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>13/07/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-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
94 </ul> <em>Launching Jalview</em>
97 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
98 through a system property
102 <td align="left" valign="top">
105 <!-- JAL-3493 -->Escape does not clear highlights on the
106 alignment (Since Jalview 2.10.3)
109 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
110 doesn't slide selected sequences
113 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
114 multiple EMBL gene products shown forĀ a single contig
117 <!-- JAL-3696 -->Errors encountered when processing variants
118 from VCF files yield "Error processing VCF: Format specifier
122 <!-- JAL-3697 -->Count of features not shown can be wrong
123 when there are both local and complementary features mapped
124 to the position under the cursor
127 <!-- JAL-2983 -->Slider with negative range values not
128 rendered correctly in VAqua4 (Since 2.10.4)
134 <td width="60" align="center" nowrap><strong><a
135 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
136 <em>22/04/2020</em></strong></td>
137 <td align="left" valign="top">
140 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
141 'virtual' codon features shown on protein (or vice versa)
142 for display in alignments, on structure views (including
143 transfer to UCSF chimera), in feature reports and for
147 <!-- JAL-3121 -->Feature attributes from VCF files can be
148 exported and re-imported as GFF3 files
151 <!-- JAL-3376 -->Capture VCF "fixed column" values
152 POS, ID, QUAL, FILTER as Feature Attributes
155 <!-- JAL-3375 -->More robust VCF numeric data field
156 validation while parsing
159 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
163 <!-- JAL-3535 -->Feature Settings dialog title includes name
167 <!-- JAL-3538 -->Font anti-aliasing in alignment views
171 <!-- JAL-3468 -->Very long feature descriptions truncated in
175 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
176 with no feature types visible
179 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
181 </ul><em>Jalview Installer</em>
184 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
185 in console (may be null when Jalview launched as executable jar or via conda)
188 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
191 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
194 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
196 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
197 </ul> <em>Release processes</em>
200 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
203 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
205 </ul> <em>Build System</em>
208 <!-- JAL-3510 -->Clover updated to 4.4.1
211 <!-- JAL-3513 -->Test code included in Clover coverage
215 <em>Groovy Scripts</em>
218 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
219 to stdout containing the consensus sequence for each
220 alignment in a Jalview session
223 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
224 genomic sequence_variant annotation from CDS as
225 missense_variant or synonymous_variant on protein products.
229 <td align="left" valign="top">
232 <!-- JAL-3581 -->Hidden sequence markers still visible when
233 'Show hidden markers' option is not ticked
236 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
237 PNG output when 'Automatically set ID width' is set in
238 jalview preferences or properties file
241 <!-- JAL-3571 -->Feature Editor dialog can be opened when
242 'Show Sequence Features' option is not ticked
245 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
246 buttons in Feature Settings dialog are clicked when no
250 <!-- JAL-3412 -->ID margins for CDS and Protein views not
251 equal when split frame is first opened
254 <!-- JAL-3296 -->Sequence position numbers in status bar not
255 correct after editing a sequence's start position
258 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
259 with annotation and exceptions thrown when only a few
260 columns shown in wrapped mode
263 <!-- JAL-3386 -->Sequence IDs missing in headless export of
264 wrapped alignment figure with annotations
267 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
268 ID fails with ClassCastException
271 <!-- JAL-3389 -->Chimera session not restored from Jalview
275 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
276 feature settings dialog also selects columns
279 <!-- JAL-3473 -->SpinnerNumberModel causes
280 IllegalArgumentException in some circumstances
283 <!-- JAL-3534 -->Multiple feature settings dialogs can be
287 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
288 alignment window is closed
291 <!-- JAL-3406 -->Credits missing some authors in Jalview
292 help documentation for 2.11.0 release
295 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
296 includes Pfam ID as sequence's accession rather than its
299 </ul> <em>Java 11 Compatibility issues</em>
302 <!-- JAL-2987 -->OSX - Can't view some search results in
303 PDB/Uniprot search panel
305 </ul> <em>Installer</em>
308 <!-- JAL-3447 -->Jalview should not create file associations
309 for 3D structure files (.pdb, .mmcif. .cif)
311 </ul> <em>Repository and Source Release</em>
314 <!-- JAL-3474 -->removed obsolete .cvsignore files from
318 <!-- JAL-3541 -->Clover report generation running out of
321 </ul> <em>New Known Issues</em>
324 <!-- JAL-3523 -->OSX - Current working directory not
325 preserved when Jalview.app launched with parameters from
329 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
330 clipped in headless figure export when Right Align option
334 <!-- JAL-3542 -->Jalview Installation type always reports
335 'Source' in console output
338 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
339 bamboo server but run fine locally.
345 <td width="60" align="center" nowrap>
346 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
347 <em>04/07/2019</em></strong>
349 <td align="left" valign="top">
352 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
353 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
354 source project) rather than InstallAnywhere
357 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
358 settings, receive over the air updates and launch specific
359 versions via (<a href="https://github.com/threerings/getdown">Three
363 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
364 formats supported by Jalview (including .jvp project files)
367 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
368 arguments and switch between different getdown channels
371 <!-- JAL-3141 -->Backup files created when saving Jalview project
376 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
377 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
379 <!-- JAL-2620 -->Alternative genetic code tables for
380 'Translate as cDNA'</li>
382 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
383 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
386 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
387 implementation that allows updates) used for Sequence Feature collections</li>
389 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
390 features can be filtered and shaded according to any
391 associated attributes (e.g. variant attributes from VCF
392 file, or key-value pairs imported from column 9 of GFF
396 <!-- JAL-2879 -->Feature Attributes and shading schemes
397 stored and restored from Jalview Projects
400 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
401 recognise variant features
404 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
405 sequences (also coloured red by default)
408 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
412 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
413 algorithm (Z-sort/transparency and filter aware)
416 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
422 <!-- JAL-3205 -->Symmetric score matrices for faster
423 tree and PCA calculations
425 <li><strong>Principal Components Analysis Viewer</strong>
428 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
429 and Viewer state saved in Jalview Project
431 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
434 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
438 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
443 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
445 <li><strong>Speed and Efficiency</strong>
448 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
449 multiple groups when working with large alignments
452 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
456 <li><strong>User Interface</strong>
459 <!-- JAL-2933 -->Finder panel remembers last position in each
463 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
464 what is shown)<br />Only visible regions of alignment are shown by
465 default (can be changed in user preferences)
468 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
469 to the Overwrite Dialog
472 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
476 <!-- JAL-1244 -->Status bar shows bounds when dragging a
477 selection region, and gap count when inserting or deleting gaps
480 <!-- JAL-3132 -->Status bar updates over sequence and annotation
484 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
488 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
492 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
495 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
499 <!-- JAL-3181 -->Consistent ordering of links in sequence id
503 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
505 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
509 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
510 <li><strong>Java 11 Support (not yet on general release)</strong>
513 <!-- -->OSX GUI integrations for App menu's 'About' entry and
518 <em>Deprecations</em>
520 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
521 capabilities removed from the Jalview Desktop
523 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
524 unmarshalling has been replaced by JAXB for Jalview projects
525 and XML based data retrieval clients</li>
526 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
527 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
528 </ul> <em>Documentation</em>
530 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
531 not supported in EPS figure export
533 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
534 </ul> <em>Development and Release Processes</em>
537 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
540 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
542 <!-- JAL-3225 -->Eclipse project configuration managed with
546 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
547 Bamboo continuous integration for unattended Test Suite
551 <!-- JAL-2864 -->Memory test suite to detect leaks in common
555 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
559 <!-- JAL-3248 -->Developer documentation migrated to
560 markdown (with HTML rendering)
563 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
566 <!-- JAL-3289 -->New URLs for publishing development
571 <td align="left" valign="top">
574 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
577 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
578 superposition in Jmol fail on Windows
581 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
582 structures for sequences with lots of PDB structures
585 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
589 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
590 project involving multiple views
593 <!-- JAL-3164 -->Overview for complementary view in a linked
594 CDS/Protein alignment is not updated when Hide Columns by
595 Annotation dialog hides columns
598 <!-- JAL-3158 -->Selection highlighting in the complement of a
599 CDS/Protein alignment stops working after making a selection in
600 one view, then making another selection in the other view
603 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
607 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
608 Settings and Jalview Preferences panels
611 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
612 overview with large alignments
615 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
616 region if columns were selected by dragging right-to-left and the
617 mouse moved to the left of the first column
620 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
621 hidden column marker via scale popup menu
624 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
625 doesn't tell users the invalid URL
628 <!-- JAL-2816 -->Tooltips displayed for features filtered by
632 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
633 show cross references or Fetch Database References are shown in
637 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
638 peptide sequence (computed variant shown as p.Res.null)
641 <!-- JAL-2060 -->'Graduated colour' option not offered for
642 manually created features (where feature score is Float.NaN)
645 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
646 when columns are hidden
649 <!-- JAL-3082 -->Regular expression error for '(' in Select
650 Columns by Annotation description
653 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
654 out of Scale or Annotation Panel
657 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
661 <!-- JAL-3074 -->Left/right drag in annotation can scroll
665 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
669 <!-- JAL-3002 -->Column display is out by one after Page Down,
670 Page Up in wrapped mode
673 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
676 <!-- JAL-2932 -->Finder searches in minimised alignments
679 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
680 on opening an alignment
683 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
687 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
688 different groups in the alignment are selected
691 <!-- JAL-2717 -->Internationalised colour scheme names not shown
695 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
699 <!-- JAL-3125 -->Value input for graduated feature colour
700 threshold gets 'unrounded'
703 <!-- JAL-2982 -->PCA image export doesn't respect background
707 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
710 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
713 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
717 <!-- JAL-2964 -->Associate Tree with All Views not restored from
721 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
722 shown in complementary view
725 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
726 without normalisation
729 <!-- JAL-3021 -->Sequence Details report should open positioned at top
733 <!-- JAL-914 -->Help page can be opened twice
736 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
738 </ul> <em>Editing</em>
741 <!-- JAL-2822 -->Start and End should be updated when sequence
742 data at beginning or end of alignment added/removed via 'Edit'
746 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
747 relocate sequence features correctly when start of sequence is
748 removed (Known defect since 2.10)
751 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
752 dialog corrupts dataset sequence
755 <!-- JAL-868 -->Structure colours not updated when associated tree
756 repartitions the alignment view (Regression in 2.10.5)
758 </ul> <em>Datamodel</em>
761 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
762 sequence's End is greater than its length
764 </ul> <em>Bugs fixed for Java 11 Support (not yet on
765 general release)</em>
768 <!-- JAL-3288 -->Menus work properly in split-screen
770 </ul> <em>New Known Defects</em>
773 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
776 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
777 regions of protein alignment.
780 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
781 is restored from a Jalview 2.11 project
784 <!-- JAL-3213 -->Alignment panel height can be too small after
788 <!-- JAL-3240 -->Display is incorrect after removing gapped
789 columns within hidden columns
792 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
793 window after dragging left to select columns to left of visible
797 <!-- JAL-2876 -->Features coloured according to their description
798 string and thresholded by score in earlier versions of Jalview are
799 not shown as thresholded features in 2.11. To workaround please
800 create a Score filter instead.
803 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
805 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
808 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
809 alignments with multiple views can close views unexpectedly
812 <em>Java 11 Specific defects</em>
815 <!-- JAL-3235 -->Jalview Properties file is not sorted
816 alphabetically when saved
822 <td width="60" nowrap>
824 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
827 <td><div align="left">
831 <!-- JAL-3101 -->Default memory for Jalview webstart and
832 InstallAnywhere increased to 1G.
835 <!-- JAL-247 -->Hidden sequence markers and representative
836 sequence bolding included when exporting alignment as EPS,
837 SVG, PNG or HTML. <em>Display is configured via the
838 Format menu, or for command-line use via a Jalview
839 properties file.</em>
842 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
843 API and sequence data now imported as JSON.
846 <!-- JAL-3065 -->Change in recommended way of starting
847 Jalview via a Java command line: add jars in lib directory
848 to CLASSPATH, rather than via the deprecated java.ext.dirs
855 <!-- JAL-3047 -->Support added to execute test suite
856 instrumented with <a href="http://openclover.org/">Open
861 <td><div align="left">
865 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
866 row shown in Feredoxin Structure alignment view of example
870 <!-- JAL-2854 -->Annotation obscures sequences if lots of
871 annotation displayed.
874 <!-- JAL-3107 -->Group conservation/consensus not shown
875 for newly created group when 'Apply to all groups'
879 <!-- JAL-3087 -->Corrupted display when switching to
880 wrapped mode when sequence panel's vertical scrollbar is
884 <!-- JAL-3003 -->Alignment is black in exported EPS file
885 when sequences are selected in exported view.</em>
888 <!-- JAL-3059 -->Groups with different coloured borders
889 aren't rendered with correct colour.
892 <!-- JAL-3092 -->Jalview could hang when importing certain
893 types of knotted RNA secondary structure.
896 <!-- JAL-3095 -->Sequence highlight and selection in
897 trimmed VARNA 2D structure is incorrect for sequences that
901 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
902 annotation when columns are inserted into an alignment,
903 and when exporting as Stockholm flatfile.
906 <!-- JAL-3053 -->Jalview annotation rows containing upper
907 and lower-case 'E' and 'H' do not automatically get
908 treated as RNA secondary structure.
911 <!-- JAL-3106 -->.jvp should be used as default extension
912 (not .jar) when saving a Jalview project file.
915 <!-- JAL-3105 -->Mac Users: closing a window correctly
916 transfers focus to previous window on OSX
919 <em>Java 10 Issues Resolved</em>
922 <!-- JAL-2988 -->OSX - Can't save new files via the File
923 or export menus by typing in a name into the Save dialog
927 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
928 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
929 'look and feel' which has improved compatibility with the
930 latest version of OSX.
937 <td width="60" nowrap>
939 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
940 <em>7/06/2018</em></strong>
943 <td><div align="left">
947 <!-- JAL-2920 -->Use HGVS nomenclature for variant
948 annotation retrieved from Uniprot
951 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
952 onto the Jalview Desktop
956 <td><div align="left">
960 <!-- JAL-3017 -->Cannot import features with multiple
961 variant elements (blocks import of some Uniprot records)
964 <!-- JAL-2997 -->Clustal files with sequence positions in
965 right-hand column parsed correctly
968 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
969 not alignment area in exported graphic
972 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
973 window has input focus
976 <!-- JAL-2992 -->Annotation panel set too high when
977 annotation added to view (Windows)
980 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
981 network connectivity is poor
984 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
985 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
986 the currently open URL and links from a page viewed in
987 Firefox or Chrome on Windows is now fully supported. If
988 you are using Edge, only links in the page can be
989 dragged, and with Internet Explorer, only the currently
990 open URL in the browser can be dropped onto Jalview.</em>
993 <em>New Known Defects</em>
995 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1000 <td width="60" nowrap>
1001 <div align="center">
1002 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1005 <td><div align="left">
1009 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1010 for disabling automatic superposition of multiple
1011 structures and open structures in existing views
1014 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1015 ID and annotation area margins can be click-dragged to
1019 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1023 <!-- JAL-2759 -->Improved performance for large alignments
1024 and lots of hidden columns
1027 <!-- JAL-2593 -->Improved performance when rendering lots
1028 of features (particularly when transparency is disabled)
1031 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1032 exchange of Jalview features and Chimera attributes made
1038 <td><div align="left">
1041 <!-- JAL-2899 -->Structure and Overview aren't updated
1042 when Colour By Annotation threshold slider is adjusted
1045 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1046 overlapping alignment panel
1049 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1053 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1054 improved: CDS not handled correctly if transcript has no
1058 <!-- JAL-2321 -->Secondary structure and temperature
1059 factor annotation not added to sequence when local PDB
1060 file associated with it by drag'n'drop or structure
1064 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1065 dialog doesn't import PDB files dropped on an alignment
1068 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1069 scroll bar doesn't work for some CDS/Protein views
1072 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1073 Java 1.8u153 onwards and Java 1.9u4+.
1076 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1077 columns in annotation row
1080 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1081 honored in batch mode
1084 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1085 for structures added to existing Jmol view
1088 <!-- JAL-2223 -->'View Mappings' includes duplicate
1089 entries after importing project with multiple views
1092 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1093 protein sequences via SIFTS from associated PDB entries
1094 with negative residue numbers or missing residues fails
1097 <!-- JAL-2952 -->Exception when shading sequence with negative
1098 Temperature Factor values from annotated PDB files (e.g.
1099 as generated by CONSURF)
1102 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1103 tooltip doesn't include a text description of mutation
1106 <!-- JAL-2922 -->Invert displayed features very slow when
1107 structure and/or overview windows are also shown
1110 <!-- JAL-2954 -->Selecting columns from highlighted regions
1111 very slow for alignments with large numbers of sequences
1114 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1115 with 'StringIndexOutOfBounds'
1118 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1119 platforms running Java 10
1122 <!-- JAL-2960 -->Adding a structure to existing structure
1123 view appears to do nothing because the view is hidden behind the alignment view
1129 <!-- JAL-2926 -->Copy consensus sequence option in applet
1130 should copy the group consensus when popup is opened on it
1136 <!-- JAL-2913 -->Fixed ID width preference is not respected
1139 <em>New Known Defects</em>
1142 <!-- JAL-2973 --> Exceptions occasionally raised when
1143 editing a large alignment and overview is displayed
1146 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1147 repeatedly after a series of edits even when the overview
1148 is no longer reflecting updates
1151 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1152 structures for protein subsequence (if 'Trim Retrieved
1153 Sequences' enabled) or Ensembl isoforms (Workaround in
1154 2.10.4 is to fail back to N&W mapping)
1157 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1158 option gives blank output
1165 <td width="60" nowrap>
1166 <div align="center">
1167 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1170 <td><div align="left">
1171 <ul><li>Updated Certum Codesigning Certificate
1172 (Valid till 30th November 2018)</li></ul></div></td>
1173 <td><div align="left">
1174 <em>Desktop</em><ul>
1176 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1177 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1178 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1179 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1180 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1181 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1182 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1188 <td width="60" nowrap>
1189 <div align="center">
1190 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1193 <td><div align="left">
1197 <!-- JAL-2446 -->Faster and more efficient management and
1198 rendering of sequence features
1201 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1202 429 rate limit request hander
1205 <!-- JAL-2773 -->Structure views don't get updated unless
1206 their colours have changed
1209 <!-- JAL-2495 -->All linked sequences are highlighted for
1210 a structure mousover (Jmol) or selection (Chimera)
1213 <!-- JAL-2790 -->'Cancel' button in progress bar for
1214 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1217 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1218 view from Ensembl locus cross-references
1221 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1225 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1226 feature can be disabled
1229 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1230 PDB easier retrieval of sequences for lists of IDs
1233 <!-- JAL-2758 -->Short names for sequences retrieved from
1239 <li>Groovy interpreter updated to 2.4.12</li>
1240 <li>Example groovy script for generating a matrix of
1241 percent identity scores for current alignment.</li>
1243 <em>Testing and Deployment</em>
1246 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1250 <td><div align="left">
1254 <!-- JAL-2643 -->Pressing tab after updating the colour
1255 threshold text field doesn't trigger an update to the
1259 <!-- JAL-2682 -->Race condition when parsing sequence ID
1263 <!-- JAL-2608 -->Overview windows are also closed when
1264 alignment window is closed
1267 <!-- JAL-2548 -->Export of features doesn't always respect
1271 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1272 takes a long time in Cursor mode
1278 <!-- JAL-2777 -->Structures with whitespace chainCode
1279 cannot be viewed in Chimera
1282 <!-- JAL-2728 -->Protein annotation panel too high in
1286 <!-- JAL-2757 -->Can't edit the query after the server
1287 error warning icon is shown in Uniprot and PDB Free Text
1291 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1294 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1297 <!-- JAL-2739 -->Hidden column marker in last column not
1298 rendered when switching back from Wrapped to normal view
1301 <!-- JAL-2768 -->Annotation display corrupted when
1302 scrolling right in unwapped alignment view
1305 <!-- JAL-2542 -->Existing features on subsequence
1306 incorrectly relocated when full sequence retrieved from
1310 <!-- JAL-2733 -->Last reported memory still shown when
1311 Desktop->Show Memory is unticked (OSX only)
1314 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1315 features of same type and group to be selected for
1319 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1320 alignments when hidden columns are present
1323 <!-- JAL-2392 -->Jalview freezes when loading and
1324 displaying several structures
1327 <!-- JAL-2732 -->Black outlines left after resizing or
1331 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1332 within the Jalview desktop on OSX
1335 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1336 when in wrapped alignment mode
1339 <!-- JAL-2636 -->Scale mark not shown when close to right
1340 hand end of alignment
1343 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1344 each selected sequence do not have correct start/end
1348 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1349 after canceling the Alignment Window's Font dialog
1352 <!-- JAL-2036 -->Show cross-references not enabled after
1353 restoring project until a new view is created
1356 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1357 URL links appears when only default EMBL-EBI link is
1358 configured (since 2.10.2b2)
1361 <!-- JAL-2775 -->Overview redraws whole window when box
1362 position is adjusted
1365 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1366 in a multi-chain structure when viewing alignment
1367 involving more than one chain (since 2.10)
1370 <!-- JAL-2811 -->Double residue highlights in cursor mode
1371 if new selection moves alignment window
1374 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1375 arrow key in cursor mode to pass hidden column marker
1378 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1379 that produces correctly annotated transcripts and products
1382 <!-- JAL-2776 -->Toggling a feature group after first time
1383 doesn't update associated structure view
1386 <em>Applet</em><br />
1389 <!-- JAL-2687 -->Concurrent modification exception when
1390 closing alignment panel
1393 <em>BioJSON</em><br />
1396 <!-- JAL-2546 -->BioJSON export does not preserve
1397 non-positional features
1400 <em>New Known Issues</em>
1403 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1404 sequence features correctly (for many previous versions of
1408 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1409 using cursor in wrapped panel other than top
1412 <!-- JAL-2791 -->Select columns containing feature ignores
1413 graduated colour threshold
1416 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1417 always preserve numbering and sequence features
1420 <em>Known Java 9 Issues</em>
1423 <!-- JAL-2902 -->Groovy Console very slow to open and is
1424 not responsive when entering characters (Webstart, Java
1431 <td width="60" nowrap>
1432 <div align="center">
1433 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1434 <em>2/10/2017</em></strong>
1437 <td><div align="left">
1438 <em>New features in Jalview Desktop</em>
1441 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1443 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1447 <td><div align="left">
1451 <td width="60" nowrap>
1452 <div align="center">
1453 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1454 <em>7/9/2017</em></strong>
1457 <td><div align="left">
1461 <!-- JAL-2588 -->Show gaps in overview window by colouring
1462 in grey (sequences used to be coloured grey, and gaps were
1466 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1470 <!-- JAL-2587 -->Overview updates immediately on increase
1471 in size and progress bar shown as higher resolution
1472 overview is recalculated
1477 <td><div align="left">
1481 <!-- JAL-2664 -->Overview window redraws every hidden
1482 column region row by row
1485 <!-- JAL-2681 -->duplicate protein sequences shown after
1486 retrieving Ensembl crossrefs for sequences from Uniprot
1489 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1490 format setting is unticked
1493 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1494 if group has show boxes format setting unticked
1497 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1498 autoscrolling whilst dragging current selection group to
1499 include sequences and columns not currently displayed
1502 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1503 assemblies are imported via CIF file
1506 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1507 displayed when threshold or conservation colouring is also
1511 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1515 <!-- JAL-2673 -->Jalview continues to scroll after
1516 dragging a selected region off the visible region of the
1520 <!-- JAL-2724 -->Cannot apply annotation based
1521 colourscheme to all groups in a view
1524 <!-- JAL-2511 -->IDs don't line up with sequences
1525 initially after font size change using the Font chooser or
1532 <td width="60" nowrap>
1533 <div align="center">
1534 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1537 <td><div align="left">
1538 <em>Calculations</em>
1542 <!-- JAL-1933 -->Occupancy annotation row shows number of
1543 ungapped positions in each column of the alignment.
1546 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1547 a calculation dialog box
1550 <!-- JAL-2379 -->Revised implementation of PCA for speed
1551 and memory efficiency (~30x faster)
1554 <!-- JAL-2403 -->Revised implementation of sequence
1555 similarity scores as used by Tree, PCA, Shading Consensus
1556 and other calculations
1559 <!-- JAL-2416 -->Score matrices are stored as resource
1560 files within the Jalview codebase
1563 <!-- JAL-2500 -->Trees computed on Sequence Feature
1564 Similarity may have different topology due to increased
1571 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1572 model for alignments and groups
1575 <!-- JAL-384 -->Custom shading schemes created via groovy
1582 <!-- JAL-2526 -->Efficiency improvements for interacting
1583 with alignment and overview windows
1586 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1590 <!-- JAL-2388 -->Hidden columns and sequences can be
1594 <!-- JAL-2611 -->Click-drag in visible area allows fine
1595 adjustment of visible position
1599 <em>Data import/export</em>
1602 <!-- JAL-2535 -->Posterior probability annotation from
1603 Stockholm files imported as sequence associated annotation
1606 <!-- JAL-2507 -->More robust per-sequence positional
1607 annotation input/output via stockholm flatfile
1610 <!-- JAL-2533 -->Sequence names don't include file
1611 extension when importing structure files without embedded
1612 names or PDB accessions
1615 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1616 format sequence substitution matrices
1619 <em>User Interface</em>
1622 <!-- JAL-2447 --> Experimental Features Checkbox in
1623 Desktop's Tools menu to hide or show untested features in
1627 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1628 via Overview or sequence motif search operations
1631 <!-- JAL-2547 -->Amend sequence features dialog box can be
1632 opened by double clicking gaps within sequence feature
1636 <!-- JAL-1476 -->Status bar message shown when not enough
1637 aligned positions were available to create a 3D structure
1641 <em>3D Structure</em>
1644 <!-- JAL-2430 -->Hidden regions in alignment views are not
1645 coloured in linked structure views
1648 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1649 file-based command exchange
1652 <!-- JAL-2375 -->Structure chooser automatically shows
1653 Cached Structures rather than querying the PDBe if
1654 structures are already available for sequences
1657 <!-- JAL-2520 -->Structures imported via URL are cached in
1658 the Jalview project rather than downloaded again when the
1659 project is reopened.
1662 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1663 to transfer Chimera's structure attributes as Jalview
1664 features, and vice-versa (<strong>Experimental
1668 <em>Web Services</em>
1671 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1674 <!-- JAL-2335 -->Filter non-standard amino acids and
1675 nucleotides when submitting to AACon and other MSA
1679 <!-- JAL-2316, -->URLs for viewing database
1680 cross-references provided by identifiers.org and the
1681 EMBL-EBI's MIRIAM DB
1688 <!-- JAL-2344 -->FileFormatI interface for describing and
1689 identifying file formats (instead of String constants)
1692 <!-- JAL-2228 -->FeatureCounter script refactored for
1693 efficiency when counting all displayed features (not
1694 backwards compatible with 2.10.1)
1697 <em>Example files</em>
1700 <!-- JAL-2631 -->Graduated feature colour style example
1701 included in the example feature file
1704 <em>Documentation</em>
1707 <!-- JAL-2339 -->Release notes reformatted for readability
1708 with the built-in Java help viewer
1711 <!-- JAL-1644 -->Find documentation updated with 'search
1712 sequence description' option
1718 <!-- JAL-2485, -->External service integration tests for
1719 Uniprot REST Free Text Search Client
1722 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1725 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1730 <td><div align="left">
1731 <em>Calculations</em>
1734 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1735 matrix - C->R should be '-3'<br />Old matrix restored
1736 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1738 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1739 Jalview's treatment of gaps in PCA and substitution matrix
1740 based Tree calculations.<br /> <br />In earlier versions
1741 of Jalview, gaps matching gaps were penalised, and gaps
1742 matching non-gaps penalised even more. In the PCA
1743 calculation, gaps were actually treated as non-gaps - so
1744 different costs were applied, which meant Jalview's PCAs
1745 were different to those produced by SeqSpace.<br />Jalview
1746 now treats gaps in the same way as SeqSpace (ie it scores
1747 them as 0). <br /> <br />Enter the following in the
1748 Groovy console to restore pre-2.10.2 behaviour:<br />
1749 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1750 // for 2.10.1 mode <br />
1751 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1752 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1753 these settings will affect all subsequent tree and PCA
1754 calculations (not recommended)</em></li>
1756 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1757 scaling of branch lengths for trees computed using
1758 Sequence Feature Similarity.
1761 <!-- JAL-2377 -->PCA calculation could hang when
1762 generating output report when working with highly
1763 redundant alignments
1766 <!-- JAL-2544 --> Sort by features includes features to
1767 right of selected region when gaps present on right-hand
1771 <em>User Interface</em>
1774 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1775 doesn't reselect a specific sequence's associated
1776 annotation after it was used for colouring a view
1779 <!-- JAL-2419 -->Current selection lost if popup menu
1780 opened on a region of alignment without groups
1783 <!-- JAL-2374 -->Popup menu not always shown for regions
1784 of an alignment with overlapping groups
1787 <!-- JAL-2310 -->Finder double counts if both a sequence's
1788 name and description match
1791 <!-- JAL-2370 -->Hiding column selection containing two
1792 hidden regions results in incorrect hidden regions
1795 <!-- JAL-2386 -->'Apply to all groups' setting when
1796 changing colour does not apply Conservation slider value
1800 <!-- JAL-2373 -->Percentage identity and conservation menu
1801 items do not show a tick or allow shading to be disabled
1804 <!-- JAL-2385 -->Conservation shading or PID threshold
1805 lost when base colourscheme changed if slider not visible
1808 <!-- JAL-2547 -->Sequence features shown in tooltip for
1809 gaps before start of features
1812 <!-- JAL-2623 -->Graduated feature colour threshold not
1813 restored to UI when feature colour is edited
1816 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1817 a time when scrolling vertically in wrapped mode.
1820 <!-- JAL-2630 -->Structure and alignment overview update
1821 as graduate feature colour settings are modified via the
1825 <!-- JAL-2034 -->Overview window doesn't always update
1826 when a group defined on the alignment is resized
1829 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1830 wrapped view result in positional status updates
1834 <!-- JAL-2563 -->Status bar doesn't show position for
1835 ambiguous amino acid and nucleotide symbols
1838 <!-- JAL-2602 -->Copy consensus sequence failed if
1839 alignment included gapped columns
1842 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1843 widgets don't permanently disappear
1846 <!-- JAL-2503 -->Cannot select or filter quantitative
1847 annotation that are shown only as column labels (e.g.
1848 T-Coffee column reliability scores)
1851 <!-- JAL-2594 -->Exception thrown if trying to create a
1852 sequence feature on gaps only
1855 <!-- JAL-2504 -->Features created with 'New feature'
1856 button from a Find inherit previously defined feature type
1857 rather than the Find query string
1860 <!-- JAL-2423 -->incorrect title in output window when
1861 exporting tree calculated in Jalview
1864 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1865 and then revealing them reorders sequences on the
1869 <!-- JAL-964 -->Group panel in sequence feature settings
1870 doesn't update to reflect available set of groups after
1871 interactively adding or modifying features
1874 <!-- JAL-2225 -->Sequence Database chooser unusable on
1878 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1879 only excluded gaps in current sequence and ignored
1886 <!-- JAL-2421 -->Overview window visible region moves
1887 erratically when hidden rows or columns are present
1890 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1891 Structure Viewer's colour menu don't correspond to
1895 <!-- JAL-2405 -->Protein specific colours only offered in
1896 colour and group colour menu for protein alignments
1899 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1900 reflect currently selected view or group's shading
1904 <!-- JAL-2624 -->Feature colour thresholds not respected
1905 when rendered on overview and structures when opacity at
1909 <!-- JAL-2589 -->User defined gap colour not shown in
1910 overview when features overlaid on alignment
1913 <!-- JAL-2567 -->Feature settings for different views not
1914 recovered correctly from Jalview project file
1917 <!-- JAL-2256 -->Feature colours in overview when first opened
1918 (automatically via preferences) are different to the main
1922 <em>Data import/export</em>
1925 <!-- JAL-2576 -->Very large alignments take a long time to
1929 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1930 added after a sequence was imported are not written to
1934 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1935 when importing RNA secondary structure via Stockholm
1938 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1939 not shown in correct direction for simple pseudoknots
1942 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1943 with lightGray or darkGray via features file (but can
1947 <!-- JAL-2383 -->Above PID colour threshold not recovered
1948 when alignment view imported from project
1951 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1952 structure and sequences extracted from structure files
1953 imported via URL and viewed in Jmol
1956 <!-- JAL-2520 -->Structures loaded via URL are saved in
1957 Jalview Projects rather than fetched via URL again when
1958 the project is loaded and the structure viewed
1961 <em>Web Services</em>
1964 <!-- JAL-2519 -->EnsemblGenomes example failing after
1965 release of Ensembl v.88
1968 <!-- JAL-2366 -->Proxy server address and port always
1969 appear enabled in Preferences->Connections
1972 <!-- JAL-2461 -->DAS registry not found exceptions
1973 removed from console output
1976 <!-- JAL-2582 -->Cannot retrieve protein products from
1977 Ensembl by Peptide ID
1980 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1981 created from SIFTs, and spurious 'Couldn't open structure
1982 in Chimera' errors raised after April 2017 update (problem
1983 due to 'null' string rather than empty string used for
1984 residues with no corresponding PDB mapping).
1987 <em>Application UI</em>
1990 <!-- JAL-2361 -->User Defined Colours not added to Colour
1994 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1995 case' residues (button in colourscheme editor debugged and
1996 new documentation and tooltips added)
1999 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2000 doesn't restore group-specific text colour thresholds
2003 <!-- JAL-2243 -->Feature settings panel does not update as
2004 new features are added to alignment
2007 <!-- JAL-2532 -->Cancel in feature settings reverts
2008 changes to feature colours via the Amend features dialog
2011 <!-- JAL-2506 -->Null pointer exception when attempting to
2012 edit graduated feature colour via amend features dialog
2016 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2017 selection menu changes colours of alignment views
2020 <!-- JAL-2426 -->Spurious exceptions in console raised
2021 from alignment calculation workers after alignment has
2025 <!-- JAL-1608 -->Typo in selection popup menu - Create
2026 groups now 'Create Group'
2029 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2030 Create/Undefine group doesn't always work
2033 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2034 shown again after pressing 'Cancel'
2037 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2038 adjusts start position in wrap mode
2041 <!-- JAL-2563 -->Status bar doesn't show positions for
2042 ambiguous amino acids
2045 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2046 CDS/Protein view after CDS sequences added for aligned
2050 <!-- JAL-2592 -->User defined colourschemes called 'User
2051 Defined' don't appear in Colours menu
2057 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2058 score models doesn't always result in an updated PCA plot
2061 <!-- JAL-2442 -->Features not rendered as transparent on
2062 overview or linked structure view
2065 <!-- JAL-2372 -->Colour group by conservation doesn't
2069 <!-- JAL-2517 -->Hitting Cancel after applying
2070 user-defined colourscheme doesn't restore original
2077 <!-- JAL-2314 -->Unit test failure:
2078 jalview.ws.jabaws.RNAStructExportImport setup fails
2081 <!-- JAL-2307 -->Unit test failure:
2082 jalview.ws.sifts.SiftsClientTest due to compatibility
2083 problems with deep array comparison equality asserts in
2084 successive versions of TestNG
2087 <!-- JAL-2479 -->Relocated StructureChooserTest and
2088 ParameterUtilsTest Unit tests to Network suite
2091 <em>New Known Issues</em>
2094 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2095 phase after a sequence motif find operation
2098 <!-- JAL-2550 -->Importing annotation file with rows
2099 containing just upper and lower case letters are
2100 interpreted as WUSS RNA secondary structure symbols
2103 <!-- JAL-2590 -->Cannot load and display Newick trees
2104 reliably from eggnog Ortholog database
2107 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2108 containing features of type Highlight' when 'B' is pressed
2109 to mark columns containing highlighted regions.
2112 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2113 doesn't always add secondary structure annotation.
2118 <td width="60" nowrap>
2119 <div align="center">
2120 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2123 <td><div align="left">
2127 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2128 for all consensus calculations
2131 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2134 <li>Updated Jalview's Certum code signing certificate
2137 <em>Application</em>
2140 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2141 set of database cross-references, sorted alphabetically
2144 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2145 from database cross references. Users with custom links
2146 will receive a <a href="webServices/urllinks.html#warning">warning
2147 dialog</a> asking them to update their preferences.
2150 <!-- JAL-2287-->Cancel button and escape listener on
2151 dialog warning user about disconnecting Jalview from a
2155 <!-- JAL-2320-->Jalview's Chimera control window closes if
2156 the Chimera it is connected to is shut down
2159 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2160 columns menu item to mark columns containing highlighted
2161 regions (e.g. from structure selections or results of a
2165 <!-- JAL-2284-->Command line option for batch-generation
2166 of HTML pages rendering alignment data with the BioJS
2176 <!-- JAL-2286 -->Columns with more than one modal residue
2177 are not coloured or thresholded according to percent
2178 identity (first observed in Jalview 2.8.2)
2181 <!-- JAL-2301 -->Threonine incorrectly reported as not
2185 <!-- JAL-2318 -->Updates to documentation pages (above PID
2186 threshold, amino acid properties)
2189 <!-- JAL-2292 -->Lower case residues in sequences are not
2190 reported as mapped to residues in a structure file in the
2194 <!--JAL-2324 -->Identical features with non-numeric scores
2195 could be added multiple times to a sequence
2198 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2199 bond features shown as two highlighted residues rather
2200 than a range in linked structure views, and treated
2201 correctly when selecting and computing trees from features
2204 <!-- JAL-2281-->Custom URL links for database
2205 cross-references are matched to database name regardless
2210 <em>Application</em>
2213 <!-- JAL-2282-->Custom URL links for specific database
2214 names without regular expressions also offer links from
2218 <!-- JAL-2315-->Removing a single configured link in the
2219 URL links pane in Connections preferences doesn't actually
2220 update Jalview configuration
2223 <!-- JAL-2272-->CTRL-Click on a selected region to open
2224 the alignment area popup menu doesn't work on El-Capitan
2227 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2228 files with similarly named sequences if dropped onto the
2232 <!-- JAL-2312 -->Additional mappings are shown for PDB
2233 entries where more chains exist in the PDB accession than
2234 are reported in the SIFTS file
2237 <!-- JAL-2317-->Certain structures do not get mapped to
2238 the structure view when displayed with Chimera
2241 <!-- JAL-2317-->No chains shown in the Chimera view
2242 panel's View->Show Chains submenu
2245 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2246 work for wrapped alignment views
2249 <!--JAL-2197 -->Rename UI components for running JPred
2250 predictions from 'JNet' to 'JPred'
2253 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2254 corrupted when annotation panel vertical scroll is not at
2255 first annotation row
2258 <!--JAL-2332 -->Attempting to view structure for Hen
2259 lysozyme results in a PDB Client error dialog box
2262 <!-- JAL-2319 -->Structure View's mapping report switched
2263 ranges for PDB and sequence for SIFTS
2266 SIFTS 'Not_Observed' residues mapped to non-existant
2270 <!-- <em>New Known Issues</em>
2277 <td width="60" nowrap>
2278 <div align="center">
2279 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2280 <em>25/10/2016</em></strong>
2283 <td><em>Application</em>
2285 <li>3D Structure chooser opens with 'Cached structures'
2286 view if structures already loaded</li>
2287 <li>Progress bar reports models as they are loaded to
2288 structure views</li>
2294 <li>Colour by conservation always enabled and no tick
2295 shown in menu when BLOSUM or PID shading applied</li>
2296 <li>FER1_ARATH and FER2_ARATH labels were switched in
2297 example sequences/projects/trees</li>
2299 <em>Application</em>
2301 <li>Jalview projects with views of local PDB structure
2302 files saved on Windows cannot be opened on OSX</li>
2303 <li>Multiple structure views can be opened and superposed
2304 without timeout for structures with multiple models or
2305 multiple sequences in alignment</li>
2306 <li>Cannot import or associated local PDB files without a
2307 PDB ID HEADER line</li>
2308 <li>RMSD is not output in Jmol console when superposition
2310 <li>Drag and drop of URL from Browser fails for Linux and
2311 OSX versions earlier than El Capitan</li>
2312 <li>ENA client ignores invalid content from ENA server</li>
2313 <li>Exceptions are not raised in console when ENA client
2314 attempts to fetch non-existent IDs via Fetch DB Refs UI
2316 <li>Exceptions are not raised in console when a new view
2317 is created on the alignment</li>
2318 <li>OSX right-click fixed for group selections: CMD-click
2319 to insert/remove gaps in groups and CTRL-click to open group
2322 <em>Build and deployment</em>
2324 <li>URL link checker now copes with multi-line anchor
2327 <em>New Known Issues</em>
2329 <li>Drag and drop from URL links in browsers do not work
2336 <td width="60" nowrap>
2337 <div align="center">
2338 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2341 <td><em>General</em>
2344 <!-- JAL-2124 -->Updated Spanish translations.
2347 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2348 for importing structure data to Jalview. Enables mmCIF and
2352 <!-- JAL-192 --->Alignment ruler shows positions relative to
2356 <!-- JAL-2202 -->Position/residue shown in status bar when
2357 mousing over sequence associated annotation
2360 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2364 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2365 '()', canonical '[]' and invalid '{}' base pair populations
2369 <!-- JAL-2092 -->Feature settings popup menu options for
2370 showing or hiding columns containing a feature
2373 <!-- JAL-1557 -->Edit selected group by double clicking on
2374 group and sequence associated annotation labels
2377 <!-- JAL-2236 -->Sequence name added to annotation label in
2378 select/hide columns by annotation and colour by annotation
2382 </ul> <em>Application</em>
2385 <!-- JAL-2050-->Automatically hide introns when opening a
2386 gene/transcript view
2389 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2393 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2394 structure mappings with the EMBL-EBI PDBe SIFTS database
2397 <!-- JAL-2079 -->Updated download sites used for Rfam and
2398 Pfam sources to xfam.org
2401 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2404 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2405 over sequences in Jalview
2408 <!-- JAL-2027-->Support for reverse-complement coding
2409 regions in ENA and EMBL
2412 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2413 for record retrieval via ENA rest API
2416 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2420 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2421 groovy script execution
2424 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2425 alignment window's Calculate menu
2428 <!-- JAL-1812 -->Allow groovy scripts that call
2429 Jalview.getAlignFrames() to run in headless mode
2432 <!-- JAL-2068 -->Support for creating new alignment
2433 calculation workers from groovy scripts
2436 <!-- JAL-1369 --->Store/restore reference sequence in
2440 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2441 associations are now saved/restored from project
2444 <!-- JAL-1993 -->Database selection dialog always shown
2445 before sequence fetcher is opened
2448 <!-- JAL-2183 -->Double click on an entry in Jalview's
2449 database chooser opens a sequence fetcher
2452 <!-- JAL-1563 -->Free-text search client for UniProt using
2453 the UniProt REST API
2456 <!-- JAL-2168 -->-nonews command line parameter to prevent
2457 the news reader opening
2460 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2461 querying stored in preferences
2464 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2468 <!-- JAL-1977-->Tooltips shown on database chooser
2471 <!-- JAL-391 -->Reverse complement function in calculate
2472 menu for nucleotide sequences
2475 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2476 and feature counts preserves alignment ordering (and
2477 debugged for complex feature sets).
2480 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2481 viewing structures with Jalview 2.10
2484 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2485 genome, transcript CCDS and gene ids via the Ensembl and
2486 Ensembl Genomes REST API
2489 <!-- JAL-2049 -->Protein sequence variant annotation
2490 computed for 'sequence_variant' annotation on CDS regions
2494 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2498 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2499 Ref Fetcher fails to match, or otherwise updates sequence
2500 data from external database records.
2503 <!-- JAL-2154 -->Revised Jalview Project format for
2504 efficient recovery of sequence coding and alignment
2505 annotation relationships.
2507 </ul> <!-- <em>Applet</em>
2518 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2522 <!-- JAL-2018-->Export features in Jalview format (again)
2523 includes graduated colourschemes
2526 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2527 working with big alignments and lots of hidden columns
2530 <!-- JAL-2053-->Hidden column markers not always rendered
2531 at right of alignment window
2534 <!-- JAL-2067 -->Tidied up links in help file table of
2538 <!-- JAL-2072 -->Feature based tree calculation not shown
2542 <!-- JAL-2075 -->Hidden columns ignored during feature
2543 based tree calculation
2546 <!-- JAL-2065 -->Alignment view stops updating when show
2547 unconserved enabled for group on alignment
2550 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2554 <!-- JAL-2146 -->Alignment column in status incorrectly
2555 shown as "Sequence position" when mousing over
2559 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2560 hidden columns present
2563 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2564 user created annotation added to alignment
2567 <!-- JAL-1841 -->RNA Structure consensus only computed for
2568 '()' base pair annotation
2571 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2572 in zero scores for all base pairs in RNA Structure
2576 <!-- JAL-2174-->Extend selection with columns containing
2580 <!-- JAL-2275 -->Pfam format writer puts extra space at
2581 beginning of sequence
2584 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2588 <!-- JAL-2238 -->Cannot create groups on an alignment from
2589 from a tree when t-coffee scores are shown
2592 <!-- JAL-1836,1967 -->Cannot import and view PDB
2593 structures with chains containing negative resnums (4q4h)
2596 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2600 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2601 to Clustal, PIR and PileUp output
2604 <!-- JAL-2008 -->Reordering sequence features that are
2605 not visible causes alignment window to repaint
2608 <!-- JAL-2006 -->Threshold sliders don't work in
2609 graduated colour and colour by annotation row for e-value
2610 scores associated with features and annotation rows
2613 <!-- JAL-1797 -->amino acid physicochemical conservation
2614 calculation should be case independent
2617 <!-- JAL-2173 -->Remove annotation also updates hidden
2621 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2622 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2623 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2626 <!-- JAL-2065 -->Null pointer exceptions and redraw
2627 problems when reference sequence defined and 'show
2628 non-conserved' enabled
2631 <!-- JAL-1306 -->Quality and Conservation are now shown on
2632 load even when Consensus calculation is disabled
2635 <!-- JAL-1932 -->Remove right on penultimate column of
2636 alignment does nothing
2639 <em>Application</em>
2642 <!-- JAL-1552-->URLs and links can't be imported by
2643 drag'n'drop on OSX when launched via webstart (note - not
2644 yet fixed for El Capitan)
2647 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2648 output when running on non-gb/us i18n platforms
2651 <!-- JAL-1944 -->Error thrown when exporting a view with
2652 hidden sequences as flat-file alignment
2655 <!-- JAL-2030-->InstallAnywhere distribution fails when
2659 <!-- JAL-2080-->Jalview very slow to launch via webstart
2660 (also hotfix for 2.9.0b2)
2663 <!-- JAL-2085 -->Cannot save project when view has a
2664 reference sequence defined
2667 <!-- JAL-1011 -->Columns are suddenly selected in other
2668 alignments and views when revealing hidden columns
2671 <!-- JAL-1989 -->Hide columns not mirrored in complement
2672 view in a cDNA/Protein splitframe
2675 <!-- JAL-1369 -->Cannot save/restore representative
2676 sequence from project when only one sequence is
2680 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2681 in Structure Chooser
2684 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2685 structure consensus didn't refresh annotation panel
2688 <!-- JAL-1962 -->View mapping in structure view shows
2689 mappings between sequence and all chains in a PDB file
2692 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2693 dialogs format columns correctly, don't display array
2694 data, sort columns according to type
2697 <!-- JAL-1975 -->Export complete shown after destination
2698 file chooser is cancelled during an image export
2701 <!-- JAL-2025 -->Error when querying PDB Service with
2702 sequence name containing special characters
2705 <!-- JAL-2024 -->Manual PDB structure querying should be
2709 <!-- JAL-2104 -->Large tooltips with broken HTML
2710 formatting don't wrap
2713 <!-- JAL-1128 -->Figures exported from wrapped view are
2714 truncated so L looks like I in consensus annotation
2717 <!-- JAL-2003 -->Export features should only export the
2718 currently displayed features for the current selection or
2722 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2723 after fetching cross-references, and restoring from
2727 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2728 followed in the structure viewer
2731 <!-- JAL-2163 -->Titles for individual alignments in
2732 splitframe not restored from project
2735 <!-- JAL-2145 -->missing autocalculated annotation at
2736 trailing end of protein alignment in transcript/product
2737 splitview when pad-gaps not enabled by default
2740 <!-- JAL-1797 -->amino acid physicochemical conservation
2744 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2745 article has been read (reopened issue due to
2746 internationalisation problems)
2749 <!-- JAL-1960 -->Only offer PDB structures in structure
2750 viewer based on sequence name, PDB and UniProt
2755 <!-- JAL-1976 -->No progress bar shown during export of
2759 <!-- JAL-2213 -->Structures not always superimposed after
2760 multiple structures are shown for one or more sequences.
2763 <!-- JAL-1370 -->Reference sequence characters should not
2764 be replaced with '.' when 'Show unconserved' format option
2768 <!-- JAL-1823 -->Cannot specify chain code when entering
2769 specific PDB id for sequence
2772 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2773 'Export hidden sequences' is enabled, but 'export hidden
2774 columns' is disabled.
2777 <!--JAL-2026-->Best Quality option in structure chooser
2778 selects lowest rather than highest resolution structures
2782 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2783 to sequence mapping in 'View Mappings' report
2786 <!-- JAL-2284 -->Unable to read old Jalview projects that
2787 contain non-XML data added after Jalvew wrote project.
2790 <!-- JAL-2118 -->Newly created annotation row reorders
2791 after clicking on it to create new annotation for a
2795 <!-- JAL-1980 -->Null Pointer Exception raised when
2796 pressing Add on an orphaned cut'n'paste window.
2798 <!-- may exclude, this is an external service stability issue JAL-1941
2799 -- > RNA 3D structure not added via DSSR service</li> -->
2804 <!-- JAL-2151 -->Incorrect columns are selected when
2805 hidden columns present before start of sequence
2808 <!-- JAL-1986 -->Missing dependencies on applet pages
2812 <!-- JAL-1947 -->Overview pixel size changes when
2813 sequences are hidden in applet
2816 <!-- JAL-1996 -->Updated instructions for applet
2817 deployment on examples pages.
2824 <td width="60" nowrap>
2825 <div align="center">
2826 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2827 <em>16/10/2015</em></strong>
2830 <td><em>General</em>
2832 <li>Time stamps for signed Jalview application and applet
2837 <em>Application</em>
2839 <li>Duplicate group consensus and conservation rows
2840 shown when tree is partitioned</li>
2841 <li>Erratic behaviour when tree partitions made with
2842 multiple cDNA/Protein split views</li>
2848 <td width="60" nowrap>
2849 <div align="center">
2850 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2851 <em>8/10/2015</em></strong>
2854 <td><em>General</em>
2856 <li>Updated Spanish translations of localized text for
2858 </ul> <em>Application</em>
2860 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2861 <li>Signed OSX InstallAnywhere installer<br></li>
2862 <li>Support for per-sequence based annotations in BioJSON</li>
2863 </ul> <em>Applet</em>
2865 <li>Split frame example added to applet examples page</li>
2866 </ul> <em>Build and Deployment</em>
2869 <!-- JAL-1888 -->New ant target for running Jalview's test
2877 <li>Mapping of cDNA to protein in split frames
2878 incorrect when sequence start > 1</li>
2879 <li>Broken images in filter column by annotation dialog
2881 <li>Feature colours not parsed from features file</li>
2882 <li>Exceptions and incomplete link URLs recovered when
2883 loading a features file containing HTML tags in feature
2887 <em>Application</em>
2889 <li>Annotations corrupted after BioJS export and
2891 <li>Incorrect sequence limits after Fetch DB References
2892 with 'trim retrieved sequences'</li>
2893 <li>Incorrect warning about deleting all data when
2894 deleting selected columns</li>
2895 <li>Patch to build system for shipping properly signed
2896 JNLP templates for webstart launch</li>
2897 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2898 unreleased structures for download or viewing</li>
2899 <li>Tab/space/return keystroke operation of EMBL-PDBe
2900 fetcher/viewer dialogs works correctly</li>
2901 <li>Disabled 'minimise' button on Jalview windows
2902 running on OSX to workaround redraw hang bug</li>
2903 <li>Split cDNA/Protein view position and geometry not
2904 recovered from jalview project</li>
2905 <li>Initial enabled/disabled state of annotation menu
2906 sorter 'show autocalculated first/last' corresponds to
2908 <li>Restoring of Clustal, RNA Helices and T-Coffee
2909 color schemes from BioJSON</li>
2913 <li>Reorder sequences mirrored in cDNA/Protein split
2915 <li>Applet with Jmol examples not loading correctly</li>
2921 <td><div align="center">
2922 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2924 <td><em>General</em>
2926 <li>Linked visualisation and analysis of DNA and Protein
2929 <li>Translated cDNA alignments shown as split protein
2930 and DNA alignment views</li>
2931 <li>Codon consensus annotation for linked protein and
2932 cDNA alignment views</li>
2933 <li>Link cDNA or Protein product sequences by loading
2934 them onto Protein or cDNA alignments</li>
2935 <li>Reconstruct linked cDNA alignment from aligned
2936 protein sequences</li>
2939 <li>Jmol integration updated to Jmol v14.2.14</li>
2940 <li>Import and export of Jalview alignment views as <a
2941 href="features/bioJsonFormat.html">BioJSON</a></li>
2942 <li>New alignment annotation file statements for
2943 reference sequences and marking hidden columns</li>
2944 <li>Reference sequence based alignment shading to
2945 highlight variation</li>
2946 <li>Select or hide columns according to alignment
2948 <li>Find option for locating sequences by description</li>
2949 <li>Conserved physicochemical properties shown in amino
2950 acid conservation row</li>
2951 <li>Alignments can be sorted by number of RNA helices</li>
2952 </ul> <em>Application</em>
2954 <li>New cDNA/Protein analysis capabilities
2956 <li>Get Cross-References should open a Split Frame
2957 view with cDNA/Protein</li>
2958 <li>Detect when nucleotide sequences and protein
2959 sequences are placed in the same alignment</li>
2960 <li>Split cDNA/Protein views are saved in Jalview
2965 <li>Use REST API to talk to Chimera</li>
2966 <li>Selected regions in Chimera are highlighted in linked
2967 Jalview windows</li>
2969 <li>VARNA RNA viewer updated to v3.93</li>
2970 <li>VARNA views are saved in Jalview Projects</li>
2971 <li>Pseudoknots displayed as Jalview RNA annotation can
2972 be shown in VARNA</li>
2974 <li>Make groups for selection uses marked columns as well
2975 as the active selected region</li>
2977 <li>Calculate UPGMA and NJ trees using sequence feature
2979 <li>New Export options
2981 <li>New Export Settings dialog to control hidden
2982 region export in flat file generation</li>
2984 <li>Export alignment views for display with the <a
2985 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2987 <li>Export scrollable SVG in HTML page</li>
2988 <li>Optional embedding of BioJSON data when exporting
2989 alignment figures to HTML</li>
2991 <li>3D structure retrieval and display
2993 <li>Free text and structured queries with the PDBe
2995 <li>PDBe Search API based discovery and selection of
2996 PDB structures for a sequence set</li>
3000 <li>JPred4 employed for protein secondary structure
3002 <li>Hide Insertions menu option to hide unaligned columns
3003 for one or a group of sequences</li>
3004 <li>Automatically hide insertions in alignments imported
3005 from the JPred4 web server</li>
3006 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3007 system on OSX<br />LGPL libraries courtesy of <a
3008 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3010 <li>changed 'View nucleotide structure' submenu to 'View
3011 VARNA 2D Structure'</li>
3012 <li>change "View protein structure" menu option to "3D
3015 </ul> <em>Applet</em>
3017 <li>New layout for applet example pages</li>
3018 <li>New parameters to enable SplitFrame view
3019 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3020 <li>New example demonstrating linked viewing of cDNA and
3021 Protein alignments</li>
3022 </ul> <em>Development and deployment</em>
3024 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3025 <li>Include installation type and git revision in build
3026 properties and console log output</li>
3027 <li>Jalview Github organisation, and new github site for
3028 storing BioJsMSA Templates</li>
3029 <li>Jalview's unit tests now managed with TestNG</li>
3032 <!-- <em>General</em>
3034 </ul> --> <!-- issues resolved --> <em>Application</em>
3036 <li>Escape should close any open find dialogs</li>
3037 <li>Typo in select-by-features status report</li>
3038 <li>Consensus RNA secondary secondary structure
3039 predictions are not highlighted in amber</li>
3040 <li>Missing gap character in v2.7 example file means
3041 alignment appears unaligned when pad-gaps is not enabled</li>
3042 <li>First switch to RNA Helices colouring doesn't colour
3043 associated structure views</li>
3044 <li>ID width preference option is greyed out when auto
3045 width checkbox not enabled</li>
3046 <li>Stopped a warning dialog from being shown when
3047 creating user defined colours</li>
3048 <li>'View Mapping' in structure viewer shows sequence
3049 mappings for just that viewer's sequences</li>
3050 <li>Workaround for superposing PDB files containing
3051 multiple models in Chimera</li>
3052 <li>Report sequence position in status bar when hovering
3053 over Jmol structure</li>
3054 <li>Cannot output gaps as '.' symbols with Selection ->
3055 output to text box</li>
3056 <li>Flat file exports of alignments with hidden columns
3057 have incorrect sequence start/end</li>
3058 <li>'Aligning' a second chain to a Chimera structure from
3060 <li>Colour schemes applied to structure viewers don't
3061 work for nucleotide</li>
3062 <li>Loading/cut'n'pasting an empty or invalid file leads
3063 to a grey/invisible alignment window</li>
3064 <li>Exported Jpred annotation from a sequence region
3065 imports to different position</li>
3066 <li>Space at beginning of sequence feature tooltips shown
3067 on some platforms</li>
3068 <li>Chimera viewer 'View | Show Chain' menu is not
3070 <li>'New View' fails with a Null Pointer Exception in
3071 console if Chimera has been opened</li>
3072 <li>Mouseover to Chimera not working</li>
3073 <li>Miscellaneous ENA XML feature qualifiers not
3075 <li>NPE in annotation renderer after 'Extract Scores'</li>
3076 <li>If two structures in one Chimera window, mouseover of
3077 either sequence shows on first structure</li>
3078 <li>'Show annotations' options should not make
3079 non-positional annotations visible</li>
3080 <li>Subsequence secondary structure annotation not shown
3081 in right place after 'view flanking regions'</li>
3082 <li>File Save As type unset when current file format is
3084 <li>Save as '.jar' option removed for saving Jalview
3086 <li>Colour by Sequence colouring in Chimera more
3088 <li>Cannot 'add reference annotation' for a sequence in
3089 several views on same alignment</li>
3090 <li>Cannot show linked products for EMBL / ENA records</li>
3091 <li>Jalview's tooltip wraps long texts containing no
3093 </ul> <em>Applet</em>
3095 <li>Jmol to JalviewLite mouseover/link not working</li>
3096 <li>JalviewLite can't import sequences with ID
3097 descriptions containing angle brackets</li>
3098 </ul> <em>General</em>
3100 <li>Cannot export and reimport RNA secondary structure
3101 via jalview annotation file</li>
3102 <li>Random helix colour palette for colour by annotation
3103 with RNA secondary structure</li>
3104 <li>Mouseover to cDNA from STOP residue in protein
3105 translation doesn't work.</li>
3106 <li>hints when using the select by annotation dialog box</li>
3107 <li>Jmol alignment incorrect if PDB file has alternate CA
3109 <li>FontChooser message dialog appears to hang after
3110 choosing 1pt font</li>
3111 <li>Peptide secondary structure incorrectly imported from
3112 annotation file when annotation display text includes 'e' or
3114 <li>Cannot set colour of new feature type whilst creating
3116 <li>cDNA translation alignment should not be sequence
3117 order dependent</li>
3118 <li>'Show unconserved' doesn't work for lower case
3120 <li>Nucleotide ambiguity codes involving R not recognised</li>
3121 </ul> <em>Deployment and Documentation</em>
3123 <li>Applet example pages appear different to the rest of
3124 www.jalview.org</li>
3125 </ul> <em>Application Known issues</em>
3127 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3128 <li>Misleading message appears after trying to delete
3130 <li>Jalview icon not shown in dock after InstallAnywhere
3131 version launches</li>
3132 <li>Fetching EMBL reference for an RNA sequence results
3133 fails with a sequence mismatch</li>
3134 <li>Corrupted or unreadable alignment display when
3135 scrolling alignment to right</li>
3136 <li>ArrayIndexOutOfBoundsException thrown when remove
3137 empty columns called on alignment with ragged gapped ends</li>
3138 <li>auto calculated alignment annotation rows do not get
3139 placed above or below non-autocalculated rows</li>
3140 <li>Jalview dekstop becomes sluggish at full screen in
3141 ultra-high resolution</li>
3142 <li>Cannot disable consensus calculation independently of
3143 quality and conservation</li>
3144 <li>Mouseover highlighting between cDNA and protein can
3145 become sluggish with more than one splitframe shown</li>
3146 </ul> <em>Applet Known Issues</em>
3148 <li>Core PDB parsing code requires Jmol</li>
3149 <li>Sequence canvas panel goes white when alignment
3150 window is being resized</li>
3156 <td><div align="center">
3157 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3159 <td><em>General</em>
3161 <li>Updated Java code signing certificate donated by
3163 <li>Features and annotation preserved when performing
3164 pairwise alignment</li>
3165 <li>RNA pseudoknot annotation can be
3166 imported/exported/displayed</li>
3167 <li>'colour by annotation' can colour by RNA and
3168 protein secondary structure</li>
3169 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3170 post-hoc with 2.9 release</em>)
3173 </ul> <em>Application</em>
3175 <li>Extract and display secondary structure for sequences
3176 with 3D structures</li>
3177 <li>Support for parsing RNAML</li>
3178 <li>Annotations menu for layout
3180 <li>sort sequence annotation rows by alignment</li>
3181 <li>place sequence annotation above/below alignment
3184 <li>Output in Stockholm format</li>
3185 <li>Internationalisation: improved Spanish (es)
3187 <li>Structure viewer preferences tab</li>
3188 <li>Disorder and Secondary Structure annotation tracks
3189 shared between alignments</li>
3190 <li>UCSF Chimera launch and linked highlighting from
3192 <li>Show/hide all sequence associated annotation rows for
3193 all or current selection</li>
3194 <li>disorder and secondary structure predictions
3195 available as dataset annotation</li>
3196 <li>Per-sequence rna helices colouring</li>
3199 <li>Sequence database accessions imported when fetching
3200 alignments from Rfam</li>
3201 <li>update VARNA version to 3.91</li>
3203 <li>New groovy scripts for exporting aligned positions,
3204 conservation values, and calculating sum of pairs scores.</li>
3205 <li>Command line argument to set default JABAWS server</li>
3206 <li>include installation type in build properties and
3207 console log output</li>
3208 <li>Updated Jalview project format to preserve dataset
3212 <!-- issues resolved --> <em>Application</em>
3214 <li>Distinguish alignment and sequence associated RNA
3215 structure in structure->view->VARNA</li>
3216 <li>Raise dialog box if user deletes all sequences in an
3218 <li>Pressing F1 results in documentation opening twice</li>
3219 <li>Sequence feature tooltip is wrapped</li>
3220 <li>Double click on sequence associated annotation
3221 selects only first column</li>
3222 <li>Redundancy removal doesn't result in unlinked
3223 leaves shown in tree</li>
3224 <li>Undos after several redundancy removals don't undo
3226 <li>Hide sequence doesn't hide associated annotation</li>
3227 <li>User defined colours dialog box too big to fit on
3228 screen and buttons not visible</li>
3229 <li>author list isn't updated if already written to
3230 Jalview properties</li>
3231 <li>Popup menu won't open after retrieving sequence
3233 <li>File open window for associate PDB doesn't open</li>
3234 <li>Left-then-right click on a sequence id opens a
3235 browser search window</li>
3236 <li>Cannot open sequence feature shading/sort popup menu
3237 in feature settings dialog</li>
3238 <li>better tooltip placement for some areas of Jalview
3240 <li>Allow addition of JABAWS Server which doesn't
3241 pass validation</li>
3242 <li>Web services parameters dialog box is too large to
3244 <li>Muscle nucleotide alignment preset obscured by
3246 <li>JABAWS preset submenus don't contain newly
3247 defined user preset</li>
3248 <li>MSA web services warns user if they were launched
3249 with invalid input</li>
3250 <li>Jalview cannot contact DAS Registy when running on
3253 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3254 'Superpose with' submenu not shown when new view
3258 </ul> <!-- <em>Applet</em>
3260 </ul> <em>General</em>
3262 </ul>--> <em>Deployment and Documentation</em>
3264 <li>2G and 1G options in launchApp have no effect on
3265 memory allocation</li>
3266 <li>launchApp service doesn't automatically open
3267 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3269 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3270 InstallAnywhere reports cannot find valid JVM when Java
3271 1.7_055 is available
3273 </ul> <em>Application Known issues</em>
3276 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3277 corrupted or unreadable alignment display when scrolling
3281 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3282 retrieval fails but progress bar continues for DAS retrieval
3283 with large number of ID
3286 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3287 flatfile output of visible region has incorrect sequence
3291 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3292 rna structure consensus doesn't update when secondary
3293 structure tracks are rearranged
3296 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3297 invalid rna structure positional highlighting does not
3298 highlight position of invalid base pairs
3301 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3302 out of memory errors are not raised when saving Jalview
3303 project from alignment window file menu
3306 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3307 Switching to RNA Helices colouring doesn't propagate to
3311 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3312 colour by RNA Helices not enabled when user created
3313 annotation added to alignment
3316 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3317 Jalview icon not shown on dock in Mountain Lion/Webstart
3319 </ul> <em>Applet Known Issues</em>
3322 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3323 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3327 Jalview and Jmol example not compatible with IE9
3330 <li>Sort by annotation score doesn't reverse order
3336 <td><div align="center">
3337 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3340 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3343 <li>Internationalisation of user interface (usually
3344 called i18n support) and translation for Spanish locale</li>
3345 <li>Define/Undefine group on current selection with
3346 Ctrl-G/Shift Ctrl-G</li>
3347 <li>Improved group creation/removal options in
3348 alignment/sequence Popup menu</li>
3349 <li>Sensible precision for symbol distribution
3350 percentages shown in logo tooltip.</li>
3351 <li>Annotation panel height set according to amount of
3352 annotation when alignment first opened</li>
3353 </ul> <em>Application</em>
3355 <li>Interactive consensus RNA secondary structure
3356 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3357 <li>Select columns containing particular features from
3358 Feature Settings dialog</li>
3359 <li>View all 'representative' PDB structures for selected
3361 <li>Update Jalview project format:
3363 <li>New file extension for Jalview projects '.jvp'</li>
3364 <li>Preserve sequence and annotation dataset (to
3365 store secondary structure annotation,etc)</li>
3366 <li>Per group and alignment annotation and RNA helix
3370 <li>New similarity measures for PCA and Tree calculation
3372 <li>Experimental support for retrieval and viewing of
3373 flanking regions for an alignment</li>
3377 <!-- issues resolved --> <em>Application</em>
3379 <li>logo keeps spinning and status remains at queued or
3380 running after job is cancelled</li>
3381 <li>cannot export features from alignments imported from
3382 Jalview/VAMSAS projects</li>
3383 <li>Buggy slider for web service parameters that take
3385 <li>Newly created RNA secondary structure line doesn't
3386 have 'display all symbols' flag set</li>
3387 <li>T-COFFEE alignment score shading scheme and other
3388 annotation shading not saved in Jalview project</li>
3389 <li>Local file cannot be loaded in freshly downloaded
3391 <li>Jalview icon not shown on dock in Mountain
3393 <li>Load file from desktop file browser fails</li>
3394 <li>Occasional NPE thrown when calculating large trees</li>
3395 <li>Cannot reorder or slide sequences after dragging an
3396 alignment onto desktop</li>
3397 <li>Colour by annotation dialog throws NPE after using
3398 'extract scores' function</li>
3399 <li>Loading/cut'n'pasting an empty file leads to a grey
3400 alignment window</li>
3401 <li>Disorder thresholds rendered incorrectly after
3402 performing IUPred disorder prediction</li>
3403 <li>Multiple group annotated consensus rows shown when
3404 changing 'normalise logo' display setting</li>
3405 <li>Find shows blank dialog after 'finished searching' if
3406 nothing matches query</li>
3407 <li>Null Pointer Exceptions raised when sorting by
3408 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3410 <li>Errors in Jmol console when structures in alignment
3411 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3413 <li>Not all working JABAWS services are shown in
3415 <li>JAVAWS version of Jalview fails to launch with
3416 'invalid literal/length code'</li>
3417 <li>Annotation/RNA Helix colourschemes cannot be applied
3418 to alignment with groups (actually fixed in 2.8.0b1)</li>
3419 <li>RNA Helices and T-Coffee Scores available as default
3422 </ul> <em>Applet</em>
3424 <li>Remove group option is shown even when selection is
3426 <li>Apply to all groups ticked but colourscheme changes
3427 don't affect groups</li>
3428 <li>Documented RNA Helices and T-Coffee Scores as valid
3429 colourscheme name</li>
3430 <li>Annotation labels drawn on sequence IDs when
3431 Annotation panel is not displayed</li>
3432 <li>Increased font size for dropdown menus on OSX and
3433 embedded windows</li>
3434 </ul> <em>Other</em>
3436 <li>Consensus sequence for alignments/groups with a
3437 single sequence were not calculated</li>
3438 <li>annotation files that contain only groups imported as
3439 annotation and junk sequences</li>
3440 <li>Fasta files with sequences containing '*' incorrectly
3441 recognised as PFAM or BLC</li>
3442 <li>conservation/PID slider apply all groups option
3443 doesn't affect background (2.8.0b1)
3445 <li>redundancy highlighting is erratic at 0% and 100%</li>
3446 <li>Remove gapped columns fails for sequences with ragged
3448 <li>AMSA annotation row with leading spaces is not
3449 registered correctly on import</li>
3450 <li>Jalview crashes when selecting PCA analysis for
3451 certain alignments</li>
3452 <li>Opening the colour by annotation dialog for an
3453 existing annotation based 'use original colours'
3454 colourscheme loses original colours setting</li>
3459 <td><div align="center">
3460 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3461 <em>30/1/2014</em></strong>
3465 <li>Trusted certificates for JalviewLite applet and
3466 Jalview Desktop application<br />Certificate was donated by
3467 <a href="https://www.certum.eu">Certum</a> to the Jalview
3468 open source project).
3470 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3471 <li>Output in Stockholm format</li>
3472 <li>Allow import of data from gzipped files</li>
3473 <li>Export/import group and sequence associated line
3474 graph thresholds</li>
3475 <li>Nucleotide substitution matrix that supports RNA and
3476 ambiguity codes</li>
3477 <li>Allow disorder predictions to be made on the current
3478 selection (or visible selection) in the same way that JPred
3480 <li>Groovy scripting for headless Jalview operation</li>
3481 </ul> <em>Other improvements</em>
3483 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3484 <li>COMBINE statement uses current SEQUENCE_REF and
3485 GROUP_REF scope to group annotation rows</li>
3486 <li>Support '' style escaping of quotes in Newick
3488 <li>Group options for JABAWS service by command line name</li>
3489 <li>Empty tooltip shown for JABA service options with a
3490 link but no description</li>
3491 <li>Select primary source when selecting authority in
3492 database fetcher GUI</li>
3493 <li>Add .mfa to FASTA file extensions recognised by
3495 <li>Annotation label tooltip text wrap</li>
3500 <li>Slow scrolling when lots of annotation rows are
3502 <li>Lots of NPE (and slowness) after creating RNA
3503 secondary structure annotation line</li>
3504 <li>Sequence database accessions not imported when
3505 fetching alignments from Rfam</li>
3506 <li>Incorrect SHMR submission for sequences with
3508 <li>View all structures does not always superpose
3510 <li>Option widgets in service parameters not updated to
3511 reflect user or preset settings</li>
3512 <li>Null pointer exceptions for some services without
3513 presets or adjustable parameters</li>
3514 <li>Discover PDB IDs entry in structure menu doesn't
3515 discover PDB xRefs</li>
3516 <li>Exception encountered while trying to retrieve
3517 features with DAS</li>
3518 <li>Lowest value in annotation row isn't coloured
3519 when colour by annotation (per sequence) is coloured</li>
3520 <li>Keyboard mode P jumps to start of gapped region when
3521 residue follows a gap</li>
3522 <li>Jalview appears to hang importing an alignment with
3523 Wrap as default or after enabling Wrap</li>
3524 <li>'Right click to add annotations' message
3525 shown in wrap mode when no annotations present</li>
3526 <li>Disorder predictions fail with NPE if no automatic
3527 annotation already exists on alignment</li>
3528 <li>oninit javascript function should be called after
3529 initialisation completes</li>
3530 <li>Remove redundancy after disorder prediction corrupts
3531 alignment window display</li>
3532 <li>Example annotation file in documentation is invalid</li>
3533 <li>Grouped line graph annotation rows are not exported
3534 to annotation file</li>
3535 <li>Multi-harmony analysis cannot be run when only two
3537 <li>Cannot create multiple groups of line graphs with
3538 several 'combine' statements in annotation file</li>
3539 <li>Pressing return several times causes Number Format
3540 exceptions in keyboard mode</li>
3541 <li>Multi-harmony (SHMMR) method doesn't submit
3542 correct partitions for input data</li>
3543 <li>Translation from DNA to Amino Acids fails</li>
3544 <li>Jalview fail to load newick tree with quoted label</li>
3545 <li>--headless flag isn't understood</li>
3546 <li>ClassCastException when generating EPS in headless
3548 <li>Adjusting sequence-associated shading threshold only
3549 changes one row's threshold</li>
3550 <li>Preferences and Feature settings panel panel
3551 doesn't open</li>
3552 <li>hide consensus histogram also hides conservation and
3553 quality histograms</li>
3558 <td><div align="center">
3559 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3561 <td><em>Application</em>
3563 <li>Support for JABAWS 2.0 Services (AACon alignment
3564 conservation, protein disorder and Clustal Omega)</li>
3565 <li>JABAWS server status indicator in Web Services
3567 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3568 in Jalview alignment window</li>
3569 <li>Updated Jalview build and deploy framework for OSX
3570 mountain lion, windows 7, and 8</li>
3571 <li>Nucleotide substitution matrix for PCA that supports
3572 RNA and ambiguity codes</li>
3574 <li>Improved sequence database retrieval GUI</li>
3575 <li>Support fetching and database reference look up
3576 against multiple DAS sources (Fetch all from in 'fetch db
3578 <li>Jalview project improvements
3580 <li>Store and retrieve the 'belowAlignment'
3581 flag for annotation</li>
3582 <li>calcId attribute to group annotation rows on the
3584 <li>Store AACon calculation settings for a view in
3585 Jalview project</li>
3589 <li>horizontal scrolling gesture support</li>
3590 <li>Visual progress indicator when PCA calculation is
3592 <li>Simpler JABA web services menus</li>
3593 <li>visual indication that web service results are still
3594 being retrieved from server</li>
3595 <li>Serialise the dialogs that are shown when Jalview
3596 starts up for first time</li>
3597 <li>Jalview user agent string for interacting with HTTP
3599 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3601 <li>Examples directory and Groovy library included in
3602 InstallAnywhere distribution</li>
3603 </ul> <em>Applet</em>
3605 <li>RNA alignment and secondary structure annotation
3606 visualization applet example</li>
3607 </ul> <em>General</em>
3609 <li>Normalise option for consensus sequence logo</li>
3610 <li>Reset button in PCA window to return dimensions to
3612 <li>Allow seqspace or Jalview variant of alignment PCA
3614 <li>PCA with either nucleic acid and protein substitution
3616 <li>Allow windows containing HTML reports to be exported
3618 <li>Interactive display and editing of RNA secondary
3619 structure contacts</li>
3620 <li>RNA Helix Alignment Colouring</li>
3621 <li>RNA base pair logo consensus</li>
3622 <li>Parse sequence associated secondary structure
3623 information in Stockholm files</li>
3624 <li>HTML Export database accessions and annotation
3625 information presented in tooltip for sequences</li>
3626 <li>Import secondary structure from LOCARNA clustalw
3627 style RNA alignment files</li>
3628 <li>import and visualise T-COFFEE quality scores for an
3630 <li>'colour by annotation' per sequence option to
3631 shade each sequence according to its associated alignment
3633 <li>New Jalview Logo</li>
3634 </ul> <em>Documentation and Development</em>
3636 <li>documentation for score matrices used in Jalview</li>
3637 <li>New Website!</li>
3639 <td><em>Application</em>
3641 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3642 wsdbfetch REST service</li>
3643 <li>Stop windows being moved outside desktop on OSX</li>
3644 <li>Filetype associations not installed for webstart
3646 <li>Jalview does not always retrieve progress of a JABAWS
3647 job execution in full once it is complete</li>
3648 <li>revise SHMR RSBS definition to ensure alignment is
3649 uploaded via ali_file parameter</li>
3650 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3651 <li>View all structures superposed fails with exception</li>
3652 <li>Jnet job queues forever if a very short sequence is
3653 submitted for prediction</li>
3654 <li>Cut and paste menu not opened when mouse clicked on
3656 <li>Putting fractional value into integer text box in
3657 alignment parameter dialog causes Jalview to hang</li>
3658 <li>Structure view highlighting doesn't work on
3660 <li>View all structures fails with exception shown in
3662 <li>Characters in filename associated with PDBEntry not
3663 escaped in a platform independent way</li>
3664 <li>Jalview desktop fails to launch with exception when
3666 <li>Tree calculation reports 'you must have 2 or more
3667 sequences selected' when selection is empty</li>
3668 <li>Jalview desktop fails to launch with jar signature
3669 failure when java web start temporary file caching is
3671 <li>DAS Sequence retrieval with range qualification
3672 results in sequence xref which includes range qualification</li>
3673 <li>Errors during processing of command line arguments
3674 cause progress bar (JAL-898) to be removed</li>
3675 <li>Replace comma for semi-colon option not disabled for
3676 DAS sources in sequence fetcher</li>
3677 <li>Cannot close news reader when JABAWS server warning
3678 dialog is shown</li>
3679 <li>Option widgets not updated to reflect user settings</li>
3680 <li>Edited sequence not submitted to web service</li>
3681 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3682 <li>InstallAnywhere installer doesn't unpack and run
3683 on OSX Mountain Lion</li>
3684 <li>Annotation panel not given a scroll bar when
3685 sequences with alignment annotation are pasted into the
3687 <li>Sequence associated annotation rows not associated
3688 when loaded from Jalview project</li>
3689 <li>Browser launch fails with NPE on java 1.7</li>
3690 <li>JABAWS alignment marked as finished when job was
3691 cancelled or job failed due to invalid input</li>
3692 <li>NPE with v2.7 example when clicking on Tree
3693 associated with all views</li>
3694 <li>Exceptions when copy/paste sequences with grouped
3695 annotation rows to new window</li>
3696 </ul> <em>Applet</em>
3698 <li>Sequence features are momentarily displayed before
3699 they are hidden using hidefeaturegroups applet parameter</li>
3700 <li>loading features via javascript API automatically
3701 enables feature display</li>
3702 <li>scrollToColumnIn javascript API method doesn't
3704 </ul> <em>General</em>
3706 <li>Redundancy removal fails for rna alignment</li>
3707 <li>PCA calculation fails when sequence has been selected
3708 and then deselected</li>
3709 <li>PCA window shows grey box when first opened on OSX</li>
3710 <li>Letters coloured pink in sequence logo when alignment
3711 coloured with clustalx</li>
3712 <li>Choosing fonts without letter symbols defined causes
3713 exceptions and redraw errors</li>
3714 <li>Initial PCA plot view is not same as manually
3715 reconfigured view</li>
3716 <li>Grouped annotation graph label has incorrect line
3718 <li>Grouped annotation graph label display is corrupted
3719 for lots of labels</li>
3724 <div align="center">
3725 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3728 <td><em>Application</em>
3730 <li>Jalview Desktop News Reader</li>
3731 <li>Tweaked default layout of web services menu</li>
3732 <li>View/alignment association menu to enable user to
3733 easily specify which alignment a multi-structure view takes
3734 its colours/correspondences from</li>
3735 <li>Allow properties file location to be specified as URL</li>
3736 <li>Extend Jalview project to preserve associations
3737 between many alignment views and a single Jmol display</li>
3738 <li>Store annotation row height in Jalview project file</li>
3739 <li>Annotation row column label formatting attributes
3740 stored in project file</li>
3741 <li>Annotation row order for auto-calculated annotation
3742 rows preserved in Jalview project file</li>
3743 <li>Visual progress indication when Jalview state is
3744 saved using Desktop window menu</li>
3745 <li>Visual indication that command line arguments are
3746 still being processed</li>
3747 <li>Groovy script execution from URL</li>
3748 <li>Colour by annotation default min and max colours in
3750 <li>Automatically associate PDB files dragged onto an
3751 alignment with sequences that have high similarity and
3753 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3754 <li>'view structures' option to open many
3755 structures in same window</li>
3756 <li>Sort associated views menu option for tree panel</li>
3757 <li>Group all JABA and non-JABA services for a particular
3758 analysis function in its own submenu</li>
3759 </ul> <em>Applet</em>
3761 <li>Userdefined and autogenerated annotation rows for
3763 <li>Adjustment of alignment annotation pane height</li>
3764 <li>Annotation scrollbar for annotation panel</li>
3765 <li>Drag to reorder annotation rows in annotation panel</li>
3766 <li>'automaticScrolling' parameter</li>
3767 <li>Allow sequences with partial ID string matches to be
3768 annotated from GFF/Jalview features files</li>
3769 <li>Sequence logo annotation row in applet</li>
3770 <li>Absolute paths relative to host server in applet
3771 parameters are treated as such</li>
3772 <li>New in the JalviewLite javascript API:
3774 <li>JalviewLite.js javascript library</li>
3775 <li>Javascript callbacks for
3777 <li>Applet initialisation</li>
3778 <li>Sequence/alignment mouse-overs and selections</li>
3781 <li>scrollTo row and column alignment scrolling
3783 <li>Select sequence/alignment regions from javascript</li>
3784 <li>javascript structure viewer harness to pass
3785 messages between Jmol and Jalview when running as
3786 distinct applets</li>
3787 <li>sortBy method</li>
3788 <li>Set of applet and application examples shipped
3789 with documentation</li>
3790 <li>New example to demonstrate JalviewLite and Jmol
3791 javascript message exchange</li>
3793 </ul> <em>General</em>
3795 <li>Enable Jmol displays to be associated with multiple
3796 multiple alignments</li>
3797 <li>Option to automatically sort alignment with new tree</li>
3798 <li>User configurable link to enable redirects to a
3799 www.Jalview.org mirror</li>
3800 <li>Jmol colours option for Jmol displays</li>
3801 <li>Configurable newline string when writing alignment
3802 and other flat files</li>
3803 <li>Allow alignment annotation description lines to
3804 contain html tags</li>
3805 </ul> <em>Documentation and Development</em>
3807 <li>Add groovy test harness for bulk load testing to
3809 <li>Groovy script to load and align a set of sequences
3810 using a web service before displaying the result in the
3811 Jalview desktop</li>
3812 <li>Restructured javascript and applet api documentation</li>
3813 <li>Ant target to publish example html files with applet
3815 <li>Netbeans project for building Jalview from source</li>
3816 <li>ant task to create online javadoc for Jalview source</li>
3818 <td><em>Application</em>
3820 <li>User defined colourscheme throws exception when
3821 current built in colourscheme is saved as new scheme</li>
3822 <li>AlignFrame->Save in application pops up save
3823 dialog for valid filename/format</li>
3824 <li>Cannot view associated structure for UniProt sequence</li>
3825 <li>PDB file association breaks for UniProt sequence
3827 <li>Associate PDB from file dialog does not tell you
3828 which sequence is to be associated with the file</li>
3829 <li>Find All raises null pointer exception when query
3830 only matches sequence IDs</li>
3831 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3832 <li>Jalview project with Jmol views created with Jalview
3833 2.4 cannot be loaded</li>
3834 <li>Filetype associations not installed for webstart
3836 <li>Two or more chains in a single PDB file associated
3837 with sequences in different alignments do not get coloured
3838 by their associated sequence</li>
3839 <li>Visibility status of autocalculated annotation row
3840 not preserved when project is loaded</li>
3841 <li>Annotation row height and visibility attributes not
3842 stored in Jalview project</li>
3843 <li>Tree bootstraps are not preserved when saved as a
3844 Jalview project</li>
3845 <li>Envision2 workflow tooltips are corrupted</li>
3846 <li>Enabling show group conservation also enables colour
3847 by conservation</li>
3848 <li>Duplicate group associated conservation or consensus
3849 created on new view</li>
3850 <li>Annotation scrollbar not displayed after 'show
3851 all hidden annotation rows' option selected</li>
3852 <li>Alignment quality not updated after alignment
3853 annotation row is hidden then shown</li>
3854 <li>Preserve colouring of structures coloured by
3855 sequences in pre Jalview 2.7 projects</li>
3856 <li>Web service job parameter dialog is not laid out
3858 <li>Web services menu not refreshed after 'reset
3859 services' button is pressed in preferences</li>
3860 <li>Annotation off by one in Jalview v2_3 example project</li>
3861 <li>Structures imported from file and saved in project
3862 get name like jalview_pdb1234.txt when reloaded</li>
3863 <li>Jalview does not always retrieve progress of a JABAWS
3864 job execution in full once it is complete</li>
3865 </ul> <em>Applet</em>
3867 <li>Alignment height set incorrectly when lots of
3868 annotation rows are displayed</li>
3869 <li>Relative URLs in feature HTML text not resolved to
3871 <li>View follows highlighting does not work for positions
3873 <li><= shown as = in tooltip</li>
3874 <li>Export features raises exception when no features
3876 <li>Separator string used for serialising lists of IDs
3877 for javascript api is modified when separator string
3878 provided as parameter</li>
3879 <li>Null pointer exception when selecting tree leaves for
3880 alignment with no existing selection</li>
3881 <li>Relative URLs for datasources assumed to be relative
3882 to applet's codebase</li>
3883 <li>Status bar not updated after finished searching and
3884 search wraps around to first result</li>
3885 <li>StructureSelectionManager instance shared between
3886 several Jalview applets causes race conditions and memory
3888 <li>Hover tooltip and mouseover of position on structure
3889 not sent from Jmol in applet</li>
3890 <li>Certain sequences of javascript method calls to
3891 applet API fatally hang browser</li>
3892 </ul> <em>General</em>
3894 <li>View follows structure mouseover scrolls beyond
3895 position with wrapped view and hidden regions</li>
3896 <li>Find sequence position moves to wrong residue
3897 with/without hidden columns</li>
3898 <li>Sequence length given in alignment properties window
3900 <li>InvalidNumberFormat exceptions thrown when trying to
3901 import PDB like structure files</li>
3902 <li>Positional search results are only highlighted
3903 between user-supplied sequence start/end bounds</li>
3904 <li>End attribute of sequence is not validated</li>
3905 <li>Find dialog only finds first sequence containing a
3906 given sequence position</li>
3907 <li>Sequence numbering not preserved in MSF alignment
3909 <li>Jalview PDB file reader does not extract sequence
3910 from nucleotide chains correctly</li>
3911 <li>Structure colours not updated when tree partition
3912 changed in alignment</li>
3913 <li>Sequence associated secondary structure not correctly
3914 parsed in interleaved stockholm</li>
3915 <li>Colour by annotation dialog does not restore current
3917 <li>Hiding (nearly) all sequences doesn't work
3919 <li>Sequences containing lowercase letters are not
3920 properly associated with their pdb files</li>
3921 </ul> <em>Documentation and Development</em>
3923 <li>schemas/JalviewWsParamSet.xsd corrupted by
3924 ApplyCopyright tool</li>
3929 <div align="center">
3930 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3933 <td><em>Application</em>
3935 <li>New warning dialog when the Jalview Desktop cannot
3936 contact web services</li>
3937 <li>JABA service parameters for a preset are shown in
3938 service job window</li>
3939 <li>JABA Service menu entries reworded</li>
3943 <li>Modeller PIR IO broken - cannot correctly import a
3944 pir file emitted by Jalview</li>
3945 <li>Existing feature settings transferred to new
3946 alignment view created from cut'n'paste</li>
3947 <li>Improved test for mixed amino/nucleotide chains when
3948 parsing PDB files</li>
3949 <li>Consensus and conservation annotation rows
3950 occasionally become blank for all new windows</li>
3951 <li>Exception raised when right clicking above sequences
3952 in wrapped view mode</li>
3953 </ul> <em>Application</em>
3955 <li>multiple multiply aligned structure views cause cpu
3956 usage to hit 100% and computer to hang</li>
3957 <li>Web Service parameter layout breaks for long user
3958 parameter names</li>
3959 <li>Jaba service discovery hangs desktop if Jaba server
3966 <div align="center">
3967 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3970 <td><em>Application</em>
3972 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3973 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3976 <li>Web Services preference tab</li>
3977 <li>Analysis parameters dialog box and user defined
3979 <li>Improved speed and layout of Envision2 service menu</li>
3980 <li>Superpose structures using associated sequence
3982 <li>Export coordinates and projection as CSV from PCA
3984 </ul> <em>Applet</em>
3986 <li>enable javascript: execution by the applet via the
3987 link out mechanism</li>
3988 </ul> <em>Other</em>
3990 <li>Updated the Jmol Jalview interface to work with Jmol
3992 <li>The Jalview Desktop and JalviewLite applet now
3993 require Java 1.5</li>
3994 <li>Allow Jalview feature colour specification for GFF
3995 sequence annotation files</li>
3996 <li>New 'colour by label' keword in Jalview feature file
3997 type colour specification</li>
3998 <li>New Jalview Desktop Groovy API method that allows a
3999 script to check if it being run in an interactive session or
4000 in a batch operation from the Jalview command line</li>
4004 <li>clustalx colourscheme colours Ds preferentially when
4005 both D+E are present in over 50% of the column</li>
4006 </ul> <em>Application</em>
4008 <li>typo in AlignmentFrame->View->Hide->all but
4009 selected Regions menu item</li>
4010 <li>sequence fetcher replaces ',' for ';' when the ',' is
4011 part of a valid accession ID</li>
4012 <li>fatal OOM if object retrieved by sequence fetcher
4013 runs out of memory</li>
4014 <li>unhandled Out of Memory Error when viewing pca
4015 analysis results</li>
4016 <li>InstallAnywhere builds fail to launch on OS X java
4017 10.5 update 4 (due to apple Java 1.6 update)</li>
4018 <li>Installanywhere Jalview silently fails to launch</li>
4019 </ul> <em>Applet</em>
4021 <li>Jalview.getFeatureGroups() raises an
4022 ArrayIndexOutOfBoundsException if no feature groups are
4029 <div align="center">
4030 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4036 <li>Alignment prettyprinter doesn't cope with long
4038 <li>clustalx colourscheme colours Ds preferentially when
4039 both D+E are present in over 50% of the column</li>
4040 <li>nucleic acid structures retrieved from PDB do not
4041 import correctly</li>
4042 <li>More columns get selected than were clicked on when a
4043 number of columns are hidden</li>
4044 <li>annotation label popup menu not providing correct
4045 add/hide/show options when rows are hidden or none are
4047 <li>Stockholm format shown in list of readable formats,
4048 and parser copes better with alignments from RFAM.</li>
4049 <li>CSV output of consensus only includes the percentage
4050 of all symbols if sequence logo display is enabled</li>
4052 </ul> <em>Applet</em>
4054 <li>annotation panel disappears when annotation is
4056 </ul> <em>Application</em>
4058 <li>Alignment view not redrawn properly when new
4059 alignment opened where annotation panel is visible but no
4060 annotations are present on alignment</li>
4061 <li>pasted region containing hidden columns is
4062 incorrectly displayed in new alignment window</li>
4063 <li>Jalview slow to complete operations when stdout is
4064 flooded (fix is to close the Jalview console)</li>
4065 <li>typo in AlignmentFrame->View->Hide->all but
4066 selected Rregions menu item.</li>
4067 <li>inconsistent group submenu and Format submenu entry
4068 'Un' or 'Non'conserved</li>
4069 <li>Sequence feature settings are being shared by
4070 multiple distinct alignments</li>
4071 <li>group annotation not recreated when tree partition is
4073 <li>double click on group annotation to select sequences
4074 does not propagate to associated trees</li>
4075 <li>Mac OSX specific issues:
4077 <li>exception raised when mouse clicked on desktop
4078 window background</li>
4079 <li>Desktop menu placed on menu bar and application
4080 name set correctly</li>
4081 <li>sequence feature settings not wide enough for the
4082 save feature colourscheme button</li>
4091 <div align="center">
4092 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4095 <td><em>New Capabilities</em>
4097 <li>URL links generated from description line for
4098 regular-expression based URL links (applet and application)
4100 <li>Non-positional feature URL links are shown in link
4102 <li>Linked viewing of nucleic acid sequences and
4104 <li>Automatic Scrolling option in View menu to display
4105 the currently highlighted region of an alignment.</li>
4106 <li>Order an alignment by sequence length, or using the
4107 average score or total feature count for each sequence.</li>
4108 <li>Shading features by score or associated description</li>
4109 <li>Subdivide alignment and groups based on identity of
4110 selected subsequence (Make Groups from Selection).</li>
4111 <li>New hide/show options including Shift+Control+H to
4112 hide everything but the currently selected region.</li>
4113 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4114 </ul> <em>Application</em>
4116 <li>Fetch DB References capabilities and UI expanded to
4117 support retrieval from DAS sequence sources</li>
4118 <li>Local DAS Sequence sources can be added via the
4119 command line or via the Add local source dialog box.</li>
4120 <li>DAS Dbref and DbxRef feature types are parsed as
4121 database references and protein_name is parsed as
4122 description line (BioSapiens terms).</li>
4123 <li>Enable or disable non-positional feature and database
4124 references in sequence ID tooltip from View menu in
4126 <!-- <li>New hidden columns and rows and representatives capabilities
4127 in annotations file (in progress - not yet fully implemented)</li> -->
4128 <li>Group-associated consensus, sequence logos and
4129 conservation plots</li>
4130 <li>Symbol distributions for each column can be exported
4131 and visualized as sequence logos</li>
4132 <li>Optionally scale multi-character column labels to fit
4133 within each column of annotation row<!-- todo for applet -->
4135 <li>Optional automatic sort of associated alignment view
4136 when a new tree is opened.</li>
4137 <li>Jalview Java Console</li>
4138 <li>Better placement of desktop window when moving
4139 between different screens.</li>
4140 <li>New preference items for sequence ID tooltip and
4141 consensus annotation</li>
4142 <li>Client to submit sequences and IDs to Envision2
4144 <li><em>Vamsas Capabilities</em>
4146 <li>Improved VAMSAS synchronization (Jalview archive
4147 used to preserve views, structures, and tree display
4149 <li>Import of vamsas documents from disk or URL via
4151 <li>Sharing of selected regions between views and
4152 with other VAMSAS applications (Experimental feature!)</li>
4153 <li>Updated API to VAMSAS version 0.2</li>
4155 </ul> <em>Applet</em>
4157 <li>Middle button resizes annotation row height</li>
4160 <li>sortByTree (true/false) - automatically sort the
4161 associated alignment view by the tree when a new tree is
4163 <li>showTreeBootstraps (true/false) - show or hide
4164 branch bootstraps (default is to show them if available)</li>
4165 <li>showTreeDistances (true/false) - show or hide
4166 branch lengths (default is to show them if available)</li>
4167 <li>showUnlinkedTreeNodes (true/false) - indicate if
4168 unassociated nodes should be highlighted in the tree
4170 <li>heightScale and widthScale (1.0 or more) -
4171 increase the height or width of a cell in the alignment
4172 grid relative to the current font size.</li>
4175 <li>Non-positional features displayed in sequence ID
4177 </ul> <em>Other</em>
4179 <li>Features format: graduated colour definitions and
4180 specification of feature scores</li>
4181 <li>Alignment Annotations format: new keywords for group
4182 associated annotation (GROUP_REF) and annotation row display
4183 properties (ROW_PROPERTIES)</li>
4184 <li>XML formats extended to support graduated feature
4185 colourschemes, group associated annotation, and profile
4186 visualization settings.</li></td>
4189 <li>Source field in GFF files parsed as feature source
4190 rather than description</li>
4191 <li>Non-positional features are now included in sequence
4192 feature and gff files (controlled via non-positional feature
4193 visibility in tooltip).</li>
4194 <li>URL links generated for all feature links (bugfix)</li>
4195 <li>Added URL embedding instructions to features file
4197 <li>Codons containing ambiguous nucleotides translated as
4198 'X' in peptide product</li>
4199 <li>Match case switch in find dialog box works for both
4200 sequence ID and sequence string and query strings do not
4201 have to be in upper case to match case-insensitively.</li>
4202 <li>AMSA files only contain first column of
4203 multi-character column annotation labels</li>
4204 <li>Jalview Annotation File generation/parsing consistent
4205 with documentation (e.g. Stockholm annotation can be
4206 exported and re-imported)</li>
4207 <li>PDB files without embedded PDB IDs given a friendly
4209 <li>Find incrementally searches ID string matches as well
4210 as subsequence matches, and correctly reports total number
4214 <li>Better handling of exceptions during sequence
4216 <li>Dasobert generated non-positional feature URL
4217 link text excludes the start_end suffix</li>
4218 <li>DAS feature and source retrieval buttons disabled
4219 when fetch or registry operations in progress.</li>
4220 <li>PDB files retrieved from URLs are cached properly</li>
4221 <li>Sequence description lines properly shared via
4223 <li>Sequence fetcher fetches multiple records for all
4225 <li>Ensured that command line das feature retrieval
4226 completes before alignment figures are generated.</li>
4227 <li>Reduced time taken when opening file browser for
4229 <li>isAligned check prior to calculating tree, PCA or
4230 submitting an MSA to JNet now excludes hidden sequences.</li>
4231 <li>User defined group colours properly recovered
4232 from Jalview projects.</li>
4241 <div align="center">
4242 <strong>2.4.0.b2</strong><br> 28/10/2009
4247 <li>Experimental support for google analytics usage
4249 <li>Jalview privacy settings (user preferences and docs).</li>
4254 <li>Race condition in applet preventing startup in
4256 <li>Exception when feature created from selection beyond
4257 length of sequence.</li>
4258 <li>Allow synthetic PDB files to be imported gracefully</li>
4259 <li>Sequence associated annotation rows associate with
4260 all sequences with a given id</li>
4261 <li>Find function matches case-insensitively for sequence
4262 ID string searches</li>
4263 <li>Non-standard characters do not cause pairwise
4264 alignment to fail with exception</li>
4265 </ul> <em>Application Issues</em>
4267 <li>Sequences are now validated against EMBL database</li>
4268 <li>Sequence fetcher fetches multiple records for all
4270 </ul> <em>InstallAnywhere Issues</em>
4272 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4273 issue with installAnywhere mechanism)</li>
4274 <li>Command line launching of JARs from InstallAnywhere
4275 version (java class versioning error fixed)</li>
4282 <div align="center">
4283 <strong>2.4</strong><br> 27/8/2008
4286 <td><em>User Interface</em>
4288 <li>Linked highlighting of codon and amino acid from
4289 translation and protein products</li>
4290 <li>Linked highlighting of structure associated with
4291 residue mapping to codon position</li>
4292 <li>Sequence Fetcher provides example accession numbers
4293 and 'clear' button</li>
4294 <li>MemoryMonitor added as an option under Desktop's
4296 <li>Extract score function to parse whitespace separated
4297 numeric data in description line</li>
4298 <li>Column labels in alignment annotation can be centred.</li>
4299 <li>Tooltip for sequence associated annotation give name
4301 </ul> <em>Web Services and URL fetching</em>
4303 <li>JPred3 web service</li>
4304 <li>Prototype sequence search client (no public services
4306 <li>Fetch either seed alignment or full alignment from
4308 <li>URL Links created for matching database cross
4309 references as well as sequence ID</li>
4310 <li>URL Links can be created using regular-expressions</li>
4311 </ul> <em>Sequence Database Connectivity</em>
4313 <li>Retrieval of cross-referenced sequences from other
4315 <li>Generalised database reference retrieval and
4316 validation to all fetchable databases</li>
4317 <li>Fetch sequences from DAS sources supporting the
4318 sequence command</li>
4319 </ul> <em>Import and Export</em>
4320 <li>export annotation rows as CSV for spreadsheet import</li>
4321 <li>Jalview projects record alignment dataset associations,
4322 EMBL products, and cDNA sequence mappings</li>
4323 <li>Sequence Group colour can be specified in Annotation
4325 <li>Ad-hoc colouring of group in Annotation File using RGB
4326 triplet as name of colourscheme</li>
4327 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4329 <li>treenode binding for VAMSAS tree exchange</li>
4330 <li>local editing and update of sequences in VAMSAS
4331 alignments (experimental)</li>
4332 <li>Create new or select existing session to join</li>
4333 <li>load and save of vamsas documents</li>
4334 </ul> <em>Application command line</em>
4336 <li>-tree parameter to open trees (introduced for passing
4338 <li>-fetchfrom command line argument to specify nicknames
4339 of DAS servers to query for alignment features</li>
4340 <li>-dasserver command line argument to add new servers
4341 that are also automatically queried for features</li>
4342 <li>-groovy command line argument executes a given groovy
4343 script after all input data has been loaded and parsed</li>
4344 </ul> <em>Applet-Application data exchange</em>
4346 <li>Trees passed as applet parameters can be passed to
4347 application (when using "View in full
4348 application")</li>
4349 </ul> <em>Applet Parameters</em>
4351 <li>feature group display control parameter</li>
4352 <li>debug parameter</li>
4353 <li>showbutton parameter</li>
4354 </ul> <em>Applet API methods</em>
4356 <li>newView public method</li>
4357 <li>Window (current view) specific get/set public methods</li>
4358 <li>Feature display control methods</li>
4359 <li>get list of currently selected sequences</li>
4360 </ul> <em>New Jalview distribution features</em>
4362 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4363 <li>RELEASE file gives build properties for the latest
4364 Jalview release.</li>
4365 <li>Java 1.1 Applet build made easier and donotobfuscate
4366 property controls execution of obfuscator</li>
4367 <li>Build target for generating source distribution</li>
4368 <li>Debug flag for javacc</li>
4369 <li>.jalview_properties file is documented (slightly) in
4370 jalview.bin.Cache</li>
4371 <li>Continuous Build Integration for stable and
4372 development version of Application, Applet and source
4377 <li>selected region output includes visible annotations
4378 (for certain formats)</li>
4379 <li>edit label/displaychar contains existing label/char
4381 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4382 <li>shorter peptide product names from EMBL records</li>
4383 <li>Newick string generator makes compact representations</li>
4384 <li>bootstrap values parsed correctly for tree files with
4386 <li>pathological filechooser bug avoided by not allowing
4387 filenames containing a ':'</li>
4388 <li>Fixed exception when parsing GFF files containing
4389 global sequence features</li>
4390 <li>Alignment datasets are finalized only when number of
4391 references from alignment sequences goes to zero</li>
4392 <li>Close of tree branch colour box without colour
4393 selection causes cascading exceptions</li>
4394 <li>occasional negative imgwidth exceptions</li>
4395 <li>better reporting of non-fatal warnings to user when
4396 file parsing fails.</li>
4397 <li>Save works when Jalview project is default format</li>
4398 <li>Save as dialog opened if current alignment format is
4399 not a valid output format</li>
4400 <li>UniProt canonical names introduced for both das and
4402 <li>Histidine should be midblue (not pink!) in Zappo</li>
4403 <li>error messages passed up and output when data read
4405 <li>edit undo recovers previous dataset sequence when
4406 sequence is edited</li>
4407 <li>allow PDB files without pdb ID HEADER lines (like
4408 those generated by MODELLER) to be read in properly</li>
4409 <li>allow reading of JPred concise files as a normal
4411 <li>Stockholm annotation parsing and alignment properties
4412 import fixed for PFAM records</li>
4413 <li>Structure view windows have correct name in Desktop
4415 <li>annotation consisting of sequence associated scores
4416 can be read and written correctly to annotation file</li>
4417 <li>Aligned cDNA translation to aligned peptide works
4419 <li>Fixed display of hidden sequence markers and
4420 non-italic font for representatives in Applet</li>
4421 <li>Applet Menus are always embedded in applet window on
4423 <li>Newly shown features appear at top of stack (in
4425 <li>Annotations added via parameter not drawn properly
4426 due to null pointer exceptions</li>
4427 <li>Secondary structure lines are drawn starting from
4428 first column of alignment</li>
4429 <li>UniProt XML import updated for new schema release in
4431 <li>Sequence feature to sequence ID match for Features
4432 file is case-insensitive</li>
4433 <li>Sequence features read from Features file appended to
4434 all sequences with matching IDs</li>
4435 <li>PDB structure coloured correctly for associated views
4436 containing a sub-sequence</li>
4437 <li>PDB files can be retrieved by applet from Jar files</li>
4438 <li>feature and annotation file applet parameters
4439 referring to different directories are retrieved correctly</li>
4440 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4441 <li>Fixed application hang whilst waiting for
4442 splash-screen version check to complete</li>
4443 <li>Applet properly URLencodes input parameter values
4444 when passing them to the launchApp service</li>
4445 <li>display name and local features preserved in results
4446 retrieved from web service</li>
4447 <li>Visual delay indication for sequence retrieval and
4448 sequence fetcher initialisation</li>
4449 <li>updated Application to use DAS 1.53e version of
4450 dasobert DAS client</li>
4451 <li>Re-instated Full AMSA support and .amsa file
4453 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4461 <div align="center">
4462 <strong>2.3</strong><br> 9/5/07
4467 <li>Jmol 11.0.2 integration</li>
4468 <li>PDB views stored in Jalview XML files</li>
4469 <li>Slide sequences</li>
4470 <li>Edit sequence in place</li>
4471 <li>EMBL CDS features</li>
4472 <li>DAS Feature mapping</li>
4473 <li>Feature ordering</li>
4474 <li>Alignment Properties</li>
4475 <li>Annotation Scores</li>
4476 <li>Sort by scores</li>
4477 <li>Feature/annotation editing in applet</li>
4482 <li>Headless state operation in 2.2.1</li>
4483 <li>Incorrect and unstable DNA pairwise alignment</li>
4484 <li>Cut and paste of sequences with annotation</li>
4485 <li>Feature group display state in XML</li>
4486 <li>Feature ordering in XML</li>
4487 <li>blc file iteration selection using filename # suffix</li>
4488 <li>Stockholm alignment properties</li>
4489 <li>Stockhom alignment secondary structure annotation</li>
4490 <li>2.2.1 applet had no feature transparency</li>
4491 <li>Number pad keys can be used in cursor mode</li>
4492 <li>Structure Viewer mirror image resolved</li>
4499 <div align="center">
4500 <strong>2.2.1</strong><br> 12/2/07
4505 <li>Non standard characters can be read and displayed
4506 <li>Annotations/Features can be imported/exported to the
4508 <li>Applet allows editing of sequence/annotation/group
4509 name & description
4510 <li>Preference setting to display sequence name in
4512 <li>Annotation file format extended to allow
4513 Sequence_groups to be defined
4514 <li>Default opening of alignment overview panel can be
4515 specified in preferences
4516 <li>PDB residue numbering annotation added to associated
4522 <li>Applet crash under certain Linux OS with Java 1.6
4524 <li>Annotation file export / import bugs fixed
4525 <li>PNG / EPS image output bugs fixed
4531 <div align="center">
4532 <strong>2.2</strong><br> 27/11/06
4537 <li>Multiple views on alignment
4538 <li>Sequence feature editing
4539 <li>"Reload" alignment
4540 <li>"Save" to current filename
4541 <li>Background dependent text colour
4542 <li>Right align sequence ids
4543 <li>User-defined lower case residue colours
4546 <li>Menu item accelerator keys
4547 <li>Control-V pastes to current alignment
4548 <li>Cancel button for DAS Feature Fetching
4549 <li>PCA and PDB Viewers zoom via mouse roller
4550 <li>User-defined sub-tree colours and sub-tree selection
4552 <li>'New Window' button on the 'Output to Text box'
4557 <li>New memory efficient Undo/Redo System
4558 <li>Optimised symbol lookups and conservation/consensus
4560 <li>Region Conservation/Consensus recalculated after
4562 <li>Fixed Remove Empty Columns Bug (empty columns at end
4564 <li>Slowed DAS Feature Fetching for increased robustness.
4566 <li>Made angle brackets in ASCII feature descriptions
4568 <li>Re-instated Zoom function for PCA
4569 <li>Sequence descriptions conserved in web service
4571 <li>UniProt ID discoverer uses any word separated by
4573 <li>WsDbFetch query/result association resolved
4574 <li>Tree leaf to sequence mapping improved
4575 <li>Smooth fonts switch moved to FontChooser dialog box.
4582 <div align="center">
4583 <strong>2.1.1</strong><br> 12/9/06
4588 <li>Copy consensus sequence to clipboard</li>
4593 <li>Image output - rightmost residues are rendered if
4594 sequence id panel has been resized</li>
4595 <li>Image output - all offscreen group boundaries are
4597 <li>Annotation files with sequence references - all
4598 elements in file are relative to sequence position</li>
4599 <li>Mac Applet users can use Alt key for group editing</li>
4605 <div align="center">
4606 <strong>2.1</strong><br> 22/8/06
4611 <li>MAFFT Multiple Alignment in default Web Service list</li>
4612 <li>DAS Feature fetching</li>
4613 <li>Hide sequences and columns</li>
4614 <li>Export Annotations and Features</li>
4615 <li>GFF file reading / writing</li>
4616 <li>Associate structures with sequences from local PDB
4618 <li>Add sequences to exisiting alignment</li>
4619 <li>Recently opened files / URL lists</li>
4620 <li>Applet can launch the full application</li>
4621 <li>Applet has transparency for features (Java 1.2
4623 <li>Applet has user defined colours parameter</li>
4624 <li>Applet can load sequences from parameter
4625 "sequence<em>x</em>"
4631 <li>Redundancy Panel reinstalled in the Applet</li>
4632 <li>Monospaced font - EPS / rescaling bug fixed</li>
4633 <li>Annotation files with sequence references bug fixed</li>
4639 <div align="center">
4640 <strong>2.08.1</strong><br> 2/5/06
4645 <li>Change case of selected region from Popup menu</li>
4646 <li>Choose to match case when searching</li>
4647 <li>Middle mouse button and mouse movement can compress /
4648 expand the visible width and height of the alignment</li>
4653 <li>Annotation Panel displays complete JNet results</li>
4659 <div align="center">
4660 <strong>2.08b</strong><br> 18/4/06
4666 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4667 <li>Righthand label on wrapped alignments shows correct
4674 <div align="center">
4675 <strong>2.08</strong><br> 10/4/06
4680 <li>Editing can be locked to the selection area</li>
4681 <li>Keyboard editing</li>
4682 <li>Create sequence features from searches</li>
4683 <li>Precalculated annotations can be loaded onto
4685 <li>Features file allows grouping of features</li>
4686 <li>Annotation Colouring scheme added</li>
4687 <li>Smooth fonts off by default - Faster rendering</li>
4688 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4693 <li>Drag & Drop fixed on Linux</li>
4694 <li>Jalview Archive file faster to load/save, sequence
4695 descriptions saved.</li>
4701 <div align="center">
4702 <strong>2.07</strong><br> 12/12/05
4707 <li>PDB Structure Viewer enhanced</li>
4708 <li>Sequence Feature retrieval and display enhanced</li>
4709 <li>Choose to output sequence start-end after sequence
4710 name for file output</li>
4711 <li>Sequence Fetcher WSDBFetch@EBI</li>
4712 <li>Applet can read feature files, PDB files and can be
4713 used for HTML form input</li>
4718 <li>HTML output writes groups and features</li>
4719 <li>Group editing is Control and mouse click</li>
4720 <li>File IO bugs</li>
4726 <div align="center">
4727 <strong>2.06</strong><br> 28/9/05
4732 <li>View annotations in wrapped mode</li>
4733 <li>More options for PCA viewer</li>
4738 <li>GUI bugs resolved</li>
4739 <li>Runs with -nodisplay from command line</li>
4745 <div align="center">
4746 <strong>2.05b</strong><br> 15/9/05
4751 <li>Choose EPS export as lineart or text</li>
4752 <li>Jar files are executable</li>
4753 <li>Can read in Uracil - maps to unknown residue</li>
4758 <li>Known OutOfMemory errors give warning message</li>
4759 <li>Overview window calculated more efficiently</li>
4760 <li>Several GUI bugs resolved</li>
4766 <div align="center">
4767 <strong>2.05</strong><br> 30/8/05
4772 <li>Edit and annotate in "Wrapped" view</li>
4777 <li>Several GUI bugs resolved</li>
4783 <div align="center">
4784 <strong>2.04</strong><br> 24/8/05
4789 <li>Hold down mouse wheel & scroll to change font
4795 <li>Improved JPred client reliability</li>
4796 <li>Improved loading of Jalview files</li>
4802 <div align="center">
4803 <strong>2.03</strong><br> 18/8/05
4808 <li>Set Proxy server name and port in preferences</li>
4809 <li>Multiple URL links from sequence ids</li>
4810 <li>User Defined Colours can have a scheme name and added
4812 <li>Choose to ignore gaps in consensus calculation</li>
4813 <li>Unix users can set default web browser</li>
4814 <li>Runs without GUI for batch processing</li>
4815 <li>Dynamically generated Web Service Menus</li>
4820 <li>InstallAnywhere download for Sparc Solaris</li>
4826 <div align="center">
4827 <strong>2.02</strong><br> 18/7/05
4833 <li>Copy & Paste order of sequences maintains
4834 alignment order.</li>
4840 <div align="center">
4841 <strong>2.01</strong><br> 12/7/05
4846 <li>Use delete key for deleting selection.</li>
4847 <li>Use Mouse wheel to scroll sequences.</li>
4848 <li>Help file updated to describe how to add alignment
4850 <li>Version and build date written to build properties
4852 <li>InstallAnywhere installation will check for updates
4853 at launch of Jalview.</li>
4858 <li>Delete gaps bug fixed.</li>
4859 <li>FileChooser sorts columns.</li>
4860 <li>Can remove groups one by one.</li>
4861 <li>Filechooser icons installed.</li>
4862 <li>Finder ignores return character when searching.
4863 Return key will initiate a search.<br>
4870 <div align="center">
4871 <strong>2.0</strong><br> 20/6/05
4876 <li>New codebase</li>