF alignment
3629 <li>Jalview PDB file reader does not extract sequence
3630 from nucleotide chains correctly</li>
3631 <li>Structure colours not updated when tree partition
3632 changed in alignment</li>
3633 <li>Sequence associated secondary structure not correctly
3634 parsed in interleaved stockholm</li>
3635 <li>Colour by annotation dialog does not restore current
3637 <li>Hiding (nearly) all sequences doesn't work
3639 <li>Sequences containing lowercase letters are not
3640 properly associated with their pdb files</li>
3641 </ul> <em>Documentation and Development</em>
3643 <li>schemas/JalviewWsParamSet.xsd corrupted by
3644 ApplyCopyright tool</li>
3649 <div align="center">
3650 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3653 <td><em>Application</em>
3655 <li>New warning dialog when the Jalview Desktop cannot
3656 contact web services</li>
3657 <li>JABA service parameters for a preset are shown in
3658 service job window</li>
3659 <li>JABA Service menu entries reworded</li>
3663 <li>Modeller PIR IO broken - cannot correctly import a
3664 pir file emitted by Jalview</li>
3665 <li>Existing feature settings transferred to new
3666 alignment view created from cut'n'paste</li>
3667 <li>Improved test for mixed amino/nucleotide chains when
3668 parsing PDB files</li>
3669 <li>Consensus and conservation annotation rows
3670 occasionally become blank for all new windows</li>
3671 <li>Exception raised when right clicking above sequences
3672 in wrapped view mode</li>
3673 </ul> <em>Application</em>
3675 <li>multiple multiply aligned structure views cause cpu
3676 usage to hit 100% and computer to hang</li>
3677 <li>Web Service parameter layout breaks for long user
3678 parameter names</li>
3679 <li>Jaba service discovery hangs desktop if Jaba server
3686 <div align="center">
3687 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3690 <td><em>Application</em>
3692 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3693 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3696 <li>Web Services preference tab</li>
3697 <li>Analysis parameters dialog box and user defined
3699 <li>Improved speed and layout of Envision2 service menu</li>
3700 <li>Superpose structures using associated sequence
3702 <li>Export coordinates and projection as CSV from PCA
3704 </ul> <em>Applet</em>
3706 <li>enable javascript: execution by the applet via the
3707 link out mechanism</li>
3708 </ul> <em>Other</em>
3710 <li>Updated the Jmol Jalview interface to work with Jmol
3712 <li>The Jalview Desktop and JalviewLite applet now
3713 require Java 1.5</li>
3714 <li>Allow Jalview feature colour specification for GFF
3715 sequence annotation files</li>
3716 <li>New 'colour by label' keword in Jalview feature file
3717 type colour specification</li>
3718 <li>New Jalview Desktop Groovy API method that allows a
3719 script to check if it being run in an interactive session or
3720 in a batch operation from the Jalview command line</li>
3724 <li>clustalx colourscheme colours Ds preferentially when
3725 both D+E are present in over 50% of the column</li>
3726 </ul> <em>Application</em>
3728 <li>typo in AlignmentFrame->View->Hide->all but
3729 selected Regions menu item</li>
3730 <li>sequence fetcher replaces ',' for ';' when the ',' is
3731 part of a valid accession ID</li>
3732 <li>fatal OOM if object retrieved by sequence fetcher
3733 runs out of memory</li>
3734 <li>unhandled Out of Memory Error when viewing pca
3735 analysis results</li>
3736 <li>InstallAnywhere builds fail to launch on OS X java
3737 10.5 update 4 (due to apple Java 1.6 update)</li>
3738 <li>Installanywhere Jalview silently fails to launch</li>
3739 </ul> <em>Applet</em>
3741 <li>Jalview.getFeatureGroups() raises an
3742 ArrayIndexOutOfBoundsException if no feature groups are
3749 <div align="center">
3750 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3756 <li>Alignment prettyprinter doesn't cope with long
3758 <li>clustalx colourscheme colours Ds preferentially when
3759 both D+E are present in over 50% of the column</li>
3760 <li>nucleic acid structures retrieved from PDB do not
3761 import correctly</li>
3762 <li>More columns get selected than were clicked on when a
3763 number of columns are hidden</li>
3764 <li>annotation label popup menu not providing correct
3765 add/hide/show options when rows are hidden or none are
3767 <li>Stockholm format shown in list of readable formats,
3768 and parser copes better with alignments from RFAM.</li>
3769 <li>CSV output of consensus only includes the percentage
3770 of all symbols if sequence logo display is enabled</li>
3772 </ul> <em>Applet</em>
3774 <li>annotation panel disappears when annotation is
3776 </ul> <em>Application</em>
3778 <li>Alignment view not redrawn properly when new
3779 alignment opened where annotation panel is visible but no
3780 annotations are present on alignment</li>
3781 <li>pasted region containing hidden columns is
3782 incorrectly displayed in new alignment window</li>
3783 <li>Jalview slow to complete operations when stdout is
3784 flooded (fix is to close the Jalview console)</li>
3785 <li>typo in AlignmentFrame->View->Hide->all but
3786 selected Rregions menu item.</li>
3787 <li>inconsistent group submenu and Format submenu entry
3788 'Un' or 'Non'conserved</li>
3789 <li>Sequence feature settings are being shared by
3790 multiple distinct alignments</li>
3791 <li>group annotation not recreated when tree partition is
3793 <li>double click on group annotation to select sequences
3794 does not propagate to associated trees</li>
3795 <li>Mac OSX specific issues:
3797 <li>exception raised when mouse clicked on desktop
3798 window background</li>
3799 <li>Desktop menu placed on menu bar and application
3800 name set correctly</li>
3801 <li>sequence feature settings not wide enough for the
3802 save feature colourscheme button</li>
3811 <div align="center">
3812 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3815 <td><em>New Capabilities</em>
3817 <li>URL links generated from description line for
3818 regular-expression based URL links (applet and application)
3820 <li>Non-positional feature URL links are shown in link
3822 <li>Linked viewing of nucleic acid sequences and
3824 <li>Automatic Scrolling option in View menu to display
3825 the currently highlighted region of an alignment.</li>
3826 <li>Order an alignment by sequence length, or using the
3827 average score or total feature count for each sequence.</li>
3828 <li>Shading features by score or associated description</li>
3829 <li>Subdivide alignment and groups based on identity of
3830 selected subsequence (Make Groups from Selection).</li>
3831 <li>New hide/show options including Shift+Control+H to
3832 hide everything but the currently selected region.</li>
3833 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3834 </ul> <em>Application</em>
3836 <li>Fetch DB References capabilities and UI expanded to
3837 support retrieval from DAS sequence sources</li>
3838 <li>Local DAS Sequence sources can be added via the
3839 command line or via the Add local source dialog box.</li>
3840 <li>DAS Dbref and DbxRef feature types are parsed as
3841 database references and protein_name is parsed as
3842 description line (BioSapiens terms).</li>
3843 <li>Enable or disable non-positional feature and database
3844 references in sequence ID tooltip from View menu in
3846 <!-- <li>New hidden columns and rows and representatives capabilities
3847 in annotations file (in progress - not yet fully implemented)</li> -->
3848 <li>Group-associated consensus, sequence logos and
3849 conservation plots</li>
3850 <li>Symbol distributions for each column can be exported
3851 and visualized as sequence logos</li>
3852 <li>Optionally scale multi-character column labels to fit
3853 within each column of annotation row<!-- todo for applet -->
3855 <li>Optional automatic sort of associated alignment view
3856 when a new tree is opened.</li>
3857 <li>Jalview Java Console</li>
3858 <li>Better placement of desktop window when moving
3859 between different screens.</li>
3860 <li>New preference items for sequence ID tooltip and
3861 consensus annotation</li>
3862 <li>Client to submit sequences and IDs to Envision2
3864 <li><em>Vamsas Capabilities</em>
3866 <li>Improved VAMSAS synchronization (Jalview archive
3867 used to preserve views, structures, and tree display
3869 <li>Import of vamsas documents from disk or URL via
3871 <li>Sharing of selected regions between views and
3872 with other VAMSAS applications (Experimental feature!)</li>
3873 <li>Updated API to VAMSAS version 0.2</li>
3875 </ul> <em>Applet</em>
3877 <li>Middle button resizes annotation row height</li>
3880 <li>sortByTree (true/false) - automatically sort the
3881 associated alignment view by the tree when a new tree is
3883 <li>showTreeBootstraps (true/false) - show or hide
3884 branch bootstraps (default is to show them if available)</li>
3885 <li>showTreeDistances (true/false) - show or hide
3886 branch lengths (default is to show them if available)</li>
3887 <li>showUnlinkedTreeNodes (true/false) - indicate if
3888 unassociated nodes should be highlighted in the tree
3890 <li>heightScale and widthScale (1.0 or more) -
3891 increase the height or width of a cell in the alignment
3892 grid relative to the current font size.</li>
3895 <li>Non-positional features displayed in sequence ID
3897 </ul> <em>Other</em>
3899 <li>Features format: graduated colour definitions and
3900 specification of feature scores</li>
3901 <li>Alignment Annotations format: new keywords for group
3902 associated annotation (GROUP_REF) and annotation row display
3903 properties (ROW_PROPERTIES)</li>
3904 <li>XML formats extended to support graduated feature
3905 colourschemes, group associated annotation, and profile
3906 visualization settings.</li></td>
3909 <li>Source field in GFF files parsed as feature source
3910 rather than description</li>
3911 <li>Non-positional features are now included in sequence
3912 feature and gff files (controlled via non-positional feature
3913 visibility in tooltip).</li>
3914 <li>URL links generated for all feature links (bugfix)</li>
3915 <li>Added URL embedding instructions to features file
3917 <li>Codons containing ambiguous nucleotides translated as
3918 'X' in peptide product</li>
3919 <li>Match case switch in find dialog box works for both
3920 sequence ID and sequence string and query strings do not
3921 have to be in upper case to match case-insensitively.</li>
3922 <li>AMSA files only contain first column of
3923 multi-character column annotation labels</li>
3924 <li>Jalview Annotation File generation/parsing consistent
3925 with documentation (e.g. Stockholm annotation can be
3926 exported and re-imported)</li>
3927 <li>PDB files without embedded PDB IDs given a friendly
3929 <li>Find incrementally searches ID string matches as well
3930 as subsequence matches, and correctly reports total number
3934 <li>Better handling of exceptions during sequence
3936 <li>Dasobert generated non-positional feature URL
3937 link text excludes the start_end suffix</li>
3938 <li>DAS feature and source retrieval buttons disabled
3939 when fetch or registry operations in progress.</li>
3940 <li>PDB files retrieved from URLs are cached properly</li>
3941 <li>Sequence description lines properly shared via
3943 <li>Sequence fetcher fetches multiple records for all
3945 <li>Ensured that command line das feature retrieval
3946 completes before alignment figures are generated.</li>
3947 <li>Reduced time taken when opening file browser for
3949 <li>isAligned check prior to calculating tree, PCA or
3950 submitting an MSA to JNet now excludes hidden sequences.</li>
3951 <li>User defined group colours properly recovered
3952 from Jalview projects.</li>
3961 <div align="center">
3962 <strong>2.4.0.b2</strong><br> 28/10/2009
3967 <li>Experimental support for google analytics usage
3969 <li>Jalview privacy settings (user preferences and docs).</li>
3974 <li>Race condition in applet preventing startup in
3976 <li>Exception when feature created from selection beyond
3977 length of sequence.</li>
3978 <li>Allow synthetic PDB files to be imported gracefully</li>
3979 <li>Sequence associated annotation rows associate with
3980 all sequences with a given id</li>
3981 <li>Find function matches case-insensitively for sequence
3982 ID string searches</li>
3983 <li>Non-standard characters do not cause pairwise
3984 alignment to fail with exception</li>
3985 </ul> <em>Application Issues</em>
3987 <li>Sequences are now validated against EMBL database</li>
3988 <li>Sequence fetcher fetches multiple records for all
3990 </ul> <em>InstallAnywhere Issues</em>
3992 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3993 issue with installAnywhere mechanism)</li>
3994 <li>Command line launching of JARs from InstallAnywhere
3995 version (java class versioning error fixed)</li>
4002 <div align="center">
4003 <strong>2.4</strong><br> 27/8/2008
4006 <td><em>User Interface</em>
4008 <li>Linked highlighting of codon and amino acid from
4009 translation and protein products</li>
4010 <li>Linked highlighting of structure associated with
4011 residue mapping to codon position</li>
4012 <li>Sequence Fetcher provides example accession numbers
4013 and 'clear' button</li>
4014 <li>MemoryMonitor added as an option under Desktop's
4016 <li>Extract score function to parse whitespace separated
4017 numeric data in description line</li>
4018 <li>Column labels in alignment annotation can be centred.</li>
4019 <li>Tooltip for sequence associated annotation give name
4021 </ul> <em>Web Services and URL fetching</em>
4023 <li>JPred3 web service</li>
4024 <li>Prototype sequence search client (no public services
4026 <li>Fetch either seed alignment or full alignment from
4028 <li>URL Links created for matching database cross
4029 references as well as sequence ID</li>
4030 <li>URL Links can be created using regular-expressions</li>
4031 </ul> <em>Sequence Database Connectivity</em>
4033 <li>Retrieval of cross-referenced sequences from other
4035 <li>Generalised database reference retrieval and
4036 validation to all fetchable databases</li>
4037 <li>Fetch sequences from DAS sources supporting the
4038 sequence command</li>
4039 </ul> <em>Import and Export</em>
4040 <li>export annotation rows as CSV for spreadsheet import</li>
4041 <li>Jalview projects record alignment dataset associations,
4042 EMBL products, and cDNA sequence mappings</li>
4043 <li>Sequence Group colour can be specified in Annotation
4045 <li>Ad-hoc colouring of group in Annotation File using RGB
4046 triplet as name of colourscheme</li>
4047 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4049 <li>treenode binding for VAMSAS tree exchange</li>
4050 <li>local editing and update of sequences in VAMSAS
4051 alignments (experimental)</li>
4052 <li>Create new or select existing session to join</li>
4053 <li>load and save of vamsas documents</li>
4054 </ul> <em>Application command line</em>
4056 <li>-tree parameter to open trees (introduced for passing
4058 <li>-fetchfrom command line argument to specify nicknames
4059 of DAS servers to query for alignment features</li>
4060 <li>-dasserver command line argument to add new servers
4061 that are also automatically queried for features</li>
4062 <li>-groovy command line argument executes a given groovy
4063 script after all input data has been loaded and parsed</li>
4064 </ul> <em>Applet-Application data exchange</em>
4066 <li>Trees passed as applet parameters can be passed to
4067 application (when using "View in full
4068 application")</li>
4069 </ul> <em>Applet Parameters</em>
4071 <li>feature group display control parameter</li>
4072 <li>debug parameter</li>
4073 <li>showbutton parameter</li>
4074 </ul> <em>Applet API methods</em>
4076 <li>newView public method</li>
4077 <li>Window (current view) specific get/set public methods</li>
4078 <li>Feature display control methods</li>
4079 <li>get list of currently selected sequences</li>
4080 </ul> <em>New Jalview distribution features</em>
4082 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4083 <li>RELEASE file gives build properties for the latest
4084 Jalview release.</li>
4085 <li>Java 1.1 Applet build made easier and donotobfuscate
4086 property controls execution of obfuscator</li>
4087 <li>Build target for generating source distribution</li>
4088 <li>Debug flag for javacc</li>
4089 <li>.jalview_properties file is documented (slightly) in
4090 jalview.bin.Cache</li>
4091 <li>Continuous Build Integration for stable and
4092 development version of Application, Applet and source
4097 <li>selected region output includes visible annotations
4098 (for certain formats)</li>
4099 <li>edit label/displaychar contains existing label/char
4101 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4102 <li>shorter peptide product names from EMBL records</li>
4103 <li>Newick string generator makes compact representations</li>
4104 <li>bootstrap values parsed correctly for tree files with
4106 <li>pathological filechooser bug avoided by not allowing
4107 filenames containing a ':'</li>
4108 <li>Fixed exception when parsing GFF files containing
4109 global sequence features</li>
4110 <li>Alignment datasets are finalized only when number of
4111 references from alignment sequences goes to zero</li>
4112 <li>Close of tree branch colour box without colour
4113 selection causes cascading exceptions</li>
4114 <li>occasional negative imgwidth exceptions</li>
4115 <li>better reporting of non-fatal warnings to user when
4116 file parsing fails.</li>
4117 <li>Save works when Jalview project is default format</li>
4118 <li>Save as dialog opened if current alignment format is
4119 not a valid output format</li>
4120 <li>UniProt canonical names introduced for both das and
4122 <li>Histidine should be midblue (not pink!) in Zappo</li>
4123 <li>error messages passed up and output when data read
4125 <li>edit undo recovers previous dataset sequence when
4126 sequence is edited</li>
4127 <li>allow PDB files without pdb ID HEADER lines (like
4128 those generated by MODELLER) to be read in properly</li>
4129 <li>allow reading of JPred concise files as a normal
4131 <li>Stockholm annotation parsing and alignment properties
4132 import fixed for PFAM records</li>
4133 <li>Structure view windows have correct name in Desktop
4135 <li>annotation consisting of sequence associated scores
4136 can be read and written correctly to annotation file</li>
4137 <li>Aligned cDNA translation to aligned peptide works
4139 <li>Fixed display of hidden sequence markers and
4140 non-italic font for representatives in Applet</li>
4141 <li>Applet Menus are always embedded in applet window on
4143 <li>Newly shown features appear at top of stack (in
4145 <li>Annotations added via parameter not drawn properly
4146 due to null pointer exceptions</li>
4147 <li>Secondary structure lines are drawn starting from
4148 first column of alignment</li>
4149 <li>UniProt XML import updated for new schema release in
4151 <li>Sequence feature to sequence ID match for Features
4152 file is case-insensitive</li>
4153 <li>Sequence features read from Features file appended to
4154 all sequences with matching IDs</li>
4155 <li>PDB structure coloured correctly for associated views
4156 containing a sub-sequence</li>
4157 <li>PDB files can be retrieved by applet from Jar files</li>
4158 <li>feature and annotation file applet parameters
4159 referring to different directories are retrieved correctly</li>
4160 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4161 <li>Fixed application hang whilst waiting for
4162 splash-screen version check to complete</li>
4163 <li>Applet properly URLencodes input parameter values
4164 when passing them to the launchApp service</li>
4165 <li>display name and local features preserved in results
4166 retrieved from web service</li>
4167 <li>Visual delay indication for sequence retrieval and
4168 sequence fetcher initialisation</li>
4169 <li>updated Application to use DAS 1.53e version of
4170 dasobert DAS client</li>
4171 <li>Re-instated Full AMSA support and .amsa file
4173 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4181 <div align="center">
4182 <strong>2.3</strong><br> 9/5/07
4187 <li>Jmol 11.0.2 integration</li>
4188 <li>PDB views stored in Jalview XML files</li>
4189 <li>Slide sequences</li>
4190 <li>Edit sequence in place</li>
4191 <li>EMBL CDS features</li>
4192 <li>DAS Feature mapping</li>
4193 <li>Feature ordering</li>
4194 <li>Alignment Properties</li>
4195 <li>Annotation Scores</li>
4196 <li>Sort by scores</li>
4197 <li>Feature/annotation editing in applet</li>
4202 <li>Headless state operation in 2.2.1</li>
4203 <li>Incorrect and unstable DNA pairwise alignment</li>
4204 <li>Cut and paste of sequences with annotation</li>
4205 <li>Feature group display state in XML</li>
4206 <li>Feature ordering in XML</li>
4207 <li>blc file iteration selection using filename # suffix</li>
4208 <li>Stockholm alignment properties</li>
4209 <li>Stockhom alignment secondary structure annotation</li>
4210 <li>2.2.1 applet had no feature transparency</li>
4211 <li>Number pad keys can be used in cursor mode</li>
4212 <li>Structure Viewer mirror image resolved</li>
4219 <div align="center">
4220 <strong>2.2.1</strong><br> 12/2/07
4225 <li>Non standard characters can be read and displayed
4226 <li>Annotations/Features can be imported/exported to the
4228 <li>Applet allows editing of sequence/annotation/group
4229 name & description
4230 <li>Preference setting to display sequence name in
4232 <li>Annotation file format extended to allow
4233 Sequence_groups to be defined
4234 <li>Default opening of alignment overview panel can be
4235 specified in preferences
4236 <li>PDB residue numbering annotation added to associated
4242 <li>Applet crash under certain Linux OS with Java 1.6
4244 <li>Annotation file export / import bugs fixed
4245 <li>PNG / EPS image output bugs fixed
4251 <div align="center">
4252 <strong>2.2</strong><br> 27/11/06
4257 <li>Multiple views on alignment
4258 <li>Sequence feature editing
4259 <li>"Reload" alignment
4260 <li>"Save" to current filename
4261 <li>Background dependent text colour
4262 <li>Right align sequence ids
4263 <li>User-defined lower case residue colours
4266 <li>Menu item accelerator keys
4267 <li>Control-V pastes to current alignment
4268 <li>Cancel button for DAS Feature Fetching
4269 <li>PCA and PDB Viewers zoom via mouse roller
4270 <li>User-defined sub-tree colours and sub-tree selection
4272 <li>'New Window' button on the 'Output to Text box'
4277 <li>New memory efficient Undo/Redo System
4278 <li>Optimised symbol lookups and conservation/consensus
4280 <li>Region Conservation/Consensus recalculated after
4282 <li>Fixed Remove Empty Columns Bug (empty columns at end
4284 <li>Slowed DAS Feature Fetching for increased robustness.
4286 <li>Made angle brackets in ASCII feature descriptions
4288 <li>Re-instated Zoom function for PCA
4289 <li>Sequence descriptions conserved in web service
4291 <li>UniProt ID discoverer uses any word separated by
4293 <li>WsDbFetch query/result association resolved
4294 <li>Tree leaf to sequence mapping improved
4295 <li>Smooth fonts switch moved to FontChooser dialog box.
4302 <div align="center">
4303 <strong>2.1.1</strong><br> 12/9/06
4308 <li>Copy consensus sequence to clipboard</li>
4313 <li>Image output - rightmost residues are rendered if
4314 sequence id panel has been resized</li>
4315 <li>Image output - all offscreen group boundaries are
4317 <li>Annotation files with sequence references - all
4318 elements in file are relative to sequence position</li>
4319 <li>Mac Applet users can use Alt key for group editing</li>
4325 <div align="center">
4326 <strong>2.1</strong><br> 22/8/06
4331 <li>MAFFT Multiple Alignment in default Web Service list</li>
4332 <li>DAS Feature fetching</li>
4333 <li>Hide sequences and columns</li>
4334 <li>Export Annotations and Features</li>
4335 <li>GFF file reading / writing</li>
4336 <li>Associate structures with sequences from local PDB
4338 <li>Add sequences to exisiting alignment</li>
4339 <li>Recently opened files / URL lists</li>
4340 <li>Applet can launch the full application</li>
4341 <li>Applet has transparency for features (Java 1.2
4343 <li>Applet has user defined colours parameter</li>
4344 <li>Applet can load sequences from parameter
4345 "sequence<em>x</em>"
4351 <li>Redundancy Panel reinstalled in the Applet</li>
4352 <li>Monospaced font - EPS / rescaling bug fixed</li>
4353 <li>Annotation files with sequence references bug fixed</li>
4359 <div align="center">
4360 <strong>2.08.1</strong><br> 2/5/06
4365 <li>Change case of selected region from Popup menu</li>
4366 <li>Choose to match case when searching</li>
4367 <li>Middle mouse button and mouse movement can compress /
4368 expand the visible width and height of the alignment</li>
4373 <li>Annotation Panel displays complete JNet results</li>
4379 <div align="center">
4380 <strong>2.08b</strong><br> 18/4/06
4386 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4387 <li>Righthand label on wrapped alignments shows correct
4394 <div align="center">
4395 <strong>2.08</strong><br> 10/4/06
4400 <li>Editing can be locked to the selection area</li>
4401 <li>Keyboard editing</li>
4402 <li>Create sequence features from searches</li>
4403 <li>Precalculated annotations can be loaded onto
4405 <li>Features file allows grouping of features</li>
4406 <li>Annotation Colouring scheme added</li>
4407 <li>Smooth fonts off by default - Faster rendering</li>
4408 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4413 <li>Drag & Drop fixed on Linux</li>
4414 <li>Jalview Archive file faster to load/save, sequence
4415 descriptions saved.</li>
4421 <div align="center">
4422 <strong>2.07</strong><br> 12/12/05
4427 <li>PDB Structure Viewer enhanced</li>
4428 <li>Sequence Feature retrieval and display enhanced</li>
4429 <li>Choose to output sequence start-end after sequence
4430 name for file output</li>
4431 <li>Sequence Fetcher WSDBFetch@EBI</li>
4432 <li>Applet can read feature files, PDB files and can be
4433 used for HTML form input</li>
4438 <li>HTML output writes groups and features</li>
4439 <li>Group editing is Control and mouse click</li>
4440 <li>File IO bugs</li>
4446 <div align="center">
4447 <strong>2.06</strong><br> 28/9/05
4452 <li>View annotations in wrapped mode</li>
4453 <li>More options for PCA viewer</li>
4458 <li>GUI bugs resolved</li>
4459 <li>Runs with -nodisplay from command line</li>
4465 <div align="center">
4466 <strong>2.05b</strong><br> 15/9/05
4471 <li>Choose EPS export as lineart or text</li>
4472 <li>Jar files are executable</li>
4473 <li>Can read in Uracil - maps to unknown residue</li>
4478 <li>Known OutOfMemory errors give warning message</li>
4479 <li>Overview window calculated more efficiently</li>
4480 <li>Several GUI bugs resolved</li>
4486 <div align="center">
4487 <strong>2.05</strong><br> 30/8/05
4492 <li>Edit and annotate in "Wrapped" view</li>
4497 <li>Several GUI bugs resolved</li>
4503 <div align="center">
4504 <strong>2.04</strong><br> 24/8/05
4509 <li>Hold down mouse wheel & scroll to change font
4515 <li>Improved JPred client reliability</li>
4516 <li>Improved loading of Jalview files</li>
4522 <div align="center">
4523 <strong>2.03</strong><br> 18/8/05
4528 <li>Set Proxy server name and port in preferences</li>
4529 <li>Multiple URL links from sequence ids</li>
4530 <li>User Defined Colours can have a scheme name and added
4532 <li>Choose to ignore gaps in consensus calculation</li>
4533 <li>Unix users can set default web browser</li>
4534 <li>Runs without GUI for batch processing</li>
4535 <li>Dynamically generated Web Service Menus</li>
4540 <li>InstallAnywhere download for Sparc Solaris</li>
4546 <div align="center">
4547 <strong>2.02</strong><br> 18/7/05
4553 <li>Copy & Paste order of sequences maintains
4554 alignment order.</li>
4560 <div align="center">
4561 <strong>2.01</strong><br> 12/7/05
4566 <li>Use delete key for deleting selection.</li>
4567 <li>Use Mouse wheel to scroll sequences.</li>
4568 <li>Help file updated to describe how to add alignment
4570 <li>Version and build date written to build properties
4572 <li>InstallAnywhere installation will check for updates
4573 at launch of Jalview.</li>
4578 <li>Delete gaps bug fixed.</li>
4579 <li>FileChooser sorts columns.</li>
4580 <li>Can remove groups one by one.</li>
4581 <li>Filechooser icons installed.</li>
4582 <li>Finder ignores return character when searching.
4583 Return key will initiate a search.<br>
4590 <div align="center">
4591 <strong>2.0</strong><br> 20/6/05
4596 <li>New codebase</li>