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">
64 <li><!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
67 <!-- JAL-3376 -->Record "fixed column" values POS,
68 ID, QUAL, FILTER from VCF as Feature Attributes
71 <!-- JAL-3375 -->More robust VCF numeric data field
72 validation while parsing (e.g. AF* attributes)
75 <!-- JAL-3538 -->Font anti-aliasing in alignment views
81 </ul> <em>Release processes</em>
84 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
86 </ul> <em>Build System</em>
89 <!-- JAL-3510 -->Clover updated to 4.4.1
92 <!-- JAL-3513 -->Test code included in Clover coverage
95 </ul> <em>Deprecations</em>
97 <td align="left" valign="top">
103 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
104 with annotation and exceptions thrown when only a few
105 columns shown in wrapped mode
108 <!-- JAL-3386 -->Sequence IDs missing in headless export of
109 wrapped alignment figure with annotations
112 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
113 ID fails with ClassCastException
116 <!-- JAL-3389 -->Chimera session not restored from Jalview
120 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
121 feature settings dialog also selects columns
124 <!-- JAL-3473 -->SpinnerNumberModel causing
125 IllegalArgumentException in some circumstances
128 <!-- JAL-3406 -->Credits missing some authors in Jalview
129 help documentation for 2.11.0 release
131 </ul> <em>Java 11 Compatibility issues</em>
134 <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
136 </ul> <em>Repository and Source Release</em>
139 <!-- JAL-3474 -->removed redundant .gitignore files from
143 <em>New Known Issues</em>
146 <!-- JAL-3523 -->OSX - Current working directory not
147 preserved when Jalview.app launched with parameters from
151 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
152 clipped in headless figure export when Right Align option
159 <td width="60" align="center" nowrap>
160 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
161 <em>04/07/2019</em></strong>
163 <td align="left" valign="top">
166 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
167 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
168 source project) rather than InstallAnywhere
171 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
172 settings, receive over the air updates and launch specific
173 versions via (<a href="https://github.com/threerings/getdown">Three
177 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
178 formats supported by Jalview (including .jvp project files)
181 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
182 arguments and switch between different getdown channels
185 <!-- JAL-3141 -->Backup files created when saving Jalview project
190 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
191 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
193 <!-- JAL-2620 -->Alternative genetic code tables for
194 'Translate as cDNA'</li>
196 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
197 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
200 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
201 implementation that allows updates) used for Sequence Feature collections</li>
203 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
204 features can be filtered and shaded according to any
205 associated attributes (e.g. variant attributes from VCF
206 file, or key-value pairs imported from column 9 of GFF
210 <!-- JAL-2879 -->Feature Attributes and shading schemes
211 stored and restored from Jalview Projects
214 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
215 recognise variant features
218 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
219 sequences (also coloured red by default)
222 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
226 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
227 algorithm (Z-sort/transparency and filter aware)
230 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
236 <!-- JAL-3205 -->Symmetric score matrices for faster
237 tree and PCA calculations
239 <li><strong>Principal Components Analysis Viewer</strong>
242 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
243 and Viewer state saved in Jalview Project
245 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
248 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
252 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
257 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
259 <li><strong>Speed and Efficiency</strong>
262 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
263 multiple groups when working with large alignments
266 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
270 <li><strong>User Interface</strong>
273 <!-- JAL-2933 -->Finder panel remembers last position in each
277 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
278 what is shown)<br />Only visible regions of alignment are shown by
279 default (can be changed in user preferences)
282 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
283 to the Overwrite Dialog
286 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
290 <!-- JAL-1244 -->Status bar shows bounds when dragging a
291 selection region, and gap count when inserting or deleting gaps
294 <!-- JAL-3132 -->Status bar updates over sequence and annotation
298 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
302 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
306 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
309 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
313 <!-- JAL-3181 -->Consistent ordering of links in sequence id
317 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
319 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
323 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
324 <li><strong>Java 11 Support (not yet on general release)</strong>
327 <!-- -->OSX GUI integrations for App menu's 'About' entry and
332 <em>Deprecations</em>
334 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
335 capabilities removed from the Jalview Desktop
337 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
338 unmarshalling has been replaced by JAXB for Jalview projects
339 and XML based data retrieval clients</li>
340 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
341 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
342 </ul> <em>Documentation</em>
344 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
345 not supported in EPS figure export
347 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
348 </ul> <em>Development and Release Processes</em>
351 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
354 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
356 <!-- JAL-3225 -->Eclipse project configuration managed with
360 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
361 Bamboo continuous integration for unattended Test Suite
365 <!-- JAL-2864 -->Memory test suite to detect leaks in common
369 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
373 <!-- JAL-3248 -->Developer documentation migrated to
374 markdown (with HTML rendering)
377 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
380 <!-- JAL-3289 -->New URLs for publishing development
385 <td align="left" valign="top">
388 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
391 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
392 superposition in Jmol fail on Windows
395 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
396 structures for sequences with lots of PDB structures
399 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
403 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
404 project involving multiple views
407 <!-- JAL-3164 -->Overview for complementary view in a linked
408 CDS/Protein alignment is not updated when Hide Columns by
409 Annotation dialog hides columns
412 <!-- JAL-3158 -->Selection highlighting in the complement of a
413 CDS/Protein alignment stops working after making a selection in
414 one view, then making another selection in the other view
417 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
421 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
422 Settings and Jalview Preferences panels
425 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
426 overview with large alignments
429 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
430 region if columns were selected by dragging right-to-left and the
431 mouse moved to the left of the first column
434 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
435 hidden column marker via scale popup menu
438 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
439 doesn't tell users the invalid URL
442 <!-- JAL-2816 -->Tooltips displayed for features filtered by
446 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
447 show cross references or Fetch Database References are shown in
451 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
452 peptide sequence (computed variant shown as p.Res.null)
455 <!-- JAL-2060 -->'Graduated colour' option not offered for
456 manually created features (where feature score is Float.NaN)
459 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
460 when columns are hidden
463 <!-- JAL-3082 -->Regular expression error for '(' in Select
464 Columns by Annotation description
467 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
468 out of Scale or Annotation Panel
471 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
475 <!-- JAL-3074 -->Left/right drag in annotation can scroll
479 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
483 <!-- JAL-3002 -->Column display is out by one after Page Down,
484 Page Up in wrapped mode
487 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
490 <!-- JAL-2932 -->Finder searches in minimised alignments
493 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
494 on opening an alignment
497 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
501 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
502 different groups in the alignment are selected
505 <!-- JAL-2717 -->Internationalised colour scheme names not shown
509 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
513 <!-- JAL-3125 -->Value input for graduated feature colour
514 threshold gets 'unrounded'
517 <!-- JAL-2982 -->PCA image export doesn't respect background
521 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
524 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
527 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
531 <!-- JAL-2964 -->Associate Tree with All Views not restored from
535 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
536 shown in complementary view
539 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
540 without normalisation
543 <!-- JAL-3021 -->Sequence Details report should open positioned at top
547 <!-- JAL-914 -->Help page can be opened twice
550 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
552 </ul> <em>Editing</em>
555 <!-- JAL-2822 -->Start and End should be updated when sequence
556 data at beginning or end of alignment added/removed via 'Edit'
560 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
561 relocate sequence features correctly when start of sequence is
562 removed (Known defect since 2.10)
565 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
566 dialog corrupts dataset sequence
569 <!-- JAL-868 -->Structure colours not updated when associated tree
570 repartitions the alignment view (Regression in 2.10.5)
572 </ul> <em>Datamodel</em>
575 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
576 sequence's End is greater than its length
578 </ul> <em>Bugs fixed for Java 11 Support (not yet on
579 general release)</em>
582 <!-- JAL-3288 -->Menus work properly in split-screen
584 </ul> <em>New Known Defects</em>
587 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
590 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
591 regions of protein alignment.
594 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
595 is restored from a Jalview 2.11 project
598 <!-- JAL-3213 -->Alignment panel height can be too small after
602 <!-- JAL-3240 -->Display is incorrect after removing gapped
603 columns within hidden columns
606 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
607 window after dragging left to select columns to left of visible
611 <!-- JAL-2876 -->Features coloured according to their description
612 string and thresholded by score in earlier versions of Jalview are
613 not shown as thresholded features in 2.11. To workaround please
614 create a Score filter instead.
617 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
619 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
622 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
623 alignments with multiple views can close views unexpectedly
626 <em>Java 11 Specific defects</em>
629 <!-- JAL-3235 -->Jalview Properties file is not sorted
630 alphabetically when saved
636 <td width="60" nowrap>
638 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
641 <td><div align="left">
645 <!-- JAL-3101 -->Default memory for Jalview webstart and
646 InstallAnywhere increased to 1G.
649 <!-- JAL-247 -->Hidden sequence markers and representative
650 sequence bolding included when exporting alignment as EPS,
651 SVG, PNG or HTML. <em>Display is configured via the
652 Format menu, or for command-line use via a Jalview
653 properties file.</em>
656 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
657 API and sequence data now imported as JSON.
660 <!-- JAL-3065 -->Change in recommended way of starting
661 Jalview via a Java command line: add jars in lib directory
662 to CLASSPATH, rather than via the deprecated java.ext.dirs
669 <!-- JAL-3047 -->Support added to execute test suite
670 instrumented with <a href="http://openclover.org/">Open
675 <td><div align="left">
679 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
680 row shown in Feredoxin Structure alignment view of example
684 <!-- JAL-2854 -->Annotation obscures sequences if lots of
685 annotation displayed.
688 <!-- JAL-3107 -->Group conservation/consensus not shown
689 for newly created group when 'Apply to all groups'
693 <!-- JAL-3087 -->Corrupted display when switching to
694 wrapped mode when sequence panel's vertical scrollbar is
698 <!-- JAL-3003 -->Alignment is black in exported EPS file
699 when sequences are selected in exported view.</em>
702 <!-- JAL-3059 -->Groups with different coloured borders
703 aren't rendered with correct colour.
706 <!-- JAL-3092 -->Jalview could hang when importing certain
707 types of knotted RNA secondary structure.
710 <!-- JAL-3095 -->Sequence highlight and selection in
711 trimmed VARNA 2D structure is incorrect for sequences that
715 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
716 annotation when columns are inserted into an alignment,
717 and when exporting as Stockholm flatfile.
720 <!-- JAL-3053 -->Jalview annotation rows containing upper
721 and lower-case 'E' and 'H' do not automatically get
722 treated as RNA secondary structure.
725 <!-- JAL-3106 -->.jvp should be used as default extension
726 (not .jar) when saving a Jalview project file.
729 <!-- JAL-3105 -->Mac Users: closing a window correctly
730 transfers focus to previous window on OSX
733 <em>Java 10 Issues Resolved</em>
736 <!-- JAL-2988 -->OSX - Can't save new files via the File
737 or export menus by typing in a name into the Save dialog
741 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
742 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
743 'look and feel' which has improved compatibility with the
744 latest version of OSX.
751 <td width="60" nowrap>
753 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
754 <em>7/06/2018</em></strong>
757 <td><div align="left">
761 <!-- JAL-2920 -->Use HGVS nomenclature for variant
762 annotation retrieved from Uniprot
765 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
766 onto the Jalview Desktop
770 <td><div align="left">
774 <!-- JAL-3017 -->Cannot import features with multiple
775 variant elements (blocks import of some Uniprot records)
778 <!-- JAL-2997 -->Clustal files with sequence positions in
779 right-hand column parsed correctly
782 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
783 not alignment area in exported graphic
786 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
787 window has input focus
790 <!-- JAL-2992 -->Annotation panel set too high when
791 annotation added to view (Windows)
794 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
795 network connectivity is poor
798 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
799 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
800 the currently open URL and links from a page viewed in
801 Firefox or Chrome on Windows is now fully supported. If
802 you are using Edge, only links in the page can be
803 dragged, and with Internet Explorer, only the currently
804 open URL in the browser can be dropped onto Jalview.</em>
807 <em>New Known Defects</em>
809 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
814 <td width="60" nowrap>
816 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
819 <td><div align="left">
823 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
824 for disabling automatic superposition of multiple
825 structures and open structures in existing views
828 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
829 ID and annotation area margins can be click-dragged to
833 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
837 <!-- JAL-2759 -->Improved performance for large alignments
838 and lots of hidden columns
841 <!-- JAL-2593 -->Improved performance when rendering lots
842 of features (particularly when transparency is disabled)
845 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
846 exchange of Jalview features and Chimera attributes made
852 <td><div align="left">
855 <!-- JAL-2899 -->Structure and Overview aren't updated
856 when Colour By Annotation threshold slider is adjusted
859 <!-- JAL-2778 -->Slow redraw when Overview panel shown
860 overlapping alignment panel
863 <!-- JAL-2929 -->Overview doesn't show end of unpadded
867 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
868 improved: CDS not handled correctly if transcript has no
872 <!-- JAL-2321 -->Secondary structure and temperature
873 factor annotation not added to sequence when local PDB
874 file associated with it by drag'n'drop or structure
878 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
879 dialog doesn't import PDB files dropped on an alignment
882 <!-- JAL-2666 -->Linked scrolling via protein horizontal
883 scroll bar doesn't work for some CDS/Protein views
886 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
887 Java 1.8u153 onwards and Java 1.9u4+.
890 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
891 columns in annotation row
894 <!-- JAL-2913 -->Preferences panel's ID Width control is not
895 honored in batch mode
898 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
899 for structures added to existing Jmol view
902 <!-- JAL-2223 -->'View Mappings' includes duplicate
903 entries after importing project with multiple views
906 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
907 protein sequences via SIFTS from associated PDB entries
908 with negative residue numbers or missing residues fails
911 <!-- JAL-2952 -->Exception when shading sequence with negative
912 Temperature Factor values from annotated PDB files (e.g.
913 as generated by CONSURF)
916 <!-- JAL-2920 -->Uniprot 'sequence variant' features
917 tooltip doesn't include a text description of mutation
920 <!-- JAL-2922 -->Invert displayed features very slow when
921 structure and/or overview windows are also shown
924 <!-- JAL-2954 -->Selecting columns from highlighted regions
925 very slow for alignments with large numbers of sequences
928 <!-- JAL-2925 -->Copy Consensus fails for group consensus
929 with 'StringIndexOutOfBounds'
932 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
933 platforms running Java 10
936 <!-- JAL-2960 -->Adding a structure to existing structure
937 view appears to do nothing because the view is hidden behind the alignment view
943 <!-- JAL-2926 -->Copy consensus sequence option in applet
944 should copy the group consensus when popup is opened on it
950 <!-- JAL-2913 -->Fixed ID width preference is not respected
953 <em>New Known Defects</em>
956 <!-- JAL-2973 --> Exceptions occasionally raised when
957 editing a large alignment and overview is displayed
960 <!-- JAL-2974 -->'Overview updating' progress bar is shown
961 repeatedly after a series of edits even when the overview
962 is no longer reflecting updates
965 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
966 structures for protein subsequence (if 'Trim Retrieved
967 Sequences' enabled) or Ensembl isoforms (Workaround in
968 2.10.4 is to fail back to N&W mapping)
971 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
972 option gives blank output
979 <td width="60" nowrap>
981 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
984 <td><div align="left">
985 <ul><li>Updated Certum Codesigning Certificate
986 (Valid till 30th November 2018)</li></ul></div></td>
987 <td><div align="left">
990 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
991 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
992 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
993 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
994 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
995 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
996 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1002 <td width="60" nowrap>
1003 <div align="center">
1004 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1007 <td><div align="left">
1011 <!-- JAL-2446 -->Faster and more efficient management and
1012 rendering of sequence features
1015 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1016 429 rate limit request hander
1019 <!-- JAL-2773 -->Structure views don't get updated unless
1020 their colours have changed
1023 <!-- JAL-2495 -->All linked sequences are highlighted for
1024 a structure mousover (Jmol) or selection (Chimera)
1027 <!-- JAL-2790 -->'Cancel' button in progress bar for
1028 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1031 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1032 view from Ensembl locus cross-references
1035 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1039 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1040 feature can be disabled
1043 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1044 PDB easier retrieval of sequences for lists of IDs
1047 <!-- JAL-2758 -->Short names for sequences retrieved from
1053 <li>Groovy interpreter updated to 2.4.12</li>
1054 <li>Example groovy script for generating a matrix of
1055 percent identity scores for current alignment.</li>
1057 <em>Testing and Deployment</em>
1060 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1064 <td><div align="left">
1068 <!-- JAL-2643 -->Pressing tab after updating the colour
1069 threshold text field doesn't trigger an update to the
1073 <!-- JAL-2682 -->Race condition when parsing sequence ID
1077 <!-- JAL-2608 -->Overview windows are also closed when
1078 alignment window is closed
1081 <!-- JAL-2548 -->Export of features doesn't always respect
1085 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1086 takes a long time in Cursor mode
1092 <!-- JAL-2777 -->Structures with whitespace chainCode
1093 cannot be viewed in Chimera
1096 <!-- JAL-2728 -->Protein annotation panel too high in
1100 <!-- JAL-2757 -->Can't edit the query after the server
1101 error warning icon is shown in Uniprot and PDB Free Text
1105 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1108 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1111 <!-- JAL-2739 -->Hidden column marker in last column not
1112 rendered when switching back from Wrapped to normal view
1115 <!-- JAL-2768 -->Annotation display corrupted when
1116 scrolling right in unwapped alignment view
1119 <!-- JAL-2542 -->Existing features on subsequence
1120 incorrectly relocated when full sequence retrieved from
1124 <!-- JAL-2733 -->Last reported memory still shown when
1125 Desktop->Show Memory is unticked (OSX only)
1128 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1129 features of same type and group to be selected for
1133 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1134 alignments when hidden columns are present
1137 <!-- JAL-2392 -->Jalview freezes when loading and
1138 displaying several structures
1141 <!-- JAL-2732 -->Black outlines left after resizing or
1145 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1146 within the Jalview desktop on OSX
1149 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1150 when in wrapped alignment mode
1153 <!-- JAL-2636 -->Scale mark not shown when close to right
1154 hand end of alignment
1157 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1158 each selected sequence do not have correct start/end
1162 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1163 after canceling the Alignment Window's Font dialog
1166 <!-- JAL-2036 -->Show cross-references not enabled after
1167 restoring project until a new view is created
1170 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1171 URL links appears when only default EMBL-EBI link is
1172 configured (since 2.10.2b2)
1175 <!-- JAL-2775 -->Overview redraws whole window when box
1176 position is adjusted
1179 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1180 in a multi-chain structure when viewing alignment
1181 involving more than one chain (since 2.10)
1184 <!-- JAL-2811 -->Double residue highlights in cursor mode
1185 if new selection moves alignment window
1188 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1189 arrow key in cursor mode to pass hidden column marker
1192 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1193 that produces correctly annotated transcripts and products
1196 <!-- JAL-2776 -->Toggling a feature group after first time
1197 doesn't update associated structure view
1200 <em>Applet</em><br />
1203 <!-- JAL-2687 -->Concurrent modification exception when
1204 closing alignment panel
1207 <em>BioJSON</em><br />
1210 <!-- JAL-2546 -->BioJSON export does not preserve
1211 non-positional features
1214 <em>New Known Issues</em>
1217 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1218 sequence features correctly (for many previous versions of
1222 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1223 using cursor in wrapped panel other than top
1226 <!-- JAL-2791 -->Select columns containing feature ignores
1227 graduated colour threshold
1230 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1231 always preserve numbering and sequence features
1234 <em>Known Java 9 Issues</em>
1237 <!-- JAL-2902 -->Groovy Console very slow to open and is
1238 not responsive when entering characters (Webstart, Java
1245 <td width="60" nowrap>
1246 <div align="center">
1247 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1248 <em>2/10/2017</em></strong>
1251 <td><div align="left">
1252 <em>New features in Jalview Desktop</em>
1255 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1257 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1261 <td><div align="left">
1265 <td width="60" nowrap>
1266 <div align="center">
1267 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1268 <em>7/9/2017</em></strong>
1271 <td><div align="left">
1275 <!-- JAL-2588 -->Show gaps in overview window by colouring
1276 in grey (sequences used to be coloured grey, and gaps were
1280 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1284 <!-- JAL-2587 -->Overview updates immediately on increase
1285 in size and progress bar shown as higher resolution
1286 overview is recalculated
1291 <td><div align="left">
1295 <!-- JAL-2664 -->Overview window redraws every hidden
1296 column region row by row
1299 <!-- JAL-2681 -->duplicate protein sequences shown after
1300 retrieving Ensembl crossrefs for sequences from Uniprot
1303 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1304 format setting is unticked
1307 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1308 if group has show boxes format setting unticked
1311 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1312 autoscrolling whilst dragging current selection group to
1313 include sequences and columns not currently displayed
1316 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1317 assemblies are imported via CIF file
1320 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1321 displayed when threshold or conservation colouring is also
1325 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1329 <!-- JAL-2673 -->Jalview continues to scroll after
1330 dragging a selected region off the visible region of the
1334 <!-- JAL-2724 -->Cannot apply annotation based
1335 colourscheme to all groups in a view
1338 <!-- JAL-2511 -->IDs don't line up with sequences
1339 initially after font size change using the Font chooser or
1346 <td width="60" nowrap>
1347 <div align="center">
1348 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1351 <td><div align="left">
1352 <em>Calculations</em>
1356 <!-- JAL-1933 -->Occupancy annotation row shows number of
1357 ungapped positions in each column of the alignment.
1360 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1361 a calculation dialog box
1364 <!-- JAL-2379 -->Revised implementation of PCA for speed
1365 and memory efficiency (~30x faster)
1368 <!-- JAL-2403 -->Revised implementation of sequence
1369 similarity scores as used by Tree, PCA, Shading Consensus
1370 and other calculations
1373 <!-- JAL-2416 -->Score matrices are stored as resource
1374 files within the Jalview codebase
1377 <!-- JAL-2500 -->Trees computed on Sequence Feature
1378 Similarity may have different topology due to increased
1385 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1386 model for alignments and groups
1389 <!-- JAL-384 -->Custom shading schemes created via groovy
1396 <!-- JAL-2526 -->Efficiency improvements for interacting
1397 with alignment and overview windows
1400 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1404 <!-- JAL-2388 -->Hidden columns and sequences can be
1408 <!-- JAL-2611 -->Click-drag in visible area allows fine
1409 adjustment of visible position
1413 <em>Data import/export</em>
1416 <!-- JAL-2535 -->Posterior probability annotation from
1417 Stockholm files imported as sequence associated annotation
1420 <!-- JAL-2507 -->More robust per-sequence positional
1421 annotation input/output via stockholm flatfile
1424 <!-- JAL-2533 -->Sequence names don't include file
1425 extension when importing structure files without embedded
1426 names or PDB accessions
1429 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1430 format sequence substitution matrices
1433 <em>User Interface</em>
1436 <!-- JAL-2447 --> Experimental Features Checkbox in
1437 Desktop's Tools menu to hide or show untested features in
1441 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1442 via Overview or sequence motif search operations
1445 <!-- JAL-2547 -->Amend sequence features dialog box can be
1446 opened by double clicking gaps within sequence feature
1450 <!-- JAL-1476 -->Status bar message shown when not enough
1451 aligned positions were available to create a 3D structure
1455 <em>3D Structure</em>
1458 <!-- JAL-2430 -->Hidden regions in alignment views are not
1459 coloured in linked structure views
1462 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1463 file-based command exchange
1466 <!-- JAL-2375 -->Structure chooser automatically shows
1467 Cached Structures rather than querying the PDBe if
1468 structures are already available for sequences
1471 <!-- JAL-2520 -->Structures imported via URL are cached in
1472 the Jalview project rather than downloaded again when the
1473 project is reopened.
1476 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1477 to transfer Chimera's structure attributes as Jalview
1478 features, and vice-versa (<strong>Experimental
1482 <em>Web Services</em>
1485 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1488 <!-- JAL-2335 -->Filter non-standard amino acids and
1489 nucleotides when submitting to AACon and other MSA
1493 <!-- JAL-2316, -->URLs for viewing database
1494 cross-references provided by identifiers.org and the
1495 EMBL-EBI's MIRIAM DB
1502 <!-- JAL-2344 -->FileFormatI interface for describing and
1503 identifying file formats (instead of String constants)
1506 <!-- JAL-2228 -->FeatureCounter script refactored for
1507 efficiency when counting all displayed features (not
1508 backwards compatible with 2.10.1)
1511 <em>Example files</em>
1514 <!-- JAL-2631 -->Graduated feature colour style example
1515 included in the example feature file
1518 <em>Documentation</em>
1521 <!-- JAL-2339 -->Release notes reformatted for readability
1522 with the built-in Java help viewer
1525 <!-- JAL-1644 -->Find documentation updated with 'search
1526 sequence description' option
1532 <!-- JAL-2485, -->External service integration tests for
1533 Uniprot REST Free Text Search Client
1536 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1539 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1544 <td><div align="left">
1545 <em>Calculations</em>
1548 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1549 matrix - C->R should be '-3'<br />Old matrix restored
1550 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1552 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1553 Jalview's treatment of gaps in PCA and substitution matrix
1554 based Tree calculations.<br /> <br />In earlier versions
1555 of Jalview, gaps matching gaps were penalised, and gaps
1556 matching non-gaps penalised even more. In the PCA
1557 calculation, gaps were actually treated as non-gaps - so
1558 different costs were applied, which meant Jalview's PCAs
1559 were different to those produced by SeqSpace.<br />Jalview
1560 now treats gaps in the same way as SeqSpace (ie it scores
1561 them as 0). <br /> <br />Enter the following in the
1562 Groovy console to restore pre-2.10.2 behaviour:<br />
1563 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1564 // for 2.10.1 mode <br />
1565 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1566 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1567 these settings will affect all subsequent tree and PCA
1568 calculations (not recommended)</em></li>
1570 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1571 scaling of branch lengths for trees computed using
1572 Sequence Feature Similarity.
1575 <!-- JAL-2377 -->PCA calculation could hang when
1576 generating output report when working with highly
1577 redundant alignments
1580 <!-- JAL-2544 --> Sort by features includes features to
1581 right of selected region when gaps present on right-hand
1585 <em>User Interface</em>
1588 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1589 doesn't reselect a specific sequence's associated
1590 annotation after it was used for colouring a view
1593 <!-- JAL-2419 -->Current selection lost if popup menu
1594 opened on a region of alignment without groups
1597 <!-- JAL-2374 -->Popup menu not always shown for regions
1598 of an alignment with overlapping groups
1601 <!-- JAL-2310 -->Finder double counts if both a sequence's
1602 name and description match
1605 <!-- JAL-2370 -->Hiding column selection containing two
1606 hidden regions results in incorrect hidden regions
1609 <!-- JAL-2386 -->'Apply to all groups' setting when
1610 changing colour does not apply Conservation slider value
1614 <!-- JAL-2373 -->Percentage identity and conservation menu
1615 items do not show a tick or allow shading to be disabled
1618 <!-- JAL-2385 -->Conservation shading or PID threshold
1619 lost when base colourscheme changed if slider not visible
1622 <!-- JAL-2547 -->Sequence features shown in tooltip for
1623 gaps before start of features
1626 <!-- JAL-2623 -->Graduated feature colour threshold not
1627 restored to UI when feature colour is edited
1630 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1631 a time when scrolling vertically in wrapped mode.
1634 <!-- JAL-2630 -->Structure and alignment overview update
1635 as graduate feature colour settings are modified via the
1639 <!-- JAL-2034 -->Overview window doesn't always update
1640 when a group defined on the alignment is resized
1643 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1644 wrapped view result in positional status updates
1648 <!-- JAL-2563 -->Status bar doesn't show position for
1649 ambiguous amino acid and nucleotide symbols
1652 <!-- JAL-2602 -->Copy consensus sequence failed if
1653 alignment included gapped columns
1656 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1657 widgets don't permanently disappear
1660 <!-- JAL-2503 -->Cannot select or filter quantitative
1661 annotation that are shown only as column labels (e.g.
1662 T-Coffee column reliability scores)
1665 <!-- JAL-2594 -->Exception thrown if trying to create a
1666 sequence feature on gaps only
1669 <!-- JAL-2504 -->Features created with 'New feature'
1670 button from a Find inherit previously defined feature type
1671 rather than the Find query string
1674 <!-- JAL-2423 -->incorrect title in output window when
1675 exporting tree calculated in Jalview
1678 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1679 and then revealing them reorders sequences on the
1683 <!-- JAL-964 -->Group panel in sequence feature settings
1684 doesn't update to reflect available set of groups after
1685 interactively adding or modifying features
1688 <!-- JAL-2225 -->Sequence Database chooser unusable on
1692 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1693 only excluded gaps in current sequence and ignored
1700 <!-- JAL-2421 -->Overview window visible region moves
1701 erratically when hidden rows or columns are present
1704 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1705 Structure Viewer's colour menu don't correspond to
1709 <!-- JAL-2405 -->Protein specific colours only offered in
1710 colour and group colour menu for protein alignments
1713 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1714 reflect currently selected view or group's shading
1718 <!-- JAL-2624 -->Feature colour thresholds not respected
1719 when rendered on overview and structures when opacity at
1723 <!-- JAL-2589 -->User defined gap colour not shown in
1724 overview when features overlaid on alignment
1727 <!-- JAL-2567 -->Feature settings for different views not
1728 recovered correctly from Jalview project file
1731 <!-- JAL-2256 -->Feature colours in overview when first opened
1732 (automatically via preferences) are different to the main
1736 <em>Data import/export</em>
1739 <!-- JAL-2576 -->Very large alignments take a long time to
1743 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1744 added after a sequence was imported are not written to
1748 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1749 when importing RNA secondary structure via Stockholm
1752 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1753 not shown in correct direction for simple pseudoknots
1756 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1757 with lightGray or darkGray via features file (but can
1761 <!-- JAL-2383 -->Above PID colour threshold not recovered
1762 when alignment view imported from project
1765 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1766 structure and sequences extracted from structure files
1767 imported via URL and viewed in Jmol
1770 <!-- JAL-2520 -->Structures loaded via URL are saved in
1771 Jalview Projects rather than fetched via URL again when
1772 the project is loaded and the structure viewed
1775 <em>Web Services</em>
1778 <!-- JAL-2519 -->EnsemblGenomes example failing after
1779 release of Ensembl v.88
1782 <!-- JAL-2366 -->Proxy server address and port always
1783 appear enabled in Preferences->Connections
1786 <!-- JAL-2461 -->DAS registry not found exceptions
1787 removed from console output
1790 <!-- JAL-2582 -->Cannot retrieve protein products from
1791 Ensembl by Peptide ID
1794 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1795 created from SIFTs, and spurious 'Couldn't open structure
1796 in Chimera' errors raised after April 2017 update (problem
1797 due to 'null' string rather than empty string used for
1798 residues with no corresponding PDB mapping).
1801 <em>Application UI</em>
1804 <!-- JAL-2361 -->User Defined Colours not added to Colour
1808 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1809 case' residues (button in colourscheme editor debugged and
1810 new documentation and tooltips added)
1813 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1814 doesn't restore group-specific text colour thresholds
1817 <!-- JAL-2243 -->Feature settings panel does not update as
1818 new features are added to alignment
1821 <!-- JAL-2532 -->Cancel in feature settings reverts
1822 changes to feature colours via the Amend features dialog
1825 <!-- JAL-2506 -->Null pointer exception when attempting to
1826 edit graduated feature colour via amend features dialog
1830 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1831 selection menu changes colours of alignment views
1834 <!-- JAL-2426 -->Spurious exceptions in console raised
1835 from alignment calculation workers after alignment has
1839 <!-- JAL-1608 -->Typo in selection popup menu - Create
1840 groups now 'Create Group'
1843 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1844 Create/Undefine group doesn't always work
1847 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1848 shown again after pressing 'Cancel'
1851 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1852 adjusts start position in wrap mode
1855 <!-- JAL-2563 -->Status bar doesn't show positions for
1856 ambiguous amino acids
1859 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1860 CDS/Protein view after CDS sequences added for aligned
1864 <!-- JAL-2592 -->User defined colourschemes called 'User
1865 Defined' don't appear in Colours menu
1871 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1872 score models doesn't always result in an updated PCA plot
1875 <!-- JAL-2442 -->Features not rendered as transparent on
1876 overview or linked structure view
1879 <!-- JAL-2372 -->Colour group by conservation doesn't
1883 <!-- JAL-2517 -->Hitting Cancel after applying
1884 user-defined colourscheme doesn't restore original
1891 <!-- JAL-2314 -->Unit test failure:
1892 jalview.ws.jabaws.RNAStructExportImport setup fails
1895 <!-- JAL-2307 -->Unit test failure:
1896 jalview.ws.sifts.SiftsClientTest due to compatibility
1897 problems with deep array comparison equality asserts in
1898 successive versions of TestNG
1901 <!-- JAL-2479 -->Relocated StructureChooserTest and
1902 ParameterUtilsTest Unit tests to Network suite
1905 <em>New Known Issues</em>
1908 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1909 phase after a sequence motif find operation
1912 <!-- JAL-2550 -->Importing annotation file with rows
1913 containing just upper and lower case letters are
1914 interpreted as WUSS RNA secondary structure symbols
1917 <!-- JAL-2590 -->Cannot load and display Newick trees
1918 reliably from eggnog Ortholog database
1921 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1922 containing features of type Highlight' when 'B' is pressed
1923 to mark columns containing highlighted regions.
1926 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1927 doesn't always add secondary structure annotation.
1932 <td width="60" nowrap>
1933 <div align="center">
1934 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1937 <td><div align="left">
1941 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1942 for all consensus calculations
1945 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1948 <li>Updated Jalview's Certum code signing certificate
1951 <em>Application</em>
1954 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1955 set of database cross-references, sorted alphabetically
1958 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1959 from database cross references. Users with custom links
1960 will receive a <a href="webServices/urllinks.html#warning">warning
1961 dialog</a> asking them to update their preferences.
1964 <!-- JAL-2287-->Cancel button and escape listener on
1965 dialog warning user about disconnecting Jalview from a
1969 <!-- JAL-2320-->Jalview's Chimera control window closes if
1970 the Chimera it is connected to is shut down
1973 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1974 columns menu item to mark columns containing highlighted
1975 regions (e.g. from structure selections or results of a
1979 <!-- JAL-2284-->Command line option for batch-generation
1980 of HTML pages rendering alignment data with the BioJS
1990 <!-- JAL-2286 -->Columns with more than one modal residue
1991 are not coloured or thresholded according to percent
1992 identity (first observed in Jalview 2.8.2)
1995 <!-- JAL-2301 -->Threonine incorrectly reported as not
1999 <!-- JAL-2318 -->Updates to documentation pages (above PID
2000 threshold, amino acid properties)
2003 <!-- JAL-2292 -->Lower case residues in sequences are not
2004 reported as mapped to residues in a structure file in the
2008 <!--JAL-2324 -->Identical features with non-numeric scores
2009 could be added multiple times to a sequence
2012 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2013 bond features shown as two highlighted residues rather
2014 than a range in linked structure views, and treated
2015 correctly when selecting and computing trees from features
2018 <!-- JAL-2281-->Custom URL links for database
2019 cross-references are matched to database name regardless
2024 <em>Application</em>
2027 <!-- JAL-2282-->Custom URL links for specific database
2028 names without regular expressions also offer links from
2032 <!-- JAL-2315-->Removing a single configured link in the
2033 URL links pane in Connections preferences doesn't actually
2034 update Jalview configuration
2037 <!-- JAL-2272-->CTRL-Click on a selected region to open
2038 the alignment area popup menu doesn't work on El-Capitan
2041 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2042 files with similarly named sequences if dropped onto the
2046 <!-- JAL-2312 -->Additional mappings are shown for PDB
2047 entries where more chains exist in the PDB accession than
2048 are reported in the SIFTS file
2051 <!-- JAL-2317-->Certain structures do not get mapped to
2052 the structure view when displayed with Chimera
2055 <!-- JAL-2317-->No chains shown in the Chimera view
2056 panel's View->Show Chains submenu
2059 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2060 work for wrapped alignment views
2063 <!--JAL-2197 -->Rename UI components for running JPred
2064 predictions from 'JNet' to 'JPred'
2067 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2068 corrupted when annotation panel vertical scroll is not at
2069 first annotation row
2072 <!--JAL-2332 -->Attempting to view structure for Hen
2073 lysozyme results in a PDB Client error dialog box
2076 <!-- JAL-2319 -->Structure View's mapping report switched
2077 ranges for PDB and sequence for SIFTS
2080 SIFTS 'Not_Observed' residues mapped to non-existant
2084 <!-- <em>New Known Issues</em>
2091 <td width="60" nowrap>
2092 <div align="center">
2093 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2094 <em>25/10/2016</em></strong>
2097 <td><em>Application</em>
2099 <li>3D Structure chooser opens with 'Cached structures'
2100 view if structures already loaded</li>
2101 <li>Progress bar reports models as they are loaded to
2102 structure views</li>
2108 <li>Colour by conservation always enabled and no tick
2109 shown in menu when BLOSUM or PID shading applied</li>
2110 <li>FER1_ARATH and FER2_ARATH labels were switched in
2111 example sequences/projects/trees</li>
2113 <em>Application</em>
2115 <li>Jalview projects with views of local PDB structure
2116 files saved on Windows cannot be opened on OSX</li>
2117 <li>Multiple structure views can be opened and superposed
2118 without timeout for structures with multiple models or
2119 multiple sequences in alignment</li>
2120 <li>Cannot import or associated local PDB files without a
2121 PDB ID HEADER line</li>
2122 <li>RMSD is not output in Jmol console when superposition
2124 <li>Drag and drop of URL from Browser fails for Linux and
2125 OSX versions earlier than El Capitan</li>
2126 <li>ENA client ignores invalid content from ENA server</li>
2127 <li>Exceptions are not raised in console when ENA client
2128 attempts to fetch non-existent IDs via Fetch DB Refs UI
2130 <li>Exceptions are not raised in console when a new view
2131 is created on the alignment</li>
2132 <li>OSX right-click fixed for group selections: CMD-click
2133 to insert/remove gaps in groups and CTRL-click to open group
2136 <em>Build and deployment</em>
2138 <li>URL link checker now copes with multi-line anchor
2141 <em>New Known Issues</em>
2143 <li>Drag and drop from URL links in browsers do not work
2150 <td width="60" nowrap>
2151 <div align="center">
2152 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2155 <td><em>General</em>
2158 <!-- JAL-2124 -->Updated Spanish translations.
2161 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2162 for importing structure data to Jalview. Enables mmCIF and
2166 <!-- JAL-192 --->Alignment ruler shows positions relative to
2170 <!-- JAL-2202 -->Position/residue shown in status bar when
2171 mousing over sequence associated annotation
2174 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2178 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2179 '()', canonical '[]' and invalid '{}' base pair populations
2183 <!-- JAL-2092 -->Feature settings popup menu options for
2184 showing or hiding columns containing a feature
2187 <!-- JAL-1557 -->Edit selected group by double clicking on
2188 group and sequence associated annotation labels
2191 <!-- JAL-2236 -->Sequence name added to annotation label in
2192 select/hide columns by annotation and colour by annotation
2196 </ul> <em>Application</em>
2199 <!-- JAL-2050-->Automatically hide introns when opening a
2200 gene/transcript view
2203 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2207 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2208 structure mappings with the EMBL-EBI PDBe SIFTS database
2211 <!-- JAL-2079 -->Updated download sites used for Rfam and
2212 Pfam sources to xfam.org
2215 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2218 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2219 over sequences in Jalview
2222 <!-- JAL-2027-->Support for reverse-complement coding
2223 regions in ENA and EMBL
2226 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2227 for record retrieval via ENA rest API
2230 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2234 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2235 groovy script execution
2238 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2239 alignment window's Calculate menu
2242 <!-- JAL-1812 -->Allow groovy scripts that call
2243 Jalview.getAlignFrames() to run in headless mode
2246 <!-- JAL-2068 -->Support for creating new alignment
2247 calculation workers from groovy scripts
2250 <!-- JAL-1369 --->Store/restore reference sequence in
2254 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2255 associations are now saved/restored from project
2258 <!-- JAL-1993 -->Database selection dialog always shown
2259 before sequence fetcher is opened
2262 <!-- JAL-2183 -->Double click on an entry in Jalview's
2263 database chooser opens a sequence fetcher
2266 <!-- JAL-1563 -->Free-text search client for UniProt using
2267 the UniProt REST API
2270 <!-- JAL-2168 -->-nonews command line parameter to prevent
2271 the news reader opening
2274 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2275 querying stored in preferences
2278 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2282 <!-- JAL-1977-->Tooltips shown on database chooser
2285 <!-- JAL-391 -->Reverse complement function in calculate
2286 menu for nucleotide sequences
2289 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2290 and feature counts preserves alignment ordering (and
2291 debugged for complex feature sets).
2294 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2295 viewing structures with Jalview 2.10
2298 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2299 genome, transcript CCDS and gene ids via the Ensembl and
2300 Ensembl Genomes REST API
2303 <!-- JAL-2049 -->Protein sequence variant annotation
2304 computed for 'sequence_variant' annotation on CDS regions
2308 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2312 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2313 Ref Fetcher fails to match, or otherwise updates sequence
2314 data from external database records.
2317 <!-- JAL-2154 -->Revised Jalview Project format for
2318 efficient recovery of sequence coding and alignment
2319 annotation relationships.
2321 </ul> <!-- <em>Applet</em>
2332 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2336 <!-- JAL-2018-->Export features in Jalview format (again)
2337 includes graduated colourschemes
2340 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2341 working with big alignments and lots of hidden columns
2344 <!-- JAL-2053-->Hidden column markers not always rendered
2345 at right of alignment window
2348 <!-- JAL-2067 -->Tidied up links in help file table of
2352 <!-- JAL-2072 -->Feature based tree calculation not shown
2356 <!-- JAL-2075 -->Hidden columns ignored during feature
2357 based tree calculation
2360 <!-- JAL-2065 -->Alignment view stops updating when show
2361 unconserved enabled for group on alignment
2364 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2368 <!-- JAL-2146 -->Alignment column in status incorrectly
2369 shown as "Sequence position" when mousing over
2373 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2374 hidden columns present
2377 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2378 user created annotation added to alignment
2381 <!-- JAL-1841 -->RNA Structure consensus only computed for
2382 '()' base pair annotation
2385 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2386 in zero scores for all base pairs in RNA Structure
2390 <!-- JAL-2174-->Extend selection with columns containing
2394 <!-- JAL-2275 -->Pfam format writer puts extra space at
2395 beginning of sequence
2398 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2402 <!-- JAL-2238 -->Cannot create groups on an alignment from
2403 from a tree when t-coffee scores are shown
2406 <!-- JAL-1836,1967 -->Cannot import and view PDB
2407 structures with chains containing negative resnums (4q4h)
2410 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2414 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2415 to Clustal, PIR and PileUp output
2418 <!-- JAL-2008 -->Reordering sequence features that are
2419 not visible causes alignment window to repaint
2422 <!-- JAL-2006 -->Threshold sliders don't work in
2423 graduated colour and colour by annotation row for e-value
2424 scores associated with features and annotation rows
2427 <!-- JAL-1797 -->amino acid physicochemical conservation
2428 calculation should be case independent
2431 <!-- JAL-2173 -->Remove annotation also updates hidden
2435 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2436 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2437 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2440 <!-- JAL-2065 -->Null pointer exceptions and redraw
2441 problems when reference sequence defined and 'show
2442 non-conserved' enabled
2445 <!-- JAL-1306 -->Quality and Conservation are now shown on
2446 load even when Consensus calculation is disabled
2449 <!-- JAL-1932 -->Remove right on penultimate column of
2450 alignment does nothing
2453 <em>Application</em>
2456 <!-- JAL-1552-->URLs and links can't be imported by
2457 drag'n'drop on OSX when launched via webstart (note - not
2458 yet fixed for El Capitan)
2461 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2462 output when running on non-gb/us i18n platforms
2465 <!-- JAL-1944 -->Error thrown when exporting a view with
2466 hidden sequences as flat-file alignment
2469 <!-- JAL-2030-->InstallAnywhere distribution fails when
2473 <!-- JAL-2080-->Jalview very slow to launch via webstart
2474 (also hotfix for 2.9.0b2)
2477 <!-- JAL-2085 -->Cannot save project when view has a
2478 reference sequence defined
2481 <!-- JAL-1011 -->Columns are suddenly selected in other
2482 alignments and views when revealing hidden columns
2485 <!-- JAL-1989 -->Hide columns not mirrored in complement
2486 view in a cDNA/Protein splitframe
2489 <!-- JAL-1369 -->Cannot save/restore representative
2490 sequence from project when only one sequence is
2494 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2495 in Structure Chooser
2498 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2499 structure consensus didn't refresh annotation panel
2502 <!-- JAL-1962 -->View mapping in structure view shows
2503 mappings between sequence and all chains in a PDB file
2506 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2507 dialogs format columns correctly, don't display array
2508 data, sort columns according to type
2511 <!-- JAL-1975 -->Export complete shown after destination
2512 file chooser is cancelled during an image export
2515 <!-- JAL-2025 -->Error when querying PDB Service with
2516 sequence name containing special characters
2519 <!-- JAL-2024 -->Manual PDB structure querying should be
2523 <!-- JAL-2104 -->Large tooltips with broken HTML
2524 formatting don't wrap
2527 <!-- JAL-1128 -->Figures exported from wrapped view are
2528 truncated so L looks like I in consensus annotation
2531 <!-- JAL-2003 -->Export features should only export the
2532 currently displayed features for the current selection or
2536 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2537 after fetching cross-references, and restoring from
2541 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2542 followed in the structure viewer
2545 <!-- JAL-2163 -->Titles for individual alignments in
2546 splitframe not restored from project
2549 <!-- JAL-2145 -->missing autocalculated annotation at
2550 trailing end of protein alignment in transcript/product
2551 splitview when pad-gaps not enabled by default
2554 <!-- JAL-1797 -->amino acid physicochemical conservation
2558 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2559 article has been read (reopened issue due to
2560 internationalisation problems)
2563 <!-- JAL-1960 -->Only offer PDB structures in structure
2564 viewer based on sequence name, PDB and UniProt
2569 <!-- JAL-1976 -->No progress bar shown during export of
2573 <!-- JAL-2213 -->Structures not always superimposed after
2574 multiple structures are shown for one or more sequences.
2577 <!-- JAL-1370 -->Reference sequence characters should not
2578 be replaced with '.' when 'Show unconserved' format option
2582 <!-- JAL-1823 -->Cannot specify chain code when entering
2583 specific PDB id for sequence
2586 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2587 'Export hidden sequences' is enabled, but 'export hidden
2588 columns' is disabled.
2591 <!--JAL-2026-->Best Quality option in structure chooser
2592 selects lowest rather than highest resolution structures
2596 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2597 to sequence mapping in 'View Mappings' report
2600 <!-- JAL-2284 -->Unable to read old Jalview projects that
2601 contain non-XML data added after Jalvew wrote project.
2604 <!-- JAL-2118 -->Newly created annotation row reorders
2605 after clicking on it to create new annotation for a
2609 <!-- JAL-1980 -->Null Pointer Exception raised when
2610 pressing Add on an orphaned cut'n'paste window.
2612 <!-- may exclude, this is an external service stability issue JAL-1941
2613 -- > RNA 3D structure not added via DSSR service</li> -->
2618 <!-- JAL-2151 -->Incorrect columns are selected when
2619 hidden columns present before start of sequence
2622 <!-- JAL-1986 -->Missing dependencies on applet pages
2626 <!-- JAL-1947 -->Overview pixel size changes when
2627 sequences are hidden in applet
2630 <!-- JAL-1996 -->Updated instructions for applet
2631 deployment on examples pages.
2638 <td width="60" nowrap>
2639 <div align="center">
2640 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2641 <em>16/10/2015</em></strong>
2644 <td><em>General</em>
2646 <li>Time stamps for signed Jalview application and applet
2651 <em>Application</em>
2653 <li>Duplicate group consensus and conservation rows
2654 shown when tree is partitioned</li>
2655 <li>Erratic behaviour when tree partitions made with
2656 multiple cDNA/Protein split views</li>
2662 <td width="60" nowrap>
2663 <div align="center">
2664 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2665 <em>8/10/2015</em></strong>
2668 <td><em>General</em>
2670 <li>Updated Spanish translations of localized text for
2672 </ul> <em>Application</em>
2674 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2675 <li>Signed OSX InstallAnywhere installer<br></li>
2676 <li>Support for per-sequence based annotations in BioJSON</li>
2677 </ul> <em>Applet</em>
2679 <li>Split frame example added to applet examples page</li>
2680 </ul> <em>Build and Deployment</em>
2683 <!-- JAL-1888 -->New ant target for running Jalview's test
2691 <li>Mapping of cDNA to protein in split frames
2692 incorrect when sequence start > 1</li>
2693 <li>Broken images in filter column by annotation dialog
2695 <li>Feature colours not parsed from features file</li>
2696 <li>Exceptions and incomplete link URLs recovered when
2697 loading a features file containing HTML tags in feature
2701 <em>Application</em>
2703 <li>Annotations corrupted after BioJS export and
2705 <li>Incorrect sequence limits after Fetch DB References
2706 with 'trim retrieved sequences'</li>
2707 <li>Incorrect warning about deleting all data when
2708 deleting selected columns</li>
2709 <li>Patch to build system for shipping properly signed
2710 JNLP templates for webstart launch</li>
2711 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2712 unreleased structures for download or viewing</li>
2713 <li>Tab/space/return keystroke operation of EMBL-PDBe
2714 fetcher/viewer dialogs works correctly</li>
2715 <li>Disabled 'minimise' button on Jalview windows
2716 running on OSX to workaround redraw hang bug</li>
2717 <li>Split cDNA/Protein view position and geometry not
2718 recovered from jalview project</li>
2719 <li>Initial enabled/disabled state of annotation menu
2720 sorter 'show autocalculated first/last' corresponds to
2722 <li>Restoring of Clustal, RNA Helices and T-Coffee
2723 color schemes from BioJSON</li>
2727 <li>Reorder sequences mirrored in cDNA/Protein split
2729 <li>Applet with Jmol examples not loading correctly</li>
2735 <td><div align="center">
2736 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2738 <td><em>General</em>
2740 <li>Linked visualisation and analysis of DNA and Protein
2743 <li>Translated cDNA alignments shown as split protein
2744 and DNA alignment views</li>
2745 <li>Codon consensus annotation for linked protein and
2746 cDNA alignment views</li>
2747 <li>Link cDNA or Protein product sequences by loading
2748 them onto Protein or cDNA alignments</li>
2749 <li>Reconstruct linked cDNA alignment from aligned
2750 protein sequences</li>
2753 <li>Jmol integration updated to Jmol v14.2.14</li>
2754 <li>Import and export of Jalview alignment views as <a
2755 href="features/bioJsonFormat.html">BioJSON</a></li>
2756 <li>New alignment annotation file statements for
2757 reference sequences and marking hidden columns</li>
2758 <li>Reference sequence based alignment shading to
2759 highlight variation</li>
2760 <li>Select or hide columns according to alignment
2762 <li>Find option for locating sequences by description</li>
2763 <li>Conserved physicochemical properties shown in amino
2764 acid conservation row</li>
2765 <li>Alignments can be sorted by number of RNA helices</li>
2766 </ul> <em>Application</em>
2768 <li>New cDNA/Protein analysis capabilities
2770 <li>Get Cross-References should open a Split Frame
2771 view with cDNA/Protein</li>
2772 <li>Detect when nucleotide sequences and protein
2773 sequences are placed in the same alignment</li>
2774 <li>Split cDNA/Protein views are saved in Jalview
2779 <li>Use REST API to talk to Chimera</li>
2780 <li>Selected regions in Chimera are highlighted in linked
2781 Jalview windows</li>
2783 <li>VARNA RNA viewer updated to v3.93</li>
2784 <li>VARNA views are saved in Jalview Projects</li>
2785 <li>Pseudoknots displayed as Jalview RNA annotation can
2786 be shown in VARNA</li>
2788 <li>Make groups for selection uses marked columns as well
2789 as the active selected region</li>
2791 <li>Calculate UPGMA and NJ trees using sequence feature
2793 <li>New Export options
2795 <li>New Export Settings dialog to control hidden
2796 region export in flat file generation</li>
2798 <li>Export alignment views for display with the <a
2799 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2801 <li>Export scrollable SVG in HTML page</li>
2802 <li>Optional embedding of BioJSON data when exporting
2803 alignment figures to HTML</li>
2805 <li>3D structure retrieval and display
2807 <li>Free text and structured queries with the PDBe
2809 <li>PDBe Search API based discovery and selection of
2810 PDB structures for a sequence set</li>
2814 <li>JPred4 employed for protein secondary structure
2816 <li>Hide Insertions menu option to hide unaligned columns
2817 for one or a group of sequences</li>
2818 <li>Automatically hide insertions in alignments imported
2819 from the JPred4 web server</li>
2820 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2821 system on OSX<br />LGPL libraries courtesy of <a
2822 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2824 <li>changed 'View nucleotide structure' submenu to 'View
2825 VARNA 2D Structure'</li>
2826 <li>change "View protein structure" menu option to "3D
2829 </ul> <em>Applet</em>
2831 <li>New layout for applet example pages</li>
2832 <li>New parameters to enable SplitFrame view
2833 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2834 <li>New example demonstrating linked viewing of cDNA and
2835 Protein alignments</li>
2836 </ul> <em>Development and deployment</em>
2838 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2839 <li>Include installation type and git revision in build
2840 properties and console log output</li>
2841 <li>Jalview Github organisation, and new github site for
2842 storing BioJsMSA Templates</li>
2843 <li>Jalview's unit tests now managed with TestNG</li>
2846 <!-- <em>General</em>
2848 </ul> --> <!-- issues resolved --> <em>Application</em>
2850 <li>Escape should close any open find dialogs</li>
2851 <li>Typo in select-by-features status report</li>
2852 <li>Consensus RNA secondary secondary structure
2853 predictions are not highlighted in amber</li>
2854 <li>Missing gap character in v2.7 example file means
2855 alignment appears unaligned when pad-gaps is not enabled</li>
2856 <li>First switch to RNA Helices colouring doesn't colour
2857 associated structure views</li>
2858 <li>ID width preference option is greyed out when auto
2859 width checkbox not enabled</li>
2860 <li>Stopped a warning dialog from being shown when
2861 creating user defined colours</li>
2862 <li>'View Mapping' in structure viewer shows sequence
2863 mappings for just that viewer's sequences</li>
2864 <li>Workaround for superposing PDB files containing
2865 multiple models in Chimera</li>
2866 <li>Report sequence position in status bar when hovering
2867 over Jmol structure</li>
2868 <li>Cannot output gaps as '.' symbols with Selection ->
2869 output to text box</li>
2870 <li>Flat file exports of alignments with hidden columns
2871 have incorrect sequence start/end</li>
2872 <li>'Aligning' a second chain to a Chimera structure from
2874 <li>Colour schemes applied to structure viewers don't
2875 work for nucleotide</li>
2876 <li>Loading/cut'n'pasting an empty or invalid file leads
2877 to a grey/invisible alignment window</li>
2878 <li>Exported Jpred annotation from a sequence region
2879 imports to different position</li>
2880 <li>Space at beginning of sequence feature tooltips shown
2881 on some platforms</li>
2882 <li>Chimera viewer 'View | Show Chain' menu is not
2884 <li>'New View' fails with a Null Pointer Exception in
2885 console if Chimera has been opened</li>
2886 <li>Mouseover to Chimera not working</li>
2887 <li>Miscellaneous ENA XML feature qualifiers not
2889 <li>NPE in annotation renderer after 'Extract Scores'</li>
2890 <li>If two structures in one Chimera window, mouseover of
2891 either sequence shows on first structure</li>
2892 <li>'Show annotations' options should not make
2893 non-positional annotations visible</li>
2894 <li>Subsequence secondary structure annotation not shown
2895 in right place after 'view flanking regions'</li>
2896 <li>File Save As type unset when current file format is
2898 <li>Save as '.jar' option removed for saving Jalview
2900 <li>Colour by Sequence colouring in Chimera more
2902 <li>Cannot 'add reference annotation' for a sequence in
2903 several views on same alignment</li>
2904 <li>Cannot show linked products for EMBL / ENA records</li>
2905 <li>Jalview's tooltip wraps long texts containing no
2907 </ul> <em>Applet</em>
2909 <li>Jmol to JalviewLite mouseover/link not working</li>
2910 <li>JalviewLite can't import sequences with ID
2911 descriptions containing angle brackets</li>
2912 </ul> <em>General</em>
2914 <li>Cannot export and reimport RNA secondary structure
2915 via jalview annotation file</li>
2916 <li>Random helix colour palette for colour by annotation
2917 with RNA secondary structure</li>
2918 <li>Mouseover to cDNA from STOP residue in protein
2919 translation doesn't work.</li>
2920 <li>hints when using the select by annotation dialog box</li>
2921 <li>Jmol alignment incorrect if PDB file has alternate CA
2923 <li>FontChooser message dialog appears to hang after
2924 choosing 1pt font</li>
2925 <li>Peptide secondary structure incorrectly imported from
2926 annotation file when annotation display text includes 'e' or
2928 <li>Cannot set colour of new feature type whilst creating
2930 <li>cDNA translation alignment should not be sequence
2931 order dependent</li>
2932 <li>'Show unconserved' doesn't work for lower case
2934 <li>Nucleotide ambiguity codes involving R not recognised</li>
2935 </ul> <em>Deployment and Documentation</em>
2937 <li>Applet example pages appear different to the rest of
2938 www.jalview.org</li>
2939 </ul> <em>Application Known issues</em>
2941 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2942 <li>Misleading message appears after trying to delete
2944 <li>Jalview icon not shown in dock after InstallAnywhere
2945 version launches</li>
2946 <li>Fetching EMBL reference for an RNA sequence results
2947 fails with a sequence mismatch</li>
2948 <li>Corrupted or unreadable alignment display when
2949 scrolling alignment to right</li>
2950 <li>ArrayIndexOutOfBoundsException thrown when remove
2951 empty columns called on alignment with ragged gapped ends</li>
2952 <li>auto calculated alignment annotation rows do not get
2953 placed above or below non-autocalculated rows</li>
2954 <li>Jalview dekstop becomes sluggish at full screen in
2955 ultra-high resolution</li>
2956 <li>Cannot disable consensus calculation independently of
2957 quality and conservation</li>
2958 <li>Mouseover highlighting between cDNA and protein can
2959 become sluggish with more than one splitframe shown</li>
2960 </ul> <em>Applet Known Issues</em>
2962 <li>Core PDB parsing code requires Jmol</li>
2963 <li>Sequence canvas panel goes white when alignment
2964 window is being resized</li>
2970 <td><div align="center">
2971 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2973 <td><em>General</em>
2975 <li>Updated Java code signing certificate donated by
2977 <li>Features and annotation preserved when performing
2978 pairwise alignment</li>
2979 <li>RNA pseudoknot annotation can be
2980 imported/exported/displayed</li>
2981 <li>'colour by annotation' can colour by RNA and
2982 protein secondary structure</li>
2983 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2984 post-hoc with 2.9 release</em>)
2987 </ul> <em>Application</em>
2989 <li>Extract and display secondary structure for sequences
2990 with 3D structures</li>
2991 <li>Support for parsing RNAML</li>
2992 <li>Annotations menu for layout
2994 <li>sort sequence annotation rows by alignment</li>
2995 <li>place sequence annotation above/below alignment
2998 <li>Output in Stockholm format</li>
2999 <li>Internationalisation: improved Spanish (es)
3001 <li>Structure viewer preferences tab</li>
3002 <li>Disorder and Secondary Structure annotation tracks
3003 shared between alignments</li>
3004 <li>UCSF Chimera launch and linked highlighting from
3006 <li>Show/hide all sequence associated annotation rows for
3007 all or current selection</li>
3008 <li>disorder and secondary structure predictions
3009 available as dataset annotation</li>
3010 <li>Per-sequence rna helices colouring</li>
3013 <li>Sequence database accessions imported when fetching
3014 alignments from Rfam</li>
3015 <li>update VARNA version to 3.91</li>
3017 <li>New groovy scripts for exporting aligned positions,
3018 conservation values, and calculating sum of pairs scores.</li>
3019 <li>Command line argument to set default JABAWS server</li>
3020 <li>include installation type in build properties and
3021 console log output</li>
3022 <li>Updated Jalview project format to preserve dataset
3026 <!-- issues resolved --> <em>Application</em>
3028 <li>Distinguish alignment and sequence associated RNA
3029 structure in structure->view->VARNA</li>
3030 <li>Raise dialog box if user deletes all sequences in an
3032 <li>Pressing F1 results in documentation opening twice</li>
3033 <li>Sequence feature tooltip is wrapped</li>
3034 <li>Double click on sequence associated annotation
3035 selects only first column</li>
3036 <li>Redundancy removal doesn't result in unlinked
3037 leaves shown in tree</li>
3038 <li>Undos after several redundancy removals don't undo
3040 <li>Hide sequence doesn't hide associated annotation</li>
3041 <li>User defined colours dialog box too big to fit on
3042 screen and buttons not visible</li>
3043 <li>author list isn't updated if already written to
3044 Jalview properties</li>
3045 <li>Popup menu won't open after retrieving sequence
3047 <li>File open window for associate PDB doesn't open</li>
3048 <li>Left-then-right click on a sequence id opens a
3049 browser search window</li>
3050 <li>Cannot open sequence feature shading/sort popup menu
3051 in feature settings dialog</li>
3052 <li>better tooltip placement for some areas of Jalview
3054 <li>Allow addition of JABAWS Server which doesn't
3055 pass validation</li>
3056 <li>Web services parameters dialog box is too large to
3058 <li>Muscle nucleotide alignment preset obscured by
3060 <li>JABAWS preset submenus don't contain newly
3061 defined user preset</li>
3062 <li>MSA web services warns user if they were launched
3063 with invalid input</li>
3064 <li>Jalview cannot contact DAS Registy when running on
3067 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3068 'Superpose with' submenu not shown when new view
3072 </ul> <!-- <em>Applet</em>
3074 </ul> <em>General</em>
3076 </ul>--> <em>Deployment and Documentation</em>
3078 <li>2G and 1G options in launchApp have no effect on
3079 memory allocation</li>
3080 <li>launchApp service doesn't automatically open
3081 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3083 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3084 InstallAnywhere reports cannot find valid JVM when Java
3085 1.7_055 is available
3087 </ul> <em>Application Known issues</em>
3090 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3091 corrupted or unreadable alignment display when scrolling
3095 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3096 retrieval fails but progress bar continues for DAS retrieval
3097 with large number of ID
3100 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3101 flatfile output of visible region has incorrect sequence
3105 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3106 rna structure consensus doesn't update when secondary
3107 structure tracks are rearranged
3110 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3111 invalid rna structure positional highlighting does not
3112 highlight position of invalid base pairs
3115 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3116 out of memory errors are not raised when saving Jalview
3117 project from alignment window file menu
3120 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3121 Switching to RNA Helices colouring doesn't propagate to
3125 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3126 colour by RNA Helices not enabled when user created
3127 annotation added to alignment
3130 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3131 Jalview icon not shown on dock in Mountain Lion/Webstart
3133 </ul> <em>Applet Known Issues</em>
3136 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3137 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3140 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3141 Jalview and Jmol example not compatible with IE9
3144 <li>Sort by annotation score doesn't reverse order
3150 <td><div align="center">
3151 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3154 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3157 <li>Internationalisation of user interface (usually
3158 called i18n support) and translation for Spanish locale</li>
3159 <li>Define/Undefine group on current selection with
3160 Ctrl-G/Shift Ctrl-G</li>
3161 <li>Improved group creation/removal options in
3162 alignment/sequence Popup menu</li>
3163 <li>Sensible precision for symbol distribution
3164 percentages shown in logo tooltip.</li>
3165 <li>Annotation panel height set according to amount of
3166 annotation when alignment first opened</li>
3167 </ul> <em>Application</em>
3169 <li>Interactive consensus RNA secondary structure
3170 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3171 <li>Select columns containing particular features from
3172 Feature Settings dialog</li>
3173 <li>View all 'representative' PDB structures for selected
3175 <li>Update Jalview project format:
3177 <li>New file extension for Jalview projects '.jvp'</li>
3178 <li>Preserve sequence and annotation dataset (to
3179 store secondary structure annotation,etc)</li>
3180 <li>Per group and alignment annotation and RNA helix
3184 <li>New similarity measures for PCA and Tree calculation
3186 <li>Experimental support for retrieval and viewing of
3187 flanking regions for an alignment</li>
3191 <!-- issues resolved --> <em>Application</em>
3193 <li>logo keeps spinning and status remains at queued or
3194 running after job is cancelled</li>
3195 <li>cannot export features from alignments imported from
3196 Jalview/VAMSAS projects</li>
3197 <li>Buggy slider for web service parameters that take
3199 <li>Newly created RNA secondary structure line doesn't
3200 have 'display all symbols' flag set</li>
3201 <li>T-COFFEE alignment score shading scheme and other
3202 annotation shading not saved in Jalview project</li>
3203 <li>Local file cannot be loaded in freshly downloaded
3205 <li>Jalview icon not shown on dock in Mountain
3207 <li>Load file from desktop file browser fails</li>
3208 <li>Occasional NPE thrown when calculating large trees</li>
3209 <li>Cannot reorder or slide sequences after dragging an
3210 alignment onto desktop</li>
3211 <li>Colour by annotation dialog throws NPE after using
3212 'extract scores' function</li>
3213 <li>Loading/cut'n'pasting an empty file leads to a grey
3214 alignment window</li>
3215 <li>Disorder thresholds rendered incorrectly after
3216 performing IUPred disorder prediction</li>
3217 <li>Multiple group annotated consensus rows shown when
3218 changing 'normalise logo' display setting</li>
3219 <li>Find shows blank dialog after 'finished searching' if
3220 nothing matches query</li>
3221 <li>Null Pointer Exceptions raised when sorting by
3222 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3224 <li>Errors in Jmol console when structures in alignment
3225 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3227 <li>Not all working JABAWS services are shown in
3229 <li>JAVAWS version of Jalview fails to launch with
3230 'invalid literal/length code'</li>
3231 <li>Annotation/RNA Helix colourschemes cannot be applied
3232 to alignment with groups (actually fixed in 2.8.0b1)</li>
3233 <li>RNA Helices and T-Coffee Scores available as default
3236 </ul> <em>Applet</em>
3238 <li>Remove group option is shown even when selection is
3240 <li>Apply to all groups ticked but colourscheme changes
3241 don't affect groups</li>
3242 <li>Documented RNA Helices and T-Coffee Scores as valid
3243 colourscheme name</li>
3244 <li>Annotation labels drawn on sequence IDs when
3245 Annotation panel is not displayed</li>
3246 <li>Increased font size for dropdown menus on OSX and
3247 embedded windows</li>
3248 </ul> <em>Other</em>
3250 <li>Consensus sequence for alignments/groups with a
3251 single sequence were not calculated</li>
3252 <li>annotation files that contain only groups imported as
3253 annotation and junk sequences</li>
3254 <li>Fasta files with sequences containing '*' incorrectly
3255 recognised as PFAM or BLC</li>
3256 <li>conservation/PID slider apply all groups option
3257 doesn't affect background (2.8.0b1)
3259 <li>redundancy highlighting is erratic at 0% and 100%</li>
3260 <li>Remove gapped columns fails for sequences with ragged
3262 <li>AMSA annotation row with leading spaces is not
3263 registered correctly on import</li>
3264 <li>Jalview crashes when selecting PCA analysis for
3265 certain alignments</li>
3266 <li>Opening the colour by annotation dialog for an
3267 existing annotation based 'use original colours'
3268 colourscheme loses original colours setting</li>
3273 <td><div align="center">
3274 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3275 <em>30/1/2014</em></strong>
3279 <li>Trusted certificates for JalviewLite applet and
3280 Jalview Desktop application<br />Certificate was donated by
3281 <a href="https://www.certum.eu">Certum</a> to the Jalview
3282 open source project).
3284 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3285 <li>Output in Stockholm format</li>
3286 <li>Allow import of data from gzipped files</li>
3287 <li>Export/import group and sequence associated line
3288 graph thresholds</li>
3289 <li>Nucleotide substitution matrix that supports RNA and
3290 ambiguity codes</li>
3291 <li>Allow disorder predictions to be made on the current
3292 selection (or visible selection) in the same way that JPred
3294 <li>Groovy scripting for headless Jalview operation</li>
3295 </ul> <em>Other improvements</em>
3297 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3298 <li>COMBINE statement uses current SEQUENCE_REF and
3299 GROUP_REF scope to group annotation rows</li>
3300 <li>Support '' style escaping of quotes in Newick
3302 <li>Group options for JABAWS service by command line name</li>
3303 <li>Empty tooltip shown for JABA service options with a
3304 link but no description</li>
3305 <li>Select primary source when selecting authority in
3306 database fetcher GUI</li>
3307 <li>Add .mfa to FASTA file extensions recognised by
3309 <li>Annotation label tooltip text wrap</li>
3314 <li>Slow scrolling when lots of annotation rows are
3316 <li>Lots of NPE (and slowness) after creating RNA
3317 secondary structure annotation line</li>
3318 <li>Sequence database accessions not imported when
3319 fetching alignments from Rfam</li>
3320 <li>Incorrect SHMR submission for sequences with
3322 <li>View all structures does not always superpose
3324 <li>Option widgets in service parameters not updated to
3325 reflect user or preset settings</li>
3326 <li>Null pointer exceptions for some services without
3327 presets or adjustable parameters</li>
3328 <li>Discover PDB IDs entry in structure menu doesn't
3329 discover PDB xRefs</li>
3330 <li>Exception encountered while trying to retrieve
3331 features with DAS</li>
3332 <li>Lowest value in annotation row isn't coloured
3333 when colour by annotation (per sequence) is coloured</li>
3334 <li>Keyboard mode P jumps to start of gapped region when
3335 residue follows a gap</li>
3336 <li>Jalview appears to hang importing an alignment with
3337 Wrap as default or after enabling Wrap</li>
3338 <li>'Right click to add annotations' message
3339 shown in wrap mode when no annotations present</li>
3340 <li>Disorder predictions fail with NPE if no automatic
3341 annotation already exists on alignment</li>
3342 <li>oninit javascript function should be called after
3343 initialisation completes</li>
3344 <li>Remove redundancy after disorder prediction corrupts
3345 alignment window display</li>
3346 <li>Example annotation file in documentation is invalid</li>
3347 <li>Grouped line graph annotation rows are not exported
3348 to annotation file</li>
3349 <li>Multi-harmony analysis cannot be run when only two
3351 <li>Cannot create multiple groups of line graphs with
3352 several 'combine' statements in annotation file</li>
3353 <li>Pressing return several times causes Number Format
3354 exceptions in keyboard mode</li>
3355 <li>Multi-harmony (SHMMR) method doesn't submit
3356 correct partitions for input data</li>
3357 <li>Translation from DNA to Amino Acids fails</li>
3358 <li>Jalview fail to load newick tree with quoted label</li>
3359 <li>--headless flag isn't understood</li>
3360 <li>ClassCastException when generating EPS in headless
3362 <li>Adjusting sequence-associated shading threshold only
3363 changes one row's threshold</li>
3364 <li>Preferences and Feature settings panel panel
3365 doesn't open</li>
3366 <li>hide consensus histogram also hides conservation and
3367 quality histograms</li>
3372 <td><div align="center">
3373 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3375 <td><em>Application</em>
3377 <li>Support for JABAWS 2.0 Services (AACon alignment
3378 conservation, protein disorder and Clustal Omega)</li>
3379 <li>JABAWS server status indicator in Web Services
3381 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3382 in Jalview alignment window</li>
3383 <li>Updated Jalview build and deploy framework for OSX
3384 mountain lion, windows 7, and 8</li>
3385 <li>Nucleotide substitution matrix for PCA that supports
3386 RNA and ambiguity codes</li>
3388 <li>Improved sequence database retrieval GUI</li>
3389 <li>Support fetching and database reference look up
3390 against multiple DAS sources (Fetch all from in 'fetch db
3392 <li>Jalview project improvements
3394 <li>Store and retrieve the 'belowAlignment'
3395 flag for annotation</li>
3396 <li>calcId attribute to group annotation rows on the
3398 <li>Store AACon calculation settings for a view in
3399 Jalview project</li>
3403 <li>horizontal scrolling gesture support</li>
3404 <li>Visual progress indicator when PCA calculation is
3406 <li>Simpler JABA web services menus</li>
3407 <li>visual indication that web service results are still
3408 being retrieved from server</li>
3409 <li>Serialise the dialogs that are shown when Jalview
3410 starts up for first time</li>
3411 <li>Jalview user agent string for interacting with HTTP
3413 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3415 <li>Examples directory and Groovy library included in
3416 InstallAnywhere distribution</li>
3417 </ul> <em>Applet</em>
3419 <li>RNA alignment and secondary structure annotation
3420 visualization applet example</li>
3421 </ul> <em>General</em>
3423 <li>Normalise option for consensus sequence logo</li>
3424 <li>Reset button in PCA window to return dimensions to
3426 <li>Allow seqspace or Jalview variant of alignment PCA
3428 <li>PCA with either nucleic acid and protein substitution
3430 <li>Allow windows containing HTML reports to be exported
3432 <li>Interactive display and editing of RNA secondary
3433 structure contacts</li>
3434 <li>RNA Helix Alignment Colouring</li>
3435 <li>RNA base pair logo consensus</li>
3436 <li>Parse sequence associated secondary structure
3437 information in Stockholm files</li>
3438 <li>HTML Export database accessions and annotation
3439 information presented in tooltip for sequences</li>
3440 <li>Import secondary structure from LOCARNA clustalw
3441 style RNA alignment files</li>
3442 <li>import and visualise T-COFFEE quality scores for an
3444 <li>'colour by annotation' per sequence option to
3445 shade each sequence according to its associated alignment
3447 <li>New Jalview Logo</li>
3448 </ul> <em>Documentation and Development</em>
3450 <li>documentation for score matrices used in Jalview</li>
3451 <li>New Website!</li>
3453 <td><em>Application</em>
3455 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3456 wsdbfetch REST service</li>
3457 <li>Stop windows being moved outside desktop on OSX</li>
3458 <li>Filetype associations not installed for webstart
3460 <li>Jalview does not always retrieve progress of a JABAWS
3461 job execution in full once it is complete</li>
3462 <li>revise SHMR RSBS definition to ensure alignment is
3463 uploaded via ali_file parameter</li>
3464 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3465 <li>View all structures superposed fails with exception</li>
3466 <li>Jnet job queues forever if a very short sequence is
3467 submitted for prediction</li>
3468 <li>Cut and paste menu not opened when mouse clicked on
3470 <li>Putting fractional value into integer text box in
3471 alignment parameter dialog causes Jalview to hang</li>
3472 <li>Structure view highlighting doesn't work on
3474 <li>View all structures fails with exception shown in
3476 <li>Characters in filename associated with PDBEntry not
3477 escaped in a platform independent way</li>
3478 <li>Jalview desktop fails to launch with exception when
3480 <li>Tree calculation reports 'you must have 2 or more
3481 sequences selected' when selection is empty</li>
3482 <li>Jalview desktop fails to launch with jar signature
3483 failure when java web start temporary file caching is
3485 <li>DAS Sequence retrieval with range qualification
3486 results in sequence xref which includes range qualification</li>
3487 <li>Errors during processing of command line arguments
3488 cause progress bar (JAL-898) to be removed</li>
3489 <li>Replace comma for semi-colon option not disabled for
3490 DAS sources in sequence fetcher</li>
3491 <li>Cannot close news reader when JABAWS server warning
3492 dialog is shown</li>
3493 <li>Option widgets not updated to reflect user settings</li>
3494 <li>Edited sequence not submitted to web service</li>
3495 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3496 <li>InstallAnywhere installer doesn't unpack and run
3497 on OSX Mountain Lion</li>
3498 <li>Annotation panel not given a scroll bar when
3499 sequences with alignment annotation are pasted into the
3501 <li>Sequence associated annotation rows not associated
3502 when loaded from Jalview project</li>
3503 <li>Browser launch fails with NPE on java 1.7</li>
3504 <li>JABAWS alignment marked as finished when job was
3505 cancelled or job failed due to invalid input</li>
3506 <li>NPE with v2.7 example when clicking on Tree
3507 associated with all views</li>
3508 <li>Exceptions when copy/paste sequences with grouped
3509 annotation rows to new window</li>
3510 </ul> <em>Applet</em>
3512 <li>Sequence features are momentarily displayed before
3513 they are hidden using hidefeaturegroups applet parameter</li>
3514 <li>loading features via javascript API automatically
3515 enables feature display</li>
3516 <li>scrollToColumnIn javascript API method doesn't
3518 </ul> <em>General</em>
3520 <li>Redundancy removal fails for rna alignment</li>
3521 <li>PCA calculation fails when sequence has been selected
3522 and then deselected</li>
3523 <li>PCA window shows grey box when first opened on OSX</li>
3524 <li>Letters coloured pink in sequence logo when alignment
3525 coloured with clustalx</li>
3526 <li>Choosing fonts without letter symbols defined causes
3527 exceptions and redraw errors</li>
3528 <li>Initial PCA plot view is not same as manually
3529 reconfigured view</li>
3530 <li>Grouped annotation graph label has incorrect line
3532 <li>Grouped annotation graph label display is corrupted
3533 for lots of labels</li>
3538 <div align="center">
3539 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3542 <td><em>Application</em>
3544 <li>Jalview Desktop News Reader</li>
3545 <li>Tweaked default layout of web services menu</li>
3546 <li>View/alignment association menu to enable user to
3547 easily specify which alignment a multi-structure view takes
3548 its colours/correspondences from</li>
3549 <li>Allow properties file location to be specified as URL</li>
3550 <li>Extend Jalview project to preserve associations
3551 between many alignment views and a single Jmol display</li>
3552 <li>Store annotation row height in Jalview project file</li>
3553 <li>Annotation row column label formatting attributes
3554 stored in project file</li>
3555 <li>Annotation row order for auto-calculated annotation
3556 rows preserved in Jalview project file</li>
3557 <li>Visual progress indication when Jalview state is
3558 saved using Desktop window menu</li>
3559 <li>Visual indication that command line arguments are
3560 still being processed</li>
3561 <li>Groovy script execution from URL</li>
3562 <li>Colour by annotation default min and max colours in
3564 <li>Automatically associate PDB files dragged onto an
3565 alignment with sequences that have high similarity and
3567 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3568 <li>'view structures' option to open many
3569 structures in same window</li>
3570 <li>Sort associated views menu option for tree panel</li>
3571 <li>Group all JABA and non-JABA services for a particular
3572 analysis function in its own submenu</li>
3573 </ul> <em>Applet</em>
3575 <li>Userdefined and autogenerated annotation rows for
3577 <li>Adjustment of alignment annotation pane height</li>
3578 <li>Annotation scrollbar for annotation panel</li>
3579 <li>Drag to reorder annotation rows in annotation panel</li>
3580 <li>'automaticScrolling' parameter</li>
3581 <li>Allow sequences with partial ID string matches to be
3582 annotated from GFF/Jalview features files</li>
3583 <li>Sequence logo annotation row in applet</li>
3584 <li>Absolute paths relative to host server in applet
3585 parameters are treated as such</li>
3586 <li>New in the JalviewLite javascript API:
3588 <li>JalviewLite.js javascript library</li>
3589 <li>Javascript callbacks for
3591 <li>Applet initialisation</li>
3592 <li>Sequence/alignment mouse-overs and selections</li>
3595 <li>scrollTo row and column alignment scrolling
3597 <li>Select sequence/alignment regions from javascript</li>
3598 <li>javascript structure viewer harness to pass
3599 messages between Jmol and Jalview when running as
3600 distinct applets</li>
3601 <li>sortBy method</li>
3602 <li>Set of applet and application examples shipped
3603 with documentation</li>
3604 <li>New example to demonstrate JalviewLite and Jmol
3605 javascript message exchange</li>
3607 </ul> <em>General</em>
3609 <li>Enable Jmol displays to be associated with multiple
3610 multiple alignments</li>
3611 <li>Option to automatically sort alignment with new tree</li>
3612 <li>User configurable link to enable redirects to a
3613 www.Jalview.org mirror</li>
3614 <li>Jmol colours option for Jmol displays</li>
3615 <li>Configurable newline string when writing alignment
3616 and other flat files</li>
3617 <li>Allow alignment annotation description lines to
3618 contain html tags</li>
3619 </ul> <em>Documentation and Development</em>
3621 <li>Add groovy test harness for bulk load testing to
3623 <li>Groovy script to load and align a set of sequences
3624 using a web service before displaying the result in the
3625 Jalview desktop</li>
3626 <li>Restructured javascript and applet api documentation</li>
3627 <li>Ant target to publish example html files with applet
3629 <li>Netbeans project for building Jalview from source</li>
3630 <li>ant task to create online javadoc for Jalview source</li>
3632 <td><em>Application</em>
3634 <li>User defined colourscheme throws exception when
3635 current built in colourscheme is saved as new scheme</li>
3636 <li>AlignFrame->Save in application pops up save
3637 dialog for valid filename/format</li>
3638 <li>Cannot view associated structure for UniProt sequence</li>
3639 <li>PDB file association breaks for UniProt sequence
3641 <li>Associate PDB from file dialog does not tell you
3642 which sequence is to be associated with the file</li>
3643 <li>Find All raises null pointer exception when query
3644 only matches sequence IDs</li>
3645 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3646 <li>Jalview project with Jmol views created with Jalview
3647 2.4 cannot be loaded</li>
3648 <li>Filetype associations not installed for webstart
3650 <li>Two or more chains in a single PDB file associated
3651 with sequences in different alignments do not get coloured
3652 by their associated sequence</li>
3653 <li>Visibility status of autocalculated annotation row
3654 not preserved when project is loaded</li>
3655 <li>Annotation row height and visibility attributes not
3656 stored in Jalview project</li>
3657 <li>Tree bootstraps are not preserved when saved as a
3658 Jalview project</li>
3659 <li>Envision2 workflow tooltips are corrupted</li>
3660 <li>Enabling show group conservation also enables colour
3661 by conservation</li>
3662 <li>Duplicate group associated conservation or consensus
3663 created on new view</li>
3664 <li>Annotation scrollbar not displayed after 'show
3665 all hidden annotation rows' option selected</li>
3666 <li>Alignment quality not updated after alignment
3667 annotation row is hidden then shown</li>
3668 <li>Preserve colouring of structures coloured by
3669 sequences in pre Jalview 2.7 projects</li>
3670 <li>Web service job parameter dialog is not laid out
3672 <li>Web services menu not refreshed after 'reset
3673 services' button is pressed in preferences</li>
3674 <li>Annotation off by one in Jalview v2_3 example project</li>
3675 <li>Structures imported from file and saved in project
3676 get name like jalview_pdb1234.txt when reloaded</li>
3677 <li>Jalview does not always retrieve progress of a JABAWS
3678 job execution in full once it is complete</li>
3679 </ul> <em>Applet</em>
3681 <li>Alignment height set incorrectly when lots of
3682 annotation rows are displayed</li>
3683 <li>Relative URLs in feature HTML text not resolved to
3685 <li>View follows highlighting does not work for positions
3687 <li><= shown as = in tooltip</li>
3688 <li>Export features raises exception when no features
3690 <li>Separator string used for serialising lists of IDs
3691 for javascript api is modified when separator string
3692 provided as parameter</li>
3693 <li>Null pointer exception when selecting tree leaves for
3694 alignment with no existing selection</li>
3695 <li>Relative URLs for datasources assumed to be relative
3696 to applet's codebase</li>
3697 <li>Status bar not updated after finished searching and
3698 search wraps around to first result</li>
3699 <li>StructureSelectionManager instance shared between
3700 several Jalview applets causes race conditions and memory
3702 <li>Hover tooltip and mouseover of position on structure
3703 not sent from Jmol in applet</li>
3704 <li>Certain sequences of javascript method calls to
3705 applet API fatally hang browser</li>
3706 </ul> <em>General</em>
3708 <li>View follows structure mouseover scrolls beyond
3709 position with wrapped view and hidden regions</li>
3710 <li>Find sequence position moves to wrong residue
3711 with/without hidden columns</li>
3712 <li>Sequence length given in alignment properties window
3714 <li>InvalidNumberFormat exceptions thrown when trying to
3715 import PDB like structure files</li>
3716 <li>Positional search results are only highlighted
3717 between user-supplied sequence start/end bounds</li>
3718 <li>End attribute of sequence is not validated</li>
3719 <li>Find dialog only finds first sequence containing a
3720 given sequence position</li>
3721 <li>Sequence numbering not preserved in MSF alignment
3723 <li>Jalview PDB file reader does not extract sequence
3724 from nucleotide chains correctly</li>
3725 <li>Structure colours not updated when tree partition
3726 changed in alignment</li>
3727 <li>Sequence associated secondary structure not correctly
3728 parsed in interleaved stockholm</li>
3729 <li>Colour by annotation dialog does not restore current
3731 <li>Hiding (nearly) all sequences doesn't work
3733 <li>Sequences containing lowercase letters are not
3734 properly associated with their pdb files</li>
3735 </ul> <em>Documentation and Development</em>
3737 <li>schemas/JalviewWsParamSet.xsd corrupted by
3738 ApplyCopyright tool</li>
3743 <div align="center">
3744 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3747 <td><em>Application</em>
3749 <li>New warning dialog when the Jalview Desktop cannot
3750 contact web services</li>
3751 <li>JABA service parameters for a preset are shown in
3752 service job window</li>
3753 <li>JABA Service menu entries reworded</li>
3757 <li>Modeller PIR IO broken - cannot correctly import a
3758 pir file emitted by Jalview</li>
3759 <li>Existing feature settings transferred to new
3760 alignment view created from cut'n'paste</li>
3761 <li>Improved test for mixed amino/nucleotide chains when
3762 parsing PDB files</li>
3763 <li>Consensus and conservation annotation rows
3764 occasionally become blank for all new windows</li>
3765 <li>Exception raised when right clicking above sequences
3766 in wrapped view mode</li>
3767 </ul> <em>Application</em>
3769 <li>multiple multiply aligned structure views cause cpu
3770 usage to hit 100% and computer to hang</li>
3771 <li>Web Service parameter layout breaks for long user
3772 parameter names</li>
3773 <li>Jaba service discovery hangs desktop if Jaba server
3780 <div align="center">
3781 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3784 <td><em>Application</em>
3786 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3787 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3790 <li>Web Services preference tab</li>
3791 <li>Analysis parameters dialog box and user defined
3793 <li>Improved speed and layout of Envision2 service menu</li>
3794 <li>Superpose structures using associated sequence
3796 <li>Export coordinates and projection as CSV from PCA
3798 </ul> <em>Applet</em>
3800 <li>enable javascript: execution by the applet via the
3801 link out mechanism</li>
3802 </ul> <em>Other</em>
3804 <li>Updated the Jmol Jalview interface to work with Jmol
3806 <li>The Jalview Desktop and JalviewLite applet now
3807 require Java 1.5</li>
3808 <li>Allow Jalview feature colour specification for GFF
3809 sequence annotation files</li>
3810 <li>New 'colour by label' keword in Jalview feature file
3811 type colour specification</li>
3812 <li>New Jalview Desktop Groovy API method that allows a
3813 script to check if it being run in an interactive session or
3814 in a batch operation from the Jalview command line</li>
3818 <li>clustalx colourscheme colours Ds preferentially when
3819 both D+E are present in over 50% of the column</li>
3820 </ul> <em>Application</em>
3822 <li>typo in AlignmentFrame->View->Hide->all but
3823 selected Regions menu item</li>
3824 <li>sequence fetcher replaces ',' for ';' when the ',' is
3825 part of a valid accession ID</li>
3826 <li>fatal OOM if object retrieved by sequence fetcher
3827 runs out of memory</li>
3828 <li>unhandled Out of Memory Error when viewing pca
3829 analysis results</li>
3830 <li>InstallAnywhere builds fail to launch on OS X java
3831 10.5 update 4 (due to apple Java 1.6 update)</li>
3832 <li>Installanywhere Jalview silently fails to launch</li>
3833 </ul> <em>Applet</em>
3835 <li>Jalview.getFeatureGroups() raises an
3836 ArrayIndexOutOfBoundsException if no feature groups are
3843 <div align="center">
3844 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3850 <li>Alignment prettyprinter doesn't cope with long
3852 <li>clustalx colourscheme colours Ds preferentially when
3853 both D+E are present in over 50% of the column</li>
3854 <li>nucleic acid structures retrieved from PDB do not
3855 import correctly</li>
3856 <li>More columns get selected than were clicked on when a
3857 number of columns are hidden</li>
3858 <li>annotation label popup menu not providing correct
3859 add/hide/show options when rows are hidden or none are
3861 <li>Stockholm format shown in list of readable formats,
3862 and parser copes better with alignments from RFAM.</li>
3863 <li>CSV output of consensus only includes the percentage
3864 of all symbols if sequence logo display is enabled</li>
3866 </ul> <em>Applet</em>
3868 <li>annotation panel disappears when annotation is
3870 </ul> <em>Application</em>
3872 <li>Alignment view not redrawn properly when new
3873 alignment opened where annotation panel is visible but no
3874 annotations are present on alignment</li>
3875 <li>pasted region containing hidden columns is
3876 incorrectly displayed in new alignment window</li>
3877 <li>Jalview slow to complete operations when stdout is
3878 flooded (fix is to close the Jalview console)</li>
3879 <li>typo in AlignmentFrame->View->Hide->all but
3880 selected Rregions menu item.</li>
3881 <li>inconsistent group submenu and Format submenu entry
3882 'Un' or 'Non'conserved</li>
3883 <li>Sequence feature settings are being shared by
3884 multiple distinct alignments</li>
3885 <li>group annotation not recreated when tree partition is
3887 <li>double click on group annotation to select sequences
3888 does not propagate to associated trees</li>
3889 <li>Mac OSX specific issues:
3891 <li>exception raised when mouse clicked on desktop
3892 window background</li>
3893 <li>Desktop menu placed on menu bar and application
3894 name set correctly</li>
3895 <li>sequence feature settings not wide enough for the
3896 save feature colourscheme button</li>
3905 <div align="center">
3906 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3909 <td><em>New Capabilities</em>
3911 <li>URL links generated from description line for
3912 regular-expression based URL links (applet and application)
3914 <li>Non-positional feature URL links are shown in link
3916 <li>Linked viewing of nucleic acid sequences and
3918 <li>Automatic Scrolling option in View menu to display
3919 the currently highlighted region of an alignment.</li>
3920 <li>Order an alignment by sequence length, or using the
3921 average score or total feature count for each sequence.</li>
3922 <li>Shading features by score or associated description</li>
3923 <li>Subdivide alignment and groups based on identity of
3924 selected subsequence (Make Groups from Selection).</li>
3925 <li>New hide/show options including Shift+Control+H to
3926 hide everything but the currently selected region.</li>
3927 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3928 </ul> <em>Application</em>
3930 <li>Fetch DB References capabilities and UI expanded to
3931 support retrieval from DAS sequence sources</li>
3932 <li>Local DAS Sequence sources can be added via the
3933 command line or via the Add local source dialog box.</li>
3934 <li>DAS Dbref and DbxRef feature types are parsed as
3935 database references and protein_name is parsed as
3936 description line (BioSapiens terms).</li>
3937 <li>Enable or disable non-positional feature and database
3938 references in sequence ID tooltip from View menu in
3940 <!-- <li>New hidden columns and rows and representatives capabilities
3941 in annotations file (in progress - not yet fully implemented)</li> -->
3942 <li>Group-associated consensus, sequence logos and
3943 conservation plots</li>
3944 <li>Symbol distributions for each column can be exported
3945 and visualized as sequence logos</li>
3946 <li>Optionally scale multi-character column labels to fit
3947 within each column of annotation row<!-- todo for applet -->
3949 <li>Optional automatic sort of associated alignment view
3950 when a new tree is opened.</li>
3951 <li>Jalview Java Console</li>
3952 <li>Better placement of desktop window when moving
3953 between different screens.</li>
3954 <li>New preference items for sequence ID tooltip and
3955 consensus annotation</li>
3956 <li>Client to submit sequences and IDs to Envision2
3958 <li><em>Vamsas Capabilities</em>
3960 <li>Improved VAMSAS synchronization (Jalview archive
3961 used to preserve views, structures, and tree display
3963 <li>Import of vamsas documents from disk or URL via
3965 <li>Sharing of selected regions between views and
3966 with other VAMSAS applications (Experimental feature!)</li>
3967 <li>Updated API to VAMSAS version 0.2</li>
3969 </ul> <em>Applet</em>
3971 <li>Middle button resizes annotation row height</li>
3974 <li>sortByTree (true/false) - automatically sort the
3975 associated alignment view by the tree when a new tree is
3977 <li>showTreeBootstraps (true/false) - show or hide
3978 branch bootstraps (default is to show them if available)</li>
3979 <li>showTreeDistances (true/false) - show or hide
3980 branch lengths (default is to show them if available)</li>
3981 <li>showUnlinkedTreeNodes (true/false) - indicate if
3982 unassociated nodes should be highlighted in the tree
3984 <li>heightScale and widthScale (1.0 or more) -
3985 increase the height or width of a cell in the alignment
3986 grid relative to the current font size.</li>
3989 <li>Non-positional features displayed in sequence ID
3991 </ul> <em>Other</em>
3993 <li>Features format: graduated colour definitions and
3994 specification of feature scores</li>
3995 <li>Alignment Annotations format: new keywords for group
3996 associated annotation (GROUP_REF) and annotation row display
3997 properties (ROW_PROPERTIES)</li>
3998 <li>XML formats extended to support graduated feature
3999 colourschemes, group associated annotation, and profile
4000 visualization settings.</li></td>
4003 <li>Source field in GFF files parsed as feature source
4004 rather than description</li>
4005 <li>Non-positional features are now included in sequence
4006 feature and gff files (controlled via non-positional feature
4007 visibility in tooltip).</li>
4008 <li>URL links generated for all feature links (bugfix)</li>
4009 <li>Added URL embedding instructions to features file
4011 <li>Codons containing ambiguous nucleotides translated as
4012 'X' in peptide product</li>
4013 <li>Match case switch in find dialog box works for both
4014 sequence ID and sequence string and query strings do not
4015 have to be in upper case to match case-insensitively.</li>
4016 <li>AMSA files only contain first column of
4017 multi-character column annotation labels</li>
4018 <li>Jalview Annotation File generation/parsing consistent
4019 with documentation (e.g. Stockholm annotation can be
4020 exported and re-imported)</li>
4021 <li>PDB files without embedded PDB IDs given a friendly
4023 <li>Find incrementally searches ID string matches as well
4024 as subsequence matches, and correctly reports total number
4028 <li>Better handling of exceptions during sequence
4030 <li>Dasobert generated non-positional feature URL
4031 link text excludes the start_end suffix</li>
4032 <li>DAS feature and source retrieval buttons disabled
4033 when fetch or registry operations in progress.</li>
4034 <li>PDB files retrieved from URLs are cached properly</li>
4035 <li>Sequence description lines properly shared via
4037 <li>Sequence fetcher fetches multiple records for all
4039 <li>Ensured that command line das feature retrieval
4040 completes before alignment figures are generated.</li>
4041 <li>Reduced time taken when opening file browser for
4043 <li>isAligned check prior to calculating tree, PCA or
4044 submitting an MSA to JNet now excludes hidden sequences.</li>
4045 <li>User defined group colours properly recovered
4046 from Jalview projects.</li>
4055 <div align="center">
4056 <strong>2.4.0.b2</strong><br> 28/10/2009
4061 <li>Experimental support for google analytics usage
4063 <li>Jalview privacy settings (user preferences and docs).</li>
4068 <li>Race condition in applet preventing startup in
4070 <li>Exception when feature created from selection beyond
4071 length of sequence.</li>
4072 <li>Allow synthetic PDB files to be imported gracefully</li>
4073 <li>Sequence associated annotation rows associate with
4074 all sequences with a given id</li>
4075 <li>Find function matches case-insensitively for sequence
4076 ID string searches</li>
4077 <li>Non-standard characters do not cause pairwise
4078 alignment to fail with exception</li>
4079 </ul> <em>Application Issues</em>
4081 <li>Sequences are now validated against EMBL database</li>
4082 <li>Sequence fetcher fetches multiple records for all
4084 </ul> <em>InstallAnywhere Issues</em>
4086 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4087 issue with installAnywhere mechanism)</li>
4088 <li>Command line launching of JARs from InstallAnywhere
4089 version (java class versioning error fixed)</li>
4096 <div align="center">
4097 <strong>2.4</strong><br> 27/8/2008
4100 <td><em>User Interface</em>
4102 <li>Linked highlighting of codon and amino acid from
4103 translation and protein products</li>
4104 <li>Linked highlighting of structure associated with
4105 residue mapping to codon position</li>
4106 <li>Sequence Fetcher provides example accession numbers
4107 and 'clear' button</li>
4108 <li>MemoryMonitor added as an option under Desktop's
4110 <li>Extract score function to parse whitespace separated
4111 numeric data in description line</li>
4112 <li>Column labels in alignment annotation can be centred.</li>
4113 <li>Tooltip for sequence associated annotation give name
4115 </ul> <em>Web Services and URL fetching</em>
4117 <li>JPred3 web service</li>
4118 <li>Prototype sequence search client (no public services
4120 <li>Fetch either seed alignment or full alignment from
4122 <li>URL Links created for matching database cross
4123 references as well as sequence ID</li>
4124 <li>URL Links can be created using regular-expressions</li>
4125 </ul> <em>Sequence Database Connectivity</em>
4127 <li>Retrieval of cross-referenced sequences from other
4129 <li>Generalised database reference retrieval and
4130 validation to all fetchable databases</li>
4131 <li>Fetch sequences from DAS sources supporting the
4132 sequence command</li>
4133 </ul> <em>Import and Export</em>
4134 <li>export annotation rows as CSV for spreadsheet import</li>
4135 <li>Jalview projects record alignment dataset associations,
4136 EMBL products, and cDNA sequence mappings</li>
4137 <li>Sequence Group colour can be specified in Annotation
4139 <li>Ad-hoc colouring of group in Annotation File using RGB
4140 triplet as name of colourscheme</li>
4141 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4143 <li>treenode binding for VAMSAS tree exchange</li>
4144 <li>local editing and update of sequences in VAMSAS
4145 alignments (experimental)</li>
4146 <li>Create new or select existing session to join</li>
4147 <li>load and save of vamsas documents</li>
4148 </ul> <em>Application command line</em>
4150 <li>-tree parameter to open trees (introduced for passing
4152 <li>-fetchfrom command line argument to specify nicknames
4153 of DAS servers to query for alignment features</li>
4154 <li>-dasserver command line argument to add new servers
4155 that are also automatically queried for features</li>
4156 <li>-groovy command line argument executes a given groovy
4157 script after all input data has been loaded and parsed</li>
4158 </ul> <em>Applet-Application data exchange</em>
4160 <li>Trees passed as applet parameters can be passed to
4161 application (when using "View in full
4162 application")</li>
4163 </ul> <em>Applet Parameters</em>
4165 <li>feature group display control parameter</li>
4166 <li>debug parameter</li>
4167 <li>showbutton parameter</li>
4168 </ul> <em>Applet API methods</em>
4170 <li>newView public method</li>
4171 <li>Window (current view) specific get/set public methods</li>
4172 <li>Feature display control methods</li>
4173 <li>get list of currently selected sequences</li>
4174 </ul> <em>New Jalview distribution features</em>
4176 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4177 <li>RELEASE file gives build properties for the latest
4178 Jalview release.</li>
4179 <li>Java 1.1 Applet build made easier and donotobfuscate
4180 property controls execution of obfuscator</li>
4181 <li>Build target for generating source distribution</li>
4182 <li>Debug flag for javacc</li>
4183 <li>.jalview_properties file is documented (slightly) in
4184 jalview.bin.Cache</li>
4185 <li>Continuous Build Integration for stable and
4186 development version of Application, Applet and source
4191 <li>selected region output includes visible annotations
4192 (for certain formats)</li>
4193 <li>edit label/displaychar contains existing label/char
4195 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4196 <li>shorter peptide product names from EMBL records</li>
4197 <li>Newick string generator makes compact representations</li>
4198 <li>bootstrap values parsed correctly for tree files with
4200 <li>pathological filechooser bug avoided by not allowing
4201 filenames containing a ':'</li>
4202 <li>Fixed exception when parsing GFF files containing
4203 global sequence features</li>
4204 <li>Alignment datasets are finalized only when number of
4205 references from alignment sequences goes to zero</li>
4206 <li>Close of tree branch colour box without colour
4207 selection causes cascading exceptions</li>
4208 <li>occasional negative imgwidth exceptions</li>
4209 <li>better reporting of non-fatal warnings to user when
4210 file parsing fails.</li>
4211 <li>Save works when Jalview project is default format</li>
4212 <li>Save as dialog opened if current alignment format is
4213 not a valid output format</li>
4214 <li>UniProt canonical names introduced for both das and
4216 <li>Histidine should be midblue (not pink!) in Zappo</li>
4217 <li>error messages passed up and output when data read
4219 <li>edit undo recovers previous dataset sequence when
4220 sequence is edited</li>
4221 <li>allow PDB files without pdb ID HEADER lines (like
4222 those generated by MODELLER) to be read in properly</li>
4223 <li>allow reading of JPred concise files as a normal
4225 <li>Stockholm annotation parsing and alignment properties
4226 import fixed for PFAM records</li>
4227 <li>Structure view windows have correct name in Desktop
4229 <li>annotation consisting of sequence associated scores
4230 can be read and written correctly to annotation file</li>
4231 <li>Aligned cDNA translation to aligned peptide works
4233 <li>Fixed display of hidden sequence markers and
4234 non-italic font for representatives in Applet</li>
4235 <li>Applet Menus are always embedded in applet window on
4237 <li>Newly shown features appear at top of stack (in
4239 <li>Annotations added via parameter not drawn properly
4240 due to null pointer exceptions</li>
4241 <li>Secondary structure lines are drawn starting from
4242 first column of alignment</li>
4243 <li>UniProt XML import updated for new schema release in
4245 <li>Sequence feature to sequence ID match for Features
4246 file is case-insensitive</li>
4247 <li>Sequence features read from Features file appended to
4248 all sequences with matching IDs</li>
4249 <li>PDB structure coloured correctly for associated views
4250 containing a sub-sequence</li>
4251 <li>PDB files can be retrieved by applet from Jar files</li>
4252 <li>feature and annotation file applet parameters
4253 referring to different directories are retrieved correctly</li>
4254 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4255 <li>Fixed application hang whilst waiting for
4256 splash-screen version check to complete</li>
4257 <li>Applet properly URLencodes input parameter values
4258 when passing them to the launchApp service</li>
4259 <li>display name and local features preserved in results
4260 retrieved from web service</li>
4261 <li>Visual delay indication for sequence retrieval and
4262 sequence fetcher initialisation</li>
4263 <li>updated Application to use DAS 1.53e version of
4264 dasobert DAS client</li>
4265 <li>Re-instated Full AMSA support and .amsa file
4267 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4275 <div align="center">
4276 <strong>2.3</strong><br> 9/5/07
4281 <li>Jmol 11.0.2 integration</li>
4282 <li>PDB views stored in Jalview XML files</li>
4283 <li>Slide sequences</li>
4284 <li>Edit sequence in place</li>
4285 <li>EMBL CDS features</li>
4286 <li>DAS Feature mapping</li>
4287 <li>Feature ordering</li>
4288 <li>Alignment Properties</li>
4289 <li>Annotation Scores</li>
4290 <li>Sort by scores</li>
4291 <li>Feature/annotation editing in applet</li>
4296 <li>Headless state operation in 2.2.1</li>
4297 <li>Incorrect and unstable DNA pairwise alignment</li>
4298 <li>Cut and paste of sequences with annotation</li>
4299 <li>Feature group display state in XML</li>
4300 <li>Feature ordering in XML</li>
4301 <li>blc file iteration selection using filename # suffix</li>
4302 <li>Stockholm alignment properties</li>
4303 <li>Stockhom alignment secondary structure annotation</li>
4304 <li>2.2.1 applet had no feature transparency</li>
4305 <li>Number pad keys can be used in cursor mode</li>
4306 <li>Structure Viewer mirror image resolved</li>
4313 <div align="center">
4314 <strong>2.2.1</strong><br> 12/2/07
4319 <li>Non standard characters can be read and displayed
4320 <li>Annotations/Features can be imported/exported to the
4322 <li>Applet allows editing of sequence/annotation/group
4323 name & description
4324 <li>Preference setting to display sequence name in
4326 <li>Annotation file format extended to allow
4327 Sequence_groups to be defined
4328 <li>Default opening of alignment overview panel can be
4329 specified in preferences
4330 <li>PDB residue numbering annotation added to associated
4336 <li>Applet crash under certain Linux OS with Java 1.6
4338 <li>Annotation file export / import bugs fixed
4339 <li>PNG / EPS image output bugs fixed
4345 <div align="center">
4346 <strong>2.2</strong><br> 27/11/06
4351 <li>Multiple views on alignment
4352 <li>Sequence feature editing
4353 <li>"Reload" alignment
4354 <li>"Save" to current filename
4355 <li>Background dependent text colour
4356 <li>Right align sequence ids
4357 <li>User-defined lower case residue colours
4360 <li>Menu item accelerator keys
4361 <li>Control-V pastes to current alignment
4362 <li>Cancel button for DAS Feature Fetching
4363 <li>PCA and PDB Viewers zoom via mouse roller
4364 <li>User-defined sub-tree colours and sub-tree selection
4366 <li>'New Window' button on the 'Output to Text box'
4371 <li>New memory efficient Undo/Redo System
4372 <li>Optimised symbol lookups and conservation/consensus
4374 <li>Region Conservation/Consensus recalculated after
4376 <li>Fixed Remove Empty Columns Bug (empty columns at end
4378 <li>Slowed DAS Feature Fetching for increased robustness.
4380 <li>Made angle brackets in ASCII feature descriptions
4382 <li>Re-instated Zoom function for PCA
4383 <li>Sequence descriptions conserved in web service
4385 <li>UniProt ID discoverer uses any word separated by
4387 <li>WsDbFetch query/result association resolved
4388 <li>Tree leaf to sequence mapping improved
4389 <li>Smooth fonts switch moved to FontChooser dialog box.
4396 <div align="center">
4397 <strong>2.1.1</strong><br> 12/9/06
4402 <li>Copy consensus sequence to clipboard</li>
4407 <li>Image output - rightmost residues are rendered if
4408 sequence id panel has been resized</li>
4409 <li>Image output - all offscreen group boundaries are
4411 <li>Annotation files with sequence references - all
4412 elements in file are relative to sequence position</li>
4413 <li>Mac Applet users can use Alt key for group editing</li>
4419 <div align="center">
4420 <strong>2.1</strong><br> 22/8/06
4425 <li>MAFFT Multiple Alignment in default Web Service list</li>
4426 <li>DAS Feature fetching</li>
4427 <li>Hide sequences and columns</li>
4428 <li>Export Annotations and Features</li>
4429 <li>GFF file reading / writing</li>
4430 <li>Associate structures with sequences from local PDB
4432 <li>Add sequences to exisiting alignment</li>
4433 <li>Recently opened files / URL lists</li>
4434 <li>Applet can launch the full application</li>
4435 <li>Applet has transparency for features (Java 1.2
4437 <li>Applet has user defined colours parameter</li>
4438 <li>Applet can load sequences from parameter
4439 "sequence<em>x</em>"
4445 <li>Redundancy Panel reinstalled in the Applet</li>
4446 <li>Monospaced font - EPS / rescaling bug fixed</li>
4447 <li>Annotation files with sequence references bug fixed</li>
4453 <div align="center">
4454 <strong>2.08.1</strong><br> 2/5/06
4459 <li>Change case of selected region from Popup menu</li>
4460 <li>Choose to match case when searching</li>
4461 <li>Middle mouse button and mouse movement can compress /
4462 expand the visible width and height of the alignment</li>
4467 <li>Annotation Panel displays complete JNet results</li>
4473 <div align="center">
4474 <strong>2.08b</strong><br> 18/4/06
4480 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4481 <li>Righthand label on wrapped alignments shows correct
4488 <div align="center">
4489 <strong>2.08</strong><br> 10/4/06
4494 <li>Editing can be locked to the selection area</li>
4495 <li>Keyboard editing</li>
4496 <li>Create sequence features from searches</li>
4497 <li>Precalculated annotations can be loaded onto
4499 <li>Features file allows grouping of features</li>
4500 <li>Annotation Colouring scheme added</li>
4501 <li>Smooth fonts off by default - Faster rendering</li>
4502 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4507 <li>Drag & Drop fixed on Linux</li>
4508 <li>Jalview Archive file faster to load/save, sequence
4509 descriptions saved.</li>
4515 <div align="center">
4516 <strong>2.07</strong><br> 12/12/05
4521 <li>PDB Structure Viewer enhanced</li>
4522 <li>Sequence Feature retrieval and display enhanced</li>
4523 <li>Choose to output sequence start-end after sequence
4524 name for file output</li>
4525 <li>Sequence Fetcher WSDBFetch@EBI</li>
4526 <li>Applet can read feature files, PDB files and can be
4527 used for HTML form input</li>
4532 <li>HTML output writes groups and features</li>
4533 <li>Group editing is Control and mouse click</li>
4534 <li>File IO bugs</li>
4540 <div align="center">
4541 <strong>2.06</strong><br> 28/9/05
4546 <li>View annotations in wrapped mode</li>
4547 <li>More options for PCA viewer</li>
4552 <li>GUI bugs resolved</li>
4553 <li>Runs with -nodisplay from command line</li>
4559 <div align="center">
4560 <strong>2.05b</strong><br> 15/9/05
4565 <li>Choose EPS export as lineart or text</li>
4566 <li>Jar files are executable</li>
4567 <li>Can read in Uracil - maps to unknown residue</li>
4572 <li>Known OutOfMemory errors give warning message</li>
4573 <li>Overview window calculated more efficiently</li>
4574 <li>Several GUI bugs resolved</li>
4580 <div align="center">
4581 <strong>2.05</strong><br> 30/8/05
4586 <li>Edit and annotate in "Wrapped" view</li>
4591 <li>Several GUI bugs resolved</li>
4597 <div align="center">
4598 <strong>2.04</strong><br> 24/8/05
4603 <li>Hold down mouse wheel & scroll to change font
4609 <li>Improved JPred client reliability</li>
4610 <li>Improved loading of Jalview files</li>
4616 <div align="center">
4617 <strong>2.03</strong><br> 18/8/05
4622 <li>Set Proxy server name and port in preferences</li>
4623 <li>Multiple URL links from sequence ids</li>
4624 <li>User Defined Colours can have a scheme name and added
4626 <li>Choose to ignore gaps in consensus calculation</li>
4627 <li>Unix users can set default web browser</li>
4628 <li>Runs without GUI for batch processing</li>
4629 <li>Dynamically generated Web Service Menus</li>
4634 <li>InstallAnywhere download for Sparc Solaris</li>
4640 <div align="center">
4641 <strong>2.02</strong><br> 18/7/05
4647 <li>Copy & Paste order of sequences maintains
4648 alignment order.</li>
4654 <div align="center">
4655 <strong>2.01</strong><br> 12/7/05
4660 <li>Use delete key for deleting selection.</li>
4661 <li>Use Mouse wheel to scroll sequences.</li>
4662 <li>Help file updated to describe how to add alignment
4664 <li>Version and build date written to build properties
4666 <li>InstallAnywhere installation will check for updates
4667 at launch of Jalview.</li>
4672 <li>Delete gaps bug fixed.</li>
4673 <li>FileChooser sorts columns.</li>
4674 <li>Can remove groups one by one.</li>
4675 <li>Filechooser icons installed.</li>
4676 <li>Finder ignores return character when searching.
4677 Return key will initiate a search.<br>
4684 <div align="center">
4685 <strong>2.0</strong><br> 20/6/05
4690 <li>New codebase</li>