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;
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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.2.11.1.1">.1</a><br />
61 <em>13/07/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-3608 -->Set choice of Look and Feel via system property or command line option, and
71 force use of Metal look and feel as default on linux.
74 <!-- JAL-3633 -->Preferences -> Connections, Proxy server settings now allow selecting "No proxy", "System proxy settings" or custom proxy settings
75 which can be configured for HTTP, HTTPS and allows for an authenticated proxy server.
78 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
79 HTSJDK from 2.12 to 2.23
82 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
83 optimisations and improvements suggested by Bob Hanson and
84 improved compatibility with JalviewJS
87 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted alignments from Pfam and Rfam
90 <!-- JAL-2656 -->Recognise GZipped content for URLs and File import (no longer based on .gz extension)
95 <td align="left" valign="top">
98 <!-- JAL-3493 -->Escape does not clear highlights on the
99 alignment (Since Jalview 2.10.3)
102 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
103 doesn't slide selected sequences
106 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
107 multiple EMBL gene products shown forĀ a single contig
110 <!-- JAL-3628 -->Unable to save update to an existing file on Windows (partially resolved)
111 and Backups -> Single backup scheme not always saving backup file.
114 <!-- JAL-3609 -->Java 11 only: Automatically set scaling for HiDPI displays in linux.
117 <!-- JAL-3632 JAL-3633 -->Proxy properties don't set HTTPS proxy for launcher or application.
120 <!-- JAL-3696 -->Errors encountered when processing variants
121 from VCF files yield "Error processing VCF: Format specifier
125 <!-- JAL-3697 -->Count of features not shown can be wrong
126 when there are both local and complementary features mapped
127 to the position under the cursor
133 <td width="60" align="center" nowrap><strong><a
134 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
135 <em>22/04/2020</em></strong></td>
136 <td align="left" valign="top">
139 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
140 'virtual' codon features shown on protein (or vice versa)
141 for display in alignments, on structure views (including
142 transfer to UCSF chimera), in feature reports and for
146 <!-- JAL-3121 -->Feature attributes from VCF files can be
147 exported and re-imported as GFF3 files
150 <!-- JAL-3376 -->Capture VCF "fixed column" values
151 POS, ID, QUAL, FILTER as Feature Attributes
154 <!-- JAL-3375 -->More robust VCF numeric data field
155 validation while parsing
158 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
162 <!-- JAL-3535 -->Feature Settings dialog title includes name
166 <!-- JAL-3538 -->Font anti-aliasing in alignment views
170 <!-- JAL-3468 -->Very long feature descriptions truncated in
174 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
175 with no feature types visible
178 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
180 </ul><em>Jalview Installer</em>
183 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
184 in console (may be null when Jalview launched as executable jar or via conda)
187 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
190 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
193 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
195 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
196 </ul> <em>Release processes</em>
199 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
202 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
204 </ul> <em>Build System</em>
207 <!-- JAL-3510 -->Clover updated to 4.4.1
210 <!-- JAL-3513 -->Test code included in Clover coverage
214 <em>Groovy Scripts</em>
217 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
218 to stdout containing the consensus sequence for each
219 alignment in a Jalview session
222 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
223 genomic sequence_variant annotation from CDS as
224 missense_variant or synonymous_variant on protein products.
228 <td align="left" valign="top">
231 <!-- JAL-3581 -->Hidden sequence markers still visible when
232 'Show hidden markers' option is not ticked
235 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
236 PNG output when 'Automatically set ID width' is set in
237 jalview preferences or properties file
240 <!-- JAL-3571 -->Feature Editor dialog can be opened when
241 'Show Sequence Features' option is not ticked
244 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
245 buttons in Feature Settings dialog are clicked when no
249 <!-- JAL-3412 -->ID margins for CDS and Protein views not
250 equal when split frame is first opened
253 <!-- JAL-3296 -->Sequence position numbers in status bar not
254 correct after editing a sequence's start position
257 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
258 with annotation and exceptions thrown when only a few
259 columns shown in wrapped mode
262 <!-- JAL-3386 -->Sequence IDs missing in headless export of
263 wrapped alignment figure with annotations
266 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
267 ID fails with ClassCastException
270 <!-- JAL-3389 -->Chimera session not restored from Jalview
274 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
275 feature settings dialog also selects columns
278 <!-- JAL-3473 -->SpinnerNumberModel causes
279 IllegalArgumentException in some circumstances
282 <!-- JAL-3534 -->Multiple feature settings dialogs can be
286 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
287 alignment window is closed
290 <!-- JAL-3406 -->Credits missing some authors in Jalview
291 help documentation for 2.11.0 release
294 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
295 includes Pfam ID as sequence's accession rather than its
298 </ul> <em>Java 11 Compatibility issues</em>
301 <!-- JAL-2987 -->OSX - Can't view some search results in
302 PDB/Uniprot search panel
304 </ul> <em>Installer</em>
307 <!-- JAL-3447 -->Jalview should not create file associations
308 for 3D structure files (.pdb, .mmcif. .cif)
310 </ul> <em>Repository and Source Release</em>
313 <!-- JAL-3474 -->removed obsolete .cvsignore files from
317 <!-- JAL-3541 -->Clover report generation running out of
320 </ul> <em>New Known Issues</em>
323 <!-- JAL-3523 -->OSX - Current working directory not
324 preserved when Jalview.app launched with parameters from
328 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
329 clipped in headless figure export when Right Align option
333 <!-- JAL-3542 -->Jalview Installation type always reports
334 'Source' in console output
337 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
338 bamboo server but run fine locally.
344 <td width="60" align="center" nowrap>
345 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
346 <em>04/07/2019</em></strong>
348 <td align="left" valign="top">
351 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
352 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
353 source project) rather than InstallAnywhere
356 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
357 settings, receive over the air updates and launch specific
358 versions via (<a href="https://github.com/threerings/getdown">Three
362 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
363 formats supported by Jalview (including .jvp project files)
366 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
367 arguments and switch between different getdown channels
370 <!-- JAL-3141 -->Backup files created when saving Jalview project
375 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
376 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
378 <!-- JAL-2620 -->Alternative genetic code tables for
379 'Translate as cDNA'</li>
381 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
382 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
385 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
386 implementation that allows updates) used for Sequence Feature collections</li>
388 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
389 features can be filtered and shaded according to any
390 associated attributes (e.g. variant attributes from VCF
391 file, or key-value pairs imported from column 9 of GFF
395 <!-- JAL-2879 -->Feature Attributes and shading schemes
396 stored and restored from Jalview Projects
399 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
400 recognise variant features
403 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
404 sequences (also coloured red by default)
407 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
411 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
412 algorithm (Z-sort/transparency and filter aware)
415 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
421 <!-- JAL-3205 -->Symmetric score matrices for faster
422 tree and PCA calculations
424 <li><strong>Principal Components Analysis Viewer</strong>
427 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
428 and Viewer state saved in Jalview Project
430 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
433 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
437 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
442 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
444 <li><strong>Speed and Efficiency</strong>
447 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
448 multiple groups when working with large alignments
451 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
455 <li><strong>User Interface</strong>
458 <!-- JAL-2933 -->Finder panel remembers last position in each
462 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
463 what is shown)<br />Only visible regions of alignment are shown by
464 default (can be changed in user preferences)
467 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
468 to the Overwrite Dialog
471 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
475 <!-- JAL-1244 -->Status bar shows bounds when dragging a
476 selection region, and gap count when inserting or deleting gaps
479 <!-- JAL-3132 -->Status bar updates over sequence and annotation
483 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
487 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
491 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
494 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
498 <!-- JAL-3181 -->Consistent ordering of links in sequence id
502 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
504 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
508 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
509 <li><strong>Java 11 Support (not yet on general release)</strong>
512 <!-- -->OSX GUI integrations for App menu's 'About' entry and
517 <em>Deprecations</em>
519 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
520 capabilities removed from the Jalview Desktop
522 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
523 unmarshalling has been replaced by JAXB for Jalview projects
524 and XML based data retrieval clients</li>
525 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
526 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
527 </ul> <em>Documentation</em>
529 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
530 not supported in EPS figure export
532 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
533 </ul> <em>Development and Release Processes</em>
536 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
539 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
541 <!-- JAL-3225 -->Eclipse project configuration managed with
545 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
546 Bamboo continuous integration for unattended Test Suite
550 <!-- JAL-2864 -->Memory test suite to detect leaks in common
554 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
558 <!-- JAL-3248 -->Developer documentation migrated to
559 markdown (with HTML rendering)
562 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
565 <!-- JAL-3289 -->New URLs for publishing development
570 <td align="left" valign="top">
573 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
576 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
577 superposition in Jmol fail on Windows
580 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
581 structures for sequences with lots of PDB structures
584 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
588 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
589 project involving multiple views
592 <!-- JAL-3164 -->Overview for complementary view in a linked
593 CDS/Protein alignment is not updated when Hide Columns by
594 Annotation dialog hides columns
597 <!-- JAL-3158 -->Selection highlighting in the complement of a
598 CDS/Protein alignment stops working after making a selection in
599 one view, then making another selection in the other view
602 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
606 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
607 Settings and Jalview Preferences panels
610 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
611 overview with large alignments
614 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
615 region if columns were selected by dragging right-to-left and the
616 mouse moved to the left of the first column
619 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
620 hidden column marker via scale popup menu
623 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
624 doesn't tell users the invalid URL
627 <!-- JAL-2816 -->Tooltips displayed for features filtered by
631 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
632 show cross references or Fetch Database References are shown in
636 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
637 peptide sequence (computed variant shown as p.Res.null)
640 <!-- JAL-2060 -->'Graduated colour' option not offered for
641 manually created features (where feature score is Float.NaN)
644 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
645 when columns are hidden
648 <!-- JAL-3082 -->Regular expression error for '(' in Select
649 Columns by Annotation description
652 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
653 out of Scale or Annotation Panel
656 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
660 <!-- JAL-3074 -->Left/right drag in annotation can scroll
664 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
668 <!-- JAL-3002 -->Column display is out by one after Page Down,
669 Page Up in wrapped mode
672 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
675 <!-- JAL-2932 -->Finder searches in minimised alignments
678 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
679 on opening an alignment
682 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
686 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
687 different groups in the alignment are selected
690 <!-- JAL-2717 -->Internationalised colour scheme names not shown
694 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
698 <!-- JAL-3125 -->Value input for graduated feature colour
699 threshold gets 'unrounded'
702 <!-- JAL-2982 -->PCA image export doesn't respect background
706 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
709 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
712 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
716 <!-- JAL-2964 -->Associate Tree with All Views not restored from
720 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
721 shown in complementary view
724 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
725 without normalisation
728 <!-- JAL-3021 -->Sequence Details report should open positioned at top
732 <!-- JAL-914 -->Help page can be opened twice
735 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
737 </ul> <em>Editing</em>
740 <!-- JAL-2822 -->Start and End should be updated when sequence
741 data at beginning or end of alignment added/removed via 'Edit'
745 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
746 relocate sequence features correctly when start of sequence is
747 removed (Known defect since 2.10)
750 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
751 dialog corrupts dataset sequence
754 <!-- JAL-868 -->Structure colours not updated when associated tree
755 repartitions the alignment view (Regression in 2.10.5)
757 </ul> <em>Datamodel</em>
760 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
761 sequence's End is greater than its length
763 </ul> <em>Bugs fixed for Java 11 Support (not yet on
764 general release)</em>
767 <!-- JAL-3288 -->Menus work properly in split-screen
769 </ul> <em>New Known Defects</em>
772 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
775 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
776 regions of protein alignment.
779 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
780 is restored from a Jalview 2.11 project
783 <!-- JAL-3213 -->Alignment panel height can be too small after
787 <!-- JAL-3240 -->Display is incorrect after removing gapped
788 columns within hidden columns
791 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
792 window after dragging left to select columns to left of visible
796 <!-- JAL-2876 -->Features coloured according to their description
797 string and thresholded by score in earlier versions of Jalview are
798 not shown as thresholded features in 2.11. To workaround please
799 create a Score filter instead.
802 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
804 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
807 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
808 alignments with multiple views can close views unexpectedly
811 <em>Java 11 Specific defects</em>
814 <!-- JAL-3235 -->Jalview Properties file is not sorted
815 alphabetically when saved
821 <td width="60" nowrap>
823 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
826 <td><div align="left">
830 <!-- JAL-3101 -->Default memory for Jalview webstart and
831 InstallAnywhere increased to 1G.
834 <!-- JAL-247 -->Hidden sequence markers and representative
835 sequence bolding included when exporting alignment as EPS,
836 SVG, PNG or HTML. <em>Display is configured via the
837 Format menu, or for command-line use via a Jalview
838 properties file.</em>
841 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
842 API and sequence data now imported as JSON.
845 <!-- JAL-3065 -->Change in recommended way of starting
846 Jalview via a Java command line: add jars in lib directory
847 to CLASSPATH, rather than via the deprecated java.ext.dirs
854 <!-- JAL-3047 -->Support added to execute test suite
855 instrumented with <a href="http://openclover.org/">Open
860 <td><div align="left">
864 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
865 row shown in Feredoxin Structure alignment view of example
869 <!-- JAL-2854 -->Annotation obscures sequences if lots of
870 annotation displayed.
873 <!-- JAL-3107 -->Group conservation/consensus not shown
874 for newly created group when 'Apply to all groups'
878 <!-- JAL-3087 -->Corrupted display when switching to
879 wrapped mode when sequence panel's vertical scrollbar is
883 <!-- JAL-3003 -->Alignment is black in exported EPS file
884 when sequences are selected in exported view.</em>
887 <!-- JAL-3059 -->Groups with different coloured borders
888 aren't rendered with correct colour.
891 <!-- JAL-3092 -->Jalview could hang when importing certain
892 types of knotted RNA secondary structure.
895 <!-- JAL-3095 -->Sequence highlight and selection in
896 trimmed VARNA 2D structure is incorrect for sequences that
900 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
901 annotation when columns are inserted into an alignment,
902 and when exporting as Stockholm flatfile.
905 <!-- JAL-3053 -->Jalview annotation rows containing upper
906 and lower-case 'E' and 'H' do not automatically get
907 treated as RNA secondary structure.
910 <!-- JAL-3106 -->.jvp should be used as default extension
911 (not .jar) when saving a Jalview project file.
914 <!-- JAL-3105 -->Mac Users: closing a window correctly
915 transfers focus to previous window on OSX
918 <em>Java 10 Issues Resolved</em>
921 <!-- JAL-2988 -->OSX - Can't save new files via the File
922 or export menus by typing in a name into the Save dialog
926 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
927 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
928 'look and feel' which has improved compatibility with the
929 latest version of OSX.
936 <td width="60" nowrap>
938 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
939 <em>7/06/2018</em></strong>
942 <td><div align="left">
946 <!-- JAL-2920 -->Use HGVS nomenclature for variant
947 annotation retrieved from Uniprot
950 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
951 onto the Jalview Desktop
955 <td><div align="left">
959 <!-- JAL-3017 -->Cannot import features with multiple
960 variant elements (blocks import of some Uniprot records)
963 <!-- JAL-2997 -->Clustal files with sequence positions in
964 right-hand column parsed correctly
967 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
968 not alignment area in exported graphic
971 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
972 window has input focus
975 <!-- JAL-2992 -->Annotation panel set too high when
976 annotation added to view (Windows)
979 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
980 network connectivity is poor
983 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
984 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
985 the currently open URL and links from a page viewed in
986 Firefox or Chrome on Windows is now fully supported. If
987 you are using Edge, only links in the page can be
988 dragged, and with Internet Explorer, only the currently
989 open URL in the browser can be dropped onto Jalview.</em>
992 <em>New Known Defects</em>
994 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
999 <td width="60" nowrap>
1000 <div align="center">
1001 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1004 <td><div align="left">
1008 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1009 for disabling automatic superposition of multiple
1010 structures and open structures in existing views
1013 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1014 ID and annotation area margins can be click-dragged to
1018 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1022 <!-- JAL-2759 -->Improved performance for large alignments
1023 and lots of hidden columns
1026 <!-- JAL-2593 -->Improved performance when rendering lots
1027 of features (particularly when transparency is disabled)
1030 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1031 exchange of Jalview features and Chimera attributes made
1037 <td><div align="left">
1040 <!-- JAL-2899 -->Structure and Overview aren't updated
1041 when Colour By Annotation threshold slider is adjusted
1044 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1045 overlapping alignment panel
1048 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1052 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1053 improved: CDS not handled correctly if transcript has no
1057 <!-- JAL-2321 -->Secondary structure and temperature
1058 factor annotation not added to sequence when local PDB
1059 file associated with it by drag'n'drop or structure
1063 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1064 dialog doesn't import PDB files dropped on an alignment
1067 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1068 scroll bar doesn't work for some CDS/Protein views
1071 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1072 Java 1.8u153 onwards and Java 1.9u4+.
1075 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1076 columns in annotation row
1079 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1080 honored in batch mode
1083 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1084 for structures added to existing Jmol view
1087 <!-- JAL-2223 -->'View Mappings' includes duplicate
1088 entries after importing project with multiple views
1091 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1092 protein sequences via SIFTS from associated PDB entries
1093 with negative residue numbers or missing residues fails
1096 <!-- JAL-2952 -->Exception when shading sequence with negative
1097 Temperature Factor values from annotated PDB files (e.g.
1098 as generated by CONSURF)
1101 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1102 tooltip doesn't include a text description of mutation
1105 <!-- JAL-2922 -->Invert displayed features very slow when
1106 structure and/or overview windows are also shown
1109 <!-- JAL-2954 -->Selecting columns from highlighted regions
1110 very slow for alignments with large numbers of sequences
1113 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1114 with 'StringIndexOutOfBounds'
1117 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1118 platforms running Java 10
1121 <!-- JAL-2960 -->Adding a structure to existing structure
1122 view appears to do nothing because the view is hidden behind the alignment view
1128 <!-- JAL-2926 -->Copy consensus sequence option in applet
1129 should copy the group consensus when popup is opened on it
1135 <!-- JAL-2913 -->Fixed ID width preference is not respected
1138 <em>New Known Defects</em>
1141 <!-- JAL-2973 --> Exceptions occasionally raised when
1142 editing a large alignment and overview is displayed
1145 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1146 repeatedly after a series of edits even when the overview
1147 is no longer reflecting updates
1150 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1151 structures for protein subsequence (if 'Trim Retrieved
1152 Sequences' enabled) or Ensembl isoforms (Workaround in
1153 2.10.4 is to fail back to N&W mapping)
1156 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1157 option gives blank output
1164 <td width="60" nowrap>
1165 <div align="center">
1166 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1169 <td><div align="left">
1170 <ul><li>Updated Certum Codesigning Certificate
1171 (Valid till 30th November 2018)</li></ul></div></td>
1172 <td><div align="left">
1173 <em>Desktop</em><ul>
1175 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1176 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1177 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1178 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1179 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1180 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1181 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1187 <td width="60" nowrap>
1188 <div align="center">
1189 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1192 <td><div align="left">
1196 <!-- JAL-2446 -->Faster and more efficient management and
1197 rendering of sequence features
1200 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1201 429 rate limit request hander
1204 <!-- JAL-2773 -->Structure views don't get updated unless
1205 their colours have changed
1208 <!-- JAL-2495 -->All linked sequences are highlighted for
1209 a structure mousover (Jmol) or selection (Chimera)
1212 <!-- JAL-2790 -->'Cancel' button in progress bar for
1213 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1216 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1217 view from Ensembl locus cross-references
1220 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1224 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1225 feature can be disabled
1228 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1229 PDB easier retrieval of sequences for lists of IDs
1232 <!-- JAL-2758 -->Short names for sequences retrieved from
1238 <li>Groovy interpreter updated to 2.4.12</li>
1239 <li>Example groovy script for generating a matrix of
1240 percent identity scores for current alignment.</li>
1242 <em>Testing and Deployment</em>
1245 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1249 <td><div align="left">
1253 <!-- JAL-2643 -->Pressing tab after updating the colour
1254 threshold text field doesn't trigger an update to the
1258 <!-- JAL-2682 -->Race condition when parsing sequence ID
1262 <!-- JAL-2608 -->Overview windows are also closed when
1263 alignment window is closed
1266 <!-- JAL-2548 -->Export of features doesn't always respect
1270 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1271 takes a long time in Cursor mode
1277 <!-- JAL-2777 -->Structures with whitespace chainCode
1278 cannot be viewed in Chimera
1281 <!-- JAL-2728 -->Protein annotation panel too high in
1285 <!-- JAL-2757 -->Can't edit the query after the server
1286 error warning icon is shown in Uniprot and PDB Free Text
1290 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1293 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1296 <!-- JAL-2739 -->Hidden column marker in last column not
1297 rendered when switching back from Wrapped to normal view
1300 <!-- JAL-2768 -->Annotation display corrupted when
1301 scrolling right in unwapped alignment view
1304 <!-- JAL-2542 -->Existing features on subsequence
1305 incorrectly relocated when full sequence retrieved from
1309 <!-- JAL-2733 -->Last reported memory still shown when
1310 Desktop->Show Memory is unticked (OSX only)
1313 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1314 features of same type and group to be selected for
1318 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1319 alignments when hidden columns are present
1322 <!-- JAL-2392 -->Jalview freezes when loading and
1323 displaying several structures
1326 <!-- JAL-2732 -->Black outlines left after resizing or
1330 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1331 within the Jalview desktop on OSX
1334 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1335 when in wrapped alignment mode
1338 <!-- JAL-2636 -->Scale mark not shown when close to right
1339 hand end of alignment
1342 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1343 each selected sequence do not have correct start/end
1347 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1348 after canceling the Alignment Window's Font dialog
1351 <!-- JAL-2036 -->Show cross-references not enabled after
1352 restoring project until a new view is created
1355 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1356 URL links appears when only default EMBL-EBI link is
1357 configured (since 2.10.2b2)
1360 <!-- JAL-2775 -->Overview redraws whole window when box
1361 position is adjusted
1364 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1365 in a multi-chain structure when viewing alignment
1366 involving more than one chain (since 2.10)
1369 <!-- JAL-2811 -->Double residue highlights in cursor mode
1370 if new selection moves alignment window
1373 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1374 arrow key in cursor mode to pass hidden column marker
1377 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1378 that produces correctly annotated transcripts and products
1381 <!-- JAL-2776 -->Toggling a feature group after first time
1382 doesn't update associated structure view
1385 <em>Applet</em><br />
1388 <!-- JAL-2687 -->Concurrent modification exception when
1389 closing alignment panel
1392 <em>BioJSON</em><br />
1395 <!-- JAL-2546 -->BioJSON export does not preserve
1396 non-positional features
1399 <em>New Known Issues</em>
1402 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1403 sequence features correctly (for many previous versions of
1407 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1408 using cursor in wrapped panel other than top
1411 <!-- JAL-2791 -->Select columns containing feature ignores
1412 graduated colour threshold
1415 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1416 always preserve numbering and sequence features
1419 <em>Known Java 9 Issues</em>
1422 <!-- JAL-2902 -->Groovy Console very slow to open and is
1423 not responsive when entering characters (Webstart, Java
1430 <td width="60" nowrap>
1431 <div align="center">
1432 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1433 <em>2/10/2017</em></strong>
1436 <td><div align="left">
1437 <em>New features in Jalview Desktop</em>
1440 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1442 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1446 <td><div align="left">
1450 <td width="60" nowrap>
1451 <div align="center">
1452 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1453 <em>7/9/2017</em></strong>
1456 <td><div align="left">
1460 <!-- JAL-2588 -->Show gaps in overview window by colouring
1461 in grey (sequences used to be coloured grey, and gaps were
1465 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1469 <!-- JAL-2587 -->Overview updates immediately on increase
1470 in size and progress bar shown as higher resolution
1471 overview is recalculated
1476 <td><div align="left">
1480 <!-- JAL-2664 -->Overview window redraws every hidden
1481 column region row by row
1484 <!-- JAL-2681 -->duplicate protein sequences shown after
1485 retrieving Ensembl crossrefs for sequences from Uniprot
1488 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1489 format setting is unticked
1492 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1493 if group has show boxes format setting unticked
1496 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1497 autoscrolling whilst dragging current selection group to
1498 include sequences and columns not currently displayed
1501 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1502 assemblies are imported via CIF file
1505 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1506 displayed when threshold or conservation colouring is also
1510 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1514 <!-- JAL-2673 -->Jalview continues to scroll after
1515 dragging a selected region off the visible region of the
1519 <!-- JAL-2724 -->Cannot apply annotation based
1520 colourscheme to all groups in a view
1523 <!-- JAL-2511 -->IDs don't line up with sequences
1524 initially after font size change using the Font chooser or
1531 <td width="60" nowrap>
1532 <div align="center">
1533 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1536 <td><div align="left">
1537 <em>Calculations</em>
1541 <!-- JAL-1933 -->Occupancy annotation row shows number of
1542 ungapped positions in each column of the alignment.
1545 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1546 a calculation dialog box
1549 <!-- JAL-2379 -->Revised implementation of PCA for speed
1550 and memory efficiency (~30x faster)
1553 <!-- JAL-2403 -->Revised implementation of sequence
1554 similarity scores as used by Tree, PCA, Shading Consensus
1555 and other calculations
1558 <!-- JAL-2416 -->Score matrices are stored as resource
1559 files within the Jalview codebase
1562 <!-- JAL-2500 -->Trees computed on Sequence Feature
1563 Similarity may have different topology due to increased
1570 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1571 model for alignments and groups
1574 <!-- JAL-384 -->Custom shading schemes created via groovy
1581 <!-- JAL-2526 -->Efficiency improvements for interacting
1582 with alignment and overview windows
1585 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1589 <!-- JAL-2388 -->Hidden columns and sequences can be
1593 <!-- JAL-2611 -->Click-drag in visible area allows fine
1594 adjustment of visible position
1598 <em>Data import/export</em>
1601 <!-- JAL-2535 -->Posterior probability annotation from
1602 Stockholm files imported as sequence associated annotation
1605 <!-- JAL-2507 -->More robust per-sequence positional
1606 annotation input/output via stockholm flatfile
1609 <!-- JAL-2533 -->Sequence names don't include file
1610 extension when importing structure files without embedded
1611 names or PDB accessions
1614 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1615 format sequence substitution matrices
1618 <em>User Interface</em>
1621 <!-- JAL-2447 --> Experimental Features Checkbox in
1622 Desktop's Tools menu to hide or show untested features in
1626 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1627 via Overview or sequence motif search operations
1630 <!-- JAL-2547 -->Amend sequence features dialog box can be
1631 opened by double clicking gaps within sequence feature
1635 <!-- JAL-1476 -->Status bar message shown when not enough
1636 aligned positions were available to create a 3D structure
1640 <em>3D Structure</em>
1643 <!-- JAL-2430 -->Hidden regions in alignment views are not
1644 coloured in linked structure views
1647 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1648 file-based command exchange
1651 <!-- JAL-2375 -->Structure chooser automatically shows
1652 Cached Structures rather than querying the PDBe if
1653 structures are already available for sequences
1656 <!-- JAL-2520 -->Structures imported via URL are cached in
1657 the Jalview project rather than downloaded again when the
1658 project is reopened.
1661 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1662 to transfer Chimera's structure attributes as Jalview
1663 features, and vice-versa (<strong>Experimental
1667 <em>Web Services</em>
1670 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1673 <!-- JAL-2335 -->Filter non-standard amino acids and
1674 nucleotides when submitting to AACon and other MSA
1678 <!-- JAL-2316, -->URLs for viewing database
1679 cross-references provided by identifiers.org and the
1680 EMBL-EBI's MIRIAM DB
1687 <!-- JAL-2344 -->FileFormatI interface for describing and
1688 identifying file formats (instead of String constants)
1691 <!-- JAL-2228 -->FeatureCounter script refactored for
1692 efficiency when counting all displayed features (not
1693 backwards compatible with 2.10.1)
1696 <em>Example files</em>
1699 <!-- JAL-2631 -->Graduated feature colour style example
1700 included in the example feature file
1703 <em>Documentation</em>
1706 <!-- JAL-2339 -->Release notes reformatted for readability
1707 with the built-in Java help viewer
1710 <!-- JAL-1644 -->Find documentation updated with 'search
1711 sequence description' option
1717 <!-- JAL-2485, -->External service integration tests for
1718 Uniprot REST Free Text Search Client
1721 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1724 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1729 <td><div align="left">
1730 <em>Calculations</em>
1733 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1734 matrix - C->R should be '-3'<br />Old matrix restored
1735 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1737 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1738 Jalview's treatment of gaps in PCA and substitution matrix
1739 based Tree calculations.<br /> <br />In earlier versions
1740 of Jalview, gaps matching gaps were penalised, and gaps
1741 matching non-gaps penalised even more. In the PCA
1742 calculation, gaps were actually treated as non-gaps - so
1743 different costs were applied, which meant Jalview's PCAs
1744 were different to those produced by SeqSpace.<br />Jalview
1745 now treats gaps in the same way as SeqSpace (ie it scores
1746 them as 0). <br /> <br />Enter the following in the
1747 Groovy console to restore pre-2.10.2 behaviour:<br />
1748 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1749 // for 2.10.1 mode <br />
1750 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1751 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1752 these settings will affect all subsequent tree and PCA
1753 calculations (not recommended)</em></li>
1755 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1756 scaling of branch lengths for trees computed using
1757 Sequence Feature Similarity.
1760 <!-- JAL-2377 -->PCA calculation could hang when
1761 generating output report when working with highly
1762 redundant alignments
1765 <!-- JAL-2544 --> Sort by features includes features to
1766 right of selected region when gaps present on right-hand
1770 <em>User Interface</em>
1773 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1774 doesn't reselect a specific sequence's associated
1775 annotation after it was used for colouring a view
1778 <!-- JAL-2419 -->Current selection lost if popup menu
1779 opened on a region of alignment without groups
1782 <!-- JAL-2374 -->Popup menu not always shown for regions
1783 of an alignment with overlapping groups
1786 <!-- JAL-2310 -->Finder double counts if both a sequence's
1787 name and description match
1790 <!-- JAL-2370 -->Hiding column selection containing two
1791 hidden regions results in incorrect hidden regions
1794 <!-- JAL-2386 -->'Apply to all groups' setting when
1795 changing colour does not apply Conservation slider value
1799 <!-- JAL-2373 -->Percentage identity and conservation menu
1800 items do not show a tick or allow shading to be disabled
1803 <!-- JAL-2385 -->Conservation shading or PID threshold
1804 lost when base colourscheme changed if slider not visible
1807 <!-- JAL-2547 -->Sequence features shown in tooltip for
1808 gaps before start of features
1811 <!-- JAL-2623 -->Graduated feature colour threshold not
1812 restored to UI when feature colour is edited
1815 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1816 a time when scrolling vertically in wrapped mode.
1819 <!-- JAL-2630 -->Structure and alignment overview update
1820 as graduate feature colour settings are modified via the
1824 <!-- JAL-2034 -->Overview window doesn't always update
1825 when a group defined on the alignment is resized
1828 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1829 wrapped view result in positional status updates
1833 <!-- JAL-2563 -->Status bar doesn't show position for
1834 ambiguous amino acid and nucleotide symbols
1837 <!-- JAL-2602 -->Copy consensus sequence failed if
1838 alignment included gapped columns
1841 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1842 widgets don't permanently disappear
1845 <!-- JAL-2503 -->Cannot select or filter quantitative
1846 annotation that are shown only as column labels (e.g.
1847 T-Coffee column reliability scores)
1850 <!-- JAL-2594 -->Exception thrown if trying to create a
1851 sequence feature on gaps only
1854 <!-- JAL-2504 -->Features created with 'New feature'
1855 button from a Find inherit previously defined feature type
1856 rather than the Find query string
1859 <!-- JAL-2423 -->incorrect title in output window when
1860 exporting tree calculated in Jalview
1863 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1864 and then revealing them reorders sequences on the
1868 <!-- JAL-964 -->Group panel in sequence feature settings
1869 doesn't update to reflect available set of groups after
1870 interactively adding or modifying features
1873 <!-- JAL-2225 -->Sequence Database chooser unusable on
1877 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1878 only excluded gaps in current sequence and ignored
1885 <!-- JAL-2421 -->Overview window visible region moves
1886 erratically when hidden rows or columns are present
1889 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1890 Structure Viewer's colour menu don't correspond to
1894 <!-- JAL-2405 -->Protein specific colours only offered in
1895 colour and group colour menu for protein alignments
1898 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1899 reflect currently selected view or group's shading
1903 <!-- JAL-2624 -->Feature colour thresholds not respected
1904 when rendered on overview and structures when opacity at
1908 <!-- JAL-2589 -->User defined gap colour not shown in
1909 overview when features overlaid on alignment
1912 <!-- JAL-2567 -->Feature settings for different views not
1913 recovered correctly from Jalview project file
1916 <!-- JAL-2256 -->Feature colours in overview when first opened
1917 (automatically via preferences) are different to the main
1921 <em>Data import/export</em>
1924 <!-- JAL-2576 -->Very large alignments take a long time to
1928 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1929 added after a sequence was imported are not written to
1933 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1934 when importing RNA secondary structure via Stockholm
1937 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1938 not shown in correct direction for simple pseudoknots
1941 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1942 with lightGray or darkGray via features file (but can
1946 <!-- JAL-2383 -->Above PID colour threshold not recovered
1947 when alignment view imported from project
1950 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1951 structure and sequences extracted from structure files
1952 imported via URL and viewed in Jmol
1955 <!-- JAL-2520 -->Structures loaded via URL are saved in
1956 Jalview Projects rather than fetched via URL again when
1957 the project is loaded and the structure viewed
1960 <em>Web Services</em>
1963 <!-- JAL-2519 -->EnsemblGenomes example failing after
1964 release of Ensembl v.88
1967 <!-- JAL-2366 -->Proxy server address and port always
1968 appear enabled in Preferences->Connections
1971 <!-- JAL-2461 -->DAS registry not found exceptions
1972 removed from console output
1975 <!-- JAL-2582 -->Cannot retrieve protein products from
1976 Ensembl by Peptide ID
1979 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1980 created from SIFTs, and spurious 'Couldn't open structure
1981 in Chimera' errors raised after April 2017 update (problem
1982 due to 'null' string rather than empty string used for
1983 residues with no corresponding PDB mapping).
1986 <em>Application UI</em>
1989 <!-- JAL-2361 -->User Defined Colours not added to Colour
1993 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1994 case' residues (button in colourscheme editor debugged and
1995 new documentation and tooltips added)
1998 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1999 doesn't restore group-specific text colour thresholds
2002 <!-- JAL-2243 -->Feature settings panel does not update as
2003 new features are added to alignment
2006 <!-- JAL-2532 -->Cancel in feature settings reverts
2007 changes to feature colours via the Amend features dialog
2010 <!-- JAL-2506 -->Null pointer exception when attempting to
2011 edit graduated feature colour via amend features dialog
2015 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2016 selection menu changes colours of alignment views
2019 <!-- JAL-2426 -->Spurious exceptions in console raised
2020 from alignment calculation workers after alignment has
2024 <!-- JAL-1608 -->Typo in selection popup menu - Create
2025 groups now 'Create Group'
2028 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2029 Create/Undefine group doesn't always work
2032 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2033 shown again after pressing 'Cancel'
2036 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2037 adjusts start position in wrap mode
2040 <!-- JAL-2563 -->Status bar doesn't show positions for
2041 ambiguous amino acids
2044 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2045 CDS/Protein view after CDS sequences added for aligned
2049 <!-- JAL-2592 -->User defined colourschemes called 'User
2050 Defined' don't appear in Colours menu
2056 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2057 score models doesn't always result in an updated PCA plot
2060 <!-- JAL-2442 -->Features not rendered as transparent on
2061 overview or linked structure view
2064 <!-- JAL-2372 -->Colour group by conservation doesn't
2068 <!-- JAL-2517 -->Hitting Cancel after applying
2069 user-defined colourscheme doesn't restore original
2076 <!-- JAL-2314 -->Unit test failure:
2077 jalview.ws.jabaws.RNAStructExportImport setup fails
2080 <!-- JAL-2307 -->Unit test failure:
2081 jalview.ws.sifts.SiftsClientTest due to compatibility
2082 problems with deep array comparison equality asserts in
2083 successive versions of TestNG
2086 <!-- JAL-2479 -->Relocated StructureChooserTest and
2087 ParameterUtilsTest Unit tests to Network suite
2090 <em>New Known Issues</em>
2093 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2094 phase after a sequence motif find operation
2097 <!-- JAL-2550 -->Importing annotation file with rows
2098 containing just upper and lower case letters are
2099 interpreted as WUSS RNA secondary structure symbols
2102 <!-- JAL-2590 -->Cannot load and display Newick trees
2103 reliably from eggnog Ortholog database
2106 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2107 containing features of type Highlight' when 'B' is pressed
2108 to mark columns containing highlighted regions.
2111 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2112 doesn't always add secondary structure annotation.
2117 <td width="60" nowrap>
2118 <div align="center">
2119 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2122 <td><div align="left">
2126 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2127 for all consensus calculations
2130 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2133 <li>Updated Jalview's Certum code signing certificate
2136 <em>Application</em>
2139 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2140 set of database cross-references, sorted alphabetically
2143 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2144 from database cross references. Users with custom links
2145 will receive a <a href="webServices/urllinks.html#warning">warning
2146 dialog</a> asking them to update their preferences.
2149 <!-- JAL-2287-->Cancel button and escape listener on
2150 dialog warning user about disconnecting Jalview from a
2154 <!-- JAL-2320-->Jalview's Chimera control window closes if
2155 the Chimera it is connected to is shut down
2158 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2159 columns menu item to mark columns containing highlighted
2160 regions (e.g. from structure selections or results of a
2164 <!-- JAL-2284-->Command line option for batch-generation
2165 of HTML pages rendering alignment data with the BioJS
2175 <!-- JAL-2286 -->Columns with more than one modal residue
2176 are not coloured or thresholded according to percent
2177 identity (first observed in Jalview 2.8.2)
2180 <!-- JAL-2301 -->Threonine incorrectly reported as not
2184 <!-- JAL-2318 -->Updates to documentation pages (above PID
2185 threshold, amino acid properties)
2188 <!-- JAL-2292 -->Lower case residues in sequences are not
2189 reported as mapped to residues in a structure file in the
2193 <!--JAL-2324 -->Identical features with non-numeric scores
2194 could be added multiple times to a sequence
2197 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2198 bond features shown as two highlighted residues rather
2199 than a range in linked structure views, and treated
2200 correctly when selecting and computing trees from features
2203 <!-- JAL-2281-->Custom URL links for database
2204 cross-references are matched to database name regardless
2209 <em>Application</em>
2212 <!-- JAL-2282-->Custom URL links for specific database
2213 names without regular expressions also offer links from
2217 <!-- JAL-2315-->Removing a single configured link in the
2218 URL links pane in Connections preferences doesn't actually
2219 update Jalview configuration
2222 <!-- JAL-2272-->CTRL-Click on a selected region to open
2223 the alignment area popup menu doesn't work on El-Capitan
2226 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2227 files with similarly named sequences if dropped onto the
2231 <!-- JAL-2312 -->Additional mappings are shown for PDB
2232 entries where more chains exist in the PDB accession than
2233 are reported in the SIFTS file
2236 <!-- JAL-2317-->Certain structures do not get mapped to
2237 the structure view when displayed with Chimera
2240 <!-- JAL-2317-->No chains shown in the Chimera view
2241 panel's View->Show Chains submenu
2244 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2245 work for wrapped alignment views
2248 <!--JAL-2197 -->Rename UI components for running JPred
2249 predictions from 'JNet' to 'JPred'
2252 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2253 corrupted when annotation panel vertical scroll is not at
2254 first annotation row
2257 <!--JAL-2332 -->Attempting to view structure for Hen
2258 lysozyme results in a PDB Client error dialog box
2261 <!-- JAL-2319 -->Structure View's mapping report switched
2262 ranges for PDB and sequence for SIFTS
2265 SIFTS 'Not_Observed' residues mapped to non-existant
2269 <!-- <em>New Known Issues</em>
2276 <td width="60" nowrap>
2277 <div align="center">
2278 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2279 <em>25/10/2016</em></strong>
2282 <td><em>Application</em>
2284 <li>3D Structure chooser opens with 'Cached structures'
2285 view if structures already loaded</li>
2286 <li>Progress bar reports models as they are loaded to
2287 structure views</li>
2293 <li>Colour by conservation always enabled and no tick
2294 shown in menu when BLOSUM or PID shading applied</li>
2295 <li>FER1_ARATH and FER2_ARATH labels were switched in
2296 example sequences/projects/trees</li>
2298 <em>Application</em>
2300 <li>Jalview projects with views of local PDB structure
2301 files saved on Windows cannot be opened on OSX</li>
2302 <li>Multiple structure views can be opened and superposed
2303 without timeout for structures with multiple models or
2304 multiple sequences in alignment</li>
2305 <li>Cannot import or associated local PDB files without a
2306 PDB ID HEADER line</li>
2307 <li>RMSD is not output in Jmol console when superposition
2309 <li>Drag and drop of URL from Browser fails for Linux and
2310 OSX versions earlier than El Capitan</li>
2311 <li>ENA client ignores invalid content from ENA server</li>
2312 <li>Exceptions are not raised in console when ENA client
2313 attempts to fetch non-existent IDs via Fetch DB Refs UI
2315 <li>Exceptions are not raised in console when a new view
2316 is created on the alignment</li>
2317 <li>OSX right-click fixed for group selections: CMD-click
2318 to insert/remove gaps in groups and CTRL-click to open group
2321 <em>Build and deployment</em>
2323 <li>URL link checker now copes with multi-line anchor
2326 <em>New Known Issues</em>
2328 <li>Drag and drop from URL links in browsers do not work
2335 <td width="60" nowrap>
2336 <div align="center">
2337 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2340 <td><em>General</em>
2343 <!-- JAL-2124 -->Updated Spanish translations.
2346 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2347 for importing structure data to Jalview. Enables mmCIF and
2351 <!-- JAL-192 --->Alignment ruler shows positions relative to
2355 <!-- JAL-2202 -->Position/residue shown in status bar when
2356 mousing over sequence associated annotation
2359 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2363 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2364 '()', canonical '[]' and invalid '{}' base pair populations
2368 <!-- JAL-2092 -->Feature settings popup menu options for
2369 showing or hiding columns containing a feature
2372 <!-- JAL-1557 -->Edit selected group by double clicking on
2373 group and sequence associated annotation labels
2376 <!-- JAL-2236 -->Sequence name added to annotation label in
2377 select/hide columns by annotation and colour by annotation
2381 </ul> <em>Application</em>
2384 <!-- JAL-2050-->Automatically hide introns when opening a
2385 gene/transcript view
2388 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2392 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2393 structure mappings with the EMBL-EBI PDBe SIFTS database
2396 <!-- JAL-2079 -->Updated download sites used for Rfam and
2397 Pfam sources to xfam.org
2400 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2403 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2404 over sequences in Jalview
2407 <!-- JAL-2027-->Support for reverse-complement coding
2408 regions in ENA and EMBL
2411 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2412 for record retrieval via ENA rest API
2415 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2419 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2420 groovy script execution
2423 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2424 alignment window's Calculate menu
2427 <!-- JAL-1812 -->Allow groovy scripts that call
2428 Jalview.getAlignFrames() to run in headless mode
2431 <!-- JAL-2068 -->Support for creating new alignment
2432 calculation workers from groovy scripts
2435 <!-- JAL-1369 --->Store/restore reference sequence in
2439 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2440 associations are now saved/restored from project
2443 <!-- JAL-1993 -->Database selection dialog always shown
2444 before sequence fetcher is opened
2447 <!-- JAL-2183 -->Double click on an entry in Jalview's
2448 database chooser opens a sequence fetcher
2451 <!-- JAL-1563 -->Free-text search client for UniProt using
2452 the UniProt REST API
2455 <!-- JAL-2168 -->-nonews command line parameter to prevent
2456 the news reader opening
2459 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2460 querying stored in preferences
2463 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2467 <!-- JAL-1977-->Tooltips shown on database chooser
2470 <!-- JAL-391 -->Reverse complement function in calculate
2471 menu for nucleotide sequences
2474 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2475 and feature counts preserves alignment ordering (and
2476 debugged for complex feature sets).
2479 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2480 viewing structures with Jalview 2.10
2483 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2484 genome, transcript CCDS and gene ids via the Ensembl and
2485 Ensembl Genomes REST API
2488 <!-- JAL-2049 -->Protein sequence variant annotation
2489 computed for 'sequence_variant' annotation on CDS regions
2493 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2497 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2498 Ref Fetcher fails to match, or otherwise updates sequence
2499 data from external database records.
2502 <!-- JAL-2154 -->Revised Jalview Project format for
2503 efficient recovery of sequence coding and alignment
2504 annotation relationships.
2506 </ul> <!-- <em>Applet</em>
2517 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2521 <!-- JAL-2018-->Export features in Jalview format (again)
2522 includes graduated colourschemes
2525 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2526 working with big alignments and lots of hidden columns
2529 <!-- JAL-2053-->Hidden column markers not always rendered
2530 at right of alignment window
2533 <!-- JAL-2067 -->Tidied up links in help file table of
2537 <!-- JAL-2072 -->Feature based tree calculation not shown
2541 <!-- JAL-2075 -->Hidden columns ignored during feature
2542 based tree calculation
2545 <!-- JAL-2065 -->Alignment view stops updating when show
2546 unconserved enabled for group on alignment
2549 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2553 <!-- JAL-2146 -->Alignment column in status incorrectly
2554 shown as "Sequence position" when mousing over
2558 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2559 hidden columns present
2562 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2563 user created annotation added to alignment
2566 <!-- JAL-1841 -->RNA Structure consensus only computed for
2567 '()' base pair annotation
2570 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2571 in zero scores for all base pairs in RNA Structure
2575 <!-- JAL-2174-->Extend selection with columns containing
2579 <!-- JAL-2275 -->Pfam format writer puts extra space at
2580 beginning of sequence
2583 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2587 <!-- JAL-2238 -->Cannot create groups on an alignment from
2588 from a tree when t-coffee scores are shown
2591 <!-- JAL-1836,1967 -->Cannot import and view PDB
2592 structures with chains containing negative resnums (4q4h)
2595 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2599 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2600 to Clustal, PIR and PileUp output
2603 <!-- JAL-2008 -->Reordering sequence features that are
2604 not visible causes alignment window to repaint
2607 <!-- JAL-2006 -->Threshold sliders don't work in
2608 graduated colour and colour by annotation row for e-value
2609 scores associated with features and annotation rows
2612 <!-- JAL-1797 -->amino acid physicochemical conservation
2613 calculation should be case independent
2616 <!-- JAL-2173 -->Remove annotation also updates hidden
2620 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2621 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2622 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2625 <!-- JAL-2065 -->Null pointer exceptions and redraw
2626 problems when reference sequence defined and 'show
2627 non-conserved' enabled
2630 <!-- JAL-1306 -->Quality and Conservation are now shown on
2631 load even when Consensus calculation is disabled
2634 <!-- JAL-1932 -->Remove right on penultimate column of
2635 alignment does nothing
2638 <em>Application</em>
2641 <!-- JAL-1552-->URLs and links can't be imported by
2642 drag'n'drop on OSX when launched via webstart (note - not
2643 yet fixed for El Capitan)
2646 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2647 output when running on non-gb/us i18n platforms
2650 <!-- JAL-1944 -->Error thrown when exporting a view with
2651 hidden sequences as flat-file alignment
2654 <!-- JAL-2030-->InstallAnywhere distribution fails when
2658 <!-- JAL-2080-->Jalview very slow to launch via webstart
2659 (also hotfix for 2.9.0b2)
2662 <!-- JAL-2085 -->Cannot save project when view has a
2663 reference sequence defined
2666 <!-- JAL-1011 -->Columns are suddenly selected in other
2667 alignments and views when revealing hidden columns
2670 <!-- JAL-1989 -->Hide columns not mirrored in complement
2671 view in a cDNA/Protein splitframe
2674 <!-- JAL-1369 -->Cannot save/restore representative
2675 sequence from project when only one sequence is
2679 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2680 in Structure Chooser
2683 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2684 structure consensus didn't refresh annotation panel
2687 <!-- JAL-1962 -->View mapping in structure view shows
2688 mappings between sequence and all chains in a PDB file
2691 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2692 dialogs format columns correctly, don't display array
2693 data, sort columns according to type
2696 <!-- JAL-1975 -->Export complete shown after destination
2697 file chooser is cancelled during an image export
2700 <!-- JAL-2025 -->Error when querying PDB Service with
2701 sequence name containing special characters
2704 <!-- JAL-2024 -->Manual PDB structure querying should be
2708 <!-- JAL-2104 -->Large tooltips with broken HTML
2709 formatting don't wrap
2712 <!-- JAL-1128 -->Figures exported from wrapped view are
2713 truncated so L looks like I in consensus annotation
2716 <!-- JAL-2003 -->Export features should only export the
2717 currently displayed features for the current selection or
2721 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2722 after fetching cross-references, and restoring from
2726 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2727 followed in the structure viewer
2730 <!-- JAL-2163 -->Titles for individual alignments in
2731 splitframe not restored from project
2734 <!-- JAL-2145 -->missing autocalculated annotation at
2735 trailing end of protein alignment in transcript/product
2736 splitview when pad-gaps not enabled by default
2739 <!-- JAL-1797 -->amino acid physicochemical conservation
2743 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2744 article has been read (reopened issue due to
2745 internationalisation problems)
2748 <!-- JAL-1960 -->Only offer PDB structures in structure
2749 viewer based on sequence name, PDB and UniProt
2754 <!-- JAL-1976 -->No progress bar shown during export of
2758 <!-- JAL-2213 -->Structures not always superimposed after
2759 multiple structures are shown for one or more sequences.
2762 <!-- JAL-1370 -->Reference sequence characters should not
2763 be replaced with '.' when 'Show unconserved' format option
2767 <!-- JAL-1823 -->Cannot specify chain code when entering
2768 specific PDB id for sequence
2771 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2772 'Export hidden sequences' is enabled, but 'export hidden
2773 columns' is disabled.
2776 <!--JAL-2026-->Best Quality option in structure chooser
2777 selects lowest rather than highest resolution structures
2781 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2782 to sequence mapping in 'View Mappings' report
2785 <!-- JAL-2284 -->Unable to read old Jalview projects that
2786 contain non-XML data added after Jalvew wrote project.
2789 <!-- JAL-2118 -->Newly created annotation row reorders
2790 after clicking on it to create new annotation for a
2794 <!-- JAL-1980 -->Null Pointer Exception raised when
2795 pressing Add on an orphaned cut'n'paste window.
2797 <!-- may exclude, this is an external service stability issue JAL-1941
2798 -- > RNA 3D structure not added via DSSR service</li> -->
2803 <!-- JAL-2151 -->Incorrect columns are selected when
2804 hidden columns present before start of sequence
2807 <!-- JAL-1986 -->Missing dependencies on applet pages
2811 <!-- JAL-1947 -->Overview pixel size changes when
2812 sequences are hidden in applet
2815 <!-- JAL-1996 -->Updated instructions for applet
2816 deployment on examples pages.
2823 <td width="60" nowrap>
2824 <div align="center">
2825 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2826 <em>16/10/2015</em></strong>
2829 <td><em>General</em>
2831 <li>Time stamps for signed Jalview application and applet
2836 <em>Application</em>
2838 <li>Duplicate group consensus and conservation rows
2839 shown when tree is partitioned</li>
2840 <li>Erratic behaviour when tree partitions made with
2841 multiple cDNA/Protein split views</li>
2847 <td width="60" nowrap>
2848 <div align="center">
2849 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2850 <em>8/10/2015</em></strong>
2853 <td><em>General</em>
2855 <li>Updated Spanish translations of localized text for
2857 </ul> <em>Application</em>
2859 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2860 <li>Signed OSX InstallAnywhere installer<br></li>
2861 <li>Support for per-sequence based annotations in BioJSON</li>
2862 </ul> <em>Applet</em>
2864 <li>Split frame example added to applet examples page</li>
2865 </ul> <em>Build and Deployment</em>
2868 <!-- JAL-1888 -->New ant target for running Jalview's test
2876 <li>Mapping of cDNA to protein in split frames
2877 incorrect when sequence start > 1</li>
2878 <li>Broken images in filter column by annotation dialog
2880 <li>Feature colours not parsed from features file</li>
2881 <li>Exceptions and incomplete link URLs recovered when
2882 loading a features file containing HTML tags in feature
2886 <em>Application</em>
2888 <li>Annotations corrupted after BioJS export and
2890 <li>Incorrect sequence limits after Fetch DB References
2891 with 'trim retrieved sequences'</li>
2892 <li>Incorrect warning about deleting all data when
2893 deleting selected columns</li>
2894 <li>Patch to build system for shipping properly signed
2895 JNLP templates for webstart launch</li>
2896 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2897 unreleased structures for download or viewing</li>
2898 <li>Tab/space/return keystroke operation of EMBL-PDBe
2899 fetcher/viewer dialogs works correctly</li>
2900 <li>Disabled 'minimise' button on Jalview windows
2901 running on OSX to workaround redraw hang bug</li>
2902 <li>Split cDNA/Protein view position and geometry not
2903 recovered from jalview project</li>
2904 <li>Initial enabled/disabled state of annotation menu
2905 sorter 'show autocalculated first/last' corresponds to
2907 <li>Restoring of Clustal, RNA Helices and T-Coffee
2908 color schemes from BioJSON</li>
2912 <li>Reorder sequences mirrored in cDNA/Protein split
2914 <li>Applet with Jmol examples not loading correctly</li>
2920 <td><div align="center">
2921 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2923 <td><em>General</em>
2925 <li>Linked visualisation and analysis of DNA and Protein
2928 <li>Translated cDNA alignments shown as split protein
2929 and DNA alignment views</li>
2930 <li>Codon consensus annotation for linked protein and
2931 cDNA alignment views</li>
2932 <li>Link cDNA or Protein product sequences by loading
2933 them onto Protein or cDNA alignments</li>
2934 <li>Reconstruct linked cDNA alignment from aligned
2935 protein sequences</li>
2938 <li>Jmol integration updated to Jmol v14.2.14</li>
2939 <li>Import and export of Jalview alignment views as <a
2940 href="features/bioJsonFormat.html">BioJSON</a></li>
2941 <li>New alignment annotation file statements for
2942 reference sequences and marking hidden columns</li>
2943 <li>Reference sequence based alignment shading to
2944 highlight variation</li>
2945 <li>Select or hide columns according to alignment
2947 <li>Find option for locating sequences by description</li>
2948 <li>Conserved physicochemical properties shown in amino
2949 acid conservation row</li>
2950 <li>Alignments can be sorted by number of RNA helices</li>
2951 </ul> <em>Application</em>
2953 <li>New cDNA/Protein analysis capabilities
2955 <li>Get Cross-References should open a Split Frame
2956 view with cDNA/Protein</li>
2957 <li>Detect when nucleotide sequences and protein
2958 sequences are placed in the same alignment</li>
2959 <li>Split cDNA/Protein views are saved in Jalview
2964 <li>Use REST API to talk to Chimera</li>
2965 <li>Selected regions in Chimera are highlighted in linked
2966 Jalview windows</li>
2968 <li>VARNA RNA viewer updated to v3.93</li>
2969 <li>VARNA views are saved in Jalview Projects</li>
2970 <li>Pseudoknots displayed as Jalview RNA annotation can
2971 be shown in VARNA</li>
2973 <li>Make groups for selection uses marked columns as well
2974 as the active selected region</li>
2976 <li>Calculate UPGMA and NJ trees using sequence feature
2978 <li>New Export options
2980 <li>New Export Settings dialog to control hidden
2981 region export in flat file generation</li>
2983 <li>Export alignment views for display with the <a
2984 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2986 <li>Export scrollable SVG in HTML page</li>
2987 <li>Optional embedding of BioJSON data when exporting
2988 alignment figures to HTML</li>
2990 <li>3D structure retrieval and display
2992 <li>Free text and structured queries with the PDBe
2994 <li>PDBe Search API based discovery and selection of
2995 PDB structures for a sequence set</li>
2999 <li>JPred4 employed for protein secondary structure
3001 <li>Hide Insertions menu option to hide unaligned columns
3002 for one or a group of sequences</li>
3003 <li>Automatically hide insertions in alignments imported
3004 from the JPred4 web server</li>
3005 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3006 system on OSX<br />LGPL libraries courtesy of <a
3007 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3009 <li>changed 'View nucleotide structure' submenu to 'View
3010 VARNA 2D Structure'</li>
3011 <li>change "View protein structure" menu option to "3D
3014 </ul> <em>Applet</em>
3016 <li>New layout for applet example pages</li>
3017 <li>New parameters to enable SplitFrame view
3018 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3019 <li>New example demonstrating linked viewing of cDNA and
3020 Protein alignments</li>
3021 </ul> <em>Development and deployment</em>
3023 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3024 <li>Include installation type and git revision in build
3025 properties and console log output</li>
3026 <li>Jalview Github organisation, and new github site for
3027 storing BioJsMSA Templates</li>
3028 <li>Jalview's unit tests now managed with TestNG</li>
3031 <!-- <em>General</em>
3033 </ul> --> <!-- issues resolved --> <em>Application</em>
3035 <li>Escape should close any open find dialogs</li>
3036 <li>Typo in select-by-features status report</li>
3037 <li>Consensus RNA secondary secondary structure
3038 predictions are not highlighted in amber</li>
3039 <li>Missing gap character in v2.7 example file means
3040 alignment appears unaligned when pad-gaps is not enabled</li>
3041 <li>First switch to RNA Helices colouring doesn't colour
3042 associated structure views</li>
3043 <li>ID width preference option is greyed out when auto
3044 width checkbox not enabled</li>
3045 <li>Stopped a warning dialog from being shown when
3046 creating user defined colours</li>
3047 <li>'View Mapping' in structure viewer shows sequence
3048 mappings for just that viewer's sequences</li>
3049 <li>Workaround for superposing PDB files containing
3050 multiple models in Chimera</li>
3051 <li>Report sequence position in status bar when hovering
3052 over Jmol structure</li>
3053 <li>Cannot output gaps as '.' symbols with Selection ->
3054 output to text box</li>
3055 <li>Flat file exports of alignments with hidden columns
3056 have incorrect sequence start/end</li>
3057 <li>'Aligning' a second chain to a Chimera structure from
3059 <li>Colour schemes applied to structure viewers don't
3060 work for nucleotide</li>
3061 <li>Loading/cut'n'pasting an empty or invalid file leads
3062 to a grey/invisible alignment window</li>
3063 <li>Exported Jpred annotation from a sequence region
3064 imports to different position</li>
3065 <li>Space at beginning of sequence feature tooltips shown
3066 on some platforms</li>
3067 <li>Chimera viewer 'View | Show Chain' menu is not
3069 <li>'New View' fails with a Null Pointer Exception in
3070 console if Chimera has been opened</li>
3071 <li>Mouseover to Chimera not working</li>
3072 <li>Miscellaneous ENA XML feature qualifiers not
3074 <li>NPE in annotation renderer after 'Extract Scores'</li>
3075 <li>If two structures in one Chimera window, mouseover of
3076 either sequence shows on first structure</li>
3077 <li>'Show annotations' options should not make
3078 non-positional annotations visible</li>
3079 <li>Subsequence secondary structure annotation not shown
3080 in right place after 'view flanking regions'</li>
3081 <li>File Save As type unset when current file format is
3083 <li>Save as '.jar' option removed for saving Jalview
3085 <li>Colour by Sequence colouring in Chimera more
3087 <li>Cannot 'add reference annotation' for a sequence in
3088 several views on same alignment</li>
3089 <li>Cannot show linked products for EMBL / ENA records</li>
3090 <li>Jalview's tooltip wraps long texts containing no
3092 </ul> <em>Applet</em>
3094 <li>Jmol to JalviewLite mouseover/link not working</li>
3095 <li>JalviewLite can't import sequences with ID
3096 descriptions containing angle brackets</li>
3097 </ul> <em>General</em>
3099 <li>Cannot export and reimport RNA secondary structure
3100 via jalview annotation file</li>
3101 <li>Random helix colour palette for colour by annotation
3102 with RNA secondary structure</li>
3103 <li>Mouseover to cDNA from STOP residue in protein
3104 translation doesn't work.</li>
3105 <li>hints when using the select by annotation dialog box</li>
3106 <li>Jmol alignment incorrect if PDB file has alternate CA
3108 <li>FontChooser message dialog appears to hang after
3109 choosing 1pt font</li>
3110 <li>Peptide secondary structure incorrectly imported from
3111 annotation file when annotation display text includes 'e' or
3113 <li>Cannot set colour of new feature type whilst creating
3115 <li>cDNA translation alignment should not be sequence
3116 order dependent</li>
3117 <li>'Show unconserved' doesn't work for lower case
3119 <li>Nucleotide ambiguity codes involving R not recognised</li>
3120 </ul> <em>Deployment and Documentation</em>
3122 <li>Applet example pages appear different to the rest of
3123 www.jalview.org</li>
3124 </ul> <em>Application Known issues</em>
3126 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3127 <li>Misleading message appears after trying to delete
3129 <li>Jalview icon not shown in dock after InstallAnywhere
3130 version launches</li>
3131 <li>Fetching EMBL reference for an RNA sequence results
3132 fails with a sequence mismatch</li>
3133 <li>Corrupted or unreadable alignment display when
3134 scrolling alignment to right</li>
3135 <li>ArrayIndexOutOfBoundsException thrown when remove
3136 empty columns called on alignment with ragged gapped ends</li>
3137 <li>auto calculated alignment annotation rows do not get
3138 placed above or below non-autocalculated rows</li>
3139 <li>Jalview dekstop becomes sluggish at full screen in
3140 ultra-high resolution</li>
3141 <li>Cannot disable consensus calculation independently of
3142 quality and conservation</li>
3143 <li>Mouseover highlighting between cDNA and protein can
3144 become sluggish with more than one splitframe shown</li>
3145 </ul> <em>Applet Known Issues</em>
3147 <li>Core PDB parsing code requires Jmol</li>
3148 <li>Sequence canvas panel goes white when alignment
3149 window is being resized</li>
3155 <td><div align="center">
3156 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3158 <td><em>General</em>
3160 <li>Updated Java code signing certificate donated by
3162 <li>Features and annotation preserved when performing
3163 pairwise alignment</li>
3164 <li>RNA pseudoknot annotation can be
3165 imported/exported/displayed</li>
3166 <li>'colour by annotation' can colour by RNA and
3167 protein secondary structure</li>
3168 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3169 post-hoc with 2.9 release</em>)
3172 </ul> <em>Application</em>
3174 <li>Extract and display secondary structure for sequences
3175 with 3D structures</li>
3176 <li>Support for parsing RNAML</li>
3177 <li>Annotations menu for layout
3179 <li>sort sequence annotation rows by alignment</li>
3180 <li>place sequence annotation above/below alignment
3183 <li>Output in Stockholm format</li>
3184 <li>Internationalisation: improved Spanish (es)
3186 <li>Structure viewer preferences tab</li>
3187 <li>Disorder and Secondary Structure annotation tracks
3188 shared between alignments</li>
3189 <li>UCSF Chimera launch and linked highlighting from
3191 <li>Show/hide all sequence associated annotation rows for
3192 all or current selection</li>
3193 <li>disorder and secondary structure predictions
3194 available as dataset annotation</li>
3195 <li>Per-sequence rna helices colouring</li>
3198 <li>Sequence database accessions imported when fetching
3199 alignments from Rfam</li>
3200 <li>update VARNA version to 3.91</li>
3202 <li>New groovy scripts for exporting aligned positions,
3203 conservation values, and calculating sum of pairs scores.</li>
3204 <li>Command line argument to set default JABAWS server</li>
3205 <li>include installation type in build properties and
3206 console log output</li>
3207 <li>Updated Jalview project format to preserve dataset
3211 <!-- issues resolved --> <em>Application</em>
3213 <li>Distinguish alignment and sequence associated RNA
3214 structure in structure->view->VARNA</li>
3215 <li>Raise dialog box if user deletes all sequences in an
3217 <li>Pressing F1 results in documentation opening twice</li>
3218 <li>Sequence feature tooltip is wrapped</li>
3219 <li>Double click on sequence associated annotation
3220 selects only first column</li>
3221 <li>Redundancy removal doesn't result in unlinked
3222 leaves shown in tree</li>
3223 <li>Undos after several redundancy removals don't undo
3225 <li>Hide sequence doesn't hide associated annotation</li>
3226 <li>User defined colours dialog box too big to fit on
3227 screen and buttons not visible</li>
3228 <li>author list isn't updated if already written to
3229 Jalview properties</li>
3230 <li>Popup menu won't open after retrieving sequence
3232 <li>File open window for associate PDB doesn't open</li>
3233 <li>Left-then-right click on a sequence id opens a
3234 browser search window</li>
3235 <li>Cannot open sequence feature shading/sort popup menu
3236 in feature settings dialog</li>
3237 <li>better tooltip placement for some areas of Jalview
3239 <li>Allow addition of JABAWS Server which doesn't
3240 pass validation</li>
3241 <li>Web services parameters dialog box is too large to
3243 <li>Muscle nucleotide alignment preset obscured by
3245 <li>JABAWS preset submenus don't contain newly
3246 defined user preset</li>
3247 <li>MSA web services warns user if they were launched
3248 with invalid input</li>
3249 <li>Jalview cannot contact DAS Registy when running on
3252 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3253 'Superpose with' submenu not shown when new view
3257 </ul> <!-- <em>Applet</em>
3259 </ul> <em>General</em>
3261 </ul>--> <em>Deployment and Documentation</em>
3263 <li>2G and 1G options in launchApp have no effect on
3264 memory allocation</li>
3265 <li>launchApp service doesn't automatically open
3266 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3268 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3269 InstallAnywhere reports cannot find valid JVM when Java
3270 1.7_055 is available
3272 </ul> <em>Application Known issues</em>
3275 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3276 corrupted or unreadable alignment display when scrolling
3280 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3281 retrieval fails but progress bar continues for DAS retrieval
3282 with large number of ID
3285 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3286 flatfile output of visible region has incorrect sequence
3290 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3291 rna structure consensus doesn't update when secondary
3292 structure tracks are rearranged
3295 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3296 invalid rna structure positional highlighting does not
3297 highlight position of invalid base pairs
3300 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3301 out of memory errors are not raised when saving Jalview
3302 project from alignment window file menu
3305 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3306 Switching to RNA Helices colouring doesn't propagate to
3310 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3311 colour by RNA Helices not enabled when user created
3312 annotation added to alignment
3315 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3316 Jalview icon not shown on dock in Mountain Lion/Webstart
3318 </ul> <em>Applet Known Issues</em>
3321 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3322 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3325 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3326 Jalview and Jmol example not compatible with IE9
3329 <li>Sort by annotation score doesn't reverse order
3335 <td><div align="center">
3336 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3339 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3342 <li>Internationalisation of user interface (usually
3343 called i18n support) and translation for Spanish locale</li>
3344 <li>Define/Undefine group on current selection with
3345 Ctrl-G/Shift Ctrl-G</li>
3346 <li>Improved group creation/removal options in
3347 alignment/sequence Popup menu</li>
3348 <li>Sensible precision for symbol distribution
3349 percentages shown in logo tooltip.</li>
3350 <li>Annotation panel height set according to amount of
3351 annotation when alignment first opened</li>
3352 </ul> <em>Application</em>
3354 <li>Interactive consensus RNA secondary structure
3355 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3356 <li>Select columns containing particular features from
3357 Feature Settings dialog</li>
3358 <li>View all 'representative' PDB structures for selected
3360 <li>Update Jalview project format:
3362 <li>New file extension for Jalview projects '.jvp'</li>
3363 <li>Preserve sequence and annotation dataset (to
3364 store secondary structure annotation,etc)</li>
3365 <li>Per group and alignment annotation and RNA helix
3369 <li>New similarity measures for PCA and Tree calculation
3371 <li>Experimental support for retrieval and viewing of
3372 flanking regions for an alignment</li>
3376 <!-- issues resolved --> <em>Application</em>
3378 <li>logo keeps spinning and status remains at queued or
3379 running after job is cancelled</li>
3380 <li>cannot export features from alignments imported from
3381 Jalview/VAMSAS projects</li>
3382 <li>Buggy slider for web service parameters that take
3384 <li>Newly created RNA secondary structure line doesn't
3385 have 'display all symbols' flag set</li>
3386 <li>T-COFFEE alignment score shading scheme and other
3387 annotation shading not saved in Jalview project</li>
3388 <li>Local file cannot be loaded in freshly downloaded
3390 <li>Jalview icon not shown on dock in Mountain
3392 <li>Load file from desktop file browser fails</li>
3393 <li>Occasional NPE thrown when calculating large trees</li>
3394 <li>Cannot reorder or slide sequences after dragging an
3395 alignment onto desktop</li>
3396 <li>Colour by annotation dialog throws NPE after using
3397 'extract scores' function</li>
3398 <li>Loading/cut'n'pasting an empty file leads to a grey
3399 alignment window</li>
3400 <li>Disorder thresholds rendered incorrectly after
3401 performing IUPred disorder prediction</li>
3402 <li>Multiple group annotated consensus rows shown when
3403 changing 'normalise logo' display setting</li>
3404 <li>Find shows blank dialog after 'finished searching' if
3405 nothing matches query</li>
3406 <li>Null Pointer Exceptions raised when sorting by
3407 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3409 <li>Errors in Jmol console when structures in alignment
3410 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3412 <li>Not all working JABAWS services are shown in
3414 <li>JAVAWS version of Jalview fails to launch with
3415 'invalid literal/length code'</li>
3416 <li>Annotation/RNA Helix colourschemes cannot be applied
3417 to alignment with groups (actually fixed in 2.8.0b1)</li>
3418 <li>RNA Helices and T-Coffee Scores available as default
3421 </ul> <em>Applet</em>
3423 <li>Remove group option is shown even when selection is
3425 <li>Apply to all groups ticked but colourscheme changes
3426 don't affect groups</li>
3427 <li>Documented RNA Helices and T-Coffee Scores as valid
3428 colourscheme name</li>
3429 <li>Annotation labels drawn on sequence IDs when
3430 Annotation panel is not displayed</li>
3431 <li>Increased font size for dropdown menus on OSX and
3432 embedded windows</li>
3433 </ul> <em>Other</em>
3435 <li>Consensus sequence for alignments/groups with a
3436 single sequence were not calculated</li>
3437 <li>annotation files that contain only groups imported as
3438 annotation and junk sequences</li>
3439 <li>Fasta files with sequences containing '*' incorrectly
3440 recognised as PFAM or BLC</li>
3441 <li>conservation/PID slider apply all groups option
3442 doesn't affect background (2.8.0b1)
3444 <li>redundancy highlighting is erratic at 0% and 100%</li>
3445 <li>Remove gapped columns fails for sequences with ragged
3447 <li>AMSA annotation row with leading spaces is not
3448 registered correctly on import</li>
3449 <li>Jalview crashes when selecting PCA analysis for
3450 certain alignments</li>
3451 <li>Opening the colour by annotation dialog for an
3452 existing annotation based 'use original colours'
3453 colourscheme loses original colours setting</li>
3458 <td><div align="center">
3459 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3460 <em>30/1/2014</em></strong>
3464 <li>Trusted certificates for JalviewLite applet and
3465 Jalview Desktop application<br />Certificate was donated by
3466 <a href="https://www.certum.eu">Certum</a> to the Jalview
3467 open source project).
3469 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3470 <li>Output in Stockholm format</li>
3471 <li>Allow import of data from gzipped files</li>
3472 <li>Export/import group and sequence associated line
3473 graph thresholds</li>
3474 <li>Nucleotide substitution matrix that supports RNA and
3475 ambiguity codes</li>
3476 <li>Allow disorder predictions to be made on the current
3477 selection (or visible selection) in the same way that JPred
3479 <li>Groovy scripting for headless Jalview operation</li>
3480 </ul> <em>Other improvements</em>
3482 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3483 <li>COMBINE statement uses current SEQUENCE_REF and
3484 GROUP_REF scope to group annotation rows</li>
3485 <li>Support '' style escaping of quotes in Newick
3487 <li>Group options for JABAWS service by command line name</li>
3488 <li>Empty tooltip shown for JABA service options with a
3489 link but no description</li>
3490 <li>Select primary source when selecting authority in
3491 database fetcher GUI</li>
3492 <li>Add .mfa to FASTA file extensions recognised by
3494 <li>Annotation label tooltip text wrap</li>
3499 <li>Slow scrolling when lots of annotation rows are
3501 <li>Lots of NPE (and slowness) after creating RNA
3502 secondary structure annotation line</li>
3503 <li>Sequence database accessions not imported when
3504 fetching alignments from Rfam</li>
3505 <li>Incorrect SHMR submission for sequences with
3507 <li>View all structures does not always superpose
3509 <li>Option widgets in service parameters not updated to
3510 reflect user or preset settings</li>
3511 <li>Null pointer exceptions for some services without
3512 presets or adjustable parameters</li>
3513 <li>Discover PDB IDs entry in structure menu doesn't
3514 discover PDB xRefs</li>
3515 <li>Exception encountered while trying to retrieve
3516 features with DAS</li>
3517 <li>Lowest value in annotation row isn't coloured
3518 when colour by annotation (per sequence) is coloured</li>
3519 <li>Keyboard mode P jumps to start of gapped region when
3520 residue follows a gap</li>
3521 <li>Jalview appears to hang importing an alignment with
3522 Wrap as default or after enabling Wrap</li>
3523 <li>'Right click to add annotations' message
3524 shown in wrap mode when no annotations present</li>
3525 <li>Disorder predictions fail with NPE if no automatic
3526 annotation already exists on alignment</li>
3527 <li>oninit javascript function should be called after
3528 initialisation completes</li>
3529 <li>Remove redundancy after disorder prediction corrupts
3530 alignment window display</li>
3531 <li>Example annotation file in documentation is invalid</li>
3532 <li>Grouped line graph annotation rows are not exported
3533 to annotation file</li>
3534 <li>Multi-harmony analysis cannot be run when only two
3536 <li>Cannot create multiple groups of line graphs with
3537 several 'combine' statements in annotation file</li>
3538 <li>Pressing return several times causes Number Format
3539 exceptions in keyboard mode</li>
3540 <li>Multi-harmony (SHMMR) method doesn't submit
3541 correct partitions for input data</li>
3542 <li>Translation from DNA to Amino Acids fails</li>
3543 <li>Jalview fail to load newick tree with quoted label</li>
3544 <li>--headless flag isn't understood</li>
3545 <li>ClassCastException when generating EPS in headless
3547 <li>Adjusting sequence-associated shading threshold only
3548 changes one row's threshold</li>
3549 <li>Preferences and Feature settings panel panel
3550 doesn't open</li>
3551 <li>hide consensus histogram also hides conservation and
3552 quality histograms</li>
3557 <td><div align="center">
3558 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3560 <td><em>Application</em>
3562 <li>Support for JABAWS 2.0 Services (AACon alignment
3563 conservation, protein disorder and Clustal Omega)</li>
3564 <li>JABAWS server status indicator in Web Services
3566 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3567 in Jalview alignment window</li>
3568 <li>Updated Jalview build and deploy framework for OSX
3569 mountain lion, windows 7, and 8</li>
3570 <li>Nucleotide substitution matrix for PCA that supports
3571 RNA and ambiguity codes</li>
3573 <li>Improved sequence database retrieval GUI</li>
3574 <li>Support fetching and database reference look up
3575 against multiple DAS sources (Fetch all from in 'fetch db
3577 <li>Jalview project improvements
3579 <li>Store and retrieve the 'belowAlignment'
3580 flag for annotation</li>
3581 <li>calcId attribute to group annotation rows on the
3583 <li>Store AACon calculation settings for a view in
3584 Jalview project</li>
3588 <li>horizontal scrolling gesture support</li>
3589 <li>Visual progress indicator when PCA calculation is
3591 <li>Simpler JABA web services menus</li>
3592 <li>visual indication that web service results are still
3593 being retrieved from server</li>
3594 <li>Serialise the dialogs that are shown when Jalview
3595 starts up for first time</li>
3596 <li>Jalview user agent string for interacting with HTTP
3598 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3600 <li>Examples directory and Groovy library included in
3601 InstallAnywhere distribution</li>
3602 </ul> <em>Applet</em>
3604 <li>RNA alignment and secondary structure annotation
3605 visualization applet example</li>
3606 </ul> <em>General</em>
3608 <li>Normalise option for consensus sequence logo</li>
3609 <li>Reset button in PCA window to return dimensions to
3611 <li>Allow seqspace or Jalview variant of alignment PCA
3613 <li>PCA with either nucleic acid and protein substitution
3615 <li>Allow windows containing HTML reports to be exported
3617 <li>Interactive display and editing of RNA secondary
3618 structure contacts</li>
3619 <li>RNA Helix Alignment Colouring</li>
3620 <li>RNA base pair logo consensus</li>
3621 <li>Parse sequence associated secondary structure
3622 information in Stockholm files</li>
3623 <li>HTML Export database accessions and annotation
3624 information presented in tooltip for sequences</li>
3625 <li>Import secondary structure from LOCARNA clustalw
3626 style RNA alignment files</li>
3627 <li>import and visualise T-COFFEE quality scores for an
3629 <li>'colour by annotation' per sequence option to
3630 shade each sequence according to its associated alignment
3632 <li>New Jalview Logo</li>
3633 </ul> <em>Documentation and Development</em>
3635 <li>documentation for score matrices used in Jalview</li>
3636 <li>New Website!</li>
3638 <td><em>Application</em>
3640 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3641 wsdbfetch REST service</li>
3642 <li>Stop windows being moved outside desktop on OSX</li>
3643 <li>Filetype associations not installed for webstart
3645 <li>Jalview does not always retrieve progress of a JABAWS
3646 job execution in full once it is complete</li>
3647 <li>revise SHMR RSBS definition to ensure alignment is
3648 uploaded via ali_file parameter</li>
3649 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3650 <li>View all structures superposed fails with exception</li>
3651 <li>Jnet job queues forever if a very short sequence is
3652 submitted for prediction</li>
3653 <li>Cut and paste menu not opened when mouse clicked on
3655 <li>Putting fractional value into integer text box in
3656 alignment parameter dialog causes Jalview to hang</li>
3657 <li>Structure view highlighting doesn't work on
3659 <li>View all structures fails with exception shown in
3661 <li>Characters in filename associated with PDBEntry not
3662 escaped in a platform independent way</li>
3663 <li>Jalview desktop fails to launch with exception when
3665 <li>Tree calculation reports 'you must have 2 or more
3666 sequences selected' when selection is empty</li>
3667 <li>Jalview desktop fails to launch with jar signature
3668 failure when java web start temporary file caching is
3670 <li>DAS Sequence retrieval with range qualification
3671 results in sequence xref which includes range qualification</li>
3672 <li>Errors during processing of command line arguments
3673 cause progress bar (JAL-898) to be removed</li>
3674 <li>Replace comma for semi-colon option not disabled for
3675 DAS sources in sequence fetcher</li>
3676 <li>Cannot close news reader when JABAWS server warning
3677 dialog is shown</li>
3678 <li>Option widgets not updated to reflect user settings</li>
3679 <li>Edited sequence not submitted to web service</li>
3680 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3681 <li>InstallAnywhere installer doesn't unpack and run
3682 on OSX Mountain Lion</li>
3683 <li>Annotation panel not given a scroll bar when
3684 sequences with alignment annotation are pasted into the
3686 <li>Sequence associated annotation rows not associated
3687 when loaded from Jalview project</li>
3688 <li>Browser launch fails with NPE on java 1.7</li>
3689 <li>JABAWS alignment marked as finished when job was
3690 cancelled or job failed due to invalid input</li>
3691 <li>NPE with v2.7 example when clicking on Tree
3692 associated with all views</li>
3693 <li>Exceptions when copy/paste sequences with grouped
3694 annotation rows to new window</li>
3695 </ul> <em>Applet</em>
3697 <li>Sequence features are momentarily displayed before
3698 they are hidden using hidefeaturegroups applet parameter</li>
3699 <li>loading features via javascript API automatically
3700 enables feature display</li>
3701 <li>scrollToColumnIn javascript API method doesn't
3703 </ul> <em>General</em>
3705 <li>Redundancy removal fails for rna alignment</li>
3706 <li>PCA calculation fails when sequence has been selected
3707 and then deselected</li>
3708 <li>PCA window shows grey box when first opened on OSX</li>
3709 <li>Letters coloured pink in sequence logo when alignment
3710 coloured with clustalx</li>
3711 <li>Choosing fonts without letter symbols defined causes
3712 exceptions and redraw errors</li>
3713 <li>Initial PCA plot view is not same as manually
3714 reconfigured view</li>
3715 <li>Grouped annotation graph label has incorrect line
3717 <li>Grouped annotation graph label display is corrupted
3718 for lots of labels</li>
3723 <div align="center">
3724 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3727 <td><em>Application</em>
3729 <li>Jalview Desktop News Reader</li>
3730 <li>Tweaked default layout of web services menu</li>
3731 <li>View/alignment association menu to enable user to
3732 easily specify which alignment a multi-structure view takes
3733 its colours/correspondences from</li>
3734 <li>Allow properties file location to be specified as URL</li>
3735 <li>Extend Jalview project to preserve associations
3736 between many alignment views and a single Jmol display</li>
3737 <li>Store annotation row height in Jalview project file</li>
3738 <li>Annotation row column label formatting attributes
3739 stored in project file</li>
3740 <li>Annotation row order for auto-calculated annotation
3741 rows preserved in Jalview project file</li>
3742 <li>Visual progress indication when Jalview state is
3743 saved using Desktop window menu</li>
3744 <li>Visual indication that command line arguments are
3745 still being processed</li>
3746 <li>Groovy script execution from URL</li>
3747 <li>Colour by annotation default min and max colours in
3749 <li>Automatically associate PDB files dragged onto an
3750 alignment with sequences that have high similarity and
3752 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3753 <li>'view structures' option to open many
3754 structures in same window</li>
3755 <li>Sort associated views menu option for tree panel</li>
3756 <li>Group all JABA and non-JABA services for a particular
3757 analysis function in its own submenu</li>
3758 </ul> <em>Applet</em>
3760 <li>Userdefined and autogenerated annotation rows for
3762 <li>Adjustment of alignment annotation pane height</li>
3763 <li>Annotation scrollbar for annotation panel</li>
3764 <li>Drag to reorder annotation rows in annotation panel</li>
3765 <li>'automaticScrolling' parameter</li>
3766 <li>Allow sequences with partial ID string matches to be
3767 annotated from GFF/Jalview features files</li>
3768 <li>Sequence logo annotation row in applet</li>
3769 <li>Absolute paths relative to host server in applet
3770 parameters are treated as such</li>
3771 <li>New in the JalviewLite javascript API:
3773 <li>JalviewLite.js javascript library</li>
3774 <li>Javascript callbacks for
3776 <li>Applet initialisation</li>
3777 <li>Sequence/alignment mouse-overs and selections</li>
3780 <li>scrollTo row and column alignment scrolling
3782 <li>Select sequence/alignment regions from javascript</li>
3783 <li>javascript structure viewer harness to pass
3784 messages between Jmol and Jalview when running as
3785 distinct applets</li>
3786 <li>sortBy method</li>
3787 <li>Set of applet and application examples shipped
3788 with documentation</li>
3789 <li>New example to demonstrate JalviewLite and Jmol
3790 javascript message exchange</li>
3792 </ul> <em>General</em>
3794 <li>Enable Jmol displays to be associated with multiple
3795 multiple alignments</li>
3796 <li>Option to automatically sort alignment with new tree</li>
3797 <li>User configurable link to enable redirects to a
3798 www.Jalview.org mirror</li>
3799 <li>Jmol colours option for Jmol displays</li>
3800 <li>Configurable newline string when writing alignment
3801 and other flat files</li>
3802 <li>Allow alignment annotation description lines to
3803 contain html tags</li>
3804 </ul> <em>Documentation and Development</em>
3806 <li>Add groovy test harness for bulk load testing to
3808 <li>Groovy script to load and align a set of sequences
3809 using a web service before displaying the result in the
3810 Jalview desktop</li>
3811 <li>Restructured javascript and applet api documentation</li>
3812 <li>Ant target to publish example html files with applet
3814 <li>Netbeans project for building Jalview from source</li>
3815 <li>ant task to create online javadoc for Jalview source</li>
3817 <td><em>Application</em>
3819 <li>User defined colourscheme throws exception when
3820 current built in colourscheme is saved as new scheme</li>
3821 <li>AlignFrame->Save in application pops up save
3822 dialog for valid filename/format</li>
3823 <li>Cannot view associated structure for UniProt sequence</li>
3824 <li>PDB file association breaks for UniProt sequence
3826 <li>Associate PDB from file dialog does not tell you
3827 which sequence is to be associated with the file</li>
3828 <li>Find All raises null pointer exception when query
3829 only matches sequence IDs</li>
3830 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3831 <li>Jalview project with Jmol views created with Jalview
3832 2.4 cannot be loaded</li>
3833 <li>Filetype associations not installed for webstart
3835 <li>Two or more chains in a single PDB file associated
3836 with sequences in different alignments do not get coloured
3837 by their associated sequence</li>
3838 <li>Visibility status of autocalculated annotation row
3839 not preserved when project is loaded</li>
3840 <li>Annotation row height and visibility attributes not
3841 stored in Jalview project</li>
3842 <li>Tree bootstraps are not preserved when saved as a
3843 Jalview project</li>
3844 <li>Envision2 workflow tooltips are corrupted</li>
3845 <li>Enabling show group conservation also enables colour
3846 by conservation</li>
3847 <li>Duplicate group associated conservation or consensus
3848 created on new view</li>
3849 <li>Annotation scrollbar not displayed after 'show
3850 all hidden annotation rows' option selected</li>
3851 <li>Alignment quality not updated after alignment
3852 annotation row is hidden then shown</li>
3853 <li>Preserve colouring of structures coloured by
3854 sequences in pre Jalview 2.7 projects</li>
3855 <li>Web service job parameter dialog is not laid out
3857 <li>Web services menu not refreshed after 'reset
3858 services' button is pressed in preferences</li>
3859 <li>Annotation off by one in Jalview v2_3 example project</li>
3860 <li>Structures imported from file and saved in project
3861 get name like jalview_pdb1234.txt when reloaded</li>
3862 <li>Jalview does not always retrieve progress of a JABAWS
3863 job execution in full once it is complete</li>
3864 </ul> <em>Applet</em>
3866 <li>Alignment height set incorrectly when lots of
3867 annotation rows are displayed</li>
3868 <li>Relative URLs in feature HTML text not resolved to
3870 <li>View follows highlighting does not work for positions
3872 <li><= shown as = in tooltip</li>
3873 <li>Export features raises exception when no features
3875 <li>Separator string used for serialising lists of IDs
3876 for javascript api is modified when separator string
3877 provided as parameter</li>
3878 <li>Null pointer exception when selecting tree leaves for
3879 alignment with no existing selection</li>
3880 <li>Relative URLs for datasources assumed to be relative
3881 to applet's codebase</li>
3882 <li>Status bar not updated after finished searching and
3883 search wraps around to first result</li>
3884 <li>StructureSelectionManager instance shared between
3885 several Jalview applets causes race conditions and memory
3887 <li>Hover tooltip and mouseover of position on structure
3888 not sent from Jmol in applet</li>
3889 <li>Certain sequences of javascript method calls to
3890 applet API fatally hang browser</li>
3891 </ul> <em>General</em>
3893 <li>View follows structure mouseover scrolls beyond
3894 position with wrapped view and hidden regions</li>
3895 <li>Find sequence position moves to wrong residue
3896 with/without hidden columns</li>
3897 <li>Sequence length given in alignment properties window
3899 <li>InvalidNumberFormat exceptions thrown when trying to
3900 import PDB like structure files</li>
3901 <li>Positional search results are only highlighted
3902 between user-supplied sequence start/end bounds</li>
3903 <li>End attribute of sequence is not validated</li>
3904 <li>Find dialog only finds first sequence containing a
3905 given sequence position</li>
3906 <li>Sequence numbering not preserved in MSF alignment
3908 <li>Jalview PDB file reader does not extract sequence
3909 from nucleotide chains correctly</li>
3910 <li>Structure colours not updated when tree partition
3911 changed in alignment</li>
3912 <li>Sequence associated secondary structure not correctly
3913 parsed in interleaved stockholm</li>
3914 <li>Colour by annotation dialog does not restore current
3916 <li>Hiding (nearly) all sequences doesn't work
3918 <li>Sequences containing lowercase letters are not
3919 properly associated with their pdb files</li>
3920 </ul> <em>Documentation and Development</em>
3922 <li>schemas/JalviewWsParamSet.xsd corrupted by
3923 ApplyCopyright tool</li>
3928 <div align="center">
3929 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3932 <td><em>Application</em>
3934 <li>New warning dialog when the Jalview Desktop cannot
3935 contact web services</li>
3936 <li>JABA service parameters for a preset are shown in
3937 service job window</li>
3938 <li>JABA Service menu entries reworded</li>
3942 <li>Modeller PIR IO broken - cannot correctly import a
3943 pir file emitted by Jalview</li>
3944 <li>Existing feature settings transferred to new
3945 alignment view created from cut'n'paste</li>
3946 <li>Improved test for mixed amino/nucleotide chains when
3947 parsing PDB files</li>
3948 <li>Consensus and conservation annotation rows
3949 occasionally become blank for all new windows</li>
3950 <li>Exception raised when right clicking above sequences
3951 in wrapped view mode</li>
3952 </ul> <em>Application</em>
3954 <li>multiple multiply aligned structure views cause cpu
3955 usage to hit 100% and computer to hang</li>
3956 <li>Web Service parameter layout breaks for long user
3957 parameter names</li>
3958 <li>Jaba service discovery hangs desktop if Jaba server
3965 <div align="center">
3966 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3969 <td><em>Application</em>
3971 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3972 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3975 <li>Web Services preference tab</li>
3976 <li>Analysis parameters dialog box and user defined
3978 <li>Improved speed and layout of Envision2 service menu</li>
3979 <li>Superpose structures using associated sequence
3981 <li>Export coordinates and projection as CSV from PCA
3983 </ul> <em>Applet</em>
3985 <li>enable javascript: execution by the applet via the
3986 link out mechanism</li>
3987 </ul> <em>Other</em>
3989 <li>Updated the Jmol Jalview interface to work with Jmol
3991 <li>The Jalview Desktop and JalviewLite applet now
3992 require Java 1.5</li>
3993 <li>Allow Jalview feature colour specification for GFF
3994 sequence annotation files</li>
3995 <li>New 'colour by label' keword in Jalview feature file
3996 type colour specification</li>
3997 <li>New Jalview Desktop Groovy API method that allows a
3998 script to check if it being run in an interactive session or
3999 in a batch operation from the Jalview command line</li>
4003 <li>clustalx colourscheme colours Ds preferentially when
4004 both D+E are present in over 50% of the column</li>
4005 </ul> <em>Application</em>
4007 <li>typo in AlignmentFrame->View->Hide->all but
4008 selected Regions menu item</li>
4009 <li>sequence fetcher replaces ',' for ';' when the ',' is
4010 part of a valid accession ID</li>
4011 <li>fatal OOM if object retrieved by sequence fetcher
4012 runs out of memory</li>
4013 <li>unhandled Out of Memory Error when viewing pca
4014 analysis results</li>
4015 <li>InstallAnywhere builds fail to launch on OS X java
4016 10.5 update 4 (due to apple Java 1.6 update)</li>
4017 <li>Installanywhere Jalview silently fails to launch</li>
4018 </ul> <em>Applet</em>
4020 <li>Jalview.getFeatureGroups() raises an
4021 ArrayIndexOutOfBoundsException if no feature groups are
4028 <div align="center">
4029 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4035 <li>Alignment prettyprinter doesn't cope with long
4037 <li>clustalx colourscheme colours Ds preferentially when
4038 both D+E are present in over 50% of the column</li>
4039 <li>nucleic acid structures retrieved from PDB do not
4040 import correctly</li>
4041 <li>More columns get selected than were clicked on when a
4042 number of columns are hidden</li>
4043 <li>annotation label popup menu not providing correct
4044 add/hide/show options when rows are hidden or none are
4046 <li>Stockholm format shown in list of readable formats,
4047 and parser copes better with alignments from RFAM.</li>
4048 <li>CSV output of consensus only includes the percentage
4049 of all symbols if sequence logo display is enabled</li>
4051 </ul> <em>Applet</em>
4053 <li>annotation panel disappears when annotation is
4055 </ul> <em>Application</em>
4057 <li>Alignment view not redrawn properly when new
4058 alignment opened where annotation panel is visible but no
4059 annotations are present on alignment</li>
4060 <li>pasted region containing hidden columns is
4061 incorrectly displayed in new alignment window</li>
4062 <li>Jalview slow to complete operations when stdout is
4063 flooded (fix is to close the Jalview console)</li>
4064 <li>typo in AlignmentFrame->View->Hide->all but
4065 selected Rregions menu item.</li>
4066 <li>inconsistent group submenu and Format submenu entry
4067 'Un' or 'Non'conserved</li>
4068 <li>Sequence feature settings are being shared by
4069 multiple distinct alignments</li>
4070 <li>group annotation not recreated when tree partition is
4072 <li>double click on group annotation to select sequences
4073 does not propagate to associated trees</li>
4074 <li>Mac OSX specific issues:
4076 <li>exception raised when mouse clicked on desktop
4077 window background</li>
4078 <li>Desktop menu placed on menu bar and application
4079 name set correctly</li>
4080 <li>sequence feature settings not wide enough for the
4081 save feature colourscheme button</li>
4090 <div align="center">
4091 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4094 <td><em>New Capabilities</em>
4096 <li>URL links generated from description line for
4097 regular-expression based URL links (applet and application)
4099 <li>Non-positional feature URL links are shown in link
4101 <li>Linked viewing of nucleic acid sequences and
4103 <li>Automatic Scrolling option in View menu to display
4104 the currently highlighted region of an alignment.</li>
4105 <li>Order an alignment by sequence length, or using the
4106 average score or total feature count for each sequence.</li>
4107 <li>Shading features by score or associated description</li>
4108 <li>Subdivide alignment and groups based on identity of
4109 selected subsequence (Make Groups from Selection).</li>
4110 <li>New hide/show options including Shift+Control+H to
4111 hide everything but the currently selected region.</li>
4112 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4113 </ul> <em>Application</em>
4115 <li>Fetch DB References capabilities and UI expanded to
4116 support retrieval from DAS sequence sources</li>
4117 <li>Local DAS Sequence sources can be added via the
4118 command line or via the Add local source dialog box.</li>
4119 <li>DAS Dbref and DbxRef feature types are parsed as
4120 database references and protein_name is parsed as
4121 description line (BioSapiens terms).</li>
4122 <li>Enable or disable non-positional feature and database
4123 references in sequence ID tooltip from View menu in
4125 <!-- <li>New hidden columns and rows and representatives capabilities
4126 in annotations file (in progress - not yet fully implemented)</li> -->
4127 <li>Group-associated consensus, sequence logos and
4128 conservation plots</li>
4129 <li>Symbol distributions for each column can be exported
4130 and visualized as sequence logos</li>
4131 <li>Optionally scale multi-character column labels to fit
4132 within each column of annotation row<!-- todo for applet -->
4134 <li>Optional automatic sort of associated alignment view
4135 when a new tree is opened.</li>
4136 <li>Jalview Java Console</li>
4137 <li>Better placement of desktop window when moving
4138 between different screens.</li>
4139 <li>New preference items for sequence ID tooltip and
4140 consensus annotation</li>
4141 <li>Client to submit sequences and IDs to Envision2
4143 <li><em>Vamsas Capabilities</em>
4145 <li>Improved VAMSAS synchronization (Jalview archive
4146 used to preserve views, structures, and tree display
4148 <li>Import of vamsas documents from disk or URL via
4150 <li>Sharing of selected regions between views and
4151 with other VAMSAS applications (Experimental feature!)</li>
4152 <li>Updated API to VAMSAS version 0.2</li>
4154 </ul> <em>Applet</em>
4156 <li>Middle button resizes annotation row height</li>
4159 <li>sortByTree (true/false) - automatically sort the
4160 associated alignment view by the tree when a new tree is
4162 <li>showTreeBootstraps (true/false) - show or hide
4163 branch bootstraps (default is to show them if available)</li>
4164 <li>showTreeDistances (true/false) - show or hide
4165 branch lengths (default is to show them if available)</li>
4166 <li>showUnlinkedTreeNodes (true/false) - indicate if
4167 unassociated nodes should be highlighted in the tree
4169 <li>heightScale and widthScale (1.0 or more) -
4170 increase the height or width of a cell in the alignment
4171 grid relative to the current font size.</li>
4174 <li>Non-positional features displayed in sequence ID
4176 </ul> <em>Other</em>
4178 <li>Features format: graduated colour definitions and
4179 specification of feature scores</li>
4180 <li>Alignment Annotations format: new keywords for group
4181 associated annotation (GROUP_REF) and annotation row display
4182 properties (ROW_PROPERTIES)</li>
4183 <li>XML formats extended to support graduated feature
4184 colourschemes, group associated annotation, and profile
4185 visualization settings.</li></td>
4188 <li>Source field in GFF files parsed as feature source
4189 rather than description</li>
4190 <li>Non-positional features are now included in sequence
4191 feature and gff files (controlled via non-positional feature
4192 visibility in tooltip).</li>
4193 <li>URL links generated for all feature links (bugfix)</li>
4194 <li>Added URL embedding instructions to features file
4196 <li>Codons containing ambiguous nucleotides translated as
4197 'X' in peptide product</li>
4198 <li>Match case switch in find dialog box works for both
4199 sequence ID and sequence string and query strings do not
4200 have to be in upper case to match case-insensitively.</li>
4201 <li>AMSA files only contain first column of
4202 multi-character column annotation labels</li>
4203 <li>Jalview Annotation File generation/parsing consistent
4204 with documentation (e.g. Stockholm annotation can be
4205 exported and re-imported)</li>
4206 <li>PDB files without embedded PDB IDs given a friendly
4208 <li>Find incrementally searches ID string matches as well
4209 as subsequence matches, and correctly reports total number
4213 <li>Better handling of exceptions during sequence
4215 <li>Dasobert generated non-positional feature URL
4216 link text excludes the start_end suffix</li>
4217 <li>DAS feature and source retrieval buttons disabled
4218 when fetch or registry operations in progress.</li>
4219 <li>PDB files retrieved from URLs are cached properly</li>
4220 <li>Sequence description lines properly shared via
4222 <li>Sequence fetcher fetches multiple records for all
4224 <li>Ensured that command line das feature retrieval
4225 completes before alignment figures are generated.</li>
4226 <li>Reduced time taken when opening file browser for
4228 <li>isAligned check prior to calculating tree, PCA or
4229 submitting an MSA to JNet now excludes hidden sequences.</li>
4230 <li>User defined group colours properly recovered
4231 from Jalview projects.</li>
4240 <div align="center">
4241 <strong>2.4.0.b2</strong><br> 28/10/2009
4246 <li>Experimental support for google analytics usage
4248 <li>Jalview privacy settings (user preferences and docs).</li>
4253 <li>Race condition in applet preventing startup in
4255 <li>Exception when feature created from selection beyond
4256 length of sequence.</li>
4257 <li>Allow synthetic PDB files to be imported gracefully</li>
4258 <li>Sequence associated annotation rows associate with
4259 all sequences with a given id</li>
4260 <li>Find function matches case-insensitively for sequence
4261 ID string searches</li>
4262 <li>Non-standard characters do not cause pairwise
4263 alignment to fail with exception</li>
4264 </ul> <em>Application Issues</em>
4266 <li>Sequences are now validated against EMBL database</li>
4267 <li>Sequence fetcher fetches multiple records for all
4269 </ul> <em>InstallAnywhere Issues</em>
4271 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4272 issue with installAnywhere mechanism)</li>
4273 <li>Command line launching of JARs from InstallAnywhere
4274 version (java class versioning error fixed)</li>
4281 <div align="center">
4282 <strong>2.4</strong><br> 27/8/2008
4285 <td><em>User Interface</em>
4287 <li>Linked highlighting of codon and amino acid from
4288 translation and protein products</li>
4289 <li>Linked highlighting of structure associated with
4290 residue mapping to codon position</li>
4291 <li>Sequence Fetcher provides example accession numbers
4292 and 'clear' button</li>
4293 <li>MemoryMonitor added as an option under Desktop's
4295 <li>Extract score function to parse whitespace separated
4296 numeric data in description line</li>
4297 <li>Column labels in alignment annotation can be centred.</li>
4298 <li>Tooltip for sequence associated annotation give name
4300 </ul> <em>Web Services and URL fetching</em>
4302 <li>JPred3 web service</li>
4303 <li>Prototype sequence search client (no public services
4305 <li>Fetch either seed alignment or full alignment from
4307 <li>URL Links created for matching database cross
4308 references as well as sequence ID</li>
4309 <li>URL Links can be created using regular-expressions</li>
4310 </ul> <em>Sequence Database Connectivity</em>
4312 <li>Retrieval of cross-referenced sequences from other
4314 <li>Generalised database reference retrieval and
4315 validation to all fetchable databases</li>
4316 <li>Fetch sequences from DAS sources supporting the
4317 sequence command</li>
4318 </ul> <em>Import and Export</em>
4319 <li>export annotation rows as CSV for spreadsheet import</li>
4320 <li>Jalview projects record alignment dataset associations,
4321 EMBL products, and cDNA sequence mappings</li>
4322 <li>Sequence Group colour can be specified in Annotation
4324 <li>Ad-hoc colouring of group in Annotation File using RGB
4325 triplet as name of colourscheme</li>
4326 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4328 <li>treenode binding for VAMSAS tree exchange</li>
4329 <li>local editing and update of sequences in VAMSAS
4330 alignments (experimental)</li>
4331 <li>Create new or select existing session to join</li>
4332 <li>load and save of vamsas documents</li>
4333 </ul> <em>Application command line</em>
4335 <li>-tree parameter to open trees (introduced for passing
4337 <li>-fetchfrom command line argument to specify nicknames
4338 of DAS servers to query for alignment features</li>
4339 <li>-dasserver command line argument to add new servers
4340 that are also automatically queried for features</li>
4341 <li>-groovy command line argument executes a given groovy
4342 script after all input data has been loaded and parsed</li>
4343 </ul> <em>Applet-Application data exchange</em>
4345 <li>Trees passed as applet parameters can be passed to
4346 application (when using "View in full
4347 application")</li>
4348 </ul> <em>Applet Parameters</em>
4350 <li>feature group display control parameter</li>
4351 <li>debug parameter</li>
4352 <li>showbutton parameter</li>
4353 </ul> <em>Applet API methods</em>
4355 <li>newView public method</li>
4356 <li>Window (current view) specific get/set public methods</li>
4357 <li>Feature display control methods</li>
4358 <li>get list of currently selected sequences</li>
4359 </ul> <em>New Jalview distribution features</em>
4361 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4362 <li>RELEASE file gives build properties for the latest
4363 Jalview release.</li>
4364 <li>Java 1.1 Applet build made easier and donotobfuscate
4365 property controls execution of obfuscator</li>
4366 <li>Build target for generating source distribution</li>
4367 <li>Debug flag for javacc</li>
4368 <li>.jalview_properties file is documented (slightly) in
4369 jalview.bin.Cache</li>
4370 <li>Continuous Build Integration for stable and
4371 development version of Application, Applet and source
4376 <li>selected region output includes visible annotations
4377 (for certain formats)</li>
4378 <li>edit label/displaychar contains existing label/char
4380 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4381 <li>shorter peptide product names from EMBL records</li>
4382 <li>Newick string generator makes compact representations</li>
4383 <li>bootstrap values parsed correctly for tree files with
4385 <li>pathological filechooser bug avoided by not allowing
4386 filenames containing a ':'</li>
4387 <li>Fixed exception when parsing GFF files containing
4388 global sequence features</li>
4389 <li>Alignment datasets are finalized only when number of
4390 references from alignment sequences goes to zero</li>
4391 <li>Close of tree branch colour box without colour
4392 selection causes cascading exceptions</li>
4393 <li>occasional negative imgwidth exceptions</li>
4394 <li>better reporting of non-fatal warnings to user when
4395 file parsing fails.</li>
4396 <li>Save works when Jalview project is default format</li>
4397 <li>Save as dialog opened if current alignment format is
4398 not a valid output format</li>
4399 <li>UniProt canonical names introduced for both das and
4401 <li>Histidine should be midblue (not pink!) in Zappo</li>
4402 <li>error messages passed up and output when data read
4404 <li>edit undo recovers previous dataset sequence when
4405 sequence is edited</li>
4406 <li>allow PDB files without pdb ID HEADER lines (like
4407 those generated by MODELLER) to be read in properly</li>
4408 <li>allow reading of JPred concise files as a normal
4410 <li>Stockholm annotation parsing and alignment properties
4411 import fixed for PFAM records</li>
4412 <li>Structure view windows have correct name in Desktop
4414 <li>annotation consisting of sequence associated scores
4415 can be read and written correctly to annotation file</li>
4416 <li>Aligned cDNA translation to aligned peptide works
4418 <li>Fixed display of hidden sequence markers and
4419 non-italic font for representatives in Applet</li>
4420 <li>Applet Menus are always embedded in applet window on
4422 <li>Newly shown features appear at top of stack (in
4424 <li>Annotations added via parameter not drawn properly
4425 due to null pointer exceptions</li>
4426 <li>Secondary structure lines are drawn starting from
4427 first column of alignment</li>
4428 <li>UniProt XML import updated for new schema release in
4430 <li>Sequence feature to sequence ID match for Features
4431 file is case-insensitive</li>
4432 <li>Sequence features read from Features file appended to
4433 all sequences with matching IDs</li>
4434 <li>PDB structure coloured correctly for associated views
4435 containing a sub-sequence</li>
4436 <li>PDB files can be retrieved by applet from Jar files</li>
4437 <li>feature and annotation file applet parameters
4438 referring to different directories are retrieved correctly</li>
4439 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4440 <li>Fixed application hang whilst waiting for
4441 splash-screen version check to complete</li>
4442 <li>Applet properly URLencodes input parameter values
4443 when passing them to the launchApp service</li>
4444 <li>display name and local features preserved in results
4445 retrieved from web service</li>
4446 <li>Visual delay indication for sequence retrieval and
4447 sequence fetcher initialisation</li>
4448 <li>updated Application to use DAS 1.53e version of
4449 dasobert DAS client</li>
4450 <li>Re-instated Full AMSA support and .amsa file
4452 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4460 <div align="center">
4461 <strong>2.3</strong><br> 9/5/07
4466 <li>Jmol 11.0.2 integration</li>
4467 <li>PDB views stored in Jalview XML files</li>
4468 <li>Slide sequences</li>
4469 <li>Edit sequence in place</li>
4470 <li>EMBL CDS features</li>
4471 <li>DAS Feature mapping</li>
4472 <li>Feature ordering</li>
4473 <li>Alignment Properties</li>
4474 <li>Annotation Scores</li>
4475 <li>Sort by scores</li>
4476 <li>Feature/annotation editing in applet</li>
4481 <li>Headless state operation in 2.2.1</li>
4482 <li>Incorrect and unstable DNA pairwise alignment</li>
4483 <li>Cut and paste of sequences with annotation</li>
4484 <li>Feature group display state in XML</li>
4485 <li>Feature ordering in XML</li>
4486 <li>blc file iteration selection using filename # suffix</li>
4487 <li>Stockholm alignment properties</li>
4488 <li>Stockhom alignment secondary structure annotation</li>
4489 <li>2.2.1 applet had no feature transparency</li>
4490 <li>Number pad keys can be used in cursor mode</li>
4491 <li>Structure Viewer mirror image resolved</li>
4498 <div align="center">
4499 <strong>2.2.1</strong><br> 12/2/07
4504 <li>Non standard characters can be read and displayed
4505 <li>Annotations/Features can be imported/exported to the
4507 <li>Applet allows editing of sequence/annotation/group
4508 name & description
4509 <li>Preference setting to display sequence name in
4511 <li>Annotation file format extended to allow
4512 Sequence_groups to be defined
4513 <li>Default opening of alignment overview panel can be
4514 specified in preferences
4515 <li>PDB residue numbering annotation added to associated
4521 <li>Applet crash under certain Linux OS with Java 1.6
4523 <li>Annotation file export / import bugs fixed
4524 <li>PNG / EPS image output bugs fixed
4530 <div align="center">
4531 <strong>2.2</strong><br> 27/11/06
4536 <li>Multiple views on alignment
4537 <li>Sequence feature editing
4538 <li>"Reload" alignment
4539 <li>"Save" to current filename
4540 <li>Background dependent text colour
4541 <li>Right align sequence ids
4542 <li>User-defined lower case residue colours
4545 <li>Menu item accelerator keys
4546 <li>Control-V pastes to current alignment
4547 <li>Cancel button for DAS Feature Fetching
4548 <li>PCA and PDB Viewers zoom via mouse roller
4549 <li>User-defined sub-tree colours and sub-tree selection
4551 <li>'New Window' button on the 'Output to Text box'
4556 <li>New memory efficient Undo/Redo System
4557 <li>Optimised symbol lookups and conservation/consensus
4559 <li>Region Conservation/Consensus recalculated after
4561 <li>Fixed Remove Empty Columns Bug (empty columns at end
4563 <li>Slowed DAS Feature Fetching for increased robustness.
4565 <li>Made angle brackets in ASCII feature descriptions
4567 <li>Re-instated Zoom function for PCA
4568 <li>Sequence descriptions conserved in web service
4570 <li>UniProt ID discoverer uses any word separated by
4572 <li>WsDbFetch query/result association resolved
4573 <li>Tree leaf to sequence mapping improved
4574 <li>Smooth fonts switch moved to FontChooser dialog box.
4581 <div align="center">
4582 <strong>2.1.1</strong><br> 12/9/06
4587 <li>Copy consensus sequence to clipboard</li>
4592 <li>Image output - rightmost residues are rendered if
4593 sequence id panel has been resized</li>
4594 <li>Image output - all offscreen group boundaries are
4596 <li>Annotation files with sequence references - all
4597 elements in file are relative to sequence position</li>
4598 <li>Mac Applet users can use Alt key for group editing</li>
4604 <div align="center">
4605 <strong>2.1</strong><br> 22/8/06
4610 <li>MAFFT Multiple Alignment in default Web Service list</li>
4611 <li>DAS Feature fetching</li>
4612 <li>Hide sequences and columns</li>
4613 <li>Export Annotations and Features</li>
4614 <li>GFF file reading / writing</li>
4615 <li>Associate structures with sequences from local PDB
4617 <li>Add sequences to exisiting alignment</li>
4618 <li>Recently opened files / URL lists</li>
4619 <li>Applet can launch the full application</li>
4620 <li>Applet has transparency for features (Java 1.2
4622 <li>Applet has user defined colours parameter</li>
4623 <li>Applet can load sequences from parameter
4624 "sequence<em>x</em>"
4630 <li>Redundancy Panel reinstalled in the Applet</li>
4631 <li>Monospaced font - EPS / rescaling bug fixed</li>
4632 <li>Annotation files with sequence references bug fixed</li>
4638 <div align="center">
4639 <strong>2.08.1</strong><br> 2/5/06
4644 <li>Change case of selected region from Popup menu</li>
4645 <li>Choose to match case when searching</li>
4646 <li>Middle mouse button and mouse movement can compress /
4647 expand the visible width and height of the alignment</li>
4652 <li>Annotation Panel displays complete JNet results</li>
4658 <div align="center">
4659 <strong>2.08b</strong><br> 18/4/06
4665 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4666 <li>Righthand label on wrapped alignments shows correct
4673 <div align="center">
4674 <strong>2.08</strong><br> 10/4/06
4679 <li>Editing can be locked to the selection area</li>
4680 <li>Keyboard editing</li>
4681 <li>Create sequence features from searches</li>
4682 <li>Precalculated annotations can be loaded onto
4684 <li>Features file allows grouping of features</li>
4685 <li>Annotation Colouring scheme added</li>
4686 <li>Smooth fonts off by default - Faster rendering</li>
4687 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4692 <li>Drag & Drop fixed on Linux</li>
4693 <li>Jalview Archive file faster to load/save, sequence
4694 descriptions saved.</li>
4700 <div align="center">
4701 <strong>2.07</strong><br> 12/12/05
4706 <li>PDB Structure Viewer enhanced</li>
4707 <li>Sequence Feature retrieval and display enhanced</li>
4708 <li>Choose to output sequence start-end after sequence
4709 name for file output</li>
4710 <li>Sequence Fetcher WSDBFetch@EBI</li>
4711 <li>Applet can read feature files, PDB files and can be
4712 used for HTML form input</li>
4717 <li>HTML output writes groups and features</li>
4718 <li>Group editing is Control and mouse click</li>
4719 <li>File IO bugs</li>
4725 <div align="center">
4726 <strong>2.06</strong><br> 28/9/05
4731 <li>View annotations in wrapped mode</li>
4732 <li>More options for PCA viewer</li>
4737 <li>GUI bugs resolved</li>
4738 <li>Runs with -nodisplay from command line</li>
4744 <div align="center">
4745 <strong>2.05b</strong><br> 15/9/05
4750 <li>Choose EPS export as lineart or text</li>
4751 <li>Jar files are executable</li>
4752 <li>Can read in Uracil - maps to unknown residue</li>
4757 <li>Known OutOfMemory errors give warning message</li>
4758 <li>Overview window calculated more efficiently</li>
4759 <li>Several GUI bugs resolved</li>
4765 <div align="center">
4766 <strong>2.05</strong><br> 30/8/05
4771 <li>Edit and annotate in "Wrapped" view</li>
4776 <li>Several GUI bugs resolved</li>
4782 <div align="center">
4783 <strong>2.04</strong><br> 24/8/05
4788 <li>Hold down mouse wheel & scroll to change font
4794 <li>Improved JPred client reliability</li>
4795 <li>Improved loading of Jalview files</li>
4801 <div align="center">
4802 <strong>2.03</strong><br> 18/8/05
4807 <li>Set Proxy server name and port in preferences</li>
4808 <li>Multiple URL links from sequence ids</li>
4809 <li>User Defined Colours can have a scheme name and added
4811 <li>Choose to ignore gaps in consensus calculation</li>
4812 <li>Unix users can set default web browser</li>
4813 <li>Runs without GUI for batch processing</li>
4814 <li>Dynamically generated Web Service Menus</li>
4819 <li>InstallAnywhere download for Sparc Solaris</li>
4825 <div align="center">
4826 <strong>2.02</strong><br> 18/7/05
4832 <li>Copy & Paste order of sequences maintains
4833 alignment order.</li>
4839 <div align="center">
4840 <strong>2.01</strong><br> 12/7/05
4845 <li>Use delete key for deleting selection.</li>
4846 <li>Use Mouse wheel to scroll sequences.</li>
4847 <li>Help file updated to describe how to add alignment
4849 <li>Version and build date written to build properties
4851 <li>InstallAnywhere installation will check for updates
4852 at launch of Jalview.</li>
4857 <li>Delete gaps bug fixed.</li>
4858 <li>FileChooser sorts columns.</li>
4859 <li>Can remove groups one by one.</li>
4860 <li>Filechooser icons installed.</li>
4861 <li>Finder ignores return character when searching.
4862 Return key will initiate a search.<br>
4869 <div align="center">
4870 <strong>2.0</strong><br> 20/6/05
4875 <li>New codebase</li>