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><strong><a
60 name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
61 <em>16/2/2020</em></strong></td>
62 <td align="left" valign="top">
67 </ul> <em>Release processes</em>
70 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
72 </ul> <em>Build System</em>
75 <!-- JAL-3510 -->Clover updated to 4.4.1
78 <!-- JAL-3513 -->Test code included in Clover coverage
81 </ul> <em>Deprecations</em>
83 <td align="left" valign="top">
95 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
96 ID fails with ClassCastException
99 <!-- JAL-3389 -->Chimera session not restored from Jalview
103 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
104 feature settings dialog also selects columns
107 <!-- JAL-3473 -->SpinnerNumberModel causing
108 IllegalArgumentException in some circumstances
111 <!-- JAL-3406 -->Credits missing some authors in Jalview
112 help documentation for 2.11.0 release
114 </ul> <em>Java 11 Compatibility issues</em>
117 <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
119 </ul> <em>Repository and Source Release</em>
122 <!-- JAL-3474 -->removed redundant .gitignore files from
129 <td width="60" align="center" nowrap>
130 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
131 <em>04/07/2019</em></strong>
133 <td align="left" valign="top">
136 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
137 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
138 source project) rather than InstallAnywhere
141 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
142 settings, receive over the air updates and launch specific
143 versions via (<a href="https://github.com/threerings/getdown">Three
147 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
148 formats supported by Jalview (including .jvp project files)
151 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
152 arguments and switch between different getdown channels
155 <!-- JAL-3141 -->Backup files created when saving Jalview project
160 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
161 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
163 <!-- JAL-2620 -->Alternative genetic code tables for
164 'Translate as cDNA'</li>
166 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
167 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
170 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
171 implementation that allows updates) used for Sequence Feature collections</li>
173 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
174 features can be filtered and shaded according to any
175 associated attributes (e.g. variant attributes from VCF
176 file, or key-value pairs imported from column 9 of GFF
180 <!-- JAL-2879 -->Feature Attributes and shading schemes
181 stored and restored from Jalview Projects
184 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
185 recognise variant features
188 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
189 sequences (also coloured red by default)
192 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
196 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
197 algorithm (Z-sort/transparency and filter aware)
200 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
206 <!-- JAL-3205 -->Symmetric score matrices for faster
207 tree and PCA calculations
209 <li><strong>Principal Components Analysis Viewer</strong>
212 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
213 and Viewer state saved in Jalview Project
215 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
218 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
222 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
227 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
229 <li><strong>Speed and Efficiency</strong>
232 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
233 multiple groups when working with large alignments
236 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
240 <li><strong>User Interface</strong>
243 <!-- JAL-2933 -->Finder panel remembers last position in each
247 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
248 what is shown)<br />Only visible regions of alignment are shown by
249 default (can be changed in user preferences)
252 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
253 to the Overwrite Dialog
256 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
260 <!-- JAL-1244 -->Status bar shows bounds when dragging a
261 selection region, and gap count when inserting or deleting gaps
264 <!-- JAL-3132 -->Status bar updates over sequence and annotation
268 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
272 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
276 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
279 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
283 <!-- JAL-3181 -->Consistent ordering of links in sequence id
287 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
289 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
293 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
294 <li><strong>Java 11 Support (not yet on general release)</strong>
297 <!-- -->OSX GUI integrations for App menu's 'About' entry and
302 <em>Deprecations</em>
304 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
305 capabilities removed from the Jalview Desktop
307 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
308 unmarshalling has been replaced by JAXB for Jalview projects
309 and XML based data retrieval clients</li>
310 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
311 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
312 </ul> <em>Documentation</em>
314 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
315 not supported in EPS figure export
317 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
318 </ul> <em>Development and Release Processes</em>
321 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
324 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
326 <!-- JAL-3225 -->Eclipse project configuration managed with
330 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
331 Bamboo continuous integration for unattended Test Suite
335 <!-- JAL-2864 -->Memory test suite to detect leaks in common
339 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
343 <!-- JAL-3248 -->Developer documentation migrated to
344 markdown (with HTML rendering)
347 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
350 <!-- JAL-3289 -->New URLs for publishing development
355 <td align="left" valign="top">
358 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
361 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
362 superposition in Jmol fail on Windows
365 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
366 structures for sequences with lots of PDB structures
369 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
373 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
374 project involving multiple views
377 <!-- JAL-3164 -->Overview for complementary view in a linked
378 CDS/Protein alignment is not updated when Hide Columns by
379 Annotation dialog hides columns
382 <!-- JAL-3158 -->Selection highlighting in the complement of a
383 CDS/Protein alignment stops working after making a selection in
384 one view, then making another selection in the other view
387 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
391 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
392 Settings and Jalview Preferences panels
395 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
396 overview with large alignments
399 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
400 region if columns were selected by dragging right-to-left and the
401 mouse moved to the left of the first column
404 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
405 hidden column marker via scale popup menu
408 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
409 doesn't tell users the invalid URL
412 <!-- JAL-2816 -->Tooltips displayed for features filtered by
416 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
417 show cross references or Fetch Database References are shown in
421 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
422 peptide sequence (computed variant shown as p.Res.null)
425 <!-- JAL-2060 -->'Graduated colour' option not offered for
426 manually created features (where feature score is Float.NaN)
429 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
430 when columns are hidden
433 <!-- JAL-3082 -->Regular expression error for '(' in Select
434 Columns by Annotation description
437 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
438 out of Scale or Annotation Panel
441 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
445 <!-- JAL-3074 -->Left/right drag in annotation can scroll
449 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
453 <!-- JAL-3002 -->Column display is out by one after Page Down,
454 Page Up in wrapped mode
457 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
460 <!-- JAL-2932 -->Finder searches in minimised alignments
463 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
464 on opening an alignment
467 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
471 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
472 different groups in the alignment are selected
475 <!-- JAL-2717 -->Internationalised colour scheme names not shown
479 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
483 <!-- JAL-3125 -->Value input for graduated feature colour
484 threshold gets 'unrounded'
487 <!-- JAL-2982 -->PCA image export doesn't respect background
491 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
494 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
497 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
501 <!-- JAL-2964 -->Associate Tree with All Views not restored from
505 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
506 shown in complementary view
509 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
510 without normalisation
513 <!-- JAL-3021 -->Sequence Details report should open positioned at top
517 <!-- JAL-914 -->Help page can be opened twice
520 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
522 </ul> <em>Editing</em>
525 <!-- JAL-2822 -->Start and End should be updated when sequence
526 data at beginning or end of alignment added/removed via 'Edit'
530 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
531 relocate sequence features correctly when start of sequence is
532 removed (Known defect since 2.10)
535 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
536 dialog corrupts dataset sequence
539 <!-- JAL-868 -->Structure colours not updated when associated tree
540 repartitions the alignment view (Regression in 2.10.5)
542 </ul> <em>Datamodel</em>
545 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
546 sequence's End is greater than its length
548 </ul> <em>Bugs fixed for Java 11 Support (not yet on
549 general release)</em>
552 <!-- JAL-3288 -->Menus work properly in split-screen
554 </ul> <em>New Known Defects</em>
557 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
560 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
561 regions of protein alignment.
564 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
565 is restored from a Jalview 2.11 project
568 <!-- JAL-3213 -->Alignment panel height can be too small after
572 <!-- JAL-3240 -->Display is incorrect after removing gapped
573 columns within hidden columns
576 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
577 window after dragging left to select columns to left of visible
581 <!-- JAL-2876 -->Features coloured according to their description
582 string and thresholded by score in earlier versions of Jalview are
583 not shown as thresholded features in 2.11. To workaround please
584 create a Score filter instead.
587 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
589 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
592 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
593 alignments with multiple views can close views unexpectedly
596 <em>Java 11 Specific defects</em>
599 <!-- JAL-3235 -->Jalview Properties file is not sorted
600 alphabetically when saved
606 <td width="60" nowrap>
608 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
611 <td><div align="left">
615 <!-- JAL-3101 -->Default memory for Jalview webstart and
616 InstallAnywhere increased to 1G.
619 <!-- JAL-247 -->Hidden sequence markers and representative
620 sequence bolding included when exporting alignment as EPS,
621 SVG, PNG or HTML. <em>Display is configured via the
622 Format menu, or for command-line use via a Jalview
623 properties file.</em>
626 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
627 API and sequence data now imported as JSON.
630 <!-- JAL-3065 -->Change in recommended way of starting
631 Jalview via a Java command line: add jars in lib directory
632 to CLASSPATH, rather than via the deprecated java.ext.dirs
639 <!-- JAL-3047 -->Support added to execute test suite
640 instrumented with <a href="http://openclover.org/">Open
645 <td><div align="left">
649 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
650 row shown in Feredoxin Structure alignment view of example
654 <!-- JAL-2854 -->Annotation obscures sequences if lots of
655 annotation displayed.
658 <!-- JAL-3107 -->Group conservation/consensus not shown
659 for newly created group when 'Apply to all groups'
663 <!-- JAL-3087 -->Corrupted display when switching to
664 wrapped mode when sequence panel's vertical scrollbar is
668 <!-- JAL-3003 -->Alignment is black in exported EPS file
669 when sequences are selected in exported view.</em>
672 <!-- JAL-3059 -->Groups with different coloured borders
673 aren't rendered with correct colour.
676 <!-- JAL-3092 -->Jalview could hang when importing certain
677 types of knotted RNA secondary structure.
680 <!-- JAL-3095 -->Sequence highlight and selection in
681 trimmed VARNA 2D structure is incorrect for sequences that
685 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
686 annotation when columns are inserted into an alignment,
687 and when exporting as Stockholm flatfile.
690 <!-- JAL-3053 -->Jalview annotation rows containing upper
691 and lower-case 'E' and 'H' do not automatically get
692 treated as RNA secondary structure.
695 <!-- JAL-3106 -->.jvp should be used as default extension
696 (not .jar) when saving a Jalview project file.
699 <!-- JAL-3105 -->Mac Users: closing a window correctly
700 transfers focus to previous window on OSX
703 <em>Java 10 Issues Resolved</em>
706 <!-- JAL-2988 -->OSX - Can't save new files via the File
707 or export menus by typing in a name into the Save dialog
711 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
712 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
713 'look and feel' which has improved compatibility with the
714 latest version of OSX.
721 <td width="60" nowrap>
723 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
724 <em>7/06/2018</em></strong>
727 <td><div align="left">
731 <!-- JAL-2920 -->Use HGVS nomenclature for variant
732 annotation retrieved from Uniprot
735 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
736 onto the Jalview Desktop
740 <td><div align="left">
744 <!-- JAL-3017 -->Cannot import features with multiple
745 variant elements (blocks import of some Uniprot records)
748 <!-- JAL-2997 -->Clustal files with sequence positions in
749 right-hand column parsed correctly
752 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
753 not alignment area in exported graphic
756 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
757 window has input focus
760 <!-- JAL-2992 -->Annotation panel set too high when
761 annotation added to view (Windows)
764 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
765 network connectivity is poor
768 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
769 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
770 the currently open URL and links from a page viewed in
771 Firefox or Chrome on Windows is now fully supported. If
772 you are using Edge, only links in the page can be
773 dragged, and with Internet Explorer, only the currently
774 open URL in the browser can be dropped onto Jalview.</em>
777 <em>New Known Defects</em>
779 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
784 <td width="60" nowrap>
786 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
789 <td><div align="left">
793 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
794 for disabling automatic superposition of multiple
795 structures and open structures in existing views
798 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
799 ID and annotation area margins can be click-dragged to
803 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
807 <!-- JAL-2759 -->Improved performance for large alignments
808 and lots of hidden columns
811 <!-- JAL-2593 -->Improved performance when rendering lots
812 of features (particularly when transparency is disabled)
815 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
816 exchange of Jalview features and Chimera attributes made
822 <td><div align="left">
825 <!-- JAL-2899 -->Structure and Overview aren't updated
826 when Colour By Annotation threshold slider is adjusted
829 <!-- JAL-2778 -->Slow redraw when Overview panel shown
830 overlapping alignment panel
833 <!-- JAL-2929 -->Overview doesn't show end of unpadded
837 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
838 improved: CDS not handled correctly if transcript has no
842 <!-- JAL-2321 -->Secondary structure and temperature
843 factor annotation not added to sequence when local PDB
844 file associated with it by drag'n'drop or structure
848 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
849 dialog doesn't import PDB files dropped on an alignment
852 <!-- JAL-2666 -->Linked scrolling via protein horizontal
853 scroll bar doesn't work for some CDS/Protein views
856 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
857 Java 1.8u153 onwards and Java 1.9u4+.
860 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
861 columns in annotation row
864 <!-- JAL-2913 -->Preferences panel's ID Width control is not
865 honored in batch mode
868 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
869 for structures added to existing Jmol view
872 <!-- JAL-2223 -->'View Mappings' includes duplicate
873 entries after importing project with multiple views
876 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
877 protein sequences via SIFTS from associated PDB entries
878 with negative residue numbers or missing residues fails
881 <!-- JAL-2952 -->Exception when shading sequence with negative
882 Temperature Factor values from annotated PDB files (e.g.
883 as generated by CONSURF)
886 <!-- JAL-2920 -->Uniprot 'sequence variant' features
887 tooltip doesn't include a text description of mutation
890 <!-- JAL-2922 -->Invert displayed features very slow when
891 structure and/or overview windows are also shown
894 <!-- JAL-2954 -->Selecting columns from highlighted regions
895 very slow for alignments with large numbers of sequences
898 <!-- JAL-2925 -->Copy Consensus fails for group consensus
899 with 'StringIndexOutOfBounds'
902 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
903 platforms running Java 10
906 <!-- JAL-2960 -->Adding a structure to existing structure
907 view appears to do nothing because the view is hidden behind the alignment view
913 <!-- JAL-2926 -->Copy consensus sequence option in applet
914 should copy the group consensus when popup is opened on it
920 <!-- JAL-2913 -->Fixed ID width preference is not respected
923 <em>New Known Defects</em>
926 <!-- JAL-2973 --> Exceptions occasionally raised when
927 editing a large alignment and overview is displayed
930 <!-- JAL-2974 -->'Overview updating' progress bar is shown
931 repeatedly after a series of edits even when the overview
932 is no longer reflecting updates
935 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
936 structures for protein subsequence (if 'Trim Retrieved
937 Sequences' enabled) or Ensembl isoforms (Workaround in
938 2.10.4 is to fail back to N&W mapping)
941 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
942 option gives blank output
949 <td width="60" nowrap>
951 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
954 <td><div align="left">
955 <ul><li>Updated Certum Codesigning Certificate
956 (Valid till 30th November 2018)</li></ul></div></td>
957 <td><div align="left">
960 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
961 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
962 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
963 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
964 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
965 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
966 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
972 <td width="60" nowrap>
974 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
977 <td><div align="left">
981 <!-- JAL-2446 -->Faster and more efficient management and
982 rendering of sequence features
985 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
986 429 rate limit request hander
989 <!-- JAL-2773 -->Structure views don't get updated unless
990 their colours have changed
993 <!-- JAL-2495 -->All linked sequences are highlighted for
994 a structure mousover (Jmol) or selection (Chimera)
997 <!-- JAL-2790 -->'Cancel' button in progress bar for
998 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1001 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1002 view from Ensembl locus cross-references
1005 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1009 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1010 feature can be disabled
1013 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1014 PDB easier retrieval of sequences for lists of IDs
1017 <!-- JAL-2758 -->Short names for sequences retrieved from
1023 <li>Groovy interpreter updated to 2.4.12</li>
1024 <li>Example groovy script for generating a matrix of
1025 percent identity scores for current alignment.</li>
1027 <em>Testing and Deployment</em>
1030 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1034 <td><div align="left">
1038 <!-- JAL-2643 -->Pressing tab after updating the colour
1039 threshold text field doesn't trigger an update to the
1043 <!-- JAL-2682 -->Race condition when parsing sequence ID
1047 <!-- JAL-2608 -->Overview windows are also closed when
1048 alignment window is closed
1051 <!-- JAL-2548 -->Export of features doesn't always respect
1055 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1056 takes a long time in Cursor mode
1062 <!-- JAL-2777 -->Structures with whitespace chainCode
1063 cannot be viewed in Chimera
1066 <!-- JAL-2728 -->Protein annotation panel too high in
1070 <!-- JAL-2757 -->Can't edit the query after the server
1071 error warning icon is shown in Uniprot and PDB Free Text
1075 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1078 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1081 <!-- JAL-2739 -->Hidden column marker in last column not
1082 rendered when switching back from Wrapped to normal view
1085 <!-- JAL-2768 -->Annotation display corrupted when
1086 scrolling right in unwapped alignment view
1089 <!-- JAL-2542 -->Existing features on subsequence
1090 incorrectly relocated when full sequence retrieved from
1094 <!-- JAL-2733 -->Last reported memory still shown when
1095 Desktop->Show Memory is unticked (OSX only)
1098 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1099 features of same type and group to be selected for
1103 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1104 alignments when hidden columns are present
1107 <!-- JAL-2392 -->Jalview freezes when loading and
1108 displaying several structures
1111 <!-- JAL-2732 -->Black outlines left after resizing or
1115 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1116 within the Jalview desktop on OSX
1119 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1120 when in wrapped alignment mode
1123 <!-- JAL-2636 -->Scale mark not shown when close to right
1124 hand end of alignment
1127 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1128 each selected sequence do not have correct start/end
1132 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1133 after canceling the Alignment Window's Font dialog
1136 <!-- JAL-2036 -->Show cross-references not enabled after
1137 restoring project until a new view is created
1140 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1141 URL links appears when only default EMBL-EBI link is
1142 configured (since 2.10.2b2)
1145 <!-- JAL-2775 -->Overview redraws whole window when box
1146 position is adjusted
1149 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1150 in a multi-chain structure when viewing alignment
1151 involving more than one chain (since 2.10)
1154 <!-- JAL-2811 -->Double residue highlights in cursor mode
1155 if new selection moves alignment window
1158 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1159 arrow key in cursor mode to pass hidden column marker
1162 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1163 that produces correctly annotated transcripts and products
1166 <!-- JAL-2776 -->Toggling a feature group after first time
1167 doesn't update associated structure view
1170 <em>Applet</em><br />
1173 <!-- JAL-2687 -->Concurrent modification exception when
1174 closing alignment panel
1177 <em>BioJSON</em><br />
1180 <!-- JAL-2546 -->BioJSON export does not preserve
1181 non-positional features
1184 <em>New Known Issues</em>
1187 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1188 sequence features correctly (for many previous versions of
1192 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1193 using cursor in wrapped panel other than top
1196 <!-- JAL-2791 -->Select columns containing feature ignores
1197 graduated colour threshold
1200 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1201 always preserve numbering and sequence features
1204 <em>Known Java 9 Issues</em>
1207 <!-- JAL-2902 -->Groovy Console very slow to open and is
1208 not responsive when entering characters (Webstart, Java
1215 <td width="60" nowrap>
1216 <div align="center">
1217 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1218 <em>2/10/2017</em></strong>
1221 <td><div align="left">
1222 <em>New features in Jalview Desktop</em>
1225 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1227 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1231 <td><div align="left">
1235 <td width="60" nowrap>
1236 <div align="center">
1237 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1238 <em>7/9/2017</em></strong>
1241 <td><div align="left">
1245 <!-- JAL-2588 -->Show gaps in overview window by colouring
1246 in grey (sequences used to be coloured grey, and gaps were
1250 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1254 <!-- JAL-2587 -->Overview updates immediately on increase
1255 in size and progress bar shown as higher resolution
1256 overview is recalculated
1261 <td><div align="left">
1265 <!-- JAL-2664 -->Overview window redraws every hidden
1266 column region row by row
1269 <!-- JAL-2681 -->duplicate protein sequences shown after
1270 retrieving Ensembl crossrefs for sequences from Uniprot
1273 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1274 format setting is unticked
1277 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1278 if group has show boxes format setting unticked
1281 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1282 autoscrolling whilst dragging current selection group to
1283 include sequences and columns not currently displayed
1286 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1287 assemblies are imported via CIF file
1290 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1291 displayed when threshold or conservation colouring is also
1295 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1299 <!-- JAL-2673 -->Jalview continues to scroll after
1300 dragging a selected region off the visible region of the
1304 <!-- JAL-2724 -->Cannot apply annotation based
1305 colourscheme to all groups in a view
1308 <!-- JAL-2511 -->IDs don't line up with sequences
1309 initially after font size change using the Font chooser or
1316 <td width="60" nowrap>
1317 <div align="center">
1318 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1321 <td><div align="left">
1322 <em>Calculations</em>
1326 <!-- JAL-1933 -->Occupancy annotation row shows number of
1327 ungapped positions in each column of the alignment.
1330 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1331 a calculation dialog box
1334 <!-- JAL-2379 -->Revised implementation of PCA for speed
1335 and memory efficiency (~30x faster)
1338 <!-- JAL-2403 -->Revised implementation of sequence
1339 similarity scores as used by Tree, PCA, Shading Consensus
1340 and other calculations
1343 <!-- JAL-2416 -->Score matrices are stored as resource
1344 files within the Jalview codebase
1347 <!-- JAL-2500 -->Trees computed on Sequence Feature
1348 Similarity may have different topology due to increased
1355 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1356 model for alignments and groups
1359 <!-- JAL-384 -->Custom shading schemes created via groovy
1366 <!-- JAL-2526 -->Efficiency improvements for interacting
1367 with alignment and overview windows
1370 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1374 <!-- JAL-2388 -->Hidden columns and sequences can be
1378 <!-- JAL-2611 -->Click-drag in visible area allows fine
1379 adjustment of visible position
1383 <em>Data import/export</em>
1386 <!-- JAL-2535 -->Posterior probability annotation from
1387 Stockholm files imported as sequence associated annotation
1390 <!-- JAL-2507 -->More robust per-sequence positional
1391 annotation input/output via stockholm flatfile
1394 <!-- JAL-2533 -->Sequence names don't include file
1395 extension when importing structure files without embedded
1396 names or PDB accessions
1399 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1400 format sequence substitution matrices
1403 <em>User Interface</em>
1406 <!-- JAL-2447 --> Experimental Features Checkbox in
1407 Desktop's Tools menu to hide or show untested features in
1411 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1412 via Overview or sequence motif search operations
1415 <!-- JAL-2547 -->Amend sequence features dialog box can be
1416 opened by double clicking gaps within sequence feature
1420 <!-- JAL-1476 -->Status bar message shown when not enough
1421 aligned positions were available to create a 3D structure
1425 <em>3D Structure</em>
1428 <!-- JAL-2430 -->Hidden regions in alignment views are not
1429 coloured in linked structure views
1432 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1433 file-based command exchange
1436 <!-- JAL-2375 -->Structure chooser automatically shows
1437 Cached Structures rather than querying the PDBe if
1438 structures are already available for sequences
1441 <!-- JAL-2520 -->Structures imported via URL are cached in
1442 the Jalview project rather than downloaded again when the
1443 project is reopened.
1446 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1447 to transfer Chimera's structure attributes as Jalview
1448 features, and vice-versa (<strong>Experimental
1452 <em>Web Services</em>
1455 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1458 <!-- JAL-2335 -->Filter non-standard amino acids and
1459 nucleotides when submitting to AACon and other MSA
1463 <!-- JAL-2316, -->URLs for viewing database
1464 cross-references provided by identifiers.org and the
1465 EMBL-EBI's MIRIAM DB
1472 <!-- JAL-2344 -->FileFormatI interface for describing and
1473 identifying file formats (instead of String constants)
1476 <!-- JAL-2228 -->FeatureCounter script refactored for
1477 efficiency when counting all displayed features (not
1478 backwards compatible with 2.10.1)
1481 <em>Example files</em>
1484 <!-- JAL-2631 -->Graduated feature colour style example
1485 included in the example feature file
1488 <em>Documentation</em>
1491 <!-- JAL-2339 -->Release notes reformatted for readability
1492 with the built-in Java help viewer
1495 <!-- JAL-1644 -->Find documentation updated with 'search
1496 sequence description' option
1502 <!-- JAL-2485, -->External service integration tests for
1503 Uniprot REST Free Text Search Client
1506 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1509 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1514 <td><div align="left">
1515 <em>Calculations</em>
1518 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1519 matrix - C->R should be '-3'<br />Old matrix restored
1520 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1522 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1523 Jalview's treatment of gaps in PCA and substitution matrix
1524 based Tree calculations.<br /> <br />In earlier versions
1525 of Jalview, gaps matching gaps were penalised, and gaps
1526 matching non-gaps penalised even more. In the PCA
1527 calculation, gaps were actually treated as non-gaps - so
1528 different costs were applied, which meant Jalview's PCAs
1529 were different to those produced by SeqSpace.<br />Jalview
1530 now treats gaps in the same way as SeqSpace (ie it scores
1531 them as 0). <br /> <br />Enter the following in the
1532 Groovy console to restore pre-2.10.2 behaviour:<br />
1533 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1534 // for 2.10.1 mode <br />
1535 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1536 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1537 these settings will affect all subsequent tree and PCA
1538 calculations (not recommended)</em></li>
1540 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1541 scaling of branch lengths for trees computed using
1542 Sequence Feature Similarity.
1545 <!-- JAL-2377 -->PCA calculation could hang when
1546 generating output report when working with highly
1547 redundant alignments
1550 <!-- JAL-2544 --> Sort by features includes features to
1551 right of selected region when gaps present on right-hand
1555 <em>User Interface</em>
1558 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1559 doesn't reselect a specific sequence's associated
1560 annotation after it was used for colouring a view
1563 <!-- JAL-2419 -->Current selection lost if popup menu
1564 opened on a region of alignment without groups
1567 <!-- JAL-2374 -->Popup menu not always shown for regions
1568 of an alignment with overlapping groups
1571 <!-- JAL-2310 -->Finder double counts if both a sequence's
1572 name and description match
1575 <!-- JAL-2370 -->Hiding column selection containing two
1576 hidden regions results in incorrect hidden regions
1579 <!-- JAL-2386 -->'Apply to all groups' setting when
1580 changing colour does not apply Conservation slider value
1584 <!-- JAL-2373 -->Percentage identity and conservation menu
1585 items do not show a tick or allow shading to be disabled
1588 <!-- JAL-2385 -->Conservation shading or PID threshold
1589 lost when base colourscheme changed if slider not visible
1592 <!-- JAL-2547 -->Sequence features shown in tooltip for
1593 gaps before start of features
1596 <!-- JAL-2623 -->Graduated feature colour threshold not
1597 restored to UI when feature colour is edited
1600 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1601 a time when scrolling vertically in wrapped mode.
1604 <!-- JAL-2630 -->Structure and alignment overview update
1605 as graduate feature colour settings are modified via the
1609 <!-- JAL-2034 -->Overview window doesn't always update
1610 when a group defined on the alignment is resized
1613 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1614 wrapped view result in positional status updates
1618 <!-- JAL-2563 -->Status bar doesn't show position for
1619 ambiguous amino acid and nucleotide symbols
1622 <!-- JAL-2602 -->Copy consensus sequence failed if
1623 alignment included gapped columns
1626 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1627 widgets don't permanently disappear
1630 <!-- JAL-2503 -->Cannot select or filter quantitative
1631 annotation that are shown only as column labels (e.g.
1632 T-Coffee column reliability scores)
1635 <!-- JAL-2594 -->Exception thrown if trying to create a
1636 sequence feature on gaps only
1639 <!-- JAL-2504 -->Features created with 'New feature'
1640 button from a Find inherit previously defined feature type
1641 rather than the Find query string
1644 <!-- JAL-2423 -->incorrect title in output window when
1645 exporting tree calculated in Jalview
1648 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1649 and then revealing them reorders sequences on the
1653 <!-- JAL-964 -->Group panel in sequence feature settings
1654 doesn't update to reflect available set of groups after
1655 interactively adding or modifying features
1658 <!-- JAL-2225 -->Sequence Database chooser unusable on
1662 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1663 only excluded gaps in current sequence and ignored
1670 <!-- JAL-2421 -->Overview window visible region moves
1671 erratically when hidden rows or columns are present
1674 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1675 Structure Viewer's colour menu don't correspond to
1679 <!-- JAL-2405 -->Protein specific colours only offered in
1680 colour and group colour menu for protein alignments
1683 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1684 reflect currently selected view or group's shading
1688 <!-- JAL-2624 -->Feature colour thresholds not respected
1689 when rendered on overview and structures when opacity at
1693 <!-- JAL-2589 -->User defined gap colour not shown in
1694 overview when features overlaid on alignment
1697 <!-- JAL-2567 -->Feature settings for different views not
1698 recovered correctly from Jalview project file
1701 <!-- JAL-2256 -->Feature colours in overview when first opened
1702 (automatically via preferences) are different to the main
1706 <em>Data import/export</em>
1709 <!-- JAL-2576 -->Very large alignments take a long time to
1713 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1714 added after a sequence was imported are not written to
1718 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1719 when importing RNA secondary structure via Stockholm
1722 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1723 not shown in correct direction for simple pseudoknots
1726 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1727 with lightGray or darkGray via features file (but can
1731 <!-- JAL-2383 -->Above PID colour threshold not recovered
1732 when alignment view imported from project
1735 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1736 structure and sequences extracted from structure files
1737 imported via URL and viewed in Jmol
1740 <!-- JAL-2520 -->Structures loaded via URL are saved in
1741 Jalview Projects rather than fetched via URL again when
1742 the project is loaded and the structure viewed
1745 <em>Web Services</em>
1748 <!-- JAL-2519 -->EnsemblGenomes example failing after
1749 release of Ensembl v.88
1752 <!-- JAL-2366 -->Proxy server address and port always
1753 appear enabled in Preferences->Connections
1756 <!-- JAL-2461 -->DAS registry not found exceptions
1757 removed from console output
1760 <!-- JAL-2582 -->Cannot retrieve protein products from
1761 Ensembl by Peptide ID
1764 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1765 created from SIFTs, and spurious 'Couldn't open structure
1766 in Chimera' errors raised after April 2017 update (problem
1767 due to 'null' string rather than empty string used for
1768 residues with no corresponding PDB mapping).
1771 <em>Application UI</em>
1774 <!-- JAL-2361 -->User Defined Colours not added to Colour
1778 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1779 case' residues (button in colourscheme editor debugged and
1780 new documentation and tooltips added)
1783 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1784 doesn't restore group-specific text colour thresholds
1787 <!-- JAL-2243 -->Feature settings panel does not update as
1788 new features are added to alignment
1791 <!-- JAL-2532 -->Cancel in feature settings reverts
1792 changes to feature colours via the Amend features dialog
1795 <!-- JAL-2506 -->Null pointer exception when attempting to
1796 edit graduated feature colour via amend features dialog
1800 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1801 selection menu changes colours of alignment views
1804 <!-- JAL-2426 -->Spurious exceptions in console raised
1805 from alignment calculation workers after alignment has
1809 <!-- JAL-1608 -->Typo in selection popup menu - Create
1810 groups now 'Create Group'
1813 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1814 Create/Undefine group doesn't always work
1817 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1818 shown again after pressing 'Cancel'
1821 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1822 adjusts start position in wrap mode
1825 <!-- JAL-2563 -->Status bar doesn't show positions for
1826 ambiguous amino acids
1829 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1830 CDS/Protein view after CDS sequences added for aligned
1834 <!-- JAL-2592 -->User defined colourschemes called 'User
1835 Defined' don't appear in Colours menu
1841 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1842 score models doesn't always result in an updated PCA plot
1845 <!-- JAL-2442 -->Features not rendered as transparent on
1846 overview or linked structure view
1849 <!-- JAL-2372 -->Colour group by conservation doesn't
1853 <!-- JAL-2517 -->Hitting Cancel after applying
1854 user-defined colourscheme doesn't restore original
1861 <!-- JAL-2314 -->Unit test failure:
1862 jalview.ws.jabaws.RNAStructExportImport setup fails
1865 <!-- JAL-2307 -->Unit test failure:
1866 jalview.ws.sifts.SiftsClientTest due to compatibility
1867 problems with deep array comparison equality asserts in
1868 successive versions of TestNG
1871 <!-- JAL-2479 -->Relocated StructureChooserTest and
1872 ParameterUtilsTest Unit tests to Network suite
1875 <em>New Known Issues</em>
1878 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1879 phase after a sequence motif find operation
1882 <!-- JAL-2550 -->Importing annotation file with rows
1883 containing just upper and lower case letters are
1884 interpreted as WUSS RNA secondary structure symbols
1887 <!-- JAL-2590 -->Cannot load and display Newick trees
1888 reliably from eggnog Ortholog database
1891 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1892 containing features of type Highlight' when 'B' is pressed
1893 to mark columns containing highlighted regions.
1896 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1897 doesn't always add secondary structure annotation.
1902 <td width="60" nowrap>
1903 <div align="center">
1904 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1907 <td><div align="left">
1911 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1912 for all consensus calculations
1915 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1918 <li>Updated Jalview's Certum code signing certificate
1921 <em>Application</em>
1924 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1925 set of database cross-references, sorted alphabetically
1928 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1929 from database cross references. Users with custom links
1930 will receive a <a href="webServices/urllinks.html#warning">warning
1931 dialog</a> asking them to update their preferences.
1934 <!-- JAL-2287-->Cancel button and escape listener on
1935 dialog warning user about disconnecting Jalview from a
1939 <!-- JAL-2320-->Jalview's Chimera control window closes if
1940 the Chimera it is connected to is shut down
1943 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1944 columns menu item to mark columns containing highlighted
1945 regions (e.g. from structure selections or results of a
1949 <!-- JAL-2284-->Command line option for batch-generation
1950 of HTML pages rendering alignment data with the BioJS
1960 <!-- JAL-2286 -->Columns with more than one modal residue
1961 are not coloured or thresholded according to percent
1962 identity (first observed in Jalview 2.8.2)
1965 <!-- JAL-2301 -->Threonine incorrectly reported as not
1969 <!-- JAL-2318 -->Updates to documentation pages (above PID
1970 threshold, amino acid properties)
1973 <!-- JAL-2292 -->Lower case residues in sequences are not
1974 reported as mapped to residues in a structure file in the
1978 <!--JAL-2324 -->Identical features with non-numeric scores
1979 could be added multiple times to a sequence
1982 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1983 bond features shown as two highlighted residues rather
1984 than a range in linked structure views, and treated
1985 correctly when selecting and computing trees from features
1988 <!-- JAL-2281-->Custom URL links for database
1989 cross-references are matched to database name regardless
1994 <em>Application</em>
1997 <!-- JAL-2282-->Custom URL links for specific database
1998 names without regular expressions also offer links from
2002 <!-- JAL-2315-->Removing a single configured link in the
2003 URL links pane in Connections preferences doesn't actually
2004 update Jalview configuration
2007 <!-- JAL-2272-->CTRL-Click on a selected region to open
2008 the alignment area popup menu doesn't work on El-Capitan
2011 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2012 files with similarly named sequences if dropped onto the
2016 <!-- JAL-2312 -->Additional mappings are shown for PDB
2017 entries where more chains exist in the PDB accession than
2018 are reported in the SIFTS file
2021 <!-- JAL-2317-->Certain structures do not get mapped to
2022 the structure view when displayed with Chimera
2025 <!-- JAL-2317-->No chains shown in the Chimera view
2026 panel's View->Show Chains submenu
2029 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2030 work for wrapped alignment views
2033 <!--JAL-2197 -->Rename UI components for running JPred
2034 predictions from 'JNet' to 'JPred'
2037 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2038 corrupted when annotation panel vertical scroll is not at
2039 first annotation row
2042 <!--JAL-2332 -->Attempting to view structure for Hen
2043 lysozyme results in a PDB Client error dialog box
2046 <!-- JAL-2319 -->Structure View's mapping report switched
2047 ranges for PDB and sequence for SIFTS
2050 SIFTS 'Not_Observed' residues mapped to non-existant
2054 <!-- <em>New Known Issues</em>
2061 <td width="60" nowrap>
2062 <div align="center">
2063 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2064 <em>25/10/2016</em></strong>
2067 <td><em>Application</em>
2069 <li>3D Structure chooser opens with 'Cached structures'
2070 view if structures already loaded</li>
2071 <li>Progress bar reports models as they are loaded to
2072 structure views</li>
2078 <li>Colour by conservation always enabled and no tick
2079 shown in menu when BLOSUM or PID shading applied</li>
2080 <li>FER1_ARATH and FER2_ARATH labels were switched in
2081 example sequences/projects/trees</li>
2083 <em>Application</em>
2085 <li>Jalview projects with views of local PDB structure
2086 files saved on Windows cannot be opened on OSX</li>
2087 <li>Multiple structure views can be opened and superposed
2088 without timeout for structures with multiple models or
2089 multiple sequences in alignment</li>
2090 <li>Cannot import or associated local PDB files without a
2091 PDB ID HEADER line</li>
2092 <li>RMSD is not output in Jmol console when superposition
2094 <li>Drag and drop of URL from Browser fails for Linux and
2095 OSX versions earlier than El Capitan</li>
2096 <li>ENA client ignores invalid content from ENA server</li>
2097 <li>Exceptions are not raised in console when ENA client
2098 attempts to fetch non-existent IDs via Fetch DB Refs UI
2100 <li>Exceptions are not raised in console when a new view
2101 is created on the alignment</li>
2102 <li>OSX right-click fixed for group selections: CMD-click
2103 to insert/remove gaps in groups and CTRL-click to open group
2106 <em>Build and deployment</em>
2108 <li>URL link checker now copes with multi-line anchor
2111 <em>New Known Issues</em>
2113 <li>Drag and drop from URL links in browsers do not work
2120 <td width="60" nowrap>
2121 <div align="center">
2122 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2125 <td><em>General</em>
2128 <!-- JAL-2124 -->Updated Spanish translations.
2131 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2132 for importing structure data to Jalview. Enables mmCIF and
2136 <!-- JAL-192 --->Alignment ruler shows positions relative to
2140 <!-- JAL-2202 -->Position/residue shown in status bar when
2141 mousing over sequence associated annotation
2144 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2148 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2149 '()', canonical '[]' and invalid '{}' base pair populations
2153 <!-- JAL-2092 -->Feature settings popup menu options for
2154 showing or hiding columns containing a feature
2157 <!-- JAL-1557 -->Edit selected group by double clicking on
2158 group and sequence associated annotation labels
2161 <!-- JAL-2236 -->Sequence name added to annotation label in
2162 select/hide columns by annotation and colour by annotation
2166 </ul> <em>Application</em>
2169 <!-- JAL-2050-->Automatically hide introns when opening a
2170 gene/transcript view
2173 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2177 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2178 structure mappings with the EMBL-EBI PDBe SIFTS database
2181 <!-- JAL-2079 -->Updated download sites used for Rfam and
2182 Pfam sources to xfam.org
2185 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2188 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2189 over sequences in Jalview
2192 <!-- JAL-2027-->Support for reverse-complement coding
2193 regions in ENA and EMBL
2196 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2197 for record retrieval via ENA rest API
2200 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2204 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2205 groovy script execution
2208 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2209 alignment window's Calculate menu
2212 <!-- JAL-1812 -->Allow groovy scripts that call
2213 Jalview.getAlignFrames() to run in headless mode
2216 <!-- JAL-2068 -->Support for creating new alignment
2217 calculation workers from groovy scripts
2220 <!-- JAL-1369 --->Store/restore reference sequence in
2224 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2225 associations are now saved/restored from project
2228 <!-- JAL-1993 -->Database selection dialog always shown
2229 before sequence fetcher is opened
2232 <!-- JAL-2183 -->Double click on an entry in Jalview's
2233 database chooser opens a sequence fetcher
2236 <!-- JAL-1563 -->Free-text search client for UniProt using
2237 the UniProt REST API
2240 <!-- JAL-2168 -->-nonews command line parameter to prevent
2241 the news reader opening
2244 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2245 querying stored in preferences
2248 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2252 <!-- JAL-1977-->Tooltips shown on database chooser
2255 <!-- JAL-391 -->Reverse complement function in calculate
2256 menu for nucleotide sequences
2259 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2260 and feature counts preserves alignment ordering (and
2261 debugged for complex feature sets).
2264 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2265 viewing structures with Jalview 2.10
2268 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2269 genome, transcript CCDS and gene ids via the Ensembl and
2270 Ensembl Genomes REST API
2273 <!-- JAL-2049 -->Protein sequence variant annotation
2274 computed for 'sequence_variant' annotation on CDS regions
2278 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2282 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2283 Ref Fetcher fails to match, or otherwise updates sequence
2284 data from external database records.
2287 <!-- JAL-2154 -->Revised Jalview Project format for
2288 efficient recovery of sequence coding and alignment
2289 annotation relationships.
2291 </ul> <!-- <em>Applet</em>
2302 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2306 <!-- JAL-2018-->Export features in Jalview format (again)
2307 includes graduated colourschemes
2310 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2311 working with big alignments and lots of hidden columns
2314 <!-- JAL-2053-->Hidden column markers not always rendered
2315 at right of alignment window
2318 <!-- JAL-2067 -->Tidied up links in help file table of
2322 <!-- JAL-2072 -->Feature based tree calculation not shown
2326 <!-- JAL-2075 -->Hidden columns ignored during feature
2327 based tree calculation
2330 <!-- JAL-2065 -->Alignment view stops updating when show
2331 unconserved enabled for group on alignment
2334 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2338 <!-- JAL-2146 -->Alignment column in status incorrectly
2339 shown as "Sequence position" when mousing over
2343 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2344 hidden columns present
2347 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2348 user created annotation added to alignment
2351 <!-- JAL-1841 -->RNA Structure consensus only computed for
2352 '()' base pair annotation
2355 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2356 in zero scores for all base pairs in RNA Structure
2360 <!-- JAL-2174-->Extend selection with columns containing
2364 <!-- JAL-2275 -->Pfam format writer puts extra space at
2365 beginning of sequence
2368 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2372 <!-- JAL-2238 -->Cannot create groups on an alignment from
2373 from a tree when t-coffee scores are shown
2376 <!-- JAL-1836,1967 -->Cannot import and view PDB
2377 structures with chains containing negative resnums (4q4h)
2380 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2384 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2385 to Clustal, PIR and PileUp output
2388 <!-- JAL-2008 -->Reordering sequence features that are
2389 not visible causes alignment window to repaint
2392 <!-- JAL-2006 -->Threshold sliders don't work in
2393 graduated colour and colour by annotation row for e-value
2394 scores associated with features and annotation rows
2397 <!-- JAL-1797 -->amino acid physicochemical conservation
2398 calculation should be case independent
2401 <!-- JAL-2173 -->Remove annotation also updates hidden
2405 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2406 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2407 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2410 <!-- JAL-2065 -->Null pointer exceptions and redraw
2411 problems when reference sequence defined and 'show
2412 non-conserved' enabled
2415 <!-- JAL-1306 -->Quality and Conservation are now shown on
2416 load even when Consensus calculation is disabled
2419 <!-- JAL-1932 -->Remove right on penultimate column of
2420 alignment does nothing
2423 <em>Application</em>
2426 <!-- JAL-1552-->URLs and links can't be imported by
2427 drag'n'drop on OSX when launched via webstart (note - not
2428 yet fixed for El Capitan)
2431 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2432 output when running on non-gb/us i18n platforms
2435 <!-- JAL-1944 -->Error thrown when exporting a view with
2436 hidden sequences as flat-file alignment
2439 <!-- JAL-2030-->InstallAnywhere distribution fails when
2443 <!-- JAL-2080-->Jalview very slow to launch via webstart
2444 (also hotfix for 2.9.0b2)
2447 <!-- JAL-2085 -->Cannot save project when view has a
2448 reference sequence defined
2451 <!-- JAL-1011 -->Columns are suddenly selected in other
2452 alignments and views when revealing hidden columns
2455 <!-- JAL-1989 -->Hide columns not mirrored in complement
2456 view in a cDNA/Protein splitframe
2459 <!-- JAL-1369 -->Cannot save/restore representative
2460 sequence from project when only one sequence is
2464 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2465 in Structure Chooser
2468 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2469 structure consensus didn't refresh annotation panel
2472 <!-- JAL-1962 -->View mapping in structure view shows
2473 mappings between sequence and all chains in a PDB file
2476 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2477 dialogs format columns correctly, don't display array
2478 data, sort columns according to type
2481 <!-- JAL-1975 -->Export complete shown after destination
2482 file chooser is cancelled during an image export
2485 <!-- JAL-2025 -->Error when querying PDB Service with
2486 sequence name containing special characters
2489 <!-- JAL-2024 -->Manual PDB structure querying should be
2493 <!-- JAL-2104 -->Large tooltips with broken HTML
2494 formatting don't wrap
2497 <!-- JAL-1128 -->Figures exported from wrapped view are
2498 truncated so L looks like I in consensus annotation
2501 <!-- JAL-2003 -->Export features should only export the
2502 currently displayed features for the current selection or
2506 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2507 after fetching cross-references, and restoring from
2511 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2512 followed in the structure viewer
2515 <!-- JAL-2163 -->Titles for individual alignments in
2516 splitframe not restored from project
2519 <!-- JAL-2145 -->missing autocalculated annotation at
2520 trailing end of protein alignment in transcript/product
2521 splitview when pad-gaps not enabled by default
2524 <!-- JAL-1797 -->amino acid physicochemical conservation
2528 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2529 article has been read (reopened issue due to
2530 internationalisation problems)
2533 <!-- JAL-1960 -->Only offer PDB structures in structure
2534 viewer based on sequence name, PDB and UniProt
2539 <!-- JAL-1976 -->No progress bar shown during export of
2543 <!-- JAL-2213 -->Structures not always superimposed after
2544 multiple structures are shown for one or more sequences.
2547 <!-- JAL-1370 -->Reference sequence characters should not
2548 be replaced with '.' when 'Show unconserved' format option
2552 <!-- JAL-1823 -->Cannot specify chain code when entering
2553 specific PDB id for sequence
2556 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2557 'Export hidden sequences' is enabled, but 'export hidden
2558 columns' is disabled.
2561 <!--JAL-2026-->Best Quality option in structure chooser
2562 selects lowest rather than highest resolution structures
2566 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2567 to sequence mapping in 'View Mappings' report
2570 <!-- JAL-2284 -->Unable to read old Jalview projects that
2571 contain non-XML data added after Jalvew wrote project.
2574 <!-- JAL-2118 -->Newly created annotation row reorders
2575 after clicking on it to create new annotation for a
2579 <!-- JAL-1980 -->Null Pointer Exception raised when
2580 pressing Add on an orphaned cut'n'paste window.
2582 <!-- may exclude, this is an external service stability issue JAL-1941
2583 -- > RNA 3D structure not added via DSSR service</li> -->
2588 <!-- JAL-2151 -->Incorrect columns are selected when
2589 hidden columns present before start of sequence
2592 <!-- JAL-1986 -->Missing dependencies on applet pages
2596 <!-- JAL-1947 -->Overview pixel size changes when
2597 sequences are hidden in applet
2600 <!-- JAL-1996 -->Updated instructions for applet
2601 deployment on examples pages.
2608 <td width="60" nowrap>
2609 <div align="center">
2610 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2611 <em>16/10/2015</em></strong>
2614 <td><em>General</em>
2616 <li>Time stamps for signed Jalview application and applet
2621 <em>Application</em>
2623 <li>Duplicate group consensus and conservation rows
2624 shown when tree is partitioned</li>
2625 <li>Erratic behaviour when tree partitions made with
2626 multiple cDNA/Protein split views</li>
2632 <td width="60" nowrap>
2633 <div align="center">
2634 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2635 <em>8/10/2015</em></strong>
2638 <td><em>General</em>
2640 <li>Updated Spanish translations of localized text for
2642 </ul> <em>Application</em>
2644 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2645 <li>Signed OSX InstallAnywhere installer<br></li>
2646 <li>Support for per-sequence based annotations in BioJSON</li>
2647 </ul> <em>Applet</em>
2649 <li>Split frame example added to applet examples page</li>
2650 </ul> <em>Build and Deployment</em>
2653 <!-- JAL-1888 -->New ant target for running Jalview's test
2661 <li>Mapping of cDNA to protein in split frames
2662 incorrect when sequence start > 1</li>
2663 <li>Broken images in filter column by annotation dialog
2665 <li>Feature colours not parsed from features file</li>
2666 <li>Exceptions and incomplete link URLs recovered when
2667 loading a features file containing HTML tags in feature
2671 <em>Application</em>
2673 <li>Annotations corrupted after BioJS export and
2675 <li>Incorrect sequence limits after Fetch DB References
2676 with 'trim retrieved sequences'</li>
2677 <li>Incorrect warning about deleting all data when
2678 deleting selected columns</li>
2679 <li>Patch to build system for shipping properly signed
2680 JNLP templates for webstart launch</li>
2681 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2682 unreleased structures for download or viewing</li>
2683 <li>Tab/space/return keystroke operation of EMBL-PDBe
2684 fetcher/viewer dialogs works correctly</li>
2685 <li>Disabled 'minimise' button on Jalview windows
2686 running on OSX to workaround redraw hang bug</li>
2687 <li>Split cDNA/Protein view position and geometry not
2688 recovered from jalview project</li>
2689 <li>Initial enabled/disabled state of annotation menu
2690 sorter 'show autocalculated first/last' corresponds to
2692 <li>Restoring of Clustal, RNA Helices and T-Coffee
2693 color schemes from BioJSON</li>
2697 <li>Reorder sequences mirrored in cDNA/Protein split
2699 <li>Applet with Jmol examples not loading correctly</li>
2705 <td><div align="center">
2706 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2708 <td><em>General</em>
2710 <li>Linked visualisation and analysis of DNA and Protein
2713 <li>Translated cDNA alignments shown as split protein
2714 and DNA alignment views</li>
2715 <li>Codon consensus annotation for linked protein and
2716 cDNA alignment views</li>
2717 <li>Link cDNA or Protein product sequences by loading
2718 them onto Protein or cDNA alignments</li>
2719 <li>Reconstruct linked cDNA alignment from aligned
2720 protein sequences</li>
2723 <li>Jmol integration updated to Jmol v14.2.14</li>
2724 <li>Import and export of Jalview alignment views as <a
2725 href="features/bioJsonFormat.html">BioJSON</a></li>
2726 <li>New alignment annotation file statements for
2727 reference sequences and marking hidden columns</li>
2728 <li>Reference sequence based alignment shading to
2729 highlight variation</li>
2730 <li>Select or hide columns according to alignment
2732 <li>Find option for locating sequences by description</li>
2733 <li>Conserved physicochemical properties shown in amino
2734 acid conservation row</li>
2735 <li>Alignments can be sorted by number of RNA helices</li>
2736 </ul> <em>Application</em>
2738 <li>New cDNA/Protein analysis capabilities
2740 <li>Get Cross-References should open a Split Frame
2741 view with cDNA/Protein</li>
2742 <li>Detect when nucleotide sequences and protein
2743 sequences are placed in the same alignment</li>
2744 <li>Split cDNA/Protein views are saved in Jalview
2749 <li>Use REST API to talk to Chimera</li>
2750 <li>Selected regions in Chimera are highlighted in linked
2751 Jalview windows</li>
2753 <li>VARNA RNA viewer updated to v3.93</li>
2754 <li>VARNA views are saved in Jalview Projects</li>
2755 <li>Pseudoknots displayed as Jalview RNA annotation can
2756 be shown in VARNA</li>
2758 <li>Make groups for selection uses marked columns as well
2759 as the active selected region</li>
2761 <li>Calculate UPGMA and NJ trees using sequence feature
2763 <li>New Export options
2765 <li>New Export Settings dialog to control hidden
2766 region export in flat file generation</li>
2768 <li>Export alignment views for display with the <a
2769 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2771 <li>Export scrollable SVG in HTML page</li>
2772 <li>Optional embedding of BioJSON data when exporting
2773 alignment figures to HTML</li>
2775 <li>3D structure retrieval and display
2777 <li>Free text and structured queries with the PDBe
2779 <li>PDBe Search API based discovery and selection of
2780 PDB structures for a sequence set</li>
2784 <li>JPred4 employed for protein secondary structure
2786 <li>Hide Insertions menu option to hide unaligned columns
2787 for one or a group of sequences</li>
2788 <li>Automatically hide insertions in alignments imported
2789 from the JPred4 web server</li>
2790 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2791 system on OSX<br />LGPL libraries courtesy of <a
2792 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2794 <li>changed 'View nucleotide structure' submenu to 'View
2795 VARNA 2D Structure'</li>
2796 <li>change "View protein structure" menu option to "3D
2799 </ul> <em>Applet</em>
2801 <li>New layout for applet example pages</li>
2802 <li>New parameters to enable SplitFrame view
2803 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2804 <li>New example demonstrating linked viewing of cDNA and
2805 Protein alignments</li>
2806 </ul> <em>Development and deployment</em>
2808 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2809 <li>Include installation type and git revision in build
2810 properties and console log output</li>
2811 <li>Jalview Github organisation, and new github site for
2812 storing BioJsMSA Templates</li>
2813 <li>Jalview's unit tests now managed with TestNG</li>
2816 <!-- <em>General</em>
2818 </ul> --> <!-- issues resolved --> <em>Application</em>
2820 <li>Escape should close any open find dialogs</li>
2821 <li>Typo in select-by-features status report</li>
2822 <li>Consensus RNA secondary secondary structure
2823 predictions are not highlighted in amber</li>
2824 <li>Missing gap character in v2.7 example file means
2825 alignment appears unaligned when pad-gaps is not enabled</li>
2826 <li>First switch to RNA Helices colouring doesn't colour
2827 associated structure views</li>
2828 <li>ID width preference option is greyed out when auto
2829 width checkbox not enabled</li>
2830 <li>Stopped a warning dialog from being shown when
2831 creating user defined colours</li>
2832 <li>'View Mapping' in structure viewer shows sequence
2833 mappings for just that viewer's sequences</li>
2834 <li>Workaround for superposing PDB files containing
2835 multiple models in Chimera</li>
2836 <li>Report sequence position in status bar when hovering
2837 over Jmol structure</li>
2838 <li>Cannot output gaps as '.' symbols with Selection ->
2839 output to text box</li>
2840 <li>Flat file exports of alignments with hidden columns
2841 have incorrect sequence start/end</li>
2842 <li>'Aligning' a second chain to a Chimera structure from
2844 <li>Colour schemes applied to structure viewers don't
2845 work for nucleotide</li>
2846 <li>Loading/cut'n'pasting an empty or invalid file leads
2847 to a grey/invisible alignment window</li>
2848 <li>Exported Jpred annotation from a sequence region
2849 imports to different position</li>
2850 <li>Space at beginning of sequence feature tooltips shown
2851 on some platforms</li>
2852 <li>Chimera viewer 'View | Show Chain' menu is not
2854 <li>'New View' fails with a Null Pointer Exception in
2855 console if Chimera has been opened</li>
2856 <li>Mouseover to Chimera not working</li>
2857 <li>Miscellaneous ENA XML feature qualifiers not
2859 <li>NPE in annotation renderer after 'Extract Scores'</li>
2860 <li>If two structures in one Chimera window, mouseover of
2861 either sequence shows on first structure</li>
2862 <li>'Show annotations' options should not make
2863 non-positional annotations visible</li>
2864 <li>Subsequence secondary structure annotation not shown
2865 in right place after 'view flanking regions'</li>
2866 <li>File Save As type unset when current file format is
2868 <li>Save as '.jar' option removed for saving Jalview
2870 <li>Colour by Sequence colouring in Chimera more
2872 <li>Cannot 'add reference annotation' for a sequence in
2873 several views on same alignment</li>
2874 <li>Cannot show linked products for EMBL / ENA records</li>
2875 <li>Jalview's tooltip wraps long texts containing no
2877 </ul> <em>Applet</em>
2879 <li>Jmol to JalviewLite mouseover/link not working</li>
2880 <li>JalviewLite can't import sequences with ID
2881 descriptions containing angle brackets</li>
2882 </ul> <em>General</em>
2884 <li>Cannot export and reimport RNA secondary structure
2885 via jalview annotation file</li>
2886 <li>Random helix colour palette for colour by annotation
2887 with RNA secondary structure</li>
2888 <li>Mouseover to cDNA from STOP residue in protein
2889 translation doesn't work.</li>
2890 <li>hints when using the select by annotation dialog box</li>
2891 <li>Jmol alignment incorrect if PDB file has alternate CA
2893 <li>FontChooser message dialog appears to hang after
2894 choosing 1pt font</li>
2895 <li>Peptide secondary structure incorrectly imported from
2896 annotation file when annotation display text includes 'e' or
2898 <li>Cannot set colour of new feature type whilst creating
2900 <li>cDNA translation alignment should not be sequence
2901 order dependent</li>
2902 <li>'Show unconserved' doesn't work for lower case
2904 <li>Nucleotide ambiguity codes involving R not recognised</li>
2905 </ul> <em>Deployment and Documentation</em>
2907 <li>Applet example pages appear different to the rest of
2908 www.jalview.org</li>
2909 </ul> <em>Application Known issues</em>
2911 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2912 <li>Misleading message appears after trying to delete
2914 <li>Jalview icon not shown in dock after InstallAnywhere
2915 version launches</li>
2916 <li>Fetching EMBL reference for an RNA sequence results
2917 fails with a sequence mismatch</li>
2918 <li>Corrupted or unreadable alignment display when
2919 scrolling alignment to right</li>
2920 <li>ArrayIndexOutOfBoundsException thrown when remove
2921 empty columns called on alignment with ragged gapped ends</li>
2922 <li>auto calculated alignment annotation rows do not get
2923 placed above or below non-autocalculated rows</li>
2924 <li>Jalview dekstop becomes sluggish at full screen in
2925 ultra-high resolution</li>
2926 <li>Cannot disable consensus calculation independently of
2927 quality and conservation</li>
2928 <li>Mouseover highlighting between cDNA and protein can
2929 become sluggish with more than one splitframe shown</li>
2930 </ul> <em>Applet Known Issues</em>
2932 <li>Core PDB parsing code requires Jmol</li>
2933 <li>Sequence canvas panel goes white when alignment
2934 window is being resized</li>
2940 <td><div align="center">
2941 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2943 <td><em>General</em>
2945 <li>Updated Java code signing certificate donated by
2947 <li>Features and annotation preserved when performing
2948 pairwise alignment</li>
2949 <li>RNA pseudoknot annotation can be
2950 imported/exported/displayed</li>
2951 <li>'colour by annotation' can colour by RNA and
2952 protein secondary structure</li>
2953 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2954 post-hoc with 2.9 release</em>)
2957 </ul> <em>Application</em>
2959 <li>Extract and display secondary structure for sequences
2960 with 3D structures</li>
2961 <li>Support for parsing RNAML</li>
2962 <li>Annotations menu for layout
2964 <li>sort sequence annotation rows by alignment</li>
2965 <li>place sequence annotation above/below alignment
2968 <li>Output in Stockholm format</li>
2969 <li>Internationalisation: improved Spanish (es)
2971 <li>Structure viewer preferences tab</li>
2972 <li>Disorder and Secondary Structure annotation tracks
2973 shared between alignments</li>
2974 <li>UCSF Chimera launch and linked highlighting from
2976 <li>Show/hide all sequence associated annotation rows for
2977 all or current selection</li>
2978 <li>disorder and secondary structure predictions
2979 available as dataset annotation</li>
2980 <li>Per-sequence rna helices colouring</li>
2983 <li>Sequence database accessions imported when fetching
2984 alignments from Rfam</li>
2985 <li>update VARNA version to 3.91</li>
2987 <li>New groovy scripts for exporting aligned positions,
2988 conservation values, and calculating sum of pairs scores.</li>
2989 <li>Command line argument to set default JABAWS server</li>
2990 <li>include installation type in build properties and
2991 console log output</li>
2992 <li>Updated Jalview project format to preserve dataset
2996 <!-- issues resolved --> <em>Application</em>
2998 <li>Distinguish alignment and sequence associated RNA
2999 structure in structure->view->VARNA</li>
3000 <li>Raise dialog box if user deletes all sequences in an
3002 <li>Pressing F1 results in documentation opening twice</li>
3003 <li>Sequence feature tooltip is wrapped</li>
3004 <li>Double click on sequence associated annotation
3005 selects only first column</li>
3006 <li>Redundancy removal doesn't result in unlinked
3007 leaves shown in tree</li>
3008 <li>Undos after several redundancy removals don't undo
3010 <li>Hide sequence doesn't hide associated annotation</li>
3011 <li>User defined colours dialog box too big to fit on
3012 screen and buttons not visible</li>
3013 <li>author list isn't updated if already written to
3014 Jalview properties</li>
3015 <li>Popup menu won't open after retrieving sequence
3017 <li>File open window for associate PDB doesn't open</li>
3018 <li>Left-then-right click on a sequence id opens a
3019 browser search window</li>
3020 <li>Cannot open sequence feature shading/sort popup menu
3021 in feature settings dialog</li>
3022 <li>better tooltip placement for some areas of Jalview
3024 <li>Allow addition of JABAWS Server which doesn't
3025 pass validation</li>
3026 <li>Web services parameters dialog box is too large to
3028 <li>Muscle nucleotide alignment preset obscured by
3030 <li>JABAWS preset submenus don't contain newly
3031 defined user preset</li>
3032 <li>MSA web services warns user if they were launched
3033 with invalid input</li>
3034 <li>Jalview cannot contact DAS Registy when running on
3037 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3038 'Superpose with' submenu not shown when new view
3042 </ul> <!-- <em>Applet</em>
3044 </ul> <em>General</em>
3046 </ul>--> <em>Deployment and Documentation</em>
3048 <li>2G and 1G options in launchApp have no effect on
3049 memory allocation</li>
3050 <li>launchApp service doesn't automatically open
3051 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3053 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3054 InstallAnywhere reports cannot find valid JVM when Java
3055 1.7_055 is available
3057 </ul> <em>Application Known issues</em>
3060 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3061 corrupted or unreadable alignment display when scrolling
3065 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3066 retrieval fails but progress bar continues for DAS retrieval
3067 with large number of ID
3070 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3071 flatfile output of visible region has incorrect sequence
3075 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3076 rna structure consensus doesn't update when secondary
3077 structure tracks are rearranged
3080 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3081 invalid rna structure positional highlighting does not
3082 highlight position of invalid base pairs
3085 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3086 out of memory errors are not raised when saving Jalview
3087 project from alignment window file menu
3090 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3091 Switching to RNA Helices colouring doesn't propagate to
3095 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3096 colour by RNA Helices not enabled when user created
3097 annotation added to alignment
3100 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3101 Jalview icon not shown on dock in Mountain Lion/Webstart
3103 </ul> <em>Applet Known Issues</em>
3106 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3107 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3110 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3111 Jalview and Jmol example not compatible with IE9
3114 <li>Sort by annotation score doesn't reverse order
3120 <td><div align="center">
3121 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3124 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3127 <li>Internationalisation of user interface (usually
3128 called i18n support) and translation for Spanish locale</li>
3129 <li>Define/Undefine group on current selection with
3130 Ctrl-G/Shift Ctrl-G</li>
3131 <li>Improved group creation/removal options in
3132 alignment/sequence Popup menu</li>
3133 <li>Sensible precision for symbol distribution
3134 percentages shown in logo tooltip.</li>
3135 <li>Annotation panel height set according to amount of
3136 annotation when alignment first opened</li>
3137 </ul> <em>Application</em>
3139 <li>Interactive consensus RNA secondary structure
3140 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3141 <li>Select columns containing particular features from
3142 Feature Settings dialog</li>
3143 <li>View all 'representative' PDB structures for selected
3145 <li>Update Jalview project format:
3147 <li>New file extension for Jalview projects '.jvp'</li>
3148 <li>Preserve sequence and annotation dataset (to
3149 store secondary structure annotation,etc)</li>
3150 <li>Per group and alignment annotation and RNA helix
3154 <li>New similarity measures for PCA and Tree calculation
3156 <li>Experimental support for retrieval and viewing of
3157 flanking regions for an alignment</li>
3161 <!-- issues resolved --> <em>Application</em>
3163 <li>logo keeps spinning and status remains at queued or
3164 running after job is cancelled</li>
3165 <li>cannot export features from alignments imported from
3166 Jalview/VAMSAS projects</li>
3167 <li>Buggy slider for web service parameters that take
3169 <li>Newly created RNA secondary structure line doesn't
3170 have 'display all symbols' flag set</li>
3171 <li>T-COFFEE alignment score shading scheme and other
3172 annotation shading not saved in Jalview project</li>
3173 <li>Local file cannot be loaded in freshly downloaded
3175 <li>Jalview icon not shown on dock in Mountain
3177 <li>Load file from desktop file browser fails</li>
3178 <li>Occasional NPE thrown when calculating large trees</li>
3179 <li>Cannot reorder or slide sequences after dragging an
3180 alignment onto desktop</li>
3181 <li>Colour by annotation dialog throws NPE after using
3182 'extract scores' function</li>
3183 <li>Loading/cut'n'pasting an empty file leads to a grey
3184 alignment window</li>
3185 <li>Disorder thresholds rendered incorrectly after
3186 performing IUPred disorder prediction</li>
3187 <li>Multiple group annotated consensus rows shown when
3188 changing 'normalise logo' display setting</li>
3189 <li>Find shows blank dialog after 'finished searching' if
3190 nothing matches query</li>
3191 <li>Null Pointer Exceptions raised when sorting by
3192 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3194 <li>Errors in Jmol console when structures in alignment
3195 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3197 <li>Not all working JABAWS services are shown in
3199 <li>JAVAWS version of Jalview fails to launch with
3200 'invalid literal/length code'</li>
3201 <li>Annotation/RNA Helix colourschemes cannot be applied
3202 to alignment with groups (actually fixed in 2.8.0b1)</li>
3203 <li>RNA Helices and T-Coffee Scores available as default
3206 </ul> <em>Applet</em>
3208 <li>Remove group option is shown even when selection is
3210 <li>Apply to all groups ticked but colourscheme changes
3211 don't affect groups</li>
3212 <li>Documented RNA Helices and T-Coffee Scores as valid
3213 colourscheme name</li>
3214 <li>Annotation labels drawn on sequence IDs when
3215 Annotation panel is not displayed</li>
3216 <li>Increased font size for dropdown menus on OSX and
3217 embedded windows</li>
3218 </ul> <em>Other</em>
3220 <li>Consensus sequence for alignments/groups with a
3221 single sequence were not calculated</li>
3222 <li>annotation files that contain only groups imported as
3223 annotation and junk sequences</li>
3224 <li>Fasta files with sequences containing '*' incorrectly
3225 recognised as PFAM or BLC</li>
3226 <li>conservation/PID slider apply all groups option
3227 doesn't affect background (2.8.0b1)
3229 <li>redundancy highlighting is erratic at 0% and 100%</li>
3230 <li>Remove gapped columns fails for sequences with ragged
3232 <li>AMSA annotation row with leading spaces is not
3233 registered correctly on import</li>
3234 <li>Jalview crashes when selecting PCA analysis for
3235 certain alignments</li>
3236 <li>Opening the colour by annotation dialog for an
3237 existing annotation based 'use original colours'
3238 colourscheme loses original colours setting</li>
3243 <td><div align="center">
3244 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3245 <em>30/1/2014</em></strong>
3249 <li>Trusted certificates for JalviewLite applet and
3250 Jalview Desktop application<br />Certificate was donated by
3251 <a href="https://www.certum.eu">Certum</a> to the Jalview
3252 open source project).
3254 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3255 <li>Output in Stockholm format</li>
3256 <li>Allow import of data from gzipped files</li>
3257 <li>Export/import group and sequence associated line
3258 graph thresholds</li>
3259 <li>Nucleotide substitution matrix that supports RNA and
3260 ambiguity codes</li>
3261 <li>Allow disorder predictions to be made on the current
3262 selection (or visible selection) in the same way that JPred
3264 <li>Groovy scripting for headless Jalview operation</li>
3265 </ul> <em>Other improvements</em>
3267 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3268 <li>COMBINE statement uses current SEQUENCE_REF and
3269 GROUP_REF scope to group annotation rows</li>
3270 <li>Support '' style escaping of quotes in Newick
3272 <li>Group options for JABAWS service by command line name</li>
3273 <li>Empty tooltip shown for JABA service options with a
3274 link but no description</li>
3275 <li>Select primary source when selecting authority in
3276 database fetcher GUI</li>
3277 <li>Add .mfa to FASTA file extensions recognised by
3279 <li>Annotation label tooltip text wrap</li>
3284 <li>Slow scrolling when lots of annotation rows are
3286 <li>Lots of NPE (and slowness) after creating RNA
3287 secondary structure annotation line</li>
3288 <li>Sequence database accessions not imported when
3289 fetching alignments from Rfam</li>
3290 <li>Incorrect SHMR submission for sequences with
3292 <li>View all structures does not always superpose
3294 <li>Option widgets in service parameters not updated to
3295 reflect user or preset settings</li>
3296 <li>Null pointer exceptions for some services without
3297 presets or adjustable parameters</li>
3298 <li>Discover PDB IDs entry in structure menu doesn't
3299 discover PDB xRefs</li>
3300 <li>Exception encountered while trying to retrieve
3301 features with DAS</li>
3302 <li>Lowest value in annotation row isn't coloured
3303 when colour by annotation (per sequence) is coloured</li>
3304 <li>Keyboard mode P jumps to start of gapped region when
3305 residue follows a gap</li>
3306 <li>Jalview appears to hang importing an alignment with
3307 Wrap as default or after enabling Wrap</li>
3308 <li>'Right click to add annotations' message
3309 shown in wrap mode when no annotations present</li>
3310 <li>Disorder predictions fail with NPE if no automatic
3311 annotation already exists on alignment</li>
3312 <li>oninit javascript function should be called after
3313 initialisation completes</li>
3314 <li>Remove redundancy after disorder prediction corrupts
3315 alignment window display</li>
3316 <li>Example annotation file in documentation is invalid</li>
3317 <li>Grouped line graph annotation rows are not exported
3318 to annotation file</li>
3319 <li>Multi-harmony analysis cannot be run when only two
3321 <li>Cannot create multiple groups of line graphs with
3322 several 'combine' statements in annotation file</li>
3323 <li>Pressing return several times causes Number Format
3324 exceptions in keyboard mode</li>
3325 <li>Multi-harmony (SHMMR) method doesn't submit
3326 correct partitions for input data</li>
3327 <li>Translation from DNA to Amino Acids fails</li>
3328 <li>Jalview fail to load newick tree with quoted label</li>
3329 <li>--headless flag isn't understood</li>
3330 <li>ClassCastException when generating EPS in headless
3332 <li>Adjusting sequence-associated shading threshold only
3333 changes one row's threshold</li>
3334 <li>Preferences and Feature settings panel panel
3335 doesn't open</li>
3336 <li>hide consensus histogram also hides conservation and
3337 quality histograms</li>
3342 <td><div align="center">
3343 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3345 <td><em>Application</em>
3347 <li>Support for JABAWS 2.0 Services (AACon alignment
3348 conservation, protein disorder and Clustal Omega)</li>
3349 <li>JABAWS server status indicator in Web Services
3351 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3352 in Jalview alignment window</li>
3353 <li>Updated Jalview build and deploy framework for OSX
3354 mountain lion, windows 7, and 8</li>
3355 <li>Nucleotide substitution matrix for PCA that supports
3356 RNA and ambiguity codes</li>
3358 <li>Improved sequence database retrieval GUI</li>
3359 <li>Support fetching and database reference look up
3360 against multiple DAS sources (Fetch all from in 'fetch db
3362 <li>Jalview project improvements
3364 <li>Store and retrieve the 'belowAlignment'
3365 flag for annotation</li>
3366 <li>calcId attribute to group annotation rows on the
3368 <li>Store AACon calculation settings for a view in
3369 Jalview project</li>
3373 <li>horizontal scrolling gesture support</li>
3374 <li>Visual progress indicator when PCA calculation is
3376 <li>Simpler JABA web services menus</li>
3377 <li>visual indication that web service results are still
3378 being retrieved from server</li>
3379 <li>Serialise the dialogs that are shown when Jalview
3380 starts up for first time</li>
3381 <li>Jalview user agent string for interacting with HTTP
3383 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3385 <li>Examples directory and Groovy library included in
3386 InstallAnywhere distribution</li>
3387 </ul> <em>Applet</em>
3389 <li>RNA alignment and secondary structure annotation
3390 visualization applet example</li>
3391 </ul> <em>General</em>
3393 <li>Normalise option for consensus sequence logo</li>
3394 <li>Reset button in PCA window to return dimensions to
3396 <li>Allow seqspace or Jalview variant of alignment PCA
3398 <li>PCA with either nucleic acid and protein substitution
3400 <li>Allow windows containing HTML reports to be exported
3402 <li>Interactive display and editing of RNA secondary
3403 structure contacts</li>
3404 <li>RNA Helix Alignment Colouring</li>
3405 <li>RNA base pair logo consensus</li>
3406 <li>Parse sequence associated secondary structure
3407 information in Stockholm files</li>
3408 <li>HTML Export database accessions and annotation
3409 information presented in tooltip for sequences</li>
3410 <li>Import secondary structure from LOCARNA clustalw
3411 style RNA alignment files</li>
3412 <li>import and visualise T-COFFEE quality scores for an
3414 <li>'colour by annotation' per sequence option to
3415 shade each sequence according to its associated alignment
3417 <li>New Jalview Logo</li>
3418 </ul> <em>Documentation and Development</em>
3420 <li>documentation for score matrices used in Jalview</li>
3421 <li>New Website!</li>
3423 <td><em>Application</em>
3425 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3426 wsdbfetch REST service</li>
3427 <li>Stop windows being moved outside desktop on OSX</li>
3428 <li>Filetype associations not installed for webstart
3430 <li>Jalview does not always retrieve progress of a JABAWS
3431 job execution in full once it is complete</li>
3432 <li>revise SHMR RSBS definition to ensure alignment is
3433 uploaded via ali_file parameter</li>
3434 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3435 <li>View all structures superposed fails with exception</li>
3436 <li>Jnet job queues forever if a very short sequence is
3437 submitted for prediction</li>
3438 <li>Cut and paste menu not opened when mouse clicked on
3440 <li>Putting fractional value into integer text box in
3441 alignment parameter dialog causes Jalview to hang</li>
3442 <li>Structure view highlighting doesn't work on
3444 <li>View all structures fails with exception shown in
3446 <li>Characters in filename associated with PDBEntry not
3447 escaped in a platform independent way</li>
3448 <li>Jalview desktop fails to launch with exception when
3450 <li>Tree calculation reports 'you must have 2 or more
3451 sequences selected' when selection is empty</li>
3452 <li>Jalview desktop fails to launch with jar signature
3453 failure when java web start temporary file caching is
3455 <li>DAS Sequence retrieval with range qualification
3456 results in sequence xref which includes range qualification</li>
3457 <li>Errors during processing of command line arguments
3458 cause progress bar (JAL-898) to be removed</li>
3459 <li>Replace comma for semi-colon option not disabled for
3460 DAS sources in sequence fetcher</li>
3461 <li>Cannot close news reader when JABAWS server warning
3462 dialog is shown</li>
3463 <li>Option widgets not updated to reflect user settings</li>
3464 <li>Edited sequence not submitted to web service</li>
3465 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3466 <li>InstallAnywhere installer doesn't unpack and run
3467 on OSX Mountain Lion</li>
3468 <li>Annotation panel not given a scroll bar when
3469 sequences with alignment annotation are pasted into the
3471 <li>Sequence associated annotation rows not associated
3472 when loaded from Jalview project</li>
3473 <li>Browser launch fails with NPE on java 1.7</li>
3474 <li>JABAWS alignment marked as finished when job was
3475 cancelled or job failed due to invalid input</li>
3476 <li>NPE with v2.7 example when clicking on Tree
3477 associated with all views</li>
3478 <li>Exceptions when copy/paste sequences with grouped
3479 annotation rows to new window</li>
3480 </ul> <em>Applet</em>
3482 <li>Sequence features are momentarily displayed before
3483 they are hidden using hidefeaturegroups applet parameter</li>
3484 <li>loading features via javascript API automatically
3485 enables feature display</li>
3486 <li>scrollToColumnIn javascript API method doesn't
3488 </ul> <em>General</em>
3490 <li>Redundancy removal fails for rna alignment</li>
3491 <li>PCA calculation fails when sequence has been selected
3492 and then deselected</li>
3493 <li>PCA window shows grey box when first opened on OSX</li>
3494 <li>Letters coloured pink in sequence logo when alignment
3495 coloured with clustalx</li>
3496 <li>Choosing fonts without letter symbols defined causes
3497 exceptions and redraw errors</li>
3498 <li>Initial PCA plot view is not same as manually
3499 reconfigured view</li>
3500 <li>Grouped annotation graph label has incorrect line
3502 <li>Grouped annotation graph label display is corrupted
3503 for lots of labels</li>
3508 <div align="center">
3509 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3512 <td><em>Application</em>
3514 <li>Jalview Desktop News Reader</li>
3515 <li>Tweaked default layout of web services menu</li>
3516 <li>View/alignment association menu to enable user to
3517 easily specify which alignment a multi-structure view takes
3518 its colours/correspondences from</li>
3519 <li>Allow properties file location to be specified as URL</li>
3520 <li>Extend Jalview project to preserve associations
3521 between many alignment views and a single Jmol display</li>
3522 <li>Store annotation row height in Jalview project file</li>
3523 <li>Annotation row column label formatting attributes
3524 stored in project file</li>
3525 <li>Annotation row order for auto-calculated annotation
3526 rows preserved in Jalview project file</li>
3527 <li>Visual progress indication when Jalview state is
3528 saved using Desktop window menu</li>
3529 <li>Visual indication that command line arguments are
3530 still being processed</li>
3531 <li>Groovy script execution from URL</li>
3532 <li>Colour by annotation default min and max colours in
3534 <li>Automatically associate PDB files dragged onto an
3535 alignment with sequences that have high similarity and
3537 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3538 <li>'view structures' option to open many
3539 structures in same window</li>
3540 <li>Sort associated views menu option for tree panel</li>
3541 <li>Group all JABA and non-JABA services for a particular
3542 analysis function in its own submenu</li>
3543 </ul> <em>Applet</em>
3545 <li>Userdefined and autogenerated annotation rows for
3547 <li>Adjustment of alignment annotation pane height</li>
3548 <li>Annotation scrollbar for annotation panel</li>
3549 <li>Drag to reorder annotation rows in annotation panel</li>
3550 <li>'automaticScrolling' parameter</li>
3551 <li>Allow sequences with partial ID string matches to be
3552 annotated from GFF/Jalview features files</li>
3553 <li>Sequence logo annotation row in applet</li>
3554 <li>Absolute paths relative to host server in applet
3555 parameters are treated as such</li>
3556 <li>New in the JalviewLite javascript API:
3558 <li>JalviewLite.js javascript library</li>
3559 <li>Javascript callbacks for
3561 <li>Applet initialisation</li>
3562 <li>Sequence/alignment mouse-overs and selections</li>
3565 <li>scrollTo row and column alignment scrolling
3567 <li>Select sequence/alignment regions from javascript</li>
3568 <li>javascript structure viewer harness to pass
3569 messages between Jmol and Jalview when running as
3570 distinct applets</li>
3571 <li>sortBy method</li>
3572 <li>Set of applet and application examples shipped
3573 with documentation</li>
3574 <li>New example to demonstrate JalviewLite and Jmol
3575 javascript message exchange</li>
3577 </ul> <em>General</em>
3579 <li>Enable Jmol displays to be associated with multiple
3580 multiple alignments</li>
3581 <li>Option to automatically sort alignment with new tree</li>
3582 <li>User configurable link to enable redirects to a
3583 www.Jalview.org mirror</li>
3584 <li>Jmol colours option for Jmol displays</li>
3585 <li>Configurable newline string when writing alignment
3586 and other flat files</li>
3587 <li>Allow alignment annotation description lines to
3588 contain html tags</li>
3589 </ul> <em>Documentation and Development</em>
3591 <li>Add groovy test harness for bulk load testing to
3593 <li>Groovy script to load and align a set of sequences
3594 using a web service before displaying the result in the
3595 Jalview desktop</li>
3596 <li>Restructured javascript and applet api documentation</li>
3597 <li>Ant target to publish example html files with applet
3599 <li>Netbeans project for building Jalview from source</li>
3600 <li>ant task to create online javadoc for Jalview source</li>
3602 <td><em>Application</em>
3604 <li>User defined colourscheme throws exception when
3605 current built in colourscheme is saved as new scheme</li>
3606 <li>AlignFrame->Save in application pops up save
3607 dialog for valid filename/format</li>
3608 <li>Cannot view associated structure for UniProt sequence</li>
3609 <li>PDB file association breaks for UniProt sequence
3611 <li>Associate PDB from file dialog does not tell you
3612 which sequence is to be associated with the file</li>
3613 <li>Find All raises null pointer exception when query
3614 only matches sequence IDs</li>
3615 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3616 <li>Jalview project with Jmol views created with Jalview
3617 2.4 cannot be loaded</li>
3618 <li>Filetype associations not installed for webstart
3620 <li>Two or more chains in a single PDB file associated
3621 with sequences in different alignments do not get coloured
3622 by their associated sequence</li>
3623 <li>Visibility status of autocalculated annotation row
3624 not preserved when project is loaded</li>
3625 <li>Annotation row height and visibility attributes not
3626 stored in Jalview project</li>
3627 <li>Tree bootstraps are not preserved when saved as a
3628 Jalview project</li>
3629 <li>Envision2 workflow tooltips are corrupted</li>
3630 <li>Enabling show group conservation also enables colour
3631 by conservation</li>
3632 <li>Duplicate group associated conservation or consensus
3633 created on new view</li>
3634 <li>Annotation scrollbar not displayed after 'show
3635 all hidden annotation rows' option selected</li>
3636 <li>Alignment quality not updated after alignment
3637 annotation row is hidden then shown</li>
3638 <li>Preserve colouring of structures coloured by
3639 sequences in pre Jalview 2.7 projects</li>
3640 <li>Web service job parameter dialog is not laid out
3642 <li>Web services menu not refreshed after 'reset
3643 services' button is pressed in preferences</li>
3644 <li>Annotation off by one in Jalview v2_3 example project</li>
3645 <li>Structures imported from file and saved in project
3646 get name like jalview_pdb1234.txt when reloaded</li>
3647 <li>Jalview does not always retrieve progress of a JABAWS
3648 job execution in full once it is complete</li>
3649 </ul> <em>Applet</em>
3651 <li>Alignment height set incorrectly when lots of
3652 annotation rows are displayed</li>
3653 <li>Relative URLs in feature HTML text not resolved to
3655 <li>View follows highlighting does not work for positions
3657 <li><= shown as = in tooltip</li>
3658 <li>Export features raises exception when no features
3660 <li>Separator string used for serialising lists of IDs
3661 for javascript api is modified when separator string
3662 provided as parameter</li>
3663 <li>Null pointer exception when selecting tree leaves for
3664 alignment with no existing selection</li>
3665 <li>Relative URLs for datasources assumed to be relative
3666 to applet's codebase</li>
3667 <li>Status bar not updated after finished searching and
3668 search wraps around to first result</li>
3669 <li>StructureSelectionManager instance shared between
3670 several Jalview applets causes race conditions and memory
3672 <li>Hover tooltip and mouseover of position on structure
3673 not sent from Jmol in applet</li>
3674 <li>Certain sequences of javascript method calls to
3675 applet API fatally hang browser</li>
3676 </ul> <em>General</em>
3678 <li>View follows structure mouseover scrolls beyond
3679 position with wrapped view and hidden regions</li>
3680 <li>Find sequence position moves to wrong residue
3681 with/without hidden columns</li>
3682 <li>Sequence length given in alignment properties window
3684 <li>InvalidNumberFormat exceptions thrown when trying to
3685 import PDB like structure files</li>
3686 <li>Positional search results are only highlighted
3687 between user-supplied sequence start/end bounds</li>
3688 <li>End attribute of sequence is not validated</li>
3689 <li>Find dialog only finds first sequence containing a
3690 given sequence position</li>
3691 <li>Sequence numbering not preserved in MSF alignment
3693 <li>Jalview PDB file reader does not extract sequence
3694 from nucleotide chains correctly</li>
3695 <li>Structure colours not updated when tree partition
3696 changed in alignment</li>
3697 <li>Sequence associated secondary structure not correctly
3698 parsed in interleaved stockholm</li>
3699 <li>Colour by annotation dialog does not restore current
3701 <li>Hiding (nearly) all sequences doesn't work
3703 <li>Sequences containing lowercase letters are not
3704 properly associated with their pdb files</li>
3705 </ul> <em>Documentation and Development</em>
3707 <li>schemas/JalviewWsParamSet.xsd corrupted by
3708 ApplyCopyright tool</li>
3713 <div align="center">
3714 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3717 <td><em>Application</em>
3719 <li>New warning dialog when the Jalview Desktop cannot
3720 contact web services</li>
3721 <li>JABA service parameters for a preset are shown in
3722 service job window</li>
3723 <li>JABA Service menu entries reworded</li>
3727 <li>Modeller PIR IO broken - cannot correctly import a
3728 pir file emitted by Jalview</li>
3729 <li>Existing feature settings transferred to new
3730 alignment view created from cut'n'paste</li>
3731 <li>Improved test for mixed amino/nucleotide chains when
3732 parsing PDB files</li>
3733 <li>Consensus and conservation annotation rows
3734 occasionally become blank for all new windows</li>
3735 <li>Exception raised when right clicking above sequences
3736 in wrapped view mode</li>
3737 </ul> <em>Application</em>
3739 <li>multiple multiply aligned structure views cause cpu
3740 usage to hit 100% and computer to hang</li>
3741 <li>Web Service parameter layout breaks for long user
3742 parameter names</li>
3743 <li>Jaba service discovery hangs desktop if Jaba server
3750 <div align="center">
3751 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3754 <td><em>Application</em>
3756 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3757 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3760 <li>Web Services preference tab</li>
3761 <li>Analysis parameters dialog box and user defined
3763 <li>Improved speed and layout of Envision2 service menu</li>
3764 <li>Superpose structures using associated sequence
3766 <li>Export coordinates and projection as CSV from PCA
3768 </ul> <em>Applet</em>
3770 <li>enable javascript: execution by the applet via the
3771 link out mechanism</li>
3772 </ul> <em>Other</em>
3774 <li>Updated the Jmol Jalview interface to work with Jmol
3776 <li>The Jalview Desktop and JalviewLite applet now
3777 require Java 1.5</li>
3778 <li>Allow Jalview feature colour specification for GFF
3779 sequence annotation files</li>
3780 <li>New 'colour by label' keword in Jalview feature file
3781 type colour specification</li>
3782 <li>New Jalview Desktop Groovy API method that allows a
3783 script to check if it being run in an interactive session or
3784 in a batch operation from the Jalview command line</li>
3788 <li>clustalx colourscheme colours Ds preferentially when
3789 both D+E are present in over 50% of the column</li>
3790 </ul> <em>Application</em>
3792 <li>typo in AlignmentFrame->View->Hide->all but
3793 selected Regions menu item</li>
3794 <li>sequence fetcher replaces ',' for ';' when the ',' is
3795 part of a valid accession ID</li>
3796 <li>fatal OOM if object retrieved by sequence fetcher
3797 runs out of memory</li>
3798 <li>unhandled Out of Memory Error when viewing pca
3799 analysis results</li>
3800 <li>InstallAnywhere builds fail to launch on OS X java
3801 10.5 update 4 (due to apple Java 1.6 update)</li>
3802 <li>Installanywhere Jalview silently fails to launch</li>
3803 </ul> <em>Applet</em>
3805 <li>Jalview.getFeatureGroups() raises an
3806 ArrayIndexOutOfBoundsException if no feature groups are
3813 <div align="center">
3814 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3820 <li>Alignment prettyprinter doesn't cope with long
3822 <li>clustalx colourscheme colours Ds preferentially when
3823 both D+E are present in over 50% of the column</li>
3824 <li>nucleic acid structures retrieved from PDB do not
3825 import correctly</li>
3826 <li>More columns get selected than were clicked on when a
3827 number of columns are hidden</li>
3828 <li>annotation label popup menu not providing correct
3829 add/hide/show options when rows are hidden or none are
3831 <li>Stockholm format shown in list of readable formats,
3832 and parser copes better with alignments from RFAM.</li>
3833 <li>CSV output of consensus only includes the percentage
3834 of all symbols if sequence logo display is enabled</li>
3836 </ul> <em>Applet</em>
3838 <li>annotation panel disappears when annotation is
3840 </ul> <em>Application</em>
3842 <li>Alignment view not redrawn properly when new
3843 alignment opened where annotation panel is visible but no
3844 annotations are present on alignment</li>
3845 <li>pasted region containing hidden columns is
3846 incorrectly displayed in new alignment window</li>
3847 <li>Jalview slow to complete operations when stdout is
3848 flooded (fix is to close the Jalview console)</li>
3849 <li>typo in AlignmentFrame->View->Hide->all but
3850 selected Rregions menu item.</li>
3851 <li>inconsistent group submenu and Format submenu entry
3852 'Un' or 'Non'conserved</li>
3853 <li>Sequence feature settings are being shared by
3854 multiple distinct alignments</li>
3855 <li>group annotation not recreated when tree partition is
3857 <li>double click on group annotation to select sequences
3858 does not propagate to associated trees</li>
3859 <li>Mac OSX specific issues:
3861 <li>exception raised when mouse clicked on desktop
3862 window background</li>
3863 <li>Desktop menu placed on menu bar and application
3864 name set correctly</li>
3865 <li>sequence feature settings not wide enough for the
3866 save feature colourscheme button</li>
3875 <div align="center">
3876 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3879 <td><em>New Capabilities</em>
3881 <li>URL links generated from description line for
3882 regular-expression based URL links (applet and application)
3884 <li>Non-positional feature URL links are shown in link
3886 <li>Linked viewing of nucleic acid sequences and
3888 <li>Automatic Scrolling option in View menu to display
3889 the currently highlighted region of an alignment.</li>
3890 <li>Order an alignment by sequence length, or using the
3891 average score or total feature count for each sequence.</li>
3892 <li>Shading features by score or associated description</li>
3893 <li>Subdivide alignment and groups based on identity of
3894 selected subsequence (Make Groups from Selection).</li>
3895 <li>New hide/show options including Shift+Control+H to
3896 hide everything but the currently selected region.</li>
3897 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3898 </ul> <em>Application</em>
3900 <li>Fetch DB References capabilities and UI expanded to
3901 support retrieval from DAS sequence sources</li>
3902 <li>Local DAS Sequence sources can be added via the
3903 command line or via the Add local source dialog box.</li>
3904 <li>DAS Dbref and DbxRef feature types are parsed as
3905 database references and protein_name is parsed as
3906 description line (BioSapiens terms).</li>
3907 <li>Enable or disable non-positional feature and database
3908 references in sequence ID tooltip from View menu in
3910 <!-- <li>New hidden columns and rows and representatives capabilities
3911 in annotations file (in progress - not yet fully implemented)</li> -->
3912 <li>Group-associated consensus, sequence logos and
3913 conservation plots</li>
3914 <li>Symbol distributions for each column can be exported
3915 and visualized as sequence logos</li>
3916 <li>Optionally scale multi-character column labels to fit
3917 within each column of annotation row<!-- todo for applet -->
3919 <li>Optional automatic sort of associated alignment view
3920 when a new tree is opened.</li>
3921 <li>Jalview Java Console</li>
3922 <li>Better placement of desktop window when moving
3923 between different screens.</li>
3924 <li>New preference items for sequence ID tooltip and
3925 consensus annotation</li>
3926 <li>Client to submit sequences and IDs to Envision2
3928 <li><em>Vamsas Capabilities</em>
3930 <li>Improved VAMSAS synchronization (Jalview archive
3931 used to preserve views, structures, and tree display
3933 <li>Import of vamsas documents from disk or URL via
3935 <li>Sharing of selected regions between views and
3936 with other VAMSAS applications (Experimental feature!)</li>
3937 <li>Updated API to VAMSAS version 0.2</li>
3939 </ul> <em>Applet</em>
3941 <li>Middle button resizes annotation row height</li>
3944 <li>sortByTree (true/false) - automatically sort the
3945 associated alignment view by the tree when a new tree is
3947 <li>showTreeBootstraps (true/false) - show or hide
3948 branch bootstraps (default is to show them if available)</li>
3949 <li>showTreeDistances (true/false) - show or hide
3950 branch lengths (default is to show them if available)</li>
3951 <li>showUnlinkedTreeNodes (true/false) - indicate if
3952 unassociated nodes should be highlighted in the tree
3954 <li>heightScale and widthScale (1.0 or more) -
3955 increase the height or width of a cell in the alignment
3956 grid relative to the current font size.</li>
3959 <li>Non-positional features displayed in sequence ID
3961 </ul> <em>Other</em>
3963 <li>Features format: graduated colour definitions and
3964 specification of feature scores</li>
3965 <li>Alignment Annotations format: new keywords for group
3966 associated annotation (GROUP_REF) and annotation row display
3967 properties (ROW_PROPERTIES)</li>
3968 <li>XML formats extended to support graduated feature
3969 colourschemes, group associated annotation, and profile
3970 visualization settings.</li></td>
3973 <li>Source field in GFF files parsed as feature source
3974 rather than description</li>
3975 <li>Non-positional features are now included in sequence
3976 feature and gff files (controlled via non-positional feature
3977 visibility in tooltip).</li>
3978 <li>URL links generated for all feature links (bugfix)</li>
3979 <li>Added URL embedding instructions to features file
3981 <li>Codons containing ambiguous nucleotides translated as
3982 'X' in peptide product</li>
3983 <li>Match case switch in find dialog box works for both
3984 sequence ID and sequence string and query strings do not
3985 have to be in upper case to match case-insensitively.</li>
3986 <li>AMSA files only contain first column of
3987 multi-character column annotation labels</li>
3988 <li>Jalview Annotation File generation/parsing consistent
3989 with documentation (e.g. Stockholm annotation can be
3990 exported and re-imported)</li>
3991 <li>PDB files without embedded PDB IDs given a friendly
3993 <li>Find incrementally searches ID string matches as well
3994 as subsequence matches, and correctly reports total number
3998 <li>Better handling of exceptions during sequence
4000 <li>Dasobert generated non-positional feature URL
4001 link text excludes the start_end suffix</li>
4002 <li>DAS feature and source retrieval buttons disabled
4003 when fetch or registry operations in progress.</li>
4004 <li>PDB files retrieved from URLs are cached properly</li>
4005 <li>Sequence description lines properly shared via
4007 <li>Sequence fetcher fetches multiple records for all
4009 <li>Ensured that command line das feature retrieval
4010 completes before alignment figures are generated.</li>
4011 <li>Reduced time taken when opening file browser for
4013 <li>isAligned check prior to calculating tree, PCA or
4014 submitting an MSA to JNet now excludes hidden sequences.</li>
4015 <li>User defined group colours properly recovered
4016 from Jalview projects.</li>
4025 <div align="center">
4026 <strong>2.4.0.b2</strong><br> 28/10/2009
4031 <li>Experimental support for google analytics usage
4033 <li>Jalview privacy settings (user preferences and docs).</li>
4038 <li>Race condition in applet preventing startup in
4040 <li>Exception when feature created from selection beyond
4041 length of sequence.</li>
4042 <li>Allow synthetic PDB files to be imported gracefully</li>
4043 <li>Sequence associated annotation rows associate with
4044 all sequences with a given id</li>
4045 <li>Find function matches case-insensitively for sequence
4046 ID string searches</li>
4047 <li>Non-standard characters do not cause pairwise
4048 alignment to fail with exception</li>
4049 </ul> <em>Application Issues</em>
4051 <li>Sequences are now validated against EMBL database</li>
4052 <li>Sequence fetcher fetches multiple records for all
4054 </ul> <em>InstallAnywhere Issues</em>
4056 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4057 issue with installAnywhere mechanism)</li>
4058 <li>Command line launching of JARs from InstallAnywhere
4059 version (java class versioning error fixed)</li>
4066 <div align="center">
4067 <strong>2.4</strong><br> 27/8/2008
4070 <td><em>User Interface</em>
4072 <li>Linked highlighting of codon and amino acid from
4073 translation and protein products</li>
4074 <li>Linked highlighting of structure associated with
4075 residue mapping to codon position</li>
4076 <li>Sequence Fetcher provides example accession numbers
4077 and 'clear' button</li>
4078 <li>MemoryMonitor added as an option under Desktop's
4080 <li>Extract score function to parse whitespace separated
4081 numeric data in description line</li>
4082 <li>Column labels in alignment annotation can be centred.</li>
4083 <li>Tooltip for sequence associated annotation give name
4085 </ul> <em>Web Services and URL fetching</em>
4087 <li>JPred3 web service</li>
4088 <li>Prototype sequence search client (no public services
4090 <li>Fetch either seed alignment or full alignment from
4092 <li>URL Links created for matching database cross
4093 references as well as sequence ID</li>
4094 <li>URL Links can be created using regular-expressions</li>
4095 </ul> <em>Sequence Database Connectivity</em>
4097 <li>Retrieval of cross-referenced sequences from other
4099 <li>Generalised database reference retrieval and
4100 validation to all fetchable databases</li>
4101 <li>Fetch sequences from DAS sources supporting the
4102 sequence command</li>
4103 </ul> <em>Import and Export</em>
4104 <li>export annotation rows as CSV for spreadsheet import</li>
4105 <li>Jalview projects record alignment dataset associations,
4106 EMBL products, and cDNA sequence mappings</li>
4107 <li>Sequence Group colour can be specified in Annotation
4109 <li>Ad-hoc colouring of group in Annotation File using RGB
4110 triplet as name of colourscheme</li>
4111 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4113 <li>treenode binding for VAMSAS tree exchange</li>
4114 <li>local editing and update of sequences in VAMSAS
4115 alignments (experimental)</li>
4116 <li>Create new or select existing session to join</li>
4117 <li>load and save of vamsas documents</li>
4118 </ul> <em>Application command line</em>
4120 <li>-tree parameter to open trees (introduced for passing
4122 <li>-fetchfrom command line argument to specify nicknames
4123 of DAS servers to query for alignment features</li>
4124 <li>-dasserver command line argument to add new servers
4125 that are also automatically queried for features</li>
4126 <li>-groovy command line argument executes a given groovy
4127 script after all input data has been loaded and parsed</li>
4128 </ul> <em>Applet-Application data exchange</em>
4130 <li>Trees passed as applet parameters can be passed to
4131 application (when using "View in full
4132 application")</li>
4133 </ul> <em>Applet Parameters</em>
4135 <li>feature group display control parameter</li>
4136 <li>debug parameter</li>
4137 <li>showbutton parameter</li>
4138 </ul> <em>Applet API methods</em>
4140 <li>newView public method</li>
4141 <li>Window (current view) specific get/set public methods</li>
4142 <li>Feature display control methods</li>
4143 <li>get list of currently selected sequences</li>
4144 </ul> <em>New Jalview distribution features</em>
4146 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4147 <li>RELEASE file gives build properties for the latest
4148 Jalview release.</li>
4149 <li>Java 1.1 Applet build made easier and donotobfuscate
4150 property controls execution of obfuscator</li>
4151 <li>Build target for generating source distribution</li>
4152 <li>Debug flag for javacc</li>
4153 <li>.jalview_properties file is documented (slightly) in
4154 jalview.bin.Cache</li>
4155 <li>Continuous Build Integration for stable and
4156 development version of Application, Applet and source
4161 <li>selected region output includes visible annotations
4162 (for certain formats)</li>
4163 <li>edit label/displaychar contains existing label/char
4165 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4166 <li>shorter peptide product names from EMBL records</li>
4167 <li>Newick string generator makes compact representations</li>
4168 <li>bootstrap values parsed correctly for tree files with
4170 <li>pathological filechooser bug avoided by not allowing
4171 filenames containing a ':'</li>
4172 <li>Fixed exception when parsing GFF files containing
4173 global sequence features</li>
4174 <li>Alignment datasets are finalized only when number of
4175 references from alignment sequences goes to zero</li>
4176 <li>Close of tree branch colour box without colour
4177 selection causes cascading exceptions</li>
4178 <li>occasional negative imgwidth exceptions</li>
4179 <li>better reporting of non-fatal warnings to user when
4180 file parsing fails.</li>
4181 <li>Save works when Jalview project is default format</li>
4182 <li>Save as dialog opened if current alignment format is
4183 not a valid output format</li>
4184 <li>UniProt canonical names introduced for both das and
4186 <li>Histidine should be midblue (not pink!) in Zappo</li>
4187 <li>error messages passed up and output when data read
4189 <li>edit undo recovers previous dataset sequence when
4190 sequence is edited</li>
4191 <li>allow PDB files without pdb ID HEADER lines (like
4192 those generated by MODELLER) to be read in properly</li>
4193 <li>allow reading of JPred concise files as a normal
4195 <li>Stockholm annotation parsing and alignment properties
4196 import fixed for PFAM records</li>
4197 <li>Structure view windows have correct name in Desktop
4199 <li>annotation consisting of sequence associated scores
4200 can be read and written correctly to annotation file</li>
4201 <li>Aligned cDNA translation to aligned peptide works
4203 <li>Fixed display of hidden sequence markers and
4204 non-italic font for representatives in Applet</li>
4205 <li>Applet Menus are always embedded in applet window on
4207 <li>Newly shown features appear at top of stack (in
4209 <li>Annotations added via parameter not drawn properly
4210 due to null pointer exceptions</li>
4211 <li>Secondary structure lines are drawn starting from
4212 first column of alignment</li>
4213 <li>UniProt XML import updated for new schema release in
4215 <li>Sequence feature to sequence ID match for Features
4216 file is case-insensitive</li>
4217 <li>Sequence features read from Features file appended to
4218 all sequences with matching IDs</li>
4219 <li>PDB structure coloured correctly for associated views
4220 containing a sub-sequence</li>
4221 <li>PDB files can be retrieved by applet from Jar files</li>
4222 <li>feature and annotation file applet parameters
4223 referring to different directories are retrieved correctly</li>
4224 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4225 <li>Fixed application hang whilst waiting for
4226 splash-screen version check to complete</li>
4227 <li>Applet properly URLencodes input parameter values
4228 when passing them to the launchApp service</li>
4229 <li>display name and local features preserved in results
4230 retrieved from web service</li>
4231 <li>Visual delay indication for sequence retrieval and
4232 sequence fetcher initialisation</li>
4233 <li>updated Application to use DAS 1.53e version of
4234 dasobert DAS client</li>
4235 <li>Re-instated Full AMSA support and .amsa file
4237 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4245 <div align="center">
4246 <strong>2.3</strong><br> 9/5/07
4251 <li>Jmol 11.0.2 integration</li>
4252 <li>PDB views stored in Jalview XML files</li>
4253 <li>Slide sequences</li>
4254 <li>Edit sequence in place</li>
4255 <li>EMBL CDS features</li>
4256 <li>DAS Feature mapping</li>
4257 <li>Feature ordering</li>
4258 <li>Alignment Properties</li>
4259 <li>Annotation Scores</li>
4260 <li>Sort by scores</li>
4261 <li>Feature/annotation editing in applet</li>
4266 <li>Headless state operation in 2.2.1</li>
4267 <li>Incorrect and unstable DNA pairwise alignment</li>
4268 <li>Cut and paste of sequences with annotation</li>
4269 <li>Feature group display state in XML</li>
4270 <li>Feature ordering in XML</li>
4271 <li>blc file iteration selection using filename # suffix</li>
4272 <li>Stockholm alignment properties</li>
4273 <li>Stockhom alignment secondary structure annotation</li>
4274 <li>2.2.1 applet had no feature transparency</li>
4275 <li>Number pad keys can be used in cursor mode</li>
4276 <li>Structure Viewer mirror image resolved</li>
4283 <div align="center">
4284 <strong>2.2.1</strong><br> 12/2/07
4289 <li>Non standard characters can be read and displayed
4290 <li>Annotations/Features can be imported/exported to the
4292 <li>Applet allows editing of sequence/annotation/group
4293 name & description
4294 <li>Preference setting to display sequence name in
4296 <li>Annotation file format extended to allow
4297 Sequence_groups to be defined
4298 <li>Default opening of alignment overview panel can be
4299 specified in preferences
4300 <li>PDB residue numbering annotation added to associated
4306 <li>Applet crash under certain Linux OS with Java 1.6
4308 <li>Annotation file export / import bugs fixed
4309 <li>PNG / EPS image output bugs fixed
4315 <div align="center">
4316 <strong>2.2</strong><br> 27/11/06
4321 <li>Multiple views on alignment
4322 <li>Sequence feature editing
4323 <li>"Reload" alignment
4324 <li>"Save" to current filename
4325 <li>Background dependent text colour
4326 <li>Right align sequence ids
4327 <li>User-defined lower case residue colours
4330 <li>Menu item accelerator keys
4331 <li>Control-V pastes to current alignment
4332 <li>Cancel button for DAS Feature Fetching
4333 <li>PCA and PDB Viewers zoom via mouse roller
4334 <li>User-defined sub-tree colours and sub-tree selection
4336 <li>'New Window' button on the 'Output to Text box'
4341 <li>New memory efficient Undo/Redo System
4342 <li>Optimised symbol lookups and conservation/consensus
4344 <li>Region Conservation/Consensus recalculated after
4346 <li>Fixed Remove Empty Columns Bug (empty columns at end
4348 <li>Slowed DAS Feature Fetching for increased robustness.
4350 <li>Made angle brackets in ASCII feature descriptions
4352 <li>Re-instated Zoom function for PCA
4353 <li>Sequence descriptions conserved in web service
4355 <li>UniProt ID discoverer uses any word separated by
4357 <li>WsDbFetch query/result association resolved
4358 <li>Tree leaf to sequence mapping improved
4359 <li>Smooth fonts switch moved to FontChooser dialog box.
4366 <div align="center">
4367 <strong>2.1.1</strong><br> 12/9/06
4372 <li>Copy consensus sequence to clipboard</li>
4377 <li>Image output - rightmost residues are rendered if
4378 sequence id panel has been resized</li>
4379 <li>Image output - all offscreen group boundaries are
4381 <li>Annotation files with sequence references - all
4382 elements in file are relative to sequence position</li>
4383 <li>Mac Applet users can use Alt key for group editing</li>
4389 <div align="center">
4390 <strong>2.1</strong><br> 22/8/06
4395 <li>MAFFT Multiple Alignment in default Web Service list</li>
4396 <li>DAS Feature fetching</li>
4397 <li>Hide sequences and columns</li>
4398 <li>Export Annotations and Features</li>
4399 <li>GFF file reading / writing</li>
4400 <li>Associate structures with sequences from local PDB
4402 <li>Add sequences to exisiting alignment</li>
4403 <li>Recently opened files / URL lists</li>
4404 <li>Applet can launch the full application</li>
4405 <li>Applet has transparency for features (Java 1.2
4407 <li>Applet has user defined colours parameter</li>
4408 <li>Applet can load sequences from parameter
4409 "sequence<em>x</em>"
4415 <li>Redundancy Panel reinstalled in the Applet</li>
4416 <li>Monospaced font - EPS / rescaling bug fixed</li>
4417 <li>Annotation files with sequence references bug fixed</li>
4423 <div align="center">
4424 <strong>2.08.1</strong><br> 2/5/06
4429 <li>Change case of selected region from Popup menu</li>
4430 <li>Choose to match case when searching</li>
4431 <li>Middle mouse button and mouse movement can compress /
4432 expand the visible width and height of the alignment</li>
4437 <li>Annotation Panel displays complete JNet results</li>
4443 <div align="center">
4444 <strong>2.08b</strong><br> 18/4/06
4450 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4451 <li>Righthand label on wrapped alignments shows correct
4458 <div align="center">
4459 <strong>2.08</strong><br> 10/4/06
4464 <li>Editing can be locked to the selection area</li>
4465 <li>Keyboard editing</li>
4466 <li>Create sequence features from searches</li>
4467 <li>Precalculated annotations can be loaded onto
4469 <li>Features file allows grouping of features</li>
4470 <li>Annotation Colouring scheme added</li>
4471 <li>Smooth fonts off by default - Faster rendering</li>
4472 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4477 <li>Drag & Drop fixed on Linux</li>
4478 <li>Jalview Archive file faster to load/save, sequence
4479 descriptions saved.</li>
4485 <div align="center">
4486 <strong>2.07</strong><br> 12/12/05
4491 <li>PDB Structure Viewer enhanced</li>
4492 <li>Sequence Feature retrieval and display enhanced</li>
4493 <li>Choose to output sequence start-end after sequence
4494 name for file output</li>
4495 <li>Sequence Fetcher WSDBFetch@EBI</li>
4496 <li>Applet can read feature files, PDB files and can be
4497 used for HTML form input</li>
4502 <li>HTML output writes groups and features</li>
4503 <li>Group editing is Control and mouse click</li>
4504 <li>File IO bugs</li>
4510 <div align="center">
4511 <strong>2.06</strong><br> 28/9/05
4516 <li>View annotations in wrapped mode</li>
4517 <li>More options for PCA viewer</li>
4522 <li>GUI bugs resolved</li>
4523 <li>Runs with -nodisplay from command line</li>
4529 <div align="center">
4530 <strong>2.05b</strong><br> 15/9/05
4535 <li>Choose EPS export as lineart or text</li>
4536 <li>Jar files are executable</li>
4537 <li>Can read in Uracil - maps to unknown residue</li>
4542 <li>Known OutOfMemory errors give warning message</li>
4543 <li>Overview window calculated more efficiently</li>
4544 <li>Several GUI bugs resolved</li>
4550 <div align="center">
4551 <strong>2.05</strong><br> 30/8/05
4556 <li>Edit and annotate in "Wrapped" view</li>
4561 <li>Several GUI bugs resolved</li>
4567 <div align="center">
4568 <strong>2.04</strong><br> 24/8/05
4573 <li>Hold down mouse wheel & scroll to change font
4579 <li>Improved JPred client reliability</li>
4580 <li>Improved loading of Jalview files</li>
4586 <div align="center">
4587 <strong>2.03</strong><br> 18/8/05
4592 <li>Set Proxy server name and port in preferences</li>
4593 <li>Multiple URL links from sequence ids</li>
4594 <li>User Defined Colours can have a scheme name and added
4596 <li>Choose to ignore gaps in consensus calculation</li>
4597 <li>Unix users can set default web browser</li>
4598 <li>Runs without GUI for batch processing</li>
4599 <li>Dynamically generated Web Service Menus</li>
4604 <li>InstallAnywhere download for Sparc Solaris</li>
4610 <div align="center">
4611 <strong>2.02</strong><br> 18/7/05
4617 <li>Copy & Paste order of sequences maintains
4618 alignment order.</li>
4624 <div align="center">
4625 <strong>2.01</strong><br> 12/7/05
4630 <li>Use delete key for deleting selection.</li>
4631 <li>Use Mouse wheel to scroll sequences.</li>
4632 <li>Help file updated to describe how to add alignment
4634 <li>Version and build date written to build properties
4636 <li>InstallAnywhere installation will check for updates
4637 at launch of Jalview.</li>
4642 <li>Delete gaps bug fixed.</li>
4643 <li>FileChooser sorts columns.</li>
4644 <li>Can remove groups one by one.</li>
4645 <li>Filechooser icons installed.</li>
4646 <li>Finder ignores return character when searching.
4647 Return key will initiate a search.<br>
4654 <div align="center">
4655 <strong>2.0</strong><br> 20/6/05
4660 <li>New codebase</li>