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>30/03/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302 -->Map 'virtual'
66 codon features shown on protein (or vice versa) for display
67 in alignments, on structure views and for export.
70 <!-- JAL-3121 -->Feature attributes from VCF files can be
71 exported and re-imported as GFF3 files
74 <!-- JAL-3376 -->Capture VCF "fixed column" values
75 POS, ID, QUAL, FILTER as Feature Attributes
78 <!-- JAL-3375 -->More robust VCF numeric data field
79 validation while parsing
82 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
86 <!-- JAL-3538 -->Font anti-aliasing in alignment views
90 <!-- JAL-3468 -->Very long feature descriptions truncated in
94 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
95 with no feature types visible
97 </ul><em>Jalview Installer</em>
100 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
101 in console (may be null when Jalview launched as executable jar or via conda)
104 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
107 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
110 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
112 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
113 </ul> <em>Release processes</em>
116 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
118 </ul> <em>Build System</em>
121 <!-- JAL-3510 -->Clover updated to 4.4.1
124 <!-- JAL-3513 -->Test code included in Clover coverage
128 <em>Groovy Scripts</em>
131 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
132 to stdout containing the consensus sequence for each
133 alignment in a Jalview session
137 <td align="left" valign="top">
140 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
141 buttons in Feature Settings dialog are clicked when no
145 <!-- JAL-3412 -->ID margins for CDS and Protein views not
146 equal when split frame is first opened
149 <!-- JAL-3296 -->Sequence position numbers in status bar not
150 correct after editing a sequence's start position
153 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
154 with annotation and exceptions thrown when only a few
155 columns shown in wrapped mode
158 <!-- JAL-3386 -->Sequence IDs missing in headless export of
159 wrapped alignment figure with annotations
162 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
163 ID fails with ClassCastException
166 <!-- JAL-3389 -->Chimera session not restored from Jalview
170 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
171 feature settings dialog also selects columns
174 <!-- JAL-3473 -->SpinnerNumberModel causes
175 IllegalArgumentException in some circumstances
178 <!-- JAL-3534 -->Multiple feature settings dialogs can be
182 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
183 alignment window is closed
186 <!-- JAL-3406 -->Credits missing some authors in Jalview
187 help documentation for 2.11.0 release
189 </ul> <em>Java 11 Compatibility issues</em>
192 <!-- JAL-2987 -->OSX - Can't view some search results in
193 PDB/Uniprot search panel
195 </ul> <em>Installer</em>
198 <!-- JAL-3447 -->Jalview should not create file associations
199 for 3D structure files (.pdb, .mmcif. .cif)
201 </ul> <em>Repository and Source Release</em>
204 <!-- JAL-3474 -->removed obsolete .cvsignore files from
208 <!-- JAL-3541 -->Clover report generation running out of
211 </ul> <em>New Known Issues</em>
214 <!-- JAL-3523 -->OSX - Current working directory not
215 preserved when Jalview.app launched with parameters from
219 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
220 clipped in headless figure export when Right Align option
224 <!-- JAL-3542 -->Jalview Installation type always reports
225 'Source' in console output
228 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
229 bamboo server but run fine locally.
235 <td width="60" align="center" nowrap>
236 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
237 <em>04/07/2019</em></strong>
239 <td align="left" valign="top">
242 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
243 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
244 source project) rather than InstallAnywhere
247 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
248 settings, receive over the air updates and launch specific
249 versions via (<a href="https://github.com/threerings/getdown">Three
253 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
254 formats supported by Jalview (including .jvp project files)
257 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
258 arguments and switch between different getdown channels
261 <!-- JAL-3141 -->Backup files created when saving Jalview project
266 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
267 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
269 <!-- JAL-2620 -->Alternative genetic code tables for
270 'Translate as cDNA'</li>
272 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
273 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
276 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
277 implementation that allows updates) used for Sequence Feature collections</li>
279 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
280 features can be filtered and shaded according to any
281 associated attributes (e.g. variant attributes from VCF
282 file, or key-value pairs imported from column 9 of GFF
286 <!-- JAL-2879 -->Feature Attributes and shading schemes
287 stored and restored from Jalview Projects
290 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
291 recognise variant features
294 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
295 sequences (also coloured red by default)
298 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
302 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
303 algorithm (Z-sort/transparency and filter aware)
306 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
312 <!-- JAL-3205 -->Symmetric score matrices for faster
313 tree and PCA calculations
315 <li><strong>Principal Components Analysis Viewer</strong>
318 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
319 and Viewer state saved in Jalview Project
321 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
324 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
328 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
333 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
335 <li><strong>Speed and Efficiency</strong>
338 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
339 multiple groups when working with large alignments
342 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
346 <li><strong>User Interface</strong>
349 <!-- JAL-2933 -->Finder panel remembers last position in each
353 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
354 what is shown)<br />Only visible regions of alignment are shown by
355 default (can be changed in user preferences)
358 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
359 to the Overwrite Dialog
362 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
366 <!-- JAL-1244 -->Status bar shows bounds when dragging a
367 selection region, and gap count when inserting or deleting gaps
370 <!-- JAL-3132 -->Status bar updates over sequence and annotation
374 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
378 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
382 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
385 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
389 <!-- JAL-3181 -->Consistent ordering of links in sequence id
393 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
395 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
399 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
400 <li><strong>Java 11 Support (not yet on general release)</strong>
403 <!-- -->OSX GUI integrations for App menu's 'About' entry and
408 <em>Deprecations</em>
410 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
411 capabilities removed from the Jalview Desktop
413 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
414 unmarshalling has been replaced by JAXB for Jalview projects
415 and XML based data retrieval clients</li>
416 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
417 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
418 </ul> <em>Documentation</em>
420 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
421 not supported in EPS figure export
423 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
424 </ul> <em>Development and Release Processes</em>
427 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
430 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
432 <!-- JAL-3225 -->Eclipse project configuration managed with
436 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
437 Bamboo continuous integration for unattended Test Suite
441 <!-- JAL-2864 -->Memory test suite to detect leaks in common
445 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
449 <!-- JAL-3248 -->Developer documentation migrated to
450 markdown (with HTML rendering)
453 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
456 <!-- JAL-3289 -->New URLs for publishing development
461 <td align="left" valign="top">
464 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
467 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
468 superposition in Jmol fail on Windows
471 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
472 structures for sequences with lots of PDB structures
475 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
479 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
480 project involving multiple views
483 <!-- JAL-3164 -->Overview for complementary view in a linked
484 CDS/Protein alignment is not updated when Hide Columns by
485 Annotation dialog hides columns
488 <!-- JAL-3158 -->Selection highlighting in the complement of a
489 CDS/Protein alignment stops working after making a selection in
490 one view, then making another selection in the other view
493 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
497 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
498 Settings and Jalview Preferences panels
501 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
502 overview with large alignments
505 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
506 region if columns were selected by dragging right-to-left and the
507 mouse moved to the left of the first column
510 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
511 hidden column marker via scale popup menu
514 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
515 doesn't tell users the invalid URL
518 <!-- JAL-2816 -->Tooltips displayed for features filtered by
522 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
523 show cross references or Fetch Database References are shown in
527 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
528 peptide sequence (computed variant shown as p.Res.null)
531 <!-- JAL-2060 -->'Graduated colour' option not offered for
532 manually created features (where feature score is Float.NaN)
535 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
536 when columns are hidden
539 <!-- JAL-3082 -->Regular expression error for '(' in Select
540 Columns by Annotation description
543 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
544 out of Scale or Annotation Panel
547 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
551 <!-- JAL-3074 -->Left/right drag in annotation can scroll
555 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
559 <!-- JAL-3002 -->Column display is out by one after Page Down,
560 Page Up in wrapped mode
563 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
566 <!-- JAL-2932 -->Finder searches in minimised alignments
569 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
570 on opening an alignment
573 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
577 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
578 different groups in the alignment are selected
581 <!-- JAL-2717 -->Internationalised colour scheme names not shown
585 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
589 <!-- JAL-3125 -->Value input for graduated feature colour
590 threshold gets 'unrounded'
593 <!-- JAL-2982 -->PCA image export doesn't respect background
597 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
600 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
603 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
607 <!-- JAL-2964 -->Associate Tree with All Views not restored from
611 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
612 shown in complementary view
615 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
616 without normalisation
619 <!-- JAL-3021 -->Sequence Details report should open positioned at top
623 <!-- JAL-914 -->Help page can be opened twice
626 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
628 </ul> <em>Editing</em>
631 <!-- JAL-2822 -->Start and End should be updated when sequence
632 data at beginning or end of alignment added/removed via 'Edit'
636 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
637 relocate sequence features correctly when start of sequence is
638 removed (Known defect since 2.10)
641 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
642 dialog corrupts dataset sequence
645 <!-- JAL-868 -->Structure colours not updated when associated tree
646 repartitions the alignment view (Regression in 2.10.5)
648 </ul> <em>Datamodel</em>
651 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
652 sequence's End is greater than its length
654 </ul> <em>Bugs fixed for Java 11 Support (not yet on
655 general release)</em>
658 <!-- JAL-3288 -->Menus work properly in split-screen
660 </ul> <em>New Known Defects</em>
663 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
666 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
667 regions of protein alignment.
670 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
671 is restored from a Jalview 2.11 project
674 <!-- JAL-3213 -->Alignment panel height can be too small after
678 <!-- JAL-3240 -->Display is incorrect after removing gapped
679 columns within hidden columns
682 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
683 window after dragging left to select columns to left of visible
687 <!-- JAL-2876 -->Features coloured according to their description
688 string and thresholded by score in earlier versions of Jalview are
689 not shown as thresholded features in 2.11. To workaround please
690 create a Score filter instead.
693 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
695 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
698 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
699 alignments with multiple views can close views unexpectedly
702 <em>Java 11 Specific defects</em>
705 <!-- JAL-3235 -->Jalview Properties file is not sorted
706 alphabetically when saved
712 <td width="60" nowrap>
714 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
717 <td><div align="left">
721 <!-- JAL-3101 -->Default memory for Jalview webstart and
722 InstallAnywhere increased to 1G.
725 <!-- JAL-247 -->Hidden sequence markers and representative
726 sequence bolding included when exporting alignment as EPS,
727 SVG, PNG or HTML. <em>Display is configured via the
728 Format menu, or for command-line use via a Jalview
729 properties file.</em>
732 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
733 API and sequence data now imported as JSON.
736 <!-- JAL-3065 -->Change in recommended way of starting
737 Jalview via a Java command line: add jars in lib directory
738 to CLASSPATH, rather than via the deprecated java.ext.dirs
745 <!-- JAL-3047 -->Support added to execute test suite
746 instrumented with <a href="http://openclover.org/">Open
751 <td><div align="left">
755 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
756 row shown in Feredoxin Structure alignment view of example
760 <!-- JAL-2854 -->Annotation obscures sequences if lots of
761 annotation displayed.
764 <!-- JAL-3107 -->Group conservation/consensus not shown
765 for newly created group when 'Apply to all groups'
769 <!-- JAL-3087 -->Corrupted display when switching to
770 wrapped mode when sequence panel's vertical scrollbar is
774 <!-- JAL-3003 -->Alignment is black in exported EPS file
775 when sequences are selected in exported view.</em>
778 <!-- JAL-3059 -->Groups with different coloured borders
779 aren't rendered with correct colour.
782 <!-- JAL-3092 -->Jalview could hang when importing certain
783 types of knotted RNA secondary structure.
786 <!-- JAL-3095 -->Sequence highlight and selection in
787 trimmed VARNA 2D structure is incorrect for sequences that
791 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
792 annotation when columns are inserted into an alignment,
793 and when exporting as Stockholm flatfile.
796 <!-- JAL-3053 -->Jalview annotation rows containing upper
797 and lower-case 'E' and 'H' do not automatically get
798 treated as RNA secondary structure.
801 <!-- JAL-3106 -->.jvp should be used as default extension
802 (not .jar) when saving a Jalview project file.
805 <!-- JAL-3105 -->Mac Users: closing a window correctly
806 transfers focus to previous window on OSX
809 <em>Java 10 Issues Resolved</em>
812 <!-- JAL-2988 -->OSX - Can't save new files via the File
813 or export menus by typing in a name into the Save dialog
817 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
818 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
819 'look and feel' which has improved compatibility with the
820 latest version of OSX.
827 <td width="60" nowrap>
829 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
830 <em>7/06/2018</em></strong>
833 <td><div align="left">
837 <!-- JAL-2920 -->Use HGVS nomenclature for variant
838 annotation retrieved from Uniprot
841 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
842 onto the Jalview Desktop
846 <td><div align="left">
850 <!-- JAL-3017 -->Cannot import features with multiple
851 variant elements (blocks import of some Uniprot records)
854 <!-- JAL-2997 -->Clustal files with sequence positions in
855 right-hand column parsed correctly
858 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
859 not alignment area in exported graphic
862 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
863 window has input focus
866 <!-- JAL-2992 -->Annotation panel set too high when
867 annotation added to view (Windows)
870 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
871 network connectivity is poor
874 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
875 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
876 the currently open URL and links from a page viewed in
877 Firefox or Chrome on Windows is now fully supported. If
878 you are using Edge, only links in the page can be
879 dragged, and with Internet Explorer, only the currently
880 open URL in the browser can be dropped onto Jalview.</em>
883 <em>New Known Defects</em>
885 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
890 <td width="60" nowrap>
892 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
895 <td><div align="left">
899 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
900 for disabling automatic superposition of multiple
901 structures and open structures in existing views
904 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
905 ID and annotation area margins can be click-dragged to
909 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
913 <!-- JAL-2759 -->Improved performance for large alignments
914 and lots of hidden columns
917 <!-- JAL-2593 -->Improved performance when rendering lots
918 of features (particularly when transparency is disabled)
921 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
922 exchange of Jalview features and Chimera attributes made
928 <td><div align="left">
931 <!-- JAL-2899 -->Structure and Overview aren't updated
932 when Colour By Annotation threshold slider is adjusted
935 <!-- JAL-2778 -->Slow redraw when Overview panel shown
936 overlapping alignment panel
939 <!-- JAL-2929 -->Overview doesn't show end of unpadded
943 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
944 improved: CDS not handled correctly if transcript has no
948 <!-- JAL-2321 -->Secondary structure and temperature
949 factor annotation not added to sequence when local PDB
950 file associated with it by drag'n'drop or structure
954 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
955 dialog doesn't import PDB files dropped on an alignment
958 <!-- JAL-2666 -->Linked scrolling via protein horizontal
959 scroll bar doesn't work for some CDS/Protein views
962 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
963 Java 1.8u153 onwards and Java 1.9u4+.
966 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
967 columns in annotation row
970 <!-- JAL-2913 -->Preferences panel's ID Width control is not
971 honored in batch mode
974 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
975 for structures added to existing Jmol view
978 <!-- JAL-2223 -->'View Mappings' includes duplicate
979 entries after importing project with multiple views
982 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
983 protein sequences via SIFTS from associated PDB entries
984 with negative residue numbers or missing residues fails
987 <!-- JAL-2952 -->Exception when shading sequence with negative
988 Temperature Factor values from annotated PDB files (e.g.
989 as generated by CONSURF)
992 <!-- JAL-2920 -->Uniprot 'sequence variant' features
993 tooltip doesn't include a text description of mutation
996 <!-- JAL-2922 -->Invert displayed features very slow when
997 structure and/or overview windows are also shown
1000 <!-- JAL-2954 -->Selecting columns from highlighted regions
1001 very slow for alignments with large numbers of sequences
1004 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1005 with 'StringIndexOutOfBounds'
1008 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1009 platforms running Java 10
1012 <!-- JAL-2960 -->Adding a structure to existing structure
1013 view appears to do nothing because the view is hidden behind the alignment view
1019 <!-- JAL-2926 -->Copy consensus sequence option in applet
1020 should copy the group consensus when popup is opened on it
1026 <!-- JAL-2913 -->Fixed ID width preference is not respected
1029 <em>New Known Defects</em>
1032 <!-- JAL-2973 --> Exceptions occasionally raised when
1033 editing a large alignment and overview is displayed
1036 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1037 repeatedly after a series of edits even when the overview
1038 is no longer reflecting updates
1041 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1042 structures for protein subsequence (if 'Trim Retrieved
1043 Sequences' enabled) or Ensembl isoforms (Workaround in
1044 2.10.4 is to fail back to N&W mapping)
1047 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1048 option gives blank output
1055 <td width="60" nowrap>
1056 <div align="center">
1057 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1060 <td><div align="left">
1061 <ul><li>Updated Certum Codesigning Certificate
1062 (Valid till 30th November 2018)</li></ul></div></td>
1063 <td><div align="left">
1064 <em>Desktop</em><ul>
1066 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1067 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1068 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1069 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1070 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1071 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1072 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1078 <td width="60" nowrap>
1079 <div align="center">
1080 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1083 <td><div align="left">
1087 <!-- JAL-2446 -->Faster and more efficient management and
1088 rendering of sequence features
1091 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1092 429 rate limit request hander
1095 <!-- JAL-2773 -->Structure views don't get updated unless
1096 their colours have changed
1099 <!-- JAL-2495 -->All linked sequences are highlighted for
1100 a structure mousover (Jmol) or selection (Chimera)
1103 <!-- JAL-2790 -->'Cancel' button in progress bar for
1104 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1107 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1108 view from Ensembl locus cross-references
1111 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1115 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1116 feature can be disabled
1119 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1120 PDB easier retrieval of sequences for lists of IDs
1123 <!-- JAL-2758 -->Short names for sequences retrieved from
1129 <li>Groovy interpreter updated to 2.4.12</li>
1130 <li>Example groovy script for generating a matrix of
1131 percent identity scores for current alignment.</li>
1133 <em>Testing and Deployment</em>
1136 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1140 <td><div align="left">
1144 <!-- JAL-2643 -->Pressing tab after updating the colour
1145 threshold text field doesn't trigger an update to the
1149 <!-- JAL-2682 -->Race condition when parsing sequence ID
1153 <!-- JAL-2608 -->Overview windows are also closed when
1154 alignment window is closed
1157 <!-- JAL-2548 -->Export of features doesn't always respect
1161 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1162 takes a long time in Cursor mode
1168 <!-- JAL-2777 -->Structures with whitespace chainCode
1169 cannot be viewed in Chimera
1172 <!-- JAL-2728 -->Protein annotation panel too high in
1176 <!-- JAL-2757 -->Can't edit the query after the server
1177 error warning icon is shown in Uniprot and PDB Free Text
1181 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1184 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1187 <!-- JAL-2739 -->Hidden column marker in last column not
1188 rendered when switching back from Wrapped to normal view
1191 <!-- JAL-2768 -->Annotation display corrupted when
1192 scrolling right in unwapped alignment view
1195 <!-- JAL-2542 -->Existing features on subsequence
1196 incorrectly relocated when full sequence retrieved from
1200 <!-- JAL-2733 -->Last reported memory still shown when
1201 Desktop->Show Memory is unticked (OSX only)
1204 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1205 features of same type and group to be selected for
1209 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1210 alignments when hidden columns are present
1213 <!-- JAL-2392 -->Jalview freezes when loading and
1214 displaying several structures
1217 <!-- JAL-2732 -->Black outlines left after resizing or
1221 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1222 within the Jalview desktop on OSX
1225 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1226 when in wrapped alignment mode
1229 <!-- JAL-2636 -->Scale mark not shown when close to right
1230 hand end of alignment
1233 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1234 each selected sequence do not have correct start/end
1238 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1239 after canceling the Alignment Window's Font dialog
1242 <!-- JAL-2036 -->Show cross-references not enabled after
1243 restoring project until a new view is created
1246 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1247 URL links appears when only default EMBL-EBI link is
1248 configured (since 2.10.2b2)
1251 <!-- JAL-2775 -->Overview redraws whole window when box
1252 position is adjusted
1255 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1256 in a multi-chain structure when viewing alignment
1257 involving more than one chain (since 2.10)
1260 <!-- JAL-2811 -->Double residue highlights in cursor mode
1261 if new selection moves alignment window
1264 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1265 arrow key in cursor mode to pass hidden column marker
1268 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1269 that produces correctly annotated transcripts and products
1272 <!-- JAL-2776 -->Toggling a feature group after first time
1273 doesn't update associated structure view
1276 <em>Applet</em><br />
1279 <!-- JAL-2687 -->Concurrent modification exception when
1280 closing alignment panel
1283 <em>BioJSON</em><br />
1286 <!-- JAL-2546 -->BioJSON export does not preserve
1287 non-positional features
1290 <em>New Known Issues</em>
1293 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1294 sequence features correctly (for many previous versions of
1298 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1299 using cursor in wrapped panel other than top
1302 <!-- JAL-2791 -->Select columns containing feature ignores
1303 graduated colour threshold
1306 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1307 always preserve numbering and sequence features
1310 <em>Known Java 9 Issues</em>
1313 <!-- JAL-2902 -->Groovy Console very slow to open and is
1314 not responsive when entering characters (Webstart, Java
1321 <td width="60" nowrap>
1322 <div align="center">
1323 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1324 <em>2/10/2017</em></strong>
1327 <td><div align="left">
1328 <em>New features in Jalview Desktop</em>
1331 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1333 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1337 <td><div align="left">
1341 <td width="60" nowrap>
1342 <div align="center">
1343 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1344 <em>7/9/2017</em></strong>
1347 <td><div align="left">
1351 <!-- JAL-2588 -->Show gaps in overview window by colouring
1352 in grey (sequences used to be coloured grey, and gaps were
1356 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1360 <!-- JAL-2587 -->Overview updates immediately on increase
1361 in size and progress bar shown as higher resolution
1362 overview is recalculated
1367 <td><div align="left">
1371 <!-- JAL-2664 -->Overview window redraws every hidden
1372 column region row by row
1375 <!-- JAL-2681 -->duplicate protein sequences shown after
1376 retrieving Ensembl crossrefs for sequences from Uniprot
1379 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1380 format setting is unticked
1383 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1384 if group has show boxes format setting unticked
1387 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1388 autoscrolling whilst dragging current selection group to
1389 include sequences and columns not currently displayed
1392 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1393 assemblies are imported via CIF file
1396 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1397 displayed when threshold or conservation colouring is also
1401 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1405 <!-- JAL-2673 -->Jalview continues to scroll after
1406 dragging a selected region off the visible region of the
1410 <!-- JAL-2724 -->Cannot apply annotation based
1411 colourscheme to all groups in a view
1414 <!-- JAL-2511 -->IDs don't line up with sequences
1415 initially after font size change using the Font chooser or
1422 <td width="60" nowrap>
1423 <div align="center">
1424 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1427 <td><div align="left">
1428 <em>Calculations</em>
1432 <!-- JAL-1933 -->Occupancy annotation row shows number of
1433 ungapped positions in each column of the alignment.
1436 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1437 a calculation dialog box
1440 <!-- JAL-2379 -->Revised implementation of PCA for speed
1441 and memory efficiency (~30x faster)
1444 <!-- JAL-2403 -->Revised implementation of sequence
1445 similarity scores as used by Tree, PCA, Shading Consensus
1446 and other calculations
1449 <!-- JAL-2416 -->Score matrices are stored as resource
1450 files within the Jalview codebase
1453 <!-- JAL-2500 -->Trees computed on Sequence Feature
1454 Similarity may have different topology due to increased
1461 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1462 model for alignments and groups
1465 <!-- JAL-384 -->Custom shading schemes created via groovy
1472 <!-- JAL-2526 -->Efficiency improvements for interacting
1473 with alignment and overview windows
1476 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1480 <!-- JAL-2388 -->Hidden columns and sequences can be
1484 <!-- JAL-2611 -->Click-drag in visible area allows fine
1485 adjustment of visible position
1489 <em>Data import/export</em>
1492 <!-- JAL-2535 -->Posterior probability annotation from
1493 Stockholm files imported as sequence associated annotation
1496 <!-- JAL-2507 -->More robust per-sequence positional
1497 annotation input/output via stockholm flatfile
1500 <!-- JAL-2533 -->Sequence names don't include file
1501 extension when importing structure files without embedded
1502 names or PDB accessions
1505 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1506 format sequence substitution matrices
1509 <em>User Interface</em>
1512 <!-- JAL-2447 --> Experimental Features Checkbox in
1513 Desktop's Tools menu to hide or show untested features in
1517 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1518 via Overview or sequence motif search operations
1521 <!-- JAL-2547 -->Amend sequence features dialog box can be
1522 opened by double clicking gaps within sequence feature
1526 <!-- JAL-1476 -->Status bar message shown when not enough
1527 aligned positions were available to create a 3D structure
1531 <em>3D Structure</em>
1534 <!-- JAL-2430 -->Hidden regions in alignment views are not
1535 coloured in linked structure views
1538 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1539 file-based command exchange
1542 <!-- JAL-2375 -->Structure chooser automatically shows
1543 Cached Structures rather than querying the PDBe if
1544 structures are already available for sequences
1547 <!-- JAL-2520 -->Structures imported via URL are cached in
1548 the Jalview project rather than downloaded again when the
1549 project is reopened.
1552 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1553 to transfer Chimera's structure attributes as Jalview
1554 features, and vice-versa (<strong>Experimental
1558 <em>Web Services</em>
1561 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1564 <!-- JAL-2335 -->Filter non-standard amino acids and
1565 nucleotides when submitting to AACon and other MSA
1569 <!-- JAL-2316, -->URLs for viewing database
1570 cross-references provided by identifiers.org and the
1571 EMBL-EBI's MIRIAM DB
1578 <!-- JAL-2344 -->FileFormatI interface for describing and
1579 identifying file formats (instead of String constants)
1582 <!-- JAL-2228 -->FeatureCounter script refactored for
1583 efficiency when counting all displayed features (not
1584 backwards compatible with 2.10.1)
1587 <em>Example files</em>
1590 <!-- JAL-2631 -->Graduated feature colour style example
1591 included in the example feature file
1594 <em>Documentation</em>
1597 <!-- JAL-2339 -->Release notes reformatted for readability
1598 with the built-in Java help viewer
1601 <!-- JAL-1644 -->Find documentation updated with 'search
1602 sequence description' option
1608 <!-- JAL-2485, -->External service integration tests for
1609 Uniprot REST Free Text Search Client
1612 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1615 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1620 <td><div align="left">
1621 <em>Calculations</em>
1624 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1625 matrix - C->R should be '-3'<br />Old matrix restored
1626 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1628 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1629 Jalview's treatment of gaps in PCA and substitution matrix
1630 based Tree calculations.<br /> <br />In earlier versions
1631 of Jalview, gaps matching gaps were penalised, and gaps
1632 matching non-gaps penalised even more. In the PCA
1633 calculation, gaps were actually treated as non-gaps - so
1634 different costs were applied, which meant Jalview's PCAs
1635 were different to those produced by SeqSpace.<br />Jalview
1636 now treats gaps in the same way as SeqSpace (ie it scores
1637 them as 0). <br /> <br />Enter the following in the
1638 Groovy console to restore pre-2.10.2 behaviour:<br />
1639 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1640 // for 2.10.1 mode <br />
1641 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1642 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1643 these settings will affect all subsequent tree and PCA
1644 calculations (not recommended)</em></li>
1646 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1647 scaling of branch lengths for trees computed using
1648 Sequence Feature Similarity.
1651 <!-- JAL-2377 -->PCA calculation could hang when
1652 generating output report when working with highly
1653 redundant alignments
1656 <!-- JAL-2544 --> Sort by features includes features to
1657 right of selected region when gaps present on right-hand
1661 <em>User Interface</em>
1664 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1665 doesn't reselect a specific sequence's associated
1666 annotation after it was used for colouring a view
1669 <!-- JAL-2419 -->Current selection lost if popup menu
1670 opened on a region of alignment without groups
1673 <!-- JAL-2374 -->Popup menu not always shown for regions
1674 of an alignment with overlapping groups
1677 <!-- JAL-2310 -->Finder double counts if both a sequence's
1678 name and description match
1681 <!-- JAL-2370 -->Hiding column selection containing two
1682 hidden regions results in incorrect hidden regions
1685 <!-- JAL-2386 -->'Apply to all groups' setting when
1686 changing colour does not apply Conservation slider value
1690 <!-- JAL-2373 -->Percentage identity and conservation menu
1691 items do not show a tick or allow shading to be disabled
1694 <!-- JAL-2385 -->Conservation shading or PID threshold
1695 lost when base colourscheme changed if slider not visible
1698 <!-- JAL-2547 -->Sequence features shown in tooltip for
1699 gaps before start of features
1702 <!-- JAL-2623 -->Graduated feature colour threshold not
1703 restored to UI when feature colour is edited
1706 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1707 a time when scrolling vertically in wrapped mode.
1710 <!-- JAL-2630 -->Structure and alignment overview update
1711 as graduate feature colour settings are modified via the
1715 <!-- JAL-2034 -->Overview window doesn't always update
1716 when a group defined on the alignment is resized
1719 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1720 wrapped view result in positional status updates
1724 <!-- JAL-2563 -->Status bar doesn't show position for
1725 ambiguous amino acid and nucleotide symbols
1728 <!-- JAL-2602 -->Copy consensus sequence failed if
1729 alignment included gapped columns
1732 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1733 widgets don't permanently disappear
1736 <!-- JAL-2503 -->Cannot select or filter quantitative
1737 annotation that are shown only as column labels (e.g.
1738 T-Coffee column reliability scores)
1741 <!-- JAL-2594 -->Exception thrown if trying to create a
1742 sequence feature on gaps only
1745 <!-- JAL-2504 -->Features created with 'New feature'
1746 button from a Find inherit previously defined feature type
1747 rather than the Find query string
1750 <!-- JAL-2423 -->incorrect title in output window when
1751 exporting tree calculated in Jalview
1754 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1755 and then revealing them reorders sequences on the
1759 <!-- JAL-964 -->Group panel in sequence feature settings
1760 doesn't update to reflect available set of groups after
1761 interactively adding or modifying features
1764 <!-- JAL-2225 -->Sequence Database chooser unusable on
1768 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1769 only excluded gaps in current sequence and ignored
1776 <!-- JAL-2421 -->Overview window visible region moves
1777 erratically when hidden rows or columns are present
1780 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1781 Structure Viewer's colour menu don't correspond to
1785 <!-- JAL-2405 -->Protein specific colours only offered in
1786 colour and group colour menu for protein alignments
1789 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1790 reflect currently selected view or group's shading
1794 <!-- JAL-2624 -->Feature colour thresholds not respected
1795 when rendered on overview and structures when opacity at
1799 <!-- JAL-2589 -->User defined gap colour not shown in
1800 overview when features overlaid on alignment
1803 <!-- JAL-2567 -->Feature settings for different views not
1804 recovered correctly from Jalview project file
1807 <!-- JAL-2256 -->Feature colours in overview when first opened
1808 (automatically via preferences) are different to the main
1812 <em>Data import/export</em>
1815 <!-- JAL-2576 -->Very large alignments take a long time to
1819 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1820 added after a sequence was imported are not written to
1824 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1825 when importing RNA secondary structure via Stockholm
1828 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1829 not shown in correct direction for simple pseudoknots
1832 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1833 with lightGray or darkGray via features file (but can
1837 <!-- JAL-2383 -->Above PID colour threshold not recovered
1838 when alignment view imported from project
1841 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1842 structure and sequences extracted from structure files
1843 imported via URL and viewed in Jmol
1846 <!-- JAL-2520 -->Structures loaded via URL are saved in
1847 Jalview Projects rather than fetched via URL again when
1848 the project is loaded and the structure viewed
1851 <em>Web Services</em>
1854 <!-- JAL-2519 -->EnsemblGenomes example failing after
1855 release of Ensembl v.88
1858 <!-- JAL-2366 -->Proxy server address and port always
1859 appear enabled in Preferences->Connections
1862 <!-- JAL-2461 -->DAS registry not found exceptions
1863 removed from console output
1866 <!-- JAL-2582 -->Cannot retrieve protein products from
1867 Ensembl by Peptide ID
1870 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1871 created from SIFTs, and spurious 'Couldn't open structure
1872 in Chimera' errors raised after April 2017 update (problem
1873 due to 'null' string rather than empty string used for
1874 residues with no corresponding PDB mapping).
1877 <em>Application UI</em>
1880 <!-- JAL-2361 -->User Defined Colours not added to Colour
1884 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1885 case' residues (button in colourscheme editor debugged and
1886 new documentation and tooltips added)
1889 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1890 doesn't restore group-specific text colour thresholds
1893 <!-- JAL-2243 -->Feature settings panel does not update as
1894 new features are added to alignment
1897 <!-- JAL-2532 -->Cancel in feature settings reverts
1898 changes to feature colours via the Amend features dialog
1901 <!-- JAL-2506 -->Null pointer exception when attempting to
1902 edit graduated feature colour via amend features dialog
1906 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1907 selection menu changes colours of alignment views
1910 <!-- JAL-2426 -->Spurious exceptions in console raised
1911 from alignment calculation workers after alignment has
1915 <!-- JAL-1608 -->Typo in selection popup menu - Create
1916 groups now 'Create Group'
1919 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1920 Create/Undefine group doesn't always work
1923 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1924 shown again after pressing 'Cancel'
1927 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1928 adjusts start position in wrap mode
1931 <!-- JAL-2563 -->Status bar doesn't show positions for
1932 ambiguous amino acids
1935 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1936 CDS/Protein view after CDS sequences added for aligned
1940 <!-- JAL-2592 -->User defined colourschemes called 'User
1941 Defined' don't appear in Colours menu
1947 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1948 score models doesn't always result in an updated PCA plot
1951 <!-- JAL-2442 -->Features not rendered as transparent on
1952 overview or linked structure view
1955 <!-- JAL-2372 -->Colour group by conservation doesn't
1959 <!-- JAL-2517 -->Hitting Cancel after applying
1960 user-defined colourscheme doesn't restore original
1967 <!-- JAL-2314 -->Unit test failure:
1968 jalview.ws.jabaws.RNAStructExportImport setup fails
1971 <!-- JAL-2307 -->Unit test failure:
1972 jalview.ws.sifts.SiftsClientTest due to compatibility
1973 problems with deep array comparison equality asserts in
1974 successive versions of TestNG
1977 <!-- JAL-2479 -->Relocated StructureChooserTest and
1978 ParameterUtilsTest Unit tests to Network suite
1981 <em>New Known Issues</em>
1984 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1985 phase after a sequence motif find operation
1988 <!-- JAL-2550 -->Importing annotation file with rows
1989 containing just upper and lower case letters are
1990 interpreted as WUSS RNA secondary structure symbols
1993 <!-- JAL-2590 -->Cannot load and display Newick trees
1994 reliably from eggnog Ortholog database
1997 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1998 containing features of type Highlight' when 'B' is pressed
1999 to mark columns containing highlighted regions.
2002 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2003 doesn't always add secondary structure annotation.
2008 <td width="60" nowrap>
2009 <div align="center">
2010 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2013 <td><div align="left">
2017 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2018 for all consensus calculations
2021 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2024 <li>Updated Jalview's Certum code signing certificate
2027 <em>Application</em>
2030 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2031 set of database cross-references, sorted alphabetically
2034 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2035 from database cross references. Users with custom links
2036 will receive a <a href="webServices/urllinks.html#warning">warning
2037 dialog</a> asking them to update their preferences.
2040 <!-- JAL-2287-->Cancel button and escape listener on
2041 dialog warning user about disconnecting Jalview from a
2045 <!-- JAL-2320-->Jalview's Chimera control window closes if
2046 the Chimera it is connected to is shut down
2049 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2050 columns menu item to mark columns containing highlighted
2051 regions (e.g. from structure selections or results of a
2055 <!-- JAL-2284-->Command line option for batch-generation
2056 of HTML pages rendering alignment data with the BioJS
2066 <!-- JAL-2286 -->Columns with more than one modal residue
2067 are not coloured or thresholded according to percent
2068 identity (first observed in Jalview 2.8.2)
2071 <!-- JAL-2301 -->Threonine incorrectly reported as not
2075 <!-- JAL-2318 -->Updates to documentation pages (above PID
2076 threshold, amino acid properties)
2079 <!-- JAL-2292 -->Lower case residues in sequences are not
2080 reported as mapped to residues in a structure file in the
2084 <!--JAL-2324 -->Identical features with non-numeric scores
2085 could be added multiple times to a sequence
2088 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2089 bond features shown as two highlighted residues rather
2090 than a range in linked structure views, and treated
2091 correctly when selecting and computing trees from features
2094 <!-- JAL-2281-->Custom URL links for database
2095 cross-references are matched to database name regardless
2100 <em>Application</em>
2103 <!-- JAL-2282-->Custom URL links for specific database
2104 names without regular expressions also offer links from
2108 <!-- JAL-2315-->Removing a single configured link in the
2109 URL links pane in Connections preferences doesn't actually
2110 update Jalview configuration
2113 <!-- JAL-2272-->CTRL-Click on a selected region to open
2114 the alignment area popup menu doesn't work on El-Capitan
2117 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2118 files with similarly named sequences if dropped onto the
2122 <!-- JAL-2312 -->Additional mappings are shown for PDB
2123 entries where more chains exist in the PDB accession than
2124 are reported in the SIFTS file
2127 <!-- JAL-2317-->Certain structures do not get mapped to
2128 the structure view when displayed with Chimera
2131 <!-- JAL-2317-->No chains shown in the Chimera view
2132 panel's View->Show Chains submenu
2135 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2136 work for wrapped alignment views
2139 <!--JAL-2197 -->Rename UI components for running JPred
2140 predictions from 'JNet' to 'JPred'
2143 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2144 corrupted when annotation panel vertical scroll is not at
2145 first annotation row
2148 <!--JAL-2332 -->Attempting to view structure for Hen
2149 lysozyme results in a PDB Client error dialog box
2152 <!-- JAL-2319 -->Structure View's mapping report switched
2153 ranges for PDB and sequence for SIFTS
2156 SIFTS 'Not_Observed' residues mapped to non-existant
2160 <!-- <em>New Known Issues</em>
2167 <td width="60" nowrap>
2168 <div align="center">
2169 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2170 <em>25/10/2016</em></strong>
2173 <td><em>Application</em>
2175 <li>3D Structure chooser opens with 'Cached structures'
2176 view if structures already loaded</li>
2177 <li>Progress bar reports models as they are loaded to
2178 structure views</li>
2184 <li>Colour by conservation always enabled and no tick
2185 shown in menu when BLOSUM or PID shading applied</li>
2186 <li>FER1_ARATH and FER2_ARATH labels were switched in
2187 example sequences/projects/trees</li>
2189 <em>Application</em>
2191 <li>Jalview projects with views of local PDB structure
2192 files saved on Windows cannot be opened on OSX</li>
2193 <li>Multiple structure views can be opened and superposed
2194 without timeout for structures with multiple models or
2195 multiple sequences in alignment</li>
2196 <li>Cannot import or associated local PDB files without a
2197 PDB ID HEADER line</li>
2198 <li>RMSD is not output in Jmol console when superposition
2200 <li>Drag and drop of URL from Browser fails for Linux and
2201 OSX versions earlier than El Capitan</li>
2202 <li>ENA client ignores invalid content from ENA server</li>
2203 <li>Exceptions are not raised in console when ENA client
2204 attempts to fetch non-existent IDs via Fetch DB Refs UI
2206 <li>Exceptions are not raised in console when a new view
2207 is created on the alignment</li>
2208 <li>OSX right-click fixed for group selections: CMD-click
2209 to insert/remove gaps in groups and CTRL-click to open group
2212 <em>Build and deployment</em>
2214 <li>URL link checker now copes with multi-line anchor
2217 <em>New Known Issues</em>
2219 <li>Drag and drop from URL links in browsers do not work
2226 <td width="60" nowrap>
2227 <div align="center">
2228 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2231 <td><em>General</em>
2234 <!-- JAL-2124 -->Updated Spanish translations.
2237 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2238 for importing structure data to Jalview. Enables mmCIF and
2242 <!-- JAL-192 --->Alignment ruler shows positions relative to
2246 <!-- JAL-2202 -->Position/residue shown in status bar when
2247 mousing over sequence associated annotation
2250 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2254 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2255 '()', canonical '[]' and invalid '{}' base pair populations
2259 <!-- JAL-2092 -->Feature settings popup menu options for
2260 showing or hiding columns containing a feature
2263 <!-- JAL-1557 -->Edit selected group by double clicking on
2264 group and sequence associated annotation labels
2267 <!-- JAL-2236 -->Sequence name added to annotation label in
2268 select/hide columns by annotation and colour by annotation
2272 </ul> <em>Application</em>
2275 <!-- JAL-2050-->Automatically hide introns when opening a
2276 gene/transcript view
2279 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2283 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2284 structure mappings with the EMBL-EBI PDBe SIFTS database
2287 <!-- JAL-2079 -->Updated download sites used for Rfam and
2288 Pfam sources to xfam.org
2291 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2294 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2295 over sequences in Jalview
2298 <!-- JAL-2027-->Support for reverse-complement coding
2299 regions in ENA and EMBL
2302 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2303 for record retrieval via ENA rest API
2306 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2310 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2311 groovy script execution
2314 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2315 alignment window's Calculate menu
2318 <!-- JAL-1812 -->Allow groovy scripts that call
2319 Jalview.getAlignFrames() to run in headless mode
2322 <!-- JAL-2068 -->Support for creating new alignment
2323 calculation workers from groovy scripts
2326 <!-- JAL-1369 --->Store/restore reference sequence in
2330 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2331 associations are now saved/restored from project
2334 <!-- JAL-1993 -->Database selection dialog always shown
2335 before sequence fetcher is opened
2338 <!-- JAL-2183 -->Double click on an entry in Jalview's
2339 database chooser opens a sequence fetcher
2342 <!-- JAL-1563 -->Free-text search client for UniProt using
2343 the UniProt REST API
2346 <!-- JAL-2168 -->-nonews command line parameter to prevent
2347 the news reader opening
2350 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2351 querying stored in preferences
2354 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2358 <!-- JAL-1977-->Tooltips shown on database chooser
2361 <!-- JAL-391 -->Reverse complement function in calculate
2362 menu for nucleotide sequences
2365 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2366 and feature counts preserves alignment ordering (and
2367 debugged for complex feature sets).
2370 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2371 viewing structures with Jalview 2.10
2374 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2375 genome, transcript CCDS and gene ids via the Ensembl and
2376 Ensembl Genomes REST API
2379 <!-- JAL-2049 -->Protein sequence variant annotation
2380 computed for 'sequence_variant' annotation on CDS regions
2384 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2388 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2389 Ref Fetcher fails to match, or otherwise updates sequence
2390 data from external database records.
2393 <!-- JAL-2154 -->Revised Jalview Project format for
2394 efficient recovery of sequence coding and alignment
2395 annotation relationships.
2397 </ul> <!-- <em>Applet</em>
2408 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2412 <!-- JAL-2018-->Export features in Jalview format (again)
2413 includes graduated colourschemes
2416 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2417 working with big alignments and lots of hidden columns
2420 <!-- JAL-2053-->Hidden column markers not always rendered
2421 at right of alignment window
2424 <!-- JAL-2067 -->Tidied up links in help file table of
2428 <!-- JAL-2072 -->Feature based tree calculation not shown
2432 <!-- JAL-2075 -->Hidden columns ignored during feature
2433 based tree calculation
2436 <!-- JAL-2065 -->Alignment view stops updating when show
2437 unconserved enabled for group on alignment
2440 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2444 <!-- JAL-2146 -->Alignment column in status incorrectly
2445 shown as "Sequence position" when mousing over
2449 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2450 hidden columns present
2453 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2454 user created annotation added to alignment
2457 <!-- JAL-1841 -->RNA Structure consensus only computed for
2458 '()' base pair annotation
2461 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2462 in zero scores for all base pairs in RNA Structure
2466 <!-- JAL-2174-->Extend selection with columns containing
2470 <!-- JAL-2275 -->Pfam format writer puts extra space at
2471 beginning of sequence
2474 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2478 <!-- JAL-2238 -->Cannot create groups on an alignment from
2479 from a tree when t-coffee scores are shown
2482 <!-- JAL-1836,1967 -->Cannot import and view PDB
2483 structures with chains containing negative resnums (4q4h)
2486 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2490 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2491 to Clustal, PIR and PileUp output
2494 <!-- JAL-2008 -->Reordering sequence features that are
2495 not visible causes alignment window to repaint
2498 <!-- JAL-2006 -->Threshold sliders don't work in
2499 graduated colour and colour by annotation row for e-value
2500 scores associated with features and annotation rows
2503 <!-- JAL-1797 -->amino acid physicochemical conservation
2504 calculation should be case independent
2507 <!-- JAL-2173 -->Remove annotation also updates hidden
2511 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2512 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2513 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2516 <!-- JAL-2065 -->Null pointer exceptions and redraw
2517 problems when reference sequence defined and 'show
2518 non-conserved' enabled
2521 <!-- JAL-1306 -->Quality and Conservation are now shown on
2522 load even when Consensus calculation is disabled
2525 <!-- JAL-1932 -->Remove right on penultimate column of
2526 alignment does nothing
2529 <em>Application</em>
2532 <!-- JAL-1552-->URLs and links can't be imported by
2533 drag'n'drop on OSX when launched via webstart (note - not
2534 yet fixed for El Capitan)
2537 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2538 output when running on non-gb/us i18n platforms
2541 <!-- JAL-1944 -->Error thrown when exporting a view with
2542 hidden sequences as flat-file alignment
2545 <!-- JAL-2030-->InstallAnywhere distribution fails when
2549 <!-- JAL-2080-->Jalview very slow to launch via webstart
2550 (also hotfix for 2.9.0b2)
2553 <!-- JAL-2085 -->Cannot save project when view has a
2554 reference sequence defined
2557 <!-- JAL-1011 -->Columns are suddenly selected in other
2558 alignments and views when revealing hidden columns
2561 <!-- JAL-1989 -->Hide columns not mirrored in complement
2562 view in a cDNA/Protein splitframe
2565 <!-- JAL-1369 -->Cannot save/restore representative
2566 sequence from project when only one sequence is
2570 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2571 in Structure Chooser
2574 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2575 structure consensus didn't refresh annotation panel
2578 <!-- JAL-1962 -->View mapping in structure view shows
2579 mappings between sequence and all chains in a PDB file
2582 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2583 dialogs format columns correctly, don't display array
2584 data, sort columns according to type
2587 <!-- JAL-1975 -->Export complete shown after destination
2588 file chooser is cancelled during an image export
2591 <!-- JAL-2025 -->Error when querying PDB Service with
2592 sequence name containing special characters
2595 <!-- JAL-2024 -->Manual PDB structure querying should be
2599 <!-- JAL-2104 -->Large tooltips with broken HTML
2600 formatting don't wrap
2603 <!-- JAL-1128 -->Figures exported from wrapped view are
2604 truncated so L looks like I in consensus annotation
2607 <!-- JAL-2003 -->Export features should only export the
2608 currently displayed features for the current selection or
2612 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2613 after fetching cross-references, and restoring from
2617 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2618 followed in the structure viewer
2621 <!-- JAL-2163 -->Titles for individual alignments in
2622 splitframe not restored from project
2625 <!-- JAL-2145 -->missing autocalculated annotation at
2626 trailing end of protein alignment in transcript/product
2627 splitview when pad-gaps not enabled by default
2630 <!-- JAL-1797 -->amino acid physicochemical conservation
2634 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2635 article has been read (reopened issue due to
2636 internationalisation problems)
2639 <!-- JAL-1960 -->Only offer PDB structures in structure
2640 viewer based on sequence name, PDB and UniProt
2645 <!-- JAL-1976 -->No progress bar shown during export of
2649 <!-- JAL-2213 -->Structures not always superimposed after
2650 multiple structures are shown for one or more sequences.
2653 <!-- JAL-1370 -->Reference sequence characters should not
2654 be replaced with '.' when 'Show unconserved' format option
2658 <!-- JAL-1823 -->Cannot specify chain code when entering
2659 specific PDB id for sequence
2662 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2663 'Export hidden sequences' is enabled, but 'export hidden
2664 columns' is disabled.
2667 <!--JAL-2026-->Best Quality option in structure chooser
2668 selects lowest rather than highest resolution structures
2672 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2673 to sequence mapping in 'View Mappings' report
2676 <!-- JAL-2284 -->Unable to read old Jalview projects that
2677 contain non-XML data added after Jalvew wrote project.
2680 <!-- JAL-2118 -->Newly created annotation row reorders
2681 after clicking on it to create new annotation for a
2685 <!-- JAL-1980 -->Null Pointer Exception raised when
2686 pressing Add on an orphaned cut'n'paste window.
2688 <!-- may exclude, this is an external service stability issue JAL-1941
2689 -- > RNA 3D structure not added via DSSR service</li> -->
2694 <!-- JAL-2151 -->Incorrect columns are selected when
2695 hidden columns present before start of sequence
2698 <!-- JAL-1986 -->Missing dependencies on applet pages
2702 <!-- JAL-1947 -->Overview pixel size changes when
2703 sequences are hidden in applet
2706 <!-- JAL-1996 -->Updated instructions for applet
2707 deployment on examples pages.
2714 <td width="60" nowrap>
2715 <div align="center">
2716 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2717 <em>16/10/2015</em></strong>
2720 <td><em>General</em>
2722 <li>Time stamps for signed Jalview application and applet
2727 <em>Application</em>
2729 <li>Duplicate group consensus and conservation rows
2730 shown when tree is partitioned</li>
2731 <li>Erratic behaviour when tree partitions made with
2732 multiple cDNA/Protein split views</li>
2738 <td width="60" nowrap>
2739 <div align="center">
2740 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2741 <em>8/10/2015</em></strong>
2744 <td><em>General</em>
2746 <li>Updated Spanish translations of localized text for
2748 </ul> <em>Application</em>
2750 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2751 <li>Signed OSX InstallAnywhere installer<br></li>
2752 <li>Support for per-sequence based annotations in BioJSON</li>
2753 </ul> <em>Applet</em>
2755 <li>Split frame example added to applet examples page</li>
2756 </ul> <em>Build and Deployment</em>
2759 <!-- JAL-1888 -->New ant target for running Jalview's test
2767 <li>Mapping of cDNA to protein in split frames
2768 incorrect when sequence start > 1</li>
2769 <li>Broken images in filter column by annotation dialog
2771 <li>Feature colours not parsed from features file</li>
2772 <li>Exceptions and incomplete link URLs recovered when
2773 loading a features file containing HTML tags in feature
2777 <em>Application</em>
2779 <li>Annotations corrupted after BioJS export and
2781 <li>Incorrect sequence limits after Fetch DB References
2782 with 'trim retrieved sequences'</li>
2783 <li>Incorrect warning about deleting all data when
2784 deleting selected columns</li>
2785 <li>Patch to build system for shipping properly signed
2786 JNLP templates for webstart launch</li>
2787 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2788 unreleased structures for download or viewing</li>
2789 <li>Tab/space/return keystroke operation of EMBL-PDBe
2790 fetcher/viewer dialogs works correctly</li>
2791 <li>Disabled 'minimise' button on Jalview windows
2792 running on OSX to workaround redraw hang bug</li>
2793 <li>Split cDNA/Protein view position and geometry not
2794 recovered from jalview project</li>
2795 <li>Initial enabled/disabled state of annotation menu
2796 sorter 'show autocalculated first/last' corresponds to
2798 <li>Restoring of Clustal, RNA Helices and T-Coffee
2799 color schemes from BioJSON</li>
2803 <li>Reorder sequences mirrored in cDNA/Protein split
2805 <li>Applet with Jmol examples not loading correctly</li>
2811 <td><div align="center">
2812 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2814 <td><em>General</em>
2816 <li>Linked visualisation and analysis of DNA and Protein
2819 <li>Translated cDNA alignments shown as split protein
2820 and DNA alignment views</li>
2821 <li>Codon consensus annotation for linked protein and
2822 cDNA alignment views</li>
2823 <li>Link cDNA or Protein product sequences by loading
2824 them onto Protein or cDNA alignments</li>
2825 <li>Reconstruct linked cDNA alignment from aligned
2826 protein sequences</li>
2829 <li>Jmol integration updated to Jmol v14.2.14</li>
2830 <li>Import and export of Jalview alignment views as <a
2831 href="features/bioJsonFormat.html">BioJSON</a></li>
2832 <li>New alignment annotation file statements for
2833 reference sequences and marking hidden columns</li>
2834 <li>Reference sequence based alignment shading to
2835 highlight variation</li>
2836 <li>Select or hide columns according to alignment
2838 <li>Find option for locating sequences by description</li>
2839 <li>Conserved physicochemical properties shown in amino
2840 acid conservation row</li>
2841 <li>Alignments can be sorted by number of RNA helices</li>
2842 </ul> <em>Application</em>
2844 <li>New cDNA/Protein analysis capabilities
2846 <li>Get Cross-References should open a Split Frame
2847 view with cDNA/Protein</li>
2848 <li>Detect when nucleotide sequences and protein
2849 sequences are placed in the same alignment</li>
2850 <li>Split cDNA/Protein views are saved in Jalview
2855 <li>Use REST API to talk to Chimera</li>
2856 <li>Selected regions in Chimera are highlighted in linked
2857 Jalview windows</li>
2859 <li>VARNA RNA viewer updated to v3.93</li>
2860 <li>VARNA views are saved in Jalview Projects</li>
2861 <li>Pseudoknots displayed as Jalview RNA annotation can
2862 be shown in VARNA</li>
2864 <li>Make groups for selection uses marked columns as well
2865 as the active selected region</li>
2867 <li>Calculate UPGMA and NJ trees using sequence feature
2869 <li>New Export options
2871 <li>New Export Settings dialog to control hidden
2872 region export in flat file generation</li>
2874 <li>Export alignment views for display with the <a
2875 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2877 <li>Export scrollable SVG in HTML page</li>
2878 <li>Optional embedding of BioJSON data when exporting
2879 alignment figures to HTML</li>
2881 <li>3D structure retrieval and display
2883 <li>Free text and structured queries with the PDBe
2885 <li>PDBe Search API based discovery and selection of
2886 PDB structures for a sequence set</li>
2890 <li>JPred4 employed for protein secondary structure
2892 <li>Hide Insertions menu option to hide unaligned columns
2893 for one or a group of sequences</li>
2894 <li>Automatically hide insertions in alignments imported
2895 from the JPred4 web server</li>
2896 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2897 system on OSX<br />LGPL libraries courtesy of <a
2898 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2900 <li>changed 'View nucleotide structure' submenu to 'View
2901 VARNA 2D Structure'</li>
2902 <li>change "View protein structure" menu option to "3D
2905 </ul> <em>Applet</em>
2907 <li>New layout for applet example pages</li>
2908 <li>New parameters to enable SplitFrame view
2909 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2910 <li>New example demonstrating linked viewing of cDNA and
2911 Protein alignments</li>
2912 </ul> <em>Development and deployment</em>
2914 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2915 <li>Include installation type and git revision in build
2916 properties and console log output</li>
2917 <li>Jalview Github organisation, and new github site for
2918 storing BioJsMSA Templates</li>
2919 <li>Jalview's unit tests now managed with TestNG</li>
2922 <!-- <em>General</em>
2924 </ul> --> <!-- issues resolved --> <em>Application</em>
2926 <li>Escape should close any open find dialogs</li>
2927 <li>Typo in select-by-features status report</li>
2928 <li>Consensus RNA secondary secondary structure
2929 predictions are not highlighted in amber</li>
2930 <li>Missing gap character in v2.7 example file means
2931 alignment appears unaligned when pad-gaps is not enabled</li>
2932 <li>First switch to RNA Helices colouring doesn't colour
2933 associated structure views</li>
2934 <li>ID width preference option is greyed out when auto
2935 width checkbox not enabled</li>
2936 <li>Stopped a warning dialog from being shown when
2937 creating user defined colours</li>
2938 <li>'View Mapping' in structure viewer shows sequence
2939 mappings for just that viewer's sequences</li>
2940 <li>Workaround for superposing PDB files containing
2941 multiple models in Chimera</li>
2942 <li>Report sequence position in status bar when hovering
2943 over Jmol structure</li>
2944 <li>Cannot output gaps as '.' symbols with Selection ->
2945 output to text box</li>
2946 <li>Flat file exports of alignments with hidden columns
2947 have incorrect sequence start/end</li>
2948 <li>'Aligning' a second chain to a Chimera structure from
2950 <li>Colour schemes applied to structure viewers don't
2951 work for nucleotide</li>
2952 <li>Loading/cut'n'pasting an empty or invalid file leads
2953 to a grey/invisible alignment window</li>
2954 <li>Exported Jpred annotation from a sequence region
2955 imports to different position</li>
2956 <li>Space at beginning of sequence feature tooltips shown
2957 on some platforms</li>
2958 <li>Chimera viewer 'View | Show Chain' menu is not
2960 <li>'New View' fails with a Null Pointer Exception in
2961 console if Chimera has been opened</li>
2962 <li>Mouseover to Chimera not working</li>
2963 <li>Miscellaneous ENA XML feature qualifiers not
2965 <li>NPE in annotation renderer after 'Extract Scores'</li>
2966 <li>If two structures in one Chimera window, mouseover of
2967 either sequence shows on first structure</li>
2968 <li>'Show annotations' options should not make
2969 non-positional annotations visible</li>
2970 <li>Subsequence secondary structure annotation not shown
2971 in right place after 'view flanking regions'</li>
2972 <li>File Save As type unset when current file format is
2974 <li>Save as '.jar' option removed for saving Jalview
2976 <li>Colour by Sequence colouring in Chimera more
2978 <li>Cannot 'add reference annotation' for a sequence in
2979 several views on same alignment</li>
2980 <li>Cannot show linked products for EMBL / ENA records</li>
2981 <li>Jalview's tooltip wraps long texts containing no
2983 </ul> <em>Applet</em>
2985 <li>Jmol to JalviewLite mouseover/link not working</li>
2986 <li>JalviewLite can't import sequences with ID
2987 descriptions containing angle brackets</li>
2988 </ul> <em>General</em>
2990 <li>Cannot export and reimport RNA secondary structure
2991 via jalview annotation file</li>
2992 <li>Random helix colour palette for colour by annotation
2993 with RNA secondary structure</li>
2994 <li>Mouseover to cDNA from STOP residue in protein
2995 translation doesn't work.</li>
2996 <li>hints when using the select by annotation dialog box</li>
2997 <li>Jmol alignment incorrect if PDB file has alternate CA
2999 <li>FontChooser message dialog appears to hang after
3000 choosing 1pt font</li>
3001 <li>Peptide secondary structure incorrectly imported from
3002 annotation file when annotation display text includes 'e' or
3004 <li>Cannot set colour of new feature type whilst creating
3006 <li>cDNA translation alignment should not be sequence
3007 order dependent</li>
3008 <li>'Show unconserved' doesn't work for lower case
3010 <li>Nucleotide ambiguity codes involving R not recognised</li>
3011 </ul> <em>Deployment and Documentation</em>
3013 <li>Applet example pages appear different to the rest of
3014 www.jalview.org</li>
3015 </ul> <em>Application Known issues</em>
3017 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3018 <li>Misleading message appears after trying to delete
3020 <li>Jalview icon not shown in dock after InstallAnywhere
3021 version launches</li>
3022 <li>Fetching EMBL reference for an RNA sequence results
3023 fails with a sequence mismatch</li>
3024 <li>Corrupted or unreadable alignment display when
3025 scrolling alignment to right</li>
3026 <li>ArrayIndexOutOfBoundsException thrown when remove
3027 empty columns called on alignment with ragged gapped ends</li>
3028 <li>auto calculated alignment annotation rows do not get
3029 placed above or below non-autocalculated rows</li>
3030 <li>Jalview dekstop becomes sluggish at full screen in
3031 ultra-high resolution</li>
3032 <li>Cannot disable consensus calculation independently of
3033 quality and conservation</li>
3034 <li>Mouseover highlighting between cDNA and protein can
3035 become sluggish with more than one splitframe shown</li>
3036 </ul> <em>Applet Known Issues</em>
3038 <li>Core PDB parsing code requires Jmol</li>
3039 <li>Sequence canvas panel goes white when alignment
3040 window is being resized</li>
3046 <td><div align="center">
3047 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3049 <td><em>General</em>
3051 <li>Updated Java code signing certificate donated by
3053 <li>Features and annotation preserved when performing
3054 pairwise alignment</li>
3055 <li>RNA pseudoknot annotation can be
3056 imported/exported/displayed</li>
3057 <li>'colour by annotation' can colour by RNA and
3058 protein secondary structure</li>
3059 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3060 post-hoc with 2.9 release</em>)
3063 </ul> <em>Application</em>
3065 <li>Extract and display secondary structure for sequences
3066 with 3D structures</li>
3067 <li>Support for parsing RNAML</li>
3068 <li>Annotations menu for layout
3070 <li>sort sequence annotation rows by alignment</li>
3071 <li>place sequence annotation above/below alignment
3074 <li>Output in Stockholm format</li>
3075 <li>Internationalisation: improved Spanish (es)
3077 <li>Structure viewer preferences tab</li>
3078 <li>Disorder and Secondary Structure annotation tracks
3079 shared between alignments</li>
3080 <li>UCSF Chimera launch and linked highlighting from
3082 <li>Show/hide all sequence associated annotation rows for
3083 all or current selection</li>
3084 <li>disorder and secondary structure predictions
3085 available as dataset annotation</li>
3086 <li>Per-sequence rna helices colouring</li>
3089 <li>Sequence database accessions imported when fetching
3090 alignments from Rfam</li>
3091 <li>update VARNA version to 3.91</li>
3093 <li>New groovy scripts for exporting aligned positions,
3094 conservation values, and calculating sum of pairs scores.</li>
3095 <li>Command line argument to set default JABAWS server</li>
3096 <li>include installation type in build properties and
3097 console log output</li>
3098 <li>Updated Jalview project format to preserve dataset
3102 <!-- issues resolved --> <em>Application</em>
3104 <li>Distinguish alignment and sequence associated RNA
3105 structure in structure->view->VARNA</li>
3106 <li>Raise dialog box if user deletes all sequences in an
3108 <li>Pressing F1 results in documentation opening twice</li>
3109 <li>Sequence feature tooltip is wrapped</li>
3110 <li>Double click on sequence associated annotation
3111 selects only first column</li>
3112 <li>Redundancy removal doesn't result in unlinked
3113 leaves shown in tree</li>
3114 <li>Undos after several redundancy removals don't undo
3116 <li>Hide sequence doesn't hide associated annotation</li>
3117 <li>User defined colours dialog box too big to fit on
3118 screen and buttons not visible</li>
3119 <li>author list isn't updated if already written to
3120 Jalview properties</li>
3121 <li>Popup menu won't open after retrieving sequence
3123 <li>File open window for associate PDB doesn't open</li>
3124 <li>Left-then-right click on a sequence id opens a
3125 browser search window</li>
3126 <li>Cannot open sequence feature shading/sort popup menu
3127 in feature settings dialog</li>
3128 <li>better tooltip placement for some areas of Jalview
3130 <li>Allow addition of JABAWS Server which doesn't
3131 pass validation</li>
3132 <li>Web services parameters dialog box is too large to
3134 <li>Muscle nucleotide alignment preset obscured by
3136 <li>JABAWS preset submenus don't contain newly
3137 defined user preset</li>
3138 <li>MSA web services warns user if they were launched
3139 with invalid input</li>
3140 <li>Jalview cannot contact DAS Registy when running on
3143 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3144 'Superpose with' submenu not shown when new view
3148 </ul> <!-- <em>Applet</em>
3150 </ul> <em>General</em>
3152 </ul>--> <em>Deployment and Documentation</em>
3154 <li>2G and 1G options in launchApp have no effect on
3155 memory allocation</li>
3156 <li>launchApp service doesn't automatically open
3157 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3159 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3160 InstallAnywhere reports cannot find valid JVM when Java
3161 1.7_055 is available
3163 </ul> <em>Application Known issues</em>
3166 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3167 corrupted or unreadable alignment display when scrolling
3171 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3172 retrieval fails but progress bar continues for DAS retrieval
3173 with large number of ID
3176 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3177 flatfile output of visible region has incorrect sequence
3181 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3182 rna structure consensus doesn't update when secondary
3183 structure tracks are rearranged
3186 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3187 invalid rna structure positional highlighting does not
3188 highlight position of invalid base pairs
3191 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3192 out of memory errors are not raised when saving Jalview
3193 project from alignment window file menu
3196 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3197 Switching to RNA Helices colouring doesn't propagate to
3201 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3202 colour by RNA Helices not enabled when user created
3203 annotation added to alignment
3206 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3207 Jalview icon not shown on dock in Mountain Lion/Webstart
3209 </ul> <em>Applet Known Issues</em>
3212 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3213 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3217 Jalview and Jmol example not compatible with IE9
3220 <li>Sort by annotation score doesn't reverse order
3226 <td><div align="center">
3227 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3230 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3233 <li>Internationalisation of user interface (usually
3234 called i18n support) and translation for Spanish locale</li>
3235 <li>Define/Undefine group on current selection with
3236 Ctrl-G/Shift Ctrl-G</li>
3237 <li>Improved group creation/removal options in
3238 alignment/sequence Popup menu</li>
3239 <li>Sensible precision for symbol distribution
3240 percentages shown in logo tooltip.</li>
3241 <li>Annotation panel height set according to amount of
3242 annotation when alignment first opened</li>
3243 </ul> <em>Application</em>
3245 <li>Interactive consensus RNA secondary structure
3246 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3247 <li>Select columns containing particular features from
3248 Feature Settings dialog</li>
3249 <li>View all 'representative' PDB structures for selected
3251 <li>Update Jalview project format:
3253 <li>New file extension for Jalview projects '.jvp'</li>
3254 <li>Preserve sequence and annotation dataset (to
3255 store secondary structure annotation,etc)</li>
3256 <li>Per group and alignment annotation and RNA helix
3260 <li>New similarity measures for PCA and Tree calculation
3262 <li>Experimental support for retrieval and viewing of
3263 flanking regions for an alignment</li>
3267 <!-- issues resolved --> <em>Application</em>
3269 <li>logo keeps spinning and status remains at queued or
3270 running after job is cancelled</li>
3271 <li>cannot export features from alignments imported from
3272 Jalview/VAMSAS projects</li>
3273 <li>Buggy slider for web service parameters that take
3275 <li>Newly created RNA secondary structure line doesn't
3276 have 'display all symbols' flag set</li>
3277 <li>T-COFFEE alignment score shading scheme and other
3278 annotation shading not saved in Jalview project</li>
3279 <li>Local file cannot be loaded in freshly downloaded
3281 <li>Jalview icon not shown on dock in Mountain
3283 <li>Load file from desktop file browser fails</li>
3284 <li>Occasional NPE thrown when calculating large trees</li>
3285 <li>Cannot reorder or slide sequences after dragging an
3286 alignment onto desktop</li>
3287 <li>Colour by annotation dialog throws NPE after using
3288 'extract scores' function</li>
3289 <li>Loading/cut'n'pasting an empty file leads to a grey
3290 alignment window</li>
3291 <li>Disorder thresholds rendered incorrectly after
3292 performing IUPred disorder prediction</li>
3293 <li>Multiple group annotated consensus rows shown when
3294 changing 'normalise logo' display setting</li>
3295 <li>Find shows blank dialog after 'finished searching' if
3296 nothing matches query</li>
3297 <li>Null Pointer Exceptions raised when sorting by
3298 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3300 <li>Errors in Jmol console when structures in alignment
3301 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3303 <li>Not all working JABAWS services are shown in
3305 <li>JAVAWS version of Jalview fails to launch with
3306 'invalid literal/length code'</li>
3307 <li>Annotation/RNA Helix colourschemes cannot be applied
3308 to alignment with groups (actually fixed in 2.8.0b1)</li>
3309 <li>RNA Helices and T-Coffee Scores available as default
3312 </ul> <em>Applet</em>
3314 <li>Remove group option is shown even when selection is
3316 <li>Apply to all groups ticked but colourscheme changes
3317 don't affect groups</li>
3318 <li>Documented RNA Helices and T-Coffee Scores as valid
3319 colourscheme name</li>
3320 <li>Annotation labels drawn on sequence IDs when
3321 Annotation panel is not displayed</li>
3322 <li>Increased font size for dropdown menus on OSX and
3323 embedded windows</li>
3324 </ul> <em>Other</em>
3326 <li>Consensus sequence for alignments/groups with a
3327 single sequence were not calculated</li>
3328 <li>annotation files that contain only groups imported as
3329 annotation and junk sequences</li>
3330 <li>Fasta files with sequences containing '*' incorrectly
3331 recognised as PFAM or BLC</li>
3332 <li>conservation/PID slider apply all groups option
3333 doesn't affect background (2.8.0b1)
3335 <li>redundancy highlighting is erratic at 0% and 100%</li>
3336 <li>Remove gapped columns fails for sequences with ragged
3338 <li>AMSA annotation row with leading spaces is not
3339 registered correctly on import</li>
3340 <li>Jalview crashes when selecting PCA analysis for
3341 certain alignments</li>
3342 <li>Opening the colour by annotation dialog for an
3343 existing annotation based 'use original colours'
3344 colourscheme loses original colours setting</li>
3349 <td><div align="center">
3350 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3351 <em>30/1/2014</em></strong>
3355 <li>Trusted certificates for JalviewLite applet and
3356 Jalview Desktop application<br />Certificate was donated by
3357 <a href="https://www.certum.eu">Certum</a> to the Jalview
3358 open source project).
3360 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3361 <li>Output in Stockholm format</li>
3362 <li>Allow import of data from gzipped files</li>
3363 <li>Export/import group and sequence associated line
3364 graph thresholds</li>
3365 <li>Nucleotide substitution matrix that supports RNA and
3366 ambiguity codes</li>
3367 <li>Allow disorder predictions to be made on the current
3368 selection (or visible selection) in the same way that JPred
3370 <li>Groovy scripting for headless Jalview operation</li>
3371 </ul> <em>Other improvements</em>
3373 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3374 <li>COMBINE statement uses current SEQUENCE_REF and
3375 GROUP_REF scope to group annotation rows</li>
3376 <li>Support '' style escaping of quotes in Newick
3378 <li>Group options for JABAWS service by command line name</li>
3379 <li>Empty tooltip shown for JABA service options with a
3380 link but no description</li>
3381 <li>Select primary source when selecting authority in
3382 database fetcher GUI</li>
3383 <li>Add .mfa to FASTA file extensions recognised by
3385 <li>Annotation label tooltip text wrap</li>
3390 <li>Slow scrolling when lots of annotation rows are
3392 <li>Lots of NPE (and slowness) after creating RNA
3393 secondary structure annotation line</li>
3394 <li>Sequence database accessions not imported when
3395 fetching alignments from Rfam</li>
3396 <li>Incorrect SHMR submission for sequences with
3398 <li>View all structures does not always superpose
3400 <li>Option widgets in service parameters not updated to
3401 reflect user or preset settings</li>
3402 <li>Null pointer exceptions for some services without
3403 presets or adjustable parameters</li>
3404 <li>Discover PDB IDs entry in structure menu doesn't
3405 discover PDB xRefs</li>
3406 <li>Exception encountered while trying to retrieve
3407 features with DAS</li>
3408 <li>Lowest value in annotation row isn't coloured
3409 when colour by annotation (per sequence) is coloured</li>
3410 <li>Keyboard mode P jumps to start of gapped region when
3411 residue follows a gap</li>
3412 <li>Jalview appears to hang importing an alignment with
3413 Wrap as default or after enabling Wrap</li>
3414 <li>'Right click to add annotations' message
3415 shown in wrap mode when no annotations present</li>
3416 <li>Disorder predictions fail with NPE if no automatic
3417 annotation already exists on alignment</li>
3418 <li>oninit javascript function should be called after
3419 initialisation completes</li>
3420 <li>Remove redundancy after disorder prediction corrupts
3421 alignment window display</li>
3422 <li>Example annotation file in documentation is invalid</li>
3423 <li>Grouped line graph annotation rows are not exported
3424 to annotation file</li>
3425 <li>Multi-harmony analysis cannot be run when only two
3427 <li>Cannot create multiple groups of line graphs with
3428 several 'combine' statements in annotation file</li>
3429 <li>Pressing return several times causes Number Format
3430 exceptions in keyboard mode</li>
3431 <li>Multi-harmony (SHMMR) method doesn't submit
3432 correct partitions for input data</li>
3433 <li>Translation from DNA to Amino Acids fails</li>
3434 <li>Jalview fail to load newick tree with quoted label</li>
3435 <li>--headless flag isn't understood</li>
3436 <li>ClassCastException when generating EPS in headless
3438 <li>Adjusting sequence-associated shading threshold only
3439 changes one row's threshold</li>
3440 <li>Preferences and Feature settings panel panel
3441 doesn't open</li>
3442 <li>hide consensus histogram also hides conservation and
3443 quality histograms</li>
3448 <td><div align="center">
3449 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3451 <td><em>Application</em>
3453 <li>Support for JABAWS 2.0 Services (AACon alignment
3454 conservation, protein disorder and Clustal Omega)</li>
3455 <li>JABAWS server status indicator in Web Services
3457 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3458 in Jalview alignment window</li>
3459 <li>Updated Jalview build and deploy framework for OSX
3460 mountain lion, windows 7, and 8</li>
3461 <li>Nucleotide substitution matrix for PCA that supports
3462 RNA and ambiguity codes</li>
3464 <li>Improved sequence database retrieval GUI</li>
3465 <li>Support fetching and database reference look up
3466 against multiple DAS sources (Fetch all from in 'fetch db
3468 <li>Jalview project improvements
3470 <li>Store and retrieve the 'belowAlignment'
3471 flag for annotation</li>
3472 <li>calcId attribute to group annotation rows on the
3474 <li>Store AACon calculation settings for a view in
3475 Jalview project</li>
3479 <li>horizontal scrolling gesture support</li>
3480 <li>Visual progress indicator when PCA calculation is
3482 <li>Simpler JABA web services menus</li>
3483 <li>visual indication that web service results are still
3484 being retrieved from server</li>
3485 <li>Serialise the dialogs that are shown when Jalview
3486 starts up for first time</li>
3487 <li>Jalview user agent string for interacting with HTTP
3489 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3491 <li>Examples directory and Groovy library included in
3492 InstallAnywhere distribution</li>
3493 </ul> <em>Applet</em>
3495 <li>RNA alignment and secondary structure annotation
3496 visualization applet example</li>
3497 </ul> <em>General</em>
3499 <li>Normalise option for consensus sequence logo</li>
3500 <li>Reset button in PCA window to return dimensions to
3502 <li>Allow seqspace or Jalview variant of alignment PCA
3504 <li>PCA with either nucleic acid and protein substitution
3506 <li>Allow windows containing HTML reports to be exported
3508 <li>Interactive display and editing of RNA secondary
3509 structure contacts</li>
3510 <li>RNA Helix Alignment Colouring</li>
3511 <li>RNA base pair logo consensus</li>
3512 <li>Parse sequence associated secondary structure
3513 information in Stockholm files</li>
3514 <li>HTML Export database accessions and annotation
3515 information presented in tooltip for sequences</li>
3516 <li>Import secondary structure from LOCARNA clustalw
3517 style RNA alignment files</li>
3518 <li>import and visualise T-COFFEE quality scores for an
3520 <li>'colour by annotation' per sequence option to
3521 shade each sequence according to its associated alignment
3523 <li>New Jalview Logo</li>
3524 </ul> <em>Documentation and Development</em>
3526 <li>documentation for score matrices used in Jalview</li>
3527 <li>New Website!</li>
3529 <td><em>Application</em>
3531 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3532 wsdbfetch REST service</li>
3533 <li>Stop windows being moved outside desktop on OSX</li>
3534 <li>Filetype associations not installed for webstart
3536 <li>Jalview does not always retrieve progress of a JABAWS
3537 job execution in full once it is complete</li>
3538 <li>revise SHMR RSBS definition to ensure alignment is
3539 uploaded via ali_file parameter</li>
3540 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3541 <li>View all structures superposed fails with exception</li>
3542 <li>Jnet job queues forever if a very short sequence is
3543 submitted for prediction</li>
3544 <li>Cut and paste menu not opened when mouse clicked on
3546 <li>Putting fractional value into integer text box in
3547 alignment parameter dialog causes Jalview to hang</li>
3548 <li>Structure view highlighting doesn't work on
3550 <li>View all structures fails with exception shown in
3552 <li>Characters in filename associated with PDBEntry not
3553 escaped in a platform independent way</li>
3554 <li>Jalview desktop fails to launch with exception when
3556 <li>Tree calculation reports 'you must have 2 or more
3557 sequences selected' when selection is empty</li>
3558 <li>Jalview desktop fails to launch with jar signature
3559 failure when java web start temporary file caching is
3561 <li>DAS Sequence retrieval with range qualification
3562 results in sequence xref which includes range qualification</li>
3563 <li>Errors during processing of command line arguments
3564 cause progress bar (JAL-898) to be removed</li>
3565 <li>Replace comma for semi-colon option not disabled for
3566 DAS sources in sequence fetcher</li>
3567 <li>Cannot close news reader when JABAWS server warning
3568 dialog is shown</li>
3569 <li>Option widgets not updated to reflect user settings</li>
3570 <li>Edited sequence not submitted to web service</li>
3571 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3572 <li>InstallAnywhere installer doesn't unpack and run
3573 on OSX Mountain Lion</li>
3574 <li>Annotation panel not given a scroll bar when
3575 sequences with alignment annotation are pasted into the
3577 <li>Sequence associated annotation rows not associated
3578 when loaded from Jalview project</li>
3579 <li>Browser launch fails with NPE on java 1.7</li>
3580 <li>JABAWS alignment marked as finished when job was
3581 cancelled or job failed due to invalid input</li>
3582 <li>NPE with v2.7 example when clicking on Tree
3583 associated with all views</li>
3584 <li>Exceptions when copy/paste sequences with grouped
3585 annotation rows to new window</li>
3586 </ul> <em>Applet</em>
3588 <li>Sequence features are momentarily displayed before
3589 they are hidden using hidefeaturegroups applet parameter</li>
3590 <li>loading features via javascript API automatically
3591 enables feature display</li>
3592 <li>scrollToColumnIn javascript API method doesn't
3594 </ul> <em>General</em>
3596 <li>Redundancy removal fails for rna alignment</li>
3597 <li>PCA calculation fails when sequence has been selected
3598 and then deselected</li>
3599 <li>PCA window shows grey box when first opened on OSX</li>
3600 <li>Letters coloured pink in sequence logo when alignment
3601 coloured with clustalx</li>
3602 <li>Choosing fonts without letter symbols defined causes
3603 exceptions and redraw errors</li>
3604 <li>Initial PCA plot view is not same as manually
3605 reconfigured view</li>
3606 <li>Grouped annotation graph label has incorrect line
3608 <li>Grouped annotation graph label display is corrupted
3609 for lots of labels</li>
3614 <div align="center">
3615 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3618 <td><em>Application</em>
3620 <li>Jalview Desktop News Reader</li>
3621 <li>Tweaked default layout of web services menu</li>
3622 <li>View/alignment association menu to enable user to
3623 easily specify which alignment a multi-structure view takes
3624 its colours/correspondences from</li>
3625 <li>Allow properties file location to be specified as URL</li>
3626 <li>Extend Jalview project to preserve associations
3627 between many alignment views and a single Jmol display</li>
3628 <li>Store annotation row height in Jalview project file</li>
3629 <li>Annotation row column label formatting attributes
3630 stored in project file</li>
3631 <li>Annotation row order for auto-calculated annotation
3632 rows preserved in Jalview project file</li>
3633 <li>Visual progress indication when Jalview state is
3634 saved using Desktop window menu</li>
3635 <li>Visual indication that command line arguments are
3636 still being processed</li>
3637 <li>Groovy script execution from URL</li>
3638 <li>Colour by annotation default min and max colours in
3640 <li>Automatically associate PDB files dragged onto an
3641 alignment with sequences that have high similarity and
3643 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3644 <li>'view structures' option to open many
3645 structures in same window</li>
3646 <li>Sort associated views menu option for tree panel</li>
3647 <li>Group all JABA and non-JABA services for a particular
3648 analysis function in its own submenu</li>
3649 </ul> <em>Applet</em>
3651 <li>Userdefined and autogenerated annotation rows for
3653 <li>Adjustment of alignment annotation pane height</li>
3654 <li>Annotation scrollbar for annotation panel</li>
3655 <li>Drag to reorder annotation rows in annotation panel</li>
3656 <li>'automaticScrolling' parameter</li>
3657 <li>Allow sequences with partial ID string matches to be
3658 annotated from GFF/Jalview features files</li>
3659 <li>Sequence logo annotation row in applet</li>
3660 <li>Absolute paths relative to host server in applet
3661 parameters are treated as such</li>
3662 <li>New in the JalviewLite javascript API:
3664 <li>JalviewLite.js javascript library</li>
3665 <li>Javascript callbacks for
3667 <li>Applet initialisation</li>
3668 <li>Sequence/alignment mouse-overs and selections</li>
3671 <li>scrollTo row and column alignment scrolling
3673 <li>Select sequence/alignment regions from javascript</li>
3674 <li>javascript structure viewer harness to pass
3675 messages between Jmol and Jalview when running as
3676 distinct applets</li>
3677 <li>sortBy method</li>
3678 <li>Set of applet and application examples shipped
3679 with documentation</li>
3680 <li>New example to demonstrate JalviewLite and Jmol
3681 javascript message exchange</li>
3683 </ul> <em>General</em>
3685 <li>Enable Jmol displays to be associated with multiple
3686 multiple alignments</li>
3687 <li>Option to automatically sort alignment with new tree</li>
3688 <li>User configurable link to enable redirects to a
3689 www.Jalview.org mirror</li>
3690 <li>Jmol colours option for Jmol displays</li>
3691 <li>Configurable newline string when writing alignment
3692 and other flat files</li>
3693 <li>Allow alignment annotation description lines to
3694 contain html tags</li>
3695 </ul> <em>Documentation and Development</em>
3697 <li>Add groovy test harness for bulk load testing to
3699 <li>Groovy script to load and align a set of sequences
3700 using a web service before displaying the result in the
3701 Jalview desktop</li>
3702 <li>Restructured javascript and applet api documentation</li>
3703 <li>Ant target to publish example html files with applet
3705 <li>Netbeans project for building Jalview from source</li>
3706 <li>ant task to create online javadoc for Jalview source</li>
3708 <td><em>Application</em>
3710 <li>User defined colourscheme throws exception when
3711 current built in colourscheme is saved as new scheme</li>
3712 <li>AlignFrame->Save in application pops up save
3713 dialog for valid filename/format</li>
3714 <li>Cannot view associated structure for UniProt sequence</li>
3715 <li>PDB file association breaks for UniProt sequence
3717 <li>Associate PDB from file dialog does not tell you
3718 which sequence is to be associated with the file</li>
3719 <li>Find All raises null pointer exception when query
3720 only matches sequence IDs</li>
3721 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3722 <li>Jalview project with Jmol views created with Jalview
3723 2.4 cannot be loaded</li>
3724 <li>Filetype associations not installed for webstart
3726 <li>Two or more chains in a single PDB file associated
3727 with sequences in different alignments do not get coloured
3728 by their associated sequence</li>
3729 <li>Visibility status of autocalculated annotation row
3730 not preserved when project is loaded</li>
3731 <li>Annotation row height and visibility attributes not
3732 stored in Jalview project</li>
3733 <li>Tree bootstraps are not preserved when saved as a
3734 Jalview project</li>
3735 <li>Envision2 workflow tooltips are corrupted</li>
3736 <li>Enabling show group conservation also enables colour
3737 by conservation</li>
3738 <li>Duplicate group associated conservation or consensus
3739 created on new view</li>
3740 <li>Annotation scrollbar not displayed after 'show
3741 all hidden annotation rows' option selected</li>
3742 <li>Alignment quality not updated after alignment
3743 annotation row is hidden then shown</li>
3744 <li>Preserve colouring of structures coloured by
3745 sequences in pre Jalview 2.7 projects</li>
3746 <li>Web service job parameter dialog is not laid out
3748 <li>Web services menu not refreshed after 'reset
3749 services' button is pressed in preferences</li>
3750 <li>Annotation off by one in Jalview v2_3 example project</li>
3751 <li>Structures imported from file and saved in project
3752 get name like jalview_pdb1234.txt when reloaded</li>
3753 <li>Jalview does not always retrieve progress of a JABAWS
3754 job execution in full once it is complete</li>
3755 </ul> <em>Applet</em>
3757 <li>Alignment height set incorrectly when lots of
3758 annotation rows are displayed</li>
3759 <li>Relative URLs in feature HTML text not resolved to
3761 <li>View follows highlighting does not work for positions
3763 <li><= shown as = in tooltip</li>
3764 <li>Export features raises exception when no features
3766 <li>Separator string used for serialising lists of IDs
3767 for javascript api is modified when separator string
3768 provided as parameter</li>
3769 <li>Null pointer exception when selecting tree leaves for
3770 alignment with no existing selection</li>
3771 <li>Relative URLs for datasources assumed to be relative
3772 to applet's codebase</li>
3773 <li>Status bar not updated after finished searching and
3774 search wraps around to first result</li>
3775 <li>StructureSelectionManager instance shared between
3776 several Jalview applets causes race conditions and memory
3778 <li>Hover tooltip and mouseover of position on structure
3779 not sent from Jmol in applet</li>
3780 <li>Certain sequences of javascript method calls to
3781 applet API fatally hang browser</li>
3782 </ul> <em>General</em>
3784 <li>View follows structure mouseover scrolls beyond
3785 position with wrapped view and hidden regions</li>
3786 <li>Find sequence position moves to wrong residue
3787 with/without hidden columns</li>
3788 <li>Sequence length given in alignment properties window
3790 <li>InvalidNumberFormat exceptions thrown when trying to
3791 import PDB like structure files</li>
3792 <li>Positional search results are only highlighted
3793 between user-supplied sequence start/end bounds</li>
3794 <li>End attribute of sequence is not validated</li>
3795 <li>Find dialog only finds first sequence containing a
3796 given sequence position</li>
3797 <li>Sequence numbering not preserved in MSF alignment
3799 <li>Jalview PDB file reader does not extract sequence
3800 from nucleotide chains correctly</li>
3801 <li>Structure colours not updated when tree partition
3802 changed in alignment</li>
3803 <li>Sequence associated secondary structure not correctly
3804 parsed in interleaved stockholm</li>
3805 <li>Colour by annotation dialog does not restore current
3807 <li>Hiding (nearly) all sequences doesn't work
3809 <li>Sequences containing lowercase letters are not
3810 properly associated with their pdb files</li>
3811 </ul> <em>Documentation and Development</em>
3813 <li>schemas/JalviewWsParamSet.xsd corrupted by
3814 ApplyCopyright tool</li>
3819 <div align="center">
3820 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3823 <td><em>Application</em>
3825 <li>New warning dialog when the Jalview Desktop cannot
3826 contact web services</li>
3827 <li>JABA service parameters for a preset are shown in
3828 service job window</li>
3829 <li>JABA Service menu entries reworded</li>
3833 <li>Modeller PIR IO broken - cannot correctly import a
3834 pir file emitted by Jalview</li>
3835 <li>Existing feature settings transferred to new
3836 alignment view created from cut'n'paste</li>
3837 <li>Improved test for mixed amino/nucleotide chains when
3838 parsing PDB files</li>
3839 <li>Consensus and conservation annotation rows
3840 occasionally become blank for all new windows</li>
3841 <li>Exception raised when right clicking above sequences
3842 in wrapped view mode</li>
3843 </ul> <em>Application</em>
3845 <li>multiple multiply aligned structure views cause cpu
3846 usage to hit 100% and computer to hang</li>
3847 <li>Web Service parameter layout breaks for long user
3848 parameter names</li>
3849 <li>Jaba service discovery hangs desktop if Jaba server
3856 <div align="center">
3857 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3860 <td><em>Application</em>
3862 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3863 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3866 <li>Web Services preference tab</li>
3867 <li>Analysis parameters dialog box and user defined
3869 <li>Improved speed and layout of Envision2 service menu</li>
3870 <li>Superpose structures using associated sequence
3872 <li>Export coordinates and projection as CSV from PCA
3874 </ul> <em>Applet</em>
3876 <li>enable javascript: execution by the applet via the
3877 link out mechanism</li>
3878 </ul> <em>Other</em>
3880 <li>Updated the Jmol Jalview interface to work with Jmol
3882 <li>The Jalview Desktop and JalviewLite applet now
3883 require Java 1.5</li>
3884 <li>Allow Jalview feature colour specification for GFF
3885 sequence annotation files</li>
3886 <li>New 'colour by label' keword in Jalview feature file
3887 type colour specification</li>
3888 <li>New Jalview Desktop Groovy API method that allows a
3889 script to check if it being run in an interactive session or
3890 in a batch operation from the Jalview command line</li>
3894 <li>clustalx colourscheme colours Ds preferentially when
3895 both D+E are present in over 50% of the column</li>
3896 </ul> <em>Application</em>
3898 <li>typo in AlignmentFrame->View->Hide->all but
3899 selected Regions menu item</li>
3900 <li>sequence fetcher replaces ',' for ';' when the ',' is
3901 part of a valid accession ID</li>
3902 <li>fatal OOM if object retrieved by sequence fetcher
3903 runs out of memory</li>
3904 <li>unhandled Out of Memory Error when viewing pca
3905 analysis results</li>
3906 <li>InstallAnywhere builds fail to launch on OS X java
3907 10.5 update 4 (due to apple Java 1.6 update)</li>
3908 <li>Installanywhere Jalview silently fails to launch</li>
3909 </ul> <em>Applet</em>
3911 <li>Jalview.getFeatureGroups() raises an
3912 ArrayIndexOutOfBoundsException if no feature groups are
3919 <div align="center">
3920 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3926 <li>Alignment prettyprinter doesn't cope with long
3928 <li>clustalx colourscheme colours Ds preferentially when
3929 both D+E are present in over 50% of the column</li>
3930 <li>nucleic acid structures retrieved from PDB do not
3931 import correctly</li>
3932 <li>More columns get selected than were clicked on when a
3933 number of columns are hidden</li>
3934 <li>annotation label popup menu not providing correct
3935 add/hide/show options when rows are hidden or none are
3937 <li>Stockholm format shown in list of readable formats,
3938 and parser copes better with alignments from RFAM.</li>
3939 <li>CSV output of consensus only includes the percentage
3940 of all symbols if sequence logo display is enabled</li>
3942 </ul> <em>Applet</em>
3944 <li>annotation panel disappears when annotation is
3946 </ul> <em>Application</em>
3948 <li>Alignment view not redrawn properly when new
3949 alignment opened where annotation panel is visible but no
3950 annotations are present on alignment</li>
3951 <li>pasted region containing hidden columns is
3952 incorrectly displayed in new alignment window</li>
3953 <li>Jalview slow to complete operations when stdout is
3954 flooded (fix is to close the Jalview console)</li>
3955 <li>typo in AlignmentFrame->View->Hide->all but
3956 selected Rregions menu item.</li>
3957 <li>inconsistent group submenu and Format submenu entry
3958 'Un' or 'Non'conserved</li>
3959 <li>Sequence feature settings are being shared by
3960 multiple distinct alignments</li>
3961 <li>group annotation not recreated when tree partition is
3963 <li>double click on group annotation to select sequences
3964 does not propagate to associated trees</li>
3965 <li>Mac OSX specific issues:
3967 <li>exception raised when mouse clicked on desktop
3968 window background</li>
3969 <li>Desktop menu placed on menu bar and application
3970 name set correctly</li>
3971 <li>sequence feature settings not wide enough for the
3972 save feature colourscheme button</li>
3981 <div align="center">
3982 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3985 <td><em>New Capabilities</em>
3987 <li>URL links generated from description line for
3988 regular-expression based URL links (applet and application)
3990 <li>Non-positional feature URL links are shown in link
3992 <li>Linked viewing of nucleic acid sequences and
3994 <li>Automatic Scrolling option in View menu to display
3995 the currently highlighted region of an alignment.</li>
3996 <li>Order an alignment by sequence length, or using the
3997 average score or total feature count for each sequence.</li>
3998 <li>Shading features by score or associated description</li>
3999 <li>Subdivide alignment and groups based on identity of
4000 selected subsequence (Make Groups from Selection).</li>
4001 <li>New hide/show options including Shift+Control+H to
4002 hide everything but the currently selected region.</li>
4003 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4004 </ul> <em>Application</em>
4006 <li>Fetch DB References capabilities and UI expanded to
4007 support retrieval from DAS sequence sources</li>
4008 <li>Local DAS Sequence sources can be added via the
4009 command line or via the Add local source dialog box.</li>
4010 <li>DAS Dbref and DbxRef feature types are parsed as
4011 database references and protein_name is parsed as
4012 description line (BioSapiens terms).</li>
4013 <li>Enable or disable non-positional feature and database
4014 references in sequence ID tooltip from View menu in
4016 <!-- <li>New hidden columns and rows and representatives capabilities
4017 in annotations file (in progress - not yet fully implemented)</li> -->
4018 <li>Group-associated consensus, sequence logos and
4019 conservation plots</li>
4020 <li>Symbol distributions for each column can be exported
4021 and visualized as sequence logos</li>
4022 <li>Optionally scale multi-character column labels to fit
4023 within each column of annotation row<!-- todo for applet -->
4025 <li>Optional automatic sort of associated alignment view
4026 when a new tree is opened.</li>
4027 <li>Jalview Java Console</li>
4028 <li>Better placement of desktop window when moving
4029 between different screens.</li>
4030 <li>New preference items for sequence ID tooltip and
4031 consensus annotation</li>
4032 <li>Client to submit sequences and IDs to Envision2
4034 <li><em>Vamsas Capabilities</em>
4036 <li>Improved VAMSAS synchronization (Jalview archive
4037 used to preserve views, structures, and tree display
4039 <li>Import of vamsas documents from disk or URL via
4041 <li>Sharing of selected regions between views and
4042 with other VAMSAS applications (Experimental feature!)</li>
4043 <li>Updated API to VAMSAS version 0.2</li>
4045 </ul> <em>Applet</em>
4047 <li>Middle button resizes annotation row height</li>
4050 <li>sortByTree (true/false) - automatically sort the
4051 associated alignment view by the tree when a new tree is
4053 <li>showTreeBootstraps (true/false) - show or hide
4054 branch bootstraps (default is to show them if available)</li>
4055 <li>showTreeDistances (true/false) - show or hide
4056 branch lengths (default is to show them if available)</li>
4057 <li>showUnlinkedTreeNodes (true/false) - indicate if
4058 unassociated nodes should be highlighted in the tree
4060 <li>heightScale and widthScale (1.0 or more) -
4061 increase the height or width of a cell in the alignment
4062 grid relative to the current font size.</li>
4065 <li>Non-positional features displayed in sequence ID
4067 </ul> <em>Other</em>
4069 <li>Features format: graduated colour definitions and
4070 specification of feature scores</li>
4071 <li>Alignment Annotations format: new keywords for group
4072 associated annotation (GROUP_REF) and annotation row display
4073 properties (ROW_PROPERTIES)</li>
4074 <li>XML formats extended to support graduated feature
4075 colourschemes, group associated annotation, and profile
4076 visualization settings.</li></td>
4079 <li>Source field in GFF files parsed as feature source
4080 rather than description</li>
4081 <li>Non-positional features are now included in sequence
4082 feature and gff files (controlled via non-positional feature
4083 visibility in tooltip).</li>
4084 <li>URL links generated for all feature links (bugfix)</li>
4085 <li>Added URL embedding instructions to features file
4087 <li>Codons containing ambiguous nucleotides translated as
4088 'X' in peptide product</li>
4089 <li>Match case switch in find dialog box works for both
4090 sequence ID and sequence string and query strings do not
4091 have to be in upper case to match case-insensitively.</li>
4092 <li>AMSA files only contain first column of
4093 multi-character column annotation labels</li>
4094 <li>Jalview Annotation File generation/parsing consistent
4095 with documentation (e.g. Stockholm annotation can be
4096 exported and re-imported)</li>
4097 <li>PDB files without embedded PDB IDs given a friendly
4099 <li>Find incrementally searches ID string matches as well
4100 as subsequence matches, and correctly reports total number
4104 <li>Better handling of exceptions during sequence
4106 <li>Dasobert generated non-positional feature URL
4107 link text excludes the start_end suffix</li>
4108 <li>DAS feature and source retrieval buttons disabled
4109 when fetch or registry operations in progress.</li>
4110 <li>PDB files retrieved from URLs are cached properly</li>
4111 <li>Sequence description lines properly shared via
4113 <li>Sequence fetcher fetches multiple records for all
4115 <li>Ensured that command line das feature retrieval
4116 completes before alignment figures are generated.</li>
4117 <li>Reduced time taken when opening file browser for
4119 <li>isAligned check prior to calculating tree, PCA or
4120 submitting an MSA to JNet now excludes hidden sequences.</li>
4121 <li>User defined group colours properly recovered
4122 from Jalview projects.</li>
4131 <div align="center">
4132 <strong>2.4.0.b2</strong><br> 28/10/2009
4137 <li>Experimental support for google analytics usage
4139 <li>Jalview privacy settings (user preferences and docs).</li>
4144 <li>Race condition in applet preventing startup in
4146 <li>Exception when feature created from selection beyond
4147 length of sequence.</li>
4148 <li>Allow synthetic PDB files to be imported gracefully</li>
4149 <li>Sequence associated annotation rows associate with
4150 all sequences with a given id</li>
4151 <li>Find function matches case-insensitively for sequence
4152 ID string searches</li>
4153 <li>Non-standard characters do not cause pairwise
4154 alignment to fail with exception</li>
4155 </ul> <em>Application Issues</em>
4157 <li>Sequences are now validated against EMBL database</li>
4158 <li>Sequence fetcher fetches multiple records for all
4160 </ul> <em>InstallAnywhere Issues</em>
4162 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4163 issue with installAnywhere mechanism)</li>
4164 <li>Command line launching of JARs from InstallAnywhere
4165 version (java class versioning error fixed)</li>
4172 <div align="center">
4173 <strong>2.4</strong><br> 27/8/2008
4176 <td><em>User Interface</em>
4178 <li>Linked highlighting of codon and amino acid from
4179 translation and protein products</li>
4180 <li>Linked highlighting of structure associated with
4181 residue mapping to codon position</li>
4182 <li>Sequence Fetcher provides example accession numbers
4183 and 'clear' button</li>
4184 <li>MemoryMonitor added as an option under Desktop's
4186 <li>Extract score function to parse whitespace separated
4187 numeric data in description line</li>
4188 <li>Column labels in alignment annotation can be centred.</li>
4189 <li>Tooltip for sequence associated annotation give name
4191 </ul> <em>Web Services and URL fetching</em>
4193 <li>JPred3 web service</li>
4194 <li>Prototype sequence search client (no public services
4196 <li>Fetch either seed alignment or full alignment from
4198 <li>URL Links created for matching database cross
4199 references as well as sequence ID</li>
4200 <li>URL Links can be created using regular-expressions</li>
4201 </ul> <em>Sequence Database Connectivity</em>
4203 <li>Retrieval of cross-referenced sequences from other
4205 <li>Generalised database reference retrieval and
4206 validation to all fetchable databases</li>
4207 <li>Fetch sequences from DAS sources supporting the
4208 sequence command</li>
4209 </ul> <em>Import and Export</em>
4210 <li>export annotation rows as CSV for spreadsheet import</li>
4211 <li>Jalview projects record alignment dataset associations,
4212 EMBL products, and cDNA sequence mappings</li>
4213 <li>Sequence Group colour can be specified in Annotation
4215 <li>Ad-hoc colouring of group in Annotation File using RGB
4216 triplet as name of colourscheme</li>
4217 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4219 <li>treenode binding for VAMSAS tree exchange</li>
4220 <li>local editing and update of sequences in VAMSAS
4221 alignments (experimental)</li>
4222 <li>Create new or select existing session to join</li>
4223 <li>load and save of vamsas documents</li>
4224 </ul> <em>Application command line</em>
4226 <li>-tree parameter to open trees (introduced for passing
4228 <li>-fetchfrom command line argument to specify nicknames
4229 of DAS servers to query for alignment features</li>
4230 <li>-dasserver command line argument to add new servers
4231 that are also automatically queried for features</li>
4232 <li>-groovy command line argument executes a given groovy
4233 script after all input data has been loaded and parsed</li>
4234 </ul> <em>Applet-Application data exchange</em>
4236 <li>Trees passed as applet parameters can be passed to
4237 application (when using "View in full
4238 application")</li>
4239 </ul> <em>Applet Parameters</em>
4241 <li>feature group display control parameter</li>
4242 <li>debug parameter</li>
4243 <li>showbutton parameter</li>
4244 </ul> <em>Applet API methods</em>
4246 <li>newView public method</li>
4247 <li>Window (current view) specific get/set public methods</li>
4248 <li>Feature display control methods</li>
4249 <li>get list of currently selected sequences</li>
4250 </ul> <em>New Jalview distribution features</em>
4252 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4253 <li>RELEASE file gives build properties for the latest
4254 Jalview release.</li>
4255 <li>Java 1.1 Applet build made easier and donotobfuscate
4256 property controls execution of obfuscator</li>
4257 <li>Build target for generating source distribution</li>
4258 <li>Debug flag for javacc</li>
4259 <li>.jalview_properties file is documented (slightly) in
4260 jalview.bin.Cache</li>
4261 <li>Continuous Build Integration for stable and
4262 development version of Application, Applet and source
4267 <li>selected region output includes visible annotations
4268 (for certain formats)</li>
4269 <li>edit label/displaychar contains existing label/char
4271 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4272 <li>shorter peptide product names from EMBL records</li>
4273 <li>Newick string generator makes compact representations</li>
4274 <li>bootstrap values parsed correctly for tree files with
4276 <li>pathological filechooser bug avoided by not allowing
4277 filenames containing a ':'</li>
4278 <li>Fixed exception when parsing GFF files containing
4279 global sequence features</li>
4280 <li>Alignment datasets are finalized only when number of
4281 references from alignment sequences goes to zero</li>
4282 <li>Close of tree branch colour box without colour
4283 selection causes cascading exceptions</li>
4284 <li>occasional negative imgwidth exceptions</li>
4285 <li>better reporting of non-fatal warnings to user when
4286 file parsing fails.</li>
4287 <li>Save works when Jalview project is default format</li>
4288 <li>Save as dialog opened if current alignment format is
4289 not a valid output format</li>
4290 <li>UniProt canonical names introduced for both das and
4292 <li>Histidine should be midblue (not pink!) in Zappo</li>
4293 <li>error messages passed up and output when data read
4295 <li>edit undo recovers previous dataset sequence when
4296 sequence is edited</li>
4297 <li>allow PDB files without pdb ID HEADER lines (like
4298 those generated by MODELLER) to be read in properly</li>
4299 <li>allow reading of JPred concise files as a normal
4301 <li>Stockholm annotation parsing and alignment properties
4302 import fixed for PFAM records</li>
4303 <li>Structure view windows have correct name in Desktop
4305 <li>annotation consisting of sequence associated scores
4306 can be read and written correctly to annotation file</li>
4307 <li>Aligned cDNA translation to aligned peptide works
4309 <li>Fixed display of hidden sequence markers and
4310 non-italic font for representatives in Applet</li>
4311 <li>Applet Menus are always embedded in applet window on
4313 <li>Newly shown features appear at top of stack (in
4315 <li>Annotations added via parameter not drawn properly
4316 due to null pointer exceptions</li>
4317 <li>Secondary structure lines are drawn starting from
4318 first column of alignment</li>
4319 <li>UniProt XML import updated for new schema release in
4321 <li>Sequence feature to sequence ID match for Features
4322 file is case-insensitive</li>
4323 <li>Sequence features read from Features file appended to
4324 all sequences with matching IDs</li>
4325 <li>PDB structure coloured correctly for associated views
4326 containing a sub-sequence</li>
4327 <li>PDB files can be retrieved by applet from Jar files</li>
4328 <li>feature and annotation file applet parameters
4329 referring to different directories are retrieved correctly</li>
4330 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4331 <li>Fixed application hang whilst waiting for
4332 splash-screen version check to complete</li>
4333 <li>Applet properly URLencodes input parameter values
4334 when passing them to the launchApp service</li>
4335 <li>display name and local features preserved in results
4336 retrieved from web service</li>
4337 <li>Visual delay indication for sequence retrieval and
4338 sequence fetcher initialisation</li>
4339 <li>updated Application to use DAS 1.53e version of
4340 dasobert DAS client</li>
4341 <li>Re-instated Full AMSA support and .amsa file
4343 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4351 <div align="center">
4352 <strong>2.3</strong><br> 9/5/07
4357 <li>Jmol 11.0.2 integration</li>
4358 <li>PDB views stored in Jalview XML files</li>
4359 <li>Slide sequences</li>
4360 <li>Edit sequence in place</li>
4361 <li>EMBL CDS features</li>
4362 <li>DAS Feature mapping</li>
4363 <li>Feature ordering</li>
4364 <li>Alignment Properties</li>
4365 <li>Annotation Scores</li>
4366 <li>Sort by scores</li>
4367 <li>Feature/annotation editing in applet</li>
4372 <li>Headless state operation in 2.2.1</li>
4373 <li>Incorrect and unstable DNA pairwise alignment</li>
4374 <li>Cut and paste of sequences with annotation</li>
4375 <li>Feature group display state in XML</li>
4376 <li>Feature ordering in XML</li>
4377 <li>blc file iteration selection using filename # suffix</li>
4378 <li>Stockholm alignment properties</li>
4379 <li>Stockhom alignment secondary structure annotation</li>
4380 <li>2.2.1 applet had no feature transparency</li>
4381 <li>Number pad keys can be used in cursor mode</li>
4382 <li>Structure Viewer mirror image resolved</li>
4389 <div align="center">
4390 <strong>2.2.1</strong><br> 12/2/07
4395 <li>Non standard characters can be read and displayed
4396 <li>Annotations/Features can be imported/exported to the
4398 <li>Applet allows editing of sequence/annotation/group
4399 name & description
4400 <li>Preference setting to display sequence name in
4402 <li>Annotation file format extended to allow
4403 Sequence_groups to be defined
4404 <li>Default opening of alignment overview panel can be
4405 specified in preferences
4406 <li>PDB residue numbering annotation added to associated
4412 <li>Applet crash under certain Linux OS with Java 1.6
4414 <li>Annotation file export / import bugs fixed
4415 <li>PNG / EPS image output bugs fixed
4421 <div align="center">
4422 <strong>2.2</strong><br> 27/11/06
4427 <li>Multiple views on alignment
4428 <li>Sequence feature editing
4429 <li>"Reload" alignment
4430 <li>"Save" to current filename
4431 <li>Background dependent text colour
4432 <li>Right align sequence ids
4433 <li>User-defined lower case residue colours
4436 <li>Menu item accelerator keys
4437 <li>Control-V pastes to current alignment
4438 <li>Cancel button for DAS Feature Fetching
4439 <li>PCA and PDB Viewers zoom via mouse roller
4440 <li>User-defined sub-tree colours and sub-tree selection
4442 <li>'New Window' button on the 'Output to Text box'
4447 <li>New memory efficient Undo/Redo System
4448 <li>Optimised symbol lookups and conservation/consensus
4450 <li>Region Conservation/Consensus recalculated after
4452 <li>Fixed Remove Empty Columns Bug (empty columns at end
4454 <li>Slowed DAS Feature Fetching for increased robustness.
4456 <li>Made angle brackets in ASCII feature descriptions
4458 <li>Re-instated Zoom function for PCA
4459 <li>Sequence descriptions conserved in web service
4461 <li>UniProt ID discoverer uses any word separated by
4463 <li>WsDbFetch query/result association resolved
4464 <li>Tree leaf to sequence mapping improved
4465 <li>Smooth fonts switch moved to FontChooser dialog box.
4472 <div align="center">
4473 <strong>2.1.1</strong><br> 12/9/06
4478 <li>Copy consensus sequence to clipboard</li>
4483 <li>Image output - rightmost residues are rendered if
4484 sequence id panel has been resized</li>
4485 <li>Image output - all offscreen group boundaries are
4487 <li>Annotation files with sequence references - all
4488 elements in file are relative to sequence position</li>
4489 <li>Mac Applet users can use Alt key for group editing</li>
4495 <div align="center">
4496 <strong>2.1</strong><br> 22/8/06
4501 <li>MAFFT Multiple Alignment in default Web Service list</li>
4502 <li>DAS Feature fetching</li>
4503 <li>Hide sequences and columns</li>
4504 <li>Export Annotations and Features</li>
4505 <li>GFF file reading / writing</li>
4506 <li>Associate structures with sequences from local PDB
4508 <li>Add sequences to exisiting alignment</li>
4509 <li>Recently opened files / URL lists</li>
4510 <li>Applet can launch the full application</li>
4511 <li>Applet has transparency for features (Java 1.2
4513 <li>Applet has user defined colours parameter</li>
4514 <li>Applet can load sequences from parameter
4515 "sequence<em>x</em>"
4521 <li>Redundancy Panel reinstalled in the Applet</li>
4522 <li>Monospaced font - EPS / rescaling bug fixed</li>
4523 <li>Annotation files with sequence references bug fixed</li>
4529 <div align="center">
4530 <strong>2.08.1</strong><br> 2/5/06
4535 <li>Change case of selected region from Popup menu</li>
4536 <li>Choose to match case when searching</li>
4537 <li>Middle mouse button and mouse movement can compress /
4538 expand the visible width and height of the alignment</li>
4543 <li>Annotation Panel displays complete JNet results</li>
4549 <div align="center">
4550 <strong>2.08b</strong><br> 18/4/06
4556 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4557 <li>Righthand label on wrapped alignments shows correct
4564 <div align="center">
4565 <strong>2.08</strong><br> 10/4/06
4570 <li>Editing can be locked to the selection area</li>
4571 <li>Keyboard editing</li>
4572 <li>Create sequence features from searches</li>
4573 <li>Precalculated annotations can be loaded onto
4575 <li>Features file allows grouping of features</li>
4576 <li>Annotation Colouring scheme added</li>
4577 <li>Smooth fonts off by default - Faster rendering</li>
4578 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4583 <li>Drag & Drop fixed on Linux</li>
4584 <li>Jalview Archive file faster to load/save, sequence
4585 descriptions saved.</li>
4591 <div align="center">
4592 <strong>2.07</strong><br> 12/12/05
4597 <li>PDB Structure Viewer enhanced</li>
4598 <li>Sequence Feature retrieval and display enhanced</li>
4599 <li>Choose to output sequence start-end after sequence
4600 name for file output</li>
4601 <li>Sequence Fetcher WSDBFetch@EBI</li>
4602 <li>Applet can read feature files, PDB files and can be
4603 used for HTML form input</li>
4608 <li>HTML output writes groups and features</li>
4609 <li>Group editing is Control and mouse click</li>
4610 <li>File IO bugs</li>
4616 <div align="center">
4617 <strong>2.06</strong><br> 28/9/05
4622 <li>View annotations in wrapped mode</li>
4623 <li>More options for PCA viewer</li>
4628 <li>GUI bugs resolved</li>
4629 <li>Runs with -nodisplay from command line</li>
4635 <div align="center">
4636 <strong>2.05b</strong><br> 15/9/05
4641 <li>Choose EPS export as lineart or text</li>
4642 <li>Jar files are executable</li>
4643 <li>Can read in Uracil - maps to unknown residue</li>
4648 <li>Known OutOfMemory errors give warning message</li>
4649 <li>Overview window calculated more efficiently</li>
4650 <li>Several GUI bugs resolved</li>
4656 <div align="center">
4657 <strong>2.05</strong><br> 30/8/05
4662 <li>Edit and annotate in "Wrapped" view</li>
4667 <li>Several GUI bugs resolved</li>
4673 <div align="center">
4674 <strong>2.04</strong><br> 24/8/05
4679 <li>Hold down mouse wheel & scroll to change font
4685 <li>Improved JPred client reliability</li>
4686 <li>Improved loading of Jalview files</li>
4692 <div align="center">
4693 <strong>2.03</strong><br> 18/8/05
4698 <li>Set Proxy server name and port in preferences</li>
4699 <li>Multiple URL links from sequence ids</li>
4700 <li>User Defined Colours can have a scheme name and added
4702 <li>Choose to ignore gaps in consensus calculation</li>
4703 <li>Unix users can set default web browser</li>
4704 <li>Runs without GUI for batch processing</li>
4705 <li>Dynamically generated Web Service Menus</li>
4710 <li>InstallAnywhere download for Sparc Solaris</li>
4716 <div align="center">
4717 <strong>2.02</strong><br> 18/7/05
4723 <li>Copy & Paste order of sequences maintains
4724 alignment order.</li>
4730 <div align="center">
4731 <strong>2.01</strong><br> 12/7/05
4736 <li>Use delete key for deleting selection.</li>
4737 <li>Use Mouse wheel to scroll sequences.</li>
4738 <li>Help file updated to describe how to add alignment
4740 <li>Version and build date written to build properties
4742 <li>InstallAnywhere installation will check for updates
4743 at launch of Jalview.</li>
4748 <li>Delete gaps bug fixed.</li>
4749 <li>FileChooser sorts columns.</li>
4750 <li>Can remove groups one by one.</li>
4751 <li>Filechooser icons installed.</li>
4752 <li>Finder ignores return character when searching.
4753 Return key will initiate a search.<br>
4760 <div align="center">
4761 <strong>2.0</strong><br> 20/6/05
4766 <li>New codebase</li>