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>25/2/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3376 -->Record "fixed column" values POS,
66 ID, QUAL, FILTER from VCF as Feature Attributes
69 <!-- JAL-3375 -->More robust VCF numeric data field
70 validation while parsing (e.g. AF* attributes)
73 <!-- JAL-3538 -->Font anti-aliasing in alignment views
79 </ul> <em>Release processes</em>
82 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
84 </ul> <em>Build System</em>
87 <!-- JAL-3510 -->Clover updated to 4.4.1
90 <!-- JAL-3513 -->Test code included in Clover coverage
93 </ul> <em>Deprecations</em>
95 <td align="left" valign="top">
101 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
102 with annotation and exceptions thrown when only a few
103 columns shown in wrapped mode
106 <!-- JAL-3386 -->Sequence IDs missing in headless export of
107 wrapped alignment figure with annotations
110 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
111 ID fails with ClassCastException
114 <!-- JAL-3389 -->Chimera session not restored from Jalview
118 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
119 feature settings dialog also selects columns
122 <!-- JAL-3473 -->SpinnerNumberModel causing
123 IllegalArgumentException in some circumstances
126 <!-- JAL-3406 -->Credits missing some authors in Jalview
127 help documentation for 2.11.0 release
129 </ul> <em>Java 11 Compatibility issues</em>
132 <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
134 </ul> <em>Repository and Source Release</em>
137 <!-- JAL-3474 -->removed redundant .gitignore files from
141 <em>New Known Issues</em>
144 <!-- JAL-3523 -->OSX - Current working directory not
145 preserved when Jalview.app launched with parameters from
149 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
150 clipped in headless figure export when Right Align option
157 <td width="60" align="center" nowrap>
158 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
159 <em>04/07/2019</em></strong>
161 <td align="left" valign="top">
164 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
165 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
166 source project) rather than InstallAnywhere
169 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
170 settings, receive over the air updates and launch specific
171 versions via (<a href="https://github.com/threerings/getdown">Three
175 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
176 formats supported by Jalview (including .jvp project files)
179 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
180 arguments and switch between different getdown channels
183 <!-- JAL-3141 -->Backup files created when saving Jalview project
188 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
189 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
191 <!-- JAL-2620 -->Alternative genetic code tables for
192 'Translate as cDNA'</li>
194 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
195 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
198 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
199 implementation that allows updates) used for Sequence Feature collections</li>
201 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
202 features can be filtered and shaded according to any
203 associated attributes (e.g. variant attributes from VCF
204 file, or key-value pairs imported from column 9 of GFF
208 <!-- JAL-2879 -->Feature Attributes and shading schemes
209 stored and restored from Jalview Projects
212 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
213 recognise variant features
216 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
217 sequences (also coloured red by default)
220 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
224 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
225 algorithm (Z-sort/transparency and filter aware)
228 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
234 <!-- JAL-3205 -->Symmetric score matrices for faster
235 tree and PCA calculations
237 <li><strong>Principal Components Analysis Viewer</strong>
240 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
241 and Viewer state saved in Jalview Project
243 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
246 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
250 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
255 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
257 <li><strong>Speed and Efficiency</strong>
260 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
261 multiple groups when working with large alignments
264 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
268 <li><strong>User Interface</strong>
271 <!-- JAL-2933 -->Finder panel remembers last position in each
275 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
276 what is shown)<br />Only visible regions of alignment are shown by
277 default (can be changed in user preferences)
280 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
281 to the Overwrite Dialog
284 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
288 <!-- JAL-1244 -->Status bar shows bounds when dragging a
289 selection region, and gap count when inserting or deleting gaps
292 <!-- JAL-3132 -->Status bar updates over sequence and annotation
296 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
300 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
304 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
307 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
311 <!-- JAL-3181 -->Consistent ordering of links in sequence id
315 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
317 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
321 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
322 <li><strong>Java 11 Support (not yet on general release)</strong>
325 <!-- -->OSX GUI integrations for App menu's 'About' entry and
330 <em>Deprecations</em>
332 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
333 capabilities removed from the Jalview Desktop
335 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
336 unmarshalling has been replaced by JAXB for Jalview projects
337 and XML based data retrieval clients</li>
338 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
339 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
340 </ul> <em>Documentation</em>
342 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
343 not supported in EPS figure export
345 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
346 </ul> <em>Development and Release Processes</em>
349 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
352 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
354 <!-- JAL-3225 -->Eclipse project configuration managed with
358 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
359 Bamboo continuous integration for unattended Test Suite
363 <!-- JAL-2864 -->Memory test suite to detect leaks in common
367 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
371 <!-- JAL-3248 -->Developer documentation migrated to
372 markdown (with HTML rendering)
375 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
378 <!-- JAL-3289 -->New URLs for publishing development
383 <td align="left" valign="top">
386 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
389 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
390 superposition in Jmol fail on Windows
393 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
394 structures for sequences with lots of PDB structures
397 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
401 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
402 project involving multiple views
405 <!-- JAL-3164 -->Overview for complementary view in a linked
406 CDS/Protein alignment is not updated when Hide Columns by
407 Annotation dialog hides columns
410 <!-- JAL-3158 -->Selection highlighting in the complement of a
411 CDS/Protein alignment stops working after making a selection in
412 one view, then making another selection in the other view
415 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
419 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
420 Settings and Jalview Preferences panels
423 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
424 overview with large alignments
427 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
428 region if columns were selected by dragging right-to-left and the
429 mouse moved to the left of the first column
432 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
433 hidden column marker via scale popup menu
436 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
437 doesn't tell users the invalid URL
440 <!-- JAL-2816 -->Tooltips displayed for features filtered by
444 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
445 show cross references or Fetch Database References are shown in
449 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
450 peptide sequence (computed variant shown as p.Res.null)
453 <!-- JAL-2060 -->'Graduated colour' option not offered for
454 manually created features (where feature score is Float.NaN)
457 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
458 when columns are hidden
461 <!-- JAL-3082 -->Regular expression error for '(' in Select
462 Columns by Annotation description
465 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
466 out of Scale or Annotation Panel
469 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
473 <!-- JAL-3074 -->Left/right drag in annotation can scroll
477 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
481 <!-- JAL-3002 -->Column display is out by one after Page Down,
482 Page Up in wrapped mode
485 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
488 <!-- JAL-2932 -->Finder searches in minimised alignments
491 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
492 on opening an alignment
495 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
499 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
500 different groups in the alignment are selected
503 <!-- JAL-2717 -->Internationalised colour scheme names not shown
507 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
511 <!-- JAL-3125 -->Value input for graduated feature colour
512 threshold gets 'unrounded'
515 <!-- JAL-2982 -->PCA image export doesn't respect background
519 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
522 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
525 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
529 <!-- JAL-2964 -->Associate Tree with All Views not restored from
533 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
534 shown in complementary view
537 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
538 without normalisation
541 <!-- JAL-3021 -->Sequence Details report should open positioned at top
545 <!-- JAL-914 -->Help page can be opened twice
548 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
550 </ul> <em>Editing</em>
553 <!-- JAL-2822 -->Start and End should be updated when sequence
554 data at beginning or end of alignment added/removed via 'Edit'
558 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
559 relocate sequence features correctly when start of sequence is
560 removed (Known defect since 2.10)
563 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
564 dialog corrupts dataset sequence
567 <!-- JAL-868 -->Structure colours not updated when associated tree
568 repartitions the alignment view (Regression in 2.10.5)
570 </ul> <em>Datamodel</em>
573 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
574 sequence's End is greater than its length
576 </ul> <em>Bugs fixed for Java 11 Support (not yet on
577 general release)</em>
580 <!-- JAL-3288 -->Menus work properly in split-screen
582 </ul> <em>New Known Defects</em>
585 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
588 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
589 regions of protein alignment.
592 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
593 is restored from a Jalview 2.11 project
596 <!-- JAL-3213 -->Alignment panel height can be too small after
600 <!-- JAL-3240 -->Display is incorrect after removing gapped
601 columns within hidden columns
604 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
605 window after dragging left to select columns to left of visible
609 <!-- JAL-2876 -->Features coloured according to their description
610 string and thresholded by score in earlier versions of Jalview are
611 not shown as thresholded features in 2.11. To workaround please
612 create a Score filter instead.
615 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
617 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
620 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
621 alignments with multiple views can close views unexpectedly
624 <em>Java 11 Specific defects</em>
627 <!-- JAL-3235 -->Jalview Properties file is not sorted
628 alphabetically when saved
634 <td width="60" nowrap>
636 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
639 <td><div align="left">
643 <!-- JAL-3101 -->Default memory for Jalview webstart and
644 InstallAnywhere increased to 1G.
647 <!-- JAL-247 -->Hidden sequence markers and representative
648 sequence bolding included when exporting alignment as EPS,
649 SVG, PNG or HTML. <em>Display is configured via the
650 Format menu, or for command-line use via a Jalview
651 properties file.</em>
654 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
655 API and sequence data now imported as JSON.
658 <!-- JAL-3065 -->Change in recommended way of starting
659 Jalview via a Java command line: add jars in lib directory
660 to CLASSPATH, rather than via the deprecated java.ext.dirs
667 <!-- JAL-3047 -->Support added to execute test suite
668 instrumented with <a href="http://openclover.org/">Open
673 <td><div align="left">
677 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
678 row shown in Feredoxin Structure alignment view of example
682 <!-- JAL-2854 -->Annotation obscures sequences if lots of
683 annotation displayed.
686 <!-- JAL-3107 -->Group conservation/consensus not shown
687 for newly created group when 'Apply to all groups'
691 <!-- JAL-3087 -->Corrupted display when switching to
692 wrapped mode when sequence panel's vertical scrollbar is
696 <!-- JAL-3003 -->Alignment is black in exported EPS file
697 when sequences are selected in exported view.</em>
700 <!-- JAL-3059 -->Groups with different coloured borders
701 aren't rendered with correct colour.
704 <!-- JAL-3092 -->Jalview could hang when importing certain
705 types of knotted RNA secondary structure.
708 <!-- JAL-3095 -->Sequence highlight and selection in
709 trimmed VARNA 2D structure is incorrect for sequences that
713 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
714 annotation when columns are inserted into an alignment,
715 and when exporting as Stockholm flatfile.
718 <!-- JAL-3053 -->Jalview annotation rows containing upper
719 and lower-case 'E' and 'H' do not automatically get
720 treated as RNA secondary structure.
723 <!-- JAL-3106 -->.jvp should be used as default extension
724 (not .jar) when saving a Jalview project file.
727 <!-- JAL-3105 -->Mac Users: closing a window correctly
728 transfers focus to previous window on OSX
731 <em>Java 10 Issues Resolved</em>
734 <!-- JAL-2988 -->OSX - Can't save new files via the File
735 or export menus by typing in a name into the Save dialog
739 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
740 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
741 'look and feel' which has improved compatibility with the
742 latest version of OSX.
749 <td width="60" nowrap>
751 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
752 <em>7/06/2018</em></strong>
755 <td><div align="left">
759 <!-- JAL-2920 -->Use HGVS nomenclature for variant
760 annotation retrieved from Uniprot
763 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
764 onto the Jalview Desktop
768 <td><div align="left">
772 <!-- JAL-3017 -->Cannot import features with multiple
773 variant elements (blocks import of some Uniprot records)
776 <!-- JAL-2997 -->Clustal files with sequence positions in
777 right-hand column parsed correctly
780 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
781 not alignment area in exported graphic
784 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
785 window has input focus
788 <!-- JAL-2992 -->Annotation panel set too high when
789 annotation added to view (Windows)
792 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
793 network connectivity is poor
796 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
797 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
798 the currently open URL and links from a page viewed in
799 Firefox or Chrome on Windows is now fully supported. If
800 you are using Edge, only links in the page can be
801 dragged, and with Internet Explorer, only the currently
802 open URL in the browser can be dropped onto Jalview.</em>
805 <em>New Known Defects</em>
807 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
812 <td width="60" nowrap>
814 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
817 <td><div align="left">
821 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
822 for disabling automatic superposition of multiple
823 structures and open structures in existing views
826 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
827 ID and annotation area margins can be click-dragged to
831 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
835 <!-- JAL-2759 -->Improved performance for large alignments
836 and lots of hidden columns
839 <!-- JAL-2593 -->Improved performance when rendering lots
840 of features (particularly when transparency is disabled)
843 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
844 exchange of Jalview features and Chimera attributes made
850 <td><div align="left">
853 <!-- JAL-2899 -->Structure and Overview aren't updated
854 when Colour By Annotation threshold slider is adjusted
857 <!-- JAL-2778 -->Slow redraw when Overview panel shown
858 overlapping alignment panel
861 <!-- JAL-2929 -->Overview doesn't show end of unpadded
865 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
866 improved: CDS not handled correctly if transcript has no
870 <!-- JAL-2321 -->Secondary structure and temperature
871 factor annotation not added to sequence when local PDB
872 file associated with it by drag'n'drop or structure
876 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
877 dialog doesn't import PDB files dropped on an alignment
880 <!-- JAL-2666 -->Linked scrolling via protein horizontal
881 scroll bar doesn't work for some CDS/Protein views
884 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
885 Java 1.8u153 onwards and Java 1.9u4+.
888 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
889 columns in annotation row
892 <!-- JAL-2913 -->Preferences panel's ID Width control is not
893 honored in batch mode
896 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
897 for structures added to existing Jmol view
900 <!-- JAL-2223 -->'View Mappings' includes duplicate
901 entries after importing project with multiple views
904 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
905 protein sequences via SIFTS from associated PDB entries
906 with negative residue numbers or missing residues fails
909 <!-- JAL-2952 -->Exception when shading sequence with negative
910 Temperature Factor values from annotated PDB files (e.g.
911 as generated by CONSURF)
914 <!-- JAL-2920 -->Uniprot 'sequence variant' features
915 tooltip doesn't include a text description of mutation
918 <!-- JAL-2922 -->Invert displayed features very slow when
919 structure and/or overview windows are also shown
922 <!-- JAL-2954 -->Selecting columns from highlighted regions
923 very slow for alignments with large numbers of sequences
926 <!-- JAL-2925 -->Copy Consensus fails for group consensus
927 with 'StringIndexOutOfBounds'
930 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
931 platforms running Java 10
934 <!-- JAL-2960 -->Adding a structure to existing structure
935 view appears to do nothing because the view is hidden behind the alignment view
941 <!-- JAL-2926 -->Copy consensus sequence option in applet
942 should copy the group consensus when popup is opened on it
948 <!-- JAL-2913 -->Fixed ID width preference is not respected
951 <em>New Known Defects</em>
954 <!-- JAL-2973 --> Exceptions occasionally raised when
955 editing a large alignment and overview is displayed
958 <!-- JAL-2974 -->'Overview updating' progress bar is shown
959 repeatedly after a series of edits even when the overview
960 is no longer reflecting updates
963 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
964 structures for protein subsequence (if 'Trim Retrieved
965 Sequences' enabled) or Ensembl isoforms (Workaround in
966 2.10.4 is to fail back to N&W mapping)
969 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
970 option gives blank output
977 <td width="60" nowrap>
979 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
982 <td><div align="left">
983 <ul><li>Updated Certum Codesigning Certificate
984 (Valid till 30th November 2018)</li></ul></div></td>
985 <td><div align="left">
988 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
989 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
990 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
991 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
992 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
993 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
994 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1000 <td width="60" nowrap>
1001 <div align="center">
1002 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1005 <td><div align="left">
1009 <!-- JAL-2446 -->Faster and more efficient management and
1010 rendering of sequence features
1013 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1014 429 rate limit request hander
1017 <!-- JAL-2773 -->Structure views don't get updated unless
1018 their colours have changed
1021 <!-- JAL-2495 -->All linked sequences are highlighted for
1022 a structure mousover (Jmol) or selection (Chimera)
1025 <!-- JAL-2790 -->'Cancel' button in progress bar for
1026 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1029 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1030 view from Ensembl locus cross-references
1033 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1037 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1038 feature can be disabled
1041 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1042 PDB easier retrieval of sequences for lists of IDs
1045 <!-- JAL-2758 -->Short names for sequences retrieved from
1051 <li>Groovy interpreter updated to 2.4.12</li>
1052 <li>Example groovy script for generating a matrix of
1053 percent identity scores for current alignment.</li>
1055 <em>Testing and Deployment</em>
1058 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1062 <td><div align="left">
1066 <!-- JAL-2643 -->Pressing tab after updating the colour
1067 threshold text field doesn't trigger an update to the
1071 <!-- JAL-2682 -->Race condition when parsing sequence ID
1075 <!-- JAL-2608 -->Overview windows are also closed when
1076 alignment window is closed
1079 <!-- JAL-2548 -->Export of features doesn't always respect
1083 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1084 takes a long time in Cursor mode
1090 <!-- JAL-2777 -->Structures with whitespace chainCode
1091 cannot be viewed in Chimera
1094 <!-- JAL-2728 -->Protein annotation panel too high in
1098 <!-- JAL-2757 -->Can't edit the query after the server
1099 error warning icon is shown in Uniprot and PDB Free Text
1103 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1106 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1109 <!-- JAL-2739 -->Hidden column marker in last column not
1110 rendered when switching back from Wrapped to normal view
1113 <!-- JAL-2768 -->Annotation display corrupted when
1114 scrolling right in unwapped alignment view
1117 <!-- JAL-2542 -->Existing features on subsequence
1118 incorrectly relocated when full sequence retrieved from
1122 <!-- JAL-2733 -->Last reported memory still shown when
1123 Desktop->Show Memory is unticked (OSX only)
1126 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1127 features of same type and group to be selected for
1131 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1132 alignments when hidden columns are present
1135 <!-- JAL-2392 -->Jalview freezes when loading and
1136 displaying several structures
1139 <!-- JAL-2732 -->Black outlines left after resizing or
1143 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1144 within the Jalview desktop on OSX
1147 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1148 when in wrapped alignment mode
1151 <!-- JAL-2636 -->Scale mark not shown when close to right
1152 hand end of alignment
1155 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1156 each selected sequence do not have correct start/end
1160 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1161 after canceling the Alignment Window's Font dialog
1164 <!-- JAL-2036 -->Show cross-references not enabled after
1165 restoring project until a new view is created
1168 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1169 URL links appears when only default EMBL-EBI link is
1170 configured (since 2.10.2b2)
1173 <!-- JAL-2775 -->Overview redraws whole window when box
1174 position is adjusted
1177 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1178 in a multi-chain structure when viewing alignment
1179 involving more than one chain (since 2.10)
1182 <!-- JAL-2811 -->Double residue highlights in cursor mode
1183 if new selection moves alignment window
1186 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1187 arrow key in cursor mode to pass hidden column marker
1190 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1191 that produces correctly annotated transcripts and products
1194 <!-- JAL-2776 -->Toggling a feature group after first time
1195 doesn't update associated structure view
1198 <em>Applet</em><br />
1201 <!-- JAL-2687 -->Concurrent modification exception when
1202 closing alignment panel
1205 <em>BioJSON</em><br />
1208 <!-- JAL-2546 -->BioJSON export does not preserve
1209 non-positional features
1212 <em>New Known Issues</em>
1215 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1216 sequence features correctly (for many previous versions of
1220 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1221 using cursor in wrapped panel other than top
1224 <!-- JAL-2791 -->Select columns containing feature ignores
1225 graduated colour threshold
1228 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1229 always preserve numbering and sequence features
1232 <em>Known Java 9 Issues</em>
1235 <!-- JAL-2902 -->Groovy Console very slow to open and is
1236 not responsive when entering characters (Webstart, Java
1243 <td width="60" nowrap>
1244 <div align="center">
1245 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1246 <em>2/10/2017</em></strong>
1249 <td><div align="left">
1250 <em>New features in Jalview Desktop</em>
1253 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1255 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1259 <td><div align="left">
1263 <td width="60" nowrap>
1264 <div align="center">
1265 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1266 <em>7/9/2017</em></strong>
1269 <td><div align="left">
1273 <!-- JAL-2588 -->Show gaps in overview window by colouring
1274 in grey (sequences used to be coloured grey, and gaps were
1278 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1282 <!-- JAL-2587 -->Overview updates immediately on increase
1283 in size and progress bar shown as higher resolution
1284 overview is recalculated
1289 <td><div align="left">
1293 <!-- JAL-2664 -->Overview window redraws every hidden
1294 column region row by row
1297 <!-- JAL-2681 -->duplicate protein sequences shown after
1298 retrieving Ensembl crossrefs for sequences from Uniprot
1301 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1302 format setting is unticked
1305 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1306 if group has show boxes format setting unticked
1309 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1310 autoscrolling whilst dragging current selection group to
1311 include sequences and columns not currently displayed
1314 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1315 assemblies are imported via CIF file
1318 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1319 displayed when threshold or conservation colouring is also
1323 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1327 <!-- JAL-2673 -->Jalview continues to scroll after
1328 dragging a selected region off the visible region of the
1332 <!-- JAL-2724 -->Cannot apply annotation based
1333 colourscheme to all groups in a view
1336 <!-- JAL-2511 -->IDs don't line up with sequences
1337 initially after font size change using the Font chooser or
1344 <td width="60" nowrap>
1345 <div align="center">
1346 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1349 <td><div align="left">
1350 <em>Calculations</em>
1354 <!-- JAL-1933 -->Occupancy annotation row shows number of
1355 ungapped positions in each column of the alignment.
1358 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1359 a calculation dialog box
1362 <!-- JAL-2379 -->Revised implementation of PCA for speed
1363 and memory efficiency (~30x faster)
1366 <!-- JAL-2403 -->Revised implementation of sequence
1367 similarity scores as used by Tree, PCA, Shading Consensus
1368 and other calculations
1371 <!-- JAL-2416 -->Score matrices are stored as resource
1372 files within the Jalview codebase
1375 <!-- JAL-2500 -->Trees computed on Sequence Feature
1376 Similarity may have different topology due to increased
1383 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1384 model for alignments and groups
1387 <!-- JAL-384 -->Custom shading schemes created via groovy
1394 <!-- JAL-2526 -->Efficiency improvements for interacting
1395 with alignment and overview windows
1398 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1402 <!-- JAL-2388 -->Hidden columns and sequences can be
1406 <!-- JAL-2611 -->Click-drag in visible area allows fine
1407 adjustment of visible position
1411 <em>Data import/export</em>
1414 <!-- JAL-2535 -->Posterior probability annotation from
1415 Stockholm files imported as sequence associated annotation
1418 <!-- JAL-2507 -->More robust per-sequence positional
1419 annotation input/output via stockholm flatfile
1422 <!-- JAL-2533 -->Sequence names don't include file
1423 extension when importing structure files without embedded
1424 names or PDB accessions
1427 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1428 format sequence substitution matrices
1431 <em>User Interface</em>
1434 <!-- JAL-2447 --> Experimental Features Checkbox in
1435 Desktop's Tools menu to hide or show untested features in
1439 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1440 via Overview or sequence motif search operations
1443 <!-- JAL-2547 -->Amend sequence features dialog box can be
1444 opened by double clicking gaps within sequence feature
1448 <!-- JAL-1476 -->Status bar message shown when not enough
1449 aligned positions were available to create a 3D structure
1453 <em>3D Structure</em>
1456 <!-- JAL-2430 -->Hidden regions in alignment views are not
1457 coloured in linked structure views
1460 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1461 file-based command exchange
1464 <!-- JAL-2375 -->Structure chooser automatically shows
1465 Cached Structures rather than querying the PDBe if
1466 structures are already available for sequences
1469 <!-- JAL-2520 -->Structures imported via URL are cached in
1470 the Jalview project rather than downloaded again when the
1471 project is reopened.
1474 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1475 to transfer Chimera's structure attributes as Jalview
1476 features, and vice-versa (<strong>Experimental
1480 <em>Web Services</em>
1483 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1486 <!-- JAL-2335 -->Filter non-standard amino acids and
1487 nucleotides when submitting to AACon and other MSA
1491 <!-- JAL-2316, -->URLs for viewing database
1492 cross-references provided by identifiers.org and the
1493 EMBL-EBI's MIRIAM DB
1500 <!-- JAL-2344 -->FileFormatI interface for describing and
1501 identifying file formats (instead of String constants)
1504 <!-- JAL-2228 -->FeatureCounter script refactored for
1505 efficiency when counting all displayed features (not
1506 backwards compatible with 2.10.1)
1509 <em>Example files</em>
1512 <!-- JAL-2631 -->Graduated feature colour style example
1513 included in the example feature file
1516 <em>Documentation</em>
1519 <!-- JAL-2339 -->Release notes reformatted for readability
1520 with the built-in Java help viewer
1523 <!-- JAL-1644 -->Find documentation updated with 'search
1524 sequence description' option
1530 <!-- JAL-2485, -->External service integration tests for
1531 Uniprot REST Free Text Search Client
1534 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1537 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1542 <td><div align="left">
1543 <em>Calculations</em>
1546 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1547 matrix - C->R should be '-3'<br />Old matrix restored
1548 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1550 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1551 Jalview's treatment of gaps in PCA and substitution matrix
1552 based Tree calculations.<br /> <br />In earlier versions
1553 of Jalview, gaps matching gaps were penalised, and gaps
1554 matching non-gaps penalised even more. In the PCA
1555 calculation, gaps were actually treated as non-gaps - so
1556 different costs were applied, which meant Jalview's PCAs
1557 were different to those produced by SeqSpace.<br />Jalview
1558 now treats gaps in the same way as SeqSpace (ie it scores
1559 them as 0). <br /> <br />Enter the following in the
1560 Groovy console to restore pre-2.10.2 behaviour:<br />
1561 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1562 // for 2.10.1 mode <br />
1563 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1564 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1565 these settings will affect all subsequent tree and PCA
1566 calculations (not recommended)</em></li>
1568 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1569 scaling of branch lengths for trees computed using
1570 Sequence Feature Similarity.
1573 <!-- JAL-2377 -->PCA calculation could hang when
1574 generating output report when working with highly
1575 redundant alignments
1578 <!-- JAL-2544 --> Sort by features includes features to
1579 right of selected region when gaps present on right-hand
1583 <em>User Interface</em>
1586 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1587 doesn't reselect a specific sequence's associated
1588 annotation after it was used for colouring a view
1591 <!-- JAL-2419 -->Current selection lost if popup menu
1592 opened on a region of alignment without groups
1595 <!-- JAL-2374 -->Popup menu not always shown for regions
1596 of an alignment with overlapping groups
1599 <!-- JAL-2310 -->Finder double counts if both a sequence's
1600 name and description match
1603 <!-- JAL-2370 -->Hiding column selection containing two
1604 hidden regions results in incorrect hidden regions
1607 <!-- JAL-2386 -->'Apply to all groups' setting when
1608 changing colour does not apply Conservation slider value
1612 <!-- JAL-2373 -->Percentage identity and conservation menu
1613 items do not show a tick or allow shading to be disabled
1616 <!-- JAL-2385 -->Conservation shading or PID threshold
1617 lost when base colourscheme changed if slider not visible
1620 <!-- JAL-2547 -->Sequence features shown in tooltip for
1621 gaps before start of features
1624 <!-- JAL-2623 -->Graduated feature colour threshold not
1625 restored to UI when feature colour is edited
1628 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1629 a time when scrolling vertically in wrapped mode.
1632 <!-- JAL-2630 -->Structure and alignment overview update
1633 as graduate feature colour settings are modified via the
1637 <!-- JAL-2034 -->Overview window doesn't always update
1638 when a group defined on the alignment is resized
1641 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1642 wrapped view result in positional status updates
1646 <!-- JAL-2563 -->Status bar doesn't show position for
1647 ambiguous amino acid and nucleotide symbols
1650 <!-- JAL-2602 -->Copy consensus sequence failed if
1651 alignment included gapped columns
1654 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1655 widgets don't permanently disappear
1658 <!-- JAL-2503 -->Cannot select or filter quantitative
1659 annotation that are shown only as column labels (e.g.
1660 T-Coffee column reliability scores)
1663 <!-- JAL-2594 -->Exception thrown if trying to create a
1664 sequence feature on gaps only
1667 <!-- JAL-2504 -->Features created with 'New feature'
1668 button from a Find inherit previously defined feature type
1669 rather than the Find query string
1672 <!-- JAL-2423 -->incorrect title in output window when
1673 exporting tree calculated in Jalview
1676 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1677 and then revealing them reorders sequences on the
1681 <!-- JAL-964 -->Group panel in sequence feature settings
1682 doesn't update to reflect available set of groups after
1683 interactively adding or modifying features
1686 <!-- JAL-2225 -->Sequence Database chooser unusable on
1690 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1691 only excluded gaps in current sequence and ignored
1698 <!-- JAL-2421 -->Overview window visible region moves
1699 erratically when hidden rows or columns are present
1702 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1703 Structure Viewer's colour menu don't correspond to
1707 <!-- JAL-2405 -->Protein specific colours only offered in
1708 colour and group colour menu for protein alignments
1711 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1712 reflect currently selected view or group's shading
1716 <!-- JAL-2624 -->Feature colour thresholds not respected
1717 when rendered on overview and structures when opacity at
1721 <!-- JAL-2589 -->User defined gap colour not shown in
1722 overview when features overlaid on alignment
1725 <!-- JAL-2567 -->Feature settings for different views not
1726 recovered correctly from Jalview project file
1729 <!-- JAL-2256 -->Feature colours in overview when first opened
1730 (automatically via preferences) are different to the main
1734 <em>Data import/export</em>
1737 <!-- JAL-2576 -->Very large alignments take a long time to
1741 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1742 added after a sequence was imported are not written to
1746 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1747 when importing RNA secondary structure via Stockholm
1750 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1751 not shown in correct direction for simple pseudoknots
1754 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1755 with lightGray or darkGray via features file (but can
1759 <!-- JAL-2383 -->Above PID colour threshold not recovered
1760 when alignment view imported from project
1763 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1764 structure and sequences extracted from structure files
1765 imported via URL and viewed in Jmol
1768 <!-- JAL-2520 -->Structures loaded via URL are saved in
1769 Jalview Projects rather than fetched via URL again when
1770 the project is loaded and the structure viewed
1773 <em>Web Services</em>
1776 <!-- JAL-2519 -->EnsemblGenomes example failing after
1777 release of Ensembl v.88
1780 <!-- JAL-2366 -->Proxy server address and port always
1781 appear enabled in Preferences->Connections
1784 <!-- JAL-2461 -->DAS registry not found exceptions
1785 removed from console output
1788 <!-- JAL-2582 -->Cannot retrieve protein products from
1789 Ensembl by Peptide ID
1792 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1793 created from SIFTs, and spurious 'Couldn't open structure
1794 in Chimera' errors raised after April 2017 update (problem
1795 due to 'null' string rather than empty string used for
1796 residues with no corresponding PDB mapping).
1799 <em>Application UI</em>
1802 <!-- JAL-2361 -->User Defined Colours not added to Colour
1806 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1807 case' residues (button in colourscheme editor debugged and
1808 new documentation and tooltips added)
1811 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1812 doesn't restore group-specific text colour thresholds
1815 <!-- JAL-2243 -->Feature settings panel does not update as
1816 new features are added to alignment
1819 <!-- JAL-2532 -->Cancel in feature settings reverts
1820 changes to feature colours via the Amend features dialog
1823 <!-- JAL-2506 -->Null pointer exception when attempting to
1824 edit graduated feature colour via amend features dialog
1828 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1829 selection menu changes colours of alignment views
1832 <!-- JAL-2426 -->Spurious exceptions in console raised
1833 from alignment calculation workers after alignment has
1837 <!-- JAL-1608 -->Typo in selection popup menu - Create
1838 groups now 'Create Group'
1841 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1842 Create/Undefine group doesn't always work
1845 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1846 shown again after pressing 'Cancel'
1849 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1850 adjusts start position in wrap mode
1853 <!-- JAL-2563 -->Status bar doesn't show positions for
1854 ambiguous amino acids
1857 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1858 CDS/Protein view after CDS sequences added for aligned
1862 <!-- JAL-2592 -->User defined colourschemes called 'User
1863 Defined' don't appear in Colours menu
1869 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1870 score models doesn't always result in an updated PCA plot
1873 <!-- JAL-2442 -->Features not rendered as transparent on
1874 overview or linked structure view
1877 <!-- JAL-2372 -->Colour group by conservation doesn't
1881 <!-- JAL-2517 -->Hitting Cancel after applying
1882 user-defined colourscheme doesn't restore original
1889 <!-- JAL-2314 -->Unit test failure:
1890 jalview.ws.jabaws.RNAStructExportImport setup fails
1893 <!-- JAL-2307 -->Unit test failure:
1894 jalview.ws.sifts.SiftsClientTest due to compatibility
1895 problems with deep array comparison equality asserts in
1896 successive versions of TestNG
1899 <!-- JAL-2479 -->Relocated StructureChooserTest and
1900 ParameterUtilsTest Unit tests to Network suite
1903 <em>New Known Issues</em>
1906 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1907 phase after a sequence motif find operation
1910 <!-- JAL-2550 -->Importing annotation file with rows
1911 containing just upper and lower case letters are
1912 interpreted as WUSS RNA secondary structure symbols
1915 <!-- JAL-2590 -->Cannot load and display Newick trees
1916 reliably from eggnog Ortholog database
1919 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1920 containing features of type Highlight' when 'B' is pressed
1921 to mark columns containing highlighted regions.
1924 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1925 doesn't always add secondary structure annotation.
1930 <td width="60" nowrap>
1931 <div align="center">
1932 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1935 <td><div align="left">
1939 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1940 for all consensus calculations
1943 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1946 <li>Updated Jalview's Certum code signing certificate
1949 <em>Application</em>
1952 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1953 set of database cross-references, sorted alphabetically
1956 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1957 from database cross references. Users with custom links
1958 will receive a <a href="webServices/urllinks.html#warning">warning
1959 dialog</a> asking them to update their preferences.
1962 <!-- JAL-2287-->Cancel button and escape listener on
1963 dialog warning user about disconnecting Jalview from a
1967 <!-- JAL-2320-->Jalview's Chimera control window closes if
1968 the Chimera it is connected to is shut down
1971 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1972 columns menu item to mark columns containing highlighted
1973 regions (e.g. from structure selections or results of a
1977 <!-- JAL-2284-->Command line option for batch-generation
1978 of HTML pages rendering alignment data with the BioJS
1988 <!-- JAL-2286 -->Columns with more than one modal residue
1989 are not coloured or thresholded according to percent
1990 identity (first observed in Jalview 2.8.2)
1993 <!-- JAL-2301 -->Threonine incorrectly reported as not
1997 <!-- JAL-2318 -->Updates to documentation pages (above PID
1998 threshold, amino acid properties)
2001 <!-- JAL-2292 -->Lower case residues in sequences are not
2002 reported as mapped to residues in a structure file in the
2006 <!--JAL-2324 -->Identical features with non-numeric scores
2007 could be added multiple times to a sequence
2010 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2011 bond features shown as two highlighted residues rather
2012 than a range in linked structure views, and treated
2013 correctly when selecting and computing trees from features
2016 <!-- JAL-2281-->Custom URL links for database
2017 cross-references are matched to database name regardless
2022 <em>Application</em>
2025 <!-- JAL-2282-->Custom URL links for specific database
2026 names without regular expressions also offer links from
2030 <!-- JAL-2315-->Removing a single configured link in the
2031 URL links pane in Connections preferences doesn't actually
2032 update Jalview configuration
2035 <!-- JAL-2272-->CTRL-Click on a selected region to open
2036 the alignment area popup menu doesn't work on El-Capitan
2039 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2040 files with similarly named sequences if dropped onto the
2044 <!-- JAL-2312 -->Additional mappings are shown for PDB
2045 entries where more chains exist in the PDB accession than
2046 are reported in the SIFTS file
2049 <!-- JAL-2317-->Certain structures do not get mapped to
2050 the structure view when displayed with Chimera
2053 <!-- JAL-2317-->No chains shown in the Chimera view
2054 panel's View->Show Chains submenu
2057 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2058 work for wrapped alignment views
2061 <!--JAL-2197 -->Rename UI components for running JPred
2062 predictions from 'JNet' to 'JPred'
2065 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2066 corrupted when annotation panel vertical scroll is not at
2067 first annotation row
2070 <!--JAL-2332 -->Attempting to view structure for Hen
2071 lysozyme results in a PDB Client error dialog box
2074 <!-- JAL-2319 -->Structure View's mapping report switched
2075 ranges for PDB and sequence for SIFTS
2078 SIFTS 'Not_Observed' residues mapped to non-existant
2082 <!-- <em>New Known Issues</em>
2089 <td width="60" nowrap>
2090 <div align="center">
2091 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2092 <em>25/10/2016</em></strong>
2095 <td><em>Application</em>
2097 <li>3D Structure chooser opens with 'Cached structures'
2098 view if structures already loaded</li>
2099 <li>Progress bar reports models as they are loaded to
2100 structure views</li>
2106 <li>Colour by conservation always enabled and no tick
2107 shown in menu when BLOSUM or PID shading applied</li>
2108 <li>FER1_ARATH and FER2_ARATH labels were switched in
2109 example sequences/projects/trees</li>
2111 <em>Application</em>
2113 <li>Jalview projects with views of local PDB structure
2114 files saved on Windows cannot be opened on OSX</li>
2115 <li>Multiple structure views can be opened and superposed
2116 without timeout for structures with multiple models or
2117 multiple sequences in alignment</li>
2118 <li>Cannot import or associated local PDB files without a
2119 PDB ID HEADER line</li>
2120 <li>RMSD is not output in Jmol console when superposition
2122 <li>Drag and drop of URL from Browser fails for Linux and
2123 OSX versions earlier than El Capitan</li>
2124 <li>ENA client ignores invalid content from ENA server</li>
2125 <li>Exceptions are not raised in console when ENA client
2126 attempts to fetch non-existent IDs via Fetch DB Refs UI
2128 <li>Exceptions are not raised in console when a new view
2129 is created on the alignment</li>
2130 <li>OSX right-click fixed for group selections: CMD-click
2131 to insert/remove gaps in groups and CTRL-click to open group
2134 <em>Build and deployment</em>
2136 <li>URL link checker now copes with multi-line anchor
2139 <em>New Known Issues</em>
2141 <li>Drag and drop from URL links in browsers do not work
2148 <td width="60" nowrap>
2149 <div align="center">
2150 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2153 <td><em>General</em>
2156 <!-- JAL-2124 -->Updated Spanish translations.
2159 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2160 for importing structure data to Jalview. Enables mmCIF and
2164 <!-- JAL-192 --->Alignment ruler shows positions relative to
2168 <!-- JAL-2202 -->Position/residue shown in status bar when
2169 mousing over sequence associated annotation
2172 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2176 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2177 '()', canonical '[]' and invalid '{}' base pair populations
2181 <!-- JAL-2092 -->Feature settings popup menu options for
2182 showing or hiding columns containing a feature
2185 <!-- JAL-1557 -->Edit selected group by double clicking on
2186 group and sequence associated annotation labels
2189 <!-- JAL-2236 -->Sequence name added to annotation label in
2190 select/hide columns by annotation and colour by annotation
2194 </ul> <em>Application</em>
2197 <!-- JAL-2050-->Automatically hide introns when opening a
2198 gene/transcript view
2201 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2205 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2206 structure mappings with the EMBL-EBI PDBe SIFTS database
2209 <!-- JAL-2079 -->Updated download sites used for Rfam and
2210 Pfam sources to xfam.org
2213 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2216 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2217 over sequences in Jalview
2220 <!-- JAL-2027-->Support for reverse-complement coding
2221 regions in ENA and EMBL
2224 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2225 for record retrieval via ENA rest API
2228 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2232 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2233 groovy script execution
2236 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2237 alignment window's Calculate menu
2240 <!-- JAL-1812 -->Allow groovy scripts that call
2241 Jalview.getAlignFrames() to run in headless mode
2244 <!-- JAL-2068 -->Support for creating new alignment
2245 calculation workers from groovy scripts
2248 <!-- JAL-1369 --->Store/restore reference sequence in
2252 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2253 associations are now saved/restored from project
2256 <!-- JAL-1993 -->Database selection dialog always shown
2257 before sequence fetcher is opened
2260 <!-- JAL-2183 -->Double click on an entry in Jalview's
2261 database chooser opens a sequence fetcher
2264 <!-- JAL-1563 -->Free-text search client for UniProt using
2265 the UniProt REST API
2268 <!-- JAL-2168 -->-nonews command line parameter to prevent
2269 the news reader opening
2272 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2273 querying stored in preferences
2276 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2280 <!-- JAL-1977-->Tooltips shown on database chooser
2283 <!-- JAL-391 -->Reverse complement function in calculate
2284 menu for nucleotide sequences
2287 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2288 and feature counts preserves alignment ordering (and
2289 debugged for complex feature sets).
2292 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2293 viewing structures with Jalview 2.10
2296 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2297 genome, transcript CCDS and gene ids via the Ensembl and
2298 Ensembl Genomes REST API
2301 <!-- JAL-2049 -->Protein sequence variant annotation
2302 computed for 'sequence_variant' annotation on CDS regions
2306 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2310 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2311 Ref Fetcher fails to match, or otherwise updates sequence
2312 data from external database records.
2315 <!-- JAL-2154 -->Revised Jalview Project format for
2316 efficient recovery of sequence coding and alignment
2317 annotation relationships.
2319 </ul> <!-- <em>Applet</em>
2330 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2334 <!-- JAL-2018-->Export features in Jalview format (again)
2335 includes graduated colourschemes
2338 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2339 working with big alignments and lots of hidden columns
2342 <!-- JAL-2053-->Hidden column markers not always rendered
2343 at right of alignment window
2346 <!-- JAL-2067 -->Tidied up links in help file table of
2350 <!-- JAL-2072 -->Feature based tree calculation not shown
2354 <!-- JAL-2075 -->Hidden columns ignored during feature
2355 based tree calculation
2358 <!-- JAL-2065 -->Alignment view stops updating when show
2359 unconserved enabled for group on alignment
2362 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2366 <!-- JAL-2146 -->Alignment column in status incorrectly
2367 shown as "Sequence position" when mousing over
2371 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2372 hidden columns present
2375 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2376 user created annotation added to alignment
2379 <!-- JAL-1841 -->RNA Structure consensus only computed for
2380 '()' base pair annotation
2383 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2384 in zero scores for all base pairs in RNA Structure
2388 <!-- JAL-2174-->Extend selection with columns containing
2392 <!-- JAL-2275 -->Pfam format writer puts extra space at
2393 beginning of sequence
2396 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2400 <!-- JAL-2238 -->Cannot create groups on an alignment from
2401 from a tree when t-coffee scores are shown
2404 <!-- JAL-1836,1967 -->Cannot import and view PDB
2405 structures with chains containing negative resnums (4q4h)
2408 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2412 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2413 to Clustal, PIR and PileUp output
2416 <!-- JAL-2008 -->Reordering sequence features that are
2417 not visible causes alignment window to repaint
2420 <!-- JAL-2006 -->Threshold sliders don't work in
2421 graduated colour and colour by annotation row for e-value
2422 scores associated with features and annotation rows
2425 <!-- JAL-1797 -->amino acid physicochemical conservation
2426 calculation should be case independent
2429 <!-- JAL-2173 -->Remove annotation also updates hidden
2433 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2434 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2435 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2438 <!-- JAL-2065 -->Null pointer exceptions and redraw
2439 problems when reference sequence defined and 'show
2440 non-conserved' enabled
2443 <!-- JAL-1306 -->Quality and Conservation are now shown on
2444 load even when Consensus calculation is disabled
2447 <!-- JAL-1932 -->Remove right on penultimate column of
2448 alignment does nothing
2451 <em>Application</em>
2454 <!-- JAL-1552-->URLs and links can't be imported by
2455 drag'n'drop on OSX when launched via webstart (note - not
2456 yet fixed for El Capitan)
2459 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2460 output when running on non-gb/us i18n platforms
2463 <!-- JAL-1944 -->Error thrown when exporting a view with
2464 hidden sequences as flat-file alignment
2467 <!-- JAL-2030-->InstallAnywhere distribution fails when
2471 <!-- JAL-2080-->Jalview very slow to launch via webstart
2472 (also hotfix for 2.9.0b2)
2475 <!-- JAL-2085 -->Cannot save project when view has a
2476 reference sequence defined
2479 <!-- JAL-1011 -->Columns are suddenly selected in other
2480 alignments and views when revealing hidden columns
2483 <!-- JAL-1989 -->Hide columns not mirrored in complement
2484 view in a cDNA/Protein splitframe
2487 <!-- JAL-1369 -->Cannot save/restore representative
2488 sequence from project when only one sequence is
2492 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2493 in Structure Chooser
2496 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2497 structure consensus didn't refresh annotation panel
2500 <!-- JAL-1962 -->View mapping in structure view shows
2501 mappings between sequence and all chains in a PDB file
2504 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2505 dialogs format columns correctly, don't display array
2506 data, sort columns according to type
2509 <!-- JAL-1975 -->Export complete shown after destination
2510 file chooser is cancelled during an image export
2513 <!-- JAL-2025 -->Error when querying PDB Service with
2514 sequence name containing special characters
2517 <!-- JAL-2024 -->Manual PDB structure querying should be
2521 <!-- JAL-2104 -->Large tooltips with broken HTML
2522 formatting don't wrap
2525 <!-- JAL-1128 -->Figures exported from wrapped view are
2526 truncated so L looks like I in consensus annotation
2529 <!-- JAL-2003 -->Export features should only export the
2530 currently displayed features for the current selection or
2534 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2535 after fetching cross-references, and restoring from
2539 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2540 followed in the structure viewer
2543 <!-- JAL-2163 -->Titles for individual alignments in
2544 splitframe not restored from project
2547 <!-- JAL-2145 -->missing autocalculated annotation at
2548 trailing end of protein alignment in transcript/product
2549 splitview when pad-gaps not enabled by default
2552 <!-- JAL-1797 -->amino acid physicochemical conservation
2556 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2557 article has been read (reopened issue due to
2558 internationalisation problems)
2561 <!-- JAL-1960 -->Only offer PDB structures in structure
2562 viewer based on sequence name, PDB and UniProt
2567 <!-- JAL-1976 -->No progress bar shown during export of
2571 <!-- JAL-2213 -->Structures not always superimposed after
2572 multiple structures are shown for one or more sequences.
2575 <!-- JAL-1370 -->Reference sequence characters should not
2576 be replaced with '.' when 'Show unconserved' format option
2580 <!-- JAL-1823 -->Cannot specify chain code when entering
2581 specific PDB id for sequence
2584 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2585 'Export hidden sequences' is enabled, but 'export hidden
2586 columns' is disabled.
2589 <!--JAL-2026-->Best Quality option in structure chooser
2590 selects lowest rather than highest resolution structures
2594 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2595 to sequence mapping in 'View Mappings' report
2598 <!-- JAL-2284 -->Unable to read old Jalview projects that
2599 contain non-XML data added after Jalvew wrote project.
2602 <!-- JAL-2118 -->Newly created annotation row reorders
2603 after clicking on it to create new annotation for a
2607 <!-- JAL-1980 -->Null Pointer Exception raised when
2608 pressing Add on an orphaned cut'n'paste window.
2610 <!-- may exclude, this is an external service stability issue JAL-1941
2611 -- > RNA 3D structure not added via DSSR service</li> -->
2616 <!-- JAL-2151 -->Incorrect columns are selected when
2617 hidden columns present before start of sequence
2620 <!-- JAL-1986 -->Missing dependencies on applet pages
2624 <!-- JAL-1947 -->Overview pixel size changes when
2625 sequences are hidden in applet
2628 <!-- JAL-1996 -->Updated instructions for applet
2629 deployment on examples pages.
2636 <td width="60" nowrap>
2637 <div align="center">
2638 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2639 <em>16/10/2015</em></strong>
2642 <td><em>General</em>
2644 <li>Time stamps for signed Jalview application and applet
2649 <em>Application</em>
2651 <li>Duplicate group consensus and conservation rows
2652 shown when tree is partitioned</li>
2653 <li>Erratic behaviour when tree partitions made with
2654 multiple cDNA/Protein split views</li>
2660 <td width="60" nowrap>
2661 <div align="center">
2662 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2663 <em>8/10/2015</em></strong>
2666 <td><em>General</em>
2668 <li>Updated Spanish translations of localized text for
2670 </ul> <em>Application</em>
2672 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2673 <li>Signed OSX InstallAnywhere installer<br></li>
2674 <li>Support for per-sequence based annotations in BioJSON</li>
2675 </ul> <em>Applet</em>
2677 <li>Split frame example added to applet examples page</li>
2678 </ul> <em>Build and Deployment</em>
2681 <!-- JAL-1888 -->New ant target for running Jalview's test
2689 <li>Mapping of cDNA to protein in split frames
2690 incorrect when sequence start > 1</li>
2691 <li>Broken images in filter column by annotation dialog
2693 <li>Feature colours not parsed from features file</li>
2694 <li>Exceptions and incomplete link URLs recovered when
2695 loading a features file containing HTML tags in feature
2699 <em>Application</em>
2701 <li>Annotations corrupted after BioJS export and
2703 <li>Incorrect sequence limits after Fetch DB References
2704 with 'trim retrieved sequences'</li>
2705 <li>Incorrect warning about deleting all data when
2706 deleting selected columns</li>
2707 <li>Patch to build system for shipping properly signed
2708 JNLP templates for webstart launch</li>
2709 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2710 unreleased structures for download or viewing</li>
2711 <li>Tab/space/return keystroke operation of EMBL-PDBe
2712 fetcher/viewer dialogs works correctly</li>
2713 <li>Disabled 'minimise' button on Jalview windows
2714 running on OSX to workaround redraw hang bug</li>
2715 <li>Split cDNA/Protein view position and geometry not
2716 recovered from jalview project</li>
2717 <li>Initial enabled/disabled state of annotation menu
2718 sorter 'show autocalculated first/last' corresponds to
2720 <li>Restoring of Clustal, RNA Helices and T-Coffee
2721 color schemes from BioJSON</li>
2725 <li>Reorder sequences mirrored in cDNA/Protein split
2727 <li>Applet with Jmol examples not loading correctly</li>
2733 <td><div align="center">
2734 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2736 <td><em>General</em>
2738 <li>Linked visualisation and analysis of DNA and Protein
2741 <li>Translated cDNA alignments shown as split protein
2742 and DNA alignment views</li>
2743 <li>Codon consensus annotation for linked protein and
2744 cDNA alignment views</li>
2745 <li>Link cDNA or Protein product sequences by loading
2746 them onto Protein or cDNA alignments</li>
2747 <li>Reconstruct linked cDNA alignment from aligned
2748 protein sequences</li>
2751 <li>Jmol integration updated to Jmol v14.2.14</li>
2752 <li>Import and export of Jalview alignment views as <a
2753 href="features/bioJsonFormat.html">BioJSON</a></li>
2754 <li>New alignment annotation file statements for
2755 reference sequences and marking hidden columns</li>
2756 <li>Reference sequence based alignment shading to
2757 highlight variation</li>
2758 <li>Select or hide columns according to alignment
2760 <li>Find option for locating sequences by description</li>
2761 <li>Conserved physicochemical properties shown in amino
2762 acid conservation row</li>
2763 <li>Alignments can be sorted by number of RNA helices</li>
2764 </ul> <em>Application</em>
2766 <li>New cDNA/Protein analysis capabilities
2768 <li>Get Cross-References should open a Split Frame
2769 view with cDNA/Protein</li>
2770 <li>Detect when nucleotide sequences and protein
2771 sequences are placed in the same alignment</li>
2772 <li>Split cDNA/Protein views are saved in Jalview
2777 <li>Use REST API to talk to Chimera</li>
2778 <li>Selected regions in Chimera are highlighted in linked
2779 Jalview windows</li>
2781 <li>VARNA RNA viewer updated to v3.93</li>
2782 <li>VARNA views are saved in Jalview Projects</li>
2783 <li>Pseudoknots displayed as Jalview RNA annotation can
2784 be shown in VARNA</li>
2786 <li>Make groups for selection uses marked columns as well
2787 as the active selected region</li>
2789 <li>Calculate UPGMA and NJ trees using sequence feature
2791 <li>New Export options
2793 <li>New Export Settings dialog to control hidden
2794 region export in flat file generation</li>
2796 <li>Export alignment views for display with the <a
2797 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2799 <li>Export scrollable SVG in HTML page</li>
2800 <li>Optional embedding of BioJSON data when exporting
2801 alignment figures to HTML</li>
2803 <li>3D structure retrieval and display
2805 <li>Free text and structured queries with the PDBe
2807 <li>PDBe Search API based discovery and selection of
2808 PDB structures for a sequence set</li>
2812 <li>JPred4 employed for protein secondary structure
2814 <li>Hide Insertions menu option to hide unaligned columns
2815 for one or a group of sequences</li>
2816 <li>Automatically hide insertions in alignments imported
2817 from the JPred4 web server</li>
2818 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2819 system on OSX<br />LGPL libraries courtesy of <a
2820 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2822 <li>changed 'View nucleotide structure' submenu to 'View
2823 VARNA 2D Structure'</li>
2824 <li>change "View protein structure" menu option to "3D
2827 </ul> <em>Applet</em>
2829 <li>New layout for applet example pages</li>
2830 <li>New parameters to enable SplitFrame view
2831 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2832 <li>New example demonstrating linked viewing of cDNA and
2833 Protein alignments</li>
2834 </ul> <em>Development and deployment</em>
2836 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2837 <li>Include installation type and git revision in build
2838 properties and console log output</li>
2839 <li>Jalview Github organisation, and new github site for
2840 storing BioJsMSA Templates</li>
2841 <li>Jalview's unit tests now managed with TestNG</li>
2844 <!-- <em>General</em>
2846 </ul> --> <!-- issues resolved --> <em>Application</em>
2848 <li>Escape should close any open find dialogs</li>
2849 <li>Typo in select-by-features status report</li>
2850 <li>Consensus RNA secondary secondary structure
2851 predictions are not highlighted in amber</li>
2852 <li>Missing gap character in v2.7 example file means
2853 alignment appears unaligned when pad-gaps is not enabled</li>
2854 <li>First switch to RNA Helices colouring doesn't colour
2855 associated structure views</li>
2856 <li>ID width preference option is greyed out when auto
2857 width checkbox not enabled</li>
2858 <li>Stopped a warning dialog from being shown when
2859 creating user defined colours</li>
2860 <li>'View Mapping' in structure viewer shows sequence
2861 mappings for just that viewer's sequences</li>
2862 <li>Workaround for superposing PDB files containing
2863 multiple models in Chimera</li>
2864 <li>Report sequence position in status bar when hovering
2865 over Jmol structure</li>
2866 <li>Cannot output gaps as '.' symbols with Selection ->
2867 output to text box</li>
2868 <li>Flat file exports of alignments with hidden columns
2869 have incorrect sequence start/end</li>
2870 <li>'Aligning' a second chain to a Chimera structure from
2872 <li>Colour schemes applied to structure viewers don't
2873 work for nucleotide</li>
2874 <li>Loading/cut'n'pasting an empty or invalid file leads
2875 to a grey/invisible alignment window</li>
2876 <li>Exported Jpred annotation from a sequence region
2877 imports to different position</li>
2878 <li>Space at beginning of sequence feature tooltips shown
2879 on some platforms</li>
2880 <li>Chimera viewer 'View | Show Chain' menu is not
2882 <li>'New View' fails with a Null Pointer Exception in
2883 console if Chimera has been opened</li>
2884 <li>Mouseover to Chimera not working</li>
2885 <li>Miscellaneous ENA XML feature qualifiers not
2887 <li>NPE in annotation renderer after 'Extract Scores'</li>
2888 <li>If two structures in one Chimera window, mouseover of
2889 either sequence shows on first structure</li>
2890 <li>'Show annotations' options should not make
2891 non-positional annotations visible</li>
2892 <li>Subsequence secondary structure annotation not shown
2893 in right place after 'view flanking regions'</li>
2894 <li>File Save As type unset when current file format is
2896 <li>Save as '.jar' option removed for saving Jalview
2898 <li>Colour by Sequence colouring in Chimera more
2900 <li>Cannot 'add reference annotation' for a sequence in
2901 several views on same alignment</li>
2902 <li>Cannot show linked products for EMBL / ENA records</li>
2903 <li>Jalview's tooltip wraps long texts containing no
2905 </ul> <em>Applet</em>
2907 <li>Jmol to JalviewLite mouseover/link not working</li>
2908 <li>JalviewLite can't import sequences with ID
2909 descriptions containing angle brackets</li>
2910 </ul> <em>General</em>
2912 <li>Cannot export and reimport RNA secondary structure
2913 via jalview annotation file</li>
2914 <li>Random helix colour palette for colour by annotation
2915 with RNA secondary structure</li>
2916 <li>Mouseover to cDNA from STOP residue in protein
2917 translation doesn't work.</li>
2918 <li>hints when using the select by annotation dialog box</li>
2919 <li>Jmol alignment incorrect if PDB file has alternate CA
2921 <li>FontChooser message dialog appears to hang after
2922 choosing 1pt font</li>
2923 <li>Peptide secondary structure incorrectly imported from
2924 annotation file when annotation display text includes 'e' or
2926 <li>Cannot set colour of new feature type whilst creating
2928 <li>cDNA translation alignment should not be sequence
2929 order dependent</li>
2930 <li>'Show unconserved' doesn't work for lower case
2932 <li>Nucleotide ambiguity codes involving R not recognised</li>
2933 </ul> <em>Deployment and Documentation</em>
2935 <li>Applet example pages appear different to the rest of
2936 www.jalview.org</li>
2937 </ul> <em>Application Known issues</em>
2939 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2940 <li>Misleading message appears after trying to delete
2942 <li>Jalview icon not shown in dock after InstallAnywhere
2943 version launches</li>
2944 <li>Fetching EMBL reference for an RNA sequence results
2945 fails with a sequence mismatch</li>
2946 <li>Corrupted or unreadable alignment display when
2947 scrolling alignment to right</li>
2948 <li>ArrayIndexOutOfBoundsException thrown when remove
2949 empty columns called on alignment with ragged gapped ends</li>
2950 <li>auto calculated alignment annotation rows do not get
2951 placed above or below non-autocalculated rows</li>
2952 <li>Jalview dekstop becomes sluggish at full screen in
2953 ultra-high resolution</li>
2954 <li>Cannot disable consensus calculation independently of
2955 quality and conservation</li>
2956 <li>Mouseover highlighting between cDNA and protein can
2957 become sluggish with more than one splitframe shown</li>
2958 </ul> <em>Applet Known Issues</em>
2960 <li>Core PDB parsing code requires Jmol</li>
2961 <li>Sequence canvas panel goes white when alignment
2962 window is being resized</li>
2968 <td><div align="center">
2969 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2971 <td><em>General</em>
2973 <li>Updated Java code signing certificate donated by
2975 <li>Features and annotation preserved when performing
2976 pairwise alignment</li>
2977 <li>RNA pseudoknot annotation can be
2978 imported/exported/displayed</li>
2979 <li>'colour by annotation' can colour by RNA and
2980 protein secondary structure</li>
2981 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2982 post-hoc with 2.9 release</em>)
2985 </ul> <em>Application</em>
2987 <li>Extract and display secondary structure for sequences
2988 with 3D structures</li>
2989 <li>Support for parsing RNAML</li>
2990 <li>Annotations menu for layout
2992 <li>sort sequence annotation rows by alignment</li>
2993 <li>place sequence annotation above/below alignment
2996 <li>Output in Stockholm format</li>
2997 <li>Internationalisation: improved Spanish (es)
2999 <li>Structure viewer preferences tab</li>
3000 <li>Disorder and Secondary Structure annotation tracks
3001 shared between alignments</li>
3002 <li>UCSF Chimera launch and linked highlighting from
3004 <li>Show/hide all sequence associated annotation rows for
3005 all or current selection</li>
3006 <li>disorder and secondary structure predictions
3007 available as dataset annotation</li>
3008 <li>Per-sequence rna helices colouring</li>
3011 <li>Sequence database accessions imported when fetching
3012 alignments from Rfam</li>
3013 <li>update VARNA version to 3.91</li>
3015 <li>New groovy scripts for exporting aligned positions,
3016 conservation values, and calculating sum of pairs scores.</li>
3017 <li>Command line argument to set default JABAWS server</li>
3018 <li>include installation type in build properties and
3019 console log output</li>
3020 <li>Updated Jalview project format to preserve dataset
3024 <!-- issues resolved --> <em>Application</em>
3026 <li>Distinguish alignment and sequence associated RNA
3027 structure in structure->view->VARNA</li>
3028 <li>Raise dialog box if user deletes all sequences in an
3030 <li>Pressing F1 results in documentation opening twice</li>
3031 <li>Sequence feature tooltip is wrapped</li>
3032 <li>Double click on sequence associated annotation
3033 selects only first column</li>
3034 <li>Redundancy removal doesn't result in unlinked
3035 leaves shown in tree</li>
3036 <li>Undos after several redundancy removals don't undo
3038 <li>Hide sequence doesn't hide associated annotation</li>
3039 <li>User defined colours dialog box too big to fit on
3040 screen and buttons not visible</li>
3041 <li>author list isn't updated if already written to
3042 Jalview properties</li>
3043 <li>Popup menu won't open after retrieving sequence
3045 <li>File open window for associate PDB doesn't open</li>
3046 <li>Left-then-right click on a sequence id opens a
3047 browser search window</li>
3048 <li>Cannot open sequence feature shading/sort popup menu
3049 in feature settings dialog</li>
3050 <li>better tooltip placement for some areas of Jalview
3052 <li>Allow addition of JABAWS Server which doesn't
3053 pass validation</li>
3054 <li>Web services parameters dialog box is too large to
3056 <li>Muscle nucleotide alignment preset obscured by
3058 <li>JABAWS preset submenus don't contain newly
3059 defined user preset</li>
3060 <li>MSA web services warns user if they were launched
3061 with invalid input</li>
3062 <li>Jalview cannot contact DAS Registy when running on
3065 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3066 'Superpose with' submenu not shown when new view
3070 </ul> <!-- <em>Applet</em>
3072 </ul> <em>General</em>
3074 </ul>--> <em>Deployment and Documentation</em>
3076 <li>2G and 1G options in launchApp have no effect on
3077 memory allocation</li>
3078 <li>launchApp service doesn't automatically open
3079 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3081 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3082 InstallAnywhere reports cannot find valid JVM when Java
3083 1.7_055 is available
3085 </ul> <em>Application Known issues</em>
3088 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3089 corrupted or unreadable alignment display when scrolling
3093 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3094 retrieval fails but progress bar continues for DAS retrieval
3095 with large number of ID
3098 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3099 flatfile output of visible region has incorrect sequence
3103 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3104 rna structure consensus doesn't update when secondary
3105 structure tracks are rearranged
3108 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3109 invalid rna structure positional highlighting does not
3110 highlight position of invalid base pairs
3113 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3114 out of memory errors are not raised when saving Jalview
3115 project from alignment window file menu
3118 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3119 Switching to RNA Helices colouring doesn't propagate to
3123 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3124 colour by RNA Helices not enabled when user created
3125 annotation added to alignment
3128 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3129 Jalview icon not shown on dock in Mountain Lion/Webstart
3131 </ul> <em>Applet Known Issues</em>
3134 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3135 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3138 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3139 Jalview and Jmol example not compatible with IE9
3142 <li>Sort by annotation score doesn't reverse order
3148 <td><div align="center">
3149 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3152 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3155 <li>Internationalisation of user interface (usually
3156 called i18n support) and translation for Spanish locale</li>
3157 <li>Define/Undefine group on current selection with
3158 Ctrl-G/Shift Ctrl-G</li>
3159 <li>Improved group creation/removal options in
3160 alignment/sequence Popup menu</li>
3161 <li>Sensible precision for symbol distribution
3162 percentages shown in logo tooltip.</li>
3163 <li>Annotation panel height set according to amount of
3164 annotation when alignment first opened</li>
3165 </ul> <em>Application</em>
3167 <li>Interactive consensus RNA secondary structure
3168 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3169 <li>Select columns containing particular features from
3170 Feature Settings dialog</li>
3171 <li>View all 'representative' PDB structures for selected
3173 <li>Update Jalview project format:
3175 <li>New file extension for Jalview projects '.jvp'</li>
3176 <li>Preserve sequence and annotation dataset (to
3177 store secondary structure annotation,etc)</li>
3178 <li>Per group and alignment annotation and RNA helix
3182 <li>New similarity measures for PCA and Tree calculation
3184 <li>Experimental support for retrieval and viewing of
3185 flanking regions for an alignment</li>
3189 <!-- issues resolved --> <em>Application</em>
3191 <li>logo keeps spinning and status remains at queued or
3192 running after job is cancelled</li>
3193 <li>cannot export features from alignments imported from
3194 Jalview/VAMSAS projects</li>
3195 <li>Buggy slider for web service parameters that take
3197 <li>Newly created RNA secondary structure line doesn't
3198 have 'display all symbols' flag set</li>
3199 <li>T-COFFEE alignment score shading scheme and other
3200 annotation shading not saved in Jalview project</li>
3201 <li>Local file cannot be loaded in freshly downloaded
3203 <li>Jalview icon not shown on dock in Mountain
3205 <li>Load file from desktop file browser fails</li>
3206 <li>Occasional NPE thrown when calculating large trees</li>
3207 <li>Cannot reorder or slide sequences after dragging an
3208 alignment onto desktop</li>
3209 <li>Colour by annotation dialog throws NPE after using
3210 'extract scores' function</li>
3211 <li>Loading/cut'n'pasting an empty file leads to a grey
3212 alignment window</li>
3213 <li>Disorder thresholds rendered incorrectly after
3214 performing IUPred disorder prediction</li>
3215 <li>Multiple group annotated consensus rows shown when
3216 changing 'normalise logo' display setting</li>
3217 <li>Find shows blank dialog after 'finished searching' if
3218 nothing matches query</li>
3219 <li>Null Pointer Exceptions raised when sorting by
3220 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3222 <li>Errors in Jmol console when structures in alignment
3223 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3225 <li>Not all working JABAWS services are shown in
3227 <li>JAVAWS version of Jalview fails to launch with
3228 'invalid literal/length code'</li>
3229 <li>Annotation/RNA Helix colourschemes cannot be applied
3230 to alignment with groups (actually fixed in 2.8.0b1)</li>
3231 <li>RNA Helices and T-Coffee Scores available as default
3234 </ul> <em>Applet</em>
3236 <li>Remove group option is shown even when selection is
3238 <li>Apply to all groups ticked but colourscheme changes
3239 don't affect groups</li>
3240 <li>Documented RNA Helices and T-Coffee Scores as valid
3241 colourscheme name</li>
3242 <li>Annotation labels drawn on sequence IDs when
3243 Annotation panel is not displayed</li>
3244 <li>Increased font size for dropdown menus on OSX and
3245 embedded windows</li>
3246 </ul> <em>Other</em>
3248 <li>Consensus sequence for alignments/groups with a
3249 single sequence were not calculated</li>
3250 <li>annotation files that contain only groups imported as
3251 annotation and junk sequences</li>
3252 <li>Fasta files with sequences containing '*' incorrectly
3253 recognised as PFAM or BLC</li>
3254 <li>conservation/PID slider apply all groups option
3255 doesn't affect background (2.8.0b1)
3257 <li>redundancy highlighting is erratic at 0% and 100%</li>
3258 <li>Remove gapped columns fails for sequences with ragged
3260 <li>AMSA annotation row with leading spaces is not
3261 registered correctly on import</li>
3262 <li>Jalview crashes when selecting PCA analysis for
3263 certain alignments</li>
3264 <li>Opening the colour by annotation dialog for an
3265 existing annotation based 'use original colours'
3266 colourscheme loses original colours setting</li>
3271 <td><div align="center">
3272 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3273 <em>30/1/2014</em></strong>
3277 <li>Trusted certificates for JalviewLite applet and
3278 Jalview Desktop application<br />Certificate was donated by
3279 <a href="https://www.certum.eu">Certum</a> to the Jalview
3280 open source project).
3282 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3283 <li>Output in Stockholm format</li>
3284 <li>Allow import of data from gzipped files</li>
3285 <li>Export/import group and sequence associated line
3286 graph thresholds</li>
3287 <li>Nucleotide substitution matrix that supports RNA and
3288 ambiguity codes</li>
3289 <li>Allow disorder predictions to be made on the current
3290 selection (or visible selection) in the same way that JPred
3292 <li>Groovy scripting for headless Jalview operation</li>
3293 </ul> <em>Other improvements</em>
3295 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3296 <li>COMBINE statement uses current SEQUENCE_REF and
3297 GROUP_REF scope to group annotation rows</li>
3298 <li>Support '' style escaping of quotes in Newick
3300 <li>Group options for JABAWS service by command line name</li>
3301 <li>Empty tooltip shown for JABA service options with a
3302 link but no description</li>
3303 <li>Select primary source when selecting authority in
3304 database fetcher GUI</li>
3305 <li>Add .mfa to FASTA file extensions recognised by
3307 <li>Annotation label tooltip text wrap</li>
3312 <li>Slow scrolling when lots of annotation rows are
3314 <li>Lots of NPE (and slowness) after creating RNA
3315 secondary structure annotation line</li>
3316 <li>Sequence database accessions not imported when
3317 fetching alignments from Rfam</li>
3318 <li>Incorrect SHMR submission for sequences with
3320 <li>View all structures does not always superpose
3322 <li>Option widgets in service parameters not updated to
3323 reflect user or preset settings</li>
3324 <li>Null pointer exceptions for some services without
3325 presets or adjustable parameters</li>
3326 <li>Discover PDB IDs entry in structure menu doesn't
3327 discover PDB xRefs</li>
3328 <li>Exception encountered while trying to retrieve
3329 features with DAS</li>
3330 <li>Lowest value in annotation row isn't coloured
3331 when colour by annotation (per sequence) is coloured</li>
3332 <li>Keyboard mode P jumps to start of gapped region when
3333 residue follows a gap</li>
3334 <li>Jalview appears to hang importing an alignment with
3335 Wrap as default or after enabling Wrap</li>
3336 <li>'Right click to add annotations' message
3337 shown in wrap mode when no annotations present</li>
3338 <li>Disorder predictions fail with NPE if no automatic
3339 annotation already exists on alignment</li>
3340 <li>oninit javascript function should be called after
3341 initialisation completes</li>
3342 <li>Remove redundancy after disorder prediction corrupts
3343 alignment window display</li>
3344 <li>Example annotation file in documentation is invalid</li>
3345 <li>Grouped line graph annotation rows are not exported
3346 to annotation file</li>
3347 <li>Multi-harmony analysis cannot be run when only two
3349 <li>Cannot create multiple groups of line graphs with
3350 several 'combine' statements in annotation file</li>
3351 <li>Pressing return several times causes Number Format
3352 exceptions in keyboard mode</li>
3353 <li>Multi-harmony (SHMMR) method doesn't submit
3354 correct partitions for input data</li>
3355 <li>Translation from DNA to Amino Acids fails</li>
3356 <li>Jalview fail to load newick tree with quoted label</li>
3357 <li>--headless flag isn't understood</li>
3358 <li>ClassCastException when generating EPS in headless
3360 <li>Adjusting sequence-associated shading threshold only
3361 changes one row's threshold</li>
3362 <li>Preferences and Feature settings panel panel
3363 doesn't open</li>
3364 <li>hide consensus histogram also hides conservation and
3365 quality histograms</li>
3370 <td><div align="center">
3371 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3373 <td><em>Application</em>
3375 <li>Support for JABAWS 2.0 Services (AACon alignment
3376 conservation, protein disorder and Clustal Omega)</li>
3377 <li>JABAWS server status indicator in Web Services
3379 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3380 in Jalview alignment window</li>
3381 <li>Updated Jalview build and deploy framework for OSX
3382 mountain lion, windows 7, and 8</li>
3383 <li>Nucleotide substitution matrix for PCA that supports
3384 RNA and ambiguity codes</li>
3386 <li>Improved sequence database retrieval GUI</li>
3387 <li>Support fetching and database reference look up
3388 against multiple DAS sources (Fetch all from in 'fetch db
3390 <li>Jalview project improvements
3392 <li>Store and retrieve the 'belowAlignment'
3393 flag for annotation</li>
3394 <li>calcId attribute to group annotation rows on the
3396 <li>Store AACon calculation settings for a view in
3397 Jalview project</li>
3401 <li>horizontal scrolling gesture support</li>
3402 <li>Visual progress indicator when PCA calculation is
3404 <li>Simpler JABA web services menus</li>
3405 <li>visual indication that web service results are still
3406 being retrieved from server</li>
3407 <li>Serialise the dialogs that are shown when Jalview
3408 starts up for first time</li>
3409 <li>Jalview user agent string for interacting with HTTP
3411 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3413 <li>Examples directory and Groovy library included in
3414 InstallAnywhere distribution</li>
3415 </ul> <em>Applet</em>
3417 <li>RNA alignment and secondary structure annotation
3418 visualization applet example</li>
3419 </ul> <em>General</em>
3421 <li>Normalise option for consensus sequence logo</li>
3422 <li>Reset button in PCA window to return dimensions to
3424 <li>Allow seqspace or Jalview variant of alignment PCA
3426 <li>PCA with either nucleic acid and protein substitution
3428 <li>Allow windows containing HTML reports to be exported
3430 <li>Interactive display and editing of RNA secondary
3431 structure contacts</li>
3432 <li>RNA Helix Alignment Colouring</li>
3433 <li>RNA base pair logo consensus</li>
3434 <li>Parse sequence associated secondary structure
3435 information in Stockholm files</li>
3436 <li>HTML Export database accessions and annotation
3437 information presented in tooltip for sequences</li>
3438 <li>Import secondary structure from LOCARNA clustalw
3439 style RNA alignment files</li>
3440 <li>import and visualise T-COFFEE quality scores for an
3442 <li>'colour by annotation' per sequence option to
3443 shade each sequence according to its associated alignment
3445 <li>New Jalview Logo</li>
3446 </ul> <em>Documentation and Development</em>
3448 <li>documentation for score matrices used in Jalview</li>
3449 <li>New Website!</li>
3451 <td><em>Application</em>
3453 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3454 wsdbfetch REST service</li>
3455 <li>Stop windows being moved outside desktop on OSX</li>
3456 <li>Filetype associations not installed for webstart
3458 <li>Jalview does not always retrieve progress of a JABAWS
3459 job execution in full once it is complete</li>
3460 <li>revise SHMR RSBS definition to ensure alignment is
3461 uploaded via ali_file parameter</li>
3462 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3463 <li>View all structures superposed fails with exception</li>
3464 <li>Jnet job queues forever if a very short sequence is
3465 submitted for prediction</li>
3466 <li>Cut and paste menu not opened when mouse clicked on
3468 <li>Putting fractional value into integer text box in
3469 alignment parameter dialog causes Jalview to hang</li>
3470 <li>Structure view highlighting doesn't work on
3472 <li>View all structures fails with exception shown in
3474 <li>Characters in filename associated with PDBEntry not
3475 escaped in a platform independent way</li>
3476 <li>Jalview desktop fails to launch with exception when
3478 <li>Tree calculation reports 'you must have 2 or more
3479 sequences selected' when selection is empty</li>
3480 <li>Jalview desktop fails to launch with jar signature
3481 failure when java web start temporary file caching is
3483 <li>DAS Sequence retrieval with range qualification
3484 results in sequence xref which includes range qualification</li>
3485 <li>Errors during processing of command line arguments
3486 cause progress bar (JAL-898) to be removed</li>
3487 <li>Replace comma for semi-colon option not disabled for
3488 DAS sources in sequence fetcher</li>
3489 <li>Cannot close news reader when JABAWS server warning
3490 dialog is shown</li>
3491 <li>Option widgets not updated to reflect user settings</li>
3492 <li>Edited sequence not submitted to web service</li>
3493 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3494 <li>InstallAnywhere installer doesn't unpack and run
3495 on OSX Mountain Lion</li>
3496 <li>Annotation panel not given a scroll bar when
3497 sequences with alignment annotation are pasted into the
3499 <li>Sequence associated annotation rows not associated
3500 when loaded from Jalview project</li>
3501 <li>Browser launch fails with NPE on java 1.7</li>
3502 <li>JABAWS alignment marked as finished when job was
3503 cancelled or job failed due to invalid input</li>
3504 <li>NPE with v2.7 example when clicking on Tree
3505 associated with all views</li>
3506 <li>Exceptions when copy/paste sequences with grouped
3507 annotation rows to new window</li>
3508 </ul> <em>Applet</em>
3510 <li>Sequence features are momentarily displayed before
3511 they are hidden using hidefeaturegroups applet parameter</li>
3512 <li>loading features via javascript API automatically
3513 enables feature display</li>
3514 <li>scrollToColumnIn javascript API method doesn't
3516 </ul> <em>General</em>
3518 <li>Redundancy removal fails for rna alignment</li>
3519 <li>PCA calculation fails when sequence has been selected
3520 and then deselected</li>
3521 <li>PCA window shows grey box when first opened on OSX</li>
3522 <li>Letters coloured pink in sequence logo when alignment
3523 coloured with clustalx</li>
3524 <li>Choosing fonts without letter symbols defined causes
3525 exceptions and redraw errors</li>
3526 <li>Initial PCA plot view is not same as manually
3527 reconfigured view</li>
3528 <li>Grouped annotation graph label has incorrect line
3530 <li>Grouped annotation graph label display is corrupted
3531 for lots of labels</li>
3536 <div align="center">
3537 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3540 <td><em>Application</em>
3542 <li>Jalview Desktop News Reader</li>
3543 <li>Tweaked default layout of web services menu</li>
3544 <li>View/alignment association menu to enable user to
3545 easily specify which alignment a multi-structure view takes
3546 its colours/correspondences from</li>
3547 <li>Allow properties file location to be specified as URL</li>
3548 <li>Extend Jalview project to preserve associations
3549 between many alignment views and a single Jmol display</li>
3550 <li>Store annotation row height in Jalview project file</li>
3551 <li>Annotation row column label formatting attributes
3552 stored in project file</li>
3553 <li>Annotation row order for auto-calculated annotation
3554 rows preserved in Jalview project file</li>
3555 <li>Visual progress indication when Jalview state is
3556 saved using Desktop window menu</li>
3557 <li>Visual indication that command line arguments are
3558 still being processed</li>
3559 <li>Groovy script execution from URL</li>
3560 <li>Colour by annotation default min and max colours in
3562 <li>Automatically associate PDB files dragged onto an
3563 alignment with sequences that have high similarity and
3565 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3566 <li>'view structures' option to open many
3567 structures in same window</li>
3568 <li>Sort associated views menu option for tree panel</li>
3569 <li>Group all JABA and non-JABA services for a particular
3570 analysis function in its own submenu</li>
3571 </ul> <em>Applet</em>
3573 <li>Userdefined and autogenerated annotation rows for
3575 <li>Adjustment of alignment annotation pane height</li>
3576 <li>Annotation scrollbar for annotation panel</li>
3577 <li>Drag to reorder annotation rows in annotation panel</li>
3578 <li>'automaticScrolling' parameter</li>
3579 <li>Allow sequences with partial ID string matches to be
3580 annotated from GFF/Jalview features files</li>
3581 <li>Sequence logo annotation row in applet</li>
3582 <li>Absolute paths relative to host server in applet
3583 parameters are treated as such</li>
3584 <li>New in the JalviewLite javascript API:
3586 <li>JalviewLite.js javascript library</li>
3587 <li>Javascript callbacks for
3589 <li>Applet initialisation</li>
3590 <li>Sequence/alignment mouse-overs and selections</li>
3593 <li>scrollTo row and column alignment scrolling
3595 <li>Select sequence/alignment regions from javascript</li>
3596 <li>javascript structure viewer harness to pass
3597 messages between Jmol and Jalview when running as
3598 distinct applets</li>
3599 <li>sortBy method</li>
3600 <li>Set of applet and application examples shipped
3601 with documentation</li>
3602 <li>New example to demonstrate JalviewLite and Jmol
3603 javascript message exchange</li>
3605 </ul> <em>General</em>
3607 <li>Enable Jmol displays to be associated with multiple
3608 multiple alignments</li>
3609 <li>Option to automatically sort alignment with new tree</li>
3610 <li>User configurable link to enable redirects to a
3611 www.Jalview.org mirror</li>
3612 <li>Jmol colours option for Jmol displays</li>
3613 <li>Configurable newline string when writing alignment
3614 and other flat files</li>
3615 <li>Allow alignment annotation description lines to
3616 contain html tags</li>
3617 </ul> <em>Documentation and Development</em>
3619 <li>Add groovy test harness for bulk load testing to
3621 <li>Groovy script to load and align a set of sequences
3622 using a web service before displaying the result in the
3623 Jalview desktop</li>
3624 <li>Restructured javascript and applet api documentation</li>
3625 <li>Ant target to publish example html files with applet
3627 <li>Netbeans project for building Jalview from source</li>
3628 <li>ant task to create online javadoc for Jalview source</li>
3630 <td><em>Application</em>
3632 <li>User defined colourscheme throws exception when
3633 current built in colourscheme is saved as new scheme</li>
3634 <li>AlignFrame->Save in application pops up save
3635 dialog for valid filename/format</li>
3636 <li>Cannot view associated structure for UniProt sequence</li>
3637 <li>PDB file association breaks for UniProt sequence
3639 <li>Associate PDB from file dialog does not tell you
3640 which sequence is to be associated with the file</li>
3641 <li>Find All raises null pointer exception when query
3642 only matches sequence IDs</li>
3643 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3644 <li>Jalview project with Jmol views created with Jalview
3645 2.4 cannot be loaded</li>
3646 <li>Filetype associations not installed for webstart
3648 <li>Two or more chains in a single PDB file associated
3649 with sequences in different alignments do not get coloured
3650 by their associated sequence</li>
3651 <li>Visibility status of autocalculated annotation row
3652 not preserved when project is loaded</li>
3653 <li>Annotation row height and visibility attributes not
3654 stored in Jalview project</li>
3655 <li>Tree bootstraps are not preserved when saved as a
3656 Jalview project</li>
3657 <li>Envision2 workflow tooltips are corrupted</li>
3658 <li>Enabling show group conservation also enables colour
3659 by conservation</li>
3660 <li>Duplicate group associated conservation or consensus
3661 created on new view</li>
3662 <li>Annotation scrollbar not displayed after 'show
3663 all hidden annotation rows' option selected</li>
3664 <li>Alignment quality not updated after alignment
3665 annotation row is hidden then shown</li>
3666 <li>Preserve colouring of structures coloured by
3667 sequences in pre Jalview 2.7 projects</li>
3668 <li>Web service job parameter dialog is not laid out
3670 <li>Web services menu not refreshed after 'reset
3671 services' button is pressed in preferences</li>
3672 <li>Annotation off by one in Jalview v2_3 example project</li>
3673 <li>Structures imported from file and saved in project
3674 get name like jalview_pdb1234.txt when reloaded</li>
3675 <li>Jalview does not always retrieve progress of a JABAWS
3676 job execution in full once it is complete</li>
3677 </ul> <em>Applet</em>
3679 <li>Alignment height set incorrectly when lots of
3680 annotation rows are displayed</li>
3681 <li>Relative URLs in feature HTML text not resolved to
3683 <li>View follows highlighting does not work for positions
3685 <li><= shown as = in tooltip</li>
3686 <li>Export features raises exception when no features
3688 <li>Separator string used for serialising lists of IDs
3689 for javascript api is modified when separator string
3690 provided as parameter</li>
3691 <li>Null pointer exception when selecting tree leaves for
3692 alignment with no existing selection</li>
3693 <li>Relative URLs for datasources assumed to be relative
3694 to applet's codebase</li>
3695 <li>Status bar not updated after finished searching and
3696 search wraps around to first result</li>
3697 <li>StructureSelectionManager instance shared between
3698 several Jalview applets causes race conditions and memory
3700 <li>Hover tooltip and mouseover of position on structure
3701 not sent from Jmol in applet</li>
3702 <li>Certain sequences of javascript method calls to
3703 applet API fatally hang browser</li>
3704 </ul> <em>General</em>
3706 <li>View follows structure mouseover scrolls beyond
3707 position with wrapped view and hidden regions</li>
3708 <li>Find sequence position moves to wrong residue
3709 with/without hidden columns</li>
3710 <li>Sequence length given in alignment properties window
3712 <li>InvalidNumberFormat exceptions thrown when trying to
3713 import PDB like structure files</li>
3714 <li>Positional search results are only highlighted
3715 between user-supplied sequence start/end bounds</li>
3716 <li>End attribute of sequence is not validated</li>
3717 <li>Find dialog only finds first sequence containing a
3718 given sequence position</li>
3719 <li>Sequence numbering not preserved in MSF alignment
3721 <li>Jalview PDB file reader does not extract sequence
3722 from nucleotide chains correctly</li>
3723 <li>Structure colours not updated when tree partition
3724 changed in alignment</li>
3725 <li>Sequence associated secondary structure not correctly
3726 parsed in interleaved stockholm</li>
3727 <li>Colour by annotation dialog does not restore current
3729 <li>Hiding (nearly) all sequences doesn't work
3731 <li>Sequences containing lowercase letters are not
3732 properly associated with their pdb files</li>
3733 </ul> <em>Documentation and Development</em>
3735 <li>schemas/JalviewWsParamSet.xsd corrupted by
3736 ApplyCopyright tool</li>
3741 <div align="center">
3742 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3745 <td><em>Application</em>
3747 <li>New warning dialog when the Jalview Desktop cannot
3748 contact web services</li>
3749 <li>JABA service parameters for a preset are shown in
3750 service job window</li>
3751 <li>JABA Service menu entries reworded</li>
3755 <li>Modeller PIR IO broken - cannot correctly import a
3756 pir file emitted by Jalview</li>
3757 <li>Existing feature settings transferred to new
3758 alignment view created from cut'n'paste</li>
3759 <li>Improved test for mixed amino/nucleotide chains when
3760 parsing PDB files</li>
3761 <li>Consensus and conservation annotation rows
3762 occasionally become blank for all new windows</li>
3763 <li>Exception raised when right clicking above sequences
3764 in wrapped view mode</li>
3765 </ul> <em>Application</em>
3767 <li>multiple multiply aligned structure views cause cpu
3768 usage to hit 100% and computer to hang</li>
3769 <li>Web Service parameter layout breaks for long user
3770 parameter names</li>
3771 <li>Jaba service discovery hangs desktop if Jaba server
3778 <div align="center">
3779 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3782 <td><em>Application</em>
3784 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3785 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3788 <li>Web Services preference tab</li>
3789 <li>Analysis parameters dialog box and user defined
3791 <li>Improved speed and layout of Envision2 service menu</li>
3792 <li>Superpose structures using associated sequence
3794 <li>Export coordinates and projection as CSV from PCA
3796 </ul> <em>Applet</em>
3798 <li>enable javascript: execution by the applet via the
3799 link out mechanism</li>
3800 </ul> <em>Other</em>
3802 <li>Updated the Jmol Jalview interface to work with Jmol
3804 <li>The Jalview Desktop and JalviewLite applet now
3805 require Java 1.5</li>
3806 <li>Allow Jalview feature colour specification for GFF
3807 sequence annotation files</li>
3808 <li>New 'colour by label' keword in Jalview feature file
3809 type colour specification</li>
3810 <li>New Jalview Desktop Groovy API method that allows a
3811 script to check if it being run in an interactive session or
3812 in a batch operation from the Jalview command line</li>
3816 <li>clustalx colourscheme colours Ds preferentially when
3817 both D+E are present in over 50% of the column</li>
3818 </ul> <em>Application</em>
3820 <li>typo in AlignmentFrame->View->Hide->all but
3821 selected Regions menu item</li>
3822 <li>sequence fetcher replaces ',' for ';' when the ',' is
3823 part of a valid accession ID</li>
3824 <li>fatal OOM if object retrieved by sequence fetcher
3825 runs out of memory</li>
3826 <li>unhandled Out of Memory Error when viewing pca
3827 analysis results</li>
3828 <li>InstallAnywhere builds fail to launch on OS X java
3829 10.5 update 4 (due to apple Java 1.6 update)</li>
3830 <li>Installanywhere Jalview silently fails to launch</li>
3831 </ul> <em>Applet</em>
3833 <li>Jalview.getFeatureGroups() raises an
3834 ArrayIndexOutOfBoundsException if no feature groups are
3841 <div align="center">
3842 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3848 <li>Alignment prettyprinter doesn't cope with long
3850 <li>clustalx colourscheme colours Ds preferentially when
3851 both D+E are present in over 50% of the column</li>
3852 <li>nucleic acid structures retrieved from PDB do not
3853 import correctly</li>
3854 <li>More columns get selected than were clicked on when a
3855 number of columns are hidden</li>
3856 <li>annotation label popup menu not providing correct
3857 add/hide/show options when rows are hidden or none are
3859 <li>Stockholm format shown in list of readable formats,
3860 and parser copes better with alignments from RFAM.</li>
3861 <li>CSV output of consensus only includes the percentage
3862 of all symbols if sequence logo display is enabled</li>
3864 </ul> <em>Applet</em>
3866 <li>annotation panel disappears when annotation is
3868 </ul> <em>Application</em>
3870 <li>Alignment view not redrawn properly when new
3871 alignment opened where annotation panel is visible but no
3872 annotations are present on alignment</li>
3873 <li>pasted region containing hidden columns is
3874 incorrectly displayed in new alignment window</li>
3875 <li>Jalview slow to complete operations when stdout is
3876 flooded (fix is to close the Jalview console)</li>
3877 <li>typo in AlignmentFrame->View->Hide->all but
3878 selected Rregions menu item.</li>
3879 <li>inconsistent group submenu and Format submenu entry
3880 'Un' or 'Non'conserved</li>
3881 <li>Sequence feature settings are being shared by
3882 multiple distinct alignments</li>
3883 <li>group annotation not recreated when tree partition is
3885 <li>double click on group annotation to select sequences
3886 does not propagate to associated trees</li>
3887 <li>Mac OSX specific issues:
3889 <li>exception raised when mouse clicked on desktop
3890 window background</li>
3891 <li>Desktop menu placed on menu bar and application
3892 name set correctly</li>
3893 <li>sequence feature settings not wide enough for the
3894 save feature colourscheme button</li>
3903 <div align="center">
3904 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3907 <td><em>New Capabilities</em>
3909 <li>URL links generated from description line for
3910 regular-expression based URL links (applet and application)
3912 <li>Non-positional feature URL links are shown in link
3914 <li>Linked viewing of nucleic acid sequences and
3916 <li>Automatic Scrolling option in View menu to display
3917 the currently highlighted region of an alignment.</li>
3918 <li>Order an alignment by sequence length, or using the
3919 average score or total feature count for each sequence.</li>
3920 <li>Shading features by score or associated description</li>
3921 <li>Subdivide alignment and groups based on identity of
3922 selected subsequence (Make Groups from Selection).</li>
3923 <li>New hide/show options including Shift+Control+H to
3924 hide everything but the currently selected region.</li>
3925 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3926 </ul> <em>Application</em>
3928 <li>Fetch DB References capabilities and UI expanded to
3929 support retrieval from DAS sequence sources</li>
3930 <li>Local DAS Sequence sources can be added via the
3931 command line or via the Add local source dialog box.</li>
3932 <li>DAS Dbref and DbxRef feature types are parsed as
3933 database references and protein_name is parsed as
3934 description line (BioSapiens terms).</li>
3935 <li>Enable or disable non-positional feature and database
3936 references in sequence ID tooltip from View menu in
3938 <!-- <li>New hidden columns and rows and representatives capabilities
3939 in annotations file (in progress - not yet fully implemented)</li> -->
3940 <li>Group-associated consensus, sequence logos and
3941 conservation plots</li>
3942 <li>Symbol distributions for each column can be exported
3943 and visualized as sequence logos</li>
3944 <li>Optionally scale multi-character column labels to fit
3945 within each column of annotation row<!-- todo for applet -->
3947 <li>Optional automatic sort of associated alignment view
3948 when a new tree is opened.</li>
3949 <li>Jalview Java Console</li>
3950 <li>Better placement of desktop window when moving
3951 between different screens.</li>
3952 <li>New preference items for sequence ID tooltip and
3953 consensus annotation</li>
3954 <li>Client to submit sequences and IDs to Envision2
3956 <li><em>Vamsas Capabilities</em>
3958 <li>Improved VAMSAS synchronization (Jalview archive
3959 used to preserve views, structures, and tree display
3961 <li>Import of vamsas documents from disk or URL via
3963 <li>Sharing of selected regions between views and
3964 with other VAMSAS applications (Experimental feature!)</li>
3965 <li>Updated API to VAMSAS version 0.2</li>
3967 </ul> <em>Applet</em>
3969 <li>Middle button resizes annotation row height</li>
3972 <li>sortByTree (true/false) - automatically sort the
3973 associated alignment view by the tree when a new tree is
3975 <li>showTreeBootstraps (true/false) - show or hide
3976 branch bootstraps (default is to show them if available)</li>
3977 <li>showTreeDistances (true/false) - show or hide
3978 branch lengths (default is to show them if available)</li>
3979 <li>showUnlinkedTreeNodes (true/false) - indicate if
3980 unassociated nodes should be highlighted in the tree
3982 <li>heightScale and widthScale (1.0 or more) -
3983 increase the height or width of a cell in the alignment
3984 grid relative to the current font size.</li>
3987 <li>Non-positional features displayed in sequence ID
3989 </ul> <em>Other</em>
3991 <li>Features format: graduated colour definitions and
3992 specification of feature scores</li>
3993 <li>Alignment Annotations format: new keywords for group
3994 associated annotation (GROUP_REF) and annotation row display
3995 properties (ROW_PROPERTIES)</li>
3996 <li>XML formats extended to support graduated feature
3997 colourschemes, group associated annotation, and profile
3998 visualization settings.</li></td>
4001 <li>Source field in GFF files parsed as feature source
4002 rather than description</li>
4003 <li>Non-positional features are now included in sequence
4004 feature and gff files (controlled via non-positional feature
4005 visibility in tooltip).</li>
4006 <li>URL links generated for all feature links (bugfix)</li>
4007 <li>Added URL embedding instructions to features file
4009 <li>Codons containing ambiguous nucleotides translated as
4010 'X' in peptide product</li>
4011 <li>Match case switch in find dialog box works for both
4012 sequence ID and sequence string and query strings do not
4013 have to be in upper case to match case-insensitively.</li>
4014 <li>AMSA files only contain first column of
4015 multi-character column annotation labels</li>
4016 <li>Jalview Annotation File generation/parsing consistent
4017 with documentation (e.g. Stockholm annotation can be
4018 exported and re-imported)</li>
4019 <li>PDB files without embedded PDB IDs given a friendly
4021 <li>Find incrementally searches ID string matches as well
4022 as subsequence matches, and correctly reports total number
4026 <li>Better handling of exceptions during sequence
4028 <li>Dasobert generated non-positional feature URL
4029 link text excludes the start_end suffix</li>
4030 <li>DAS feature and source retrieval buttons disabled
4031 when fetch or registry operations in progress.</li>
4032 <li>PDB files retrieved from URLs are cached properly</li>
4033 <li>Sequence description lines properly shared via
4035 <li>Sequence fetcher fetches multiple records for all
4037 <li>Ensured that command line das feature retrieval
4038 completes before alignment figures are generated.</li>
4039 <li>Reduced time taken when opening file browser for
4041 <li>isAligned check prior to calculating tree, PCA or
4042 submitting an MSA to JNet now excludes hidden sequences.</li>
4043 <li>User defined group colours properly recovered
4044 from Jalview projects.</li>
4053 <div align="center">
4054 <strong>2.4.0.b2</strong><br> 28/10/2009
4059 <li>Experimental support for google analytics usage
4061 <li>Jalview privacy settings (user preferences and docs).</li>
4066 <li>Race condition in applet preventing startup in
4068 <li>Exception when feature created from selection beyond
4069 length of sequence.</li>
4070 <li>Allow synthetic PDB files to be imported gracefully</li>
4071 <li>Sequence associated annotation rows associate with
4072 all sequences with a given id</li>
4073 <li>Find function matches case-insensitively for sequence
4074 ID string searches</li>
4075 <li>Non-standard characters do not cause pairwise
4076 alignment to fail with exception</li>
4077 </ul> <em>Application Issues</em>
4079 <li>Sequences are now validated against EMBL database</li>
4080 <li>Sequence fetcher fetches multiple records for all
4082 </ul> <em>InstallAnywhere Issues</em>
4084 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4085 issue with installAnywhere mechanism)</li>
4086 <li>Command line launching of JARs from InstallAnywhere
4087 version (java class versioning error fixed)</li>
4094 <div align="center">
4095 <strong>2.4</strong><br> 27/8/2008
4098 <td><em>User Interface</em>
4100 <li>Linked highlighting of codon and amino acid from
4101 translation and protein products</li>
4102 <li>Linked highlighting of structure associated with
4103 residue mapping to codon position</li>
4104 <li>Sequence Fetcher provides example accession numbers
4105 and 'clear' button</li>
4106 <li>MemoryMonitor added as an option under Desktop's
4108 <li>Extract score function to parse whitespace separated
4109 numeric data in description line</li>
4110 <li>Column labels in alignment annotation can be centred.</li>
4111 <li>Tooltip for sequence associated annotation give name
4113 </ul> <em>Web Services and URL fetching</em>
4115 <li>JPred3 web service</li>
4116 <li>Prototype sequence search client (no public services
4118 <li>Fetch either seed alignment or full alignment from
4120 <li>URL Links created for matching database cross
4121 references as well as sequence ID</li>
4122 <li>URL Links can be created using regular-expressions</li>
4123 </ul> <em>Sequence Database Connectivity</em>
4125 <li>Retrieval of cross-referenced sequences from other
4127 <li>Generalised database reference retrieval and
4128 validation to all fetchable databases</li>
4129 <li>Fetch sequences from DAS sources supporting the
4130 sequence command</li>
4131 </ul> <em>Import and Export</em>
4132 <li>export annotation rows as CSV for spreadsheet import</li>
4133 <li>Jalview projects record alignment dataset associations,
4134 EMBL products, and cDNA sequence mappings</li>
4135 <li>Sequence Group colour can be specified in Annotation
4137 <li>Ad-hoc colouring of group in Annotation File using RGB
4138 triplet as name of colourscheme</li>
4139 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4141 <li>treenode binding for VAMSAS tree exchange</li>
4142 <li>local editing and update of sequences in VAMSAS
4143 alignments (experimental)</li>
4144 <li>Create new or select existing session to join</li>
4145 <li>load and save of vamsas documents</li>
4146 </ul> <em>Application command line</em>
4148 <li>-tree parameter to open trees (introduced for passing
4150 <li>-fetchfrom command line argument to specify nicknames
4151 of DAS servers to query for alignment features</li>
4152 <li>-dasserver command line argument to add new servers
4153 that are also automatically queried for features</li>
4154 <li>-groovy command line argument executes a given groovy
4155 script after all input data has been loaded and parsed</li>
4156 </ul> <em>Applet-Application data exchange</em>
4158 <li>Trees passed as applet parameters can be passed to
4159 application (when using "View in full
4160 application")</li>
4161 </ul> <em>Applet Parameters</em>
4163 <li>feature group display control parameter</li>
4164 <li>debug parameter</li>
4165 <li>showbutton parameter</li>
4166 </ul> <em>Applet API methods</em>
4168 <li>newView public method</li>
4169 <li>Window (current view) specific get/set public methods</li>
4170 <li>Feature display control methods</li>
4171 <li>get list of currently selected sequences</li>
4172 </ul> <em>New Jalview distribution features</em>
4174 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4175 <li>RELEASE file gives build properties for the latest
4176 Jalview release.</li>
4177 <li>Java 1.1 Applet build made easier and donotobfuscate
4178 property controls execution of obfuscator</li>
4179 <li>Build target for generating source distribution</li>
4180 <li>Debug flag for javacc</li>
4181 <li>.jalview_properties file is documented (slightly) in
4182 jalview.bin.Cache</li>
4183 <li>Continuous Build Integration for stable and
4184 development version of Application, Applet and source
4189 <li>selected region output includes visible annotations
4190 (for certain formats)</li>
4191 <li>edit label/displaychar contains existing label/char
4193 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4194 <li>shorter peptide product names from EMBL records</li>
4195 <li>Newick string generator makes compact representations</li>
4196 <li>bootstrap values parsed correctly for tree files with
4198 <li>pathological filechooser bug avoided by not allowing
4199 filenames containing a ':'</li>
4200 <li>Fixed exception when parsing GFF files containing
4201 global sequence features</li>
4202 <li>Alignment datasets are finalized only when number of
4203 references from alignment sequences goes to zero</li>
4204 <li>Close of tree branch colour box without colour
4205 selection causes cascading exceptions</li>
4206 <li>occasional negative imgwidth exceptions</li>
4207 <li>better reporting of non-fatal warnings to user when
4208 file parsing fails.</li>
4209 <li>Save works when Jalview project is default format</li>
4210 <li>Save as dialog opened if current alignment format is
4211 not a valid output format</li>
4212 <li>UniProt canonical names introduced for both das and
4214 <li>Histidine should be midblue (not pink!) in Zappo</li>
4215 <li>error messages passed up and output when data read
4217 <li>edit undo recovers previous dataset sequence when
4218 sequence is edited</li>
4219 <li>allow PDB files without pdb ID HEADER lines (like
4220 those generated by MODELLER) to be read in properly</li>
4221 <li>allow reading of JPred concise files as a normal
4223 <li>Stockholm annotation parsing and alignment properties
4224 import fixed for PFAM records</li>
4225 <li>Structure view windows have correct name in Desktop
4227 <li>annotation consisting of sequence associated scores
4228 can be read and written correctly to annotation file</li>
4229 <li>Aligned cDNA translation to aligned peptide works
4231 <li>Fixed display of hidden sequence markers and
4232 non-italic font for representatives in Applet</li>
4233 <li>Applet Menus are always embedded in applet window on
4235 <li>Newly shown features appear at top of stack (in
4237 <li>Annotations added via parameter not drawn properly
4238 due to null pointer exceptions</li>
4239 <li>Secondary structure lines are drawn starting from
4240 first column of alignment</li>
4241 <li>UniProt XML import updated for new schema release in
4243 <li>Sequence feature to sequence ID match for Features
4244 file is case-insensitive</li>
4245 <li>Sequence features read from Features file appended to
4246 all sequences with matching IDs</li>
4247 <li>PDB structure coloured correctly for associated views
4248 containing a sub-sequence</li>
4249 <li>PDB files can be retrieved by applet from Jar files</li>
4250 <li>feature and annotation file applet parameters
4251 referring to different directories are retrieved correctly</li>
4252 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4253 <li>Fixed application hang whilst waiting for
4254 splash-screen version check to complete</li>
4255 <li>Applet properly URLencodes input parameter values
4256 when passing them to the launchApp service</li>
4257 <li>display name and local features preserved in results
4258 retrieved from web service</li>
4259 <li>Visual delay indication for sequence retrieval and
4260 sequence fetcher initialisation</li>
4261 <li>updated Application to use DAS 1.53e version of
4262 dasobert DAS client</li>
4263 <li>Re-instated Full AMSA support and .amsa file
4265 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4273 <div align="center">
4274 <strong>2.3</strong><br> 9/5/07
4279 <li>Jmol 11.0.2 integration</li>
4280 <li>PDB views stored in Jalview XML files</li>
4281 <li>Slide sequences</li>
4282 <li>Edit sequence in place</li>
4283 <li>EMBL CDS features</li>
4284 <li>DAS Feature mapping</li>
4285 <li>Feature ordering</li>
4286 <li>Alignment Properties</li>
4287 <li>Annotation Scores</li>
4288 <li>Sort by scores</li>
4289 <li>Feature/annotation editing in applet</li>
4294 <li>Headless state operation in 2.2.1</li>
4295 <li>Incorrect and unstable DNA pairwise alignment</li>
4296 <li>Cut and paste of sequences with annotation</li>
4297 <li>Feature group display state in XML</li>
4298 <li>Feature ordering in XML</li>
4299 <li>blc file iteration selection using filename # suffix</li>
4300 <li>Stockholm alignment properties</li>
4301 <li>Stockhom alignment secondary structure annotation</li>
4302 <li>2.2.1 applet had no feature transparency</li>
4303 <li>Number pad keys can be used in cursor mode</li>
4304 <li>Structure Viewer mirror image resolved</li>
4311 <div align="center">
4312 <strong>2.2.1</strong><br> 12/2/07
4317 <li>Non standard characters can be read and displayed
4318 <li>Annotations/Features can be imported/exported to the
4320 <li>Applet allows editing of sequence/annotation/group
4321 name & description
4322 <li>Preference setting to display sequence name in
4324 <li>Annotation file format extended to allow
4325 Sequence_groups to be defined
4326 <li>Default opening of alignment overview panel can be
4327 specified in preferences
4328 <li>PDB residue numbering annotation added to associated
4334 <li>Applet crash under certain Linux OS with Java 1.6
4336 <li>Annotation file export / import bugs fixed
4337 <li>PNG / EPS image output bugs fixed
4343 <div align="center">
4344 <strong>2.2</strong><br> 27/11/06
4349 <li>Multiple views on alignment
4350 <li>Sequence feature editing
4351 <li>"Reload" alignment
4352 <li>"Save" to current filename
4353 <li>Background dependent text colour
4354 <li>Right align sequence ids
4355 <li>User-defined lower case residue colours
4358 <li>Menu item accelerator keys
4359 <li>Control-V pastes to current alignment
4360 <li>Cancel button for DAS Feature Fetching
4361 <li>PCA and PDB Viewers zoom via mouse roller
4362 <li>User-defined sub-tree colours and sub-tree selection
4364 <li>'New Window' button on the 'Output to Text box'
4369 <li>New memory efficient Undo/Redo System
4370 <li>Optimised symbol lookups and conservation/consensus
4372 <li>Region Conservation/Consensus recalculated after
4374 <li>Fixed Remove Empty Columns Bug (empty columns at end
4376 <li>Slowed DAS Feature Fetching for increased robustness.
4378 <li>Made angle brackets in ASCII feature descriptions
4380 <li>Re-instated Zoom function for PCA
4381 <li>Sequence descriptions conserved in web service
4383 <li>UniProt ID discoverer uses any word separated by
4385 <li>WsDbFetch query/result association resolved
4386 <li>Tree leaf to sequence mapping improved
4387 <li>Smooth fonts switch moved to FontChooser dialog box.
4394 <div align="center">
4395 <strong>2.1.1</strong><br> 12/9/06
4400 <li>Copy consensus sequence to clipboard</li>
4405 <li>Image output - rightmost residues are rendered if
4406 sequence id panel has been resized</li>
4407 <li>Image output - all offscreen group boundaries are
4409 <li>Annotation files with sequence references - all
4410 elements in file are relative to sequence position</li>
4411 <li>Mac Applet users can use Alt key for group editing</li>
4417 <div align="center">
4418 <strong>2.1</strong><br> 22/8/06
4423 <li>MAFFT Multiple Alignment in default Web Service list</li>
4424 <li>DAS Feature fetching</li>
4425 <li>Hide sequences and columns</li>
4426 <li>Export Annotations and Features</li>
4427 <li>GFF file reading / writing</li>
4428 <li>Associate structures with sequences from local PDB
4430 <li>Add sequences to exisiting alignment</li>
4431 <li>Recently opened files / URL lists</li>
4432 <li>Applet can launch the full application</li>
4433 <li>Applet has transparency for features (Java 1.2
4435 <li>Applet has user defined colours parameter</li>
4436 <li>Applet can load sequences from parameter
4437 "sequence<em>x</em>"
4443 <li>Redundancy Panel reinstalled in the Applet</li>
4444 <li>Monospaced font - EPS / rescaling bug fixed</li>
4445 <li>Annotation files with sequence references bug fixed</li>
4451 <div align="center">
4452 <strong>2.08.1</strong><br> 2/5/06
4457 <li>Change case of selected region from Popup menu</li>
4458 <li>Choose to match case when searching</li>
4459 <li>Middle mouse button and mouse movement can compress /
4460 expand the visible width and height of the alignment</li>
4465 <li>Annotation Panel displays complete JNet results</li>
4471 <div align="center">
4472 <strong>2.08b</strong><br> 18/4/06
4478 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4479 <li>Righthand label on wrapped alignments shows correct
4486 <div align="center">
4487 <strong>2.08</strong><br> 10/4/06
4492 <li>Editing can be locked to the selection area</li>
4493 <li>Keyboard editing</li>
4494 <li>Create sequence features from searches</li>
4495 <li>Precalculated annotations can be loaded onto
4497 <li>Features file allows grouping of features</li>
4498 <li>Annotation Colouring scheme added</li>
4499 <li>Smooth fonts off by default - Faster rendering</li>
4500 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4505 <li>Drag & Drop fixed on Linux</li>
4506 <li>Jalview Archive file faster to load/save, sequence
4507 descriptions saved.</li>
4513 <div align="center">
4514 <strong>2.07</strong><br> 12/12/05
4519 <li>PDB Structure Viewer enhanced</li>
4520 <li>Sequence Feature retrieval and display enhanced</li>
4521 <li>Choose to output sequence start-end after sequence
4522 name for file output</li>
4523 <li>Sequence Fetcher WSDBFetch@EBI</li>
4524 <li>Applet can read feature files, PDB files and can be
4525 used for HTML form input</li>
4530 <li>HTML output writes groups and features</li>
4531 <li>Group editing is Control and mouse click</li>
4532 <li>File IO bugs</li>
4538 <div align="center">
4539 <strong>2.06</strong><br> 28/9/05
4544 <li>View annotations in wrapped mode</li>
4545 <li>More options for PCA viewer</li>
4550 <li>GUI bugs resolved</li>
4551 <li>Runs with -nodisplay from command line</li>
4557 <div align="center">
4558 <strong>2.05b</strong><br> 15/9/05
4563 <li>Choose EPS export as lineart or text</li>
4564 <li>Jar files are executable</li>
4565 <li>Can read in Uracil - maps to unknown residue</li>
4570 <li>Known OutOfMemory errors give warning message</li>
4571 <li>Overview window calculated more efficiently</li>
4572 <li>Several GUI bugs resolved</li>
4578 <div align="center">
4579 <strong>2.05</strong><br> 30/8/05
4584 <li>Edit and annotate in "Wrapped" view</li>
4589 <li>Several GUI bugs resolved</li>
4595 <div align="center">
4596 <strong>2.04</strong><br> 24/8/05
4601 <li>Hold down mouse wheel & scroll to change font
4607 <li>Improved JPred client reliability</li>
4608 <li>Improved loading of Jalview files</li>
4614 <div align="center">
4615 <strong>2.03</strong><br> 18/8/05
4620 <li>Set Proxy server name and port in preferences</li>
4621 <li>Multiple URL links from sequence ids</li>
4622 <li>User Defined Colours can have a scheme name and added
4624 <li>Choose to ignore gaps in consensus calculation</li>
4625 <li>Unix users can set default web browser</li>
4626 <li>Runs without GUI for batch processing</li>
4627 <li>Dynamically generated Web Service Menus</li>
4632 <li>InstallAnywhere download for Sparc Solaris</li>
4638 <div align="center">
4639 <strong>2.02</strong><br> 18/7/05
4645 <li>Copy & Paste order of sequences maintains
4646 alignment order.</li>
4652 <div align="center">
4653 <strong>2.01</strong><br> 12/7/05
4658 <li>Use delete key for deleting selection.</li>
4659 <li>Use Mouse wheel to scroll sequences.</li>
4660 <li>Help file updated to describe how to add alignment
4662 <li>Version and build date written to build properties
4664 <li>InstallAnywhere installation will check for updates
4665 at launch of Jalview.</li>
4670 <li>Delete gaps bug fixed.</li>
4671 <li>FileChooser sorts columns.</li>
4672 <li>Can remove groups one by one.</li>
4673 <li>Filechooser icons installed.</li>
4674 <li>Finder ignores return character when searching.
4675 Return key will initiate a search.<br>
4682 <div align="center">
4683 <strong>2.0</strong><br> 20/6/05
4688 <li>New codebase</li>