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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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>11/08/2020</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-3695 -->Support import of VCF 4.3 by updating
71 HTSJDK from 2.12 to 2.23
74 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
75 optimisations and improvements suggested by Bob Hanson and
76 improved compatibility with JalviewJS
79 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
80 alignments from Pfam and Rfam
83 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
84 import (no longer based on .gz extension)
87 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
90 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
91 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
95 <!-- JAL-3667 -->Improved warning messages, debug logging
96 and fixed Retry action when Jalview encounters errors when
97 saving or making backup files.
100 <!-- JAL-3676 -->Enhanced Jalview Java Console:
102 <li>Jalview's logging level can be configured</li>
103 <li>Copy to Clipboard Buttion</li>
107 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
108 when running on Linux (Requires Java 11+)
110 </ul> <em>Launching Jalview</em>
113 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
114 through a system property
117 <!-- JAL-3477 -->Improved built-in documentation and command
118 line help for configuring Jalview's memory
122 <td align="left" valign="top">
125 <!-- JAL-3493 -->Escape does not clear highlights on the
126 alignment (Since Jalview 2.10.3)
129 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
130 doesn't slide selected sequences, just sequence under cursor
133 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
134 multiple EMBL gene products shown forĀ a single contig
137 <!-- JAL-3696 -->Errors encountered when processing variants
138 from VCF files yield "Error processing VCF: Format specifier
142 <!-- JAL-3697 -->Count of features not shown can be wrong
143 when there are both local and complementary features mapped
144 to the position under the cursor
147 <!-- JAL-3673 -->Sequence ID for reference sequence is
148 clipped when Right align Sequence IDs enabled
151 <!-- JAL-2983 -->Slider with negative range values not
152 rendered correctly in VAqua4 (Since 2.10.4)
155 <!-- JAL-3685 -->Single quotes not displayed correctly in
156 internationalised text for some messages and log output
159 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
160 panels, Alignment viewport and annotation renderer.
162 </ul> <em>Developing Jalview</em>
165 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
166 data, causing cloverReport gradle task to fail with an
169 </ul> <em>New Known defects</em>
172 <!-- JAL-3576 -->Co-located features exported and re-imported
173 are ordered differently when shown on alignment and in
174 tooltips. (Also affects v2.11.1.0)
177 <!-- JAL-3667 -->Windows 10: For a minority of users, if
178 backups are not enabled, Jalview sometimes fails to
179 overwrite an existing file and raises a warning dialog.
180 Workaround is to try to save the file again, and if that
181 fails, delete the original file and save in place.
184 <!-- JAL-3701 -->Stale build data in jalview standalone jar
185 builds (only affects 2.11.1.1 branch)
191 <td width="60" align="center" nowrap><strong><a
192 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
193 <em>22/04/2020</em></strong></td>
194 <td align="left" valign="top">
197 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
198 'virtual' codon features shown on protein (or vice versa)
199 for display in alignments, on structure views (including
200 transfer to UCSF chimera), in feature reports and for
204 <!-- JAL-3121 -->Feature attributes from VCF files can be
205 exported and re-imported as GFF3 files
208 <!-- JAL-3376 -->Capture VCF "fixed column" values
209 POS, ID, QUAL, FILTER as Feature Attributes
212 <!-- JAL-3375 -->More robust VCF numeric data field
213 validation while parsing
216 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
220 <!-- JAL-3535 -->Feature Settings dialog title includes name
224 <!-- JAL-3538 -->Font anti-aliasing in alignment views
228 <!-- JAL-3468 -->Very long feature descriptions truncated in
232 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
233 with no feature types visible
236 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
238 </ul><em>Jalview Installer</em>
241 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
242 in console (may be null when Jalview launched as executable jar or via conda)
245 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
248 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
251 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
253 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
254 </ul> <em>Release processes</em>
257 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
260 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
262 </ul> <em>Build System</em>
265 <!-- JAL-3510 -->Clover updated to 4.4.1
268 <!-- JAL-3513 -->Test code included in Clover coverage
272 <em>Groovy Scripts</em>
275 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
276 to stdout containing the consensus sequence for each
277 alignment in a Jalview session
280 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
281 genomic sequence_variant annotation from CDS as
282 missense_variant or synonymous_variant on protein products.
286 <td align="left" valign="top">
289 <!-- JAL-3581 -->Hidden sequence markers still visible when
290 'Show hidden markers' option is not ticked
293 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
294 PNG output when 'Automatically set ID width' is set in
295 jalview preferences or properties file
298 <!-- JAL-3571 -->Feature Editor dialog can be opened when
299 'Show Sequence Features' option is not ticked
302 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
303 buttons in Feature Settings dialog are clicked when no
307 <!-- JAL-3412 -->ID margins for CDS and Protein views not
308 equal when split frame is first opened
311 <!-- JAL-3296 -->Sequence position numbers in status bar not
312 correct after editing a sequence's start position
315 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
316 with annotation and exceptions thrown when only a few
317 columns shown in wrapped mode
320 <!-- JAL-3386 -->Sequence IDs missing in headless export of
321 wrapped alignment figure with annotations
324 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
325 ID fails with ClassCastException
328 <!-- JAL-3389 -->Chimera session not restored from Jalview
332 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
333 feature settings dialog also selects columns
336 <!-- JAL-3473 -->SpinnerNumberModel causes
337 IllegalArgumentException in some circumstances
340 <!-- JAL-3534 -->Multiple feature settings dialogs can be
344 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
345 alignment window is closed
348 <!-- JAL-3406 -->Credits missing some authors in Jalview
349 help documentation for 2.11.0 release
352 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
353 includes Pfam ID as sequence's accession rather than its
356 </ul> <em>Java 11 Compatibility issues</em>
359 <!-- JAL-2987 -->OSX - Can't view some search results in
360 PDB/Uniprot search panel
362 </ul> <em>Installer</em>
365 <!-- JAL-3447 -->Jalview should not create file associations
366 for 3D structure files (.pdb, .mmcif. .cif)
368 </ul> <em>Repository and Source Release</em>
371 <!-- JAL-3474 -->removed obsolete .cvsignore files from
375 <!-- JAL-3541 -->Clover report generation running out of
378 </ul> <em>New Known Issues</em>
381 <!-- JAL-3523 -->OSX - Current working directory not
382 preserved when Jalview.app launched with parameters from
386 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
387 clipped in headless figure export when Right Align option
391 <!-- JAL-3542 -->Jalview Installation type always reports
392 'Source' in console output
395 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
396 bamboo server but run fine locally.
402 <td width="60" align="center" nowrap>
403 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
404 <em>04/07/2019</em></strong>
406 <td align="left" valign="top">
409 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
410 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
411 source project) rather than InstallAnywhere
414 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
415 settings, receive over the air updates and launch specific
416 versions via (<a href="https://github.com/threerings/getdown">Three
420 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
421 formats supported by Jalview (including .jvp project files)
424 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
425 arguments and switch between different getdown channels
428 <!-- JAL-3141 -->Backup files created when saving Jalview project
433 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
434 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
436 <!-- JAL-2620 -->Alternative genetic code tables for
437 'Translate as cDNA'</li>
439 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
440 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
443 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
444 implementation that allows updates) used for Sequence Feature collections</li>
446 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
447 features can be filtered and shaded according to any
448 associated attributes (e.g. variant attributes from VCF
449 file, or key-value pairs imported from column 9 of GFF
453 <!-- JAL-2879 -->Feature Attributes and shading schemes
454 stored and restored from Jalview Projects
457 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
458 recognise variant features
461 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
462 sequences (also coloured red by default)
465 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
469 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
470 algorithm (Z-sort/transparency and filter aware)
473 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
479 <!-- JAL-3205 -->Symmetric score matrices for faster
480 tree and PCA calculations
482 <li><strong>Principal Components Analysis Viewer</strong>
485 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
486 and Viewer state saved in Jalview Project
488 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
491 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
495 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
500 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
502 <li><strong>Speed and Efficiency</strong>
505 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
506 multiple groups when working with large alignments
509 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
513 <li><strong>User Interface</strong>
516 <!-- JAL-2933 -->Finder panel remembers last position in each
520 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
521 what is shown)<br />Only visible regions of alignment are shown by
522 default (can be changed in user preferences)
525 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
526 to the Overwrite Dialog
529 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
533 <!-- JAL-1244 -->Status bar shows bounds when dragging a
534 selection region, and gap count when inserting or deleting gaps
537 <!-- JAL-3132 -->Status bar updates over sequence and annotation
541 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
545 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
549 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
552 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
556 <!-- JAL-3181 -->Consistent ordering of links in sequence id
560 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
562 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
566 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
567 <li><strong>Java 11 Support (not yet on general release)</strong>
570 <!-- -->OSX GUI integrations for App menu's 'About' entry and
575 <em>Deprecations</em>
577 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
578 capabilities removed from the Jalview Desktop
580 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
581 unmarshalling has been replaced by JAXB for Jalview projects
582 and XML based data retrieval clients</li>
583 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
584 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
585 </ul> <em>Documentation</em>
587 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
588 not supported in EPS figure export
590 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
591 </ul> <em>Development and Release Processes</em>
594 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
597 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
599 <!-- JAL-3225 -->Eclipse project configuration managed with
603 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
604 Bamboo continuous integration for unattended Test Suite
608 <!-- JAL-2864 -->Memory test suite to detect leaks in common
612 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
616 <!-- JAL-3248 -->Developer documentation migrated to
617 markdown (with HTML rendering)
620 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
623 <!-- JAL-3289 -->New URLs for publishing development
628 <td align="left" valign="top">
631 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
634 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
635 superposition in Jmol fail on Windows
638 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
639 structures for sequences with lots of PDB structures
642 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
646 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
647 project involving multiple views
650 <!-- JAL-3164 -->Overview for complementary view in a linked
651 CDS/Protein alignment is not updated when Hide Columns by
652 Annotation dialog hides columns
655 <!-- JAL-3158 -->Selection highlighting in the complement of a
656 CDS/Protein alignment stops working after making a selection in
657 one view, then making another selection in the other view
660 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
664 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
665 Settings and Jalview Preferences panels
668 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
669 overview with large alignments
672 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
673 region if columns were selected by dragging right-to-left and the
674 mouse moved to the left of the first column
677 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
678 hidden column marker via scale popup menu
681 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
682 doesn't tell users the invalid URL
685 <!-- JAL-2816 -->Tooltips displayed for features filtered by
689 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
690 show cross references or Fetch Database References are shown in
694 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
695 peptide sequence (computed variant shown as p.Res.null)
698 <!-- JAL-2060 -->'Graduated colour' option not offered for
699 manually created features (where feature score is Float.NaN)
702 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
703 when columns are hidden
706 <!-- JAL-3082 -->Regular expression error for '(' in Select
707 Columns by Annotation description
710 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
711 out of Scale or Annotation Panel
714 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
718 <!-- JAL-3074 -->Left/right drag in annotation can scroll
722 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
726 <!-- JAL-3002 -->Column display is out by one after Page Down,
727 Page Up in wrapped mode
730 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
733 <!-- JAL-2932 -->Finder searches in minimised alignments
736 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
737 on opening an alignment
740 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
744 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
745 different groups in the alignment are selected
748 <!-- JAL-2717 -->Internationalised colour scheme names not shown
752 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
756 <!-- JAL-3125 -->Value input for graduated feature colour
757 threshold gets 'unrounded'
760 <!-- JAL-2982 -->PCA image export doesn't respect background
764 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
767 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
770 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
774 <!-- JAL-2964 -->Associate Tree with All Views not restored from
778 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
779 shown in complementary view
782 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
783 without normalisation
786 <!-- JAL-3021 -->Sequence Details report should open positioned at top
790 <!-- JAL-914 -->Help page can be opened twice
793 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
795 </ul> <em>Editing</em>
798 <!-- JAL-2822 -->Start and End should be updated when sequence
799 data at beginning or end of alignment added/removed via 'Edit'
803 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
804 relocate sequence features correctly when start of sequence is
805 removed (Known defect since 2.10)
808 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
809 dialog corrupts dataset sequence
812 <!-- JAL-868 -->Structure colours not updated when associated tree
813 repartitions the alignment view (Regression in 2.10.5)
815 </ul> <em>Datamodel</em>
818 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
819 sequence's End is greater than its length
821 </ul> <em>Bugs fixed for Java 11 Support (not yet on
822 general release)</em>
825 <!-- JAL-3288 -->Menus work properly in split-screen
827 </ul> <em>New Known Defects</em>
830 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
833 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
834 regions of protein alignment.
837 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
838 is restored from a Jalview 2.11 project
841 <!-- JAL-3213 -->Alignment panel height can be too small after
845 <!-- JAL-3240 -->Display is incorrect after removing gapped
846 columns within hidden columns
849 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
850 window after dragging left to select columns to left of visible
854 <!-- JAL-2876 -->Features coloured according to their description
855 string and thresholded by score in earlier versions of Jalview are
856 not shown as thresholded features in 2.11. To workaround please
857 create a Score filter instead.
860 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
862 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
865 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
866 alignments with multiple views can close views unexpectedly
869 <em>Java 11 Specific defects</em>
872 <!-- JAL-3235 -->Jalview Properties file is not sorted
873 alphabetically when saved
879 <td width="60" nowrap>
881 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
884 <td><div align="left">
888 <!-- JAL-3101 -->Default memory for Jalview webstart and
889 InstallAnywhere increased to 1G.
892 <!-- JAL-247 -->Hidden sequence markers and representative
893 sequence bolding included when exporting alignment as EPS,
894 SVG, PNG or HTML. <em>Display is configured via the
895 Format menu, or for command-line use via a Jalview
896 properties file.</em>
899 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
900 API and sequence data now imported as JSON.
903 <!-- JAL-3065 -->Change in recommended way of starting
904 Jalview via a Java command line: add jars in lib directory
905 to CLASSPATH, rather than via the deprecated java.ext.dirs
912 <!-- JAL-3047 -->Support added to execute test suite
913 instrumented with <a href="http://openclover.org/">Open
918 <td><div align="left">
922 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
923 row shown in Feredoxin Structure alignment view of example
927 <!-- JAL-2854 -->Annotation obscures sequences if lots of
928 annotation displayed.
931 <!-- JAL-3107 -->Group conservation/consensus not shown
932 for newly created group when 'Apply to all groups'
936 <!-- JAL-3087 -->Corrupted display when switching to
937 wrapped mode when sequence panel's vertical scrollbar is
941 <!-- JAL-3003 -->Alignment is black in exported EPS file
942 when sequences are selected in exported view.</em>
945 <!-- JAL-3059 -->Groups with different coloured borders
946 aren't rendered with correct colour.
949 <!-- JAL-3092 -->Jalview could hang when importing certain
950 types of knotted RNA secondary structure.
953 <!-- JAL-3095 -->Sequence highlight and selection in
954 trimmed VARNA 2D structure is incorrect for sequences that
958 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
959 annotation when columns are inserted into an alignment,
960 and when exporting as Stockholm flatfile.
963 <!-- JAL-3053 -->Jalview annotation rows containing upper
964 and lower-case 'E' and 'H' do not automatically get
965 treated as RNA secondary structure.
968 <!-- JAL-3106 -->.jvp should be used as default extension
969 (not .jar) when saving a Jalview project file.
972 <!-- JAL-3105 -->Mac Users: closing a window correctly
973 transfers focus to previous window on OSX
976 <em>Java 10 Issues Resolved</em>
979 <!-- JAL-2988 -->OSX - Can't save new files via the File
980 or export menus by typing in a name into the Save dialog
984 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
985 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
986 'look and feel' which has improved compatibility with the
987 latest version of OSX.
994 <td width="60" nowrap>
996 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
997 <em>7/06/2018</em></strong>
1000 <td><div align="left">
1004 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1005 annotation retrieved from Uniprot
1008 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1009 onto the Jalview Desktop
1013 <td><div align="left">
1017 <!-- JAL-3017 -->Cannot import features with multiple
1018 variant elements (blocks import of some Uniprot records)
1021 <!-- JAL-2997 -->Clustal files with sequence positions in
1022 right-hand column parsed correctly
1025 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1026 not alignment area in exported graphic
1029 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1030 window has input focus
1033 <!-- JAL-2992 -->Annotation panel set too high when
1034 annotation added to view (Windows)
1037 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1038 network connectivity is poor
1041 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1042 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1043 the currently open URL and links from a page viewed in
1044 Firefox or Chrome on Windows is now fully supported. If
1045 you are using Edge, only links in the page can be
1046 dragged, and with Internet Explorer, only the currently
1047 open URL in the browser can be dropped onto Jalview.</em>
1050 <em>New Known Defects</em>
1052 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1057 <td width="60" nowrap>
1058 <div align="center">
1059 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1062 <td><div align="left">
1066 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1067 for disabling automatic superposition of multiple
1068 structures and open structures in existing views
1071 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1072 ID and annotation area margins can be click-dragged to
1076 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1080 <!-- JAL-2759 -->Improved performance for large alignments
1081 and lots of hidden columns
1084 <!-- JAL-2593 -->Improved performance when rendering lots
1085 of features (particularly when transparency is disabled)
1088 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1089 exchange of Jalview features and Chimera attributes made
1095 <td><div align="left">
1098 <!-- JAL-2899 -->Structure and Overview aren't updated
1099 when Colour By Annotation threshold slider is adjusted
1102 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1103 overlapping alignment panel
1106 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1110 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1111 improved: CDS not handled correctly if transcript has no
1115 <!-- JAL-2321 -->Secondary structure and temperature
1116 factor annotation not added to sequence when local PDB
1117 file associated with it by drag'n'drop or structure
1121 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1122 dialog doesn't import PDB files dropped on an alignment
1125 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1126 scroll bar doesn't work for some CDS/Protein views
1129 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1130 Java 1.8u153 onwards and Java 1.9u4+.
1133 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1134 columns in annotation row
1137 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1138 honored in batch mode
1141 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1142 for structures added to existing Jmol view
1145 <!-- JAL-2223 -->'View Mappings' includes duplicate
1146 entries after importing project with multiple views
1149 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1150 protein sequences via SIFTS from associated PDB entries
1151 with negative residue numbers or missing residues fails
1154 <!-- JAL-2952 -->Exception when shading sequence with negative
1155 Temperature Factor values from annotated PDB files (e.g.
1156 as generated by CONSURF)
1159 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1160 tooltip doesn't include a text description of mutation
1163 <!-- JAL-2922 -->Invert displayed features very slow when
1164 structure and/or overview windows are also shown
1167 <!-- JAL-2954 -->Selecting columns from highlighted regions
1168 very slow for alignments with large numbers of sequences
1171 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1172 with 'StringIndexOutOfBounds'
1175 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1176 platforms running Java 10
1179 <!-- JAL-2960 -->Adding a structure to existing structure
1180 view appears to do nothing because the view is hidden behind the alignment view
1186 <!-- JAL-2926 -->Copy consensus sequence option in applet
1187 should copy the group consensus when popup is opened on it
1193 <!-- JAL-2913 -->Fixed ID width preference is not respected
1196 <em>New Known Defects</em>
1199 <!-- JAL-2973 --> Exceptions occasionally raised when
1200 editing a large alignment and overview is displayed
1203 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1204 repeatedly after a series of edits even when the overview
1205 is no longer reflecting updates
1208 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1209 structures for protein subsequence (if 'Trim Retrieved
1210 Sequences' enabled) or Ensembl isoforms (Workaround in
1211 2.10.4 is to fail back to N&W mapping)
1214 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1215 option gives blank output
1222 <td width="60" nowrap>
1223 <div align="center">
1224 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1227 <td><div align="left">
1228 <ul><li>Updated Certum Codesigning Certificate
1229 (Valid till 30th November 2018)</li></ul></div></td>
1230 <td><div align="left">
1231 <em>Desktop</em><ul>
1233 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1234 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1235 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1236 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1237 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1238 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1239 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1245 <td width="60" nowrap>
1246 <div align="center">
1247 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1250 <td><div align="left">
1254 <!-- JAL-2446 -->Faster and more efficient management and
1255 rendering of sequence features
1258 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1259 429 rate limit request hander
1262 <!-- JAL-2773 -->Structure views don't get updated unless
1263 their colours have changed
1266 <!-- JAL-2495 -->All linked sequences are highlighted for
1267 a structure mousover (Jmol) or selection (Chimera)
1270 <!-- JAL-2790 -->'Cancel' button in progress bar for
1271 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1274 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1275 view from Ensembl locus cross-references
1278 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1282 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1283 feature can be disabled
1286 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1287 PDB easier retrieval of sequences for lists of IDs
1290 <!-- JAL-2758 -->Short names for sequences retrieved from
1296 <li>Groovy interpreter updated to 2.4.12</li>
1297 <li>Example groovy script for generating a matrix of
1298 percent identity scores for current alignment.</li>
1300 <em>Testing and Deployment</em>
1303 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1307 <td><div align="left">
1311 <!-- JAL-2643 -->Pressing tab after updating the colour
1312 threshold text field doesn't trigger an update to the
1316 <!-- JAL-2682 -->Race condition when parsing sequence ID
1320 <!-- JAL-2608 -->Overview windows are also closed when
1321 alignment window is closed
1324 <!-- JAL-2548 -->Export of features doesn't always respect
1328 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1329 takes a long time in Cursor mode
1335 <!-- JAL-2777 -->Structures with whitespace chainCode
1336 cannot be viewed in Chimera
1339 <!-- JAL-2728 -->Protein annotation panel too high in
1343 <!-- JAL-2757 -->Can't edit the query after the server
1344 error warning icon is shown in Uniprot and PDB Free Text
1348 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1351 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1354 <!-- JAL-2739 -->Hidden column marker in last column not
1355 rendered when switching back from Wrapped to normal view
1358 <!-- JAL-2768 -->Annotation display corrupted when
1359 scrolling right in unwapped alignment view
1362 <!-- JAL-2542 -->Existing features on subsequence
1363 incorrectly relocated when full sequence retrieved from
1367 <!-- JAL-2733 -->Last reported memory still shown when
1368 Desktop->Show Memory is unticked (OSX only)
1371 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1372 features of same type and group to be selected for
1376 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1377 alignments when hidden columns are present
1380 <!-- JAL-2392 -->Jalview freezes when loading and
1381 displaying several structures
1384 <!-- JAL-2732 -->Black outlines left after resizing or
1388 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1389 within the Jalview desktop on OSX
1392 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1393 when in wrapped alignment mode
1396 <!-- JAL-2636 -->Scale mark not shown when close to right
1397 hand end of alignment
1400 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1401 each selected sequence do not have correct start/end
1405 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1406 after canceling the Alignment Window's Font dialog
1409 <!-- JAL-2036 -->Show cross-references not enabled after
1410 restoring project until a new view is created
1413 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1414 URL links appears when only default EMBL-EBI link is
1415 configured (since 2.10.2b2)
1418 <!-- JAL-2775 -->Overview redraws whole window when box
1419 position is adjusted
1422 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1423 in a multi-chain structure when viewing alignment
1424 involving more than one chain (since 2.10)
1427 <!-- JAL-2811 -->Double residue highlights in cursor mode
1428 if new selection moves alignment window
1431 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1432 arrow key in cursor mode to pass hidden column marker
1435 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1436 that produces correctly annotated transcripts and products
1439 <!-- JAL-2776 -->Toggling a feature group after first time
1440 doesn't update associated structure view
1443 <em>Applet</em><br />
1446 <!-- JAL-2687 -->Concurrent modification exception when
1447 closing alignment panel
1450 <em>BioJSON</em><br />
1453 <!-- JAL-2546 -->BioJSON export does not preserve
1454 non-positional features
1457 <em>New Known Issues</em>
1460 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1461 sequence features correctly (for many previous versions of
1465 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1466 using cursor in wrapped panel other than top
1469 <!-- JAL-2791 -->Select columns containing feature ignores
1470 graduated colour threshold
1473 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1474 always preserve numbering and sequence features
1477 <em>Known Java 9 Issues</em>
1480 <!-- JAL-2902 -->Groovy Console very slow to open and is
1481 not responsive when entering characters (Webstart, Java
1488 <td width="60" nowrap>
1489 <div align="center">
1490 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1491 <em>2/10/2017</em></strong>
1494 <td><div align="left">
1495 <em>New features in Jalview Desktop</em>
1498 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1500 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1504 <td><div align="left">
1508 <td width="60" nowrap>
1509 <div align="center">
1510 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1511 <em>7/9/2017</em></strong>
1514 <td><div align="left">
1518 <!-- JAL-2588 -->Show gaps in overview window by colouring
1519 in grey (sequences used to be coloured grey, and gaps were
1523 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1527 <!-- JAL-2587 -->Overview updates immediately on increase
1528 in size and progress bar shown as higher resolution
1529 overview is recalculated
1534 <td><div align="left">
1538 <!-- JAL-2664 -->Overview window redraws every hidden
1539 column region row by row
1542 <!-- JAL-2681 -->duplicate protein sequences shown after
1543 retrieving Ensembl crossrefs for sequences from Uniprot
1546 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1547 format setting is unticked
1550 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1551 if group has show boxes format setting unticked
1554 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1555 autoscrolling whilst dragging current selection group to
1556 include sequences and columns not currently displayed
1559 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1560 assemblies are imported via CIF file
1563 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1564 displayed when threshold or conservation colouring is also
1568 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1572 <!-- JAL-2673 -->Jalview continues to scroll after
1573 dragging a selected region off the visible region of the
1577 <!-- JAL-2724 -->Cannot apply annotation based
1578 colourscheme to all groups in a view
1581 <!-- JAL-2511 -->IDs don't line up with sequences
1582 initially after font size change using the Font chooser or
1589 <td width="60" nowrap>
1590 <div align="center">
1591 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1594 <td><div align="left">
1595 <em>Calculations</em>
1599 <!-- JAL-1933 -->Occupancy annotation row shows number of
1600 ungapped positions in each column of the alignment.
1603 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1604 a calculation dialog box
1607 <!-- JAL-2379 -->Revised implementation of PCA for speed
1608 and memory efficiency (~30x faster)
1611 <!-- JAL-2403 -->Revised implementation of sequence
1612 similarity scores as used by Tree, PCA, Shading Consensus
1613 and other calculations
1616 <!-- JAL-2416 -->Score matrices are stored as resource
1617 files within the Jalview codebase
1620 <!-- JAL-2500 -->Trees computed on Sequence Feature
1621 Similarity may have different topology due to increased
1628 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1629 model for alignments and groups
1632 <!-- JAL-384 -->Custom shading schemes created via groovy
1639 <!-- JAL-2526 -->Efficiency improvements for interacting
1640 with alignment and overview windows
1643 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1647 <!-- JAL-2388 -->Hidden columns and sequences can be
1651 <!-- JAL-2611 -->Click-drag in visible area allows fine
1652 adjustment of visible position
1656 <em>Data import/export</em>
1659 <!-- JAL-2535 -->Posterior probability annotation from
1660 Stockholm files imported as sequence associated annotation
1663 <!-- JAL-2507 -->More robust per-sequence positional
1664 annotation input/output via stockholm flatfile
1667 <!-- JAL-2533 -->Sequence names don't include file
1668 extension when importing structure files without embedded
1669 names or PDB accessions
1672 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1673 format sequence substitution matrices
1676 <em>User Interface</em>
1679 <!-- JAL-2447 --> Experimental Features Checkbox in
1680 Desktop's Tools menu to hide or show untested features in
1684 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1685 via Overview or sequence motif search operations
1688 <!-- JAL-2547 -->Amend sequence features dialog box can be
1689 opened by double clicking gaps within sequence feature
1693 <!-- JAL-1476 -->Status bar message shown when not enough
1694 aligned positions were available to create a 3D structure
1698 <em>3D Structure</em>
1701 <!-- JAL-2430 -->Hidden regions in alignment views are not
1702 coloured in linked structure views
1705 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1706 file-based command exchange
1709 <!-- JAL-2375 -->Structure chooser automatically shows
1710 Cached Structures rather than querying the PDBe if
1711 structures are already available for sequences
1714 <!-- JAL-2520 -->Structures imported via URL are cached in
1715 the Jalview project rather than downloaded again when the
1716 project is reopened.
1719 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1720 to transfer Chimera's structure attributes as Jalview
1721 features, and vice-versa (<strong>Experimental
1725 <em>Web Services</em>
1728 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1731 <!-- JAL-2335 -->Filter non-standard amino acids and
1732 nucleotides when submitting to AACon and other MSA
1736 <!-- JAL-2316, -->URLs for viewing database
1737 cross-references provided by identifiers.org and the
1738 EMBL-EBI's MIRIAM DB
1745 <!-- JAL-2344 -->FileFormatI interface for describing and
1746 identifying file formats (instead of String constants)
1749 <!-- JAL-2228 -->FeatureCounter script refactored for
1750 efficiency when counting all displayed features (not
1751 backwards compatible with 2.10.1)
1754 <em>Example files</em>
1757 <!-- JAL-2631 -->Graduated feature colour style example
1758 included in the example feature file
1761 <em>Documentation</em>
1764 <!-- JAL-2339 -->Release notes reformatted for readability
1765 with the built-in Java help viewer
1768 <!-- JAL-1644 -->Find documentation updated with 'search
1769 sequence description' option
1775 <!-- JAL-2485, -->External service integration tests for
1776 Uniprot REST Free Text Search Client
1779 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1782 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1787 <td><div align="left">
1788 <em>Calculations</em>
1791 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1792 matrix - C->R should be '-3'<br />Old matrix restored
1793 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1795 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1796 Jalview's treatment of gaps in PCA and substitution matrix
1797 based Tree calculations.<br /> <br />In earlier versions
1798 of Jalview, gaps matching gaps were penalised, and gaps
1799 matching non-gaps penalised even more. In the PCA
1800 calculation, gaps were actually treated as non-gaps - so
1801 different costs were applied, which meant Jalview's PCAs
1802 were different to those produced by SeqSpace.<br />Jalview
1803 now treats gaps in the same way as SeqSpace (ie it scores
1804 them as 0). <br /> <br />Enter the following in the
1805 Groovy console to restore pre-2.10.2 behaviour:<br />
1806 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1807 // for 2.10.1 mode <br />
1808 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1809 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1810 these settings will affect all subsequent tree and PCA
1811 calculations (not recommended)</em></li>
1813 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1814 scaling of branch lengths for trees computed using
1815 Sequence Feature Similarity.
1818 <!-- JAL-2377 -->PCA calculation could hang when
1819 generating output report when working with highly
1820 redundant alignments
1823 <!-- JAL-2544 --> Sort by features includes features to
1824 right of selected region when gaps present on right-hand
1828 <em>User Interface</em>
1831 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1832 doesn't reselect a specific sequence's associated
1833 annotation after it was used for colouring a view
1836 <!-- JAL-2419 -->Current selection lost if popup menu
1837 opened on a region of alignment without groups
1840 <!-- JAL-2374 -->Popup menu not always shown for regions
1841 of an alignment with overlapping groups
1844 <!-- JAL-2310 -->Finder double counts if both a sequence's
1845 name and description match
1848 <!-- JAL-2370 -->Hiding column selection containing two
1849 hidden regions results in incorrect hidden regions
1852 <!-- JAL-2386 -->'Apply to all groups' setting when
1853 changing colour does not apply Conservation slider value
1857 <!-- JAL-2373 -->Percentage identity and conservation menu
1858 items do not show a tick or allow shading to be disabled
1861 <!-- JAL-2385 -->Conservation shading or PID threshold
1862 lost when base colourscheme changed if slider not visible
1865 <!-- JAL-2547 -->Sequence features shown in tooltip for
1866 gaps before start of features
1869 <!-- JAL-2623 -->Graduated feature colour threshold not
1870 restored to UI when feature colour is edited
1873 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1874 a time when scrolling vertically in wrapped mode.
1877 <!-- JAL-2630 -->Structure and alignment overview update
1878 as graduate feature colour settings are modified via the
1882 <!-- JAL-2034 -->Overview window doesn't always update
1883 when a group defined on the alignment is resized
1886 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1887 wrapped view result in positional status updates
1891 <!-- JAL-2563 -->Status bar doesn't show position for
1892 ambiguous amino acid and nucleotide symbols
1895 <!-- JAL-2602 -->Copy consensus sequence failed if
1896 alignment included gapped columns
1899 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1900 widgets don't permanently disappear
1903 <!-- JAL-2503 -->Cannot select or filter quantitative
1904 annotation that are shown only as column labels (e.g.
1905 T-Coffee column reliability scores)
1908 <!-- JAL-2594 -->Exception thrown if trying to create a
1909 sequence feature on gaps only
1912 <!-- JAL-2504 -->Features created with 'New feature'
1913 button from a Find inherit previously defined feature type
1914 rather than the Find query string
1917 <!-- JAL-2423 -->incorrect title in output window when
1918 exporting tree calculated in Jalview
1921 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1922 and then revealing them reorders sequences on the
1926 <!-- JAL-964 -->Group panel in sequence feature settings
1927 doesn't update to reflect available set of groups after
1928 interactively adding or modifying features
1931 <!-- JAL-2225 -->Sequence Database chooser unusable on
1935 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1936 only excluded gaps in current sequence and ignored
1943 <!-- JAL-2421 -->Overview window visible region moves
1944 erratically when hidden rows or columns are present
1947 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1948 Structure Viewer's colour menu don't correspond to
1952 <!-- JAL-2405 -->Protein specific colours only offered in
1953 colour and group colour menu for protein alignments
1956 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1957 reflect currently selected view or group's shading
1961 <!-- JAL-2624 -->Feature colour thresholds not respected
1962 when rendered on overview and structures when opacity at
1966 <!-- JAL-2589 -->User defined gap colour not shown in
1967 overview when features overlaid on alignment
1970 <!-- JAL-2567 -->Feature settings for different views not
1971 recovered correctly from Jalview project file
1974 <!-- JAL-2256 -->Feature colours in overview when first opened
1975 (automatically via preferences) are different to the main
1979 <em>Data import/export</em>
1982 <!-- JAL-2576 -->Very large alignments take a long time to
1986 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1987 added after a sequence was imported are not written to
1991 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1992 when importing RNA secondary structure via Stockholm
1995 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1996 not shown in correct direction for simple pseudoknots
1999 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2000 with lightGray or darkGray via features file (but can
2004 <!-- JAL-2383 -->Above PID colour threshold not recovered
2005 when alignment view imported from project
2008 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2009 structure and sequences extracted from structure files
2010 imported via URL and viewed in Jmol
2013 <!-- JAL-2520 -->Structures loaded via URL are saved in
2014 Jalview Projects rather than fetched via URL again when
2015 the project is loaded and the structure viewed
2018 <em>Web Services</em>
2021 <!-- JAL-2519 -->EnsemblGenomes example failing after
2022 release of Ensembl v.88
2025 <!-- JAL-2366 -->Proxy server address and port always
2026 appear enabled in Preferences->Connections
2029 <!-- JAL-2461 -->DAS registry not found exceptions
2030 removed from console output
2033 <!-- JAL-2582 -->Cannot retrieve protein products from
2034 Ensembl by Peptide ID
2037 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2038 created from SIFTs, and spurious 'Couldn't open structure
2039 in Chimera' errors raised after April 2017 update (problem
2040 due to 'null' string rather than empty string used for
2041 residues with no corresponding PDB mapping).
2044 <em>Application UI</em>
2047 <!-- JAL-2361 -->User Defined Colours not added to Colour
2051 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2052 case' residues (button in colourscheme editor debugged and
2053 new documentation and tooltips added)
2056 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2057 doesn't restore group-specific text colour thresholds
2060 <!-- JAL-2243 -->Feature settings panel does not update as
2061 new features are added to alignment
2064 <!-- JAL-2532 -->Cancel in feature settings reverts
2065 changes to feature colours via the Amend features dialog
2068 <!-- JAL-2506 -->Null pointer exception when attempting to
2069 edit graduated feature colour via amend features dialog
2073 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2074 selection menu changes colours of alignment views
2077 <!-- JAL-2426 -->Spurious exceptions in console raised
2078 from alignment calculation workers after alignment has
2082 <!-- JAL-1608 -->Typo in selection popup menu - Create
2083 groups now 'Create Group'
2086 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2087 Create/Undefine group doesn't always work
2090 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2091 shown again after pressing 'Cancel'
2094 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2095 adjusts start position in wrap mode
2098 <!-- JAL-2563 -->Status bar doesn't show positions for
2099 ambiguous amino acids
2102 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2103 CDS/Protein view after CDS sequences added for aligned
2107 <!-- JAL-2592 -->User defined colourschemes called 'User
2108 Defined' don't appear in Colours menu
2114 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2115 score models doesn't always result in an updated PCA plot
2118 <!-- JAL-2442 -->Features not rendered as transparent on
2119 overview or linked structure view
2122 <!-- JAL-2372 -->Colour group by conservation doesn't
2126 <!-- JAL-2517 -->Hitting Cancel after applying
2127 user-defined colourscheme doesn't restore original
2134 <!-- JAL-2314 -->Unit test failure:
2135 jalview.ws.jabaws.RNAStructExportImport setup fails
2138 <!-- JAL-2307 -->Unit test failure:
2139 jalview.ws.sifts.SiftsClientTest due to compatibility
2140 problems with deep array comparison equality asserts in
2141 successive versions of TestNG
2144 <!-- JAL-2479 -->Relocated StructureChooserTest and
2145 ParameterUtilsTest Unit tests to Network suite
2148 <em>New Known Issues</em>
2151 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2152 phase after a sequence motif find operation
2155 <!-- JAL-2550 -->Importing annotation file with rows
2156 containing just upper and lower case letters are
2157 interpreted as WUSS RNA secondary structure symbols
2160 <!-- JAL-2590 -->Cannot load and display Newick trees
2161 reliably from eggnog Ortholog database
2164 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2165 containing features of type Highlight' when 'B' is pressed
2166 to mark columns containing highlighted regions.
2169 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2170 doesn't always add secondary structure annotation.
2175 <td width="60" nowrap>
2176 <div align="center">
2177 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2180 <td><div align="left">
2184 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2185 for all consensus calculations
2188 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2191 <li>Updated Jalview's Certum code signing certificate
2194 <em>Application</em>
2197 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2198 set of database cross-references, sorted alphabetically
2201 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2202 from database cross references. Users with custom links
2203 will receive a <a href="webServices/urllinks.html#warning">warning
2204 dialog</a> asking them to update their preferences.
2207 <!-- JAL-2287-->Cancel button and escape listener on
2208 dialog warning user about disconnecting Jalview from a
2212 <!-- JAL-2320-->Jalview's Chimera control window closes if
2213 the Chimera it is connected to is shut down
2216 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2217 columns menu item to mark columns containing highlighted
2218 regions (e.g. from structure selections or results of a
2222 <!-- JAL-2284-->Command line option for batch-generation
2223 of HTML pages rendering alignment data with the BioJS
2233 <!-- JAL-2286 -->Columns with more than one modal residue
2234 are not coloured or thresholded according to percent
2235 identity (first observed in Jalview 2.8.2)
2238 <!-- JAL-2301 -->Threonine incorrectly reported as not
2242 <!-- JAL-2318 -->Updates to documentation pages (above PID
2243 threshold, amino acid properties)
2246 <!-- JAL-2292 -->Lower case residues in sequences are not
2247 reported as mapped to residues in a structure file in the
2251 <!--JAL-2324 -->Identical features with non-numeric scores
2252 could be added multiple times to a sequence
2255 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2256 bond features shown as two highlighted residues rather
2257 than a range in linked structure views, and treated
2258 correctly when selecting and computing trees from features
2261 <!-- JAL-2281-->Custom URL links for database
2262 cross-references are matched to database name regardless
2267 <em>Application</em>
2270 <!-- JAL-2282-->Custom URL links for specific database
2271 names without regular expressions also offer links from
2275 <!-- JAL-2315-->Removing a single configured link in the
2276 URL links pane in Connections preferences doesn't actually
2277 update Jalview configuration
2280 <!-- JAL-2272-->CTRL-Click on a selected region to open
2281 the alignment area popup menu doesn't work on El-Capitan
2284 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2285 files with similarly named sequences if dropped onto the
2289 <!-- JAL-2312 -->Additional mappings are shown for PDB
2290 entries where more chains exist in the PDB accession than
2291 are reported in the SIFTS file
2294 <!-- JAL-2317-->Certain structures do not get mapped to
2295 the structure view when displayed with Chimera
2298 <!-- JAL-2317-->No chains shown in the Chimera view
2299 panel's View->Show Chains submenu
2302 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2303 work for wrapped alignment views
2306 <!--JAL-2197 -->Rename UI components for running JPred
2307 predictions from 'JNet' to 'JPred'
2310 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2311 corrupted when annotation panel vertical scroll is not at
2312 first annotation row
2315 <!--JAL-2332 -->Attempting to view structure for Hen
2316 lysozyme results in a PDB Client error dialog box
2319 <!-- JAL-2319 -->Structure View's mapping report switched
2320 ranges for PDB and sequence for SIFTS
2323 SIFTS 'Not_Observed' residues mapped to non-existant
2327 <!-- <em>New Known Issues</em>
2334 <td width="60" nowrap>
2335 <div align="center">
2336 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2337 <em>25/10/2016</em></strong>
2340 <td><em>Application</em>
2342 <li>3D Structure chooser opens with 'Cached structures'
2343 view if structures already loaded</li>
2344 <li>Progress bar reports models as they are loaded to
2345 structure views</li>
2351 <li>Colour by conservation always enabled and no tick
2352 shown in menu when BLOSUM or PID shading applied</li>
2353 <li>FER1_ARATH and FER2_ARATH labels were switched in
2354 example sequences/projects/trees</li>
2356 <em>Application</em>
2358 <li>Jalview projects with views of local PDB structure
2359 files saved on Windows cannot be opened on OSX</li>
2360 <li>Multiple structure views can be opened and superposed
2361 without timeout for structures with multiple models or
2362 multiple sequences in alignment</li>
2363 <li>Cannot import or associated local PDB files without a
2364 PDB ID HEADER line</li>
2365 <li>RMSD is not output in Jmol console when superposition
2367 <li>Drag and drop of URL from Browser fails for Linux and
2368 OSX versions earlier than El Capitan</li>
2369 <li>ENA client ignores invalid content from ENA server</li>
2370 <li>Exceptions are not raised in console when ENA client
2371 attempts to fetch non-existent IDs via Fetch DB Refs UI
2373 <li>Exceptions are not raised in console when a new view
2374 is created on the alignment</li>
2375 <li>OSX right-click fixed for group selections: CMD-click
2376 to insert/remove gaps in groups and CTRL-click to open group
2379 <em>Build and deployment</em>
2381 <li>URL link checker now copes with multi-line anchor
2384 <em>New Known Issues</em>
2386 <li>Drag and drop from URL links in browsers do not work
2393 <td width="60" nowrap>
2394 <div align="center">
2395 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2398 <td><em>General</em>
2401 <!-- JAL-2124 -->Updated Spanish translations.
2404 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2405 for importing structure data to Jalview. Enables mmCIF and
2409 <!-- JAL-192 --->Alignment ruler shows positions relative to
2413 <!-- JAL-2202 -->Position/residue shown in status bar when
2414 mousing over sequence associated annotation
2417 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2421 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2422 '()', canonical '[]' and invalid '{}' base pair populations
2426 <!-- JAL-2092 -->Feature settings popup menu options for
2427 showing or hiding columns containing a feature
2430 <!-- JAL-1557 -->Edit selected group by double clicking on
2431 group and sequence associated annotation labels
2434 <!-- JAL-2236 -->Sequence name added to annotation label in
2435 select/hide columns by annotation and colour by annotation
2439 </ul> <em>Application</em>
2442 <!-- JAL-2050-->Automatically hide introns when opening a
2443 gene/transcript view
2446 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2450 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2451 structure mappings with the EMBL-EBI PDBe SIFTS database
2454 <!-- JAL-2079 -->Updated download sites used for Rfam and
2455 Pfam sources to xfam.org
2458 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2461 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2462 over sequences in Jalview
2465 <!-- JAL-2027-->Support for reverse-complement coding
2466 regions in ENA and EMBL
2469 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2470 for record retrieval via ENA rest API
2473 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2477 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2478 groovy script execution
2481 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2482 alignment window's Calculate menu
2485 <!-- JAL-1812 -->Allow groovy scripts that call
2486 Jalview.getAlignFrames() to run in headless mode
2489 <!-- JAL-2068 -->Support for creating new alignment
2490 calculation workers from groovy scripts
2493 <!-- JAL-1369 --->Store/restore reference sequence in
2497 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2498 associations are now saved/restored from project
2501 <!-- JAL-1993 -->Database selection dialog always shown
2502 before sequence fetcher is opened
2505 <!-- JAL-2183 -->Double click on an entry in Jalview's
2506 database chooser opens a sequence fetcher
2509 <!-- JAL-1563 -->Free-text search client for UniProt using
2510 the UniProt REST API
2513 <!-- JAL-2168 -->-nonews command line parameter to prevent
2514 the news reader opening
2517 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2518 querying stored in preferences
2521 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2525 <!-- JAL-1977-->Tooltips shown on database chooser
2528 <!-- JAL-391 -->Reverse complement function in calculate
2529 menu for nucleotide sequences
2532 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2533 and feature counts preserves alignment ordering (and
2534 debugged for complex feature sets).
2537 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2538 viewing structures with Jalview 2.10
2541 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2542 genome, transcript CCDS and gene ids via the Ensembl and
2543 Ensembl Genomes REST API
2546 <!-- JAL-2049 -->Protein sequence variant annotation
2547 computed for 'sequence_variant' annotation on CDS regions
2551 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2555 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2556 Ref Fetcher fails to match, or otherwise updates sequence
2557 data from external database records.
2560 <!-- JAL-2154 -->Revised Jalview Project format for
2561 efficient recovery of sequence coding and alignment
2562 annotation relationships.
2564 </ul> <!-- <em>Applet</em>
2575 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2579 <!-- JAL-2018-->Export features in Jalview format (again)
2580 includes graduated colourschemes
2583 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2584 working with big alignments and lots of hidden columns
2587 <!-- JAL-2053-->Hidden column markers not always rendered
2588 at right of alignment window
2591 <!-- JAL-2067 -->Tidied up links in help file table of
2595 <!-- JAL-2072 -->Feature based tree calculation not shown
2599 <!-- JAL-2075 -->Hidden columns ignored during feature
2600 based tree calculation
2603 <!-- JAL-2065 -->Alignment view stops updating when show
2604 unconserved enabled for group on alignment
2607 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2611 <!-- JAL-2146 -->Alignment column in status incorrectly
2612 shown as "Sequence position" when mousing over
2616 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2617 hidden columns present
2620 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2621 user created annotation added to alignment
2624 <!-- JAL-1841 -->RNA Structure consensus only computed for
2625 '()' base pair annotation
2628 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2629 in zero scores for all base pairs in RNA Structure
2633 <!-- JAL-2174-->Extend selection with columns containing
2637 <!-- JAL-2275 -->Pfam format writer puts extra space at
2638 beginning of sequence
2641 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2645 <!-- JAL-2238 -->Cannot create groups on an alignment from
2646 from a tree when t-coffee scores are shown
2649 <!-- JAL-1836,1967 -->Cannot import and view PDB
2650 structures with chains containing negative resnums (4q4h)
2653 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2657 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2658 to Clustal, PIR and PileUp output
2661 <!-- JAL-2008 -->Reordering sequence features that are
2662 not visible causes alignment window to repaint
2665 <!-- JAL-2006 -->Threshold sliders don't work in
2666 graduated colour and colour by annotation row for e-value
2667 scores associated with features and annotation rows
2670 <!-- JAL-1797 -->amino acid physicochemical conservation
2671 calculation should be case independent
2674 <!-- JAL-2173 -->Remove annotation also updates hidden
2678 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2679 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2680 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2683 <!-- JAL-2065 -->Null pointer exceptions and redraw
2684 problems when reference sequence defined and 'show
2685 non-conserved' enabled
2688 <!-- JAL-1306 -->Quality and Conservation are now shown on
2689 load even when Consensus calculation is disabled
2692 <!-- JAL-1932 -->Remove right on penultimate column of
2693 alignment does nothing
2696 <em>Application</em>
2699 <!-- JAL-1552-->URLs and links can't be imported by
2700 drag'n'drop on OSX when launched via webstart (note - not
2701 yet fixed for El Capitan)
2704 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2705 output when running on non-gb/us i18n platforms
2708 <!-- JAL-1944 -->Error thrown when exporting a view with
2709 hidden sequences as flat-file alignment
2712 <!-- JAL-2030-->InstallAnywhere distribution fails when
2716 <!-- JAL-2080-->Jalview very slow to launch via webstart
2717 (also hotfix for 2.9.0b2)
2720 <!-- JAL-2085 -->Cannot save project when view has a
2721 reference sequence defined
2724 <!-- JAL-1011 -->Columns are suddenly selected in other
2725 alignments and views when revealing hidden columns
2728 <!-- JAL-1989 -->Hide columns not mirrored in complement
2729 view in a cDNA/Protein splitframe
2732 <!-- JAL-1369 -->Cannot save/restore representative
2733 sequence from project when only one sequence is
2737 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2738 in Structure Chooser
2741 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2742 structure consensus didn't refresh annotation panel
2745 <!-- JAL-1962 -->View mapping in structure view shows
2746 mappings between sequence and all chains in a PDB file
2749 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2750 dialogs format columns correctly, don't display array
2751 data, sort columns according to type
2754 <!-- JAL-1975 -->Export complete shown after destination
2755 file chooser is cancelled during an image export
2758 <!-- JAL-2025 -->Error when querying PDB Service with
2759 sequence name containing special characters
2762 <!-- JAL-2024 -->Manual PDB structure querying should be
2766 <!-- JAL-2104 -->Large tooltips with broken HTML
2767 formatting don't wrap
2770 <!-- JAL-1128 -->Figures exported from wrapped view are
2771 truncated so L looks like I in consensus annotation
2774 <!-- JAL-2003 -->Export features should only export the
2775 currently displayed features for the current selection or
2779 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2780 after fetching cross-references, and restoring from
2784 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2785 followed in the structure viewer
2788 <!-- JAL-2163 -->Titles for individual alignments in
2789 splitframe not restored from project
2792 <!-- JAL-2145 -->missing autocalculated annotation at
2793 trailing end of protein alignment in transcript/product
2794 splitview when pad-gaps not enabled by default
2797 <!-- JAL-1797 -->amino acid physicochemical conservation
2801 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2802 article has been read (reopened issue due to
2803 internationalisation problems)
2806 <!-- JAL-1960 -->Only offer PDB structures in structure
2807 viewer based on sequence name, PDB and UniProt
2812 <!-- JAL-1976 -->No progress bar shown during export of
2816 <!-- JAL-2213 -->Structures not always superimposed after
2817 multiple structures are shown for one or more sequences.
2820 <!-- JAL-1370 -->Reference sequence characters should not
2821 be replaced with '.' when 'Show unconserved' format option
2825 <!-- JAL-1823 -->Cannot specify chain code when entering
2826 specific PDB id for sequence
2829 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2830 'Export hidden sequences' is enabled, but 'export hidden
2831 columns' is disabled.
2834 <!--JAL-2026-->Best Quality option in structure chooser
2835 selects lowest rather than highest resolution structures
2839 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2840 to sequence mapping in 'View Mappings' report
2843 <!-- JAL-2284 -->Unable to read old Jalview projects that
2844 contain non-XML data added after Jalvew wrote project.
2847 <!-- JAL-2118 -->Newly created annotation row reorders
2848 after clicking on it to create new annotation for a
2852 <!-- JAL-1980 -->Null Pointer Exception raised when
2853 pressing Add on an orphaned cut'n'paste window.
2855 <!-- may exclude, this is an external service stability issue JAL-1941
2856 -- > RNA 3D structure not added via DSSR service</li> -->
2861 <!-- JAL-2151 -->Incorrect columns are selected when
2862 hidden columns present before start of sequence
2865 <!-- JAL-1986 -->Missing dependencies on applet pages
2869 <!-- JAL-1947 -->Overview pixel size changes when
2870 sequences are hidden in applet
2873 <!-- JAL-1996 -->Updated instructions for applet
2874 deployment on examples pages.
2881 <td width="60" nowrap>
2882 <div align="center">
2883 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2884 <em>16/10/2015</em></strong>
2887 <td><em>General</em>
2889 <li>Time stamps for signed Jalview application and applet
2894 <em>Application</em>
2896 <li>Duplicate group consensus and conservation rows
2897 shown when tree is partitioned</li>
2898 <li>Erratic behaviour when tree partitions made with
2899 multiple cDNA/Protein split views</li>
2905 <td width="60" nowrap>
2906 <div align="center">
2907 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2908 <em>8/10/2015</em></strong>
2911 <td><em>General</em>
2913 <li>Updated Spanish translations of localized text for
2915 </ul> <em>Application</em>
2917 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2918 <li>Signed OSX InstallAnywhere installer<br></li>
2919 <li>Support for per-sequence based annotations in BioJSON</li>
2920 </ul> <em>Applet</em>
2922 <li>Split frame example added to applet examples page</li>
2923 </ul> <em>Build and Deployment</em>
2926 <!-- JAL-1888 -->New ant target for running Jalview's test
2934 <li>Mapping of cDNA to protein in split frames
2935 incorrect when sequence start > 1</li>
2936 <li>Broken images in filter column by annotation dialog
2938 <li>Feature colours not parsed from features file</li>
2939 <li>Exceptions and incomplete link URLs recovered when
2940 loading a features file containing HTML tags in feature
2944 <em>Application</em>
2946 <li>Annotations corrupted after BioJS export and
2948 <li>Incorrect sequence limits after Fetch DB References
2949 with 'trim retrieved sequences'</li>
2950 <li>Incorrect warning about deleting all data when
2951 deleting selected columns</li>
2952 <li>Patch to build system for shipping properly signed
2953 JNLP templates for webstart launch</li>
2954 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2955 unreleased structures for download or viewing</li>
2956 <li>Tab/space/return keystroke operation of EMBL-PDBe
2957 fetcher/viewer dialogs works correctly</li>
2958 <li>Disabled 'minimise' button on Jalview windows
2959 running on OSX to workaround redraw hang bug</li>
2960 <li>Split cDNA/Protein view position and geometry not
2961 recovered from jalview project</li>
2962 <li>Initial enabled/disabled state of annotation menu
2963 sorter 'show autocalculated first/last' corresponds to
2965 <li>Restoring of Clustal, RNA Helices and T-Coffee
2966 color schemes from BioJSON</li>
2970 <li>Reorder sequences mirrored in cDNA/Protein split
2972 <li>Applet with Jmol examples not loading correctly</li>
2978 <td><div align="center">
2979 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2981 <td><em>General</em>
2983 <li>Linked visualisation and analysis of DNA and Protein
2986 <li>Translated cDNA alignments shown as split protein
2987 and DNA alignment views</li>
2988 <li>Codon consensus annotation for linked protein and
2989 cDNA alignment views</li>
2990 <li>Link cDNA or Protein product sequences by loading
2991 them onto Protein or cDNA alignments</li>
2992 <li>Reconstruct linked cDNA alignment from aligned
2993 protein sequences</li>
2996 <li>Jmol integration updated to Jmol v14.2.14</li>
2997 <li>Import and export of Jalview alignment views as <a
2998 href="features/bioJsonFormat.html">BioJSON</a></li>
2999 <li>New alignment annotation file statements for
3000 reference sequences and marking hidden columns</li>
3001 <li>Reference sequence based alignment shading to
3002 highlight variation</li>
3003 <li>Select or hide columns according to alignment
3005 <li>Find option for locating sequences by description</li>
3006 <li>Conserved physicochemical properties shown in amino
3007 acid conservation row</li>
3008 <li>Alignments can be sorted by number of RNA helices</li>
3009 </ul> <em>Application</em>
3011 <li>New cDNA/Protein analysis capabilities
3013 <li>Get Cross-References should open a Split Frame
3014 view with cDNA/Protein</li>
3015 <li>Detect when nucleotide sequences and protein
3016 sequences are placed in the same alignment</li>
3017 <li>Split cDNA/Protein views are saved in Jalview
3022 <li>Use REST API to talk to Chimera</li>
3023 <li>Selected regions in Chimera are highlighted in linked
3024 Jalview windows</li>
3026 <li>VARNA RNA viewer updated to v3.93</li>
3027 <li>VARNA views are saved in Jalview Projects</li>
3028 <li>Pseudoknots displayed as Jalview RNA annotation can
3029 be shown in VARNA</li>
3031 <li>Make groups for selection uses marked columns as well
3032 as the active selected region</li>
3034 <li>Calculate UPGMA and NJ trees using sequence feature
3036 <li>New Export options
3038 <li>New Export Settings dialog to control hidden
3039 region export in flat file generation</li>
3041 <li>Export alignment views for display with the <a
3042 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3044 <li>Export scrollable SVG in HTML page</li>
3045 <li>Optional embedding of BioJSON data when exporting
3046 alignment figures to HTML</li>
3048 <li>3D structure retrieval and display
3050 <li>Free text and structured queries with the PDBe
3052 <li>PDBe Search API based discovery and selection of
3053 PDB structures for a sequence set</li>
3057 <li>JPred4 employed for protein secondary structure
3059 <li>Hide Insertions menu option to hide unaligned columns
3060 for one or a group of sequences</li>
3061 <li>Automatically hide insertions in alignments imported
3062 from the JPred4 web server</li>
3063 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3064 system on OSX<br />LGPL libraries courtesy of <a
3065 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3067 <li>changed 'View nucleotide structure' submenu to 'View
3068 VARNA 2D Structure'</li>
3069 <li>change "View protein structure" menu option to "3D
3072 </ul> <em>Applet</em>
3074 <li>New layout for applet example pages</li>
3075 <li>New parameters to enable SplitFrame view
3076 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3077 <li>New example demonstrating linked viewing of cDNA and
3078 Protein alignments</li>
3079 </ul> <em>Development and deployment</em>
3081 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3082 <li>Include installation type and git revision in build
3083 properties and console log output</li>
3084 <li>Jalview Github organisation, and new github site for
3085 storing BioJsMSA Templates</li>
3086 <li>Jalview's unit tests now managed with TestNG</li>
3089 <!-- <em>General</em>
3091 </ul> --> <!-- issues resolved --> <em>Application</em>
3093 <li>Escape should close any open find dialogs</li>
3094 <li>Typo in select-by-features status report</li>
3095 <li>Consensus RNA secondary secondary structure
3096 predictions are not highlighted in amber</li>
3097 <li>Missing gap character in v2.7 example file means
3098 alignment appears unaligned when pad-gaps is not enabled</li>
3099 <li>First switch to RNA Helices colouring doesn't colour
3100 associated structure views</li>
3101 <li>ID width preference option is greyed out when auto
3102 width checkbox not enabled</li>
3103 <li>Stopped a warning dialog from being shown when
3104 creating user defined colours</li>
3105 <li>'View Mapping' in structure viewer shows sequence
3106 mappings for just that viewer's sequences</li>
3107 <li>Workaround for superposing PDB files containing
3108 multiple models in Chimera</li>
3109 <li>Report sequence position in status bar when hovering
3110 over Jmol structure</li>
3111 <li>Cannot output gaps as '.' symbols with Selection ->
3112 output to text box</li>
3113 <li>Flat file exports of alignments with hidden columns
3114 have incorrect sequence start/end</li>
3115 <li>'Aligning' a second chain to a Chimera structure from
3117 <li>Colour schemes applied to structure viewers don't
3118 work for nucleotide</li>
3119 <li>Loading/cut'n'pasting an empty or invalid file leads
3120 to a grey/invisible alignment window</li>
3121 <li>Exported Jpred annotation from a sequence region
3122 imports to different position</li>
3123 <li>Space at beginning of sequence feature tooltips shown
3124 on some platforms</li>
3125 <li>Chimera viewer 'View | Show Chain' menu is not
3127 <li>'New View' fails with a Null Pointer Exception in
3128 console if Chimera has been opened</li>
3129 <li>Mouseover to Chimera not working</li>
3130 <li>Miscellaneous ENA XML feature qualifiers not
3132 <li>NPE in annotation renderer after 'Extract Scores'</li>
3133 <li>If two structures in one Chimera window, mouseover of
3134 either sequence shows on first structure</li>
3135 <li>'Show annotations' options should not make
3136 non-positional annotations visible</li>
3137 <li>Subsequence secondary structure annotation not shown
3138 in right place after 'view flanking regions'</li>
3139 <li>File Save As type unset when current file format is
3141 <li>Save as '.jar' option removed for saving Jalview
3143 <li>Colour by Sequence colouring in Chimera more
3145 <li>Cannot 'add reference annotation' for a sequence in
3146 several views on same alignment</li>
3147 <li>Cannot show linked products for EMBL / ENA records</li>
3148 <li>Jalview's tooltip wraps long texts containing no
3150 </ul> <em>Applet</em>
3152 <li>Jmol to JalviewLite mouseover/link not working</li>
3153 <li>JalviewLite can't import sequences with ID
3154 descriptions containing angle brackets</li>
3155 </ul> <em>General</em>
3157 <li>Cannot export and reimport RNA secondary structure
3158 via jalview annotation file</li>
3159 <li>Random helix colour palette for colour by annotation
3160 with RNA secondary structure</li>
3161 <li>Mouseover to cDNA from STOP residue in protein
3162 translation doesn't work.</li>
3163 <li>hints when using the select by annotation dialog box</li>
3164 <li>Jmol alignment incorrect if PDB file has alternate CA
3166 <li>FontChooser message dialog appears to hang after
3167 choosing 1pt font</li>
3168 <li>Peptide secondary structure incorrectly imported from
3169 annotation file when annotation display text includes 'e' or
3171 <li>Cannot set colour of new feature type whilst creating
3173 <li>cDNA translation alignment should not be sequence
3174 order dependent</li>
3175 <li>'Show unconserved' doesn't work for lower case
3177 <li>Nucleotide ambiguity codes involving R not recognised</li>
3178 </ul> <em>Deployment and Documentation</em>
3180 <li>Applet example pages appear different to the rest of
3181 www.jalview.org</li>
3182 </ul> <em>Application Known issues</em>
3184 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3185 <li>Misleading message appears after trying to delete
3187 <li>Jalview icon not shown in dock after InstallAnywhere
3188 version launches</li>
3189 <li>Fetching EMBL reference for an RNA sequence results
3190 fails with a sequence mismatch</li>
3191 <li>Corrupted or unreadable alignment display when
3192 scrolling alignment to right</li>
3193 <li>ArrayIndexOutOfBoundsException thrown when remove
3194 empty columns called on alignment with ragged gapped ends</li>
3195 <li>auto calculated alignment annotation rows do not get
3196 placed above or below non-autocalculated rows</li>
3197 <li>Jalview dekstop becomes sluggish at full screen in
3198 ultra-high resolution</li>
3199 <li>Cannot disable consensus calculation independently of
3200 quality and conservation</li>
3201 <li>Mouseover highlighting between cDNA and protein can
3202 become sluggish with more than one splitframe shown</li>
3203 </ul> <em>Applet Known Issues</em>
3205 <li>Core PDB parsing code requires Jmol</li>
3206 <li>Sequence canvas panel goes white when alignment
3207 window is being resized</li>
3213 <td><div align="center">
3214 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3216 <td><em>General</em>
3218 <li>Updated Java code signing certificate donated by
3220 <li>Features and annotation preserved when performing
3221 pairwise alignment</li>
3222 <li>RNA pseudoknot annotation can be
3223 imported/exported/displayed</li>
3224 <li>'colour by annotation' can colour by RNA and
3225 protein secondary structure</li>
3226 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3227 post-hoc with 2.9 release</em>)
3230 </ul> <em>Application</em>
3232 <li>Extract and display secondary structure for sequences
3233 with 3D structures</li>
3234 <li>Support for parsing RNAML</li>
3235 <li>Annotations menu for layout
3237 <li>sort sequence annotation rows by alignment</li>
3238 <li>place sequence annotation above/below alignment
3241 <li>Output in Stockholm format</li>
3242 <li>Internationalisation: improved Spanish (es)
3244 <li>Structure viewer preferences tab</li>
3245 <li>Disorder and Secondary Structure annotation tracks
3246 shared between alignments</li>
3247 <li>UCSF Chimera launch and linked highlighting from
3249 <li>Show/hide all sequence associated annotation rows for
3250 all or current selection</li>
3251 <li>disorder and secondary structure predictions
3252 available as dataset annotation</li>
3253 <li>Per-sequence rna helices colouring</li>
3256 <li>Sequence database accessions imported when fetching
3257 alignments from Rfam</li>
3258 <li>update VARNA version to 3.91</li>
3260 <li>New groovy scripts for exporting aligned positions,
3261 conservation values, and calculating sum of pairs scores.</li>
3262 <li>Command line argument to set default JABAWS server</li>
3263 <li>include installation type in build properties and
3264 console log output</li>
3265 <li>Updated Jalview project format to preserve dataset
3269 <!-- issues resolved --> <em>Application</em>
3271 <li>Distinguish alignment and sequence associated RNA
3272 structure in structure->view->VARNA</li>
3273 <li>Raise dialog box if user deletes all sequences in an
3275 <li>Pressing F1 results in documentation opening twice</li>
3276 <li>Sequence feature tooltip is wrapped</li>
3277 <li>Double click on sequence associated annotation
3278 selects only first column</li>
3279 <li>Redundancy removal doesn't result in unlinked
3280 leaves shown in tree</li>
3281 <li>Undos after several redundancy removals don't undo
3283 <li>Hide sequence doesn't hide associated annotation</li>
3284 <li>User defined colours dialog box too big to fit on
3285 screen and buttons not visible</li>
3286 <li>author list isn't updated if already written to
3287 Jalview properties</li>
3288 <li>Popup menu won't open after retrieving sequence
3290 <li>File open window for associate PDB doesn't open</li>
3291 <li>Left-then-right click on a sequence id opens a
3292 browser search window</li>
3293 <li>Cannot open sequence feature shading/sort popup menu
3294 in feature settings dialog</li>
3295 <li>better tooltip placement for some areas of Jalview
3297 <li>Allow addition of JABAWS Server which doesn't
3298 pass validation</li>
3299 <li>Web services parameters dialog box is too large to
3301 <li>Muscle nucleotide alignment preset obscured by
3303 <li>JABAWS preset submenus don't contain newly
3304 defined user preset</li>
3305 <li>MSA web services warns user if they were launched
3306 with invalid input</li>
3307 <li>Jalview cannot contact DAS Registy when running on
3310 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3311 'Superpose with' submenu not shown when new view
3315 </ul> <!-- <em>Applet</em>
3317 </ul> <em>General</em>
3319 </ul>--> <em>Deployment and Documentation</em>
3321 <li>2G and 1G options in launchApp have no effect on
3322 memory allocation</li>
3323 <li>launchApp service doesn't automatically open
3324 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3327 InstallAnywhere reports cannot find valid JVM when Java
3328 1.7_055 is available
3330 </ul> <em>Application Known issues</em>
3333 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3334 corrupted or unreadable alignment display when scrolling
3338 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3339 retrieval fails but progress bar continues for DAS retrieval
3340 with large number of ID
3343 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3344 flatfile output of visible region has incorrect sequence
3348 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3349 rna structure consensus doesn't update when secondary
3350 structure tracks are rearranged
3353 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3354 invalid rna structure positional highlighting does not
3355 highlight position of invalid base pairs
3358 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3359 out of memory errors are not raised when saving Jalview
3360 project from alignment window file menu
3363 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3364 Switching to RNA Helices colouring doesn't propagate to
3368 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3369 colour by RNA Helices not enabled when user created
3370 annotation added to alignment
3373 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3374 Jalview icon not shown on dock in Mountain Lion/Webstart
3376 </ul> <em>Applet Known Issues</em>
3379 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3380 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3383 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3384 Jalview and Jmol example not compatible with IE9
3387 <li>Sort by annotation score doesn't reverse order
3393 <td><div align="center">
3394 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3397 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3400 <li>Internationalisation of user interface (usually
3401 called i18n support) and translation for Spanish locale</li>
3402 <li>Define/Undefine group on current selection with
3403 Ctrl-G/Shift Ctrl-G</li>
3404 <li>Improved group creation/removal options in
3405 alignment/sequence Popup menu</li>
3406 <li>Sensible precision for symbol distribution
3407 percentages shown in logo tooltip.</li>
3408 <li>Annotation panel height set according to amount of
3409 annotation when alignment first opened</li>
3410 </ul> <em>Application</em>
3412 <li>Interactive consensus RNA secondary structure
3413 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3414 <li>Select columns containing particular features from
3415 Feature Settings dialog</li>
3416 <li>View all 'representative' PDB structures for selected
3418 <li>Update Jalview project format:
3420 <li>New file extension for Jalview projects '.jvp'</li>
3421 <li>Preserve sequence and annotation dataset (to
3422 store secondary structure annotation,etc)</li>
3423 <li>Per group and alignment annotation and RNA helix
3427 <li>New similarity measures for PCA and Tree calculation
3429 <li>Experimental support for retrieval and viewing of
3430 flanking regions for an alignment</li>
3434 <!-- issues resolved --> <em>Application</em>
3436 <li>logo keeps spinning and status remains at queued or
3437 running after job is cancelled</li>
3438 <li>cannot export features from alignments imported from
3439 Jalview/VAMSAS projects</li>
3440 <li>Buggy slider for web service parameters that take
3442 <li>Newly created RNA secondary structure line doesn't
3443 have 'display all symbols' flag set</li>
3444 <li>T-COFFEE alignment score shading scheme and other
3445 annotation shading not saved in Jalview project</li>
3446 <li>Local file cannot be loaded in freshly downloaded
3448 <li>Jalview icon not shown on dock in Mountain
3450 <li>Load file from desktop file browser fails</li>
3451 <li>Occasional NPE thrown when calculating large trees</li>
3452 <li>Cannot reorder or slide sequences after dragging an
3453 alignment onto desktop</li>
3454 <li>Colour by annotation dialog throws NPE after using
3455 'extract scores' function</li>
3456 <li>Loading/cut'n'pasting an empty file leads to a grey
3457 alignment window</li>
3458 <li>Disorder thresholds rendered incorrectly after
3459 performing IUPred disorder prediction</li>
3460 <li>Multiple group annotated consensus rows shown when
3461 changing 'normalise logo' display setting</li>
3462 <li>Find shows blank dialog after 'finished searching' if
3463 nothing matches query</li>
3464 <li>Null Pointer Exceptions raised when sorting by
3465 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3467 <li>Errors in Jmol console when structures in alignment
3468 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3470 <li>Not all working JABAWS services are shown in
3472 <li>JAVAWS version of Jalview fails to launch with
3473 'invalid literal/length code'</li>
3474 <li>Annotation/RNA Helix colourschemes cannot be applied
3475 to alignment with groups (actually fixed in 2.8.0b1)</li>
3476 <li>RNA Helices and T-Coffee Scores available as default
3479 </ul> <em>Applet</em>
3481 <li>Remove group option is shown even when selection is
3483 <li>Apply to all groups ticked but colourscheme changes
3484 don't affect groups</li>
3485 <li>Documented RNA Helices and T-Coffee Scores as valid
3486 colourscheme name</li>
3487 <li>Annotation labels drawn on sequence IDs when
3488 Annotation panel is not displayed</li>
3489 <li>Increased font size for dropdown menus on OSX and
3490 embedded windows</li>
3491 </ul> <em>Other</em>
3493 <li>Consensus sequence for alignments/groups with a
3494 single sequence were not calculated</li>
3495 <li>annotation files that contain only groups imported as
3496 annotation and junk sequences</li>
3497 <li>Fasta files with sequences containing '*' incorrectly
3498 recognised as PFAM or BLC</li>
3499 <li>conservation/PID slider apply all groups option
3500 doesn't affect background (2.8.0b1)
3502 <li>redundancy highlighting is erratic at 0% and 100%</li>
3503 <li>Remove gapped columns fails for sequences with ragged
3505 <li>AMSA annotation row with leading spaces is not
3506 registered correctly on import</li>
3507 <li>Jalview crashes when selecting PCA analysis for
3508 certain alignments</li>
3509 <li>Opening the colour by annotation dialog for an
3510 existing annotation based 'use original colours'
3511 colourscheme loses original colours setting</li>
3516 <td><div align="center">
3517 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3518 <em>30/1/2014</em></strong>
3522 <li>Trusted certificates for JalviewLite applet and
3523 Jalview Desktop application<br />Certificate was donated by
3524 <a href="https://www.certum.eu">Certum</a> to the Jalview
3525 open source project).
3527 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3528 <li>Output in Stockholm format</li>
3529 <li>Allow import of data from gzipped files</li>
3530 <li>Export/import group and sequence associated line
3531 graph thresholds</li>
3532 <li>Nucleotide substitution matrix that supports RNA and
3533 ambiguity codes</li>
3534 <li>Allow disorder predictions to be made on the current
3535 selection (or visible selection) in the same way that JPred
3537 <li>Groovy scripting for headless Jalview operation</li>
3538 </ul> <em>Other improvements</em>
3540 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3541 <li>COMBINE statement uses current SEQUENCE_REF and
3542 GROUP_REF scope to group annotation rows</li>
3543 <li>Support '' style escaping of quotes in Newick
3545 <li>Group options for JABAWS service by command line name</li>
3546 <li>Empty tooltip shown for JABA service options with a
3547 link but no description</li>
3548 <li>Select primary source when selecting authority in
3549 database fetcher GUI</li>
3550 <li>Add .mfa to FASTA file extensions recognised by
3552 <li>Annotation label tooltip text wrap</li>
3557 <li>Slow scrolling when lots of annotation rows are
3559 <li>Lots of NPE (and slowness) after creating RNA
3560 secondary structure annotation line</li>
3561 <li>Sequence database accessions not imported when
3562 fetching alignments from Rfam</li>
3563 <li>Incorrect SHMR submission for sequences with
3565 <li>View all structures does not always superpose
3567 <li>Option widgets in service parameters not updated to
3568 reflect user or preset settings</li>
3569 <li>Null pointer exceptions for some services without
3570 presets or adjustable parameters</li>
3571 <li>Discover PDB IDs entry in structure menu doesn't
3572 discover PDB xRefs</li>
3573 <li>Exception encountered while trying to retrieve
3574 features with DAS</li>
3575 <li>Lowest value in annotation row isn't coloured
3576 when colour by annotation (per sequence) is coloured</li>
3577 <li>Keyboard mode P jumps to start of gapped region when
3578 residue follows a gap</li>
3579 <li>Jalview appears to hang importing an alignment with
3580 Wrap as default or after enabling Wrap</li>
3581 <li>'Right click to add annotations' message
3582 shown in wrap mode when no annotations present</li>
3583 <li>Disorder predictions fail with NPE if no automatic
3584 annotation already exists on alignment</li>
3585 <li>oninit javascript function should be called after
3586 initialisation completes</li>
3587 <li>Remove redundancy after disorder prediction corrupts
3588 alignment window display</li>
3589 <li>Example annotation file in documentation is invalid</li>
3590 <li>Grouped line graph annotation rows are not exported
3591 to annotation file</li>
3592 <li>Multi-harmony analysis cannot be run when only two
3594 <li>Cannot create multiple groups of line graphs with
3595 several 'combine' statements in annotation file</li>
3596 <li>Pressing return several times causes Number Format
3597 exceptions in keyboard mode</li>
3598 <li>Multi-harmony (SHMMR) method doesn't submit
3599 correct partitions for input data</li>
3600 <li>Translation from DNA to Amino Acids fails</li>
3601 <li>Jalview fail to load newick tree with quoted label</li>
3602 <li>--headless flag isn't understood</li>
3603 <li>ClassCastException when generating EPS in headless
3605 <li>Adjusting sequence-associated shading threshold only
3606 changes one row's threshold</li>
3607 <li>Preferences and Feature settings panel panel
3608 doesn't open</li>
3609 <li>hide consensus histogram also hides conservation and
3610 quality histograms</li>
3615 <td><div align="center">
3616 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3618 <td><em>Application</em>
3620 <li>Support for JABAWS 2.0 Services (AACon alignment
3621 conservation, protein disorder and Clustal Omega)</li>
3622 <li>JABAWS server status indicator in Web Services
3624 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3625 in Jalview alignment window</li>
3626 <li>Updated Jalview build and deploy framework for OSX
3627 mountain lion, windows 7, and 8</li>
3628 <li>Nucleotide substitution matrix for PCA that supports
3629 RNA and ambiguity codes</li>
3631 <li>Improved sequence database retrieval GUI</li>
3632 <li>Support fetching and database reference look up
3633 against multiple DAS sources (Fetch all from in 'fetch db
3635 <li>Jalview project improvements
3637 <li>Store and retrieve the 'belowAlignment'
3638 flag for annotation</li>
3639 <li>calcId attribute to group annotation rows on the
3641 <li>Store AACon calculation settings for a view in
3642 Jalview project</li>
3646 <li>horizontal scrolling gesture support</li>
3647 <li>Visual progress indicator when PCA calculation is
3649 <li>Simpler JABA web services menus</li>
3650 <li>visual indication that web service results are still
3651 being retrieved from server</li>
3652 <li>Serialise the dialogs that are shown when Jalview
3653 starts up for first time</li>
3654 <li>Jalview user agent string for interacting with HTTP
3656 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3658 <li>Examples directory and Groovy library included in
3659 InstallAnywhere distribution</li>
3660 </ul> <em>Applet</em>
3662 <li>RNA alignment and secondary structure annotation
3663 visualization applet example</li>
3664 </ul> <em>General</em>
3666 <li>Normalise option for consensus sequence logo</li>
3667 <li>Reset button in PCA window to return dimensions to
3669 <li>Allow seqspace or Jalview variant of alignment PCA
3671 <li>PCA with either nucleic acid and protein substitution
3673 <li>Allow windows containing HTML reports to be exported
3675 <li>Interactive display and editing of RNA secondary
3676 structure contacts</li>
3677 <li>RNA Helix Alignment Colouring</li>
3678 <li>RNA base pair logo consensus</li>
3679 <li>Parse sequence associated secondary structure
3680 information in Stockholm files</li>
3681 <li>HTML Export database accessions and annotation
3682 information presented in tooltip for sequences</li>
3683 <li>Import secondary structure from LOCARNA clustalw
3684 style RNA alignment files</li>
3685 <li>import and visualise T-COFFEE quality scores for an
3687 <li>'colour by annotation' per sequence option to
3688 shade each sequence according to its associated alignment
3690 <li>New Jalview Logo</li>
3691 </ul> <em>Documentation and Development</em>
3693 <li>documentation for score matrices used in Jalview</li>
3694 <li>New Website!</li>
3696 <td><em>Application</em>
3698 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3699 wsdbfetch REST service</li>
3700 <li>Stop windows being moved outside desktop on OSX</li>
3701 <li>Filetype associations not installed for webstart
3703 <li>Jalview does not always retrieve progress of a JABAWS
3704 job execution in full once it is complete</li>
3705 <li>revise SHMR RSBS definition to ensure alignment is
3706 uploaded via ali_file parameter</li>
3707 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3708 <li>View all structures superposed fails with exception</li>
3709 <li>Jnet job queues forever if a very short sequence is
3710 submitted for prediction</li>
3711 <li>Cut and paste menu not opened when mouse clicked on
3713 <li>Putting fractional value into integer text box in
3714 alignment parameter dialog causes Jalview to hang</li>
3715 <li>Structure view highlighting doesn't work on
3717 <li>View all structures fails with exception shown in
3719 <li>Characters in filename associated with PDBEntry not
3720 escaped in a platform independent way</li>
3721 <li>Jalview desktop fails to launch with exception when
3723 <li>Tree calculation reports 'you must have 2 or more
3724 sequences selected' when selection is empty</li>
3725 <li>Jalview desktop fails to launch with jar signature
3726 failure when java web start temporary file caching is
3728 <li>DAS Sequence retrieval with range qualification
3729 results in sequence xref which includes range qualification</li>
3730 <li>Errors during processing of command line arguments
3731 cause progress bar (JAL-898) to be removed</li>
3732 <li>Replace comma for semi-colon option not disabled for
3733 DAS sources in sequence fetcher</li>
3734 <li>Cannot close news reader when JABAWS server warning
3735 dialog is shown</li>
3736 <li>Option widgets not updated to reflect user settings</li>
3737 <li>Edited sequence not submitted to web service</li>
3738 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3739 <li>InstallAnywhere installer doesn't unpack and run
3740 on OSX Mountain Lion</li>
3741 <li>Annotation panel not given a scroll bar when
3742 sequences with alignment annotation are pasted into the
3744 <li>Sequence associated annotation rows not associated
3745 when loaded from Jalview project</li>
3746 <li>Browser launch fails with NPE on java 1.7</li>
3747 <li>JABAWS alignment marked as finished when job was
3748 cancelled or job failed due to invalid input</li>
3749 <li>NPE with v2.7 example when clicking on Tree
3750 associated with all views</li>
3751 <li>Exceptions when copy/paste sequences with grouped
3752 annotation rows to new window</li>
3753 </ul> <em>Applet</em>
3755 <li>Sequence features are momentarily displayed before
3756 they are hidden using hidefeaturegroups applet parameter</li>
3757 <li>loading features via javascript API automatically
3758 enables feature display</li>
3759 <li>scrollToColumnIn javascript API method doesn't
3761 </ul> <em>General</em>
3763 <li>Redundancy removal fails for rna alignment</li>
3764 <li>PCA calculation fails when sequence has been selected
3765 and then deselected</li>
3766 <li>PCA window shows grey box when first opened on OSX</li>
3767 <li>Letters coloured pink in sequence logo when alignment
3768 coloured with clustalx</li>
3769 <li>Choosing fonts without letter symbols defined causes
3770 exceptions and redraw errors</li>
3771 <li>Initial PCA plot view is not same as manually
3772 reconfigured view</li>
3773 <li>Grouped annotation graph label has incorrect line
3775 <li>Grouped annotation graph label display is corrupted
3776 for lots of labels</li>
3781 <div align="center">
3782 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3785 <td><em>Application</em>
3787 <li>Jalview Desktop News Reader</li>
3788 <li>Tweaked default layout of web services menu</li>
3789 <li>View/alignment association menu to enable user to
3790 easily specify which alignment a multi-structure view takes
3791 its colours/correspondences from</li>
3792 <li>Allow properties file location to be specified as URL</li>
3793 <li>Extend Jalview project to preserve associations
3794 between many alignment views and a single Jmol display</li>
3795 <li>Store annotation row height in Jalview project file</li>
3796 <li>Annotation row column label formatting attributes
3797 stored in project file</li>
3798 <li>Annotation row order for auto-calculated annotation
3799 rows preserved in Jalview project file</li>
3800 <li>Visual progress indication when Jalview state is
3801 saved using Desktop window menu</li>
3802 <li>Visual indication that command line arguments are
3803 still being processed</li>
3804 <li>Groovy script execution from URL</li>
3805 <li>Colour by annotation default min and max colours in
3807 <li>Automatically associate PDB files dragged onto an
3808 alignment with sequences that have high similarity and
3810 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3811 <li>'view structures' option to open many
3812 structures in same window</li>
3813 <li>Sort associated views menu option for tree panel</li>
3814 <li>Group all JABA and non-JABA services for a particular
3815 analysis function in its own submenu</li>
3816 </ul> <em>Applet</em>
3818 <li>Userdefined and autogenerated annotation rows for
3820 <li>Adjustment of alignment annotation pane height</li>
3821 <li>Annotation scrollbar for annotation panel</li>
3822 <li>Drag to reorder annotation rows in annotation panel</li>
3823 <li>'automaticScrolling' parameter</li>
3824 <li>Allow sequences with partial ID string matches to be
3825 annotated from GFF/Jalview features files</li>
3826 <li>Sequence logo annotation row in applet</li>
3827 <li>Absolute paths relative to host server in applet
3828 parameters are treated as such</li>
3829 <li>New in the JalviewLite javascript API:
3831 <li>JalviewLite.js javascript library</li>
3832 <li>Javascript callbacks for
3834 <li>Applet initialisation</li>
3835 <li>Sequence/alignment mouse-overs and selections</li>
3838 <li>scrollTo row and column alignment scrolling
3840 <li>Select sequence/alignment regions from javascript</li>
3841 <li>javascript structure viewer harness to pass
3842 messages between Jmol and Jalview when running as
3843 distinct applets</li>
3844 <li>sortBy method</li>
3845 <li>Set of applet and application examples shipped
3846 with documentation</li>
3847 <li>New example to demonstrate JalviewLite and Jmol
3848 javascript message exchange</li>
3850 </ul> <em>General</em>
3852 <li>Enable Jmol displays to be associated with multiple
3853 multiple alignments</li>
3854 <li>Option to automatically sort alignment with new tree</li>
3855 <li>User configurable link to enable redirects to a
3856 www.Jalview.org mirror</li>
3857 <li>Jmol colours option for Jmol displays</li>
3858 <li>Configurable newline string when writing alignment
3859 and other flat files</li>
3860 <li>Allow alignment annotation description lines to
3861 contain html tags</li>
3862 </ul> <em>Documentation and Development</em>
3864 <li>Add groovy test harness for bulk load testing to
3866 <li>Groovy script to load and align a set of sequences
3867 using a web service before displaying the result in the
3868 Jalview desktop</li>
3869 <li>Restructured javascript and applet api documentation</li>
3870 <li>Ant target to publish example html files with applet
3872 <li>Netbeans project for building Jalview from source</li>
3873 <li>ant task to create online javadoc for Jalview source</li>
3875 <td><em>Application</em>
3877 <li>User defined colourscheme throws exception when
3878 current built in colourscheme is saved as new scheme</li>
3879 <li>AlignFrame->Save in application pops up save
3880 dialog for valid filename/format</li>
3881 <li>Cannot view associated structure for UniProt sequence</li>
3882 <li>PDB file association breaks for UniProt sequence
3884 <li>Associate PDB from file dialog does not tell you
3885 which sequence is to be associated with the file</li>
3886 <li>Find All raises null pointer exception when query
3887 only matches sequence IDs</li>
3888 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3889 <li>Jalview project with Jmol views created with Jalview
3890 2.4 cannot be loaded</li>
3891 <li>Filetype associations not installed for webstart
3893 <li>Two or more chains in a single PDB file associated
3894 with sequences in different alignments do not get coloured
3895 by their associated sequence</li>
3896 <li>Visibility status of autocalculated annotation row
3897 not preserved when project is loaded</li>
3898 <li>Annotation row height and visibility attributes not
3899 stored in Jalview project</li>
3900 <li>Tree bootstraps are not preserved when saved as a
3901 Jalview project</li>
3902 <li>Envision2 workflow tooltips are corrupted</li>
3903 <li>Enabling show group conservation also enables colour
3904 by conservation</li>
3905 <li>Duplicate group associated conservation or consensus
3906 created on new view</li>
3907 <li>Annotation scrollbar not displayed after 'show
3908 all hidden annotation rows' option selected</li>
3909 <li>Alignment quality not updated after alignment
3910 annotation row is hidden then shown</li>
3911 <li>Preserve colouring of structures coloured by
3912 sequences in pre Jalview 2.7 projects</li>
3913 <li>Web service job parameter dialog is not laid out
3915 <li>Web services menu not refreshed after 'reset
3916 services' button is pressed in preferences</li>
3917 <li>Annotation off by one in Jalview v2_3 example project</li>
3918 <li>Structures imported from file and saved in project
3919 get name like jalview_pdb1234.txt when reloaded</li>
3920 <li>Jalview does not always retrieve progress of a JABAWS
3921 job execution in full once it is complete</li>
3922 </ul> <em>Applet</em>
3924 <li>Alignment height set incorrectly when lots of
3925 annotation rows are displayed</li>
3926 <li>Relative URLs in feature HTML text not resolved to
3928 <li>View follows highlighting does not work for positions
3930 <li><= shown as = in tooltip</li>
3931 <li>Export features raises exception when no features
3933 <li>Separator string used for serialising lists of IDs
3934 for javascript api is modified when separator string
3935 provided as parameter</li>
3936 <li>Null pointer exception when selecting tree leaves for
3937 alignment with no existing selection</li>
3938 <li>Relative URLs for datasources assumed to be relative
3939 to applet's codebase</li>
3940 <li>Status bar not updated after finished searching and
3941 search wraps around to first result</li>
3942 <li>StructureSelectionManager instance shared between
3943 several Jalview applets causes race conditions and memory
3945 <li>Hover tooltip and mouseover of position on structure
3946 not sent from Jmol in applet</li>
3947 <li>Certain sequences of javascript method calls to
3948 applet API fatally hang browser</li>
3949 </ul> <em>General</em>
3951 <li>View follows structure mouseover scrolls beyond
3952 position with wrapped view and hidden regions</li>
3953 <li>Find sequence position moves to wrong residue
3954 with/without hidden columns</li>
3955 <li>Sequence length given in alignment properties window
3957 <li>InvalidNumberFormat exceptions thrown when trying to
3958 import PDB like structure files</li>
3959 <li>Positional search results are only highlighted
3960 between user-supplied sequence start/end bounds</li>
3961 <li>End attribute of sequence is not validated</li>
3962 <li>Find dialog only finds first sequence containing a
3963 given sequence position</li>
3964 <li>Sequence numbering not preserved in MSF alignment
3966 <li>Jalview PDB file reader does not extract sequence
3967 from nucleotide chains correctly</li>
3968 <li>Structure colours not updated when tree partition
3969 changed in alignment</li>
3970 <li>Sequence associated secondary structure not correctly
3971 parsed in interleaved stockholm</li>
3972 <li>Colour by annotation dialog does not restore current
3974 <li>Hiding (nearly) all sequences doesn't work
3976 <li>Sequences containing lowercase letters are not
3977 properly associated with their pdb files</li>
3978 </ul> <em>Documentation and Development</em>
3980 <li>schemas/JalviewWsParamSet.xsd corrupted by
3981 ApplyCopyright tool</li>
3986 <div align="center">
3987 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3990 <td><em>Application</em>
3992 <li>New warning dialog when the Jalview Desktop cannot
3993 contact web services</li>
3994 <li>JABA service parameters for a preset are shown in
3995 service job window</li>
3996 <li>JABA Service menu entries reworded</li>
4000 <li>Modeller PIR IO broken - cannot correctly import a
4001 pir file emitted by Jalview</li>
4002 <li>Existing feature settings transferred to new
4003 alignment view created from cut'n'paste</li>
4004 <li>Improved test for mixed amino/nucleotide chains when
4005 parsing PDB files</li>
4006 <li>Consensus and conservation annotation rows
4007 occasionally become blank for all new windows</li>
4008 <li>Exception raised when right clicking above sequences
4009 in wrapped view mode</li>
4010 </ul> <em>Application</em>
4012 <li>multiple multiply aligned structure views cause cpu
4013 usage to hit 100% and computer to hang</li>
4014 <li>Web Service parameter layout breaks for long user
4015 parameter names</li>
4016 <li>Jaba service discovery hangs desktop if Jaba server
4023 <div align="center">
4024 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4027 <td><em>Application</em>
4029 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4030 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4033 <li>Web Services preference tab</li>
4034 <li>Analysis parameters dialog box and user defined
4036 <li>Improved speed and layout of Envision2 service menu</li>
4037 <li>Superpose structures using associated sequence
4039 <li>Export coordinates and projection as CSV from PCA
4041 </ul> <em>Applet</em>
4043 <li>enable javascript: execution by the applet via the
4044 link out mechanism</li>
4045 </ul> <em>Other</em>
4047 <li>Updated the Jmol Jalview interface to work with Jmol
4049 <li>The Jalview Desktop and JalviewLite applet now
4050 require Java 1.5</li>
4051 <li>Allow Jalview feature colour specification for GFF
4052 sequence annotation files</li>
4053 <li>New 'colour by label' keword in Jalview feature file
4054 type colour specification</li>
4055 <li>New Jalview Desktop Groovy API method that allows a
4056 script to check if it being run in an interactive session or
4057 in a batch operation from the Jalview command line</li>
4061 <li>clustalx colourscheme colours Ds preferentially when
4062 both D+E are present in over 50% of the column</li>
4063 </ul> <em>Application</em>
4065 <li>typo in AlignmentFrame->View->Hide->all but
4066 selected Regions menu item</li>
4067 <li>sequence fetcher replaces ',' for ';' when the ',' is
4068 part of a valid accession ID</li>
4069 <li>fatal OOM if object retrieved by sequence fetcher
4070 runs out of memory</li>
4071 <li>unhandled Out of Memory Error when viewing pca
4072 analysis results</li>
4073 <li>InstallAnywhere builds fail to launch on OS X java
4074 10.5 update 4 (due to apple Java 1.6 update)</li>
4075 <li>Installanywhere Jalview silently fails to launch</li>
4076 </ul> <em>Applet</em>
4078 <li>Jalview.getFeatureGroups() raises an
4079 ArrayIndexOutOfBoundsException if no feature groups are
4086 <div align="center">
4087 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4093 <li>Alignment prettyprinter doesn't cope with long
4095 <li>clustalx colourscheme colours Ds preferentially when
4096 both D+E are present in over 50% of the column</li>
4097 <li>nucleic acid structures retrieved from PDB do not
4098 import correctly</li>
4099 <li>More columns get selected than were clicked on when a
4100 number of columns are hidden</li>
4101 <li>annotation label popup menu not providing correct
4102 add/hide/show options when rows are hidden or none are
4104 <li>Stockholm format shown in list of readable formats,
4105 and parser copes better with alignments from RFAM.</li>
4106 <li>CSV output of consensus only includes the percentage
4107 of all symbols if sequence logo display is enabled</li>
4109 </ul> <em>Applet</em>
4111 <li>annotation panel disappears when annotation is
4113 </ul> <em>Application</em>
4115 <li>Alignment view not redrawn properly when new
4116 alignment opened where annotation panel is visible but no
4117 annotations are present on alignment</li>
4118 <li>pasted region containing hidden columns is
4119 incorrectly displayed in new alignment window</li>
4120 <li>Jalview slow to complete operations when stdout is
4121 flooded (fix is to close the Jalview console)</li>
4122 <li>typo in AlignmentFrame->View->Hide->all but
4123 selected Rregions menu item.</li>
4124 <li>inconsistent group submenu and Format submenu entry
4125 'Un' or 'Non'conserved</li>
4126 <li>Sequence feature settings are being shared by
4127 multiple distinct alignments</li>
4128 <li>group annotation not recreated when tree partition is
4130 <li>double click on group annotation to select sequences
4131 does not propagate to associated trees</li>
4132 <li>Mac OSX specific issues:
4134 <li>exception raised when mouse clicked on desktop
4135 window background</li>
4136 <li>Desktop menu placed on menu bar and application
4137 name set correctly</li>
4138 <li>sequence feature settings not wide enough for the
4139 save feature colourscheme button</li>
4148 <div align="center">
4149 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4152 <td><em>New Capabilities</em>
4154 <li>URL links generated from description line for
4155 regular-expression based URL links (applet and application)
4157 <li>Non-positional feature URL links are shown in link
4159 <li>Linked viewing of nucleic acid sequences and
4161 <li>Automatic Scrolling option in View menu to display
4162 the currently highlighted region of an alignment.</li>
4163 <li>Order an alignment by sequence length, or using the
4164 average score or total feature count for each sequence.</li>
4165 <li>Shading features by score or associated description</li>
4166 <li>Subdivide alignment and groups based on identity of
4167 selected subsequence (Make Groups from Selection).</li>
4168 <li>New hide/show options including Shift+Control+H to
4169 hide everything but the currently selected region.</li>
4170 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4171 </ul> <em>Application</em>
4173 <li>Fetch DB References capabilities and UI expanded to
4174 support retrieval from DAS sequence sources</li>
4175 <li>Local DAS Sequence sources can be added via the
4176 command line or via the Add local source dialog box.</li>
4177 <li>DAS Dbref and DbxRef feature types are parsed as
4178 database references and protein_name is parsed as
4179 description line (BioSapiens terms).</li>
4180 <li>Enable or disable non-positional feature and database
4181 references in sequence ID tooltip from View menu in
4183 <!-- <li>New hidden columns and rows and representatives capabilities
4184 in annotations file (in progress - not yet fully implemented)</li> -->
4185 <li>Group-associated consensus, sequence logos and
4186 conservation plots</li>
4187 <li>Symbol distributions for each column can be exported
4188 and visualized as sequence logos</li>
4189 <li>Optionally scale multi-character column labels to fit
4190 within each column of annotation row<!-- todo for applet -->
4192 <li>Optional automatic sort of associated alignment view
4193 when a new tree is opened.</li>
4194 <li>Jalview Java Console</li>
4195 <li>Better placement of desktop window when moving
4196 between different screens.</li>
4197 <li>New preference items for sequence ID tooltip and
4198 consensus annotation</li>
4199 <li>Client to submit sequences and IDs to Envision2
4201 <li><em>Vamsas Capabilities</em>
4203 <li>Improved VAMSAS synchronization (Jalview archive
4204 used to preserve views, structures, and tree display
4206 <li>Import of vamsas documents from disk or URL via
4208 <li>Sharing of selected regions between views and
4209 with other VAMSAS applications (Experimental feature!)</li>
4210 <li>Updated API to VAMSAS version 0.2</li>
4212 </ul> <em>Applet</em>
4214 <li>Middle button resizes annotation row height</li>
4217 <li>sortByTree (true/false) - automatically sort the
4218 associated alignment view by the tree when a new tree is
4220 <li>showTreeBootstraps (true/false) - show or hide
4221 branch bootstraps (default is to show them if available)</li>
4222 <li>showTreeDistances (true/false) - show or hide
4223 branch lengths (default is to show them if available)</li>
4224 <li>showUnlinkedTreeNodes (true/false) - indicate if
4225 unassociated nodes should be highlighted in the tree
4227 <li>heightScale and widthScale (1.0 or more) -
4228 increase the height or width of a cell in the alignment
4229 grid relative to the current font size.</li>
4232 <li>Non-positional features displayed in sequence ID
4234 </ul> <em>Other</em>
4236 <li>Features format: graduated colour definitions and
4237 specification of feature scores</li>
4238 <li>Alignment Annotations format: new keywords for group
4239 associated annotation (GROUP_REF) and annotation row display
4240 properties (ROW_PROPERTIES)</li>
4241 <li>XML formats extended to support graduated feature
4242 colourschemes, group associated annotation, and profile
4243 visualization settings.</li></td>
4246 <li>Source field in GFF files parsed as feature source
4247 rather than description</li>
4248 <li>Non-positional features are now included in sequence
4249 feature and gff files (controlled via non-positional feature
4250 visibility in tooltip).</li>
4251 <li>URL links generated for all feature links (bugfix)</li>
4252 <li>Added URL embedding instructions to features file
4254 <li>Codons containing ambiguous nucleotides translated as
4255 'X' in peptide product</li>
4256 <li>Match case switch in find dialog box works for both
4257 sequence ID and sequence string and query strings do not
4258 have to be in upper case to match case-insensitively.</li>
4259 <li>AMSA files only contain first column of
4260 multi-character column annotation labels</li>
4261 <li>Jalview Annotation File generation/parsing consistent
4262 with documentation (e.g. Stockholm annotation can be
4263 exported and re-imported)</li>
4264 <li>PDB files without embedded PDB IDs given a friendly
4266 <li>Find incrementally searches ID string matches as well
4267 as subsequence matches, and correctly reports total number
4271 <li>Better handling of exceptions during sequence
4273 <li>Dasobert generated non-positional feature URL
4274 link text excludes the start_end suffix</li>
4275 <li>DAS feature and source retrieval buttons disabled
4276 when fetch or registry operations in progress.</li>
4277 <li>PDB files retrieved from URLs are cached properly</li>
4278 <li>Sequence description lines properly shared via
4280 <li>Sequence fetcher fetches multiple records for all
4282 <li>Ensured that command line das feature retrieval
4283 completes before alignment figures are generated.</li>
4284 <li>Reduced time taken when opening file browser for
4286 <li>isAligned check prior to calculating tree, PCA or
4287 submitting an MSA to JNet now excludes hidden sequences.</li>
4288 <li>User defined group colours properly recovered
4289 from Jalview projects.</li>
4298 <div align="center">
4299 <strong>2.4.0.b2</strong><br> 28/10/2009
4304 <li>Experimental support for google analytics usage
4306 <li>Jalview privacy settings (user preferences and docs).</li>
4311 <li>Race condition in applet preventing startup in
4313 <li>Exception when feature created from selection beyond
4314 length of sequence.</li>
4315 <li>Allow synthetic PDB files to be imported gracefully</li>
4316 <li>Sequence associated annotation rows associate with
4317 all sequences with a given id</li>
4318 <li>Find function matches case-insensitively for sequence
4319 ID string searches</li>
4320 <li>Non-standard characters do not cause pairwise
4321 alignment to fail with exception</li>
4322 </ul> <em>Application Issues</em>
4324 <li>Sequences are now validated against EMBL database</li>
4325 <li>Sequence fetcher fetches multiple records for all
4327 </ul> <em>InstallAnywhere Issues</em>
4329 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4330 issue with installAnywhere mechanism)</li>
4331 <li>Command line launching of JARs from InstallAnywhere
4332 version (java class versioning error fixed)</li>
4339 <div align="center">
4340 <strong>2.4</strong><br> 27/8/2008
4343 <td><em>User Interface</em>
4345 <li>Linked highlighting of codon and amino acid from
4346 translation and protein products</li>
4347 <li>Linked highlighting of structure associated with
4348 residue mapping to codon position</li>
4349 <li>Sequence Fetcher provides example accession numbers
4350 and 'clear' button</li>
4351 <li>MemoryMonitor added as an option under Desktop's
4353 <li>Extract score function to parse whitespace separated
4354 numeric data in description line</li>
4355 <li>Column labels in alignment annotation can be centred.</li>
4356 <li>Tooltip for sequence associated annotation give name
4358 </ul> <em>Web Services and URL fetching</em>
4360 <li>JPred3 web service</li>
4361 <li>Prototype sequence search client (no public services
4363 <li>Fetch either seed alignment or full alignment from
4365 <li>URL Links created for matching database cross
4366 references as well as sequence ID</li>
4367 <li>URL Links can be created using regular-expressions</li>
4368 </ul> <em>Sequence Database Connectivity</em>
4370 <li>Retrieval of cross-referenced sequences from other
4372 <li>Generalised database reference retrieval and
4373 validation to all fetchable databases</li>
4374 <li>Fetch sequences from DAS sources supporting the
4375 sequence command</li>
4376 </ul> <em>Import and Export</em>
4377 <li>export annotation rows as CSV for spreadsheet import</li>
4378 <li>Jalview projects record alignment dataset associations,
4379 EMBL products, and cDNA sequence mappings</li>
4380 <li>Sequence Group colour can be specified in Annotation
4382 <li>Ad-hoc colouring of group in Annotation File using RGB
4383 triplet as name of colourscheme</li>
4384 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4386 <li>treenode binding for VAMSAS tree exchange</li>
4387 <li>local editing and update of sequences in VAMSAS
4388 alignments (experimental)</li>
4389 <li>Create new or select existing session to join</li>
4390 <li>load and save of vamsas documents</li>
4391 </ul> <em>Application command line</em>
4393 <li>-tree parameter to open trees (introduced for passing
4395 <li>-fetchfrom command line argument to specify nicknames
4396 of DAS servers to query for alignment features</li>
4397 <li>-dasserver command line argument to add new servers
4398 that are also automatically queried for features</li>
4399 <li>-groovy command line argument executes a given groovy
4400 script after all input data has been loaded and parsed</li>
4401 </ul> <em>Applet-Application data exchange</em>
4403 <li>Trees passed as applet parameters can be passed to
4404 application (when using "View in full
4405 application")</li>
4406 </ul> <em>Applet Parameters</em>
4408 <li>feature group display control parameter</li>
4409 <li>debug parameter</li>
4410 <li>showbutton parameter</li>
4411 </ul> <em>Applet API methods</em>
4413 <li>newView public method</li>
4414 <li>Window (current view) specific get/set public methods</li>
4415 <li>Feature display control methods</li>
4416 <li>get list of currently selected sequences</li>
4417 </ul> <em>New Jalview distribution features</em>
4419 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4420 <li>RELEASE file gives build properties for the latest
4421 Jalview release.</li>
4422 <li>Java 1.1 Applet build made easier and donotobfuscate
4423 property controls execution of obfuscator</li>
4424 <li>Build target for generating source distribution</li>
4425 <li>Debug flag for javacc</li>
4426 <li>.jalview_properties file is documented (slightly) in
4427 jalview.bin.Cache</li>
4428 <li>Continuous Build Integration for stable and
4429 development version of Application, Applet and source
4434 <li>selected region output includes visible annotations
4435 (for certain formats)</li>
4436 <li>edit label/displaychar contains existing label/char
4438 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4439 <li>shorter peptide product names from EMBL records</li>
4440 <li>Newick string generator makes compact representations</li>
4441 <li>bootstrap values parsed correctly for tree files with
4443 <li>pathological filechooser bug avoided by not allowing
4444 filenames containing a ':'</li>
4445 <li>Fixed exception when parsing GFF files containing
4446 global sequence features</li>
4447 <li>Alignment datasets are finalized only when number of
4448 references from alignment sequences goes to zero</li>
4449 <li>Close of tree branch colour box without colour
4450 selection causes cascading exceptions</li>
4451 <li>occasional negative imgwidth exceptions</li>
4452 <li>better reporting of non-fatal warnings to user when
4453 file parsing fails.</li>
4454 <li>Save works when Jalview project is default format</li>
4455 <li>Save as dialog opened if current alignment format is
4456 not a valid output format</li>
4457 <li>UniProt canonical names introduced for both das and
4459 <li>Histidine should be midblue (not pink!) in Zappo</li>
4460 <li>error messages passed up and output when data read
4462 <li>edit undo recovers previous dataset sequence when
4463 sequence is edited</li>
4464 <li>allow PDB files without pdb ID HEADER lines (like
4465 those generated by MODELLER) to be read in properly</li>
4466 <li>allow reading of JPred concise files as a normal
4468 <li>Stockholm annotation parsing and alignment properties
4469 import fixed for PFAM records</li>
4470 <li>Structure view windows have correct name in Desktop
4472 <li>annotation consisting of sequence associated scores
4473 can be read and written correctly to annotation file</li>
4474 <li>Aligned cDNA translation to aligned peptide works
4476 <li>Fixed display of hidden sequence markers and
4477 non-italic font for representatives in Applet</li>
4478 <li>Applet Menus are always embedded in applet window on
4480 <li>Newly shown features appear at top of stack (in
4482 <li>Annotations added via parameter not drawn properly
4483 due to null pointer exceptions</li>
4484 <li>Secondary structure lines are drawn starting from
4485 first column of alignment</li>
4486 <li>UniProt XML import updated for new schema release in
4488 <li>Sequence feature to sequence ID match for Features
4489 file is case-insensitive</li>
4490 <li>Sequence features read from Features file appended to
4491 all sequences with matching IDs</li>
4492 <li>PDB structure coloured correctly for associated views
4493 containing a sub-sequence</li>
4494 <li>PDB files can be retrieved by applet from Jar files</li>
4495 <li>feature and annotation file applet parameters
4496 referring to different directories are retrieved correctly</li>
4497 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4498 <li>Fixed application hang whilst waiting for
4499 splash-screen version check to complete</li>
4500 <li>Applet properly URLencodes input parameter values
4501 when passing them to the launchApp service</li>
4502 <li>display name and local features preserved in results
4503 retrieved from web service</li>
4504 <li>Visual delay indication for sequence retrieval and
4505 sequence fetcher initialisation</li>
4506 <li>updated Application to use DAS 1.53e version of
4507 dasobert DAS client</li>
4508 <li>Re-instated Full AMSA support and .amsa file
4510 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4518 <div align="center">
4519 <strong>2.3</strong><br> 9/5/07
4524 <li>Jmol 11.0.2 integration</li>
4525 <li>PDB views stored in Jalview XML files</li>
4526 <li>Slide sequences</li>
4527 <li>Edit sequence in place</li>
4528 <li>EMBL CDS features</li>
4529 <li>DAS Feature mapping</li>
4530 <li>Feature ordering</li>
4531 <li>Alignment Properties</li>
4532 <li>Annotation Scores</li>
4533 <li>Sort by scores</li>
4534 <li>Feature/annotation editing in applet</li>
4539 <li>Headless state operation in 2.2.1</li>
4540 <li>Incorrect and unstable DNA pairwise alignment</li>
4541 <li>Cut and paste of sequences with annotation</li>
4542 <li>Feature group display state in XML</li>
4543 <li>Feature ordering in XML</li>
4544 <li>blc file iteration selection using filename # suffix</li>
4545 <li>Stockholm alignment properties</li>
4546 <li>Stockhom alignment secondary structure annotation</li>
4547 <li>2.2.1 applet had no feature transparency</li>
4548 <li>Number pad keys can be used in cursor mode</li>
4549 <li>Structure Viewer mirror image resolved</li>
4556 <div align="center">
4557 <strong>2.2.1</strong><br> 12/2/07
4562 <li>Non standard characters can be read and displayed
4563 <li>Annotations/Features can be imported/exported to the
4565 <li>Applet allows editing of sequence/annotation/group
4566 name & description
4567 <li>Preference setting to display sequence name in
4569 <li>Annotation file format extended to allow
4570 Sequence_groups to be defined
4571 <li>Default opening of alignment overview panel can be
4572 specified in preferences
4573 <li>PDB residue numbering annotation added to associated
4579 <li>Applet crash under certain Linux OS with Java 1.6
4581 <li>Annotation file export / import bugs fixed
4582 <li>PNG / EPS image output bugs fixed
4588 <div align="center">
4589 <strong>2.2</strong><br> 27/11/06
4594 <li>Multiple views on alignment
4595 <li>Sequence feature editing
4596 <li>"Reload" alignment
4597 <li>"Save" to current filename
4598 <li>Background dependent text colour
4599 <li>Right align sequence ids
4600 <li>User-defined lower case residue colours
4603 <li>Menu item accelerator keys
4604 <li>Control-V pastes to current alignment
4605 <li>Cancel button for DAS Feature Fetching
4606 <li>PCA and PDB Viewers zoom via mouse roller
4607 <li>User-defined sub-tree colours and sub-tree selection
4609 <li>'New Window' button on the 'Output to Text box'
4614 <li>New memory efficient Undo/Redo System
4615 <li>Optimised symbol lookups and conservation/consensus
4617 <li>Region Conservation/Consensus recalculated after
4619 <li>Fixed Remove Empty Columns Bug (empty columns at end
4621 <li>Slowed DAS Feature Fetching for increased robustness.
4623 <li>Made angle brackets in ASCII feature descriptions
4625 <li>Re-instated Zoom function for PCA
4626 <li>Sequence descriptions conserved in web service
4628 <li>UniProt ID discoverer uses any word separated by
4630 <li>WsDbFetch query/result association resolved
4631 <li>Tree leaf to sequence mapping improved
4632 <li>Smooth fonts switch moved to FontChooser dialog box.
4639 <div align="center">
4640 <strong>2.1.1</strong><br> 12/9/06
4645 <li>Copy consensus sequence to clipboard</li>
4650 <li>Image output - rightmost residues are rendered if
4651 sequence id panel has been resized</li>
4652 <li>Image output - all offscreen group boundaries are
4654 <li>Annotation files with sequence references - all
4655 elements in file are relative to sequence position</li>
4656 <li>Mac Applet users can use Alt key for group editing</li>
4662 <div align="center">
4663 <strong>2.1</strong><br> 22/8/06
4668 <li>MAFFT Multiple Alignment in default Web Service list</li>
4669 <li>DAS Feature fetching</li>
4670 <li>Hide sequences and columns</li>
4671 <li>Export Annotations and Features</li>
4672 <li>GFF file reading / writing</li>
4673 <li>Associate structures with sequences from local PDB
4675 <li>Add sequences to exisiting alignment</li>
4676 <li>Recently opened files / URL lists</li>
4677 <li>Applet can launch the full application</li>
4678 <li>Applet has transparency for features (Java 1.2
4680 <li>Applet has user defined colours parameter</li>
4681 <li>Applet can load sequences from parameter
4682 "sequence<em>x</em>"
4688 <li>Redundancy Panel reinstalled in the Applet</li>
4689 <li>Monospaced font - EPS / rescaling bug fixed</li>
4690 <li>Annotation files with sequence references bug fixed</li>
4696 <div align="center">
4697 <strong>2.08.1</strong><br> 2/5/06
4702 <li>Change case of selected region from Popup menu</li>
4703 <li>Choose to match case when searching</li>
4704 <li>Middle mouse button and mouse movement can compress /
4705 expand the visible width and height of the alignment</li>
4710 <li>Annotation Panel displays complete JNet results</li>
4716 <div align="center">
4717 <strong>2.08b</strong><br> 18/4/06
4723 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4724 <li>Righthand label on wrapped alignments shows correct
4731 <div align="center">
4732 <strong>2.08</strong><br> 10/4/06
4737 <li>Editing can be locked to the selection area</li>
4738 <li>Keyboard editing</li>
4739 <li>Create sequence features from searches</li>
4740 <li>Precalculated annotations can be loaded onto
4742 <li>Features file allows grouping of features</li>
4743 <li>Annotation Colouring scheme added</li>
4744 <li>Smooth fonts off by default - Faster rendering</li>
4745 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4750 <li>Drag & Drop fixed on Linux</li>
4751 <li>Jalview Archive file faster to load/save, sequence
4752 descriptions saved.</li>
4758 <div align="center">
4759 <strong>2.07</strong><br> 12/12/05
4764 <li>PDB Structure Viewer enhanced</li>
4765 <li>Sequence Feature retrieval and display enhanced</li>
4766 <li>Choose to output sequence start-end after sequence
4767 name for file output</li>
4768 <li>Sequence Fetcher WSDBFetch@EBI</li>
4769 <li>Applet can read feature files, PDB files and can be
4770 used for HTML form input</li>
4775 <li>HTML output writes groups and features</li>
4776 <li>Group editing is Control and mouse click</li>
4777 <li>File IO bugs</li>
4783 <div align="center">
4784 <strong>2.06</strong><br> 28/9/05
4789 <li>View annotations in wrapped mode</li>
4790 <li>More options for PCA viewer</li>
4795 <li>GUI bugs resolved</li>
4796 <li>Runs with -nodisplay from command line</li>
4802 <div align="center">
4803 <strong>2.05b</strong><br> 15/9/05
4808 <li>Choose EPS export as lineart or text</li>
4809 <li>Jar files are executable</li>
4810 <li>Can read in Uracil - maps to unknown residue</li>
4815 <li>Known OutOfMemory errors give warning message</li>
4816 <li>Overview window calculated more efficiently</li>
4817 <li>Several GUI bugs resolved</li>
4823 <div align="center">
4824 <strong>2.05</strong><br> 30/8/05
4829 <li>Edit and annotate in "Wrapped" view</li>
4834 <li>Several GUI bugs resolved</li>
4840 <div align="center">
4841 <strong>2.04</strong><br> 24/8/05
4846 <li>Hold down mouse wheel & scroll to change font
4852 <li>Improved JPred client reliability</li>
4853 <li>Improved loading of Jalview files</li>
4859 <div align="center">
4860 <strong>2.03</strong><br> 18/8/05
4865 <li>Set Proxy server name and port in preferences</li>
4866 <li>Multiple URL links from sequence ids</li>
4867 <li>User Defined Colours can have a scheme name and added
4869 <li>Choose to ignore gaps in consensus calculation</li>
4870 <li>Unix users can set default web browser</li>
4871 <li>Runs without GUI for batch processing</li>
4872 <li>Dynamically generated Web Service Menus</li>
4877 <li>InstallAnywhere download for Sparc Solaris</li>
4883 <div align="center">
4884 <strong>2.02</strong><br> 18/7/05
4890 <li>Copy & Paste order of sequences maintains
4891 alignment order.</li>
4897 <div align="center">
4898 <strong>2.01</strong><br> 12/7/05
4903 <li>Use delete key for deleting selection.</li>
4904 <li>Use Mouse wheel to scroll sequences.</li>
4905 <li>Help file updated to describe how to add alignment
4907 <li>Version and build date written to build properties
4909 <li>InstallAnywhere installation will check for updates
4910 at launch of Jalview.</li>
4915 <li>Delete gaps bug fixed.</li>
4916 <li>FileChooser sorts columns.</li>
4917 <li>Can remove groups one by one.</li>
4918 <li>Filechooser icons installed.</li>
4919 <li>Finder ignores return character when searching.
4920 Return key will initiate a search.<br>
4927 <div align="center">
4928 <strong>2.0</strong><br> 20/6/05
4933 <li>New codebase</li>