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 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
61 <em>27/03/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3187 -->Option to show 'virtual' codon features on protein (or vice versa)
68 <!-- JAL-3304 -->Option to export virtual features if shown
71 <!-- JAL-3302 -->Option to transfer virtual features to Chimera
74 <!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
77 <!-- JAL-3376 -->Capture VCF "fixed column" values POS,
78 ID, QUAL, FILTER as Feature Attributes
81 <!-- JAL-3375 -->More robust VCF numeric data field validation while parsing
84 <!-- JAL-3533 -->Feature Settings dialog keeps same screen position if reopened
87 <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
90 <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
93 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted with no feature types visible
95 </ul><em>Jalview Installer</em>
98 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
99 in console (may be null when Jalview launched as executable jar or via conda)
102 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
105 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
108 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
110 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
111 </ul> <em>Release processes</em>
114 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
116 </ul> <em>Build System</em>
119 <!-- JAL-3510 -->Clover updated to 4.4.1
122 <!-- JAL-3513 -->Test code included in Clover coverage
127 <td align="left" valign="top">
130 <!-- JAL-3412 -->ID margins for CDS and Protein views not equal when split frame is first opened
133 <!-- JAL-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position
136 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
137 with annotation and exceptions thrown when only a few
138 columns shown in wrapped mode
141 <!-- JAL-3386 -->Sequence IDs missing in headless export of
142 wrapped alignment figure with annotations
145 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
146 ID fails with ClassCastException
149 <!-- JAL-3389 -->Chimera session not restored from Jalview
153 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
154 feature settings dialog also selects columns
157 <!-- JAL-3473 -->SpinnerNumberModel causes
158 IllegalArgumentException in some circumstances
161 <!-- JAL-3534 -->Multiple feature settings dialogs can be opened for a view
164 <!-- JAL-2764 -->Feature Settings dialog is orphaned if alignment window is closed
167 <!-- JAL-3406 -->Credits missing some authors in Jalview
168 help documentation for 2.11.0 release
170 </ul> <em>Java 11 Compatibility issues</em>
173 <!-- JAL-2987 -->OSX - Can't view some search results in PDB/Uniprot search panel
175 </ul> <em>Installer</em>
177 <li><!-- JAL-3447 -->Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
179 </ul> <em>Repository and Source Release</em>
182 <!-- JAL-3474 -->removed obsolete .cvsignore files from repository
185 <!-- JAL-3541 -->Clover report generation running out of memory
188 <em>New Known Issues</em>
191 <!-- JAL-3523 -->OSX - Current working directory not
192 preserved when Jalview.app launched with parameters from
196 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
197 clipped in headless figure export when Right Align option
201 <!-- JAL-3542 -->Jalview Installation type always reports 'Source' in console output
207 <td width="60" align="center" nowrap>
208 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
209 <em>04/07/2019</em></strong>
211 <td align="left" valign="top">
214 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
215 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
216 source project) rather than InstallAnywhere
219 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
220 settings, receive over the air updates and launch specific
221 versions via (<a href="https://github.com/threerings/getdown">Three
225 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
226 formats supported by Jalview (including .jvp project files)
229 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
230 arguments and switch between different getdown channels
233 <!-- JAL-3141 -->Backup files created when saving Jalview project
238 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
239 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
241 <!-- JAL-2620 -->Alternative genetic code tables for
242 'Translate as cDNA'</li>
244 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
245 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
248 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
249 implementation that allows updates) used for Sequence Feature collections</li>
251 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
252 features can be filtered and shaded according to any
253 associated attributes (e.g. variant attributes from VCF
254 file, or key-value pairs imported from column 9 of GFF
258 <!-- JAL-2879 -->Feature Attributes and shading schemes
259 stored and restored from Jalview Projects
262 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
263 recognise variant features
266 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
267 sequences (also coloured red by default)
270 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
274 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
275 algorithm (Z-sort/transparency and filter aware)
278 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
284 <!-- JAL-3205 -->Symmetric score matrices for faster
285 tree and PCA calculations
287 <li><strong>Principal Components Analysis Viewer</strong>
290 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
291 and Viewer state saved in Jalview Project
293 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
296 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
300 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
305 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
307 <li><strong>Speed and Efficiency</strong>
310 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
311 multiple groups when working with large alignments
314 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
318 <li><strong>User Interface</strong>
321 <!-- JAL-2933 -->Finder panel remembers last position in each
325 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
326 what is shown)<br />Only visible regions of alignment are shown by
327 default (can be changed in user preferences)
330 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
331 to the Overwrite Dialog
334 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
338 <!-- JAL-1244 -->Status bar shows bounds when dragging a
339 selection region, and gap count when inserting or deleting gaps
342 <!-- JAL-3132 -->Status bar updates over sequence and annotation
346 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
350 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
354 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
357 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
361 <!-- JAL-3181 -->Consistent ordering of links in sequence id
365 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
367 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
371 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
372 <li><strong>Java 11 Support (not yet on general release)</strong>
375 <!-- -->OSX GUI integrations for App menu's 'About' entry and
380 <em>Deprecations</em>
382 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
383 capabilities removed from the Jalview Desktop
385 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
386 unmarshalling has been replaced by JAXB for Jalview projects
387 and XML based data retrieval clients</li>
388 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
389 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
390 </ul> <em>Documentation</em>
392 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
393 not supported in EPS figure export
395 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
396 </ul> <em>Development and Release Processes</em>
399 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
402 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
404 <!-- JAL-3225 -->Eclipse project configuration managed with
408 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
409 Bamboo continuous integration for unattended Test Suite
413 <!-- JAL-2864 -->Memory test suite to detect leaks in common
417 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
421 <!-- JAL-3248 -->Developer documentation migrated to
422 markdown (with HTML rendering)
425 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
428 <!-- JAL-3289 -->New URLs for publishing development
433 <td align="left" valign="top">
436 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
439 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
440 superposition in Jmol fail on Windows
443 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
444 structures for sequences with lots of PDB structures
447 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
451 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
452 project involving multiple views
455 <!-- JAL-3164 -->Overview for complementary view in a linked
456 CDS/Protein alignment is not updated when Hide Columns by
457 Annotation dialog hides columns
460 <!-- JAL-3158 -->Selection highlighting in the complement of a
461 CDS/Protein alignment stops working after making a selection in
462 one view, then making another selection in the other view
465 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
469 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
470 Settings and Jalview Preferences panels
473 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
474 overview with large alignments
477 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
478 region if columns were selected by dragging right-to-left and the
479 mouse moved to the left of the first column
482 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
483 hidden column marker via scale popup menu
486 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
487 doesn't tell users the invalid URL
490 <!-- JAL-2816 -->Tooltips displayed for features filtered by
494 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
495 show cross references or Fetch Database References are shown in
499 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
500 peptide sequence (computed variant shown as p.Res.null)
503 <!-- JAL-2060 -->'Graduated colour' option not offered for
504 manually created features (where feature score is Float.NaN)
507 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
508 when columns are hidden
511 <!-- JAL-3082 -->Regular expression error for '(' in Select
512 Columns by Annotation description
515 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
516 out of Scale or Annotation Panel
519 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
523 <!-- JAL-3074 -->Left/right drag in annotation can scroll
527 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
531 <!-- JAL-3002 -->Column display is out by one after Page Down,
532 Page Up in wrapped mode
535 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
538 <!-- JAL-2932 -->Finder searches in minimised alignments
541 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
542 on opening an alignment
545 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
549 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
550 different groups in the alignment are selected
553 <!-- JAL-2717 -->Internationalised colour scheme names not shown
557 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
561 <!-- JAL-3125 -->Value input for graduated feature colour
562 threshold gets 'unrounded'
565 <!-- JAL-2982 -->PCA image export doesn't respect background
569 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
572 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
575 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
579 <!-- JAL-2964 -->Associate Tree with All Views not restored from
583 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
584 shown in complementary view
587 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
588 without normalisation
591 <!-- JAL-3021 -->Sequence Details report should open positioned at top
595 <!-- JAL-914 -->Help page can be opened twice
598 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
600 </ul> <em>Editing</em>
603 <!-- JAL-2822 -->Start and End should be updated when sequence
604 data at beginning or end of alignment added/removed via 'Edit'
608 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
609 relocate sequence features correctly when start of sequence is
610 removed (Known defect since 2.10)
613 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
614 dialog corrupts dataset sequence
617 <!-- JAL-868 -->Structure colours not updated when associated tree
618 repartitions the alignment view (Regression in 2.10.5)
620 </ul> <em>Datamodel</em>
623 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
624 sequence's End is greater than its length
626 </ul> <em>Bugs fixed for Java 11 Support (not yet on
627 general release)</em>
630 <!-- JAL-3288 -->Menus work properly in split-screen
632 </ul> <em>New Known Defects</em>
635 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
638 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
639 regions of protein alignment.
642 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
643 is restored from a Jalview 2.11 project
646 <!-- JAL-3213 -->Alignment panel height can be too small after
650 <!-- JAL-3240 -->Display is incorrect after removing gapped
651 columns within hidden columns
654 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
655 window after dragging left to select columns to left of visible
659 <!-- JAL-2876 -->Features coloured according to their description
660 string and thresholded by score in earlier versions of Jalview are
661 not shown as thresholded features in 2.11. To workaround please
662 create a Score filter instead.
665 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
667 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
670 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
671 alignments with multiple views can close views unexpectedly
674 <em>Java 11 Specific defects</em>
677 <!-- JAL-3235 -->Jalview Properties file is not sorted
678 alphabetically when saved
684 <td width="60" nowrap>
686 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
689 <td><div align="left">
693 <!-- JAL-3101 -->Default memory for Jalview webstart and
694 InstallAnywhere increased to 1G.
697 <!-- JAL-247 -->Hidden sequence markers and representative
698 sequence bolding included when exporting alignment as EPS,
699 SVG, PNG or HTML. <em>Display is configured via the
700 Format menu, or for command-line use via a Jalview
701 properties file.</em>
704 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
705 API and sequence data now imported as JSON.
708 <!-- JAL-3065 -->Change in recommended way of starting
709 Jalview via a Java command line: add jars in lib directory
710 to CLASSPATH, rather than via the deprecated java.ext.dirs
717 <!-- JAL-3047 -->Support added to execute test suite
718 instrumented with <a href="http://openclover.org/">Open
723 <td><div align="left">
727 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
728 row shown in Feredoxin Structure alignment view of example
732 <!-- JAL-2854 -->Annotation obscures sequences if lots of
733 annotation displayed.
736 <!-- JAL-3107 -->Group conservation/consensus not shown
737 for newly created group when 'Apply to all groups'
741 <!-- JAL-3087 -->Corrupted display when switching to
742 wrapped mode when sequence panel's vertical scrollbar is
746 <!-- JAL-3003 -->Alignment is black in exported EPS file
747 when sequences are selected in exported view.</em>
750 <!-- JAL-3059 -->Groups with different coloured borders
751 aren't rendered with correct colour.
754 <!-- JAL-3092 -->Jalview could hang when importing certain
755 types of knotted RNA secondary structure.
758 <!-- JAL-3095 -->Sequence highlight and selection in
759 trimmed VARNA 2D structure is incorrect for sequences that
763 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
764 annotation when columns are inserted into an alignment,
765 and when exporting as Stockholm flatfile.
768 <!-- JAL-3053 -->Jalview annotation rows containing upper
769 and lower-case 'E' and 'H' do not automatically get
770 treated as RNA secondary structure.
773 <!-- JAL-3106 -->.jvp should be used as default extension
774 (not .jar) when saving a Jalview project file.
777 <!-- JAL-3105 -->Mac Users: closing a window correctly
778 transfers focus to previous window on OSX
781 <em>Java 10 Issues Resolved</em>
784 <!-- JAL-2988 -->OSX - Can't save new files via the File
785 or export menus by typing in a name into the Save dialog
789 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
790 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
791 'look and feel' which has improved compatibility with the
792 latest version of OSX.
799 <td width="60" nowrap>
801 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
802 <em>7/06/2018</em></strong>
805 <td><div align="left">
809 <!-- JAL-2920 -->Use HGVS nomenclature for variant
810 annotation retrieved from Uniprot
813 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
814 onto the Jalview Desktop
818 <td><div align="left">
822 <!-- JAL-3017 -->Cannot import features with multiple
823 variant elements (blocks import of some Uniprot records)
826 <!-- JAL-2997 -->Clustal files with sequence positions in
827 right-hand column parsed correctly
830 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
831 not alignment area in exported graphic
834 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
835 window has input focus
838 <!-- JAL-2992 -->Annotation panel set too high when
839 annotation added to view (Windows)
842 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
843 network connectivity is poor
846 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
847 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
848 the currently open URL and links from a page viewed in
849 Firefox or Chrome on Windows is now fully supported. If
850 you are using Edge, only links in the page can be
851 dragged, and with Internet Explorer, only the currently
852 open URL in the browser can be dropped onto Jalview.</em>
855 <em>New Known Defects</em>
857 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
862 <td width="60" nowrap>
864 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
867 <td><div align="left">
871 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
872 for disabling automatic superposition of multiple
873 structures and open structures in existing views
876 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
877 ID and annotation area margins can be click-dragged to
881 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
885 <!-- JAL-2759 -->Improved performance for large alignments
886 and lots of hidden columns
889 <!-- JAL-2593 -->Improved performance when rendering lots
890 of features (particularly when transparency is disabled)
893 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
894 exchange of Jalview features and Chimera attributes made
900 <td><div align="left">
903 <!-- JAL-2899 -->Structure and Overview aren't updated
904 when Colour By Annotation threshold slider is adjusted
907 <!-- JAL-2778 -->Slow redraw when Overview panel shown
908 overlapping alignment panel
911 <!-- JAL-2929 -->Overview doesn't show end of unpadded
915 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
916 improved: CDS not handled correctly if transcript has no
920 <!-- JAL-2321 -->Secondary structure and temperature
921 factor annotation not added to sequence when local PDB
922 file associated with it by drag'n'drop or structure
926 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
927 dialog doesn't import PDB files dropped on an alignment
930 <!-- JAL-2666 -->Linked scrolling via protein horizontal
931 scroll bar doesn't work for some CDS/Protein views
934 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
935 Java 1.8u153 onwards and Java 1.9u4+.
938 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
939 columns in annotation row
942 <!-- JAL-2913 -->Preferences panel's ID Width control is not
943 honored in batch mode
946 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
947 for structures added to existing Jmol view
950 <!-- JAL-2223 -->'View Mappings' includes duplicate
951 entries after importing project with multiple views
954 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
955 protein sequences via SIFTS from associated PDB entries
956 with negative residue numbers or missing residues fails
959 <!-- JAL-2952 -->Exception when shading sequence with negative
960 Temperature Factor values from annotated PDB files (e.g.
961 as generated by CONSURF)
964 <!-- JAL-2920 -->Uniprot 'sequence variant' features
965 tooltip doesn't include a text description of mutation
968 <!-- JAL-2922 -->Invert displayed features very slow when
969 structure and/or overview windows are also shown
972 <!-- JAL-2954 -->Selecting columns from highlighted regions
973 very slow for alignments with large numbers of sequences
976 <!-- JAL-2925 -->Copy Consensus fails for group consensus
977 with 'StringIndexOutOfBounds'
980 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
981 platforms running Java 10
984 <!-- JAL-2960 -->Adding a structure to existing structure
985 view appears to do nothing because the view is hidden behind the alignment view
991 <!-- JAL-2926 -->Copy consensus sequence option in applet
992 should copy the group consensus when popup is opened on it
998 <!-- JAL-2913 -->Fixed ID width preference is not respected
1001 <em>New Known Defects</em>
1004 <!-- JAL-2973 --> Exceptions occasionally raised when
1005 editing a large alignment and overview is displayed
1008 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1009 repeatedly after a series of edits even when the overview
1010 is no longer reflecting updates
1013 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1014 structures for protein subsequence (if 'Trim Retrieved
1015 Sequences' enabled) or Ensembl isoforms (Workaround in
1016 2.10.4 is to fail back to N&W mapping)
1019 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1020 option gives blank output
1027 <td width="60" nowrap>
1028 <div align="center">
1029 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1032 <td><div align="left">
1033 <ul><li>Updated Certum Codesigning Certificate
1034 (Valid till 30th November 2018)</li></ul></div></td>
1035 <td><div align="left">
1036 <em>Desktop</em><ul>
1038 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1039 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1040 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1041 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1042 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1043 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1044 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1050 <td width="60" nowrap>
1051 <div align="center">
1052 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1055 <td><div align="left">
1059 <!-- JAL-2446 -->Faster and more efficient management and
1060 rendering of sequence features
1063 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1064 429 rate limit request hander
1067 <!-- JAL-2773 -->Structure views don't get updated unless
1068 their colours have changed
1071 <!-- JAL-2495 -->All linked sequences are highlighted for
1072 a structure mousover (Jmol) or selection (Chimera)
1075 <!-- JAL-2790 -->'Cancel' button in progress bar for
1076 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1079 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1080 view from Ensembl locus cross-references
1083 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1087 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1088 feature can be disabled
1091 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1092 PDB easier retrieval of sequences for lists of IDs
1095 <!-- JAL-2758 -->Short names for sequences retrieved from
1101 <li>Groovy interpreter updated to 2.4.12</li>
1102 <li>Example groovy script for generating a matrix of
1103 percent identity scores for current alignment.</li>
1105 <em>Testing and Deployment</em>
1108 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1112 <td><div align="left">
1116 <!-- JAL-2643 -->Pressing tab after updating the colour
1117 threshold text field doesn't trigger an update to the
1121 <!-- JAL-2682 -->Race condition when parsing sequence ID
1125 <!-- JAL-2608 -->Overview windows are also closed when
1126 alignment window is closed
1129 <!-- JAL-2548 -->Export of features doesn't always respect
1133 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1134 takes a long time in Cursor mode
1140 <!-- JAL-2777 -->Structures with whitespace chainCode
1141 cannot be viewed in Chimera
1144 <!-- JAL-2728 -->Protein annotation panel too high in
1148 <!-- JAL-2757 -->Can't edit the query after the server
1149 error warning icon is shown in Uniprot and PDB Free Text
1153 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1156 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1159 <!-- JAL-2739 -->Hidden column marker in last column not
1160 rendered when switching back from Wrapped to normal view
1163 <!-- JAL-2768 -->Annotation display corrupted when
1164 scrolling right in unwapped alignment view
1167 <!-- JAL-2542 -->Existing features on subsequence
1168 incorrectly relocated when full sequence retrieved from
1172 <!-- JAL-2733 -->Last reported memory still shown when
1173 Desktop->Show Memory is unticked (OSX only)
1176 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1177 features of same type and group to be selected for
1181 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1182 alignments when hidden columns are present
1185 <!-- JAL-2392 -->Jalview freezes when loading and
1186 displaying several structures
1189 <!-- JAL-2732 -->Black outlines left after resizing or
1193 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1194 within the Jalview desktop on OSX
1197 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1198 when in wrapped alignment mode
1201 <!-- JAL-2636 -->Scale mark not shown when close to right
1202 hand end of alignment
1205 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1206 each selected sequence do not have correct start/end
1210 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1211 after canceling the Alignment Window's Font dialog
1214 <!-- JAL-2036 -->Show cross-references not enabled after
1215 restoring project until a new view is created
1218 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1219 URL links appears when only default EMBL-EBI link is
1220 configured (since 2.10.2b2)
1223 <!-- JAL-2775 -->Overview redraws whole window when box
1224 position is adjusted
1227 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1228 in a multi-chain structure when viewing alignment
1229 involving more than one chain (since 2.10)
1232 <!-- JAL-2811 -->Double residue highlights in cursor mode
1233 if new selection moves alignment window
1236 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1237 arrow key in cursor mode to pass hidden column marker
1240 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1241 that produces correctly annotated transcripts and products
1244 <!-- JAL-2776 -->Toggling a feature group after first time
1245 doesn't update associated structure view
1248 <em>Applet</em><br />
1251 <!-- JAL-2687 -->Concurrent modification exception when
1252 closing alignment panel
1255 <em>BioJSON</em><br />
1258 <!-- JAL-2546 -->BioJSON export does not preserve
1259 non-positional features
1262 <em>New Known Issues</em>
1265 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1266 sequence features correctly (for many previous versions of
1270 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1271 using cursor in wrapped panel other than top
1274 <!-- JAL-2791 -->Select columns containing feature ignores
1275 graduated colour threshold
1278 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1279 always preserve numbering and sequence features
1282 <em>Known Java 9 Issues</em>
1285 <!-- JAL-2902 -->Groovy Console very slow to open and is
1286 not responsive when entering characters (Webstart, Java
1293 <td width="60" nowrap>
1294 <div align="center">
1295 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1296 <em>2/10/2017</em></strong>
1299 <td><div align="left">
1300 <em>New features in Jalview Desktop</em>
1303 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1305 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1309 <td><div align="left">
1313 <td width="60" nowrap>
1314 <div align="center">
1315 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1316 <em>7/9/2017</em></strong>
1319 <td><div align="left">
1323 <!-- JAL-2588 -->Show gaps in overview window by colouring
1324 in grey (sequences used to be coloured grey, and gaps were
1328 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1332 <!-- JAL-2587 -->Overview updates immediately on increase
1333 in size and progress bar shown as higher resolution
1334 overview is recalculated
1339 <td><div align="left">
1343 <!-- JAL-2664 -->Overview window redraws every hidden
1344 column region row by row
1347 <!-- JAL-2681 -->duplicate protein sequences shown after
1348 retrieving Ensembl crossrefs for sequences from Uniprot
1351 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1352 format setting is unticked
1355 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1356 if group has show boxes format setting unticked
1359 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1360 autoscrolling whilst dragging current selection group to
1361 include sequences and columns not currently displayed
1364 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1365 assemblies are imported via CIF file
1368 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1369 displayed when threshold or conservation colouring is also
1373 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1377 <!-- JAL-2673 -->Jalview continues to scroll after
1378 dragging a selected region off the visible region of the
1382 <!-- JAL-2724 -->Cannot apply annotation based
1383 colourscheme to all groups in a view
1386 <!-- JAL-2511 -->IDs don't line up with sequences
1387 initially after font size change using the Font chooser or
1394 <td width="60" nowrap>
1395 <div align="center">
1396 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1399 <td><div align="left">
1400 <em>Calculations</em>
1404 <!-- JAL-1933 -->Occupancy annotation row shows number of
1405 ungapped positions in each column of the alignment.
1408 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1409 a calculation dialog box
1412 <!-- JAL-2379 -->Revised implementation of PCA for speed
1413 and memory efficiency (~30x faster)
1416 <!-- JAL-2403 -->Revised implementation of sequence
1417 similarity scores as used by Tree, PCA, Shading Consensus
1418 and other calculations
1421 <!-- JAL-2416 -->Score matrices are stored as resource
1422 files within the Jalview codebase
1425 <!-- JAL-2500 -->Trees computed on Sequence Feature
1426 Similarity may have different topology due to increased
1433 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1434 model for alignments and groups
1437 <!-- JAL-384 -->Custom shading schemes created via groovy
1444 <!-- JAL-2526 -->Efficiency improvements for interacting
1445 with alignment and overview windows
1448 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1452 <!-- JAL-2388 -->Hidden columns and sequences can be
1456 <!-- JAL-2611 -->Click-drag in visible area allows fine
1457 adjustment of visible position
1461 <em>Data import/export</em>
1464 <!-- JAL-2535 -->Posterior probability annotation from
1465 Stockholm files imported as sequence associated annotation
1468 <!-- JAL-2507 -->More robust per-sequence positional
1469 annotation input/output via stockholm flatfile
1472 <!-- JAL-2533 -->Sequence names don't include file
1473 extension when importing structure files without embedded
1474 names or PDB accessions
1477 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1478 format sequence substitution matrices
1481 <em>User Interface</em>
1484 <!-- JAL-2447 --> Experimental Features Checkbox in
1485 Desktop's Tools menu to hide or show untested features in
1489 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1490 via Overview or sequence motif search operations
1493 <!-- JAL-2547 -->Amend sequence features dialog box can be
1494 opened by double clicking gaps within sequence feature
1498 <!-- JAL-1476 -->Status bar message shown when not enough
1499 aligned positions were available to create a 3D structure
1503 <em>3D Structure</em>
1506 <!-- JAL-2430 -->Hidden regions in alignment views are not
1507 coloured in linked structure views
1510 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1511 file-based command exchange
1514 <!-- JAL-2375 -->Structure chooser automatically shows
1515 Cached Structures rather than querying the PDBe if
1516 structures are already available for sequences
1519 <!-- JAL-2520 -->Structures imported via URL are cached in
1520 the Jalview project rather than downloaded again when the
1521 project is reopened.
1524 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1525 to transfer Chimera's structure attributes as Jalview
1526 features, and vice-versa (<strong>Experimental
1530 <em>Web Services</em>
1533 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1536 <!-- JAL-2335 -->Filter non-standard amino acids and
1537 nucleotides when submitting to AACon and other MSA
1541 <!-- JAL-2316, -->URLs for viewing database
1542 cross-references provided by identifiers.org and the
1543 EMBL-EBI's MIRIAM DB
1550 <!-- JAL-2344 -->FileFormatI interface for describing and
1551 identifying file formats (instead of String constants)
1554 <!-- JAL-2228 -->FeatureCounter script refactored for
1555 efficiency when counting all displayed features (not
1556 backwards compatible with 2.10.1)
1559 <em>Example files</em>
1562 <!-- JAL-2631 -->Graduated feature colour style example
1563 included in the example feature file
1566 <em>Documentation</em>
1569 <!-- JAL-2339 -->Release notes reformatted for readability
1570 with the built-in Java help viewer
1573 <!-- JAL-1644 -->Find documentation updated with 'search
1574 sequence description' option
1580 <!-- JAL-2485, -->External service integration tests for
1581 Uniprot REST Free Text Search Client
1584 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1587 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1592 <td><div align="left">
1593 <em>Calculations</em>
1596 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1597 matrix - C->R should be '-3'<br />Old matrix restored
1598 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1600 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1601 Jalview's treatment of gaps in PCA and substitution matrix
1602 based Tree calculations.<br /> <br />In earlier versions
1603 of Jalview, gaps matching gaps were penalised, and gaps
1604 matching non-gaps penalised even more. In the PCA
1605 calculation, gaps were actually treated as non-gaps - so
1606 different costs were applied, which meant Jalview's PCAs
1607 were different to those produced by SeqSpace.<br />Jalview
1608 now treats gaps in the same way as SeqSpace (ie it scores
1609 them as 0). <br /> <br />Enter the following in the
1610 Groovy console to restore pre-2.10.2 behaviour:<br />
1611 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1612 // for 2.10.1 mode <br />
1613 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1614 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1615 these settings will affect all subsequent tree and PCA
1616 calculations (not recommended)</em></li>
1618 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1619 scaling of branch lengths for trees computed using
1620 Sequence Feature Similarity.
1623 <!-- JAL-2377 -->PCA calculation could hang when
1624 generating output report when working with highly
1625 redundant alignments
1628 <!-- JAL-2544 --> Sort by features includes features to
1629 right of selected region when gaps present on right-hand
1633 <em>User Interface</em>
1636 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1637 doesn't reselect a specific sequence's associated
1638 annotation after it was used for colouring a view
1641 <!-- JAL-2419 -->Current selection lost if popup menu
1642 opened on a region of alignment without groups
1645 <!-- JAL-2374 -->Popup menu not always shown for regions
1646 of an alignment with overlapping groups
1649 <!-- JAL-2310 -->Finder double counts if both a sequence's
1650 name and description match
1653 <!-- JAL-2370 -->Hiding column selection containing two
1654 hidden regions results in incorrect hidden regions
1657 <!-- JAL-2386 -->'Apply to all groups' setting when
1658 changing colour does not apply Conservation slider value
1662 <!-- JAL-2373 -->Percentage identity and conservation menu
1663 items do not show a tick or allow shading to be disabled
1666 <!-- JAL-2385 -->Conservation shading or PID threshold
1667 lost when base colourscheme changed if slider not visible
1670 <!-- JAL-2547 -->Sequence features shown in tooltip for
1671 gaps before start of features
1674 <!-- JAL-2623 -->Graduated feature colour threshold not
1675 restored to UI when feature colour is edited
1678 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1679 a time when scrolling vertically in wrapped mode.
1682 <!-- JAL-2630 -->Structure and alignment overview update
1683 as graduate feature colour settings are modified via the
1687 <!-- JAL-2034 -->Overview window doesn't always update
1688 when a group defined on the alignment is resized
1691 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1692 wrapped view result in positional status updates
1696 <!-- JAL-2563 -->Status bar doesn't show position for
1697 ambiguous amino acid and nucleotide symbols
1700 <!-- JAL-2602 -->Copy consensus sequence failed if
1701 alignment included gapped columns
1704 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1705 widgets don't permanently disappear
1708 <!-- JAL-2503 -->Cannot select or filter quantitative
1709 annotation that are shown only as column labels (e.g.
1710 T-Coffee column reliability scores)
1713 <!-- JAL-2594 -->Exception thrown if trying to create a
1714 sequence feature on gaps only
1717 <!-- JAL-2504 -->Features created with 'New feature'
1718 button from a Find inherit previously defined feature type
1719 rather than the Find query string
1722 <!-- JAL-2423 -->incorrect title in output window when
1723 exporting tree calculated in Jalview
1726 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1727 and then revealing them reorders sequences on the
1731 <!-- JAL-964 -->Group panel in sequence feature settings
1732 doesn't update to reflect available set of groups after
1733 interactively adding or modifying features
1736 <!-- JAL-2225 -->Sequence Database chooser unusable on
1740 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1741 only excluded gaps in current sequence and ignored
1748 <!-- JAL-2421 -->Overview window visible region moves
1749 erratically when hidden rows or columns are present
1752 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1753 Structure Viewer's colour menu don't correspond to
1757 <!-- JAL-2405 -->Protein specific colours only offered in
1758 colour and group colour menu for protein alignments
1761 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1762 reflect currently selected view or group's shading
1766 <!-- JAL-2624 -->Feature colour thresholds not respected
1767 when rendered on overview and structures when opacity at
1771 <!-- JAL-2589 -->User defined gap colour not shown in
1772 overview when features overlaid on alignment
1775 <!-- JAL-2567 -->Feature settings for different views not
1776 recovered correctly from Jalview project file
1779 <!-- JAL-2256 -->Feature colours in overview when first opened
1780 (automatically via preferences) are different to the main
1784 <em>Data import/export</em>
1787 <!-- JAL-2576 -->Very large alignments take a long time to
1791 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1792 added after a sequence was imported are not written to
1796 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1797 when importing RNA secondary structure via Stockholm
1800 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1801 not shown in correct direction for simple pseudoknots
1804 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1805 with lightGray or darkGray via features file (but can
1809 <!-- JAL-2383 -->Above PID colour threshold not recovered
1810 when alignment view imported from project
1813 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1814 structure and sequences extracted from structure files
1815 imported via URL and viewed in Jmol
1818 <!-- JAL-2520 -->Structures loaded via URL are saved in
1819 Jalview Projects rather than fetched via URL again when
1820 the project is loaded and the structure viewed
1823 <em>Web Services</em>
1826 <!-- JAL-2519 -->EnsemblGenomes example failing after
1827 release of Ensembl v.88
1830 <!-- JAL-2366 -->Proxy server address and port always
1831 appear enabled in Preferences->Connections
1834 <!-- JAL-2461 -->DAS registry not found exceptions
1835 removed from console output
1838 <!-- JAL-2582 -->Cannot retrieve protein products from
1839 Ensembl by Peptide ID
1842 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1843 created from SIFTs, and spurious 'Couldn't open structure
1844 in Chimera' errors raised after April 2017 update (problem
1845 due to 'null' string rather than empty string used for
1846 residues with no corresponding PDB mapping).
1849 <em>Application UI</em>
1852 <!-- JAL-2361 -->User Defined Colours not added to Colour
1856 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1857 case' residues (button in colourscheme editor debugged and
1858 new documentation and tooltips added)
1861 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1862 doesn't restore group-specific text colour thresholds
1865 <!-- JAL-2243 -->Feature settings panel does not update as
1866 new features are added to alignment
1869 <!-- JAL-2532 -->Cancel in feature settings reverts
1870 changes to feature colours via the Amend features dialog
1873 <!-- JAL-2506 -->Null pointer exception when attempting to
1874 edit graduated feature colour via amend features dialog
1878 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1879 selection menu changes colours of alignment views
1882 <!-- JAL-2426 -->Spurious exceptions in console raised
1883 from alignment calculation workers after alignment has
1887 <!-- JAL-1608 -->Typo in selection popup menu - Create
1888 groups now 'Create Group'
1891 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1892 Create/Undefine group doesn't always work
1895 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1896 shown again after pressing 'Cancel'
1899 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1900 adjusts start position in wrap mode
1903 <!-- JAL-2563 -->Status bar doesn't show positions for
1904 ambiguous amino acids
1907 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1908 CDS/Protein view after CDS sequences added for aligned
1912 <!-- JAL-2592 -->User defined colourschemes called 'User
1913 Defined' don't appear in Colours menu
1919 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1920 score models doesn't always result in an updated PCA plot
1923 <!-- JAL-2442 -->Features not rendered as transparent on
1924 overview or linked structure view
1927 <!-- JAL-2372 -->Colour group by conservation doesn't
1931 <!-- JAL-2517 -->Hitting Cancel after applying
1932 user-defined colourscheme doesn't restore original
1939 <!-- JAL-2314 -->Unit test failure:
1940 jalview.ws.jabaws.RNAStructExportImport setup fails
1943 <!-- JAL-2307 -->Unit test failure:
1944 jalview.ws.sifts.SiftsClientTest due to compatibility
1945 problems with deep array comparison equality asserts in
1946 successive versions of TestNG
1949 <!-- JAL-2479 -->Relocated StructureChooserTest and
1950 ParameterUtilsTest Unit tests to Network suite
1953 <em>New Known Issues</em>
1956 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1957 phase after a sequence motif find operation
1960 <!-- JAL-2550 -->Importing annotation file with rows
1961 containing just upper and lower case letters are
1962 interpreted as WUSS RNA secondary structure symbols
1965 <!-- JAL-2590 -->Cannot load and display Newick trees
1966 reliably from eggnog Ortholog database
1969 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1970 containing features of type Highlight' when 'B' is pressed
1971 to mark columns containing highlighted regions.
1974 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1975 doesn't always add secondary structure annotation.
1980 <td width="60" nowrap>
1981 <div align="center">
1982 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1985 <td><div align="left">
1989 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1990 for all consensus calculations
1993 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1996 <li>Updated Jalview's Certum code signing certificate
1999 <em>Application</em>
2002 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2003 set of database cross-references, sorted alphabetically
2006 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2007 from database cross references. Users with custom links
2008 will receive a <a href="webServices/urllinks.html#warning">warning
2009 dialog</a> asking them to update their preferences.
2012 <!-- JAL-2287-->Cancel button and escape listener on
2013 dialog warning user about disconnecting Jalview from a
2017 <!-- JAL-2320-->Jalview's Chimera control window closes if
2018 the Chimera it is connected to is shut down
2021 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2022 columns menu item to mark columns containing highlighted
2023 regions (e.g. from structure selections or results of a
2027 <!-- JAL-2284-->Command line option for batch-generation
2028 of HTML pages rendering alignment data with the BioJS
2038 <!-- JAL-2286 -->Columns with more than one modal residue
2039 are not coloured or thresholded according to percent
2040 identity (first observed in Jalview 2.8.2)
2043 <!-- JAL-2301 -->Threonine incorrectly reported as not
2047 <!-- JAL-2318 -->Updates to documentation pages (above PID
2048 threshold, amino acid properties)
2051 <!-- JAL-2292 -->Lower case residues in sequences are not
2052 reported as mapped to residues in a structure file in the
2056 <!--JAL-2324 -->Identical features with non-numeric scores
2057 could be added multiple times to a sequence
2060 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2061 bond features shown as two highlighted residues rather
2062 than a range in linked structure views, and treated
2063 correctly when selecting and computing trees from features
2066 <!-- JAL-2281-->Custom URL links for database
2067 cross-references are matched to database name regardless
2072 <em>Application</em>
2075 <!-- JAL-2282-->Custom URL links for specific database
2076 names without regular expressions also offer links from
2080 <!-- JAL-2315-->Removing a single configured link in the
2081 URL links pane in Connections preferences doesn't actually
2082 update Jalview configuration
2085 <!-- JAL-2272-->CTRL-Click on a selected region to open
2086 the alignment area popup menu doesn't work on El-Capitan
2089 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2090 files with similarly named sequences if dropped onto the
2094 <!-- JAL-2312 -->Additional mappings are shown for PDB
2095 entries where more chains exist in the PDB accession than
2096 are reported in the SIFTS file
2099 <!-- JAL-2317-->Certain structures do not get mapped to
2100 the structure view when displayed with Chimera
2103 <!-- JAL-2317-->No chains shown in the Chimera view
2104 panel's View->Show Chains submenu
2107 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2108 work for wrapped alignment views
2111 <!--JAL-2197 -->Rename UI components for running JPred
2112 predictions from 'JNet' to 'JPred'
2115 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2116 corrupted when annotation panel vertical scroll is not at
2117 first annotation row
2120 <!--JAL-2332 -->Attempting to view structure for Hen
2121 lysozyme results in a PDB Client error dialog box
2124 <!-- JAL-2319 -->Structure View's mapping report switched
2125 ranges for PDB and sequence for SIFTS
2128 SIFTS 'Not_Observed' residues mapped to non-existant
2132 <!-- <em>New Known Issues</em>
2139 <td width="60" nowrap>
2140 <div align="center">
2141 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2142 <em>25/10/2016</em></strong>
2145 <td><em>Application</em>
2147 <li>3D Structure chooser opens with 'Cached structures'
2148 view if structures already loaded</li>
2149 <li>Progress bar reports models as they are loaded to
2150 structure views</li>
2156 <li>Colour by conservation always enabled and no tick
2157 shown in menu when BLOSUM or PID shading applied</li>
2158 <li>FER1_ARATH and FER2_ARATH labels were switched in
2159 example sequences/projects/trees</li>
2161 <em>Application</em>
2163 <li>Jalview projects with views of local PDB structure
2164 files saved on Windows cannot be opened on OSX</li>
2165 <li>Multiple structure views can be opened and superposed
2166 without timeout for structures with multiple models or
2167 multiple sequences in alignment</li>
2168 <li>Cannot import or associated local PDB files without a
2169 PDB ID HEADER line</li>
2170 <li>RMSD is not output in Jmol console when superposition
2172 <li>Drag and drop of URL from Browser fails for Linux and
2173 OSX versions earlier than El Capitan</li>
2174 <li>ENA client ignores invalid content from ENA server</li>
2175 <li>Exceptions are not raised in console when ENA client
2176 attempts to fetch non-existent IDs via Fetch DB Refs UI
2178 <li>Exceptions are not raised in console when a new view
2179 is created on the alignment</li>
2180 <li>OSX right-click fixed for group selections: CMD-click
2181 to insert/remove gaps in groups and CTRL-click to open group
2184 <em>Build and deployment</em>
2186 <li>URL link checker now copes with multi-line anchor
2189 <em>New Known Issues</em>
2191 <li>Drag and drop from URL links in browsers do not work
2198 <td width="60" nowrap>
2199 <div align="center">
2200 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2203 <td><em>General</em>
2206 <!-- JAL-2124 -->Updated Spanish translations.
2209 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2210 for importing structure data to Jalview. Enables mmCIF and
2214 <!-- JAL-192 --->Alignment ruler shows positions relative to
2218 <!-- JAL-2202 -->Position/residue shown in status bar when
2219 mousing over sequence associated annotation
2222 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2226 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2227 '()', canonical '[]' and invalid '{}' base pair populations
2231 <!-- JAL-2092 -->Feature settings popup menu options for
2232 showing or hiding columns containing a feature
2235 <!-- JAL-1557 -->Edit selected group by double clicking on
2236 group and sequence associated annotation labels
2239 <!-- JAL-2236 -->Sequence name added to annotation label in
2240 select/hide columns by annotation and colour by annotation
2244 </ul> <em>Application</em>
2247 <!-- JAL-2050-->Automatically hide introns when opening a
2248 gene/transcript view
2251 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2255 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2256 structure mappings with the EMBL-EBI PDBe SIFTS database
2259 <!-- JAL-2079 -->Updated download sites used for Rfam and
2260 Pfam sources to xfam.org
2263 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2266 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2267 over sequences in Jalview
2270 <!-- JAL-2027-->Support for reverse-complement coding
2271 regions in ENA and EMBL
2274 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2275 for record retrieval via ENA rest API
2278 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2282 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2283 groovy script execution
2286 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2287 alignment window's Calculate menu
2290 <!-- JAL-1812 -->Allow groovy scripts that call
2291 Jalview.getAlignFrames() to run in headless mode
2294 <!-- JAL-2068 -->Support for creating new alignment
2295 calculation workers from groovy scripts
2298 <!-- JAL-1369 --->Store/restore reference sequence in
2302 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2303 associations are now saved/restored from project
2306 <!-- JAL-1993 -->Database selection dialog always shown
2307 before sequence fetcher is opened
2310 <!-- JAL-2183 -->Double click on an entry in Jalview's
2311 database chooser opens a sequence fetcher
2314 <!-- JAL-1563 -->Free-text search client for UniProt using
2315 the UniProt REST API
2318 <!-- JAL-2168 -->-nonews command line parameter to prevent
2319 the news reader opening
2322 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2323 querying stored in preferences
2326 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2330 <!-- JAL-1977-->Tooltips shown on database chooser
2333 <!-- JAL-391 -->Reverse complement function in calculate
2334 menu for nucleotide sequences
2337 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2338 and feature counts preserves alignment ordering (and
2339 debugged for complex feature sets).
2342 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2343 viewing structures with Jalview 2.10
2346 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2347 genome, transcript CCDS and gene ids via the Ensembl and
2348 Ensembl Genomes REST API
2351 <!-- JAL-2049 -->Protein sequence variant annotation
2352 computed for 'sequence_variant' annotation on CDS regions
2356 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2360 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2361 Ref Fetcher fails to match, or otherwise updates sequence
2362 data from external database records.
2365 <!-- JAL-2154 -->Revised Jalview Project format for
2366 efficient recovery of sequence coding and alignment
2367 annotation relationships.
2369 </ul> <!-- <em>Applet</em>
2380 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2384 <!-- JAL-2018-->Export features in Jalview format (again)
2385 includes graduated colourschemes
2388 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2389 working with big alignments and lots of hidden columns
2392 <!-- JAL-2053-->Hidden column markers not always rendered
2393 at right of alignment window
2396 <!-- JAL-2067 -->Tidied up links in help file table of
2400 <!-- JAL-2072 -->Feature based tree calculation not shown
2404 <!-- JAL-2075 -->Hidden columns ignored during feature
2405 based tree calculation
2408 <!-- JAL-2065 -->Alignment view stops updating when show
2409 unconserved enabled for group on alignment
2412 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2416 <!-- JAL-2146 -->Alignment column in status incorrectly
2417 shown as "Sequence position" when mousing over
2421 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2422 hidden columns present
2425 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2426 user created annotation added to alignment
2429 <!-- JAL-1841 -->RNA Structure consensus only computed for
2430 '()' base pair annotation
2433 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2434 in zero scores for all base pairs in RNA Structure
2438 <!-- JAL-2174-->Extend selection with columns containing
2442 <!-- JAL-2275 -->Pfam format writer puts extra space at
2443 beginning of sequence
2446 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2450 <!-- JAL-2238 -->Cannot create groups on an alignment from
2451 from a tree when t-coffee scores are shown
2454 <!-- JAL-1836,1967 -->Cannot import and view PDB
2455 structures with chains containing negative resnums (4q4h)
2458 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2462 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2463 to Clustal, PIR and PileUp output
2466 <!-- JAL-2008 -->Reordering sequence features that are
2467 not visible causes alignment window to repaint
2470 <!-- JAL-2006 -->Threshold sliders don't work in
2471 graduated colour and colour by annotation row for e-value
2472 scores associated with features and annotation rows
2475 <!-- JAL-1797 -->amino acid physicochemical conservation
2476 calculation should be case independent
2479 <!-- JAL-2173 -->Remove annotation also updates hidden
2483 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2484 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2485 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2488 <!-- JAL-2065 -->Null pointer exceptions and redraw
2489 problems when reference sequence defined and 'show
2490 non-conserved' enabled
2493 <!-- JAL-1306 -->Quality and Conservation are now shown on
2494 load even when Consensus calculation is disabled
2497 <!-- JAL-1932 -->Remove right on penultimate column of
2498 alignment does nothing
2501 <em>Application</em>
2504 <!-- JAL-1552-->URLs and links can't be imported by
2505 drag'n'drop on OSX when launched via webstart (note - not
2506 yet fixed for El Capitan)
2509 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2510 output when running on non-gb/us i18n platforms
2513 <!-- JAL-1944 -->Error thrown when exporting a view with
2514 hidden sequences as flat-file alignment
2517 <!-- JAL-2030-->InstallAnywhere distribution fails when
2521 <!-- JAL-2080-->Jalview very slow to launch via webstart
2522 (also hotfix for 2.9.0b2)
2525 <!-- JAL-2085 -->Cannot save project when view has a
2526 reference sequence defined
2529 <!-- JAL-1011 -->Columns are suddenly selected in other
2530 alignments and views when revealing hidden columns
2533 <!-- JAL-1989 -->Hide columns not mirrored in complement
2534 view in a cDNA/Protein splitframe
2537 <!-- JAL-1369 -->Cannot save/restore representative
2538 sequence from project when only one sequence is
2542 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2543 in Structure Chooser
2546 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2547 structure consensus didn't refresh annotation panel
2550 <!-- JAL-1962 -->View mapping in structure view shows
2551 mappings between sequence and all chains in a PDB file
2554 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2555 dialogs format columns correctly, don't display array
2556 data, sort columns according to type
2559 <!-- JAL-1975 -->Export complete shown after destination
2560 file chooser is cancelled during an image export
2563 <!-- JAL-2025 -->Error when querying PDB Service with
2564 sequence name containing special characters
2567 <!-- JAL-2024 -->Manual PDB structure querying should be
2571 <!-- JAL-2104 -->Large tooltips with broken HTML
2572 formatting don't wrap
2575 <!-- JAL-1128 -->Figures exported from wrapped view are
2576 truncated so L looks like I in consensus annotation
2579 <!-- JAL-2003 -->Export features should only export the
2580 currently displayed features for the current selection or
2584 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2585 after fetching cross-references, and restoring from
2589 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2590 followed in the structure viewer
2593 <!-- JAL-2163 -->Titles for individual alignments in
2594 splitframe not restored from project
2597 <!-- JAL-2145 -->missing autocalculated annotation at
2598 trailing end of protein alignment in transcript/product
2599 splitview when pad-gaps not enabled by default
2602 <!-- JAL-1797 -->amino acid physicochemical conservation
2606 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2607 article has been read (reopened issue due to
2608 internationalisation problems)
2611 <!-- JAL-1960 -->Only offer PDB structures in structure
2612 viewer based on sequence name, PDB and UniProt
2617 <!-- JAL-1976 -->No progress bar shown during export of
2621 <!-- JAL-2213 -->Structures not always superimposed after
2622 multiple structures are shown for one or more sequences.
2625 <!-- JAL-1370 -->Reference sequence characters should not
2626 be replaced with '.' when 'Show unconserved' format option
2630 <!-- JAL-1823 -->Cannot specify chain code when entering
2631 specific PDB id for sequence
2634 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2635 'Export hidden sequences' is enabled, but 'export hidden
2636 columns' is disabled.
2639 <!--JAL-2026-->Best Quality option in structure chooser
2640 selects lowest rather than highest resolution structures
2644 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2645 to sequence mapping in 'View Mappings' report
2648 <!-- JAL-2284 -->Unable to read old Jalview projects that
2649 contain non-XML data added after Jalvew wrote project.
2652 <!-- JAL-2118 -->Newly created annotation row reorders
2653 after clicking on it to create new annotation for a
2657 <!-- JAL-1980 -->Null Pointer Exception raised when
2658 pressing Add on an orphaned cut'n'paste window.
2660 <!-- may exclude, this is an external service stability issue JAL-1941
2661 -- > RNA 3D structure not added via DSSR service</li> -->
2666 <!-- JAL-2151 -->Incorrect columns are selected when
2667 hidden columns present before start of sequence
2670 <!-- JAL-1986 -->Missing dependencies on applet pages
2674 <!-- JAL-1947 -->Overview pixel size changes when
2675 sequences are hidden in applet
2678 <!-- JAL-1996 -->Updated instructions for applet
2679 deployment on examples pages.
2686 <td width="60" nowrap>
2687 <div align="center">
2688 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2689 <em>16/10/2015</em></strong>
2692 <td><em>General</em>
2694 <li>Time stamps for signed Jalview application and applet
2699 <em>Application</em>
2701 <li>Duplicate group consensus and conservation rows
2702 shown when tree is partitioned</li>
2703 <li>Erratic behaviour when tree partitions made with
2704 multiple cDNA/Protein split views</li>
2710 <td width="60" nowrap>
2711 <div align="center">
2712 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2713 <em>8/10/2015</em></strong>
2716 <td><em>General</em>
2718 <li>Updated Spanish translations of localized text for
2720 </ul> <em>Application</em>
2722 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2723 <li>Signed OSX InstallAnywhere installer<br></li>
2724 <li>Support for per-sequence based annotations in BioJSON</li>
2725 </ul> <em>Applet</em>
2727 <li>Split frame example added to applet examples page</li>
2728 </ul> <em>Build and Deployment</em>
2731 <!-- JAL-1888 -->New ant target for running Jalview's test
2739 <li>Mapping of cDNA to protein in split frames
2740 incorrect when sequence start > 1</li>
2741 <li>Broken images in filter column by annotation dialog
2743 <li>Feature colours not parsed from features file</li>
2744 <li>Exceptions and incomplete link URLs recovered when
2745 loading a features file containing HTML tags in feature
2749 <em>Application</em>
2751 <li>Annotations corrupted after BioJS export and
2753 <li>Incorrect sequence limits after Fetch DB References
2754 with 'trim retrieved sequences'</li>
2755 <li>Incorrect warning about deleting all data when
2756 deleting selected columns</li>
2757 <li>Patch to build system for shipping properly signed
2758 JNLP templates for webstart launch</li>
2759 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2760 unreleased structures for download or viewing</li>
2761 <li>Tab/space/return keystroke operation of EMBL-PDBe
2762 fetcher/viewer dialogs works correctly</li>
2763 <li>Disabled 'minimise' button on Jalview windows
2764 running on OSX to workaround redraw hang bug</li>
2765 <li>Split cDNA/Protein view position and geometry not
2766 recovered from jalview project</li>
2767 <li>Initial enabled/disabled state of annotation menu
2768 sorter 'show autocalculated first/last' corresponds to
2770 <li>Restoring of Clustal, RNA Helices and T-Coffee
2771 color schemes from BioJSON</li>
2775 <li>Reorder sequences mirrored in cDNA/Protein split
2777 <li>Applet with Jmol examples not loading correctly</li>
2783 <td><div align="center">
2784 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2786 <td><em>General</em>
2788 <li>Linked visualisation and analysis of DNA and Protein
2791 <li>Translated cDNA alignments shown as split protein
2792 and DNA alignment views</li>
2793 <li>Codon consensus annotation for linked protein and
2794 cDNA alignment views</li>
2795 <li>Link cDNA or Protein product sequences by loading
2796 them onto Protein or cDNA alignments</li>
2797 <li>Reconstruct linked cDNA alignment from aligned
2798 protein sequences</li>
2801 <li>Jmol integration updated to Jmol v14.2.14</li>
2802 <li>Import and export of Jalview alignment views as <a
2803 href="features/bioJsonFormat.html">BioJSON</a></li>
2804 <li>New alignment annotation file statements for
2805 reference sequences and marking hidden columns</li>
2806 <li>Reference sequence based alignment shading to
2807 highlight variation</li>
2808 <li>Select or hide columns according to alignment
2810 <li>Find option for locating sequences by description</li>
2811 <li>Conserved physicochemical properties shown in amino
2812 acid conservation row</li>
2813 <li>Alignments can be sorted by number of RNA helices</li>
2814 </ul> <em>Application</em>
2816 <li>New cDNA/Protein analysis capabilities
2818 <li>Get Cross-References should open a Split Frame
2819 view with cDNA/Protein</li>
2820 <li>Detect when nucleotide sequences and protein
2821 sequences are placed in the same alignment</li>
2822 <li>Split cDNA/Protein views are saved in Jalview
2827 <li>Use REST API to talk to Chimera</li>
2828 <li>Selected regions in Chimera are highlighted in linked
2829 Jalview windows</li>
2831 <li>VARNA RNA viewer updated to v3.93</li>
2832 <li>VARNA views are saved in Jalview Projects</li>
2833 <li>Pseudoknots displayed as Jalview RNA annotation can
2834 be shown in VARNA</li>
2836 <li>Make groups for selection uses marked columns as well
2837 as the active selected region</li>
2839 <li>Calculate UPGMA and NJ trees using sequence feature
2841 <li>New Export options
2843 <li>New Export Settings dialog to control hidden
2844 region export in flat file generation</li>
2846 <li>Export alignment views for display with the <a
2847 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2849 <li>Export scrollable SVG in HTML page</li>
2850 <li>Optional embedding of BioJSON data when exporting
2851 alignment figures to HTML</li>
2853 <li>3D structure retrieval and display
2855 <li>Free text and structured queries with the PDBe
2857 <li>PDBe Search API based discovery and selection of
2858 PDB structures for a sequence set</li>
2862 <li>JPred4 employed for protein secondary structure
2864 <li>Hide Insertions menu option to hide unaligned columns
2865 for one or a group of sequences</li>
2866 <li>Automatically hide insertions in alignments imported
2867 from the JPred4 web server</li>
2868 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2869 system on OSX<br />LGPL libraries courtesy of <a
2870 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2872 <li>changed 'View nucleotide structure' submenu to 'View
2873 VARNA 2D Structure'</li>
2874 <li>change "View protein structure" menu option to "3D
2877 </ul> <em>Applet</em>
2879 <li>New layout for applet example pages</li>
2880 <li>New parameters to enable SplitFrame view
2881 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2882 <li>New example demonstrating linked viewing of cDNA and
2883 Protein alignments</li>
2884 </ul> <em>Development and deployment</em>
2886 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2887 <li>Include installation type and git revision in build
2888 properties and console log output</li>
2889 <li>Jalview Github organisation, and new github site for
2890 storing BioJsMSA Templates</li>
2891 <li>Jalview's unit tests now managed with TestNG</li>
2894 <!-- <em>General</em>
2896 </ul> --> <!-- issues resolved --> <em>Application</em>
2898 <li>Escape should close any open find dialogs</li>
2899 <li>Typo in select-by-features status report</li>
2900 <li>Consensus RNA secondary secondary structure
2901 predictions are not highlighted in amber</li>
2902 <li>Missing gap character in v2.7 example file means
2903 alignment appears unaligned when pad-gaps is not enabled</li>
2904 <li>First switch to RNA Helices colouring doesn't colour
2905 associated structure views</li>
2906 <li>ID width preference option is greyed out when auto
2907 width checkbox not enabled</li>
2908 <li>Stopped a warning dialog from being shown when
2909 creating user defined colours</li>
2910 <li>'View Mapping' in structure viewer shows sequence
2911 mappings for just that viewer's sequences</li>
2912 <li>Workaround for superposing PDB files containing
2913 multiple models in Chimera</li>
2914 <li>Report sequence position in status bar when hovering
2915 over Jmol structure</li>
2916 <li>Cannot output gaps as '.' symbols with Selection ->
2917 output to text box</li>
2918 <li>Flat file exports of alignments with hidden columns
2919 have incorrect sequence start/end</li>
2920 <li>'Aligning' a second chain to a Chimera structure from
2922 <li>Colour schemes applied to structure viewers don't
2923 work for nucleotide</li>
2924 <li>Loading/cut'n'pasting an empty or invalid file leads
2925 to a grey/invisible alignment window</li>
2926 <li>Exported Jpred annotation from a sequence region
2927 imports to different position</li>
2928 <li>Space at beginning of sequence feature tooltips shown
2929 on some platforms</li>
2930 <li>Chimera viewer 'View | Show Chain' menu is not
2932 <li>'New View' fails with a Null Pointer Exception in
2933 console if Chimera has been opened</li>
2934 <li>Mouseover to Chimera not working</li>
2935 <li>Miscellaneous ENA XML feature qualifiers not
2937 <li>NPE in annotation renderer after 'Extract Scores'</li>
2938 <li>If two structures in one Chimera window, mouseover of
2939 either sequence shows on first structure</li>
2940 <li>'Show annotations' options should not make
2941 non-positional annotations visible</li>
2942 <li>Subsequence secondary structure annotation not shown
2943 in right place after 'view flanking regions'</li>
2944 <li>File Save As type unset when current file format is
2946 <li>Save as '.jar' option removed for saving Jalview
2948 <li>Colour by Sequence colouring in Chimera more
2950 <li>Cannot 'add reference annotation' for a sequence in
2951 several views on same alignment</li>
2952 <li>Cannot show linked products for EMBL / ENA records</li>
2953 <li>Jalview's tooltip wraps long texts containing no
2955 </ul> <em>Applet</em>
2957 <li>Jmol to JalviewLite mouseover/link not working</li>
2958 <li>JalviewLite can't import sequences with ID
2959 descriptions containing angle brackets</li>
2960 </ul> <em>General</em>
2962 <li>Cannot export and reimport RNA secondary structure
2963 via jalview annotation file</li>
2964 <li>Random helix colour palette for colour by annotation
2965 with RNA secondary structure</li>
2966 <li>Mouseover to cDNA from STOP residue in protein
2967 translation doesn't work.</li>
2968 <li>hints when using the select by annotation dialog box</li>
2969 <li>Jmol alignment incorrect if PDB file has alternate CA
2971 <li>FontChooser message dialog appears to hang after
2972 choosing 1pt font</li>
2973 <li>Peptide secondary structure incorrectly imported from
2974 annotation file when annotation display text includes 'e' or
2976 <li>Cannot set colour of new feature type whilst creating
2978 <li>cDNA translation alignment should not be sequence
2979 order dependent</li>
2980 <li>'Show unconserved' doesn't work for lower case
2982 <li>Nucleotide ambiguity codes involving R not recognised</li>
2983 </ul> <em>Deployment and Documentation</em>
2985 <li>Applet example pages appear different to the rest of
2986 www.jalview.org</li>
2987 </ul> <em>Application Known issues</em>
2989 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2990 <li>Misleading message appears after trying to delete
2992 <li>Jalview icon not shown in dock after InstallAnywhere
2993 version launches</li>
2994 <li>Fetching EMBL reference for an RNA sequence results
2995 fails with a sequence mismatch</li>
2996 <li>Corrupted or unreadable alignment display when
2997 scrolling alignment to right</li>
2998 <li>ArrayIndexOutOfBoundsException thrown when remove
2999 empty columns called on alignment with ragged gapped ends</li>
3000 <li>auto calculated alignment annotation rows do not get
3001 placed above or below non-autocalculated rows</li>
3002 <li>Jalview dekstop becomes sluggish at full screen in
3003 ultra-high resolution</li>
3004 <li>Cannot disable consensus calculation independently of
3005 quality and conservation</li>
3006 <li>Mouseover highlighting between cDNA and protein can
3007 become sluggish with more than one splitframe shown</li>
3008 </ul> <em>Applet Known Issues</em>
3010 <li>Core PDB parsing code requires Jmol</li>
3011 <li>Sequence canvas panel goes white when alignment
3012 window is being resized</li>
3018 <td><div align="center">
3019 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3021 <td><em>General</em>
3023 <li>Updated Java code signing certificate donated by
3025 <li>Features and annotation preserved when performing
3026 pairwise alignment</li>
3027 <li>RNA pseudoknot annotation can be
3028 imported/exported/displayed</li>
3029 <li>'colour by annotation' can colour by RNA and
3030 protein secondary structure</li>
3031 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3032 post-hoc with 2.9 release</em>)
3035 </ul> <em>Application</em>
3037 <li>Extract and display secondary structure for sequences
3038 with 3D structures</li>
3039 <li>Support for parsing RNAML</li>
3040 <li>Annotations menu for layout
3042 <li>sort sequence annotation rows by alignment</li>
3043 <li>place sequence annotation above/below alignment
3046 <li>Output in Stockholm format</li>
3047 <li>Internationalisation: improved Spanish (es)
3049 <li>Structure viewer preferences tab</li>
3050 <li>Disorder and Secondary Structure annotation tracks
3051 shared between alignments</li>
3052 <li>UCSF Chimera launch and linked highlighting from
3054 <li>Show/hide all sequence associated annotation rows for
3055 all or current selection</li>
3056 <li>disorder and secondary structure predictions
3057 available as dataset annotation</li>
3058 <li>Per-sequence rna helices colouring</li>
3061 <li>Sequence database accessions imported when fetching
3062 alignments from Rfam</li>
3063 <li>update VARNA version to 3.91</li>
3065 <li>New groovy scripts for exporting aligned positions,
3066 conservation values, and calculating sum of pairs scores.</li>
3067 <li>Command line argument to set default JABAWS server</li>
3068 <li>include installation type in build properties and
3069 console log output</li>
3070 <li>Updated Jalview project format to preserve dataset
3074 <!-- issues resolved --> <em>Application</em>
3076 <li>Distinguish alignment and sequence associated RNA
3077 structure in structure->view->VARNA</li>
3078 <li>Raise dialog box if user deletes all sequences in an
3080 <li>Pressing F1 results in documentation opening twice</li>
3081 <li>Sequence feature tooltip is wrapped</li>
3082 <li>Double click on sequence associated annotation
3083 selects only first column</li>
3084 <li>Redundancy removal doesn't result in unlinked
3085 leaves shown in tree</li>
3086 <li>Undos after several redundancy removals don't undo
3088 <li>Hide sequence doesn't hide associated annotation</li>
3089 <li>User defined colours dialog box too big to fit on
3090 screen and buttons not visible</li>
3091 <li>author list isn't updated if already written to
3092 Jalview properties</li>
3093 <li>Popup menu won't open after retrieving sequence
3095 <li>File open window for associate PDB doesn't open</li>
3096 <li>Left-then-right click on a sequence id opens a
3097 browser search window</li>
3098 <li>Cannot open sequence feature shading/sort popup menu
3099 in feature settings dialog</li>
3100 <li>better tooltip placement for some areas of Jalview
3102 <li>Allow addition of JABAWS Server which doesn't
3103 pass validation</li>
3104 <li>Web services parameters dialog box is too large to
3106 <li>Muscle nucleotide alignment preset obscured by
3108 <li>JABAWS preset submenus don't contain newly
3109 defined user preset</li>
3110 <li>MSA web services warns user if they were launched
3111 with invalid input</li>
3112 <li>Jalview cannot contact DAS Registy when running on
3115 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3116 'Superpose with' submenu not shown when new view
3120 </ul> <!-- <em>Applet</em>
3122 </ul> <em>General</em>
3124 </ul>--> <em>Deployment and Documentation</em>
3126 <li>2G and 1G options in launchApp have no effect on
3127 memory allocation</li>
3128 <li>launchApp service doesn't automatically open
3129 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3131 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3132 InstallAnywhere reports cannot find valid JVM when Java
3133 1.7_055 is available
3135 </ul> <em>Application Known issues</em>
3138 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3139 corrupted or unreadable alignment display when scrolling
3143 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3144 retrieval fails but progress bar continues for DAS retrieval
3145 with large number of ID
3148 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3149 flatfile output of visible region has incorrect sequence
3153 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3154 rna structure consensus doesn't update when secondary
3155 structure tracks are rearranged
3158 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3159 invalid rna structure positional highlighting does not
3160 highlight position of invalid base pairs
3163 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3164 out of memory errors are not raised when saving Jalview
3165 project from alignment window file menu
3168 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3169 Switching to RNA Helices colouring doesn't propagate to
3173 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3174 colour by RNA Helices not enabled when user created
3175 annotation added to alignment
3178 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3179 Jalview icon not shown on dock in Mountain Lion/Webstart
3181 </ul> <em>Applet Known Issues</em>
3184 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3185 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3188 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3189 Jalview and Jmol example not compatible with IE9
3192 <li>Sort by annotation score doesn't reverse order
3198 <td><div align="center">
3199 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3202 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3205 <li>Internationalisation of user interface (usually
3206 called i18n support) and translation for Spanish locale</li>
3207 <li>Define/Undefine group on current selection with
3208 Ctrl-G/Shift Ctrl-G</li>
3209 <li>Improved group creation/removal options in
3210 alignment/sequence Popup menu</li>
3211 <li>Sensible precision for symbol distribution
3212 percentages shown in logo tooltip.</li>
3213 <li>Annotation panel height set according to amount of
3214 annotation when alignment first opened</li>
3215 </ul> <em>Application</em>
3217 <li>Interactive consensus RNA secondary structure
3218 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3219 <li>Select columns containing particular features from
3220 Feature Settings dialog</li>
3221 <li>View all 'representative' PDB structures for selected
3223 <li>Update Jalview project format:
3225 <li>New file extension for Jalview projects '.jvp'</li>
3226 <li>Preserve sequence and annotation dataset (to
3227 store secondary structure annotation,etc)</li>
3228 <li>Per group and alignment annotation and RNA helix
3232 <li>New similarity measures for PCA and Tree calculation
3234 <li>Experimental support for retrieval and viewing of
3235 flanking regions for an alignment</li>
3239 <!-- issues resolved --> <em>Application</em>
3241 <li>logo keeps spinning and status remains at queued or
3242 running after job is cancelled</li>
3243 <li>cannot export features from alignments imported from
3244 Jalview/VAMSAS projects</li>
3245 <li>Buggy slider for web service parameters that take
3247 <li>Newly created RNA secondary structure line doesn't
3248 have 'display all symbols' flag set</li>
3249 <li>T-COFFEE alignment score shading scheme and other
3250 annotation shading not saved in Jalview project</li>
3251 <li>Local file cannot be loaded in freshly downloaded
3253 <li>Jalview icon not shown on dock in Mountain
3255 <li>Load file from desktop file browser fails</li>
3256 <li>Occasional NPE thrown when calculating large trees</li>
3257 <li>Cannot reorder or slide sequences after dragging an
3258 alignment onto desktop</li>
3259 <li>Colour by annotation dialog throws NPE after using
3260 'extract scores' function</li>
3261 <li>Loading/cut'n'pasting an empty file leads to a grey
3262 alignment window</li>
3263 <li>Disorder thresholds rendered incorrectly after
3264 performing IUPred disorder prediction</li>
3265 <li>Multiple group annotated consensus rows shown when
3266 changing 'normalise logo' display setting</li>
3267 <li>Find shows blank dialog after 'finished searching' if
3268 nothing matches query</li>
3269 <li>Null Pointer Exceptions raised when sorting by
3270 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3272 <li>Errors in Jmol console when structures in alignment
3273 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3275 <li>Not all working JABAWS services are shown in
3277 <li>JAVAWS version of Jalview fails to launch with
3278 'invalid literal/length code'</li>
3279 <li>Annotation/RNA Helix colourschemes cannot be applied
3280 to alignment with groups (actually fixed in 2.8.0b1)</li>
3281 <li>RNA Helices and T-Coffee Scores available as default
3284 </ul> <em>Applet</em>
3286 <li>Remove group option is shown even when selection is
3288 <li>Apply to all groups ticked but colourscheme changes
3289 don't affect groups</li>
3290 <li>Documented RNA Helices and T-Coffee Scores as valid
3291 colourscheme name</li>
3292 <li>Annotation labels drawn on sequence IDs when
3293 Annotation panel is not displayed</li>
3294 <li>Increased font size for dropdown menus on OSX and
3295 embedded windows</li>
3296 </ul> <em>Other</em>
3298 <li>Consensus sequence for alignments/groups with a
3299 single sequence were not calculated</li>
3300 <li>annotation files that contain only groups imported as
3301 annotation and junk sequences</li>
3302 <li>Fasta files with sequences containing '*' incorrectly
3303 recognised as PFAM or BLC</li>
3304 <li>conservation/PID slider apply all groups option
3305 doesn't affect background (2.8.0b1)
3307 <li>redundancy highlighting is erratic at 0% and 100%</li>
3308 <li>Remove gapped columns fails for sequences with ragged
3310 <li>AMSA annotation row with leading spaces is not
3311 registered correctly on import</li>
3312 <li>Jalview crashes when selecting PCA analysis for
3313 certain alignments</li>
3314 <li>Opening the colour by annotation dialog for an
3315 existing annotation based 'use original colours'
3316 colourscheme loses original colours setting</li>
3321 <td><div align="center">
3322 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3323 <em>30/1/2014</em></strong>
3327 <li>Trusted certificates for JalviewLite applet and
3328 Jalview Desktop application<br />Certificate was donated by
3329 <a href="https://www.certum.eu">Certum</a> to the Jalview
3330 open source project).
3332 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3333 <li>Output in Stockholm format</li>
3334 <li>Allow import of data from gzipped files</li>
3335 <li>Export/import group and sequence associated line
3336 graph thresholds</li>
3337 <li>Nucleotide substitution matrix that supports RNA and
3338 ambiguity codes</li>
3339 <li>Allow disorder predictions to be made on the current
3340 selection (or visible selection) in the same way that JPred
3342 <li>Groovy scripting for headless Jalview operation</li>
3343 </ul> <em>Other improvements</em>
3345 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3346 <li>COMBINE statement uses current SEQUENCE_REF and
3347 GROUP_REF scope to group annotation rows</li>
3348 <li>Support '' style escaping of quotes in Newick
3350 <li>Group options for JABAWS service by command line name</li>
3351 <li>Empty tooltip shown for JABA service options with a
3352 link but no description</li>
3353 <li>Select primary source when selecting authority in
3354 database fetcher GUI</li>
3355 <li>Add .mfa to FASTA file extensions recognised by
3357 <li>Annotation label tooltip text wrap</li>
3362 <li>Slow scrolling when lots of annotation rows are
3364 <li>Lots of NPE (and slowness) after creating RNA
3365 secondary structure annotation line</li>
3366 <li>Sequence database accessions not imported when
3367 fetching alignments from Rfam</li>
3368 <li>Incorrect SHMR submission for sequences with
3370 <li>View all structures does not always superpose
3372 <li>Option widgets in service parameters not updated to
3373 reflect user or preset settings</li>
3374 <li>Null pointer exceptions for some services without
3375 presets or adjustable parameters</li>
3376 <li>Discover PDB IDs entry in structure menu doesn't
3377 discover PDB xRefs</li>
3378 <li>Exception encountered while trying to retrieve
3379 features with DAS</li>
3380 <li>Lowest value in annotation row isn't coloured
3381 when colour by annotation (per sequence) is coloured</li>
3382 <li>Keyboard mode P jumps to start of gapped region when
3383 residue follows a gap</li>
3384 <li>Jalview appears to hang importing an alignment with
3385 Wrap as default or after enabling Wrap</li>
3386 <li>'Right click to add annotations' message
3387 shown in wrap mode when no annotations present</li>
3388 <li>Disorder predictions fail with NPE if no automatic
3389 annotation already exists on alignment</li>
3390 <li>oninit javascript function should be called after
3391 initialisation completes</li>
3392 <li>Remove redundancy after disorder prediction corrupts
3393 alignment window display</li>
3394 <li>Example annotation file in documentation is invalid</li>
3395 <li>Grouped line graph annotation rows are not exported
3396 to annotation file</li>
3397 <li>Multi-harmony analysis cannot be run when only two
3399 <li>Cannot create multiple groups of line graphs with
3400 several 'combine' statements in annotation file</li>
3401 <li>Pressing return several times causes Number Format
3402 exceptions in keyboard mode</li>
3403 <li>Multi-harmony (SHMMR) method doesn't submit
3404 correct partitions for input data</li>
3405 <li>Translation from DNA to Amino Acids fails</li>
3406 <li>Jalview fail to load newick tree with quoted label</li>
3407 <li>--headless flag isn't understood</li>
3408 <li>ClassCastException when generating EPS in headless
3410 <li>Adjusting sequence-associated shading threshold only
3411 changes one row's threshold</li>
3412 <li>Preferences and Feature settings panel panel
3413 doesn't open</li>
3414 <li>hide consensus histogram also hides conservation and
3415 quality histograms</li>
3420 <td><div align="center">
3421 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3423 <td><em>Application</em>
3425 <li>Support for JABAWS 2.0 Services (AACon alignment
3426 conservation, protein disorder and Clustal Omega)</li>
3427 <li>JABAWS server status indicator in Web Services
3429 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3430 in Jalview alignment window</li>
3431 <li>Updated Jalview build and deploy framework for OSX
3432 mountain lion, windows 7, and 8</li>
3433 <li>Nucleotide substitution matrix for PCA that supports
3434 RNA and ambiguity codes</li>
3436 <li>Improved sequence database retrieval GUI</li>
3437 <li>Support fetching and database reference look up
3438 against multiple DAS sources (Fetch all from in 'fetch db
3440 <li>Jalview project improvements
3442 <li>Store and retrieve the 'belowAlignment'
3443 flag for annotation</li>
3444 <li>calcId attribute to group annotation rows on the
3446 <li>Store AACon calculation settings for a view in
3447 Jalview project</li>
3451 <li>horizontal scrolling gesture support</li>
3452 <li>Visual progress indicator when PCA calculation is
3454 <li>Simpler JABA web services menus</li>
3455 <li>visual indication that web service results are still
3456 being retrieved from server</li>
3457 <li>Serialise the dialogs that are shown when Jalview
3458 starts up for first time</li>
3459 <li>Jalview user agent string for interacting with HTTP
3461 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3463 <li>Examples directory and Groovy library included in
3464 InstallAnywhere distribution</li>
3465 </ul> <em>Applet</em>
3467 <li>RNA alignment and secondary structure annotation
3468 visualization applet example</li>
3469 </ul> <em>General</em>
3471 <li>Normalise option for consensus sequence logo</li>
3472 <li>Reset button in PCA window to return dimensions to
3474 <li>Allow seqspace or Jalview variant of alignment PCA
3476 <li>PCA with either nucleic acid and protein substitution
3478 <li>Allow windows containing HTML reports to be exported
3480 <li>Interactive display and editing of RNA secondary
3481 structure contacts</li>
3482 <li>RNA Helix Alignment Colouring</li>
3483 <li>RNA base pair logo consensus</li>
3484 <li>Parse sequence associated secondary structure
3485 information in Stockholm files</li>
3486 <li>HTML Export database accessions and annotation
3487 information presented in tooltip for sequences</li>
3488 <li>Import secondary structure from LOCARNA clustalw
3489 style RNA alignment files</li>
3490 <li>import and visualise T-COFFEE quality scores for an
3492 <li>'colour by annotation' per sequence option to
3493 shade each sequence according to its associated alignment
3495 <li>New Jalview Logo</li>
3496 </ul> <em>Documentation and Development</em>
3498 <li>documentation for score matrices used in Jalview</li>
3499 <li>New Website!</li>
3501 <td><em>Application</em>
3503 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3504 wsdbfetch REST service</li>
3505 <li>Stop windows being moved outside desktop on OSX</li>
3506 <li>Filetype associations not installed for webstart
3508 <li>Jalview does not always retrieve progress of a JABAWS
3509 job execution in full once it is complete</li>
3510 <li>revise SHMR RSBS definition to ensure alignment is
3511 uploaded via ali_file parameter</li>
3512 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3513 <li>View all structures superposed fails with exception</li>
3514 <li>Jnet job queues forever if a very short sequence is
3515 submitted for prediction</li>
3516 <li>Cut and paste menu not opened when mouse clicked on
3518 <li>Putting fractional value into integer text box in
3519 alignment parameter dialog causes Jalview to hang</li>
3520 <li>Structure view highlighting doesn't work on
3522 <li>View all structures fails with exception shown in
3524 <li>Characters in filename associated with PDBEntry not
3525 escaped in a platform independent way</li>
3526 <li>Jalview desktop fails to launch with exception when
3528 <li>Tree calculation reports 'you must have 2 or more
3529 sequences selected' when selection is empty</li>
3530 <li>Jalview desktop fails to launch with jar signature
3531 failure when java web start temporary file caching is
3533 <li>DAS Sequence retrieval with range qualification
3534 results in sequence xref which includes range qualification</li>
3535 <li>Errors during processing of command line arguments
3536 cause progress bar (JAL-898) to be removed</li>
3537 <li>Replace comma for semi-colon option not disabled for
3538 DAS sources in sequence fetcher</li>
3539 <li>Cannot close news reader when JABAWS server warning
3540 dialog is shown</li>
3541 <li>Option widgets not updated to reflect user settings</li>
3542 <li>Edited sequence not submitted to web service</li>
3543 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3544 <li>InstallAnywhere installer doesn't unpack and run
3545 on OSX Mountain Lion</li>
3546 <li>Annotation panel not given a scroll bar when
3547 sequences with alignment annotation are pasted into the
3549 <li>Sequence associated annotation rows not associated
3550 when loaded from Jalview project</li>
3551 <li>Browser launch fails with NPE on java 1.7</li>
3552 <li>JABAWS alignment marked as finished when job was
3553 cancelled or job failed due to invalid input</li>
3554 <li>NPE with v2.7 example when clicking on Tree
3555 associated with all views</li>
3556 <li>Exceptions when copy/paste sequences with grouped
3557 annotation rows to new window</li>
3558 </ul> <em>Applet</em>
3560 <li>Sequence features are momentarily displayed before
3561 they are hidden using hidefeaturegroups applet parameter</li>
3562 <li>loading features via javascript API automatically
3563 enables feature display</li>
3564 <li>scrollToColumnIn javascript API method doesn't
3566 </ul> <em>General</em>
3568 <li>Redundancy removal fails for rna alignment</li>
3569 <li>PCA calculation fails when sequence has been selected
3570 and then deselected</li>
3571 <li>PCA window shows grey box when first opened on OSX</li>
3572 <li>Letters coloured pink in sequence logo when alignment
3573 coloured with clustalx</li>
3574 <li>Choosing fonts without letter symbols defined causes
3575 exceptions and redraw errors</li>
3576 <li>Initial PCA plot view is not same as manually
3577 reconfigured view</li>
3578 <li>Grouped annotation graph label has incorrect line
3580 <li>Grouped annotation graph label display is corrupted
3581 for lots of labels</li>
3586 <div align="center">
3587 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3590 <td><em>Application</em>
3592 <li>Jalview Desktop News Reader</li>
3593 <li>Tweaked default layout of web services menu</li>
3594 <li>View/alignment association menu to enable user to
3595 easily specify which alignment a multi-structure view takes
3596 its colours/correspondences from</li>
3597 <li>Allow properties file location to be specified as URL</li>
3598 <li>Extend Jalview project to preserve associations
3599 between many alignment views and a single Jmol display</li>
3600 <li>Store annotation row height in Jalview project file</li>
3601 <li>Annotation row column label formatting attributes
3602 stored in project file</li>
3603 <li>Annotation row order for auto-calculated annotation
3604 rows preserved in Jalview project file</li>
3605 <li>Visual progress indication when Jalview state is
3606 saved using Desktop window menu</li>
3607 <li>Visual indication that command line arguments are
3608 still being processed</li>
3609 <li>Groovy script execution from URL</li>
3610 <li>Colour by annotation default min and max colours in
3612 <li>Automatically associate PDB files dragged onto an
3613 alignment with sequences that have high similarity and
3615 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3616 <li>'view structures' option to open many
3617 structures in same window</li>
3618 <li>Sort associated views menu option for tree panel</li>
3619 <li>Group all JABA and non-JABA services for a particular
3620 analysis function in its own submenu</li>
3621 </ul> <em>Applet</em>
3623 <li>Userdefined and autogenerated annotation rows for
3625 <li>Adjustment of alignment annotation pane height</li>
3626 <li>Annotation scrollbar for annotation panel</li>
3627 <li>Drag to reorder annotation rows in annotation panel</li>
3628 <li>'automaticScrolling' parameter</li>
3629 <li>Allow sequences with partial ID string matches to be
3630 annotated from GFF/Jalview features files</li>
3631 <li>Sequence logo annotation row in applet</li>
3632 <li>Absolute paths relative to host server in applet
3633 parameters are treated as such</li>
3634 <li>New in the JalviewLite javascript API:
3636 <li>JalviewLite.js javascript library</li>
3637 <li>Javascript callbacks for
3639 <li>Applet initialisation</li>
3640 <li>Sequence/alignment mouse-overs and selections</li>
3643 <li>scrollTo row and column alignment scrolling
3645 <li>Select sequence/alignment regions from javascript</li>
3646 <li>javascript structure viewer harness to pass
3647 messages between Jmol and Jalview when running as
3648 distinct applets</li>
3649 <li>sortBy method</li>
3650 <li>Set of applet and application examples shipped
3651 with documentation</li>
3652 <li>New example to demonstrate JalviewLite and Jmol
3653 javascript message exchange</li>
3655 </ul> <em>General</em>
3657 <li>Enable Jmol displays to be associated with multiple
3658 multiple alignments</li>
3659 <li>Option to automatically sort alignment with new tree</li>
3660 <li>User configurable link to enable redirects to a
3661 www.Jalview.org mirror</li>
3662 <li>Jmol colours option for Jmol displays</li>
3663 <li>Configurable newline string when writing alignment
3664 and other flat files</li>
3665 <li>Allow alignment annotation description lines to
3666 contain html tags</li>
3667 </ul> <em>Documentation and Development</em>
3669 <li>Add groovy test harness for bulk load testing to
3671 <li>Groovy script to load and align a set of sequences
3672 using a web service before displaying the result in the
3673 Jalview desktop</li>
3674 <li>Restructured javascript and applet api documentation</li>
3675 <li>Ant target to publish example html files with applet
3677 <li>Netbeans project for building Jalview from source</li>
3678 <li>ant task to create online javadoc for Jalview source</li>
3680 <td><em>Application</em>
3682 <li>User defined colourscheme throws exception when
3683 current built in colourscheme is saved as new scheme</li>
3684 <li>AlignFrame->Save in application pops up save
3685 dialog for valid filename/format</li>
3686 <li>Cannot view associated structure for UniProt sequence</li>
3687 <li>PDB file association breaks for UniProt sequence
3689 <li>Associate PDB from file dialog does not tell you
3690 which sequence is to be associated with the file</li>
3691 <li>Find All raises null pointer exception when query
3692 only matches sequence IDs</li>
3693 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3694 <li>Jalview project with Jmol views created with Jalview
3695 2.4 cannot be loaded</li>
3696 <li>Filetype associations not installed for webstart
3698 <li>Two or more chains in a single PDB file associated
3699 with sequences in different alignments do not get coloured
3700 by their associated sequence</li>
3701 <li>Visibility status of autocalculated annotation row
3702 not preserved when project is loaded</li>
3703 <li>Annotation row height and visibility attributes not
3704 stored in Jalview project</li>
3705 <li>Tree bootstraps are not preserved when saved as a
3706 Jalview project</li>
3707 <li>Envision2 workflow tooltips are corrupted</li>
3708 <li>Enabling show group conservation also enables colour
3709 by conservation</li>
3710 <li>Duplicate group associated conservation or consensus
3711 created on new view</li>
3712 <li>Annotation scrollbar not displayed after 'show
3713 all hidden annotation rows' option selected</li>
3714 <li>Alignment quality not updated after alignment
3715 annotation row is hidden then shown</li>
3716 <li>Preserve colouring of structures coloured by
3717 sequences in pre Jalview 2.7 projects</li>
3718 <li>Web service job parameter dialog is not laid out
3720 <li>Web services menu not refreshed after 'reset
3721 services' button is pressed in preferences</li>
3722 <li>Annotation off by one in Jalview v2_3 example project</li>
3723 <li>Structures imported from file and saved in project
3724 get name like jalview_pdb1234.txt when reloaded</li>
3725 <li>Jalview does not always retrieve progress of a JABAWS
3726 job execution in full once it is complete</li>
3727 </ul> <em>Applet</em>
3729 <li>Alignment height set incorrectly when lots of
3730 annotation rows are displayed</li>
3731 <li>Relative URLs in feature HTML text not resolved to
3733 <li>View follows highlighting does not work for positions
3735 <li><= shown as = in tooltip</li>
3736 <li>Export features raises exception when no features
3738 <li>Separator string used for serialising lists of IDs
3739 for javascript api is modified when separator string
3740 provided as parameter</li>
3741 <li>Null pointer exception when selecting tree leaves for
3742 alignment with no existing selection</li>
3743 <li>Relative URLs for datasources assumed to be relative
3744 to applet's codebase</li>
3745 <li>Status bar not updated after finished searching and
3746 search wraps around to first result</li>
3747 <li>StructureSelectionManager instance shared between
3748 several Jalview applets causes race conditions and memory
3750 <li>Hover tooltip and mouseover of position on structure
3751 not sent from Jmol in applet</li>
3752 <li>Certain sequences of javascript method calls to
3753 applet API fatally hang browser</li>
3754 </ul> <em>General</em>
3756 <li>View follows structure mouseover scrolls beyond
3757 position with wrapped view and hidden regions</li>
3758 <li>Find sequence position moves to wrong residue
3759 with/without hidden columns</li>
3760 <li>Sequence length given in alignment properties window
3762 <li>InvalidNumberFormat exceptions thrown when trying to
3763 import PDB like structure files</li>
3764 <li>Positional search results are only highlighted
3765 between user-supplied sequence start/end bounds</li>
3766 <li>End attribute of sequence is not validated</li>
3767 <li>Find dialog only finds first sequence containing a
3768 given sequence position</li>
3769 <li>Sequence numbering not preserved in MSF alignment
3771 <li>Jalview PDB file reader does not extract sequence
3772 from nucleotide chains correctly</li>
3773 <li>Structure colours not updated when tree partition
3774 changed in alignment</li>
3775 <li>Sequence associated secondary structure not correctly
3776 parsed in interleaved stockholm</li>
3777 <li>Colour by annotation dialog does not restore current
3779 <li>Hiding (nearly) all sequences doesn't work
3781 <li>Sequences containing lowercase letters are not
3782 properly associated with their pdb files</li>
3783 </ul> <em>Documentation and Development</em>
3785 <li>schemas/JalviewWsParamSet.xsd corrupted by
3786 ApplyCopyright tool</li>
3791 <div align="center">
3792 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3795 <td><em>Application</em>
3797 <li>New warning dialog when the Jalview Desktop cannot
3798 contact web services</li>
3799 <li>JABA service parameters for a preset are shown in
3800 service job window</li>
3801 <li>JABA Service menu entries reworded</li>
3805 <li>Modeller PIR IO broken - cannot correctly import a
3806 pir file emitted by Jalview</li>
3807 <li>Existing feature settings transferred to new
3808 alignment view created from cut'n'paste</li>
3809 <li>Improved test for mixed amino/nucleotide chains when
3810 parsing PDB files</li>
3811 <li>Consensus and conservation annotation rows
3812 occasionally become blank for all new windows</li>
3813 <li>Exception raised when right clicking above sequences
3814 in wrapped view mode</li>
3815 </ul> <em>Application</em>
3817 <li>multiple multiply aligned structure views cause cpu
3818 usage to hit 100% and computer to hang</li>
3819 <li>Web Service parameter layout breaks for long user
3820 parameter names</li>
3821 <li>Jaba service discovery hangs desktop if Jaba server
3828 <div align="center">
3829 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3832 <td><em>Application</em>
3834 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3835 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3838 <li>Web Services preference tab</li>
3839 <li>Analysis parameters dialog box and user defined
3841 <li>Improved speed and layout of Envision2 service menu</li>
3842 <li>Superpose structures using associated sequence
3844 <li>Export coordinates and projection as CSV from PCA
3846 </ul> <em>Applet</em>
3848 <li>enable javascript: execution by the applet via the
3849 link out mechanism</li>
3850 </ul> <em>Other</em>
3852 <li>Updated the Jmol Jalview interface to work with Jmol
3854 <li>The Jalview Desktop and JalviewLite applet now
3855 require Java 1.5</li>
3856 <li>Allow Jalview feature colour specification for GFF
3857 sequence annotation files</li>
3858 <li>New 'colour by label' keword in Jalview feature file
3859 type colour specification</li>
3860 <li>New Jalview Desktop Groovy API method that allows a
3861 script to check if it being run in an interactive session or
3862 in a batch operation from the Jalview command line</li>
3866 <li>clustalx colourscheme colours Ds preferentially when
3867 both D+E are present in over 50% of the column</li>
3868 </ul> <em>Application</em>
3870 <li>typo in AlignmentFrame->View->Hide->all but
3871 selected Regions menu item</li>
3872 <li>sequence fetcher replaces ',' for ';' when the ',' is
3873 part of a valid accession ID</li>
3874 <li>fatal OOM if object retrieved by sequence fetcher
3875 runs out of memory</li>
3876 <li>unhandled Out of Memory Error when viewing pca
3877 analysis results</li>
3878 <li>InstallAnywhere builds fail to launch on OS X java
3879 10.5 update 4 (due to apple Java 1.6 update)</li>
3880 <li>Installanywhere Jalview silently fails to launch</li>
3881 </ul> <em>Applet</em>
3883 <li>Jalview.getFeatureGroups() raises an
3884 ArrayIndexOutOfBoundsException if no feature groups are
3891 <div align="center">
3892 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3898 <li>Alignment prettyprinter doesn't cope with long
3900 <li>clustalx colourscheme colours Ds preferentially when
3901 both D+E are present in over 50% of the column</li>
3902 <li>nucleic acid structures retrieved from PDB do not
3903 import correctly</li>
3904 <li>More columns get selected than were clicked on when a
3905 number of columns are hidden</li>
3906 <li>annotation label popup menu not providing correct
3907 add/hide/show options when rows are hidden or none are
3909 <li>Stockholm format shown in list of readable formats,
3910 and parser copes better with alignments from RFAM.</li>
3911 <li>CSV output of consensus only includes the percentage
3912 of all symbols if sequence logo display is enabled</li>
3914 </ul> <em>Applet</em>
3916 <li>annotation panel disappears when annotation is
3918 </ul> <em>Application</em>
3920 <li>Alignment view not redrawn properly when new
3921 alignment opened where annotation panel is visible but no
3922 annotations are present on alignment</li>
3923 <li>pasted region containing hidden columns is
3924 incorrectly displayed in new alignment window</li>
3925 <li>Jalview slow to complete operations when stdout is
3926 flooded (fix is to close the Jalview console)</li>
3927 <li>typo in AlignmentFrame->View->Hide->all but
3928 selected Rregions menu item.</li>
3929 <li>inconsistent group submenu and Format submenu entry
3930 'Un' or 'Non'conserved</li>
3931 <li>Sequence feature settings are being shared by
3932 multiple distinct alignments</li>
3933 <li>group annotation not recreated when tree partition is
3935 <li>double click on group annotation to select sequences
3936 does not propagate to associated trees</li>
3937 <li>Mac OSX specific issues:
3939 <li>exception raised when mouse clicked on desktop
3940 window background</li>
3941 <li>Desktop menu placed on menu bar and application
3942 name set correctly</li>
3943 <li>sequence feature settings not wide enough for the
3944 save feature colourscheme button</li>
3953 <div align="center">
3954 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3957 <td><em>New Capabilities</em>
3959 <li>URL links generated from description line for
3960 regular-expression based URL links (applet and application)
3962 <li>Non-positional feature URL links are shown in link
3964 <li>Linked viewing of nucleic acid sequences and
3966 <li>Automatic Scrolling option in View menu to display
3967 the currently highlighted region of an alignment.</li>
3968 <li>Order an alignment by sequence length, or using the
3969 average score or total feature count for each sequence.</li>
3970 <li>Shading features by score or associated description</li>
3971 <li>Subdivide alignment and groups based on identity of
3972 selected subsequence (Make Groups from Selection).</li>
3973 <li>New hide/show options including Shift+Control+H to
3974 hide everything but the currently selected region.</li>
3975 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3976 </ul> <em>Application</em>
3978 <li>Fetch DB References capabilities and UI expanded to
3979 support retrieval from DAS sequence sources</li>
3980 <li>Local DAS Sequence sources can be added via the
3981 command line or via the Add local source dialog box.</li>
3982 <li>DAS Dbref and DbxRef feature types are parsed as
3983 database references and protein_name is parsed as
3984 description line (BioSapiens terms).</li>
3985 <li>Enable or disable non-positional feature and database
3986 references in sequence ID tooltip from View menu in
3988 <!-- <li>New hidden columns and rows and representatives capabilities
3989 in annotations file (in progress - not yet fully implemented)</li> -->
3990 <li>Group-associated consensus, sequence logos and
3991 conservation plots</li>
3992 <li>Symbol distributions for each column can be exported
3993 and visualized as sequence logos</li>
3994 <li>Optionally scale multi-character column labels to fit
3995 within each column of annotation row<!-- todo for applet -->
3997 <li>Optional automatic sort of associated alignment view
3998 when a new tree is opened.</li>
3999 <li>Jalview Java Console</li>
4000 <li>Better placement of desktop window when moving
4001 between different screens.</li>
4002 <li>New preference items for sequence ID tooltip and
4003 consensus annotation</li>
4004 <li>Client to submit sequences and IDs to Envision2
4006 <li><em>Vamsas Capabilities</em>
4008 <li>Improved VAMSAS synchronization (Jalview archive
4009 used to preserve views, structures, and tree display
4011 <li>Import of vamsas documents from disk or URL via
4013 <li>Sharing of selected regions between views and
4014 with other VAMSAS applications (Experimental feature!)</li>
4015 <li>Updated API to VAMSAS version 0.2</li>
4017 </ul> <em>Applet</em>
4019 <li>Middle button resizes annotation row height</li>
4022 <li>sortByTree (true/false) - automatically sort the
4023 associated alignment view by the tree when a new tree is
4025 <li>showTreeBootstraps (true/false) - show or hide
4026 branch bootstraps (default is to show them if available)</li>
4027 <li>showTreeDistances (true/false) - show or hide
4028 branch lengths (default is to show them if available)</li>
4029 <li>showUnlinkedTreeNodes (true/false) - indicate if
4030 unassociated nodes should be highlighted in the tree
4032 <li>heightScale and widthScale (1.0 or more) -
4033 increase the height or width of a cell in the alignment
4034 grid relative to the current font size.</li>
4037 <li>Non-positional features displayed in sequence ID
4039 </ul> <em>Other</em>
4041 <li>Features format: graduated colour definitions and
4042 specification of feature scores</li>
4043 <li>Alignment Annotations format: new keywords for group
4044 associated annotation (GROUP_REF) and annotation row display
4045 properties (ROW_PROPERTIES)</li>
4046 <li>XML formats extended to support graduated feature
4047 colourschemes, group associated annotation, and profile
4048 visualization settings.</li></td>
4051 <li>Source field in GFF files parsed as feature source
4052 rather than description</li>
4053 <li>Non-positional features are now included in sequence
4054 feature and gff files (controlled via non-positional feature
4055 visibility in tooltip).</li>
4056 <li>URL links generated for all feature links (bugfix)</li>
4057 <li>Added URL embedding instructions to features file
4059 <li>Codons containing ambiguous nucleotides translated as
4060 'X' in peptide product</li>
4061 <li>Match case switch in find dialog box works for both
4062 sequence ID and sequence string and query strings do not
4063 have to be in upper case to match case-insensitively.</li>
4064 <li>AMSA files only contain first column of
4065 multi-character column annotation labels</li>
4066 <li>Jalview Annotation File generation/parsing consistent
4067 with documentation (e.g. Stockholm annotation can be
4068 exported and re-imported)</li>
4069 <li>PDB files without embedded PDB IDs given a friendly
4071 <li>Find incrementally searches ID string matches as well
4072 as subsequence matches, and correctly reports total number
4076 <li>Better handling of exceptions during sequence
4078 <li>Dasobert generated non-positional feature URL
4079 link text excludes the start_end suffix</li>
4080 <li>DAS feature and source retrieval buttons disabled
4081 when fetch or registry operations in progress.</li>
4082 <li>PDB files retrieved from URLs are cached properly</li>
4083 <li>Sequence description lines properly shared via
4085 <li>Sequence fetcher fetches multiple records for all
4087 <li>Ensured that command line das feature retrieval
4088 completes before alignment figures are generated.</li>
4089 <li>Reduced time taken when opening file browser for
4091 <li>isAligned check prior to calculating tree, PCA or
4092 submitting an MSA to JNet now excludes hidden sequences.</li>
4093 <li>User defined group colours properly recovered
4094 from Jalview projects.</li>
4103 <div align="center">
4104 <strong>2.4.0.b2</strong><br> 28/10/2009
4109 <li>Experimental support for google analytics usage
4111 <li>Jalview privacy settings (user preferences and docs).</li>
4116 <li>Race condition in applet preventing startup in
4118 <li>Exception when feature created from selection beyond
4119 length of sequence.</li>
4120 <li>Allow synthetic PDB files to be imported gracefully</li>
4121 <li>Sequence associated annotation rows associate with
4122 all sequences with a given id</li>
4123 <li>Find function matches case-insensitively for sequence
4124 ID string searches</li>
4125 <li>Non-standard characters do not cause pairwise
4126 alignment to fail with exception</li>
4127 </ul> <em>Application Issues</em>
4129 <li>Sequences are now validated against EMBL database</li>
4130 <li>Sequence fetcher fetches multiple records for all
4132 </ul> <em>InstallAnywhere Issues</em>
4134 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4135 issue with installAnywhere mechanism)</li>
4136 <li>Command line launching of JARs from InstallAnywhere
4137 version (java class versioning error fixed)</li>
4144 <div align="center">
4145 <strong>2.4</strong><br> 27/8/2008
4148 <td><em>User Interface</em>
4150 <li>Linked highlighting of codon and amino acid from
4151 translation and protein products</li>
4152 <li>Linked highlighting of structure associated with
4153 residue mapping to codon position</li>
4154 <li>Sequence Fetcher provides example accession numbers
4155 and 'clear' button</li>
4156 <li>MemoryMonitor added as an option under Desktop's
4158 <li>Extract score function to parse whitespace separated
4159 numeric data in description line</li>
4160 <li>Column labels in alignment annotation can be centred.</li>
4161 <li>Tooltip for sequence associated annotation give name
4163 </ul> <em>Web Services and URL fetching</em>
4165 <li>JPred3 web service</li>
4166 <li>Prototype sequence search client (no public services
4168 <li>Fetch either seed alignment or full alignment from
4170 <li>URL Links created for matching database cross
4171 references as well as sequence ID</li>
4172 <li>URL Links can be created using regular-expressions</li>
4173 </ul> <em>Sequence Database Connectivity</em>
4175 <li>Retrieval of cross-referenced sequences from other
4177 <li>Generalised database reference retrieval and
4178 validation to all fetchable databases</li>
4179 <li>Fetch sequences from DAS sources supporting the
4180 sequence command</li>
4181 </ul> <em>Import and Export</em>
4182 <li>export annotation rows as CSV for spreadsheet import</li>
4183 <li>Jalview projects record alignment dataset associations,
4184 EMBL products, and cDNA sequence mappings</li>
4185 <li>Sequence Group colour can be specified in Annotation
4187 <li>Ad-hoc colouring of group in Annotation File using RGB
4188 triplet as name of colourscheme</li>
4189 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4191 <li>treenode binding for VAMSAS tree exchange</li>
4192 <li>local editing and update of sequences in VAMSAS
4193 alignments (experimental)</li>
4194 <li>Create new or select existing session to join</li>
4195 <li>load and save of vamsas documents</li>
4196 </ul> <em>Application command line</em>
4198 <li>-tree parameter to open trees (introduced for passing
4200 <li>-fetchfrom command line argument to specify nicknames
4201 of DAS servers to query for alignment features</li>
4202 <li>-dasserver command line argument to add new servers
4203 that are also automatically queried for features</li>
4204 <li>-groovy command line argument executes a given groovy
4205 script after all input data has been loaded and parsed</li>
4206 </ul> <em>Applet-Application data exchange</em>
4208 <li>Trees passed as applet parameters can be passed to
4209 application (when using "View in full
4210 application")</li>
4211 </ul> <em>Applet Parameters</em>
4213 <li>feature group display control parameter</li>
4214 <li>debug parameter</li>
4215 <li>showbutton parameter</li>
4216 </ul> <em>Applet API methods</em>
4218 <li>newView public method</li>
4219 <li>Window (current view) specific get/set public methods</li>
4220 <li>Feature display control methods</li>
4221 <li>get list of currently selected sequences</li>
4222 </ul> <em>New Jalview distribution features</em>
4224 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4225 <li>RELEASE file gives build properties for the latest
4226 Jalview release.</li>
4227 <li>Java 1.1 Applet build made easier and donotobfuscate
4228 property controls execution of obfuscator</li>
4229 <li>Build target for generating source distribution</li>
4230 <li>Debug flag for javacc</li>
4231 <li>.jalview_properties file is documented (slightly) in
4232 jalview.bin.Cache</li>
4233 <li>Continuous Build Integration for stable and
4234 development version of Application, Applet and source
4239 <li>selected region output includes visible annotations
4240 (for certain formats)</li>
4241 <li>edit label/displaychar contains existing label/char
4243 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4244 <li>shorter peptide product names from EMBL records</li>
4245 <li>Newick string generator makes compact representations</li>
4246 <li>bootstrap values parsed correctly for tree files with
4248 <li>pathological filechooser bug avoided by not allowing
4249 filenames containing a ':'</li>
4250 <li>Fixed exception when parsing GFF files containing
4251 global sequence features</li>
4252 <li>Alignment datasets are finalized only when number of
4253 references from alignment sequences goes to zero</li>
4254 <li>Close of tree branch colour box without colour
4255 selection causes cascading exceptions</li>
4256 <li>occasional negative imgwidth exceptions</li>
4257 <li>better reporting of non-fatal warnings to user when
4258 file parsing fails.</li>
4259 <li>Save works when Jalview project is default format</li>
4260 <li>Save as dialog opened if current alignment format is
4261 not a valid output format</li>
4262 <li>UniProt canonical names introduced for both das and
4264 <li>Histidine should be midblue (not pink!) in Zappo</li>
4265 <li>error messages passed up and output when data read
4267 <li>edit undo recovers previous dataset sequence when
4268 sequence is edited</li>
4269 <li>allow PDB files without pdb ID HEADER lines (like
4270 those generated by MODELLER) to be read in properly</li>
4271 <li>allow reading of JPred concise files as a normal
4273 <li>Stockholm annotation parsing and alignment properties
4274 import fixed for PFAM records</li>
4275 <li>Structure view windows have correct name in Desktop
4277 <li>annotation consisting of sequence associated scores
4278 can be read and written correctly to annotation file</li>
4279 <li>Aligned cDNA translation to aligned peptide works
4281 <li>Fixed display of hidden sequence markers and
4282 non-italic font for representatives in Applet</li>
4283 <li>Applet Menus are always embedded in applet window on
4285 <li>Newly shown features appear at top of stack (in
4287 <li>Annotations added via parameter not drawn properly
4288 due to null pointer exceptions</li>
4289 <li>Secondary structure lines are drawn starting from
4290 first column of alignment</li>
4291 <li>UniProt XML import updated for new schema release in
4293 <li>Sequence feature to sequence ID match for Features
4294 file is case-insensitive</li>
4295 <li>Sequence features read from Features file appended to
4296 all sequences with matching IDs</li>
4297 <li>PDB structure coloured correctly for associated views
4298 containing a sub-sequence</li>
4299 <li>PDB files can be retrieved by applet from Jar files</li>
4300 <li>feature and annotation file applet parameters
4301 referring to different directories are retrieved correctly</li>
4302 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4303 <li>Fixed application hang whilst waiting for
4304 splash-screen version check to complete</li>
4305 <li>Applet properly URLencodes input parameter values
4306 when passing them to the launchApp service</li>
4307 <li>display name and local features preserved in results
4308 retrieved from web service</li>
4309 <li>Visual delay indication for sequence retrieval and
4310 sequence fetcher initialisation</li>
4311 <li>updated Application to use DAS 1.53e version of
4312 dasobert DAS client</li>
4313 <li>Re-instated Full AMSA support and .amsa file
4315 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4323 <div align="center">
4324 <strong>2.3</strong><br> 9/5/07
4329 <li>Jmol 11.0.2 integration</li>
4330 <li>PDB views stored in Jalview XML files</li>
4331 <li>Slide sequences</li>
4332 <li>Edit sequence in place</li>
4333 <li>EMBL CDS features</li>
4334 <li>DAS Feature mapping</li>
4335 <li>Feature ordering</li>
4336 <li>Alignment Properties</li>
4337 <li>Annotation Scores</li>
4338 <li>Sort by scores</li>
4339 <li>Feature/annotation editing in applet</li>
4344 <li>Headless state operation in 2.2.1</li>
4345 <li>Incorrect and unstable DNA pairwise alignment</li>
4346 <li>Cut and paste of sequences with annotation</li>
4347 <li>Feature group display state in XML</li>
4348 <li>Feature ordering in XML</li>
4349 <li>blc file iteration selection using filename # suffix</li>
4350 <li>Stockholm alignment properties</li>
4351 <li>Stockhom alignment secondary structure annotation</li>
4352 <li>2.2.1 applet had no feature transparency</li>
4353 <li>Number pad keys can be used in cursor mode</li>
4354 <li>Structure Viewer mirror image resolved</li>
4361 <div align="center">
4362 <strong>2.2.1</strong><br> 12/2/07
4367 <li>Non standard characters can be read and displayed
4368 <li>Annotations/Features can be imported/exported to the
4370 <li>Applet allows editing of sequence/annotation/group
4371 name & description
4372 <li>Preference setting to display sequence name in
4374 <li>Annotation file format extended to allow
4375 Sequence_groups to be defined
4376 <li>Default opening of alignment overview panel can be
4377 specified in preferences
4378 <li>PDB residue numbering annotation added to associated
4384 <li>Applet crash under certain Linux OS with Java 1.6
4386 <li>Annotation file export / import bugs fixed
4387 <li>PNG / EPS image output bugs fixed
4393 <div align="center">
4394 <strong>2.2</strong><br> 27/11/06
4399 <li>Multiple views on alignment
4400 <li>Sequence feature editing
4401 <li>"Reload" alignment
4402 <li>"Save" to current filename
4403 <li>Background dependent text colour
4404 <li>Right align sequence ids
4405 <li>User-defined lower case residue colours
4408 <li>Menu item accelerator keys
4409 <li>Control-V pastes to current alignment
4410 <li>Cancel button for DAS Feature Fetching
4411 <li>PCA and PDB Viewers zoom via mouse roller
4412 <li>User-defined sub-tree colours and sub-tree selection
4414 <li>'New Window' button on the 'Output to Text box'
4419 <li>New memory efficient Undo/Redo System
4420 <li>Optimised symbol lookups and conservation/consensus
4422 <li>Region Conservation/Consensus recalculated after
4424 <li>Fixed Remove Empty Columns Bug (empty columns at end
4426 <li>Slowed DAS Feature Fetching for increased robustness.
4428 <li>Made angle brackets in ASCII feature descriptions
4430 <li>Re-instated Zoom function for PCA
4431 <li>Sequence descriptions conserved in web service
4433 <li>UniProt ID discoverer uses any word separated by
4435 <li>WsDbFetch query/result association resolved
4436 <li>Tree leaf to sequence mapping improved
4437 <li>Smooth fonts switch moved to FontChooser dialog box.
4444 <div align="center">
4445 <strong>2.1.1</strong><br> 12/9/06
4450 <li>Copy consensus sequence to clipboard</li>
4455 <li>Image output - rightmost residues are rendered if
4456 sequence id panel has been resized</li>
4457 <li>Image output - all offscreen group boundaries are
4459 <li>Annotation files with sequence references - all
4460 elements in file are relative to sequence position</li>
4461 <li>Mac Applet users can use Alt key for group editing</li>
4467 <div align="center">
4468 <strong>2.1</strong><br> 22/8/06
4473 <li>MAFFT Multiple Alignment in default Web Service list</li>
4474 <li>DAS Feature fetching</li>
4475 <li>Hide sequences and columns</li>
4476 <li>Export Annotations and Features</li>
4477 <li>GFF file reading / writing</li>
4478 <li>Associate structures with sequences from local PDB
4480 <li>Add sequences to exisiting alignment</li>
4481 <li>Recently opened files / URL lists</li>
4482 <li>Applet can launch the full application</li>
4483 <li>Applet has transparency for features (Java 1.2
4485 <li>Applet has user defined colours parameter</li>
4486 <li>Applet can load sequences from parameter
4487 "sequence<em>x</em>"
4493 <li>Redundancy Panel reinstalled in the Applet</li>
4494 <li>Monospaced font - EPS / rescaling bug fixed</li>
4495 <li>Annotation files with sequence references bug fixed</li>
4501 <div align="center">
4502 <strong>2.08.1</strong><br> 2/5/06
4507 <li>Change case of selected region from Popup menu</li>
4508 <li>Choose to match case when searching</li>
4509 <li>Middle mouse button and mouse movement can compress /
4510 expand the visible width and height of the alignment</li>
4515 <li>Annotation Panel displays complete JNet results</li>
4521 <div align="center">
4522 <strong>2.08b</strong><br> 18/4/06
4528 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4529 <li>Righthand label on wrapped alignments shows correct
4536 <div align="center">
4537 <strong>2.08</strong><br> 10/4/06
4542 <li>Editing can be locked to the selection area</li>
4543 <li>Keyboard editing</li>
4544 <li>Create sequence features from searches</li>
4545 <li>Precalculated annotations can be loaded onto
4547 <li>Features file allows grouping of features</li>
4548 <li>Annotation Colouring scheme added</li>
4549 <li>Smooth fonts off by default - Faster rendering</li>
4550 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4555 <li>Drag & Drop fixed on Linux</li>
4556 <li>Jalview Archive file faster to load/save, sequence
4557 descriptions saved.</li>
4563 <div align="center">
4564 <strong>2.07</strong><br> 12/12/05
4569 <li>PDB Structure Viewer enhanced</li>
4570 <li>Sequence Feature retrieval and display enhanced</li>
4571 <li>Choose to output sequence start-end after sequence
4572 name for file output</li>
4573 <li>Sequence Fetcher WSDBFetch@EBI</li>
4574 <li>Applet can read feature files, PDB files and can be
4575 used for HTML form input</li>
4580 <li>HTML output writes groups and features</li>
4581 <li>Group editing is Control and mouse click</li>
4582 <li>File IO bugs</li>
4588 <div align="center">
4589 <strong>2.06</strong><br> 28/9/05
4594 <li>View annotations in wrapped mode</li>
4595 <li>More options for PCA viewer</li>
4600 <li>GUI bugs resolved</li>
4601 <li>Runs with -nodisplay from command line</li>
4607 <div align="center">
4608 <strong>2.05b</strong><br> 15/9/05
4613 <li>Choose EPS export as lineart or text</li>
4614 <li>Jar files are executable</li>
4615 <li>Can read in Uracil - maps to unknown residue</li>
4620 <li>Known OutOfMemory errors give warning message</li>
4621 <li>Overview window calculated more efficiently</li>
4622 <li>Several GUI bugs resolved</li>
4628 <div align="center">
4629 <strong>2.05</strong><br> 30/8/05
4634 <li>Edit and annotate in "Wrapped" view</li>
4639 <li>Several GUI bugs resolved</li>
4645 <div align="center">
4646 <strong>2.04</strong><br> 24/8/05
4651 <li>Hold down mouse wheel & scroll to change font
4657 <li>Improved JPred client reliability</li>
4658 <li>Improved loading of Jalview files</li>
4664 <div align="center">
4665 <strong>2.03</strong><br> 18/8/05
4670 <li>Set Proxy server name and port in preferences</li>
4671 <li>Multiple URL links from sequence ids</li>
4672 <li>User Defined Colours can have a scheme name and added
4674 <li>Choose to ignore gaps in consensus calculation</li>
4675 <li>Unix users can set default web browser</li>
4676 <li>Runs without GUI for batch processing</li>
4677 <li>Dynamically generated Web Service Menus</li>
4682 <li>InstallAnywhere download for Sparc Solaris</li>
4688 <div align="center">
4689 <strong>2.02</strong><br> 18/7/05
4695 <li>Copy & Paste order of sequences maintains
4696 alignment order.</li>
4702 <div align="center">
4703 <strong>2.01</strong><br> 12/7/05
4708 <li>Use delete key for deleting selection.</li>
4709 <li>Use Mouse wheel to scroll sequences.</li>
4710 <li>Help file updated to describe how to add alignment
4712 <li>Version and build date written to build properties
4714 <li>InstallAnywhere installation will check for updates
4715 at launch of Jalview.</li>
4720 <li>Delete gaps bug fixed.</li>
4721 <li>FileChooser sorts columns.</li>
4722 <li>Can remove groups one by one.</li>
4723 <li>Filechooser icons installed.</li>
4724 <li>Finder ignores return character when searching.
4725 Return key will initiate a search.<br>
4732 <div align="center">
4733 <strong>2.0</strong><br> 20/6/05
4738 <li>New codebase</li>