3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
61 <em>16/2/2020</em></strong></td>
62 <td align="left" valign="top">
67 </ul> <em>Release processes</em>
70 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
72 </ul> <em>Build System</em>
75 <!-- JAL-3510 -->Clover updated to 4.4.1
78 <!-- JAL-3513 -->Test code included in Clover coverage
81 </ul> <em>Deprecations</em>
83 <td align="left" valign="top">
92 <!-- JAL-3386 -->Sequence IDs missing in headless export of
93 wrapped alignment figure with annotations
96 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
97 ID fails with ClassCastException
100 <!-- JAL-3389 -->Chimera session not restored from Jalview
104 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
105 feature settings dialog also selects columns
108 <!-- JAL-3473 -->SpinnerNumberModel causing
109 IllegalArgumentException in some circumstances
112 <!-- JAL-3406 -->Credits missing some authors in Jalview
113 help documentation for 2.11.0 release
115 </ul> <em>Java 11 Compatibility issues</em>
118 <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
120 </ul> <em>Repository and Source Release</em>
123 <!-- JAL-3474 -->removed redundant .gitignore files from
127 <em>New Known Issues</em>
130 <!-- JAL-3523 -->OSX - Current working directory not
131 preserved when Jalview.app launched with parameters from
135 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
136 clipped in headless figure export when Right Align option
143 <td width="60" align="center" nowrap>
144 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
145 <em>04/07/2019</em></strong>
147 <td align="left" valign="top">
150 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
151 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
152 source project) rather than InstallAnywhere
155 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
156 settings, receive over the air updates and launch specific
157 versions via (<a href="https://github.com/threerings/getdown">Three
161 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
162 formats supported by Jalview (including .jvp project files)
165 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
166 arguments and switch between different getdown channels
169 <!-- JAL-3141 -->Backup files created when saving Jalview project
174 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
175 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
177 <!-- JAL-2620 -->Alternative genetic code tables for
178 'Translate as cDNA'</li>
180 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
181 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
184 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
185 implementation that allows updates) used for Sequence Feature collections</li>
187 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
188 features can be filtered and shaded according to any
189 associated attributes (e.g. variant attributes from VCF
190 file, or key-value pairs imported from column 9 of GFF
194 <!-- JAL-2879 -->Feature Attributes and shading schemes
195 stored and restored from Jalview Projects
198 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
199 recognise variant features
202 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
203 sequences (also coloured red by default)
206 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
210 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
211 algorithm (Z-sort/transparency and filter aware)
214 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
220 <!-- JAL-3205 -->Symmetric score matrices for faster
221 tree and PCA calculations
223 <li><strong>Principal Components Analysis Viewer</strong>
226 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
227 and Viewer state saved in Jalview Project
229 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
232 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
236 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
241 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
243 <li><strong>Speed and Efficiency</strong>
246 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
247 multiple groups when working with large alignments
250 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
254 <li><strong>User Interface</strong>
257 <!-- JAL-2933 -->Finder panel remembers last position in each
261 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
262 what is shown)<br />Only visible regions of alignment are shown by
263 default (can be changed in user preferences)
266 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
267 to the Overwrite Dialog
270 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
274 <!-- JAL-1244 -->Status bar shows bounds when dragging a
275 selection region, and gap count when inserting or deleting gaps
278 <!-- JAL-3132 -->Status bar updates over sequence and annotation
282 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
286 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
290 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
293 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
297 <!-- JAL-3181 -->Consistent ordering of links in sequence id
301 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
303 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
307 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
308 <li><strong>Java 11 Support (not yet on general release)</strong>
311 <!-- -->OSX GUI integrations for App menu's 'About' entry and
316 <em>Deprecations</em>
318 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
319 capabilities removed from the Jalview Desktop
321 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
322 unmarshalling has been replaced by JAXB for Jalview projects
323 and XML based data retrieval clients</li>
324 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
325 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
326 </ul> <em>Documentation</em>
328 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
329 not supported in EPS figure export
331 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
332 </ul> <em>Development and Release Processes</em>
335 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
338 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
340 <!-- JAL-3225 -->Eclipse project configuration managed with
344 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
345 Bamboo continuous integration for unattended Test Suite
349 <!-- JAL-2864 -->Memory test suite to detect leaks in common
353 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
357 <!-- JAL-3248 -->Developer documentation migrated to
358 markdown (with HTML rendering)
361 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
364 <!-- JAL-3289 -->New URLs for publishing development
369 <td align="left" valign="top">
372 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
375 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
376 superposition in Jmol fail on Windows
379 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
380 structures for sequences with lots of PDB structures
383 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
387 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
388 project involving multiple views
391 <!-- JAL-3164 -->Overview for complementary view in a linked
392 CDS/Protein alignment is not updated when Hide Columns by
393 Annotation dialog hides columns
396 <!-- JAL-3158 -->Selection highlighting in the complement of a
397 CDS/Protein alignment stops working after making a selection in
398 one view, then making another selection in the other view
401 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
405 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
406 Settings and Jalview Preferences panels
409 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
410 overview with large alignments
413 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
414 region if columns were selected by dragging right-to-left and the
415 mouse moved to the left of the first column
418 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
419 hidden column marker via scale popup menu
422 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
423 doesn't tell users the invalid URL
426 <!-- JAL-2816 -->Tooltips displayed for features filtered by
430 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
431 show cross references or Fetch Database References are shown in
435 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
436 peptide sequence (computed variant shown as p.Res.null)
439 <!-- JAL-2060 -->'Graduated colour' option not offered for
440 manually created features (where feature score is Float.NaN)
443 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
444 when columns are hidden
447 <!-- JAL-3082 -->Regular expression error for '(' in Select
448 Columns by Annotation description
451 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
452 out of Scale or Annotation Panel
455 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
459 <!-- JAL-3074 -->Left/right drag in annotation can scroll
463 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
467 <!-- JAL-3002 -->Column display is out by one after Page Down,
468 Page Up in wrapped mode
471 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
474 <!-- JAL-2932 -->Finder searches in minimised alignments
477 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
478 on opening an alignment
481 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
485 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
486 different groups in the alignment are selected
489 <!-- JAL-2717 -->Internationalised colour scheme names not shown
493 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
497 <!-- JAL-3125 -->Value input for graduated feature colour
498 threshold gets 'unrounded'
501 <!-- JAL-2982 -->PCA image export doesn't respect background
505 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
508 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
511 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
515 <!-- JAL-2964 -->Associate Tree with All Views not restored from
519 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
520 shown in complementary view
523 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
524 without normalisation
527 <!-- JAL-3021 -->Sequence Details report should open positioned at top
531 <!-- JAL-914 -->Help page can be opened twice
534 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
536 </ul> <em>Editing</em>
539 <!-- JAL-2822 -->Start and End should be updated when sequence
540 data at beginning or end of alignment added/removed via 'Edit'
544 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
545 relocate sequence features correctly when start of sequence is
546 removed (Known defect since 2.10)
549 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
550 dialog corrupts dataset sequence
553 <!-- JAL-868 -->Structure colours not updated when associated tree
554 repartitions the alignment view (Regression in 2.10.5)
556 </ul> <em>Datamodel</em>
559 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
560 sequence's End is greater than its length
562 </ul> <em>Bugs fixed for Java 11 Support (not yet on
563 general release)</em>
566 <!-- JAL-3288 -->Menus work properly in split-screen
568 </ul> <em>New Known Defects</em>
571 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
574 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
575 regions of protein alignment.
578 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
579 is restored from a Jalview 2.11 project
582 <!-- JAL-3213 -->Alignment panel height can be too small after
586 <!-- JAL-3240 -->Display is incorrect after removing gapped
587 columns within hidden columns
590 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
591 window after dragging left to select columns to left of visible
595 <!-- JAL-2876 -->Features coloured according to their description
596 string and thresholded by score in earlier versions of Jalview are
597 not shown as thresholded features in 2.11. To workaround please
598 create a Score filter instead.
601 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
603 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
606 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
607 alignments with multiple views can close views unexpectedly
610 <em>Java 11 Specific defects</em>
613 <!-- JAL-3235 -->Jalview Properties file is not sorted
614 alphabetically when saved
620 <td width="60" nowrap>
622 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
625 <td><div align="left">
629 <!-- JAL-3101 -->Default memory for Jalview webstart and
630 InstallAnywhere increased to 1G.
633 <!-- JAL-247 -->Hidden sequence markers and representative
634 sequence bolding included when exporting alignment as EPS,
635 SVG, PNG or HTML. <em>Display is configured via the
636 Format menu, or for command-line use via a Jalview
637 properties file.</em>
640 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
641 API and sequence data now imported as JSON.
644 <!-- JAL-3065 -->Change in recommended way of starting
645 Jalview via a Java command line: add jars in lib directory
646 to CLASSPATH, rather than via the deprecated java.ext.dirs
653 <!-- JAL-3047 -->Support added to execute test suite
654 instrumented with <a href="http://openclover.org/">Open
659 <td><div align="left">
663 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
664 row shown in Feredoxin Structure alignment view of example
668 <!-- JAL-2854 -->Annotation obscures sequences if lots of
669 annotation displayed.
672 <!-- JAL-3107 -->Group conservation/consensus not shown
673 for newly created group when 'Apply to all groups'
677 <!-- JAL-3087 -->Corrupted display when switching to
678 wrapped mode when sequence panel's vertical scrollbar is
682 <!-- JAL-3003 -->Alignment is black in exported EPS file
683 when sequences are selected in exported view.</em>
686 <!-- JAL-3059 -->Groups with different coloured borders
687 aren't rendered with correct colour.
690 <!-- JAL-3092 -->Jalview could hang when importing certain
691 types of knotted RNA secondary structure.
694 <!-- JAL-3095 -->Sequence highlight and selection in
695 trimmed VARNA 2D structure is incorrect for sequences that
699 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
700 annotation when columns are inserted into an alignment,
701 and when exporting as Stockholm flatfile.
704 <!-- JAL-3053 -->Jalview annotation rows containing upper
705 and lower-case 'E' and 'H' do not automatically get
706 treated as RNA secondary structure.
709 <!-- JAL-3106 -->.jvp should be used as default extension
710 (not .jar) when saving a Jalview project file.
713 <!-- JAL-3105 -->Mac Users: closing a window correctly
714 transfers focus to previous window on OSX
717 <em>Java 10 Issues Resolved</em>
720 <!-- JAL-2988 -->OSX - Can't save new files via the File
721 or export menus by typing in a name into the Save dialog
725 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
726 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
727 'look and feel' which has improved compatibility with the
728 latest version of OSX.
735 <td width="60" nowrap>
737 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
738 <em>7/06/2018</em></strong>
741 <td><div align="left">
745 <!-- JAL-2920 -->Use HGVS nomenclature for variant
746 annotation retrieved from Uniprot
749 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
750 onto the Jalview Desktop
754 <td><div align="left">
758 <!-- JAL-3017 -->Cannot import features with multiple
759 variant elements (blocks import of some Uniprot records)
762 <!-- JAL-2997 -->Clustal files with sequence positions in
763 right-hand column parsed correctly
766 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
767 not alignment area in exported graphic
770 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
771 window has input focus
774 <!-- JAL-2992 -->Annotation panel set too high when
775 annotation added to view (Windows)
778 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
779 network connectivity is poor
782 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
783 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
784 the currently open URL and links from a page viewed in
785 Firefox or Chrome on Windows is now fully supported. If
786 you are using Edge, only links in the page can be
787 dragged, and with Internet Explorer, only the currently
788 open URL in the browser can be dropped onto Jalview.</em>
791 <em>New Known Defects</em>
793 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
798 <td width="60" nowrap>
800 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
803 <td><div align="left">
807 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
808 for disabling automatic superposition of multiple
809 structures and open structures in existing views
812 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
813 ID and annotation area margins can be click-dragged to
817 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
821 <!-- JAL-2759 -->Improved performance for large alignments
822 and lots of hidden columns
825 <!-- JAL-2593 -->Improved performance when rendering lots
826 of features (particularly when transparency is disabled)
829 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
830 exchange of Jalview features and Chimera attributes made
836 <td><div align="left">
839 <!-- JAL-2899 -->Structure and Overview aren't updated
840 when Colour By Annotation threshold slider is adjusted
843 <!-- JAL-2778 -->Slow redraw when Overview panel shown
844 overlapping alignment panel
847 <!-- JAL-2929 -->Overview doesn't show end of unpadded
851 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
852 improved: CDS not handled correctly if transcript has no
856 <!-- JAL-2321 -->Secondary structure and temperature
857 factor annotation not added to sequence when local PDB
858 file associated with it by drag'n'drop or structure
862 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
863 dialog doesn't import PDB files dropped on an alignment
866 <!-- JAL-2666 -->Linked scrolling via protein horizontal
867 scroll bar doesn't work for some CDS/Protein views
870 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
871 Java 1.8u153 onwards and Java 1.9u4+.
874 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
875 columns in annotation row
878 <!-- JAL-2913 -->Preferences panel's ID Width control is not
879 honored in batch mode
882 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
883 for structures added to existing Jmol view
886 <!-- JAL-2223 -->'View Mappings' includes duplicate
887 entries after importing project with multiple views
890 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
891 protein sequences via SIFTS from associated PDB entries
892 with negative residue numbers or missing residues fails
895 <!-- JAL-2952 -->Exception when shading sequence with negative
896 Temperature Factor values from annotated PDB files (e.g.
897 as generated by CONSURF)
900 <!-- JAL-2920 -->Uniprot 'sequence variant' features
901 tooltip doesn't include a text description of mutation
904 <!-- JAL-2922 -->Invert displayed features very slow when
905 structure and/or overview windows are also shown
908 <!-- JAL-2954 -->Selecting columns from highlighted regions
909 very slow for alignments with large numbers of sequences
912 <!-- JAL-2925 -->Copy Consensus fails for group consensus
913 with 'StringIndexOutOfBounds'
916 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
917 platforms running Java 10
920 <!-- JAL-2960 -->Adding a structure to existing structure
921 view appears to do nothing because the view is hidden behind the alignment view
927 <!-- JAL-2926 -->Copy consensus sequence option in applet
928 should copy the group consensus when popup is opened on it
934 <!-- JAL-2913 -->Fixed ID width preference is not respected
937 <em>New Known Defects</em>
940 <!-- JAL-2973 --> Exceptions occasionally raised when
941 editing a large alignment and overview is displayed
944 <!-- JAL-2974 -->'Overview updating' progress bar is shown
945 repeatedly after a series of edits even when the overview
946 is no longer reflecting updates
949 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
950 structures for protein subsequence (if 'Trim Retrieved
951 Sequences' enabled) or Ensembl isoforms (Workaround in
952 2.10.4 is to fail back to N&W mapping)
955 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
956 option gives blank output
963 <td width="60" nowrap>
965 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
968 <td><div align="left">
969 <ul><li>Updated Certum Codesigning Certificate
970 (Valid till 30th November 2018)</li></ul></div></td>
971 <td><div align="left">
974 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
975 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
976 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
977 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
978 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
979 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
980 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
986 <td width="60" nowrap>
988 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
991 <td><div align="left">
995 <!-- JAL-2446 -->Faster and more efficient management and
996 rendering of sequence features
999 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1000 429 rate limit request hander
1003 <!-- JAL-2773 -->Structure views don't get updated unless
1004 their colours have changed
1007 <!-- JAL-2495 -->All linked sequences are highlighted for
1008 a structure mousover (Jmol) or selection (Chimera)
1011 <!-- JAL-2790 -->'Cancel' button in progress bar for
1012 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1015 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1016 view from Ensembl locus cross-references
1019 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1023 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1024 feature can be disabled
1027 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1028 PDB easier retrieval of sequences for lists of IDs
1031 <!-- JAL-2758 -->Short names for sequences retrieved from
1037 <li>Groovy interpreter updated to 2.4.12</li>
1038 <li>Example groovy script for generating a matrix of
1039 percent identity scores for current alignment.</li>
1041 <em>Testing and Deployment</em>
1044 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1048 <td><div align="left">
1052 <!-- JAL-2643 -->Pressing tab after updating the colour
1053 threshold text field doesn't trigger an update to the
1057 <!-- JAL-2682 -->Race condition when parsing sequence ID
1061 <!-- JAL-2608 -->Overview windows are also closed when
1062 alignment window is closed
1065 <!-- JAL-2548 -->Export of features doesn't always respect
1069 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1070 takes a long time in Cursor mode
1076 <!-- JAL-2777 -->Structures with whitespace chainCode
1077 cannot be viewed in Chimera
1080 <!-- JAL-2728 -->Protein annotation panel too high in
1084 <!-- JAL-2757 -->Can't edit the query after the server
1085 error warning icon is shown in Uniprot and PDB Free Text
1089 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1092 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1095 <!-- JAL-2739 -->Hidden column marker in last column not
1096 rendered when switching back from Wrapped to normal view
1099 <!-- JAL-2768 -->Annotation display corrupted when
1100 scrolling right in unwapped alignment view
1103 <!-- JAL-2542 -->Existing features on subsequence
1104 incorrectly relocated when full sequence retrieved from
1108 <!-- JAL-2733 -->Last reported memory still shown when
1109 Desktop->Show Memory is unticked (OSX only)
1112 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1113 features of same type and group to be selected for
1117 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1118 alignments when hidden columns are present
1121 <!-- JAL-2392 -->Jalview freezes when loading and
1122 displaying several structures
1125 <!-- JAL-2732 -->Black outlines left after resizing or
1129 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1130 within the Jalview desktop on OSX
1133 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1134 when in wrapped alignment mode
1137 <!-- JAL-2636 -->Scale mark not shown when close to right
1138 hand end of alignment
1141 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1142 each selected sequence do not have correct start/end
1146 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1147 after canceling the Alignment Window's Font dialog
1150 <!-- JAL-2036 -->Show cross-references not enabled after
1151 restoring project until a new view is created
1154 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1155 URL links appears when only default EMBL-EBI link is
1156 configured (since 2.10.2b2)
1159 <!-- JAL-2775 -->Overview redraws whole window when box
1160 position is adjusted
1163 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1164 in a multi-chain structure when viewing alignment
1165 involving more than one chain (since 2.10)
1168 <!-- JAL-2811 -->Double residue highlights in cursor mode
1169 if new selection moves alignment window
1172 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1173 arrow key in cursor mode to pass hidden column marker
1176 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1177 that produces correctly annotated transcripts and products
1180 <!-- JAL-2776 -->Toggling a feature group after first time
1181 doesn't update associated structure view
1184 <em>Applet</em><br />
1187 <!-- JAL-2687 -->Concurrent modification exception when
1188 closing alignment panel
1191 <em>BioJSON</em><br />
1194 <!-- JAL-2546 -->BioJSON export does not preserve
1195 non-positional features
1198 <em>New Known Issues</em>
1201 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1202 sequence features correctly (for many previous versions of
1206 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1207 using cursor in wrapped panel other than top
1210 <!-- JAL-2791 -->Select columns containing feature ignores
1211 graduated colour threshold
1214 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1215 always preserve numbering and sequence features
1218 <em>Known Java 9 Issues</em>
1221 <!-- JAL-2902 -->Groovy Console very slow to open and is
1222 not responsive when entering characters (Webstart, Java
1229 <td width="60" nowrap>
1230 <div align="center">
1231 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1232 <em>2/10/2017</em></strong>
1235 <td><div align="left">
1236 <em>New features in Jalview Desktop</em>
1239 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1241 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1245 <td><div align="left">
1249 <td width="60" nowrap>
1250 <div align="center">
1251 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1252 <em>7/9/2017</em></strong>
1255 <td><div align="left">
1259 <!-- JAL-2588 -->Show gaps in overview window by colouring
1260 in grey (sequences used to be coloured grey, and gaps were
1264 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1268 <!-- JAL-2587 -->Overview updates immediately on increase
1269 in size and progress bar shown as higher resolution
1270 overview is recalculated
1275 <td><div align="left">
1279 <!-- JAL-2664 -->Overview window redraws every hidden
1280 column region row by row
1283 <!-- JAL-2681 -->duplicate protein sequences shown after
1284 retrieving Ensembl crossrefs for sequences from Uniprot
1287 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1288 format setting is unticked
1291 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1292 if group has show boxes format setting unticked
1295 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1296 autoscrolling whilst dragging current selection group to
1297 include sequences and columns not currently displayed
1300 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1301 assemblies are imported via CIF file
1304 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1305 displayed when threshold or conservation colouring is also
1309 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1313 <!-- JAL-2673 -->Jalview continues to scroll after
1314 dragging a selected region off the visible region of the
1318 <!-- JAL-2724 -->Cannot apply annotation based
1319 colourscheme to all groups in a view
1322 <!-- JAL-2511 -->IDs don't line up with sequences
1323 initially after font size change using the Font chooser or
1330 <td width="60" nowrap>
1331 <div align="center">
1332 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1335 <td><div align="left">
1336 <em>Calculations</em>
1340 <!-- JAL-1933 -->Occupancy annotation row shows number of
1341 ungapped positions in each column of the alignment.
1344 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1345 a calculation dialog box
1348 <!-- JAL-2379 -->Revised implementation of PCA for speed
1349 and memory efficiency (~30x faster)
1352 <!-- JAL-2403 -->Revised implementation of sequence
1353 similarity scores as used by Tree, PCA, Shading Consensus
1354 and other calculations
1357 <!-- JAL-2416 -->Score matrices are stored as resource
1358 files within the Jalview codebase
1361 <!-- JAL-2500 -->Trees computed on Sequence Feature
1362 Similarity may have different topology due to increased
1369 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1370 model for alignments and groups
1373 <!-- JAL-384 -->Custom shading schemes created via groovy
1380 <!-- JAL-2526 -->Efficiency improvements for interacting
1381 with alignment and overview windows
1384 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1388 <!-- JAL-2388 -->Hidden columns and sequences can be
1392 <!-- JAL-2611 -->Click-drag in visible area allows fine
1393 adjustment of visible position
1397 <em>Data import/export</em>
1400 <!-- JAL-2535 -->Posterior probability annotation from
1401 Stockholm files imported as sequence associated annotation
1404 <!-- JAL-2507 -->More robust per-sequence positional
1405 annotation input/output via stockholm flatfile
1408 <!-- JAL-2533 -->Sequence names don't include file
1409 extension when importing structure files without embedded
1410 names or PDB accessions
1413 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1414 format sequence substitution matrices
1417 <em>User Interface</em>
1420 <!-- JAL-2447 --> Experimental Features Checkbox in
1421 Desktop's Tools menu to hide or show untested features in
1425 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1426 via Overview or sequence motif search operations
1429 <!-- JAL-2547 -->Amend sequence features dialog box can be
1430 opened by double clicking gaps within sequence feature
1434 <!-- JAL-1476 -->Status bar message shown when not enough
1435 aligned positions were available to create a 3D structure
1439 <em>3D Structure</em>
1442 <!-- JAL-2430 -->Hidden regions in alignment views are not
1443 coloured in linked structure views
1446 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1447 file-based command exchange
1450 <!-- JAL-2375 -->Structure chooser automatically shows
1451 Cached Structures rather than querying the PDBe if
1452 structures are already available for sequences
1455 <!-- JAL-2520 -->Structures imported via URL are cached in
1456 the Jalview project rather than downloaded again when the
1457 project is reopened.
1460 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1461 to transfer Chimera's structure attributes as Jalview
1462 features, and vice-versa (<strong>Experimental
1466 <em>Web Services</em>
1469 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1472 <!-- JAL-2335 -->Filter non-standard amino acids and
1473 nucleotides when submitting to AACon and other MSA
1477 <!-- JAL-2316, -->URLs for viewing database
1478 cross-references provided by identifiers.org and the
1479 EMBL-EBI's MIRIAM DB
1486 <!-- JAL-2344 -->FileFormatI interface for describing and
1487 identifying file formats (instead of String constants)
1490 <!-- JAL-2228 -->FeatureCounter script refactored for
1491 efficiency when counting all displayed features (not
1492 backwards compatible with 2.10.1)
1495 <em>Example files</em>
1498 <!-- JAL-2631 -->Graduated feature colour style example
1499 included in the example feature file
1502 <em>Documentation</em>
1505 <!-- JAL-2339 -->Release notes reformatted for readability
1506 with the built-in Java help viewer
1509 <!-- JAL-1644 -->Find documentation updated with 'search
1510 sequence description' option
1516 <!-- JAL-2485, -->External service integration tests for
1517 Uniprot REST Free Text Search Client
1520 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1523 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1528 <td><div align="left">
1529 <em>Calculations</em>
1532 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1533 matrix - C->R should be '-3'<br />Old matrix restored
1534 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1536 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1537 Jalview's treatment of gaps in PCA and substitution matrix
1538 based Tree calculations.<br /> <br />In earlier versions
1539 of Jalview, gaps matching gaps were penalised, and gaps
1540 matching non-gaps penalised even more. In the PCA
1541 calculation, gaps were actually treated as non-gaps - so
1542 different costs were applied, which meant Jalview's PCAs
1543 were different to those produced by SeqSpace.<br />Jalview
1544 now treats gaps in the same way as SeqSpace (ie it scores
1545 them as 0). <br /> <br />Enter the following in the
1546 Groovy console to restore pre-2.10.2 behaviour:<br />
1547 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1548 // for 2.10.1 mode <br />
1549 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1550 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1551 these settings will affect all subsequent tree and PCA
1552 calculations (not recommended)</em></li>
1554 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1555 scaling of branch lengths for trees computed using
1556 Sequence Feature Similarity.
1559 <!-- JAL-2377 -->PCA calculation could hang when
1560 generating output report when working with highly
1561 redundant alignments
1564 <!-- JAL-2544 --> Sort by features includes features to
1565 right of selected region when gaps present on right-hand
1569 <em>User Interface</em>
1572 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1573 doesn't reselect a specific sequence's associated
1574 annotation after it was used for colouring a view
1577 <!-- JAL-2419 -->Current selection lost if popup menu
1578 opened on a region of alignment without groups
1581 <!-- JAL-2374 -->Popup menu not always shown for regions
1582 of an alignment with overlapping groups
1585 <!-- JAL-2310 -->Finder double counts if both a sequence's
1586 name and description match
1589 <!-- JAL-2370 -->Hiding column selection containing two
1590 hidden regions results in incorrect hidden regions
1593 <!-- JAL-2386 -->'Apply to all groups' setting when
1594 changing colour does not apply Conservation slider value
1598 <!-- JAL-2373 -->Percentage identity and conservation menu
1599 items do not show a tick or allow shading to be disabled
1602 <!-- JAL-2385 -->Conservation shading or PID threshold
1603 lost when base colourscheme changed if slider not visible
1606 <!-- JAL-2547 -->Sequence features shown in tooltip for
1607 gaps before start of features
1610 <!-- JAL-2623 -->Graduated feature colour threshold not
1611 restored to UI when feature colour is edited
1614 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1615 a time when scrolling vertically in wrapped mode.
1618 <!-- JAL-2630 -->Structure and alignment overview update
1619 as graduate feature colour settings are modified via the
1623 <!-- JAL-2034 -->Overview window doesn't always update
1624 when a group defined on the alignment is resized
1627 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1628 wrapped view result in positional status updates
1632 <!-- JAL-2563 -->Status bar doesn't show position for
1633 ambiguous amino acid and nucleotide symbols
1636 <!-- JAL-2602 -->Copy consensus sequence failed if
1637 alignment included gapped columns
1640 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1641 widgets don't permanently disappear
1644 <!-- JAL-2503 -->Cannot select or filter quantitative
1645 annotation that are shown only as column labels (e.g.
1646 T-Coffee column reliability scores)
1649 <!-- JAL-2594 -->Exception thrown if trying to create a
1650 sequence feature on gaps only
1653 <!-- JAL-2504 -->Features created with 'New feature'
1654 button from a Find inherit previously defined feature type
1655 rather than the Find query string
1658 <!-- JAL-2423 -->incorrect title in output window when
1659 exporting tree calculated in Jalview
1662 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1663 and then revealing them reorders sequences on the
1667 <!-- JAL-964 -->Group panel in sequence feature settings
1668 doesn't update to reflect available set of groups after
1669 interactively adding or modifying features
1672 <!-- JAL-2225 -->Sequence Database chooser unusable on
1676 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1677 only excluded gaps in current sequence and ignored
1684 <!-- JAL-2421 -->Overview window visible region moves
1685 erratically when hidden rows or columns are present
1688 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1689 Structure Viewer's colour menu don't correspond to
1693 <!-- JAL-2405 -->Protein specific colours only offered in
1694 colour and group colour menu for protein alignments
1697 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1698 reflect currently selected view or group's shading
1702 <!-- JAL-2624 -->Feature colour thresholds not respected
1703 when rendered on overview and structures when opacity at
1707 <!-- JAL-2589 -->User defined gap colour not shown in
1708 overview when features overlaid on alignment
1711 <!-- JAL-2567 -->Feature settings for different views not
1712 recovered correctly from Jalview project file
1715 <!-- JAL-2256 -->Feature colours in overview when first opened
1716 (automatically via preferences) are different to the main
1720 <em>Data import/export</em>
1723 <!-- JAL-2576 -->Very large alignments take a long time to
1727 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1728 added after a sequence was imported are not written to
1732 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1733 when importing RNA secondary structure via Stockholm
1736 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1737 not shown in correct direction for simple pseudoknots
1740 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1741 with lightGray or darkGray via features file (but can
1745 <!-- JAL-2383 -->Above PID colour threshold not recovered
1746 when alignment view imported from project
1749 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1750 structure and sequences extracted from structure files
1751 imported via URL and viewed in Jmol
1754 <!-- JAL-2520 -->Structures loaded via URL are saved in
1755 Jalview Projects rather than fetched via URL again when
1756 the project is loaded and the structure viewed
1759 <em>Web Services</em>
1762 <!-- JAL-2519 -->EnsemblGenomes example failing after
1763 release of Ensembl v.88
1766 <!-- JAL-2366 -->Proxy server address and port always
1767 appear enabled in Preferences->Connections
1770 <!-- JAL-2461 -->DAS registry not found exceptions
1771 removed from console output
1774 <!-- JAL-2582 -->Cannot retrieve protein products from
1775 Ensembl by Peptide ID
1778 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1779 created from SIFTs, and spurious 'Couldn't open structure
1780 in Chimera' errors raised after April 2017 update (problem
1781 due to 'null' string rather than empty string used for
1782 residues with no corresponding PDB mapping).
1785 <em>Application UI</em>
1788 <!-- JAL-2361 -->User Defined Colours not added to Colour
1792 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1793 case' residues (button in colourscheme editor debugged and
1794 new documentation and tooltips added)
1797 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1798 doesn't restore group-specific text colour thresholds
1801 <!-- JAL-2243 -->Feature settings panel does not update as
1802 new features are added to alignment
1805 <!-- JAL-2532 -->Cancel in feature settings reverts
1806 changes to feature colours via the Amend features dialog
1809 <!-- JAL-2506 -->Null pointer exception when attempting to
1810 edit graduated feature colour via amend features dialog
1814 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1815 selection menu changes colours of alignment views
1818 <!-- JAL-2426 -->Spurious exceptions in console raised
1819 from alignment calculation workers after alignment has
1823 <!-- JAL-1608 -->Typo in selection popup menu - Create
1824 groups now 'Create Group'
1827 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1828 Create/Undefine group doesn't always work
1831 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1832 shown again after pressing 'Cancel'
1835 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1836 adjusts start position in wrap mode
1839 <!-- JAL-2563 -->Status bar doesn't show positions for
1840 ambiguous amino acids
1843 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1844 CDS/Protein view after CDS sequences added for aligned
1848 <!-- JAL-2592 -->User defined colourschemes called 'User
1849 Defined' don't appear in Colours menu
1855 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1856 score models doesn't always result in an updated PCA plot
1859 <!-- JAL-2442 -->Features not rendered as transparent on
1860 overview or linked structure view
1863 <!-- JAL-2372 -->Colour group by conservation doesn't
1867 <!-- JAL-2517 -->Hitting Cancel after applying
1868 user-defined colourscheme doesn't restore original
1875 <!-- JAL-2314 -->Unit test failure:
1876 jalview.ws.jabaws.RNAStructExportImport setup fails
1879 <!-- JAL-2307 -->Unit test failure:
1880 jalview.ws.sifts.SiftsClientTest due to compatibility
1881 problems with deep array comparison equality asserts in
1882 successive versions of TestNG
1885 <!-- JAL-2479 -->Relocated StructureChooserTest and
1886 ParameterUtilsTest Unit tests to Network suite
1889 <em>New Known Issues</em>
1892 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1893 phase after a sequence motif find operation
1896 <!-- JAL-2550 -->Importing annotation file with rows
1897 containing just upper and lower case letters are
1898 interpreted as WUSS RNA secondary structure symbols
1901 <!-- JAL-2590 -->Cannot load and display Newick trees
1902 reliably from eggnog Ortholog database
1905 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1906 containing features of type Highlight' when 'B' is pressed
1907 to mark columns containing highlighted regions.
1910 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1911 doesn't always add secondary structure annotation.
1916 <td width="60" nowrap>
1917 <div align="center">
1918 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1921 <td><div align="left">
1925 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1926 for all consensus calculations
1929 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1932 <li>Updated Jalview's Certum code signing certificate
1935 <em>Application</em>
1938 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1939 set of database cross-references, sorted alphabetically
1942 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1943 from database cross references. Users with custom links
1944 will receive a <a href="webServices/urllinks.html#warning">warning
1945 dialog</a> asking them to update their preferences.
1948 <!-- JAL-2287-->Cancel button and escape listener on
1949 dialog warning user about disconnecting Jalview from a
1953 <!-- JAL-2320-->Jalview's Chimera control window closes if
1954 the Chimera it is connected to is shut down
1957 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1958 columns menu item to mark columns containing highlighted
1959 regions (e.g. from structure selections or results of a
1963 <!-- JAL-2284-->Command line option for batch-generation
1964 of HTML pages rendering alignment data with the BioJS
1974 <!-- JAL-2286 -->Columns with more than one modal residue
1975 are not coloured or thresholded according to percent
1976 identity (first observed in Jalview 2.8.2)
1979 <!-- JAL-2301 -->Threonine incorrectly reported as not
1983 <!-- JAL-2318 -->Updates to documentation pages (above PID
1984 threshold, amino acid properties)
1987 <!-- JAL-2292 -->Lower case residues in sequences are not
1988 reported as mapped to residues in a structure file in the
1992 <!--JAL-2324 -->Identical features with non-numeric scores
1993 could be added multiple times to a sequence
1996 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1997 bond features shown as two highlighted residues rather
1998 than a range in linked structure views, and treated
1999 correctly when selecting and computing trees from features
2002 <!-- JAL-2281-->Custom URL links for database
2003 cross-references are matched to database name regardless
2008 <em>Application</em>
2011 <!-- JAL-2282-->Custom URL links for specific database
2012 names without regular expressions also offer links from
2016 <!-- JAL-2315-->Removing a single configured link in the
2017 URL links pane in Connections preferences doesn't actually
2018 update Jalview configuration
2021 <!-- JAL-2272-->CTRL-Click on a selected region to open
2022 the alignment area popup menu doesn't work on El-Capitan
2025 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2026 files with similarly named sequences if dropped onto the
2030 <!-- JAL-2312 -->Additional mappings are shown for PDB
2031 entries where more chains exist in the PDB accession than
2032 are reported in the SIFTS file
2035 <!-- JAL-2317-->Certain structures do not get mapped to
2036 the structure view when displayed with Chimera
2039 <!-- JAL-2317-->No chains shown in the Chimera view
2040 panel's View->Show Chains submenu
2043 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2044 work for wrapped alignment views
2047 <!--JAL-2197 -->Rename UI components for running JPred
2048 predictions from 'JNet' to 'JPred'
2051 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2052 corrupted when annotation panel vertical scroll is not at
2053 first annotation row
2056 <!--JAL-2332 -->Attempting to view structure for Hen
2057 lysozyme results in a PDB Client error dialog box
2060 <!-- JAL-2319 -->Structure View's mapping report switched
2061 ranges for PDB and sequence for SIFTS
2064 SIFTS 'Not_Observed' residues mapped to non-existant
2068 <!-- <em>New Known Issues</em>
2075 <td width="60" nowrap>
2076 <div align="center">
2077 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2078 <em>25/10/2016</em></strong>
2081 <td><em>Application</em>
2083 <li>3D Structure chooser opens with 'Cached structures'
2084 view if structures already loaded</li>
2085 <li>Progress bar reports models as they are loaded to
2086 structure views</li>
2092 <li>Colour by conservation always enabled and no tick
2093 shown in menu when BLOSUM or PID shading applied</li>
2094 <li>FER1_ARATH and FER2_ARATH labels were switched in
2095 example sequences/projects/trees</li>
2097 <em>Application</em>
2099 <li>Jalview projects with views of local PDB structure
2100 files saved on Windows cannot be opened on OSX</li>
2101 <li>Multiple structure views can be opened and superposed
2102 without timeout for structures with multiple models or
2103 multiple sequences in alignment</li>
2104 <li>Cannot import or associated local PDB files without a
2105 PDB ID HEADER line</li>
2106 <li>RMSD is not output in Jmol console when superposition
2108 <li>Drag and drop of URL from Browser fails for Linux and
2109 OSX versions earlier than El Capitan</li>
2110 <li>ENA client ignores invalid content from ENA server</li>
2111 <li>Exceptions are not raised in console when ENA client
2112 attempts to fetch non-existent IDs via Fetch DB Refs UI
2114 <li>Exceptions are not raised in console when a new view
2115 is created on the alignment</li>
2116 <li>OSX right-click fixed for group selections: CMD-click
2117 to insert/remove gaps in groups and CTRL-click to open group
2120 <em>Build and deployment</em>
2122 <li>URL link checker now copes with multi-line anchor
2125 <em>New Known Issues</em>
2127 <li>Drag and drop from URL links in browsers do not work
2134 <td width="60" nowrap>
2135 <div align="center">
2136 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2139 <td><em>General</em>
2142 <!-- JAL-2124 -->Updated Spanish translations.
2145 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2146 for importing structure data to Jalview. Enables mmCIF and
2150 <!-- JAL-192 --->Alignment ruler shows positions relative to
2154 <!-- JAL-2202 -->Position/residue shown in status bar when
2155 mousing over sequence associated annotation
2158 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2162 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2163 '()', canonical '[]' and invalid '{}' base pair populations
2167 <!-- JAL-2092 -->Feature settings popup menu options for
2168 showing or hiding columns containing a feature
2171 <!-- JAL-1557 -->Edit selected group by double clicking on
2172 group and sequence associated annotation labels
2175 <!-- JAL-2236 -->Sequence name added to annotation label in
2176 select/hide columns by annotation and colour by annotation
2180 </ul> <em>Application</em>
2183 <!-- JAL-2050-->Automatically hide introns when opening a
2184 gene/transcript view
2187 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2191 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2192 structure mappings with the EMBL-EBI PDBe SIFTS database
2195 <!-- JAL-2079 -->Updated download sites used for Rfam and
2196 Pfam sources to xfam.org
2199 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2202 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2203 over sequences in Jalview
2206 <!-- JAL-2027-->Support for reverse-complement coding
2207 regions in ENA and EMBL
2210 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2211 for record retrieval via ENA rest API
2214 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2218 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2219 groovy script execution
2222 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2223 alignment window's Calculate menu
2226 <!-- JAL-1812 -->Allow groovy scripts that call
2227 Jalview.getAlignFrames() to run in headless mode
2230 <!-- JAL-2068 -->Support for creating new alignment
2231 calculation workers from groovy scripts
2234 <!-- JAL-1369 --->Store/restore reference sequence in
2238 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2239 associations are now saved/restored from project
2242 <!-- JAL-1993 -->Database selection dialog always shown
2243 before sequence fetcher is opened
2246 <!-- JAL-2183 -->Double click on an entry in Jalview's
2247 database chooser opens a sequence fetcher
2250 <!-- JAL-1563 -->Free-text search client for UniProt using
2251 the UniProt REST API
2254 <!-- JAL-2168 -->-nonews command line parameter to prevent
2255 the news reader opening
2258 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2259 querying stored in preferences
2262 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2266 <!-- JAL-1977-->Tooltips shown on database chooser
2269 <!-- JAL-391 -->Reverse complement function in calculate
2270 menu for nucleotide sequences
2273 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2274 and feature counts preserves alignment ordering (and
2275 debugged for complex feature sets).
2278 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2279 viewing structures with Jalview 2.10
2282 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2283 genome, transcript CCDS and gene ids via the Ensembl and
2284 Ensembl Genomes REST API
2287 <!-- JAL-2049 -->Protein sequence variant annotation
2288 computed for 'sequence_variant' annotation on CDS regions
2292 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2296 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2297 Ref Fetcher fails to match, or otherwise updates sequence
2298 data from external database records.
2301 <!-- JAL-2154 -->Revised Jalview Project format for
2302 efficient recovery of sequence coding and alignment
2303 annotation relationships.
2305 </ul> <!-- <em>Applet</em>
2316 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2320 <!-- JAL-2018-->Export features in Jalview format (again)
2321 includes graduated colourschemes
2324 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2325 working with big alignments and lots of hidden columns
2328 <!-- JAL-2053-->Hidden column markers not always rendered
2329 at right of alignment window
2332 <!-- JAL-2067 -->Tidied up links in help file table of
2336 <!-- JAL-2072 -->Feature based tree calculation not shown
2340 <!-- JAL-2075 -->Hidden columns ignored during feature
2341 based tree calculation
2344 <!-- JAL-2065 -->Alignment view stops updating when show
2345 unconserved enabled for group on alignment
2348 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2352 <!-- JAL-2146 -->Alignment column in status incorrectly
2353 shown as "Sequence position" when mousing over
2357 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2358 hidden columns present
2361 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2362 user created annotation added to alignment
2365 <!-- JAL-1841 -->RNA Structure consensus only computed for
2366 '()' base pair annotation
2369 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2370 in zero scores for all base pairs in RNA Structure
2374 <!-- JAL-2174-->Extend selection with columns containing
2378 <!-- JAL-2275 -->Pfam format writer puts extra space at
2379 beginning of sequence
2382 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2386 <!-- JAL-2238 -->Cannot create groups on an alignment from
2387 from a tree when t-coffee scores are shown
2390 <!-- JAL-1836,1967 -->Cannot import and view PDB
2391 structures with chains containing negative resnums (4q4h)
2394 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2398 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2399 to Clustal, PIR and PileUp output
2402 <!-- JAL-2008 -->Reordering sequence features that are
2403 not visible causes alignment window to repaint
2406 <!-- JAL-2006 -->Threshold sliders don't work in
2407 graduated colour and colour by annotation row for e-value
2408 scores associated with features and annotation rows
2411 <!-- JAL-1797 -->amino acid physicochemical conservation
2412 calculation should be case independent
2415 <!-- JAL-2173 -->Remove annotation also updates hidden
2419 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2420 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2421 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2424 <!-- JAL-2065 -->Null pointer exceptions and redraw
2425 problems when reference sequence defined and 'show
2426 non-conserved' enabled
2429 <!-- JAL-1306 -->Quality and Conservation are now shown on
2430 load even when Consensus calculation is disabled
2433 <!-- JAL-1932 -->Remove right on penultimate column of
2434 alignment does nothing
2437 <em>Application</em>
2440 <!-- JAL-1552-->URLs and links can't be imported by
2441 drag'n'drop on OSX when launched via webstart (note - not
2442 yet fixed for El Capitan)
2445 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2446 output when running on non-gb/us i18n platforms
2449 <!-- JAL-1944 -->Error thrown when exporting a view with
2450 hidden sequences as flat-file alignment
2453 <!-- JAL-2030-->InstallAnywhere distribution fails when
2457 <!-- JAL-2080-->Jalview very slow to launch via webstart
2458 (also hotfix for 2.9.0b2)
2461 <!-- JAL-2085 -->Cannot save project when view has a
2462 reference sequence defined
2465 <!-- JAL-1011 -->Columns are suddenly selected in other
2466 alignments and views when revealing hidden columns
2469 <!-- JAL-1989 -->Hide columns not mirrored in complement
2470 view in a cDNA/Protein splitframe
2473 <!-- JAL-1369 -->Cannot save/restore representative
2474 sequence from project when only one sequence is
2478 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2479 in Structure Chooser
2482 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2483 structure consensus didn't refresh annotation panel
2486 <!-- JAL-1962 -->View mapping in structure view shows
2487 mappings between sequence and all chains in a PDB file
2490 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2491 dialogs format columns correctly, don't display array
2492 data, sort columns according to type
2495 <!-- JAL-1975 -->Export complete shown after destination
2496 file chooser is cancelled during an image export
2499 <!-- JAL-2025 -->Error when querying PDB Service with
2500 sequence name containing special characters
2503 <!-- JAL-2024 -->Manual PDB structure querying should be
2507 <!-- JAL-2104 -->Large tooltips with broken HTML
2508 formatting don't wrap
2511 <!-- JAL-1128 -->Figures exported from wrapped view are
2512 truncated so L looks like I in consensus annotation
2515 <!-- JAL-2003 -->Export features should only export the
2516 currently displayed features for the current selection or
2520 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2521 after fetching cross-references, and restoring from
2525 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2526 followed in the structure viewer
2529 <!-- JAL-2163 -->Titles for individual alignments in
2530 splitframe not restored from project
2533 <!-- JAL-2145 -->missing autocalculated annotation at
2534 trailing end of protein alignment in transcript/product
2535 splitview when pad-gaps not enabled by default
2538 <!-- JAL-1797 -->amino acid physicochemical conservation
2542 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2543 article has been read (reopened issue due to
2544 internationalisation problems)
2547 <!-- JAL-1960 -->Only offer PDB structures in structure
2548 viewer based on sequence name, PDB and UniProt
2553 <!-- JAL-1976 -->No progress bar shown during export of
2557 <!-- JAL-2213 -->Structures not always superimposed after
2558 multiple structures are shown for one or more sequences.
2561 <!-- JAL-1370 -->Reference sequence characters should not
2562 be replaced with '.' when 'Show unconserved' format option
2566 <!-- JAL-1823 -->Cannot specify chain code when entering
2567 specific PDB id for sequence
2570 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2571 'Export hidden sequences' is enabled, but 'export hidden
2572 columns' is disabled.
2575 <!--JAL-2026-->Best Quality option in structure chooser
2576 selects lowest rather than highest resolution structures
2580 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2581 to sequence mapping in 'View Mappings' report
2584 <!-- JAL-2284 -->Unable to read old Jalview projects that
2585 contain non-XML data added after Jalvew wrote project.
2588 <!-- JAL-2118 -->Newly created annotation row reorders
2589 after clicking on it to create new annotation for a
2593 <!-- JAL-1980 -->Null Pointer Exception raised when
2594 pressing Add on an orphaned cut'n'paste window.
2596 <!-- may exclude, this is an external service stability issue JAL-1941
2597 -- > RNA 3D structure not added via DSSR service</li> -->
2602 <!-- JAL-2151 -->Incorrect columns are selected when
2603 hidden columns present before start of sequence
2606 <!-- JAL-1986 -->Missing dependencies on applet pages
2610 <!-- JAL-1947 -->Overview pixel size changes when
2611 sequences are hidden in applet
2614 <!-- JAL-1996 -->Updated instructions for applet
2615 deployment on examples pages.
2622 <td width="60" nowrap>
2623 <div align="center">
2624 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2625 <em>16/10/2015</em></strong>
2628 <td><em>General</em>
2630 <li>Time stamps for signed Jalview application and applet
2635 <em>Application</em>
2637 <li>Duplicate group consensus and conservation rows
2638 shown when tree is partitioned</li>
2639 <li>Erratic behaviour when tree partitions made with
2640 multiple cDNA/Protein split views</li>
2646 <td width="60" nowrap>
2647 <div align="center">
2648 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2649 <em>8/10/2015</em></strong>
2652 <td><em>General</em>
2654 <li>Updated Spanish translations of localized text for
2656 </ul> <em>Application</em>
2658 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2659 <li>Signed OSX InstallAnywhere installer<br></li>
2660 <li>Support for per-sequence based annotations in BioJSON</li>
2661 </ul> <em>Applet</em>
2663 <li>Split frame example added to applet examples page</li>
2664 </ul> <em>Build and Deployment</em>
2667 <!-- JAL-1888 -->New ant target for running Jalview's test
2675 <li>Mapping of cDNA to protein in split frames
2676 incorrect when sequence start > 1</li>
2677 <li>Broken images in filter column by annotation dialog
2679 <li>Feature colours not parsed from features file</li>
2680 <li>Exceptions and incomplete link URLs recovered when
2681 loading a features file containing HTML tags in feature
2685 <em>Application</em>
2687 <li>Annotations corrupted after BioJS export and
2689 <li>Incorrect sequence limits after Fetch DB References
2690 with 'trim retrieved sequences'</li>
2691 <li>Incorrect warning about deleting all data when
2692 deleting selected columns</li>
2693 <li>Patch to build system for shipping properly signed
2694 JNLP templates for webstart launch</li>
2695 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2696 unreleased structures for download or viewing</li>
2697 <li>Tab/space/return keystroke operation of EMBL-PDBe
2698 fetcher/viewer dialogs works correctly</li>
2699 <li>Disabled 'minimise' button on Jalview windows
2700 running on OSX to workaround redraw hang bug</li>
2701 <li>Split cDNA/Protein view position and geometry not
2702 recovered from jalview project</li>
2703 <li>Initial enabled/disabled state of annotation menu
2704 sorter 'show autocalculated first/last' corresponds to
2706 <li>Restoring of Clustal, RNA Helices and T-Coffee
2707 color schemes from BioJSON</li>
2711 <li>Reorder sequences mirrored in cDNA/Protein split
2713 <li>Applet with Jmol examples not loading correctly</li>
2719 <td><div align="center">
2720 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2722 <td><em>General</em>
2724 <li>Linked visualisation and analysis of DNA and Protein
2727 <li>Translated cDNA alignments shown as split protein
2728 and DNA alignment views</li>
2729 <li>Codon consensus annotation for linked protein and
2730 cDNA alignment views</li>
2731 <li>Link cDNA or Protein product sequences by loading
2732 them onto Protein or cDNA alignments</li>
2733 <li>Reconstruct linked cDNA alignment from aligned
2734 protein sequences</li>
2737 <li>Jmol integration updated to Jmol v14.2.14</li>
2738 <li>Import and export of Jalview alignment views as <a
2739 href="features/bioJsonFormat.html">BioJSON</a></li>
2740 <li>New alignment annotation file statements for
2741 reference sequences and marking hidden columns</li>
2742 <li>Reference sequence based alignment shading to
2743 highlight variation</li>
2744 <li>Select or hide columns according to alignment
2746 <li>Find option for locating sequences by description</li>
2747 <li>Conserved physicochemical properties shown in amino
2748 acid conservation row</li>
2749 <li>Alignments can be sorted by number of RNA helices</li>
2750 </ul> <em>Application</em>
2752 <li>New cDNA/Protein analysis capabilities
2754 <li>Get Cross-References should open a Split Frame
2755 view with cDNA/Protein</li>
2756 <li>Detect when nucleotide sequences and protein
2757 sequences are placed in the same alignment</li>
2758 <li>Split cDNA/Protein views are saved in Jalview
2763 <li>Use REST API to talk to Chimera</li>
2764 <li>Selected regions in Chimera are highlighted in linked
2765 Jalview windows</li>
2767 <li>VARNA RNA viewer updated to v3.93</li>
2768 <li>VARNA views are saved in Jalview Projects</li>
2769 <li>Pseudoknots displayed as Jalview RNA annotation can
2770 be shown in VARNA</li>
2772 <li>Make groups for selection uses marked columns as well
2773 as the active selected region</li>
2775 <li>Calculate UPGMA and NJ trees using sequence feature
2777 <li>New Export options
2779 <li>New Export Settings dialog to control hidden
2780 region export in flat file generation</li>
2782 <li>Export alignment views for display with the <a
2783 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2785 <li>Export scrollable SVG in HTML page</li>
2786 <li>Optional embedding of BioJSON data when exporting
2787 alignment figures to HTML</li>
2789 <li>3D structure retrieval and display
2791 <li>Free text and structured queries with the PDBe
2793 <li>PDBe Search API based discovery and selection of
2794 PDB structures for a sequence set</li>
2798 <li>JPred4 employed for protein secondary structure
2800 <li>Hide Insertions menu option to hide unaligned columns
2801 for one or a group of sequences</li>
2802 <li>Automatically hide insertions in alignments imported
2803 from the JPred4 web server</li>
2804 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2805 system on OSX<br />LGPL libraries courtesy of <a
2806 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2808 <li>changed 'View nucleotide structure' submenu to 'View
2809 VARNA 2D Structure'</li>
2810 <li>change "View protein structure" menu option to "3D
2813 </ul> <em>Applet</em>
2815 <li>New layout for applet example pages</li>
2816 <li>New parameters to enable SplitFrame view
2817 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2818 <li>New example demonstrating linked viewing of cDNA and
2819 Protein alignments</li>
2820 </ul> <em>Development and deployment</em>
2822 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2823 <li>Include installation type and git revision in build
2824 properties and console log output</li>
2825 <li>Jalview Github organisation, and new github site for
2826 storing BioJsMSA Templates</li>
2827 <li>Jalview's unit tests now managed with TestNG</li>
2830 <!-- <em>General</em>
2832 </ul> --> <!-- issues resolved --> <em>Application</em>
2834 <li>Escape should close any open find dialogs</li>
2835 <li>Typo in select-by-features status report</li>
2836 <li>Consensus RNA secondary secondary structure
2837 predictions are not highlighted in amber</li>
2838 <li>Missing gap character in v2.7 example file means
2839 alignment appears unaligned when pad-gaps is not enabled</li>
2840 <li>First switch to RNA Helices colouring doesn't colour
2841 associated structure views</li>
2842 <li>ID width preference option is greyed out when auto
2843 width checkbox not enabled</li>
2844 <li>Stopped a warning dialog from being shown when
2845 creating user defined colours</li>
2846 <li>'View Mapping' in structure viewer shows sequence
2847 mappings for just that viewer's sequences</li>
2848 <li>Workaround for superposing PDB files containing
2849 multiple models in Chimera</li>
2850 <li>Report sequence position in status bar when hovering
2851 over Jmol structure</li>
2852 <li>Cannot output gaps as '.' symbols with Selection ->
2853 output to text box</li>
2854 <li>Flat file exports of alignments with hidden columns
2855 have incorrect sequence start/end</li>
2856 <li>'Aligning' a second chain to a Chimera structure from
2858 <li>Colour schemes applied to structure viewers don't
2859 work for nucleotide</li>
2860 <li>Loading/cut'n'pasting an empty or invalid file leads
2861 to a grey/invisible alignment window</li>
2862 <li>Exported Jpred annotation from a sequence region
2863 imports to different position</li>
2864 <li>Space at beginning of sequence feature tooltips shown
2865 on some platforms</li>
2866 <li>Chimera viewer 'View | Show Chain' menu is not
2868 <li>'New View' fails with a Null Pointer Exception in
2869 console if Chimera has been opened</li>
2870 <li>Mouseover to Chimera not working</li>
2871 <li>Miscellaneous ENA XML feature qualifiers not
2873 <li>NPE in annotation renderer after 'Extract Scores'</li>
2874 <li>If two structures in one Chimera window, mouseover of
2875 either sequence shows on first structure</li>
2876 <li>'Show annotations' options should not make
2877 non-positional annotations visible</li>
2878 <li>Subsequence secondary structure annotation not shown
2879 in right place after 'view flanking regions'</li>
2880 <li>File Save As type unset when current file format is
2882 <li>Save as '.jar' option removed for saving Jalview
2884 <li>Colour by Sequence colouring in Chimera more
2886 <li>Cannot 'add reference annotation' for a sequence in
2887 several views on same alignment</li>
2888 <li>Cannot show linked products for EMBL / ENA records</li>
2889 <li>Jalview's tooltip wraps long texts containing no
2891 </ul> <em>Applet</em>
2893 <li>Jmol to JalviewLite mouseover/link not working</li>
2894 <li>JalviewLite can't import sequences with ID
2895 descriptions containing angle brackets</li>
2896 </ul> <em>General</em>
2898 <li>Cannot export and reimport RNA secondary structure
2899 via jalview annotation file</li>
2900 <li>Random helix colour palette for colour by annotation
2901 with RNA secondary structure</li>
2902 <li>Mouseover to cDNA from STOP residue in protein
2903 translation doesn't work.</li>
2904 <li>hints when using the select by annotation dialog box</li>
2905 <li>Jmol alignment incorrect if PDB file has alternate CA
2907 <li>FontChooser message dialog appears to hang after
2908 choosing 1pt font</li>
2909 <li>Peptide secondary structure incorrectly imported from
2910 annotation file when annotation display text includes 'e' or
2912 <li>Cannot set colour of new feature type whilst creating
2914 <li>cDNA translation alignment should not be sequence
2915 order dependent</li>
2916 <li>'Show unconserved' doesn't work for lower case
2918 <li>Nucleotide ambiguity codes involving R not recognised</li>
2919 </ul> <em>Deployment and Documentation</em>
2921 <li>Applet example pages appear different to the rest of
2922 www.jalview.org</li>
2923 </ul> <em>Application Known issues</em>
2925 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2926 <li>Misleading message appears after trying to delete
2928 <li>Jalview icon not shown in dock after InstallAnywhere
2929 version launches</li>
2930 <li>Fetching EMBL reference for an RNA sequence results
2931 fails with a sequence mismatch</li>
2932 <li>Corrupted or unreadable alignment display when
2933 scrolling alignment to right</li>
2934 <li>ArrayIndexOutOfBoundsException thrown when remove
2935 empty columns called on alignment with ragged gapped ends</li>
2936 <li>auto calculated alignment annotation rows do not get
2937 placed above or below non-autocalculated rows</li>
2938 <li>Jalview dekstop becomes sluggish at full screen in
2939 ultra-high resolution</li>
2940 <li>Cannot disable consensus calculation independently of
2941 quality and conservation</li>
2942 <li>Mouseover highlighting between cDNA and protein can
2943 become sluggish with more than one splitframe shown</li>
2944 </ul> <em>Applet Known Issues</em>
2946 <li>Core PDB parsing code requires Jmol</li>
2947 <li>Sequence canvas panel goes white when alignment
2948 window is being resized</li>
2954 <td><div align="center">
2955 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2957 <td><em>General</em>
2959 <li>Updated Java code signing certificate donated by
2961 <li>Features and annotation preserved when performing
2962 pairwise alignment</li>
2963 <li>RNA pseudoknot annotation can be
2964 imported/exported/displayed</li>
2965 <li>'colour by annotation' can colour by RNA and
2966 protein secondary structure</li>
2967 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2968 post-hoc with 2.9 release</em>)
2971 </ul> <em>Application</em>
2973 <li>Extract and display secondary structure for sequences
2974 with 3D structures</li>
2975 <li>Support for parsing RNAML</li>
2976 <li>Annotations menu for layout
2978 <li>sort sequence annotation rows by alignment</li>
2979 <li>place sequence annotation above/below alignment
2982 <li>Output in Stockholm format</li>
2983 <li>Internationalisation: improved Spanish (es)
2985 <li>Structure viewer preferences tab</li>
2986 <li>Disorder and Secondary Structure annotation tracks
2987 shared between alignments</li>
2988 <li>UCSF Chimera launch and linked highlighting from
2990 <li>Show/hide all sequence associated annotation rows for
2991 all or current selection</li>
2992 <li>disorder and secondary structure predictions
2993 available as dataset annotation</li>
2994 <li>Per-sequence rna helices colouring</li>
2997 <li>Sequence database accessions imported when fetching
2998 alignments from Rfam</li>
2999 <li>update VARNA version to 3.91</li>
3001 <li>New groovy scripts for exporting aligned positions,
3002 conservation values, and calculating sum of pairs scores.</li>
3003 <li>Command line argument to set default JABAWS server</li>
3004 <li>include installation type in build properties and
3005 console log output</li>
3006 <li>Updated Jalview project format to preserve dataset
3010 <!-- issues resolved --> <em>Application</em>
3012 <li>Distinguish alignment and sequence associated RNA
3013 structure in structure->view->VARNA</li>
3014 <li>Raise dialog box if user deletes all sequences in an
3016 <li>Pressing F1 results in documentation opening twice</li>
3017 <li>Sequence feature tooltip is wrapped</li>
3018 <li>Double click on sequence associated annotation
3019 selects only first column</li>
3020 <li>Redundancy removal doesn't result in unlinked
3021 leaves shown in tree</li>
3022 <li>Undos after several redundancy removals don't undo
3024 <li>Hide sequence doesn't hide associated annotation</li>
3025 <li>User defined colours dialog box too big to fit on
3026 screen and buttons not visible</li>
3027 <li>author list isn't updated if already written to
3028 Jalview properties</li>
3029 <li>Popup menu won't open after retrieving sequence
3031 <li>File open window for associate PDB doesn't open</li>
3032 <li>Left-then-right click on a sequence id opens a
3033 browser search window</li>
3034 <li>Cannot open sequence feature shading/sort popup menu
3035 in feature settings dialog</li>
3036 <li>better tooltip placement for some areas of Jalview
3038 <li>Allow addition of JABAWS Server which doesn't
3039 pass validation</li>
3040 <li>Web services parameters dialog box is too large to
3042 <li>Muscle nucleotide alignment preset obscured by
3044 <li>JABAWS preset submenus don't contain newly
3045 defined user preset</li>
3046 <li>MSA web services warns user if they were launched
3047 with invalid input</li>
3048 <li>Jalview cannot contact DAS Registy when running on
3051 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3052 'Superpose with' submenu not shown when new view
3056 </ul> <!-- <em>Applet</em>
3058 </ul> <em>General</em>
3060 </ul>--> <em>Deployment and Documentation</em>
3062 <li>2G and 1G options in launchApp have no effect on
3063 memory allocation</li>
3064 <li>launchApp service doesn't automatically open
3065 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3067 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3068 InstallAnywhere reports cannot find valid JVM when Java
3069 1.7_055 is available
3071 </ul> <em>Application Known issues</em>
3074 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3075 corrupted or unreadable alignment display when scrolling
3079 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3080 retrieval fails but progress bar continues for DAS retrieval
3081 with large number of ID
3084 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3085 flatfile output of visible region has incorrect sequence
3089 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3090 rna structure consensus doesn't update when secondary
3091 structure tracks are rearranged
3094 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3095 invalid rna structure positional highlighting does not
3096 highlight position of invalid base pairs
3099 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3100 out of memory errors are not raised when saving Jalview
3101 project from alignment window file menu
3104 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3105 Switching to RNA Helices colouring doesn't propagate to
3109 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3110 colour by RNA Helices not enabled when user created
3111 annotation added to alignment
3114 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3115 Jalview icon not shown on dock in Mountain Lion/Webstart
3117 </ul> <em>Applet Known Issues</em>
3120 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3121 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3124 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3125 Jalview and Jmol example not compatible with IE9
3128 <li>Sort by annotation score doesn't reverse order
3134 <td><div align="center">
3135 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3138 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3141 <li>Internationalisation of user interface (usually
3142 called i18n support) and translation for Spanish locale</li>
3143 <li>Define/Undefine group on current selection with
3144 Ctrl-G/Shift Ctrl-G</li>
3145 <li>Improved group creation/removal options in
3146 alignment/sequence Popup menu</li>
3147 <li>Sensible precision for symbol distribution
3148 percentages shown in logo tooltip.</li>
3149 <li>Annotation panel height set according to amount of
3150 annotation when alignment first opened</li>
3151 </ul> <em>Application</em>
3153 <li>Interactive consensus RNA secondary structure
3154 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3155 <li>Select columns containing particular features from
3156 Feature Settings dialog</li>
3157 <li>View all 'representative' PDB structures for selected
3159 <li>Update Jalview project format:
3161 <li>New file extension for Jalview projects '.jvp'</li>
3162 <li>Preserve sequence and annotation dataset (to
3163 store secondary structure annotation,etc)</li>
3164 <li>Per group and alignment annotation and RNA helix
3168 <li>New similarity measures for PCA and Tree calculation
3170 <li>Experimental support for retrieval and viewing of
3171 flanking regions for an alignment</li>
3175 <!-- issues resolved --> <em>Application</em>
3177 <li>logo keeps spinning and status remains at queued or
3178 running after job is cancelled</li>
3179 <li>cannot export features from alignments imported from
3180 Jalview/VAMSAS projects</li>
3181 <li>Buggy slider for web service parameters that take
3183 <li>Newly created RNA secondary structure line doesn't
3184 have 'display all symbols' flag set</li>
3185 <li>T-COFFEE alignment score shading scheme and other
3186 annotation shading not saved in Jalview project</li>
3187 <li>Local file cannot be loaded in freshly downloaded
3189 <li>Jalview icon not shown on dock in Mountain
3191 <li>Load file from desktop file browser fails</li>
3192 <li>Occasional NPE thrown when calculating large trees</li>
3193 <li>Cannot reorder or slide sequences after dragging an
3194 alignment onto desktop</li>
3195 <li>Colour by annotation dialog throws NPE after using
3196 'extract scores' function</li>
3197 <li>Loading/cut'n'pasting an empty file leads to a grey
3198 alignment window</li>
3199 <li>Disorder thresholds rendered incorrectly after
3200 performing IUPred disorder prediction</li>
3201 <li>Multiple group annotated consensus rows shown when
3202 changing 'normalise logo' display setting</li>
3203 <li>Find shows blank dialog after 'finished searching' if
3204 nothing matches query</li>
3205 <li>Null Pointer Exceptions raised when sorting by
3206 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3208 <li>Errors in Jmol console when structures in alignment
3209 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3211 <li>Not all working JABAWS services are shown in
3213 <li>JAVAWS version of Jalview fails to launch with
3214 'invalid literal/length code'</li>
3215 <li>Annotation/RNA Helix colourschemes cannot be applied
3216 to alignment with groups (actually fixed in 2.8.0b1)</li>
3217 <li>RNA Helices and T-Coffee Scores available as default
3220 </ul> <em>Applet</em>
3222 <li>Remove group option is shown even when selection is
3224 <li>Apply to all groups ticked but colourscheme changes
3225 don't affect groups</li>
3226 <li>Documented RNA Helices and T-Coffee Scores as valid
3227 colourscheme name</li>
3228 <li>Annotation labels drawn on sequence IDs when
3229 Annotation panel is not displayed</li>
3230 <li>Increased font size for dropdown menus on OSX and
3231 embedded windows</li>
3232 </ul> <em>Other</em>
3234 <li>Consensus sequence for alignments/groups with a
3235 single sequence were not calculated</li>
3236 <li>annotation files that contain only groups imported as
3237 annotation and junk sequences</li>
3238 <li>Fasta files with sequences containing '*' incorrectly
3239 recognised as PFAM or BLC</li>
3240 <li>conservation/PID slider apply all groups option
3241 doesn't affect background (2.8.0b1)
3243 <li>redundancy highlighting is erratic at 0% and 100%</li>
3244 <li>Remove gapped columns fails for sequences with ragged
3246 <li>AMSA annotation row with leading spaces is not
3247 registered correctly on import</li>
3248 <li>Jalview crashes when selecting PCA analysis for
3249 certain alignments</li>
3250 <li>Opening the colour by annotation dialog for an
3251 existing annotation based 'use original colours'
3252 colourscheme loses original colours setting</li>
3257 <td><div align="center">
3258 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3259 <em>30/1/2014</em></strong>
3263 <li>Trusted certificates for JalviewLite applet and
3264 Jalview Desktop application<br />Certificate was donated by
3265 <a href="https://www.certum.eu">Certum</a> to the Jalview
3266 open source project).
3268 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3269 <li>Output in Stockholm format</li>
3270 <li>Allow import of data from gzipped files</li>
3271 <li>Export/import group and sequence associated line
3272 graph thresholds</li>
3273 <li>Nucleotide substitution matrix that supports RNA and
3274 ambiguity codes</li>
3275 <li>Allow disorder predictions to be made on the current
3276 selection (or visible selection) in the same way that JPred
3278 <li>Groovy scripting for headless Jalview operation</li>
3279 </ul> <em>Other improvements</em>
3281 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3282 <li>COMBINE statement uses current SEQUENCE_REF and
3283 GROUP_REF scope to group annotation rows</li>
3284 <li>Support '' style escaping of quotes in Newick
3286 <li>Group options for JABAWS service by command line name</li>
3287 <li>Empty tooltip shown for JABA service options with a
3288 link but no description</li>
3289 <li>Select primary source when selecting authority in
3290 database fetcher GUI</li>
3291 <li>Add .mfa to FASTA file extensions recognised by
3293 <li>Annotation label tooltip text wrap</li>
3298 <li>Slow scrolling when lots of annotation rows are
3300 <li>Lots of NPE (and slowness) after creating RNA
3301 secondary structure annotation line</li>
3302 <li>Sequence database accessions not imported when
3303 fetching alignments from Rfam</li>
3304 <li>Incorrect SHMR submission for sequences with
3306 <li>View all structures does not always superpose
3308 <li>Option widgets in service parameters not updated to
3309 reflect user or preset settings</li>
3310 <li>Null pointer exceptions for some services without
3311 presets or adjustable parameters</li>
3312 <li>Discover PDB IDs entry in structure menu doesn't
3313 discover PDB xRefs</li>
3314 <li>Exception encountered while trying to retrieve
3315 features with DAS</li>
3316 <li>Lowest value in annotation row isn't coloured
3317 when colour by annotation (per sequence) is coloured</li>
3318 <li>Keyboard mode P jumps to start of gapped region when
3319 residue follows a gap</li>
3320 <li>Jalview appears to hang importing an alignment with
3321 Wrap as default or after enabling Wrap</li>
3322 <li>'Right click to add annotations' message
3323 shown in wrap mode when no annotations present</li>
3324 <li>Disorder predictions fail with NPE if no automatic
3325 annotation already exists on alignment</li>
3326 <li>oninit javascript function should be called after
3327 initialisation completes</li>
3328 <li>Remove redundancy after disorder prediction corrupts
3329 alignment window display</li>
3330 <li>Example annotation file in documentation is invalid</li>
3331 <li>Grouped line graph annotation rows are not exported
3332 to annotation file</li>
3333 <li>Multi-harmony analysis cannot be run when only two
3335 <li>Cannot create multiple groups of line graphs with
3336 several 'combine' statements in annotation file</li>
3337 <li>Pressing return several times causes Number Format
3338 exceptions in keyboard mode</li>
3339 <li>Multi-harmony (SHMMR) method doesn't submit
3340 correct partitions for input data</li>
3341 <li>Translation from DNA to Amino Acids fails</li>
3342 <li>Jalview fail to load newick tree with quoted label</li>
3343 <li>--headless flag isn't understood</li>
3344 <li>ClassCastException when generating EPS in headless
3346 <li>Adjusting sequence-associated shading threshold only
3347 changes one row's threshold</li>
3348 <li>Preferences and Feature settings panel panel
3349 doesn't open</li>
3350 <li>hide consensus histogram also hides conservation and
3351 quality histograms</li>
3356 <td><div align="center">
3357 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3359 <td><em>Application</em>
3361 <li>Support for JABAWS 2.0 Services (AACon alignment
3362 conservation, protein disorder and Clustal Omega)</li>
3363 <li>JABAWS server status indicator in Web Services
3365 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3366 in Jalview alignment window</li>
3367 <li>Updated Jalview build and deploy framework for OSX
3368 mountain lion, windows 7, and 8</li>
3369 <li>Nucleotide substitution matrix for PCA that supports
3370 RNA and ambiguity codes</li>
3372 <li>Improved sequence database retrieval GUI</li>
3373 <li>Support fetching and database reference look up
3374 against multiple DAS sources (Fetch all from in 'fetch db
3376 <li>Jalview project improvements
3378 <li>Store and retrieve the 'belowAlignment'
3379 flag for annotation</li>
3380 <li>calcId attribute to group annotation rows on the
3382 <li>Store AACon calculation settings for a view in
3383 Jalview project</li>
3387 <li>horizontal scrolling gesture support</li>
3388 <li>Visual progress indicator when PCA calculation is
3390 <li>Simpler JABA web services menus</li>
3391 <li>visual indication that web service results are still
3392 being retrieved from server</li>
3393 <li>Serialise the dialogs that are shown when Jalview
3394 starts up for first time</li>
3395 <li>Jalview user agent string for interacting with HTTP
3397 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3399 <li>Examples directory and Groovy library included in
3400 InstallAnywhere distribution</li>
3401 </ul> <em>Applet</em>
3403 <li>RNA alignment and secondary structure annotation
3404 visualization applet example</li>
3405 </ul> <em>General</em>
3407 <li>Normalise option for consensus sequence logo</li>
3408 <li>Reset button in PCA window to return dimensions to
3410 <li>Allow seqspace or Jalview variant of alignment PCA
3412 <li>PCA with either nucleic acid and protein substitution
3414 <li>Allow windows containing HTML reports to be exported
3416 <li>Interactive display and editing of RNA secondary
3417 structure contacts</li>
3418 <li>RNA Helix Alignment Colouring</li>
3419 <li>RNA base pair logo consensus</li>
3420 <li>Parse sequence associated secondary structure
3421 information in Stockholm files</li>
3422 <li>HTML Export database accessions and annotation
3423 information presented in tooltip for sequences</li>
3424 <li>Import secondary structure from LOCARNA clustalw
3425 style RNA alignment files</li>
3426 <li>import and visualise T-COFFEE quality scores for an
3428 <li>'colour by annotation' per sequence option to
3429 shade each sequence according to its associated alignment
3431 <li>New Jalview Logo</li>
3432 </ul> <em>Documentation and Development</em>
3434 <li>documentation for score matrices used in Jalview</li>
3435 <li>New Website!</li>
3437 <td><em>Application</em>
3439 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3440 wsdbfetch REST service</li>
3441 <li>Stop windows being moved outside desktop on OSX</li>
3442 <li>Filetype associations not installed for webstart
3444 <li>Jalview does not always retrieve progress of a JABAWS
3445 job execution in full once it is complete</li>
3446 <li>revise SHMR RSBS definition to ensure alignment is
3447 uploaded via ali_file parameter</li>
3448 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3449 <li>View all structures superposed fails with exception</li>
3450 <li>Jnet job queues forever if a very short sequence is
3451 submitted for prediction</li>
3452 <li>Cut and paste menu not opened when mouse clicked on
3454 <li>Putting fractional value into integer text box in
3455 alignment parameter dialog causes Jalview to hang</li>
3456 <li>Structure view highlighting doesn't work on
3458 <li>View all structures fails with exception shown in
3460 <li>Characters in filename associated with PDBEntry not
3461 escaped in a platform independent way</li>
3462 <li>Jalview desktop fails to launch with exception when
3464 <li>Tree calculation reports 'you must have 2 or more
3465 sequences selected' when selection is empty</li>
3466 <li>Jalview desktop fails to launch with jar signature
3467 failure when java web start temporary file caching is
3469 <li>DAS Sequence retrieval with range qualification
3470 results in sequence xref which includes range qualification</li>
3471 <li>Errors during processing of command line arguments
3472 cause progress bar (JAL-898) to be removed</li>
3473 <li>Replace comma for semi-colon option not disabled for
3474 DAS sources in sequence fetcher</li>
3475 <li>Cannot close news reader when JABAWS server warning
3476 dialog is shown</li>
3477 <li>Option widgets not updated to reflect user settings</li>
3478 <li>Edited sequence not submitted to web service</li>
3479 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3480 <li>InstallAnywhere installer doesn't unpack and run
3481 on OSX Mountain Lion</li>
3482 <li>Annotation panel not given a scroll bar when
3483 sequences with alignment annotation are pasted into the
3485 <li>Sequence associated annotation rows not associated
3486 when loaded from Jalview project</li>
3487 <li>Browser launch fails with NPE on java 1.7</li>
3488 <li>JABAWS alignment marked as finished when job was
3489 cancelled or job failed due to invalid input</li>
3490 <li>NPE with v2.7 example when clicking on Tree
3491 associated with all views</li>
3492 <li>Exceptions when copy/paste sequences with grouped
3493 annotation rows to new window</li>
3494 </ul> <em>Applet</em>
3496 <li>Sequence features are momentarily displayed before
3497 they are hidden using hidefeaturegroups applet parameter</li>
3498 <li>loading features via javascript API automatically
3499 enables feature display</li>
3500 <li>scrollToColumnIn javascript API method doesn't
3502 </ul> <em>General</em>
3504 <li>Redundancy removal fails for rna alignment</li>
3505 <li>PCA calculation fails when sequence has been selected
3506 and then deselected</li>
3507 <li>PCA window shows grey box when first opened on OSX</li>
3508 <li>Letters coloured pink in sequence logo when alignment
3509 coloured with clustalx</li>
3510 <li>Choosing fonts without letter symbols defined causes
3511 exceptions and redraw errors</li>
3512 <li>Initial PCA plot view is not same as manually
3513 reconfigured view</li>
3514 <li>Grouped annotation graph label has incorrect line
3516 <li>Grouped annotation graph label display is corrupted
3517 for lots of labels</li>
3522 <div align="center">
3523 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3526 <td><em>Application</em>
3528 <li>Jalview Desktop News Reader</li>
3529 <li>Tweaked default layout of web services menu</li>
3530 <li>View/alignment association menu to enable user to
3531 easily specify which alignment a multi-structure view takes
3532 its colours/correspondences from</li>
3533 <li>Allow properties file location to be specified as URL</li>
3534 <li>Extend Jalview project to preserve associations
3535 between many alignment views and a single Jmol display</li>
3536 <li>Store annotation row height in Jalview project file</li>
3537 <li>Annotation row column label formatting attributes
3538 stored in project file</li>
3539 <li>Annotation row order for auto-calculated annotation
3540 rows preserved in Jalview project file</li>
3541 <li>Visual progress indication when Jalview state is
3542 saved using Desktop window menu</li>
3543 <li>Visual indication that command line arguments are
3544 still being processed</li>
3545 <li>Groovy script execution from URL</li>
3546 <li>Colour by annotation default min and max colours in
3548 <li>Automatically associate PDB files dragged onto an
3549 alignment with sequences that have high similarity and
3551 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3552 <li>'view structures' option to open many
3553 structures in same window</li>
3554 <li>Sort associated views menu option for tree panel</li>
3555 <li>Group all JABA and non-JABA services for a particular
3556 analysis function in its own submenu</li>
3557 </ul> <em>Applet</em>
3559 <li>Userdefined and autogenerated annotation rows for
3561 <li>Adjustment of alignment annotation pane height</li>
3562 <li>Annotation scrollbar for annotation panel</li>
3563 <li>Drag to reorder annotation rows in annotation panel</li>
3564 <li>'automaticScrolling' parameter</li>
3565 <li>Allow sequences with partial ID string matches to be
3566 annotated from GFF/Jalview features files</li>
3567 <li>Sequence logo annotation row in applet</li>
3568 <li>Absolute paths relative to host server in applet
3569 parameters are treated as such</li>
3570 <li>New in the JalviewLite javascript API:
3572 <li>JalviewLite.js javascript library</li>
3573 <li>Javascript callbacks for
3575 <li>Applet initialisation</li>
3576 <li>Sequence/alignment mouse-overs and selections</li>
3579 <li>scrollTo row and column alignment scrolling
3581 <li>Select sequence/alignment regions from javascript</li>
3582 <li>javascript structure viewer harness to pass
3583 messages between Jmol and Jalview when running as
3584 distinct applets</li>
3585 <li>sortBy method</li>
3586 <li>Set of applet and application examples shipped
3587 with documentation</li>
3588 <li>New example to demonstrate JalviewLite and Jmol
3589 javascript message exchange</li>
3591 </ul> <em>General</em>
3593 <li>Enable Jmol displays to be associated with multiple
3594 multiple alignments</li>
3595 <li>Option to automatically sort alignment with new tree</li>
3596 <li>User configurable link to enable redirects to a
3597 www.Jalview.org mirror</li>
3598 <li>Jmol colours option for Jmol displays</li>
3599 <li>Configurable newline string when writing alignment
3600 and other flat files</li>
3601 <li>Allow alignment annotation description lines to
3602 contain html tags</li>
3603 </ul> <em>Documentation and Development</em>
3605 <li>Add groovy test harness for bulk load testing to
3607 <li>Groovy script to load and align a set of sequences
3608 using a web service before displaying the result in the
3609 Jalview desktop</li>
3610 <li>Restructured javascript and applet api documentation</li>
3611 <li>Ant target to publish example html files with applet
3613 <li>Netbeans project for building Jalview from source</li>
3614 <li>ant task to create online javadoc for Jalview source</li>
3616 <td><em>Application</em>
3618 <li>User defined colourscheme throws exception when
3619 current built in colourscheme is saved as new scheme</li>
3620 <li>AlignFrame->Save in application pops up save
3621 dialog for valid filename/format</li>
3622 <li>Cannot view associated structure for UniProt sequence</li>
3623 <li>PDB file association breaks for UniProt sequence
3625 <li>Associate PDB from file dialog does not tell you
3626 which sequence is to be associated with the file</li>
3627 <li>Find All raises null pointer exception when query
3628 only matches sequence IDs</li>
3629 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3630 <li>Jalview project with Jmol views created with Jalview
3631 2.4 cannot be loaded</li>
3632 <li>Filetype associations not installed for webstart
3634 <li>Two or more chains in a single PDB file associated
3635 with sequences in different alignments do not get coloured
3636 by their associated sequence</li>
3637 <li>Visibility status of autocalculated annotation row
3638 not preserved when project is loaded</li>
3639 <li>Annotation row height and visibility attributes not
3640 stored in Jalview project</li>
3641 <li>Tree bootstraps are not preserved when saved as a
3642 Jalview project</li>
3643 <li>Envision2 workflow tooltips are corrupted</li>
3644 <li>Enabling show group conservation also enables colour
3645 by conservation</li>
3646 <li>Duplicate group associated conservation or consensus
3647 created on new view</li>
3648 <li>Annotation scrollbar not displayed after 'show
3649 all hidden annotation rows' option selected</li>
3650 <li>Alignment quality not updated after alignment
3651 annotation row is hidden then shown</li>
3652 <li>Preserve colouring of structures coloured by
3653 sequences in pre Jalview 2.7 projects</li>
3654 <li>Web service job parameter dialog is not laid out
3656 <li>Web services menu not refreshed after 'reset
3657 services' button is pressed in preferences</li>
3658 <li>Annotation off by one in Jalview v2_3 example project</li>
3659 <li>Structures imported from file and saved in project
3660 get name like jalview_pdb1234.txt when reloaded</li>
3661 <li>Jalview does not always retrieve progress of a JABAWS
3662 job execution in full once it is complete</li>
3663 </ul> <em>Applet</em>
3665 <li>Alignment height set incorrectly when lots of
3666 annotation rows are displayed</li>
3667 <li>Relative URLs in feature HTML text not resolved to
3669 <li>View follows highlighting does not work for positions
3671 <li><= shown as = in tooltip</li>
3672 <li>Export features raises exception when no features
3674 <li>Separator string used for serialising lists of IDs
3675 for javascript api is modified when separator string
3676 provided as parameter</li>
3677 <li>Null pointer exception when selecting tree leaves for
3678 alignment with no existing selection</li>
3679 <li>Relative URLs for datasources assumed to be relative
3680 to applet's codebase</li>
3681 <li>Status bar not updated after finished searching and
3682 search wraps around to first result</li>
3683 <li>StructureSelectionManager instance shared between
3684 several Jalview applets causes race conditions and memory
3686 <li>Hover tooltip and mouseover of position on structure
3687 not sent from Jmol in applet</li>
3688 <li>Certain sequences of javascript method calls to
3689 applet API fatally hang browser</li>
3690 </ul> <em>General</em>
3692 <li>View follows structure mouseover scrolls beyond
3693 position with wrapped view and hidden regions</li>
3694 <li>Find sequence position moves to wrong residue
3695 with/without hidden columns</li>
3696 <li>Sequence length given in alignment properties window
3698 <li>InvalidNumberFormat exceptions thrown when trying to
3699 import PDB like structure files</li>
3700 <li>Positional search results are only highlighted
3701 between user-supplied sequence start/end bounds</li>
3702 <li>End attribute of sequence is not validated</li>
3703 <li>Find dialog only finds first sequence containing a
3704 given sequence position</li>
3705 <li>Sequence numbering not preserved in MSF alignment
3707 <li>Jalview PDB file reader does not extract sequence
3708 from nucleotide chains correctly</li>
3709 <li>Structure colours not updated when tree partition
3710 changed in alignment</li>
3711 <li>Sequence associated secondary structure not correctly
3712 parsed in interleaved stockholm</li>
3713 <li>Colour by annotation dialog does not restore current
3715 <li>Hiding (nearly) all sequences doesn't work
3717 <li>Sequences containing lowercase letters are not
3718 properly associated with their pdb files</li>
3719 </ul> <em>Documentation and Development</em>
3721 <li>schemas/JalviewWsParamSet.xsd corrupted by
3722 ApplyCopyright tool</li>
3727 <div align="center">
3728 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3731 <td><em>Application</em>
3733 <li>New warning dialog when the Jalview Desktop cannot
3734 contact web services</li>
3735 <li>JABA service parameters for a preset are shown in
3736 service job window</li>
3737 <li>JABA Service menu entries reworded</li>
3741 <li>Modeller PIR IO broken - cannot correctly import a
3742 pir file emitted by Jalview</li>
3743 <li>Existing feature settings transferred to new
3744 alignment view created from cut'n'paste</li>
3745 <li>Improved test for mixed amino/nucleotide chains when
3746 parsing PDB files</li>
3747 <li>Consensus and conservation annotation rows
3748 occasionally become blank for all new windows</li>
3749 <li>Exception raised when right clicking above sequences
3750 in wrapped view mode</li>
3751 </ul> <em>Application</em>
3753 <li>multiple multiply aligned structure views cause cpu
3754 usage to hit 100% and computer to hang</li>
3755 <li>Web Service parameter layout breaks for long user
3756 parameter names</li>
3757 <li>Jaba service discovery hangs desktop if Jaba server
3764 <div align="center">
3765 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3768 <td><em>Application</em>
3770 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3771 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3774 <li>Web Services preference tab</li>
3775 <li>Analysis parameters dialog box and user defined
3777 <li>Improved speed and layout of Envision2 service menu</li>
3778 <li>Superpose structures using associated sequence
3780 <li>Export coordinates and projection as CSV from PCA
3782 </ul> <em>Applet</em>
3784 <li>enable javascript: execution by the applet via the
3785 link out mechanism</li>
3786 </ul> <em>Other</em>
3788 <li>Updated the Jmol Jalview interface to work with Jmol
3790 <li>The Jalview Desktop and JalviewLite applet now
3791 require Java 1.5</li>
3792 <li>Allow Jalview feature colour specification for GFF
3793 sequence annotation files</li>
3794 <li>New 'colour by label' keword in Jalview feature file
3795 type colour specification</li>
3796 <li>New Jalview Desktop Groovy API method that allows a
3797 script to check if it being run in an interactive session or
3798 in a batch operation from the Jalview command line</li>
3802 <li>clustalx colourscheme colours Ds preferentially when
3803 both D+E are present in over 50% of the column</li>
3804 </ul> <em>Application</em>
3806 <li>typo in AlignmentFrame->View->Hide->all but
3807 selected Regions menu item</li>
3808 <li>sequence fetcher replaces ',' for ';' when the ',' is
3809 part of a valid accession ID</li>
3810 <li>fatal OOM if object retrieved by sequence fetcher
3811 runs out of memory</li>
3812 <li>unhandled Out of Memory Error when viewing pca
3813 analysis results</li>
3814 <li>InstallAnywhere builds fail to launch on OS X java
3815 10.5 update 4 (due to apple Java 1.6 update)</li>
3816 <li>Installanywhere Jalview silently fails to launch</li>
3817 </ul> <em>Applet</em>
3819 <li>Jalview.getFeatureGroups() raises an
3820 ArrayIndexOutOfBoundsException if no feature groups are
3827 <div align="center">
3828 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3834 <li>Alignment prettyprinter doesn't cope with long
3836 <li>clustalx colourscheme colours Ds preferentially when
3837 both D+E are present in over 50% of the column</li>
3838 <li>nucleic acid structures retrieved from PDB do not
3839 import correctly</li>
3840 <li>More columns get selected than were clicked on when a
3841 number of columns are hidden</li>
3842 <li>annotation label popup menu not providing correct
3843 add/hide/show options when rows are hidden or none are
3845 <li>Stockholm format shown in list of readable formats,
3846 and parser copes better with alignments from RFAM.</li>
3847 <li>CSV output of consensus only includes the percentage
3848 of all symbols if sequence logo display is enabled</li>
3850 </ul> <em>Applet</em>
3852 <li>annotation panel disappears when annotation is
3854 </ul> <em>Application</em>
3856 <li>Alignment view not redrawn properly when new
3857 alignment opened where annotation panel is visible but no
3858 annotations are present on alignment</li>
3859 <li>pasted region containing hidden columns is
3860 incorrectly displayed in new alignment window</li>
3861 <li>Jalview slow to complete operations when stdout is
3862 flooded (fix is to close the Jalview console)</li>
3863 <li>typo in AlignmentFrame->View->Hide->all but
3864 selected Rregions menu item.</li>
3865 <li>inconsistent group submenu and Format submenu entry
3866 'Un' or 'Non'conserved</li>
3867 <li>Sequence feature settings are being shared by
3868 multiple distinct alignments</li>
3869 <li>group annotation not recreated when tree partition is
3871 <li>double click on group annotation to select sequences
3872 does not propagate to associated trees</li>
3873 <li>Mac OSX specific issues:
3875 <li>exception raised when mouse clicked on desktop
3876 window background</li>
3877 <li>Desktop menu placed on menu bar and application
3878 name set correctly</li>
3879 <li>sequence feature settings not wide enough for the
3880 save feature colourscheme button</li>
3889 <div align="center">
3890 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3893 <td><em>New Capabilities</em>
3895 <li>URL links generated from description line for
3896 regular-expression based URL links (applet and application)
3898 <li>Non-positional feature URL links are shown in link
3900 <li>Linked viewing of nucleic acid sequences and
3902 <li>Automatic Scrolling option in View menu to display
3903 the currently highlighted region of an alignment.</li>
3904 <li>Order an alignment by sequence length, or using the
3905 average score or total feature count for each sequence.</li>
3906 <li>Shading features by score or associated description</li>
3907 <li>Subdivide alignment and groups based on identity of
3908 selected subsequence (Make Groups from Selection).</li>
3909 <li>New hide/show options including Shift+Control+H to
3910 hide everything but the currently selected region.</li>
3911 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3912 </ul> <em>Application</em>
3914 <li>Fetch DB References capabilities and UI expanded to
3915 support retrieval from DAS sequence sources</li>
3916 <li>Local DAS Sequence sources can be added via the
3917 command line or via the Add local source dialog box.</li>
3918 <li>DAS Dbref and DbxRef feature types are parsed as
3919 database references and protein_name is parsed as
3920 description line (BioSapiens terms).</li>
3921 <li>Enable or disable non-positional feature and database
3922 references in sequence ID tooltip from View menu in
3924 <!-- <li>New hidden columns and rows and representatives capabilities
3925 in annotations file (in progress - not yet fully implemented)</li> -->
3926 <li>Group-associated consensus, sequence logos and
3927 conservation plots</li>
3928 <li>Symbol distributions for each column can be exported
3929 and visualized as sequence logos</li>
3930 <li>Optionally scale multi-character column labels to fit
3931 within each column of annotation row<!-- todo for applet -->
3933 <li>Optional automatic sort of associated alignment view
3934 when a new tree is opened.</li>
3935 <li>Jalview Java Console</li>
3936 <li>Better placement of desktop window when moving
3937 between different screens.</li>
3938 <li>New preference items for sequence ID tooltip and
3939 consensus annotation</li>
3940 <li>Client to submit sequences and IDs to Envision2
3942 <li><em>Vamsas Capabilities</em>
3944 <li>Improved VAMSAS synchronization (Jalview archive
3945 used to preserve views, structures, and tree display
3947 <li>Import of vamsas documents from disk or URL via
3949 <li>Sharing of selected regions between views and
3950 with other VAMSAS applications (Experimental feature!)</li>
3951 <li>Updated API to VAMSAS version 0.2</li>
3953 </ul> <em>Applet</em>
3955 <li>Middle button resizes annotation row height</li>
3958 <li>sortByTree (true/false) - automatically sort the
3959 associated alignment view by the tree when a new tree is
3961 <li>showTreeBootstraps (true/false) - show or hide
3962 branch bootstraps (default is to show them if available)</li>
3963 <li>showTreeDistances (true/false) - show or hide
3964 branch lengths (default is to show them if available)</li>
3965 <li>showUnlinkedTreeNodes (true/false) - indicate if
3966 unassociated nodes should be highlighted in the tree
3968 <li>heightScale and widthScale (1.0 or more) -
3969 increase the height or width of a cell in the alignment
3970 grid relative to the current font size.</li>
3973 <li>Non-positional features displayed in sequence ID
3975 </ul> <em>Other</em>
3977 <li>Features format: graduated colour definitions and
3978 specification of feature scores</li>
3979 <li>Alignment Annotations format: new keywords for group
3980 associated annotation (GROUP_REF) and annotation row display
3981 properties (ROW_PROPERTIES)</li>
3982 <li>XML formats extended to support graduated feature
3983 colourschemes, group associated annotation, and profile
3984 visualization settings.</li></td>
3987 <li>Source field in GFF files parsed as feature source
3988 rather than description</li>
3989 <li>Non-positional features are now included in sequence
3990 feature and gff files (controlled via non-positional feature
3991 visibility in tooltip).</li>
3992 <li>URL links generated for all feature links (bugfix)</li>
3993 <li>Added URL embedding instructions to features file
3995 <li>Codons containing ambiguous nucleotides translated as
3996 'X' in peptide product</li>
3997 <li>Match case switch in find dialog box works for both
3998 sequence ID and sequence string and query strings do not
3999 have to be in upper case to match case-insensitively.</li>
4000 <li>AMSA files only contain first column of
4001 multi-character column annotation labels</li>
4002 <li>Jalview Annotation File generation/parsing consistent
4003 with documentation (e.g. Stockholm annotation can be
4004 exported and re-imported)</li>
4005 <li>PDB files without embedded PDB IDs given a friendly
4007 <li>Find incrementally searches ID string matches as well
4008 as subsequence matches, and correctly reports total number
4012 <li>Better handling of exceptions during sequence
4014 <li>Dasobert generated non-positional feature URL
4015 link text excludes the start_end suffix</li>
4016 <li>DAS feature and source retrieval buttons disabled
4017 when fetch or registry operations in progress.</li>
4018 <li>PDB files retrieved from URLs are cached properly</li>
4019 <li>Sequence description lines properly shared via
4021 <li>Sequence fetcher fetches multiple records for all
4023 <li>Ensured that command line das feature retrieval
4024 completes before alignment figures are generated.</li>
4025 <li>Reduced time taken when opening file browser for
4027 <li>isAligned check prior to calculating tree, PCA or
4028 submitting an MSA to JNet now excludes hidden sequences.</li>
4029 <li>User defined group colours properly recovered
4030 from Jalview projects.</li>
4039 <div align="center">
4040 <strong>2.4.0.b2</strong><br> 28/10/2009
4045 <li>Experimental support for google analytics usage
4047 <li>Jalview privacy settings (user preferences and docs).</li>
4052 <li>Race condition in applet preventing startup in
4054 <li>Exception when feature created from selection beyond
4055 length of sequence.</li>
4056 <li>Allow synthetic PDB files to be imported gracefully</li>
4057 <li>Sequence associated annotation rows associate with
4058 all sequences with a given id</li>
4059 <li>Find function matches case-insensitively for sequence
4060 ID string searches</li>
4061 <li>Non-standard characters do not cause pairwise
4062 alignment to fail with exception</li>
4063 </ul> <em>Application Issues</em>
4065 <li>Sequences are now validated against EMBL database</li>
4066 <li>Sequence fetcher fetches multiple records for all
4068 </ul> <em>InstallAnywhere Issues</em>
4070 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4071 issue with installAnywhere mechanism)</li>
4072 <li>Command line launching of JARs from InstallAnywhere
4073 version (java class versioning error fixed)</li>
4080 <div align="center">
4081 <strong>2.4</strong><br> 27/8/2008
4084 <td><em>User Interface</em>
4086 <li>Linked highlighting of codon and amino acid from
4087 translation and protein products</li>
4088 <li>Linked highlighting of structure associated with
4089 residue mapping to codon position</li>
4090 <li>Sequence Fetcher provides example accession numbers
4091 and 'clear' button</li>
4092 <li>MemoryMonitor added as an option under Desktop's
4094 <li>Extract score function to parse whitespace separated
4095 numeric data in description line</li>
4096 <li>Column labels in alignment annotation can be centred.</li>
4097 <li>Tooltip for sequence associated annotation give name
4099 </ul> <em>Web Services and URL fetching</em>
4101 <li>JPred3 web service</li>
4102 <li>Prototype sequence search client (no public services
4104 <li>Fetch either seed alignment or full alignment from
4106 <li>URL Links created for matching database cross
4107 references as well as sequence ID</li>
4108 <li>URL Links can be created using regular-expressions</li>
4109 </ul> <em>Sequence Database Connectivity</em>
4111 <li>Retrieval of cross-referenced sequences from other
4113 <li>Generalised database reference retrieval and
4114 validation to all fetchable databases</li>
4115 <li>Fetch sequences from DAS sources supporting the
4116 sequence command</li>
4117 </ul> <em>Import and Export</em>
4118 <li>export annotation rows as CSV for spreadsheet import</li>
4119 <li>Jalview projects record alignment dataset associations,
4120 EMBL products, and cDNA sequence mappings</li>
4121 <li>Sequence Group colour can be specified in Annotation
4123 <li>Ad-hoc colouring of group in Annotation File using RGB
4124 triplet as name of colourscheme</li>
4125 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4127 <li>treenode binding for VAMSAS tree exchange</li>
4128 <li>local editing and update of sequences in VAMSAS
4129 alignments (experimental)</li>
4130 <li>Create new or select existing session to join</li>
4131 <li>load and save of vamsas documents</li>
4132 </ul> <em>Application command line</em>
4134 <li>-tree parameter to open trees (introduced for passing
4136 <li>-fetchfrom command line argument to specify nicknames
4137 of DAS servers to query for alignment features</li>
4138 <li>-dasserver command line argument to add new servers
4139 that are also automatically queried for features</li>
4140 <li>-groovy command line argument executes a given groovy
4141 script after all input data has been loaded and parsed</li>
4142 </ul> <em>Applet-Application data exchange</em>
4144 <li>Trees passed as applet parameters can be passed to
4145 application (when using "View in full
4146 application")</li>
4147 </ul> <em>Applet Parameters</em>
4149 <li>feature group display control parameter</li>
4150 <li>debug parameter</li>
4151 <li>showbutton parameter</li>
4152 </ul> <em>Applet API methods</em>
4154 <li>newView public method</li>
4155 <li>Window (current view) specific get/set public methods</li>
4156 <li>Feature display control methods</li>
4157 <li>get list of currently selected sequences</li>
4158 </ul> <em>New Jalview distribution features</em>
4160 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4161 <li>RELEASE file gives build properties for the latest
4162 Jalview release.</li>
4163 <li>Java 1.1 Applet build made easier and donotobfuscate
4164 property controls execution of obfuscator</li>
4165 <li>Build target for generating source distribution</li>
4166 <li>Debug flag for javacc</li>
4167 <li>.jalview_properties file is documented (slightly) in
4168 jalview.bin.Cache</li>
4169 <li>Continuous Build Integration for stable and
4170 development version of Application, Applet and source
4175 <li>selected region output includes visible annotations
4176 (for certain formats)</li>
4177 <li>edit label/displaychar contains existing label/char
4179 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4180 <li>shorter peptide product names from EMBL records</li>
4181 <li>Newick string generator makes compact representations</li>
4182 <li>bootstrap values parsed correctly for tree files with
4184 <li>pathological filechooser bug avoided by not allowing
4185 filenames containing a ':'</li>
4186 <li>Fixed exception when parsing GFF files containing
4187 global sequence features</li>
4188 <li>Alignment datasets are finalized only when number of
4189 references from alignment sequences goes to zero</li>
4190 <li>Close of tree branch colour box without colour
4191 selection causes cascading exceptions</li>
4192 <li>occasional negative imgwidth exceptions</li>
4193 <li>better reporting of non-fatal warnings to user when
4194 file parsing fails.</li>
4195 <li>Save works when Jalview project is default format</li>
4196 <li>Save as dialog opened if current alignment format is
4197 not a valid output format</li>
4198 <li>UniProt canonical names introduced for both das and
4200 <li>Histidine should be midblue (not pink!) in Zappo</li>
4201 <li>error messages passed up and output when data read
4203 <li>edit undo recovers previous dataset sequence when
4204 sequence is edited</li>
4205 <li>allow PDB files without pdb ID HEADER lines (like
4206 those generated by MODELLER) to be read in properly</li>
4207 <li>allow reading of JPred concise files as a normal
4209 <li>Stockholm annotation parsing and alignment properties
4210 import fixed for PFAM records</li>
4211 <li>Structure view windows have correct name in Desktop
4213 <li>annotation consisting of sequence associated scores
4214 can be read and written correctly to annotation file</li>
4215 <li>Aligned cDNA translation to aligned peptide works
4217 <li>Fixed display of hidden sequence markers and
4218 non-italic font for representatives in Applet</li>
4219 <li>Applet Menus are always embedded in applet window on
4221 <li>Newly shown features appear at top of stack (in
4223 <li>Annotations added via parameter not drawn properly
4224 due to null pointer exceptions</li>
4225 <li>Secondary structure lines are drawn starting from
4226 first column of alignment</li>
4227 <li>UniProt XML import updated for new schema release in
4229 <li>Sequence feature to sequence ID match for Features
4230 file is case-insensitive</li>
4231 <li>Sequence features read from Features file appended to
4232 all sequences with matching IDs</li>
4233 <li>PDB structure coloured correctly for associated views
4234 containing a sub-sequence</li>
4235 <li>PDB files can be retrieved by applet from Jar files</li>
4236 <li>feature and annotation file applet parameters
4237 referring to different directories are retrieved correctly</li>
4238 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4239 <li>Fixed application hang whilst waiting for
4240 splash-screen version check to complete</li>
4241 <li>Applet properly URLencodes input parameter values
4242 when passing them to the launchApp service</li>
4243 <li>display name and local features preserved in results
4244 retrieved from web service</li>
4245 <li>Visual delay indication for sequence retrieval and
4246 sequence fetcher initialisation</li>
4247 <li>updated Application to use DAS 1.53e version of
4248 dasobert DAS client</li>
4249 <li>Re-instated Full AMSA support and .amsa file
4251 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4259 <div align="center">
4260 <strong>2.3</strong><br> 9/5/07
4265 <li>Jmol 11.0.2 integration</li>
4266 <li>PDB views stored in Jalview XML files</li>
4267 <li>Slide sequences</li>
4268 <li>Edit sequence in place</li>
4269 <li>EMBL CDS features</li>
4270 <li>DAS Feature mapping</li>
4271 <li>Feature ordering</li>
4272 <li>Alignment Properties</li>
4273 <li>Annotation Scores</li>
4274 <li>Sort by scores</li>
4275 <li>Feature/annotation editing in applet</li>
4280 <li>Headless state operation in 2.2.1</li>
4281 <li>Incorrect and unstable DNA pairwise alignment</li>
4282 <li>Cut and paste of sequences with annotation</li>
4283 <li>Feature group display state in XML</li>
4284 <li>Feature ordering in XML</li>
4285 <li>blc file iteration selection using filename # suffix</li>
4286 <li>Stockholm alignment properties</li>
4287 <li>Stockhom alignment secondary structure annotation</li>
4288 <li>2.2.1 applet had no feature transparency</li>
4289 <li>Number pad keys can be used in cursor mode</li>
4290 <li>Structure Viewer mirror image resolved</li>
4297 <div align="center">
4298 <strong>2.2.1</strong><br> 12/2/07
4303 <li>Non standard characters can be read and displayed
4304 <li>Annotations/Features can be imported/exported to the
4306 <li>Applet allows editing of sequence/annotation/group
4307 name & description
4308 <li>Preference setting to display sequence name in
4310 <li>Annotation file format extended to allow
4311 Sequence_groups to be defined
4312 <li>Default opening of alignment overview panel can be
4313 specified in preferences
4314 <li>PDB residue numbering annotation added to associated
4320 <li>Applet crash under certain Linux OS with Java 1.6
4322 <li>Annotation file export / import bugs fixed
4323 <li>PNG / EPS image output bugs fixed
4329 <div align="center">
4330 <strong>2.2</strong><br> 27/11/06
4335 <li>Multiple views on alignment
4336 <li>Sequence feature editing
4337 <li>"Reload" alignment
4338 <li>"Save" to current filename
4339 <li>Background dependent text colour
4340 <li>Right align sequence ids
4341 <li>User-defined lower case residue colours
4344 <li>Menu item accelerator keys
4345 <li>Control-V pastes to current alignment
4346 <li>Cancel button for DAS Feature Fetching
4347 <li>PCA and PDB Viewers zoom via mouse roller
4348 <li>User-defined sub-tree colours and sub-tree selection
4350 <li>'New Window' button on the 'Output to Text box'
4355 <li>New memory efficient Undo/Redo System
4356 <li>Optimised symbol lookups and conservation/consensus
4358 <li>Region Conservation/Consensus recalculated after
4360 <li>Fixed Remove Empty Columns Bug (empty columns at end
4362 <li>Slowed DAS Feature Fetching for increased robustness.
4364 <li>Made angle brackets in ASCII feature descriptions
4366 <li>Re-instated Zoom function for PCA
4367 <li>Sequence descriptions conserved in web service
4369 <li>UniProt ID discoverer uses any word separated by
4371 <li>WsDbFetch query/result association resolved
4372 <li>Tree leaf to sequence mapping improved
4373 <li>Smooth fonts switch moved to FontChooser dialog box.
4380 <div align="center">
4381 <strong>2.1.1</strong><br> 12/9/06
4386 <li>Copy consensus sequence to clipboard</li>
4391 <li>Image output - rightmost residues are rendered if
4392 sequence id panel has been resized</li>
4393 <li>Image output - all offscreen group boundaries are
4395 <li>Annotation files with sequence references - all
4396 elements in file are relative to sequence position</li>
4397 <li>Mac Applet users can use Alt key for group editing</li>
4403 <div align="center">
4404 <strong>2.1</strong><br> 22/8/06
4409 <li>MAFFT Multiple Alignment in default Web Service list</li>
4410 <li>DAS Feature fetching</li>
4411 <li>Hide sequences and columns</li>
4412 <li>Export Annotations and Features</li>
4413 <li>GFF file reading / writing</li>
4414 <li>Associate structures with sequences from local PDB
4416 <li>Add sequences to exisiting alignment</li>
4417 <li>Recently opened files / URL lists</li>
4418 <li>Applet can launch the full application</li>
4419 <li>Applet has transparency for features (Java 1.2
4421 <li>Applet has user defined colours parameter</li>
4422 <li>Applet can load sequences from parameter
4423 "sequence<em>x</em>"
4429 <li>Redundancy Panel reinstalled in the Applet</li>
4430 <li>Monospaced font - EPS / rescaling bug fixed</li>
4431 <li>Annotation files with sequence references bug fixed</li>
4437 <div align="center">
4438 <strong>2.08.1</strong><br> 2/5/06
4443 <li>Change case of selected region from Popup menu</li>
4444 <li>Choose to match case when searching</li>
4445 <li>Middle mouse button and mouse movement can compress /
4446 expand the visible width and height of the alignment</li>
4451 <li>Annotation Panel displays complete JNet results</li>
4457 <div align="center">
4458 <strong>2.08b</strong><br> 18/4/06
4464 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4465 <li>Righthand label on wrapped alignments shows correct
4472 <div align="center">
4473 <strong>2.08</strong><br> 10/4/06
4478 <li>Editing can be locked to the selection area</li>
4479 <li>Keyboard editing</li>
4480 <li>Create sequence features from searches</li>
4481 <li>Precalculated annotations can be loaded onto
4483 <li>Features file allows grouping of features</li>
4484 <li>Annotation Colouring scheme added</li>
4485 <li>Smooth fonts off by default - Faster rendering</li>
4486 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4491 <li>Drag & Drop fixed on Linux</li>
4492 <li>Jalview Archive file faster to load/save, sequence
4493 descriptions saved.</li>
4499 <div align="center">
4500 <strong>2.07</strong><br> 12/12/05
4505 <li>PDB Structure Viewer enhanced</li>
4506 <li>Sequence Feature retrieval and display enhanced</li>
4507 <li>Choose to output sequence start-end after sequence
4508 name for file output</li>
4509 <li>Sequence Fetcher WSDBFetch@EBI</li>
4510 <li>Applet can read feature files, PDB files and can be
4511 used for HTML form input</li>
4516 <li>HTML output writes groups and features</li>
4517 <li>Group editing is Control and mouse click</li>
4518 <li>File IO bugs</li>
4524 <div align="center">
4525 <strong>2.06</strong><br> 28/9/05
4530 <li>View annotations in wrapped mode</li>
4531 <li>More options for PCA viewer</li>
4536 <li>GUI bugs resolved</li>
4537 <li>Runs with -nodisplay from command line</li>
4543 <div align="center">
4544 <strong>2.05b</strong><br> 15/9/05
4549 <li>Choose EPS export as lineart or text</li>
4550 <li>Jar files are executable</li>
4551 <li>Can read in Uracil - maps to unknown residue</li>
4556 <li>Known OutOfMemory errors give warning message</li>
4557 <li>Overview window calculated more efficiently</li>
4558 <li>Several GUI bugs resolved</li>
4564 <div align="center">
4565 <strong>2.05</strong><br> 30/8/05
4570 <li>Edit and annotate in "Wrapped" view</li>
4575 <li>Several GUI bugs resolved</li>
4581 <div align="center">
4582 <strong>2.04</strong><br> 24/8/05
4587 <li>Hold down mouse wheel & scroll to change font
4593 <li>Improved JPred client reliability</li>
4594 <li>Improved loading of Jalview files</li>
4600 <div align="center">
4601 <strong>2.03</strong><br> 18/8/05
4606 <li>Set Proxy server name and port in preferences</li>
4607 <li>Multiple URL links from sequence ids</li>
4608 <li>User Defined Colours can have a scheme name and added
4610 <li>Choose to ignore gaps in consensus calculation</li>
4611 <li>Unix users can set default web browser</li>
4612 <li>Runs without GUI for batch processing</li>
4613 <li>Dynamically generated Web Service Menus</li>
4618 <li>InstallAnywhere download for Sparc Solaris</li>
4624 <div align="center">
4625 <strong>2.02</strong><br> 18/7/05
4631 <li>Copy & Paste order of sequences maintains
4632 alignment order.</li>
4638 <div align="center">
4639 <strong>2.01</strong><br> 12/7/05
4644 <li>Use delete key for deleting selection.</li>
4645 <li>Use Mouse wheel to scroll sequences.</li>
4646 <li>Help file updated to describe how to add alignment
4648 <li>Version and build date written to build properties
4650 <li>InstallAnywhere installation will check for updates
4651 at launch of Jalview.</li>
4656 <li>Delete gaps bug fixed.</li>
4657 <li>FileChooser sorts columns.</li>
4658 <li>Can remove groups one by one.</li>
4659 <li>Filechooser icons installed.</li>
4660 <li>Finder ignores return character when searching.
4661 Return key will initiate a search.<br>
4668 <div align="center">
4669 <strong>2.0</strong><br> 20/6/05
4674 <li>New codebase</li>