3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>11/08/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
71 HTSJDK from 2.12 to 2.23
74 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
75 optimisations and improvements suggested by Bob Hanson and
76 improved compatibility with JalviewJS
79 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
80 alignments from Pfam and Rfam
83 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
84 import (no longer based on .gz extension)
87 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
90 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
91 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
95 <!-- JAL-3677 -->Improved warning messages, debug logging
96 and fixed Retry action when Jalview encounters errors when
97 saving or making backup files.
100 <!-- JAL-3676 -->Enhanced Jalview Java Console:
102 <li>Jalview's logging level can be configured</li>
103 <li>Copy to Clipboard Buttion</li>
107 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
108 when running on Linux (Requires Java 11+)
110 </ul> <em>Launching Jalview</em>
113 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
114 through a system property
117 <!-- JAL-3477 -->Improved built-in documentation and command
118 line help for configuring Jalview's memory
122 <td align="left" valign="top">
125 <!-- JAL-3493 -->Escape does not clear highlights on the
126 alignment (Since Jalview 2.10.3)
129 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
130 doesn't slide selected sequences, just sequence under cursor
133 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
134 multiple EMBL gene products shown forĀ a single contig
137 <!-- JAL-3696 -->Errors encountered when processing variants
138 from VCF files yield "Error processing VCF: Format specifier
142 <!-- JAL-3697 -->Count of features not shown can be wrong
143 when there are both local and complementary features mapped
144 to the position under the cursor
147 <!-- JAL-2983 -->Slider with negative range values not
148 rendered correctly in VAqua4 (Since 2.10.4)
151 <!-- JAL-3685 -->Single quotes not displayed correctly in
152 internationalised text for some messages and log output
154 </ul> <em>Developing Jalview</em>
157 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
158 data, causing cloverReport gradle task to fail with an
161 </ul> <em>New Known defects</em>
164 <!-- JAL-3701 -->Stale build data in jalview standalone jar
165 builds (only affects 2.11.1.1 branch)
168 <!-- JAL-3667 -->Windows 10: For a minority of users, if
169 backups are not enabled, Jalview sometimes fails to
170 overwrite an existing file and raises a warning dialog.
171 Workaround is to try to save the file again, and if that
172 fails, delete the original file and save in place.
178 <td width="60" align="center" nowrap><strong><a
179 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
180 <em>22/04/2020</em></strong></td>
181 <td align="left" valign="top">
184 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
185 'virtual' codon features shown on protein (or vice versa)
186 for display in alignments, on structure views (including
187 transfer to UCSF chimera), in feature reports and for
191 <!-- JAL-3121 -->Feature attributes from VCF files can be
192 exported and re-imported as GFF3 files
195 <!-- JAL-3376 -->Capture VCF "fixed column" values
196 POS, ID, QUAL, FILTER as Feature Attributes
199 <!-- JAL-3375 -->More robust VCF numeric data field
200 validation while parsing
203 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
207 <!-- JAL-3535 -->Feature Settings dialog title includes name
211 <!-- JAL-3538 -->Font anti-aliasing in alignment views
215 <!-- JAL-3468 -->Very long feature descriptions truncated in
219 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
220 with no feature types visible
223 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
225 </ul><em>Jalview Installer</em>
228 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
229 in console (may be null when Jalview launched as executable jar or via conda)
232 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
235 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
238 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
240 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
241 </ul> <em>Release processes</em>
244 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
247 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
249 </ul> <em>Build System</em>
252 <!-- JAL-3510 -->Clover updated to 4.4.1
255 <!-- JAL-3513 -->Test code included in Clover coverage
259 <em>Groovy Scripts</em>
262 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
263 to stdout containing the consensus sequence for each
264 alignment in a Jalview session
267 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
268 genomic sequence_variant annotation from CDS as
269 missense_variant or synonymous_variant on protein products.
273 <td align="left" valign="top">
276 <!-- JAL-3581 -->Hidden sequence markers still visible when
277 'Show hidden markers' option is not ticked
280 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
281 PNG output when 'Automatically set ID width' is set in
282 jalview preferences or properties file
285 <!-- JAL-3571 -->Feature Editor dialog can be opened when
286 'Show Sequence Features' option is not ticked
289 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
290 buttons in Feature Settings dialog are clicked when no
294 <!-- JAL-3412 -->ID margins for CDS and Protein views not
295 equal when split frame is first opened
298 <!-- JAL-3296 -->Sequence position numbers in status bar not
299 correct after editing a sequence's start position
302 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
303 with annotation and exceptions thrown when only a few
304 columns shown in wrapped mode
307 <!-- JAL-3386 -->Sequence IDs missing in headless export of
308 wrapped alignment figure with annotations
311 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
312 ID fails with ClassCastException
315 <!-- JAL-3389 -->Chimera session not restored from Jalview
319 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
320 feature settings dialog also selects columns
323 <!-- JAL-3473 -->SpinnerNumberModel causes
324 IllegalArgumentException in some circumstances
327 <!-- JAL-3534 -->Multiple feature settings dialogs can be
331 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
332 alignment window is closed
335 <!-- JAL-3406 -->Credits missing some authors in Jalview
336 help documentation for 2.11.0 release
339 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
340 includes Pfam ID as sequence's accession rather than its
343 </ul> <em>Java 11 Compatibility issues</em>
346 <!-- JAL-2987 -->OSX - Can't view some search results in
347 PDB/Uniprot search panel
349 </ul> <em>Installer</em>
352 <!-- JAL-3447 -->Jalview should not create file associations
353 for 3D structure files (.pdb, .mmcif. .cif)
355 </ul> <em>Repository and Source Release</em>
358 <!-- JAL-3474 -->removed obsolete .cvsignore files from
362 <!-- JAL-3541 -->Clover report generation running out of
365 </ul> <em>New Known Issues</em>
368 <!-- JAL-3523 -->OSX - Current working directory not
369 preserved when Jalview.app launched with parameters from
373 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
374 clipped in headless figure export when Right Align option
378 <!-- JAL-3542 -->Jalview Installation type always reports
379 'Source' in console output
382 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
383 bamboo server but run fine locally.
389 <td width="60" align="center" nowrap>
390 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
391 <em>04/07/2019</em></strong>
393 <td align="left" valign="top">
396 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
397 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
398 source project) rather than InstallAnywhere
401 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
402 settings, receive over the air updates and launch specific
403 versions via (<a href="https://github.com/threerings/getdown">Three
407 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
408 formats supported by Jalview (including .jvp project files)
411 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
412 arguments and switch between different getdown channels
415 <!-- JAL-3141 -->Backup files created when saving Jalview project
420 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
421 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
423 <!-- JAL-2620 -->Alternative genetic code tables for
424 'Translate as cDNA'</li>
426 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
427 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
430 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
431 implementation that allows updates) used for Sequence Feature collections</li>
433 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
434 features can be filtered and shaded according to any
435 associated attributes (e.g. variant attributes from VCF
436 file, or key-value pairs imported from column 9 of GFF
440 <!-- JAL-2879 -->Feature Attributes and shading schemes
441 stored and restored from Jalview Projects
444 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
445 recognise variant features
448 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
449 sequences (also coloured red by default)
452 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
456 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
457 algorithm (Z-sort/transparency and filter aware)
460 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
466 <!-- JAL-3205 -->Symmetric score matrices for faster
467 tree and PCA calculations
469 <li><strong>Principal Components Analysis Viewer</strong>
472 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
473 and Viewer state saved in Jalview Project
475 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
478 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
482 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
487 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
489 <li><strong>Speed and Efficiency</strong>
492 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
493 multiple groups when working with large alignments
496 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
500 <li><strong>User Interface</strong>
503 <!-- JAL-2933 -->Finder panel remembers last position in each
507 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
508 what is shown)<br />Only visible regions of alignment are shown by
509 default (can be changed in user preferences)
512 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
513 to the Overwrite Dialog
516 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
520 <!-- JAL-1244 -->Status bar shows bounds when dragging a
521 selection region, and gap count when inserting or deleting gaps
524 <!-- JAL-3132 -->Status bar updates over sequence and annotation
528 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
532 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
536 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
539 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
543 <!-- JAL-3181 -->Consistent ordering of links in sequence id
547 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
549 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
553 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
554 <li><strong>Java 11 Support (not yet on general release)</strong>
557 <!-- -->OSX GUI integrations for App menu's 'About' entry and
562 <em>Deprecations</em>
564 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
565 capabilities removed from the Jalview Desktop
567 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
568 unmarshalling has been replaced by JAXB for Jalview projects
569 and XML based data retrieval clients</li>
570 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
571 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
572 </ul> <em>Documentation</em>
574 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
575 not supported in EPS figure export
577 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
578 </ul> <em>Development and Release Processes</em>
581 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
584 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
586 <!-- JAL-3225 -->Eclipse project configuration managed with
590 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
591 Bamboo continuous integration for unattended Test Suite
595 <!-- JAL-2864 -->Memory test suite to detect leaks in common
599 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
603 <!-- JAL-3248 -->Developer documentation migrated to
604 markdown (with HTML rendering)
607 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
610 <!-- JAL-3289 -->New URLs for publishing development
615 <td align="left" valign="top">
618 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
621 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
622 superposition in Jmol fail on Windows
625 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
626 structures for sequences with lots of PDB structures
629 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
633 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
634 project involving multiple views
637 <!-- JAL-3164 -->Overview for complementary view in a linked
638 CDS/Protein alignment is not updated when Hide Columns by
639 Annotation dialog hides columns
642 <!-- JAL-3158 -->Selection highlighting in the complement of a
643 CDS/Protein alignment stops working after making a selection in
644 one view, then making another selection in the other view
647 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
651 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
652 Settings and Jalview Preferences panels
655 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
656 overview with large alignments
659 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
660 region if columns were selected by dragging right-to-left and the
661 mouse moved to the left of the first column
664 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
665 hidden column marker via scale popup menu
668 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
669 doesn't tell users the invalid URL
672 <!-- JAL-2816 -->Tooltips displayed for features filtered by
676 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
677 show cross references or Fetch Database References are shown in
681 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
682 peptide sequence (computed variant shown as p.Res.null)
685 <!-- JAL-2060 -->'Graduated colour' option not offered for
686 manually created features (where feature score is Float.NaN)
689 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
690 when columns are hidden
693 <!-- JAL-3082 -->Regular expression error for '(' in Select
694 Columns by Annotation description
697 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
698 out of Scale or Annotation Panel
701 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
705 <!-- JAL-3074 -->Left/right drag in annotation can scroll
709 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
713 <!-- JAL-3002 -->Column display is out by one after Page Down,
714 Page Up in wrapped mode
717 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
720 <!-- JAL-2932 -->Finder searches in minimised alignments
723 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
724 on opening an alignment
727 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
731 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
732 different groups in the alignment are selected
735 <!-- JAL-2717 -->Internationalised colour scheme names not shown
739 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
743 <!-- JAL-3125 -->Value input for graduated feature colour
744 threshold gets 'unrounded'
747 <!-- JAL-2982 -->PCA image export doesn't respect background
751 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
754 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
757 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
761 <!-- JAL-2964 -->Associate Tree with All Views not restored from
765 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
766 shown in complementary view
769 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
770 without normalisation
773 <!-- JAL-3021 -->Sequence Details report should open positioned at top
777 <!-- JAL-914 -->Help page can be opened twice
780 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
782 </ul> <em>Editing</em>
785 <!-- JAL-2822 -->Start and End should be updated when sequence
786 data at beginning or end of alignment added/removed via 'Edit'
790 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
791 relocate sequence features correctly when start of sequence is
792 removed (Known defect since 2.10)
795 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
796 dialog corrupts dataset sequence
799 <!-- JAL-868 -->Structure colours not updated when associated tree
800 repartitions the alignment view (Regression in 2.10.5)
802 </ul> <em>Datamodel</em>
805 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
806 sequence's End is greater than its length
808 </ul> <em>Bugs fixed for Java 11 Support (not yet on
809 general release)</em>
812 <!-- JAL-3288 -->Menus work properly in split-screen
814 </ul> <em>New Known Defects</em>
817 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
820 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
821 regions of protein alignment.
824 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
825 is restored from a Jalview 2.11 project
828 <!-- JAL-3213 -->Alignment panel height can be too small after
832 <!-- JAL-3240 -->Display is incorrect after removing gapped
833 columns within hidden columns
836 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
837 window after dragging left to select columns to left of visible
841 <!-- JAL-2876 -->Features coloured according to their description
842 string and thresholded by score in earlier versions of Jalview are
843 not shown as thresholded features in 2.11. To workaround please
844 create a Score filter instead.
847 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
849 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
852 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
853 alignments with multiple views can close views unexpectedly
856 <em>Java 11 Specific defects</em>
859 <!-- JAL-3235 -->Jalview Properties file is not sorted
860 alphabetically when saved
866 <td width="60" nowrap>
868 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
871 <td><div align="left">
875 <!-- JAL-3101 -->Default memory for Jalview webstart and
876 InstallAnywhere increased to 1G.
879 <!-- JAL-247 -->Hidden sequence markers and representative
880 sequence bolding included when exporting alignment as EPS,
881 SVG, PNG or HTML. <em>Display is configured via the
882 Format menu, or for command-line use via a Jalview
883 properties file.</em>
886 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
887 API and sequence data now imported as JSON.
890 <!-- JAL-3065 -->Change in recommended way of starting
891 Jalview via a Java command line: add jars in lib directory
892 to CLASSPATH, rather than via the deprecated java.ext.dirs
899 <!-- JAL-3047 -->Support added to execute test suite
900 instrumented with <a href="http://openclover.org/">Open
905 <td><div align="left">
909 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
910 row shown in Feredoxin Structure alignment view of example
914 <!-- JAL-2854 -->Annotation obscures sequences if lots of
915 annotation displayed.
918 <!-- JAL-3107 -->Group conservation/consensus not shown
919 for newly created group when 'Apply to all groups'
923 <!-- JAL-3087 -->Corrupted display when switching to
924 wrapped mode when sequence panel's vertical scrollbar is
928 <!-- JAL-3003 -->Alignment is black in exported EPS file
929 when sequences are selected in exported view.</em>
932 <!-- JAL-3059 -->Groups with different coloured borders
933 aren't rendered with correct colour.
936 <!-- JAL-3092 -->Jalview could hang when importing certain
937 types of knotted RNA secondary structure.
940 <!-- JAL-3095 -->Sequence highlight and selection in
941 trimmed VARNA 2D structure is incorrect for sequences that
945 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
946 annotation when columns are inserted into an alignment,
947 and when exporting as Stockholm flatfile.
950 <!-- JAL-3053 -->Jalview annotation rows containing upper
951 and lower-case 'E' and 'H' do not automatically get
952 treated as RNA secondary structure.
955 <!-- JAL-3106 -->.jvp should be used as default extension
956 (not .jar) when saving a Jalview project file.
959 <!-- JAL-3105 -->Mac Users: closing a window correctly
960 transfers focus to previous window on OSX
963 <em>Java 10 Issues Resolved</em>
966 <!-- JAL-2988 -->OSX - Can't save new files via the File
967 or export menus by typing in a name into the Save dialog
971 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
972 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
973 'look and feel' which has improved compatibility with the
974 latest version of OSX.
981 <td width="60" nowrap>
983 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
984 <em>7/06/2018</em></strong>
987 <td><div align="left">
991 <!-- JAL-2920 -->Use HGVS nomenclature for variant
992 annotation retrieved from Uniprot
995 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
996 onto the Jalview Desktop
1000 <td><div align="left">
1004 <!-- JAL-3017 -->Cannot import features with multiple
1005 variant elements (blocks import of some Uniprot records)
1008 <!-- JAL-2997 -->Clustal files with sequence positions in
1009 right-hand column parsed correctly
1012 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1013 not alignment area in exported graphic
1016 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1017 window has input focus
1020 <!-- JAL-2992 -->Annotation panel set too high when
1021 annotation added to view (Windows)
1024 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1025 network connectivity is poor
1028 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1029 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1030 the currently open URL and links from a page viewed in
1031 Firefox or Chrome on Windows is now fully supported. If
1032 you are using Edge, only links in the page can be
1033 dragged, and with Internet Explorer, only the currently
1034 open URL in the browser can be dropped onto Jalview.</em>
1037 <em>New Known Defects</em>
1039 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1044 <td width="60" nowrap>
1045 <div align="center">
1046 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1049 <td><div align="left">
1053 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1054 for disabling automatic superposition of multiple
1055 structures and open structures in existing views
1058 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1059 ID and annotation area margins can be click-dragged to
1063 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1067 <!-- JAL-2759 -->Improved performance for large alignments
1068 and lots of hidden columns
1071 <!-- JAL-2593 -->Improved performance when rendering lots
1072 of features (particularly when transparency is disabled)
1075 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1076 exchange of Jalview features and Chimera attributes made
1082 <td><div align="left">
1085 <!-- JAL-2899 -->Structure and Overview aren't updated
1086 when Colour By Annotation threshold slider is adjusted
1089 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1090 overlapping alignment panel
1093 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1097 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1098 improved: CDS not handled correctly if transcript has no
1102 <!-- JAL-2321 -->Secondary structure and temperature
1103 factor annotation not added to sequence when local PDB
1104 file associated with it by drag'n'drop or structure
1108 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1109 dialog doesn't import PDB files dropped on an alignment
1112 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1113 scroll bar doesn't work for some CDS/Protein views
1116 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1117 Java 1.8u153 onwards and Java 1.9u4+.
1120 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1121 columns in annotation row
1124 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1125 honored in batch mode
1128 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1129 for structures added to existing Jmol view
1132 <!-- JAL-2223 -->'View Mappings' includes duplicate
1133 entries after importing project with multiple views
1136 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1137 protein sequences via SIFTS from associated PDB entries
1138 with negative residue numbers or missing residues fails
1141 <!-- JAL-2952 -->Exception when shading sequence with negative
1142 Temperature Factor values from annotated PDB files (e.g.
1143 as generated by CONSURF)
1146 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1147 tooltip doesn't include a text description of mutation
1150 <!-- JAL-2922 -->Invert displayed features very slow when
1151 structure and/or overview windows are also shown
1154 <!-- JAL-2954 -->Selecting columns from highlighted regions
1155 very slow for alignments with large numbers of sequences
1158 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1159 with 'StringIndexOutOfBounds'
1162 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1163 platforms running Java 10
1166 <!-- JAL-2960 -->Adding a structure to existing structure
1167 view appears to do nothing because the view is hidden behind the alignment view
1173 <!-- JAL-2926 -->Copy consensus sequence option in applet
1174 should copy the group consensus when popup is opened on it
1180 <!-- JAL-2913 -->Fixed ID width preference is not respected
1183 <em>New Known Defects</em>
1186 <!-- JAL-2973 --> Exceptions occasionally raised when
1187 editing a large alignment and overview is displayed
1190 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1191 repeatedly after a series of edits even when the overview
1192 is no longer reflecting updates
1195 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1196 structures for protein subsequence (if 'Trim Retrieved
1197 Sequences' enabled) or Ensembl isoforms (Workaround in
1198 2.10.4 is to fail back to N&W mapping)
1201 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1202 option gives blank output
1209 <td width="60" nowrap>
1210 <div align="center">
1211 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1214 <td><div align="left">
1215 <ul><li>Updated Certum Codesigning Certificate
1216 (Valid till 30th November 2018)</li></ul></div></td>
1217 <td><div align="left">
1218 <em>Desktop</em><ul>
1220 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1221 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1222 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1223 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1224 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1225 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1226 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1232 <td width="60" nowrap>
1233 <div align="center">
1234 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1237 <td><div align="left">
1241 <!-- JAL-2446 -->Faster and more efficient management and
1242 rendering of sequence features
1245 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1246 429 rate limit request hander
1249 <!-- JAL-2773 -->Structure views don't get updated unless
1250 their colours have changed
1253 <!-- JAL-2495 -->All linked sequences are highlighted for
1254 a structure mousover (Jmol) or selection (Chimera)
1257 <!-- JAL-2790 -->'Cancel' button in progress bar for
1258 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1261 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1262 view from Ensembl locus cross-references
1265 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1269 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1270 feature can be disabled
1273 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1274 PDB easier retrieval of sequences for lists of IDs
1277 <!-- JAL-2758 -->Short names for sequences retrieved from
1283 <li>Groovy interpreter updated to 2.4.12</li>
1284 <li>Example groovy script for generating a matrix of
1285 percent identity scores for current alignment.</li>
1287 <em>Testing and Deployment</em>
1290 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1294 <td><div align="left">
1298 <!-- JAL-2643 -->Pressing tab after updating the colour
1299 threshold text field doesn't trigger an update to the
1303 <!-- JAL-2682 -->Race condition when parsing sequence ID
1307 <!-- JAL-2608 -->Overview windows are also closed when
1308 alignment window is closed
1311 <!-- JAL-2548 -->Export of features doesn't always respect
1315 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1316 takes a long time in Cursor mode
1322 <!-- JAL-2777 -->Structures with whitespace chainCode
1323 cannot be viewed in Chimera
1326 <!-- JAL-2728 -->Protein annotation panel too high in
1330 <!-- JAL-2757 -->Can't edit the query after the server
1331 error warning icon is shown in Uniprot and PDB Free Text
1335 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1338 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1341 <!-- JAL-2739 -->Hidden column marker in last column not
1342 rendered when switching back from Wrapped to normal view
1345 <!-- JAL-2768 -->Annotation display corrupted when
1346 scrolling right in unwapped alignment view
1349 <!-- JAL-2542 -->Existing features on subsequence
1350 incorrectly relocated when full sequence retrieved from
1354 <!-- JAL-2733 -->Last reported memory still shown when
1355 Desktop->Show Memory is unticked (OSX only)
1358 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1359 features of same type and group to be selected for
1363 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1364 alignments when hidden columns are present
1367 <!-- JAL-2392 -->Jalview freezes when loading and
1368 displaying several structures
1371 <!-- JAL-2732 -->Black outlines left after resizing or
1375 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1376 within the Jalview desktop on OSX
1379 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1380 when in wrapped alignment mode
1383 <!-- JAL-2636 -->Scale mark not shown when close to right
1384 hand end of alignment
1387 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1388 each selected sequence do not have correct start/end
1392 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1393 after canceling the Alignment Window's Font dialog
1396 <!-- JAL-2036 -->Show cross-references not enabled after
1397 restoring project until a new view is created
1400 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1401 URL links appears when only default EMBL-EBI link is
1402 configured (since 2.10.2b2)
1405 <!-- JAL-2775 -->Overview redraws whole window when box
1406 position is adjusted
1409 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1410 in a multi-chain structure when viewing alignment
1411 involving more than one chain (since 2.10)
1414 <!-- JAL-2811 -->Double residue highlights in cursor mode
1415 if new selection moves alignment window
1418 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1419 arrow key in cursor mode to pass hidden column marker
1422 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1423 that produces correctly annotated transcripts and products
1426 <!-- JAL-2776 -->Toggling a feature group after first time
1427 doesn't update associated structure view
1430 <em>Applet</em><br />
1433 <!-- JAL-2687 -->Concurrent modification exception when
1434 closing alignment panel
1437 <em>BioJSON</em><br />
1440 <!-- JAL-2546 -->BioJSON export does not preserve
1441 non-positional features
1444 <em>New Known Issues</em>
1447 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1448 sequence features correctly (for many previous versions of
1452 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1453 using cursor in wrapped panel other than top
1456 <!-- JAL-2791 -->Select columns containing feature ignores
1457 graduated colour threshold
1460 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1461 always preserve numbering and sequence features
1464 <em>Known Java 9 Issues</em>
1467 <!-- JAL-2902 -->Groovy Console very slow to open and is
1468 not responsive when entering characters (Webstart, Java
1475 <td width="60" nowrap>
1476 <div align="center">
1477 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1478 <em>2/10/2017</em></strong>
1481 <td><div align="left">
1482 <em>New features in Jalview Desktop</em>
1485 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1487 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1491 <td><div align="left">
1495 <td width="60" nowrap>
1496 <div align="center">
1497 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1498 <em>7/9/2017</em></strong>
1501 <td><div align="left">
1505 <!-- JAL-2588 -->Show gaps in overview window by colouring
1506 in grey (sequences used to be coloured grey, and gaps were
1510 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1514 <!-- JAL-2587 -->Overview updates immediately on increase
1515 in size and progress bar shown as higher resolution
1516 overview is recalculated
1521 <td><div align="left">
1525 <!-- JAL-2664 -->Overview window redraws every hidden
1526 column region row by row
1529 <!-- JAL-2681 -->duplicate protein sequences shown after
1530 retrieving Ensembl crossrefs for sequences from Uniprot
1533 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1534 format setting is unticked
1537 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1538 if group has show boxes format setting unticked
1541 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1542 autoscrolling whilst dragging current selection group to
1543 include sequences and columns not currently displayed
1546 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1547 assemblies are imported via CIF file
1550 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1551 displayed when threshold or conservation colouring is also
1555 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1559 <!-- JAL-2673 -->Jalview continues to scroll after
1560 dragging a selected region off the visible region of the
1564 <!-- JAL-2724 -->Cannot apply annotation based
1565 colourscheme to all groups in a view
1568 <!-- JAL-2511 -->IDs don't line up with sequences
1569 initially after font size change using the Font chooser or
1576 <td width="60" nowrap>
1577 <div align="center">
1578 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1581 <td><div align="left">
1582 <em>Calculations</em>
1586 <!-- JAL-1933 -->Occupancy annotation row shows number of
1587 ungapped positions in each column of the alignment.
1590 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1591 a calculation dialog box
1594 <!-- JAL-2379 -->Revised implementation of PCA for speed
1595 and memory efficiency (~30x faster)
1598 <!-- JAL-2403 -->Revised implementation of sequence
1599 similarity scores as used by Tree, PCA, Shading Consensus
1600 and other calculations
1603 <!-- JAL-2416 -->Score matrices are stored as resource
1604 files within the Jalview codebase
1607 <!-- JAL-2500 -->Trees computed on Sequence Feature
1608 Similarity may have different topology due to increased
1615 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1616 model for alignments and groups
1619 <!-- JAL-384 -->Custom shading schemes created via groovy
1626 <!-- JAL-2526 -->Efficiency improvements for interacting
1627 with alignment and overview windows
1630 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1634 <!-- JAL-2388 -->Hidden columns and sequences can be
1638 <!-- JAL-2611 -->Click-drag in visible area allows fine
1639 adjustment of visible position
1643 <em>Data import/export</em>
1646 <!-- JAL-2535 -->Posterior probability annotation from
1647 Stockholm files imported as sequence associated annotation
1650 <!-- JAL-2507 -->More robust per-sequence positional
1651 annotation input/output via stockholm flatfile
1654 <!-- JAL-2533 -->Sequence names don't include file
1655 extension when importing structure files without embedded
1656 names or PDB accessions
1659 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1660 format sequence substitution matrices
1663 <em>User Interface</em>
1666 <!-- JAL-2447 --> Experimental Features Checkbox in
1667 Desktop's Tools menu to hide or show untested features in
1671 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1672 via Overview or sequence motif search operations
1675 <!-- JAL-2547 -->Amend sequence features dialog box can be
1676 opened by double clicking gaps within sequence feature
1680 <!-- JAL-1476 -->Status bar message shown when not enough
1681 aligned positions were available to create a 3D structure
1685 <em>3D Structure</em>
1688 <!-- JAL-2430 -->Hidden regions in alignment views are not
1689 coloured in linked structure views
1692 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1693 file-based command exchange
1696 <!-- JAL-2375 -->Structure chooser automatically shows
1697 Cached Structures rather than querying the PDBe if
1698 structures are already available for sequences
1701 <!-- JAL-2520 -->Structures imported via URL are cached in
1702 the Jalview project rather than downloaded again when the
1703 project is reopened.
1706 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1707 to transfer Chimera's structure attributes as Jalview
1708 features, and vice-versa (<strong>Experimental
1712 <em>Web Services</em>
1715 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1718 <!-- JAL-2335 -->Filter non-standard amino acids and
1719 nucleotides when submitting to AACon and other MSA
1723 <!-- JAL-2316, -->URLs for viewing database
1724 cross-references provided by identifiers.org and the
1725 EMBL-EBI's MIRIAM DB
1732 <!-- JAL-2344 -->FileFormatI interface for describing and
1733 identifying file formats (instead of String constants)
1736 <!-- JAL-2228 -->FeatureCounter script refactored for
1737 efficiency when counting all displayed features (not
1738 backwards compatible with 2.10.1)
1741 <em>Example files</em>
1744 <!-- JAL-2631 -->Graduated feature colour style example
1745 included in the example feature file
1748 <em>Documentation</em>
1751 <!-- JAL-2339 -->Release notes reformatted for readability
1752 with the built-in Java help viewer
1755 <!-- JAL-1644 -->Find documentation updated with 'search
1756 sequence description' option
1762 <!-- JAL-2485, -->External service integration tests for
1763 Uniprot REST Free Text Search Client
1766 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1769 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1774 <td><div align="left">
1775 <em>Calculations</em>
1778 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1779 matrix - C->R should be '-3'<br />Old matrix restored
1780 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1782 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1783 Jalview's treatment of gaps in PCA and substitution matrix
1784 based Tree calculations.<br /> <br />In earlier versions
1785 of Jalview, gaps matching gaps were penalised, and gaps
1786 matching non-gaps penalised even more. In the PCA
1787 calculation, gaps were actually treated as non-gaps - so
1788 different costs were applied, which meant Jalview's PCAs
1789 were different to those produced by SeqSpace.<br />Jalview
1790 now treats gaps in the same way as SeqSpace (ie it scores
1791 them as 0). <br /> <br />Enter the following in the
1792 Groovy console to restore pre-2.10.2 behaviour:<br />
1793 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1794 // for 2.10.1 mode <br />
1795 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1796 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1797 these settings will affect all subsequent tree and PCA
1798 calculations (not recommended)</em></li>
1800 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1801 scaling of branch lengths for trees computed using
1802 Sequence Feature Similarity.
1805 <!-- JAL-2377 -->PCA calculation could hang when
1806 generating output report when working with highly
1807 redundant alignments
1810 <!-- JAL-2544 --> Sort by features includes features to
1811 right of selected region when gaps present on right-hand
1815 <em>User Interface</em>
1818 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1819 doesn't reselect a specific sequence's associated
1820 annotation after it was used for colouring a view
1823 <!-- JAL-2419 -->Current selection lost if popup menu
1824 opened on a region of alignment without groups
1827 <!-- JAL-2374 -->Popup menu not always shown for regions
1828 of an alignment with overlapping groups
1831 <!-- JAL-2310 -->Finder double counts if both a sequence's
1832 name and description match
1835 <!-- JAL-2370 -->Hiding column selection containing two
1836 hidden regions results in incorrect hidden regions
1839 <!-- JAL-2386 -->'Apply to all groups' setting when
1840 changing colour does not apply Conservation slider value
1844 <!-- JAL-2373 -->Percentage identity and conservation menu
1845 items do not show a tick or allow shading to be disabled
1848 <!-- JAL-2385 -->Conservation shading or PID threshold
1849 lost when base colourscheme changed if slider not visible
1852 <!-- JAL-2547 -->Sequence features shown in tooltip for
1853 gaps before start of features
1856 <!-- JAL-2623 -->Graduated feature colour threshold not
1857 restored to UI when feature colour is edited
1860 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1861 a time when scrolling vertically in wrapped mode.
1864 <!-- JAL-2630 -->Structure and alignment overview update
1865 as graduate feature colour settings are modified via the
1869 <!-- JAL-2034 -->Overview window doesn't always update
1870 when a group defined on the alignment is resized
1873 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1874 wrapped view result in positional status updates
1878 <!-- JAL-2563 -->Status bar doesn't show position for
1879 ambiguous amino acid and nucleotide symbols
1882 <!-- JAL-2602 -->Copy consensus sequence failed if
1883 alignment included gapped columns
1886 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1887 widgets don't permanently disappear
1890 <!-- JAL-2503 -->Cannot select or filter quantitative
1891 annotation that are shown only as column labels (e.g.
1892 T-Coffee column reliability scores)
1895 <!-- JAL-2594 -->Exception thrown if trying to create a
1896 sequence feature on gaps only
1899 <!-- JAL-2504 -->Features created with 'New feature'
1900 button from a Find inherit previously defined feature type
1901 rather than the Find query string
1904 <!-- JAL-2423 -->incorrect title in output window when
1905 exporting tree calculated in Jalview
1908 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1909 and then revealing them reorders sequences on the
1913 <!-- JAL-964 -->Group panel in sequence feature settings
1914 doesn't update to reflect available set of groups after
1915 interactively adding or modifying features
1918 <!-- JAL-2225 -->Sequence Database chooser unusable on
1922 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1923 only excluded gaps in current sequence and ignored
1930 <!-- JAL-2421 -->Overview window visible region moves
1931 erratically when hidden rows or columns are present
1934 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1935 Structure Viewer's colour menu don't correspond to
1939 <!-- JAL-2405 -->Protein specific colours only offered in
1940 colour and group colour menu for protein alignments
1943 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1944 reflect currently selected view or group's shading
1948 <!-- JAL-2624 -->Feature colour thresholds not respected
1949 when rendered on overview and structures when opacity at
1953 <!-- JAL-2589 -->User defined gap colour not shown in
1954 overview when features overlaid on alignment
1957 <!-- JAL-2567 -->Feature settings for different views not
1958 recovered correctly from Jalview project file
1961 <!-- JAL-2256 -->Feature colours in overview when first opened
1962 (automatically via preferences) are different to the main
1966 <em>Data import/export</em>
1969 <!-- JAL-2576 -->Very large alignments take a long time to
1973 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1974 added after a sequence was imported are not written to
1978 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1979 when importing RNA secondary structure via Stockholm
1982 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1983 not shown in correct direction for simple pseudoknots
1986 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1987 with lightGray or darkGray via features file (but can
1991 <!-- JAL-2383 -->Above PID colour threshold not recovered
1992 when alignment view imported from project
1995 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1996 structure and sequences extracted from structure files
1997 imported via URL and viewed in Jmol
2000 <!-- JAL-2520 -->Structures loaded via URL are saved in
2001 Jalview Projects rather than fetched via URL again when
2002 the project is loaded and the structure viewed
2005 <em>Web Services</em>
2008 <!-- JAL-2519 -->EnsemblGenomes example failing after
2009 release of Ensembl v.88
2012 <!-- JAL-2366 -->Proxy server address and port always
2013 appear enabled in Preferences->Connections
2016 <!-- JAL-2461 -->DAS registry not found exceptions
2017 removed from console output
2020 <!-- JAL-2582 -->Cannot retrieve protein products from
2021 Ensembl by Peptide ID
2024 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2025 created from SIFTs, and spurious 'Couldn't open structure
2026 in Chimera' errors raised after April 2017 update (problem
2027 due to 'null' string rather than empty string used for
2028 residues with no corresponding PDB mapping).
2031 <em>Application UI</em>
2034 <!-- JAL-2361 -->User Defined Colours not added to Colour
2038 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2039 case' residues (button in colourscheme editor debugged and
2040 new documentation and tooltips added)
2043 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2044 doesn't restore group-specific text colour thresholds
2047 <!-- JAL-2243 -->Feature settings panel does not update as
2048 new features are added to alignment
2051 <!-- JAL-2532 -->Cancel in feature settings reverts
2052 changes to feature colours via the Amend features dialog
2055 <!-- JAL-2506 -->Null pointer exception when attempting to
2056 edit graduated feature colour via amend features dialog
2060 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2061 selection menu changes colours of alignment views
2064 <!-- JAL-2426 -->Spurious exceptions in console raised
2065 from alignment calculation workers after alignment has
2069 <!-- JAL-1608 -->Typo in selection popup menu - Create
2070 groups now 'Create Group'
2073 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2074 Create/Undefine group doesn't always work
2077 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2078 shown again after pressing 'Cancel'
2081 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2082 adjusts start position in wrap mode
2085 <!-- JAL-2563 -->Status bar doesn't show positions for
2086 ambiguous amino acids
2089 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2090 CDS/Protein view after CDS sequences added for aligned
2094 <!-- JAL-2592 -->User defined colourschemes called 'User
2095 Defined' don't appear in Colours menu
2101 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2102 score models doesn't always result in an updated PCA plot
2105 <!-- JAL-2442 -->Features not rendered as transparent on
2106 overview or linked structure view
2109 <!-- JAL-2372 -->Colour group by conservation doesn't
2113 <!-- JAL-2517 -->Hitting Cancel after applying
2114 user-defined colourscheme doesn't restore original
2121 <!-- JAL-2314 -->Unit test failure:
2122 jalview.ws.jabaws.RNAStructExportImport setup fails
2125 <!-- JAL-2307 -->Unit test failure:
2126 jalview.ws.sifts.SiftsClientTest due to compatibility
2127 problems with deep array comparison equality asserts in
2128 successive versions of TestNG
2131 <!-- JAL-2479 -->Relocated StructureChooserTest and
2132 ParameterUtilsTest Unit tests to Network suite
2135 <em>New Known Issues</em>
2138 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2139 phase after a sequence motif find operation
2142 <!-- JAL-2550 -->Importing annotation file with rows
2143 containing just upper and lower case letters are
2144 interpreted as WUSS RNA secondary structure symbols
2147 <!-- JAL-2590 -->Cannot load and display Newick trees
2148 reliably from eggnog Ortholog database
2151 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2152 containing features of type Highlight' when 'B' is pressed
2153 to mark columns containing highlighted regions.
2156 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2157 doesn't always add secondary structure annotation.
2162 <td width="60" nowrap>
2163 <div align="center">
2164 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2167 <td><div align="left">
2171 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2172 for all consensus calculations
2175 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2178 <li>Updated Jalview's Certum code signing certificate
2181 <em>Application</em>
2184 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2185 set of database cross-references, sorted alphabetically
2188 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2189 from database cross references. Users with custom links
2190 will receive a <a href="webServices/urllinks.html#warning">warning
2191 dialog</a> asking them to update their preferences.
2194 <!-- JAL-2287-->Cancel button and escape listener on
2195 dialog warning user about disconnecting Jalview from a
2199 <!-- JAL-2320-->Jalview's Chimera control window closes if
2200 the Chimera it is connected to is shut down
2203 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2204 columns menu item to mark columns containing highlighted
2205 regions (e.g. from structure selections or results of a
2209 <!-- JAL-2284-->Command line option for batch-generation
2210 of HTML pages rendering alignment data with the BioJS
2220 <!-- JAL-2286 -->Columns with more than one modal residue
2221 are not coloured or thresholded according to percent
2222 identity (first observed in Jalview 2.8.2)
2225 <!-- JAL-2301 -->Threonine incorrectly reported as not
2229 <!-- JAL-2318 -->Updates to documentation pages (above PID
2230 threshold, amino acid properties)
2233 <!-- JAL-2292 -->Lower case residues in sequences are not
2234 reported as mapped to residues in a structure file in the
2238 <!--JAL-2324 -->Identical features with non-numeric scores
2239 could be added multiple times to a sequence
2242 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2243 bond features shown as two highlighted residues rather
2244 than a range in linked structure views, and treated
2245 correctly when selecting and computing trees from features
2248 <!-- JAL-2281-->Custom URL links for database
2249 cross-references are matched to database name regardless
2254 <em>Application</em>
2257 <!-- JAL-2282-->Custom URL links for specific database
2258 names without regular expressions also offer links from
2262 <!-- JAL-2315-->Removing a single configured link in the
2263 URL links pane in Connections preferences doesn't actually
2264 update Jalview configuration
2267 <!-- JAL-2272-->CTRL-Click on a selected region to open
2268 the alignment area popup menu doesn't work on El-Capitan
2271 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2272 files with similarly named sequences if dropped onto the
2276 <!-- JAL-2312 -->Additional mappings are shown for PDB
2277 entries where more chains exist in the PDB accession than
2278 are reported in the SIFTS file
2281 <!-- JAL-2317-->Certain structures do not get mapped to
2282 the structure view when displayed with Chimera
2285 <!-- JAL-2317-->No chains shown in the Chimera view
2286 panel's View->Show Chains submenu
2289 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2290 work for wrapped alignment views
2293 <!--JAL-2197 -->Rename UI components for running JPred
2294 predictions from 'JNet' to 'JPred'
2297 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2298 corrupted when annotation panel vertical scroll is not at
2299 first annotation row
2302 <!--JAL-2332 -->Attempting to view structure for Hen
2303 lysozyme results in a PDB Client error dialog box
2306 <!-- JAL-2319 -->Structure View's mapping report switched
2307 ranges for PDB and sequence for SIFTS
2310 SIFTS 'Not_Observed' residues mapped to non-existant
2314 <!-- <em>New Known Issues</em>
2321 <td width="60" nowrap>
2322 <div align="center">
2323 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2324 <em>25/10/2016</em></strong>
2327 <td><em>Application</em>
2329 <li>3D Structure chooser opens with 'Cached structures'
2330 view if structures already loaded</li>
2331 <li>Progress bar reports models as they are loaded to
2332 structure views</li>
2338 <li>Colour by conservation always enabled and no tick
2339 shown in menu when BLOSUM or PID shading applied</li>
2340 <li>FER1_ARATH and FER2_ARATH labels were switched in
2341 example sequences/projects/trees</li>
2343 <em>Application</em>
2345 <li>Jalview projects with views of local PDB structure
2346 files saved on Windows cannot be opened on OSX</li>
2347 <li>Multiple structure views can be opened and superposed
2348 without timeout for structures with multiple models or
2349 multiple sequences in alignment</li>
2350 <li>Cannot import or associated local PDB files without a
2351 PDB ID HEADER line</li>
2352 <li>RMSD is not output in Jmol console when superposition
2354 <li>Drag and drop of URL from Browser fails for Linux and
2355 OSX versions earlier than El Capitan</li>
2356 <li>ENA client ignores invalid content from ENA server</li>
2357 <li>Exceptions are not raised in console when ENA client
2358 attempts to fetch non-existent IDs via Fetch DB Refs UI
2360 <li>Exceptions are not raised in console when a new view
2361 is created on the alignment</li>
2362 <li>OSX right-click fixed for group selections: CMD-click
2363 to insert/remove gaps in groups and CTRL-click to open group
2366 <em>Build and deployment</em>
2368 <li>URL link checker now copes with multi-line anchor
2371 <em>New Known Issues</em>
2373 <li>Drag and drop from URL links in browsers do not work
2380 <td width="60" nowrap>
2381 <div align="center">
2382 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2385 <td><em>General</em>
2388 <!-- JAL-2124 -->Updated Spanish translations.
2391 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2392 for importing structure data to Jalview. Enables mmCIF and
2396 <!-- JAL-192 --->Alignment ruler shows positions relative to
2400 <!-- JAL-2202 -->Position/residue shown in status bar when
2401 mousing over sequence associated annotation
2404 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2408 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2409 '()', canonical '[]' and invalid '{}' base pair populations
2413 <!-- JAL-2092 -->Feature settings popup menu options for
2414 showing or hiding columns containing a feature
2417 <!-- JAL-1557 -->Edit selected group by double clicking on
2418 group and sequence associated annotation labels
2421 <!-- JAL-2236 -->Sequence name added to annotation label in
2422 select/hide columns by annotation and colour by annotation
2426 </ul> <em>Application</em>
2429 <!-- JAL-2050-->Automatically hide introns when opening a
2430 gene/transcript view
2433 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2437 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2438 structure mappings with the EMBL-EBI PDBe SIFTS database
2441 <!-- JAL-2079 -->Updated download sites used for Rfam and
2442 Pfam sources to xfam.org
2445 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2448 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2449 over sequences in Jalview
2452 <!-- JAL-2027-->Support for reverse-complement coding
2453 regions in ENA and EMBL
2456 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2457 for record retrieval via ENA rest API
2460 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2464 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2465 groovy script execution
2468 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2469 alignment window's Calculate menu
2472 <!-- JAL-1812 -->Allow groovy scripts that call
2473 Jalview.getAlignFrames() to run in headless mode
2476 <!-- JAL-2068 -->Support for creating new alignment
2477 calculation workers from groovy scripts
2480 <!-- JAL-1369 --->Store/restore reference sequence in
2484 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2485 associations are now saved/restored from project
2488 <!-- JAL-1993 -->Database selection dialog always shown
2489 before sequence fetcher is opened
2492 <!-- JAL-2183 -->Double click on an entry in Jalview's
2493 database chooser opens a sequence fetcher
2496 <!-- JAL-1563 -->Free-text search client for UniProt using
2497 the UniProt REST API
2500 <!-- JAL-2168 -->-nonews command line parameter to prevent
2501 the news reader opening
2504 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2505 querying stored in preferences
2508 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2512 <!-- JAL-1977-->Tooltips shown on database chooser
2515 <!-- JAL-391 -->Reverse complement function in calculate
2516 menu for nucleotide sequences
2519 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2520 and feature counts preserves alignment ordering (and
2521 debugged for complex feature sets).
2524 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2525 viewing structures with Jalview 2.10
2528 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2529 genome, transcript CCDS and gene ids via the Ensembl and
2530 Ensembl Genomes REST API
2533 <!-- JAL-2049 -->Protein sequence variant annotation
2534 computed for 'sequence_variant' annotation on CDS regions
2538 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2542 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2543 Ref Fetcher fails to match, or otherwise updates sequence
2544 data from external database records.
2547 <!-- JAL-2154 -->Revised Jalview Project format for
2548 efficient recovery of sequence coding and alignment
2549 annotation relationships.
2551 </ul> <!-- <em>Applet</em>
2562 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2566 <!-- JAL-2018-->Export features in Jalview format (again)
2567 includes graduated colourschemes
2570 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2571 working with big alignments and lots of hidden columns
2574 <!-- JAL-2053-->Hidden column markers not always rendered
2575 at right of alignment window
2578 <!-- JAL-2067 -->Tidied up links in help file table of
2582 <!-- JAL-2072 -->Feature based tree calculation not shown
2586 <!-- JAL-2075 -->Hidden columns ignored during feature
2587 based tree calculation
2590 <!-- JAL-2065 -->Alignment view stops updating when show
2591 unconserved enabled for group on alignment
2594 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2598 <!-- JAL-2146 -->Alignment column in status incorrectly
2599 shown as "Sequence position" when mousing over
2603 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2604 hidden columns present
2607 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2608 user created annotation added to alignment
2611 <!-- JAL-1841 -->RNA Structure consensus only computed for
2612 '()' base pair annotation
2615 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2616 in zero scores for all base pairs in RNA Structure
2620 <!-- JAL-2174-->Extend selection with columns containing
2624 <!-- JAL-2275 -->Pfam format writer puts extra space at
2625 beginning of sequence
2628 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2632 <!-- JAL-2238 -->Cannot create groups on an alignment from
2633 from a tree when t-coffee scores are shown
2636 <!-- JAL-1836,1967 -->Cannot import and view PDB
2637 structures with chains containing negative resnums (4q4h)
2640 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2644 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2645 to Clustal, PIR and PileUp output
2648 <!-- JAL-2008 -->Reordering sequence features that are
2649 not visible causes alignment window to repaint
2652 <!-- JAL-2006 -->Threshold sliders don't work in
2653 graduated colour and colour by annotation row for e-value
2654 scores associated with features and annotation rows
2657 <!-- JAL-1797 -->amino acid physicochemical conservation
2658 calculation should be case independent
2661 <!-- JAL-2173 -->Remove annotation also updates hidden
2665 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2666 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2667 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2670 <!-- JAL-2065 -->Null pointer exceptions and redraw
2671 problems when reference sequence defined and 'show
2672 non-conserved' enabled
2675 <!-- JAL-1306 -->Quality and Conservation are now shown on
2676 load even when Consensus calculation is disabled
2679 <!-- JAL-1932 -->Remove right on penultimate column of
2680 alignment does nothing
2683 <em>Application</em>
2686 <!-- JAL-1552-->URLs and links can't be imported by
2687 drag'n'drop on OSX when launched via webstart (note - not
2688 yet fixed for El Capitan)
2691 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2692 output when running on non-gb/us i18n platforms
2695 <!-- JAL-1944 -->Error thrown when exporting a view with
2696 hidden sequences as flat-file alignment
2699 <!-- JAL-2030-->InstallAnywhere distribution fails when
2703 <!-- JAL-2080-->Jalview very slow to launch via webstart
2704 (also hotfix for 2.9.0b2)
2707 <!-- JAL-2085 -->Cannot save project when view has a
2708 reference sequence defined
2711 <!-- JAL-1011 -->Columns are suddenly selected in other
2712 alignments and views when revealing hidden columns
2715 <!-- JAL-1989 -->Hide columns not mirrored in complement
2716 view in a cDNA/Protein splitframe
2719 <!-- JAL-1369 -->Cannot save/restore representative
2720 sequence from project when only one sequence is
2724 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2725 in Structure Chooser
2728 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2729 structure consensus didn't refresh annotation panel
2732 <!-- JAL-1962 -->View mapping in structure view shows
2733 mappings between sequence and all chains in a PDB file
2736 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2737 dialogs format columns correctly, don't display array
2738 data, sort columns according to type
2741 <!-- JAL-1975 -->Export complete shown after destination
2742 file chooser is cancelled during an image export
2745 <!-- JAL-2025 -->Error when querying PDB Service with
2746 sequence name containing special characters
2749 <!-- JAL-2024 -->Manual PDB structure querying should be
2753 <!-- JAL-2104 -->Large tooltips with broken HTML
2754 formatting don't wrap
2757 <!-- JAL-1128 -->Figures exported from wrapped view are
2758 truncated so L looks like I in consensus annotation
2761 <!-- JAL-2003 -->Export features should only export the
2762 currently displayed features for the current selection or
2766 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2767 after fetching cross-references, and restoring from
2771 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2772 followed in the structure viewer
2775 <!-- JAL-2163 -->Titles for individual alignments in
2776 splitframe not restored from project
2779 <!-- JAL-2145 -->missing autocalculated annotation at
2780 trailing end of protein alignment in transcript/product
2781 splitview when pad-gaps not enabled by default
2784 <!-- JAL-1797 -->amino acid physicochemical conservation
2788 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2789 article has been read (reopened issue due to
2790 internationalisation problems)
2793 <!-- JAL-1960 -->Only offer PDB structures in structure
2794 viewer based on sequence name, PDB and UniProt
2799 <!-- JAL-1976 -->No progress bar shown during export of
2803 <!-- JAL-2213 -->Structures not always superimposed after
2804 multiple structures are shown for one or more sequences.
2807 <!-- JAL-1370 -->Reference sequence characters should not
2808 be replaced with '.' when 'Show unconserved' format option
2812 <!-- JAL-1823 -->Cannot specify chain code when entering
2813 specific PDB id for sequence
2816 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2817 'Export hidden sequences' is enabled, but 'export hidden
2818 columns' is disabled.
2821 <!--JAL-2026-->Best Quality option in structure chooser
2822 selects lowest rather than highest resolution structures
2826 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2827 to sequence mapping in 'View Mappings' report
2830 <!-- JAL-2284 -->Unable to read old Jalview projects that
2831 contain non-XML data added after Jalvew wrote project.
2834 <!-- JAL-2118 -->Newly created annotation row reorders
2835 after clicking on it to create new annotation for a
2839 <!-- JAL-1980 -->Null Pointer Exception raised when
2840 pressing Add on an orphaned cut'n'paste window.
2842 <!-- may exclude, this is an external service stability issue JAL-1941
2843 -- > RNA 3D structure not added via DSSR service</li> -->
2848 <!-- JAL-2151 -->Incorrect columns are selected when
2849 hidden columns present before start of sequence
2852 <!-- JAL-1986 -->Missing dependencies on applet pages
2856 <!-- JAL-1947 -->Overview pixel size changes when
2857 sequences are hidden in applet
2860 <!-- JAL-1996 -->Updated instructions for applet
2861 deployment on examples pages.
2868 <td width="60" nowrap>
2869 <div align="center">
2870 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2871 <em>16/10/2015</em></strong>
2874 <td><em>General</em>
2876 <li>Time stamps for signed Jalview application and applet
2881 <em>Application</em>
2883 <li>Duplicate group consensus and conservation rows
2884 shown when tree is partitioned</li>
2885 <li>Erratic behaviour when tree partitions made with
2886 multiple cDNA/Protein split views</li>
2892 <td width="60" nowrap>
2893 <div align="center">
2894 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2895 <em>8/10/2015</em></strong>
2898 <td><em>General</em>
2900 <li>Updated Spanish translations of localized text for
2902 </ul> <em>Application</em>
2904 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2905 <li>Signed OSX InstallAnywhere installer<br></li>
2906 <li>Support for per-sequence based annotations in BioJSON</li>
2907 </ul> <em>Applet</em>
2909 <li>Split frame example added to applet examples page</li>
2910 </ul> <em>Build and Deployment</em>
2913 <!-- JAL-1888 -->New ant target for running Jalview's test
2921 <li>Mapping of cDNA to protein in split frames
2922 incorrect when sequence start > 1</li>
2923 <li>Broken images in filter column by annotation dialog
2925 <li>Feature colours not parsed from features file</li>
2926 <li>Exceptions and incomplete link URLs recovered when
2927 loading a features file containing HTML tags in feature
2931 <em>Application</em>
2933 <li>Annotations corrupted after BioJS export and
2935 <li>Incorrect sequence limits after Fetch DB References
2936 with 'trim retrieved sequences'</li>
2937 <li>Incorrect warning about deleting all data when
2938 deleting selected columns</li>
2939 <li>Patch to build system for shipping properly signed
2940 JNLP templates for webstart launch</li>
2941 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2942 unreleased structures for download or viewing</li>
2943 <li>Tab/space/return keystroke operation of EMBL-PDBe
2944 fetcher/viewer dialogs works correctly</li>
2945 <li>Disabled 'minimise' button on Jalview windows
2946 running on OSX to workaround redraw hang bug</li>
2947 <li>Split cDNA/Protein view position and geometry not
2948 recovered from jalview project</li>
2949 <li>Initial enabled/disabled state of annotation menu
2950 sorter 'show autocalculated first/last' corresponds to
2952 <li>Restoring of Clustal, RNA Helices and T-Coffee
2953 color schemes from BioJSON</li>
2957 <li>Reorder sequences mirrored in cDNA/Protein split
2959 <li>Applet with Jmol examples not loading correctly</li>
2965 <td><div align="center">
2966 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2968 <td><em>General</em>
2970 <li>Linked visualisation and analysis of DNA and Protein
2973 <li>Translated cDNA alignments shown as split protein
2974 and DNA alignment views</li>
2975 <li>Codon consensus annotation for linked protein and
2976 cDNA alignment views</li>
2977 <li>Link cDNA or Protein product sequences by loading
2978 them onto Protein or cDNA alignments</li>
2979 <li>Reconstruct linked cDNA alignment from aligned
2980 protein sequences</li>
2983 <li>Jmol integration updated to Jmol v14.2.14</li>
2984 <li>Import and export of Jalview alignment views as <a
2985 href="features/bioJsonFormat.html">BioJSON</a></li>
2986 <li>New alignment annotation file statements for
2987 reference sequences and marking hidden columns</li>
2988 <li>Reference sequence based alignment shading to
2989 highlight variation</li>
2990 <li>Select or hide columns according to alignment
2992 <li>Find option for locating sequences by description</li>
2993 <li>Conserved physicochemical properties shown in amino
2994 acid conservation row</li>
2995 <li>Alignments can be sorted by number of RNA helices</li>
2996 </ul> <em>Application</em>
2998 <li>New cDNA/Protein analysis capabilities
3000 <li>Get Cross-References should open a Split Frame
3001 view with cDNA/Protein</li>
3002 <li>Detect when nucleotide sequences and protein
3003 sequences are placed in the same alignment</li>
3004 <li>Split cDNA/Protein views are saved in Jalview
3009 <li>Use REST API to talk to Chimera</li>
3010 <li>Selected regions in Chimera are highlighted in linked
3011 Jalview windows</li>
3013 <li>VARNA RNA viewer updated to v3.93</li>
3014 <li>VARNA views are saved in Jalview Projects</li>
3015 <li>Pseudoknots displayed as Jalview RNA annotation can
3016 be shown in VARNA</li>
3018 <li>Make groups for selection uses marked columns as well
3019 as the active selected region</li>
3021 <li>Calculate UPGMA and NJ trees using sequence feature
3023 <li>New Export options
3025 <li>New Export Settings dialog to control hidden
3026 region export in flat file generation</li>
3028 <li>Export alignment views for display with the <a
3029 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3031 <li>Export scrollable SVG in HTML page</li>
3032 <li>Optional embedding of BioJSON data when exporting
3033 alignment figures to HTML</li>
3035 <li>3D structure retrieval and display
3037 <li>Free text and structured queries with the PDBe
3039 <li>PDBe Search API based discovery and selection of
3040 PDB structures for a sequence set</li>
3044 <li>JPred4 employed for protein secondary structure
3046 <li>Hide Insertions menu option to hide unaligned columns
3047 for one or a group of sequences</li>
3048 <li>Automatically hide insertions in alignments imported
3049 from the JPred4 web server</li>
3050 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3051 system on OSX<br />LGPL libraries courtesy of <a
3052 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3054 <li>changed 'View nucleotide structure' submenu to 'View
3055 VARNA 2D Structure'</li>
3056 <li>change "View protein structure" menu option to "3D
3059 </ul> <em>Applet</em>
3061 <li>New layout for applet example pages</li>
3062 <li>New parameters to enable SplitFrame view
3063 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3064 <li>New example demonstrating linked viewing of cDNA and
3065 Protein alignments</li>
3066 </ul> <em>Development and deployment</em>
3068 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3069 <li>Include installation type and git revision in build
3070 properties and console log output</li>
3071 <li>Jalview Github organisation, and new github site for
3072 storing BioJsMSA Templates</li>
3073 <li>Jalview's unit tests now managed with TestNG</li>
3076 <!-- <em>General</em>
3078 </ul> --> <!-- issues resolved --> <em>Application</em>
3080 <li>Escape should close any open find dialogs</li>
3081 <li>Typo in select-by-features status report</li>
3082 <li>Consensus RNA secondary secondary structure
3083 predictions are not highlighted in amber</li>
3084 <li>Missing gap character in v2.7 example file means
3085 alignment appears unaligned when pad-gaps is not enabled</li>
3086 <li>First switch to RNA Helices colouring doesn't colour
3087 associated structure views</li>
3088 <li>ID width preference option is greyed out when auto
3089 width checkbox not enabled</li>
3090 <li>Stopped a warning dialog from being shown when
3091 creating user defined colours</li>
3092 <li>'View Mapping' in structure viewer shows sequence
3093 mappings for just that viewer's sequences</li>
3094 <li>Workaround for superposing PDB files containing
3095 multiple models in Chimera</li>
3096 <li>Report sequence position in status bar when hovering
3097 over Jmol structure</li>
3098 <li>Cannot output gaps as '.' symbols with Selection ->
3099 output to text box</li>
3100 <li>Flat file exports of alignments with hidden columns
3101 have incorrect sequence start/end</li>
3102 <li>'Aligning' a second chain to a Chimera structure from
3104 <li>Colour schemes applied to structure viewers don't
3105 work for nucleotide</li>
3106 <li>Loading/cut'n'pasting an empty or invalid file leads
3107 to a grey/invisible alignment window</li>
3108 <li>Exported Jpred annotation from a sequence region
3109 imports to different position</li>
3110 <li>Space at beginning of sequence feature tooltips shown
3111 on some platforms</li>
3112 <li>Chimera viewer 'View | Show Chain' menu is not
3114 <li>'New View' fails with a Null Pointer Exception in
3115 console if Chimera has been opened</li>
3116 <li>Mouseover to Chimera not working</li>
3117 <li>Miscellaneous ENA XML feature qualifiers not
3119 <li>NPE in annotation renderer after 'Extract Scores'</li>
3120 <li>If two structures in one Chimera window, mouseover of
3121 either sequence shows on first structure</li>
3122 <li>'Show annotations' options should not make
3123 non-positional annotations visible</li>
3124 <li>Subsequence secondary structure annotation not shown
3125 in right place after 'view flanking regions'</li>
3126 <li>File Save As type unset when current file format is
3128 <li>Save as '.jar' option removed for saving Jalview
3130 <li>Colour by Sequence colouring in Chimera more
3132 <li>Cannot 'add reference annotation' for a sequence in
3133 several views on same alignment</li>
3134 <li>Cannot show linked products for EMBL / ENA records</li>
3135 <li>Jalview's tooltip wraps long texts containing no
3137 </ul> <em>Applet</em>
3139 <li>Jmol to JalviewLite mouseover/link not working</li>
3140 <li>JalviewLite can't import sequences with ID
3141 descriptions containing angle brackets</li>
3142 </ul> <em>General</em>
3144 <li>Cannot export and reimport RNA secondary structure
3145 via jalview annotation file</li>
3146 <li>Random helix colour palette for colour by annotation
3147 with RNA secondary structure</li>
3148 <li>Mouseover to cDNA from STOP residue in protein
3149 translation doesn't work.</li>
3150 <li>hints when using the select by annotation dialog box</li>
3151 <li>Jmol alignment incorrect if PDB file has alternate CA
3153 <li>FontChooser message dialog appears to hang after
3154 choosing 1pt font</li>
3155 <li>Peptide secondary structure incorrectly imported from
3156 annotation file when annotation display text includes 'e' or
3158 <li>Cannot set colour of new feature type whilst creating
3160 <li>cDNA translation alignment should not be sequence
3161 order dependent</li>
3162 <li>'Show unconserved' doesn't work for lower case
3164 <li>Nucleotide ambiguity codes involving R not recognised</li>
3165 </ul> <em>Deployment and Documentation</em>
3167 <li>Applet example pages appear different to the rest of
3168 www.jalview.org</li>
3169 </ul> <em>Application Known issues</em>
3171 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3172 <li>Misleading message appears after trying to delete
3174 <li>Jalview icon not shown in dock after InstallAnywhere
3175 version launches</li>
3176 <li>Fetching EMBL reference for an RNA sequence results
3177 fails with a sequence mismatch</li>
3178 <li>Corrupted or unreadable alignment display when
3179 scrolling alignment to right</li>
3180 <li>ArrayIndexOutOfBoundsException thrown when remove
3181 empty columns called on alignment with ragged gapped ends</li>
3182 <li>auto calculated alignment annotation rows do not get
3183 placed above or below non-autocalculated rows</li>
3184 <li>Jalview dekstop becomes sluggish at full screen in
3185 ultra-high resolution</li>
3186 <li>Cannot disable consensus calculation independently of
3187 quality and conservation</li>
3188 <li>Mouseover highlighting between cDNA and protein can
3189 become sluggish with more than one splitframe shown</li>
3190 </ul> <em>Applet Known Issues</em>
3192 <li>Core PDB parsing code requires Jmol</li>
3193 <li>Sequence canvas panel goes white when alignment
3194 window is being resized</li>
3200 <td><div align="center">
3201 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3203 <td><em>General</em>
3205 <li>Updated Java code signing certificate donated by
3207 <li>Features and annotation preserved when performing
3208 pairwise alignment</li>
3209 <li>RNA pseudoknot annotation can be
3210 imported/exported/displayed</li>
3211 <li>'colour by annotation' can colour by RNA and
3212 protein secondary structure</li>
3213 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3214 post-hoc with 2.9 release</em>)
3217 </ul> <em>Application</em>
3219 <li>Extract and display secondary structure for sequences
3220 with 3D structures</li>
3221 <li>Support for parsing RNAML</li>
3222 <li>Annotations menu for layout
3224 <li>sort sequence annotation rows by alignment</li>
3225 <li>place sequence annotation above/below alignment
3228 <li>Output in Stockholm format</li>
3229 <li>Internationalisation: improved Spanish (es)
3231 <li>Structure viewer preferences tab</li>
3232 <li>Disorder and Secondary Structure annotation tracks
3233 shared between alignments</li>
3234 <li>UCSF Chimera launch and linked highlighting from
3236 <li>Show/hide all sequence associated annotation rows for
3237 all or current selection</li>
3238 <li>disorder and secondary structure predictions
3239 available as dataset annotation</li>
3240 <li>Per-sequence rna helices colouring</li>
3243 <li>Sequence database accessions imported when fetching
3244 alignments from Rfam</li>
3245 <li>update VARNA version to 3.91</li>
3247 <li>New groovy scripts for exporting aligned positions,
3248 conservation values, and calculating sum of pairs scores.</li>
3249 <li>Command line argument to set default JABAWS server</li>
3250 <li>include installation type in build properties and
3251 console log output</li>
3252 <li>Updated Jalview project format to preserve dataset
3256 <!-- issues resolved --> <em>Application</em>
3258 <li>Distinguish alignment and sequence associated RNA
3259 structure in structure->view->VARNA</li>
3260 <li>Raise dialog box if user deletes all sequences in an
3262 <li>Pressing F1 results in documentation opening twice</li>
3263 <li>Sequence feature tooltip is wrapped</li>
3264 <li>Double click on sequence associated annotation
3265 selects only first column</li>
3266 <li>Redundancy removal doesn't result in unlinked
3267 leaves shown in tree</li>
3268 <li>Undos after several redundancy removals don't undo
3270 <li>Hide sequence doesn't hide associated annotation</li>
3271 <li>User defined colours dialog box too big to fit on
3272 screen and buttons not visible</li>
3273 <li>author list isn't updated if already written to
3274 Jalview properties</li>
3275 <li>Popup menu won't open after retrieving sequence
3277 <li>File open window for associate PDB doesn't open</li>
3278 <li>Left-then-right click on a sequence id opens a
3279 browser search window</li>
3280 <li>Cannot open sequence feature shading/sort popup menu
3281 in feature settings dialog</li>
3282 <li>better tooltip placement for some areas of Jalview
3284 <li>Allow addition of JABAWS Server which doesn't
3285 pass validation</li>
3286 <li>Web services parameters dialog box is too large to
3288 <li>Muscle nucleotide alignment preset obscured by
3290 <li>JABAWS preset submenus don't contain newly
3291 defined user preset</li>
3292 <li>MSA web services warns user if they were launched
3293 with invalid input</li>
3294 <li>Jalview cannot contact DAS Registy when running on
3297 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3298 'Superpose with' submenu not shown when new view
3302 </ul> <!-- <em>Applet</em>
3304 </ul> <em>General</em>
3306 </ul>--> <em>Deployment and Documentation</em>
3308 <li>2G and 1G options in launchApp have no effect on
3309 memory allocation</li>
3310 <li>launchApp service doesn't automatically open
3311 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3313 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3314 InstallAnywhere reports cannot find valid JVM when Java
3315 1.7_055 is available
3317 </ul> <em>Application Known issues</em>
3320 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3321 corrupted or unreadable alignment display when scrolling
3325 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3326 retrieval fails but progress bar continues for DAS retrieval
3327 with large number of ID
3330 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3331 flatfile output of visible region has incorrect sequence
3335 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3336 rna structure consensus doesn't update when secondary
3337 structure tracks are rearranged
3340 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3341 invalid rna structure positional highlighting does not
3342 highlight position of invalid base pairs
3345 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3346 out of memory errors are not raised when saving Jalview
3347 project from alignment window file menu
3350 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3351 Switching to RNA Helices colouring doesn't propagate to
3355 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3356 colour by RNA Helices not enabled when user created
3357 annotation added to alignment
3360 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3361 Jalview icon not shown on dock in Mountain Lion/Webstart
3363 </ul> <em>Applet Known Issues</em>
3366 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3367 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3370 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3371 Jalview and Jmol example not compatible with IE9
3374 <li>Sort by annotation score doesn't reverse order
3380 <td><div align="center">
3381 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3384 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3387 <li>Internationalisation of user interface (usually
3388 called i18n support) and translation for Spanish locale</li>
3389 <li>Define/Undefine group on current selection with
3390 Ctrl-G/Shift Ctrl-G</li>
3391 <li>Improved group creation/removal options in
3392 alignment/sequence Popup menu</li>
3393 <li>Sensible precision for symbol distribution
3394 percentages shown in logo tooltip.</li>
3395 <li>Annotation panel height set according to amount of
3396 annotation when alignment first opened</li>
3397 </ul> <em>Application</em>
3399 <li>Interactive consensus RNA secondary structure
3400 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3401 <li>Select columns containing particular features from
3402 Feature Settings dialog</li>
3403 <li>View all 'representative' PDB structures for selected
3405 <li>Update Jalview project format:
3407 <li>New file extension for Jalview projects '.jvp'</li>
3408 <li>Preserve sequence and annotation dataset (to
3409 store secondary structure annotation,etc)</li>
3410 <li>Per group and alignment annotation and RNA helix
3414 <li>New similarity measures for PCA and Tree calculation
3416 <li>Experimental support for retrieval and viewing of
3417 flanking regions for an alignment</li>
3421 <!-- issues resolved --> <em>Application</em>
3423 <li>logo keeps spinning and status remains at queued or
3424 running after job is cancelled</li>
3425 <li>cannot export features from alignments imported from
3426 Jalview/VAMSAS projects</li>
3427 <li>Buggy slider for web service parameters that take
3429 <li>Newly created RNA secondary structure line doesn't
3430 have 'display all symbols' flag set</li>
3431 <li>T-COFFEE alignment score shading scheme and other
3432 annotation shading not saved in Jalview project</li>
3433 <li>Local file cannot be loaded in freshly downloaded
3435 <li>Jalview icon not shown on dock in Mountain
3437 <li>Load file from desktop file browser fails</li>
3438 <li>Occasional NPE thrown when calculating large trees</li>
3439 <li>Cannot reorder or slide sequences after dragging an
3440 alignment onto desktop</li>
3441 <li>Colour by annotation dialog throws NPE after using
3442 'extract scores' function</li>
3443 <li>Loading/cut'n'pasting an empty file leads to a grey
3444 alignment window</li>
3445 <li>Disorder thresholds rendered incorrectly after
3446 performing IUPred disorder prediction</li>
3447 <li>Multiple group annotated consensus rows shown when
3448 changing 'normalise logo' display setting</li>
3449 <li>Find shows blank dialog after 'finished searching' if
3450 nothing matches query</li>
3451 <li>Null Pointer Exceptions raised when sorting by
3452 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3454 <li>Errors in Jmol console when structures in alignment
3455 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3457 <li>Not all working JABAWS services are shown in
3459 <li>JAVAWS version of Jalview fails to launch with
3460 'invalid literal/length code'</li>
3461 <li>Annotation/RNA Helix colourschemes cannot be applied
3462 to alignment with groups (actually fixed in 2.8.0b1)</li>
3463 <li>RNA Helices and T-Coffee Scores available as default
3466 </ul> <em>Applet</em>
3468 <li>Remove group option is shown even when selection is
3470 <li>Apply to all groups ticked but colourscheme changes
3471 don't affect groups</li>
3472 <li>Documented RNA Helices and T-Coffee Scores as valid
3473 colourscheme name</li>
3474 <li>Annotation labels drawn on sequence IDs when
3475 Annotation panel is not displayed</li>
3476 <li>Increased font size for dropdown menus on OSX and
3477 embedded windows</li>
3478 </ul> <em>Other</em>
3480 <li>Consensus sequence for alignments/groups with a
3481 single sequence were not calculated</li>
3482 <li>annotation files that contain only groups imported as
3483 annotation and junk sequences</li>
3484 <li>Fasta files with sequences containing '*' incorrectly
3485 recognised as PFAM or BLC</li>
3486 <li>conservation/PID slider apply all groups option
3487 doesn't affect background (2.8.0b1)
3489 <li>redundancy highlighting is erratic at 0% and 100%</li>
3490 <li>Remove gapped columns fails for sequences with ragged
3492 <li>AMSA annotation row with leading spaces is not
3493 registered correctly on import</li>
3494 <li>Jalview crashes when selecting PCA analysis for
3495 certain alignments</li>
3496 <li>Opening the colour by annotation dialog for an
3497 existing annotation based 'use original colours'
3498 colourscheme loses original colours setting</li>
3503 <td><div align="center">
3504 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3505 <em>30/1/2014</em></strong>
3509 <li>Trusted certificates for JalviewLite applet and
3510 Jalview Desktop application<br />Certificate was donated by
3511 <a href="https://www.certum.eu">Certum</a> to the Jalview
3512 open source project).
3514 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3515 <li>Output in Stockholm format</li>
3516 <li>Allow import of data from gzipped files</li>
3517 <li>Export/import group and sequence associated line
3518 graph thresholds</li>
3519 <li>Nucleotide substitution matrix that supports RNA and
3520 ambiguity codes</li>
3521 <li>Allow disorder predictions to be made on the current
3522 selection (or visible selection) in the same way that JPred
3524 <li>Groovy scripting for headless Jalview operation</li>
3525 </ul> <em>Other improvements</em>
3527 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3528 <li>COMBINE statement uses current SEQUENCE_REF and
3529 GROUP_REF scope to group annotation rows</li>
3530 <li>Support '' style escaping of quotes in Newick
3532 <li>Group options for JABAWS service by command line name</li>
3533 <li>Empty tooltip shown for JABA service options with a
3534 link but no description</li>
3535 <li>Select primary source when selecting authority in
3536 database fetcher GUI</li>
3537 <li>Add .mfa to FASTA file extensions recognised by
3539 <li>Annotation label tooltip text wrap</li>
3544 <li>Slow scrolling when lots of annotation rows are
3546 <li>Lots of NPE (and slowness) after creating RNA
3547 secondary structure annotation line</li>
3548 <li>Sequence database accessions not imported when
3549 fetching alignments from Rfam</li>
3550 <li>Incorrect SHMR submission for sequences with
3552 <li>View all structures does not always superpose
3554 <li>Option widgets in service parameters not updated to
3555 reflect user or preset settings</li>
3556 <li>Null pointer exceptions for some services without
3557 presets or adjustable parameters</li>
3558 <li>Discover PDB IDs entry in structure menu doesn't
3559 discover PDB xRefs</li>
3560 <li>Exception encountered while trying to retrieve
3561 features with DAS</li>
3562 <li>Lowest value in annotation row isn't coloured
3563 when colour by annotation (per sequence) is coloured</li>
3564 <li>Keyboard mode P jumps to start of gapped region when
3565 residue follows a gap</li>
3566 <li>Jalview appears to hang importing an alignment with
3567 Wrap as default or after enabling Wrap</li>
3568 <li>'Right click to add annotations' message
3569 shown in wrap mode when no annotations present</li>
3570 <li>Disorder predictions fail with NPE if no automatic
3571 annotation already exists on alignment</li>
3572 <li>oninit javascript function should be called after
3573 initialisation completes</li>
3574 <li>Remove redundancy after disorder prediction corrupts
3575 alignment window display</li>
3576 <li>Example annotation file in documentation is invalid</li>
3577 <li>Grouped line graph annotation rows are not exported
3578 to annotation file</li>
3579 <li>Multi-harmony analysis cannot be run when only two
3581 <li>Cannot create multiple groups of line graphs with
3582 several 'combine' statements in annotation file</li>
3583 <li>Pressing return several times causes Number Format
3584 exceptions in keyboard mode</li>
3585 <li>Multi-harmony (SHMMR) method doesn't submit
3586 correct partitions for input data</li>
3587 <li>Translation from DNA to Amino Acids fails</li>
3588 <li>Jalview fail to load newick tree with quoted label</li>
3589 <li>--headless flag isn't understood</li>
3590 <li>ClassCastException when generating EPS in headless
3592 <li>Adjusting sequence-associated shading threshold only
3593 changes one row's threshold</li>
3594 <li>Preferences and Feature settings panel panel
3595 doesn't open</li>
3596 <li>hide consensus histogram also hides conservation and
3597 quality histograms</li>
3602 <td><div align="center">
3603 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3605 <td><em>Application</em>
3607 <li>Support for JABAWS 2.0 Services (AACon alignment
3608 conservation, protein disorder and Clustal Omega)</li>
3609 <li>JABAWS server status indicator in Web Services
3611 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3612 in Jalview alignment window</li>
3613 <li>Updated Jalview build and deploy framework for OSX
3614 mountain lion, windows 7, and 8</li>
3615 <li>Nucleotide substitution matrix for PCA that supports
3616 RNA and ambiguity codes</li>
3618 <li>Improved sequence database retrieval GUI</li>
3619 <li>Support fetching and database reference look up
3620 against multiple DAS sources (Fetch all from in 'fetch db
3622 <li>Jalview project improvements
3624 <li>Store and retrieve the 'belowAlignment'
3625 flag for annotation</li>
3626 <li>calcId attribute to group annotation rows on the
3628 <li>Store AACon calculation settings for a view in
3629 Jalview project</li>
3633 <li>horizontal scrolling gesture support</li>
3634 <li>Visual progress indicator when PCA calculation is
3636 <li>Simpler JABA web services menus</li>
3637 <li>visual indication that web service results are still
3638 being retrieved from server</li>
3639 <li>Serialise the dialogs that are shown when Jalview
3640 starts up for first time</li>
3641 <li>Jalview user agent string for interacting with HTTP
3643 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3645 <li>Examples directory and Groovy library included in
3646 InstallAnywhere distribution</li>
3647 </ul> <em>Applet</em>
3649 <li>RNA alignment and secondary structure annotation
3650 visualization applet example</li>
3651 </ul> <em>General</em>
3653 <li>Normalise option for consensus sequence logo</li>
3654 <li>Reset button in PCA window to return dimensions to
3656 <li>Allow seqspace or Jalview variant of alignment PCA
3658 <li>PCA with either nucleic acid and protein substitution
3660 <li>Allow windows containing HTML reports to be exported
3662 <li>Interactive display and editing of RNA secondary
3663 structure contacts</li>
3664 <li>RNA Helix Alignment Colouring</li>
3665 <li>RNA base pair logo consensus</li>
3666 <li>Parse sequence associated secondary structure
3667 information in Stockholm files</li>
3668 <li>HTML Export database accessions and annotation
3669 information presented in tooltip for sequences</li>
3670 <li>Import secondary structure from LOCARNA clustalw
3671 style RNA alignment files</li>
3672 <li>import and visualise T-COFFEE quality scores for an
3674 <li>'colour by annotation' per sequence option to
3675 shade each sequence according to its associated alignment
3677 <li>New Jalview Logo</li>
3678 </ul> <em>Documentation and Development</em>
3680 <li>documentation for score matrices used in Jalview</li>
3681 <li>New Website!</li>
3683 <td><em>Application</em>
3685 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3686 wsdbfetch REST service</li>
3687 <li>Stop windows being moved outside desktop on OSX</li>
3688 <li>Filetype associations not installed for webstart
3690 <li>Jalview does not always retrieve progress of a JABAWS
3691 job execution in full once it is complete</li>
3692 <li>revise SHMR RSBS definition to ensure alignment is
3693 uploaded via ali_file parameter</li>
3694 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3695 <li>View all structures superposed fails with exception</li>
3696 <li>Jnet job queues forever if a very short sequence is
3697 submitted for prediction</li>
3698 <li>Cut and paste menu not opened when mouse clicked on
3700 <li>Putting fractional value into integer text box in
3701 alignment parameter dialog causes Jalview to hang</li>
3702 <li>Structure view highlighting doesn't work on
3704 <li>View all structures fails with exception shown in
3706 <li>Characters in filename associated with PDBEntry not
3707 escaped in a platform independent way</li>
3708 <li>Jalview desktop fails to launch with exception when
3710 <li>Tree calculation reports 'you must have 2 or more
3711 sequences selected' when selection is empty</li>
3712 <li>Jalview desktop fails to launch with jar signature
3713 failure when java web start temporary file caching is
3715 <li>DAS Sequence retrieval with range qualification
3716 results in sequence xref which includes range qualification</li>
3717 <li>Errors during processing of command line arguments
3718 cause progress bar (JAL-898) to be removed</li>
3719 <li>Replace comma for semi-colon option not disabled for
3720 DAS sources in sequence fetcher</li>
3721 <li>Cannot close news reader when JABAWS server warning
3722 dialog is shown</li>
3723 <li>Option widgets not updated to reflect user settings</li>
3724 <li>Edited sequence not submitted to web service</li>
3725 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3726 <li>InstallAnywhere installer doesn't unpack and run
3727 on OSX Mountain Lion</li>
3728 <li>Annotation panel not given a scroll bar when
3729 sequences with alignment annotation are pasted into the
3731 <li>Sequence associated annotation rows not associated
3732 when loaded from Jalview project</li>
3733 <li>Browser launch fails with NPE on java 1.7</li>
3734 <li>JABAWS alignment marked as finished when job was
3735 cancelled or job failed due to invalid input</li>
3736 <li>NPE with v2.7 example when clicking on Tree
3737 associated with all views</li>
3738 <li>Exceptions when copy/paste sequences with grouped
3739 annotation rows to new window</li>
3740 </ul> <em>Applet</em>
3742 <li>Sequence features are momentarily displayed before
3743 they are hidden using hidefeaturegroups applet parameter</li>
3744 <li>loading features via javascript API automatically
3745 enables feature display</li>
3746 <li>scrollToColumnIn javascript API method doesn't
3748 </ul> <em>General</em>
3750 <li>Redundancy removal fails for rna alignment</li>
3751 <li>PCA calculation fails when sequence has been selected
3752 and then deselected</li>
3753 <li>PCA window shows grey box when first opened on OSX</li>
3754 <li>Letters coloured pink in sequence logo when alignment
3755 coloured with clustalx</li>
3756 <li>Choosing fonts without letter symbols defined causes
3757 exceptions and redraw errors</li>
3758 <li>Initial PCA plot view is not same as manually
3759 reconfigured view</li>
3760 <li>Grouped annotation graph label has incorrect line
3762 <li>Grouped annotation graph label display is corrupted
3763 for lots of labels</li>
3768 <div align="center">
3769 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3772 <td><em>Application</em>
3774 <li>Jalview Desktop News Reader</li>
3775 <li>Tweaked default layout of web services menu</li>
3776 <li>View/alignment association menu to enable user to
3777 easily specify which alignment a multi-structure view takes
3778 its colours/correspondences from</li>
3779 <li>Allow properties file location to be specified as URL</li>
3780 <li>Extend Jalview project to preserve associations
3781 between many alignment views and a single Jmol display</li>
3782 <li>Store annotation row height in Jalview project file</li>
3783 <li>Annotation row column label formatting attributes
3784 stored in project file</li>
3785 <li>Annotation row order for auto-calculated annotation
3786 rows preserved in Jalview project file</li>
3787 <li>Visual progress indication when Jalview state is
3788 saved using Desktop window menu</li>
3789 <li>Visual indication that command line arguments are
3790 still being processed</li>
3791 <li>Groovy script execution from URL</li>
3792 <li>Colour by annotation default min and max colours in
3794 <li>Automatically associate PDB files dragged onto an
3795 alignment with sequences that have high similarity and
3797 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3798 <li>'view structures' option to open many
3799 structures in same window</li>
3800 <li>Sort associated views menu option for tree panel</li>
3801 <li>Group all JABA and non-JABA services for a particular
3802 analysis function in its own submenu</li>
3803 </ul> <em>Applet</em>
3805 <li>Userdefined and autogenerated annotation rows for
3807 <li>Adjustment of alignment annotation pane height</li>
3808 <li>Annotation scrollbar for annotation panel</li>
3809 <li>Drag to reorder annotation rows in annotation panel</li>
3810 <li>'automaticScrolling' parameter</li>
3811 <li>Allow sequences with partial ID string matches to be
3812 annotated from GFF/Jalview features files</li>
3813 <li>Sequence logo annotation row in applet</li>
3814 <li>Absolute paths relative to host server in applet
3815 parameters are treated as such</li>
3816 <li>New in the JalviewLite javascript API:
3818 <li>JalviewLite.js javascript library</li>
3819 <li>Javascript callbacks for
3821 <li>Applet initialisation</li>
3822 <li>Sequence/alignment mouse-overs and selections</li>
3825 <li>scrollTo row and column alignment scrolling
3827 <li>Select sequence/alignment regions from javascript</li>
3828 <li>javascript structure viewer harness to pass
3829 messages between Jmol and Jalview when running as
3830 distinct applets</li>
3831 <li>sortBy method</li>
3832 <li>Set of applet and application examples shipped
3833 with documentation</li>
3834 <li>New example to demonstrate JalviewLite and Jmol
3835 javascript message exchange</li>
3837 </ul> <em>General</em>
3839 <li>Enable Jmol displays to be associated with multiple
3840 multiple alignments</li>
3841 <li>Option to automatically sort alignment with new tree</li>
3842 <li>User configurable link to enable redirects to a
3843 www.Jalview.org mirror</li>
3844 <li>Jmol colours option for Jmol displays</li>
3845 <li>Configurable newline string when writing alignment
3846 and other flat files</li>
3847 <li>Allow alignment annotation description lines to
3848 contain html tags</li>
3849 </ul> <em>Documentation and Development</em>
3851 <li>Add groovy test harness for bulk load testing to
3853 <li>Groovy script to load and align a set of sequences
3854 using a web service before displaying the result in the
3855 Jalview desktop</li>
3856 <li>Restructured javascript and applet api documentation</li>
3857 <li>Ant target to publish example html files with applet
3859 <li>Netbeans project for building Jalview from source</li>
3860 <li>ant task to create online javadoc for Jalview source</li>
3862 <td><em>Application</em>
3864 <li>User defined colourscheme throws exception when
3865 current built in colourscheme is saved as new scheme</li>
3866 <li>AlignFrame->Save in application pops up save
3867 dialog for valid filename/format</li>
3868 <li>Cannot view associated structure for UniProt sequence</li>
3869 <li>PDB file association breaks for UniProt sequence
3871 <li>Associate PDB from file dialog does not tell you
3872 which sequence is to be associated with the file</li>
3873 <li>Find All raises null pointer exception when query
3874 only matches sequence IDs</li>
3875 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3876 <li>Jalview project with Jmol views created with Jalview
3877 2.4 cannot be loaded</li>
3878 <li>Filetype associations not installed for webstart
3880 <li>Two or more chains in a single PDB file associated
3881 with sequences in different alignments do not get coloured
3882 by their associated sequence</li>
3883 <li>Visibility status of autocalculated annotation row
3884 not preserved when project is loaded</li>
3885 <li>Annotation row height and visibility attributes not
3886 stored in Jalview project</li>
3887 <li>Tree bootstraps are not preserved when saved as a
3888 Jalview project</li>
3889 <li>Envision2 workflow tooltips are corrupted</li>
3890 <li>Enabling show group conservation also enables colour
3891 by conservation</li>
3892 <li>Duplicate group associated conservation or consensus
3893 created on new view</li>
3894 <li>Annotation scrollbar not displayed after 'show
3895 all hidden annotation rows' option selected</li>
3896 <li>Alignment quality not updated after alignment
3897 annotation row is hidden then shown</li>
3898 <li>Preserve colouring of structures coloured by
3899 sequences in pre Jalview 2.7 projects</li>
3900 <li>Web service job parameter dialog is not laid out
3902 <li>Web services menu not refreshed after 'reset
3903 services' button is pressed in preferences</li>
3904 <li>Annotation off by one in Jalview v2_3 example project</li>
3905 <li>Structures imported from file and saved in project
3906 get name like jalview_pdb1234.txt when reloaded</li>
3907 <li>Jalview does not always retrieve progress of a JABAWS
3908 job execution in full once it is complete</li>
3909 </ul> <em>Applet</em>
3911 <li>Alignment height set incorrectly when lots of
3912 annotation rows are displayed</li>
3913 <li>Relative URLs in feature HTML text not resolved to
3915 <li>View follows highlighting does not work for positions
3917 <li><= shown as = in tooltip</li>
3918 <li>Export features raises exception when no features
3920 <li>Separator string used for serialising lists of IDs
3921 for javascript api is modified when separator string
3922 provided as parameter</li>
3923 <li>Null pointer exception when selecting tree leaves for
3924 alignment with no existing selection</li>
3925 <li>Relative URLs for datasources assumed to be relative
3926 to applet's codebase</li>
3927 <li>Status bar not updated after finished searching and
3928 search wraps around to first result</li>
3929 <li>StructureSelectionManager instance shared between
3930 several Jalview applets causes race conditions and memory
3932 <li>Hover tooltip and mouseover of position on structure
3933 not sent from Jmol in applet</li>
3934 <li>Certain sequences of javascript method calls to
3935 applet API fatally hang browser</li>
3936 </ul> <em>General</em>
3938 <li>View follows structure mouseover scrolls beyond
3939 position with wrapped view and hidden regions</li>
3940 <li>Find sequence position moves to wrong residue
3941 with/without hidden columns</li>
3942 <li>Sequence length given in alignment properties window
3944 <li>InvalidNumberFormat exceptions thrown when trying to
3945 import PDB like structure files</li>
3946 <li>Positional search results are only highlighted
3947 between user-supplied sequence start/end bounds</li>
3948 <li>End attribute of sequence is not validated</li>
3949 <li>Find dialog only finds first sequence containing a
3950 given sequence position</li>
3951 <li>Sequence numbering not preserved in MSF alignment
3953 <li>Jalview PDB file reader does not extract sequence
3954 from nucleotide chains correctly</li>
3955 <li>Structure colours not updated when tree partition
3956 changed in alignment</li>
3957 <li>Sequence associated secondary structure not correctly
3958 parsed in interleaved stockholm</li>
3959 <li>Colour by annotation dialog does not restore current
3961 <li>Hiding (nearly) all sequences doesn't work
3963 <li>Sequences containing lowercase letters are not
3964 properly associated with their pdb files</li>
3965 </ul> <em>Documentation and Development</em>
3967 <li>schemas/JalviewWsParamSet.xsd corrupted by
3968 ApplyCopyright tool</li>
3973 <div align="center">
3974 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3977 <td><em>Application</em>
3979 <li>New warning dialog when the Jalview Desktop cannot
3980 contact web services</li>
3981 <li>JABA service parameters for a preset are shown in
3982 service job window</li>
3983 <li>JABA Service menu entries reworded</li>
3987 <li>Modeller PIR IO broken - cannot correctly import a
3988 pir file emitted by Jalview</li>
3989 <li>Existing feature settings transferred to new
3990 alignment view created from cut'n'paste</li>
3991 <li>Improved test for mixed amino/nucleotide chains when
3992 parsing PDB files</li>
3993 <li>Consensus and conservation annotation rows
3994 occasionally become blank for all new windows</li>
3995 <li>Exception raised when right clicking above sequences
3996 in wrapped view mode</li>
3997 </ul> <em>Application</em>
3999 <li>multiple multiply aligned structure views cause cpu
4000 usage to hit 100% and computer to hang</li>
4001 <li>Web Service parameter layout breaks for long user
4002 parameter names</li>
4003 <li>Jaba service discovery hangs desktop if Jaba server
4010 <div align="center">
4011 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4014 <td><em>Application</em>
4016 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4017 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4020 <li>Web Services preference tab</li>
4021 <li>Analysis parameters dialog box and user defined
4023 <li>Improved speed and layout of Envision2 service menu</li>
4024 <li>Superpose structures using associated sequence
4026 <li>Export coordinates and projection as CSV from PCA
4028 </ul> <em>Applet</em>
4030 <li>enable javascript: execution by the applet via the
4031 link out mechanism</li>
4032 </ul> <em>Other</em>
4034 <li>Updated the Jmol Jalview interface to work with Jmol
4036 <li>The Jalview Desktop and JalviewLite applet now
4037 require Java 1.5</li>
4038 <li>Allow Jalview feature colour specification for GFF
4039 sequence annotation files</li>
4040 <li>New 'colour by label' keword in Jalview feature file
4041 type colour specification</li>
4042 <li>New Jalview Desktop Groovy API method that allows a
4043 script to check if it being run in an interactive session or
4044 in a batch operation from the Jalview command line</li>
4048 <li>clustalx colourscheme colours Ds preferentially when
4049 both D+E are present in over 50% of the column</li>
4050 </ul> <em>Application</em>
4052 <li>typo in AlignmentFrame->View->Hide->all but
4053 selected Regions menu item</li>
4054 <li>sequence fetcher replaces ',' for ';' when the ',' is
4055 part of a valid accession ID</li>
4056 <li>fatal OOM if object retrieved by sequence fetcher
4057 runs out of memory</li>
4058 <li>unhandled Out of Memory Error when viewing pca
4059 analysis results</li>
4060 <li>InstallAnywhere builds fail to launch on OS X java
4061 10.5 update 4 (due to apple Java 1.6 update)</li>
4062 <li>Installanywhere Jalview silently fails to launch</li>
4063 </ul> <em>Applet</em>
4065 <li>Jalview.getFeatureGroups() raises an
4066 ArrayIndexOutOfBoundsException if no feature groups are
4073 <div align="center">
4074 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4080 <li>Alignment prettyprinter doesn't cope with long
4082 <li>clustalx colourscheme colours Ds preferentially when
4083 both D+E are present in over 50% of the column</li>
4084 <li>nucleic acid structures retrieved from PDB do not
4085 import correctly</li>
4086 <li>More columns get selected than were clicked on when a
4087 number of columns are hidden</li>
4088 <li>annotation label popup menu not providing correct
4089 add/hide/show options when rows are hidden or none are
4091 <li>Stockholm format shown in list of readable formats,
4092 and parser copes better with alignments from RFAM.</li>
4093 <li>CSV output of consensus only includes the percentage
4094 of all symbols if sequence logo display is enabled</li>
4096 </ul> <em>Applet</em>
4098 <li>annotation panel disappears when annotation is
4100 </ul> <em>Application</em>
4102 <li>Alignment view not redrawn properly when new
4103 alignment opened where annotation panel is visible but no
4104 annotations are present on alignment</li>
4105 <li>pasted region containing hidden columns is
4106 incorrectly displayed in new alignment window</li>
4107 <li>Jalview slow to complete operations when stdout is
4108 flooded (fix is to close the Jalview console)</li>
4109 <li>typo in AlignmentFrame->View->Hide->all but
4110 selected Rregions menu item.</li>
4111 <li>inconsistent group submenu and Format submenu entry
4112 'Un' or 'Non'conserved</li>
4113 <li>Sequence feature settings are being shared by
4114 multiple distinct alignments</li>
4115 <li>group annotation not recreated when tree partition is
4117 <li>double click on group annotation to select sequences
4118 does not propagate to associated trees</li>
4119 <li>Mac OSX specific issues:
4121 <li>exception raised when mouse clicked on desktop
4122 window background</li>
4123 <li>Desktop menu placed on menu bar and application
4124 name set correctly</li>
4125 <li>sequence feature settings not wide enough for the
4126 save feature colourscheme button</li>
4135 <div align="center">
4136 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4139 <td><em>New Capabilities</em>
4141 <li>URL links generated from description line for
4142 regular-expression based URL links (applet and application)
4144 <li>Non-positional feature URL links are shown in link
4146 <li>Linked viewing of nucleic acid sequences and
4148 <li>Automatic Scrolling option in View menu to display
4149 the currently highlighted region of an alignment.</li>
4150 <li>Order an alignment by sequence length, or using the
4151 average score or total feature count for each sequence.</li>
4152 <li>Shading features by score or associated description</li>
4153 <li>Subdivide alignment and groups based on identity of
4154 selected subsequence (Make Groups from Selection).</li>
4155 <li>New hide/show options including Shift+Control+H to
4156 hide everything but the currently selected region.</li>
4157 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4158 </ul> <em>Application</em>
4160 <li>Fetch DB References capabilities and UI expanded to
4161 support retrieval from DAS sequence sources</li>
4162 <li>Local DAS Sequence sources can be added via the
4163 command line or via the Add local source dialog box.</li>
4164 <li>DAS Dbref and DbxRef feature types are parsed as
4165 database references and protein_name is parsed as
4166 description line (BioSapiens terms).</li>
4167 <li>Enable or disable non-positional feature and database
4168 references in sequence ID tooltip from View menu in
4170 <!-- <li>New hidden columns and rows and representatives capabilities
4171 in annotations file (in progress - not yet fully implemented)</li> -->
4172 <li>Group-associated consensus, sequence logos and
4173 conservation plots</li>
4174 <li>Symbol distributions for each column can be exported
4175 and visualized as sequence logos</li>
4176 <li>Optionally scale multi-character column labels to fit
4177 within each column of annotation row<!-- todo for applet -->
4179 <li>Optional automatic sort of associated alignment view
4180 when a new tree is opened.</li>
4181 <li>Jalview Java Console</li>
4182 <li>Better placement of desktop window when moving
4183 between different screens.</li>
4184 <li>New preference items for sequence ID tooltip and
4185 consensus annotation</li>
4186 <li>Client to submit sequences and IDs to Envision2
4188 <li><em>Vamsas Capabilities</em>
4190 <li>Improved VAMSAS synchronization (Jalview archive
4191 used to preserve views, structures, and tree display
4193 <li>Import of vamsas documents from disk or URL via
4195 <li>Sharing of selected regions between views and
4196 with other VAMSAS applications (Experimental feature!)</li>
4197 <li>Updated API to VAMSAS version 0.2</li>
4199 </ul> <em>Applet</em>
4201 <li>Middle button resizes annotation row height</li>
4204 <li>sortByTree (true/false) - automatically sort the
4205 associated alignment view by the tree when a new tree is
4207 <li>showTreeBootstraps (true/false) - show or hide
4208 branch bootstraps (default is to show them if available)</li>
4209 <li>showTreeDistances (true/false) - show or hide
4210 branch lengths (default is to show them if available)</li>
4211 <li>showUnlinkedTreeNodes (true/false) - indicate if
4212 unassociated nodes should be highlighted in the tree
4214 <li>heightScale and widthScale (1.0 or more) -
4215 increase the height or width of a cell in the alignment
4216 grid relative to the current font size.</li>
4219 <li>Non-positional features displayed in sequence ID
4221 </ul> <em>Other</em>
4223 <li>Features format: graduated colour definitions and
4224 specification of feature scores</li>
4225 <li>Alignment Annotations format: new keywords for group
4226 associated annotation (GROUP_REF) and annotation row display
4227 properties (ROW_PROPERTIES)</li>
4228 <li>XML formats extended to support graduated feature
4229 colourschemes, group associated annotation, and profile
4230 visualization settings.</li></td>
4233 <li>Source field in GFF files parsed as feature source
4234 rather than description</li>
4235 <li>Non-positional features are now included in sequence
4236 feature and gff files (controlled via non-positional feature
4237 visibility in tooltip).</li>
4238 <li>URL links generated for all feature links (bugfix)</li>
4239 <li>Added URL embedding instructions to features file
4241 <li>Codons containing ambiguous nucleotides translated as
4242 'X' in peptide product</li>
4243 <li>Match case switch in find dialog box works for both
4244 sequence ID and sequence string and query strings do not
4245 have to be in upper case to match case-insensitively.</li>
4246 <li>AMSA files only contain first column of
4247 multi-character column annotation labels</li>
4248 <li>Jalview Annotation File generation/parsing consistent
4249 with documentation (e.g. Stockholm annotation can be
4250 exported and re-imported)</li>
4251 <li>PDB files without embedded PDB IDs given a friendly
4253 <li>Find incrementally searches ID string matches as well
4254 as subsequence matches, and correctly reports total number
4258 <li>Better handling of exceptions during sequence
4260 <li>Dasobert generated non-positional feature URL
4261 link text excludes the start_end suffix</li>
4262 <li>DAS feature and source retrieval buttons disabled
4263 when fetch or registry operations in progress.</li>
4264 <li>PDB files retrieved from URLs are cached properly</li>
4265 <li>Sequence description lines properly shared via
4267 <li>Sequence fetcher fetches multiple records for all
4269 <li>Ensured that command line das feature retrieval
4270 completes before alignment figures are generated.</li>
4271 <li>Reduced time taken when opening file browser for
4273 <li>isAligned check prior to calculating tree, PCA or
4274 submitting an MSA to JNet now excludes hidden sequences.</li>
4275 <li>User defined group colours properly recovered
4276 from Jalview projects.</li>
4285 <div align="center">
4286 <strong>2.4.0.b2</strong><br> 28/10/2009
4291 <li>Experimental support for google analytics usage
4293 <li>Jalview privacy settings (user preferences and docs).</li>
4298 <li>Race condition in applet preventing startup in
4300 <li>Exception when feature created from selection beyond
4301 length of sequence.</li>
4302 <li>Allow synthetic PDB files to be imported gracefully</li>
4303 <li>Sequence associated annotation rows associate with
4304 all sequences with a given id</li>
4305 <li>Find function matches case-insensitively for sequence
4306 ID string searches</li>
4307 <li>Non-standard characters do not cause pairwise
4308 alignment to fail with exception</li>
4309 </ul> <em>Application Issues</em>
4311 <li>Sequences are now validated against EMBL database</li>
4312 <li>Sequence fetcher fetches multiple records for all
4314 </ul> <em>InstallAnywhere Issues</em>
4316 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4317 issue with installAnywhere mechanism)</li>
4318 <li>Command line launching of JARs from InstallAnywhere
4319 version (java class versioning error fixed)</li>
4326 <div align="center">
4327 <strong>2.4</strong><br> 27/8/2008
4330 <td><em>User Interface</em>
4332 <li>Linked highlighting of codon and amino acid from
4333 translation and protein products</li>
4334 <li>Linked highlighting of structure associated with
4335 residue mapping to codon position</li>
4336 <li>Sequence Fetcher provides example accession numbers
4337 and 'clear' button</li>
4338 <li>MemoryMonitor added as an option under Desktop's
4340 <li>Extract score function to parse whitespace separated
4341 numeric data in description line</li>
4342 <li>Column labels in alignment annotation can be centred.</li>
4343 <li>Tooltip for sequence associated annotation give name
4345 </ul> <em>Web Services and URL fetching</em>
4347 <li>JPred3 web service</li>
4348 <li>Prototype sequence search client (no public services
4350 <li>Fetch either seed alignment or full alignment from
4352 <li>URL Links created for matching database cross
4353 references as well as sequence ID</li>
4354 <li>URL Links can be created using regular-expressions</li>
4355 </ul> <em>Sequence Database Connectivity</em>
4357 <li>Retrieval of cross-referenced sequences from other
4359 <li>Generalised database reference retrieval and
4360 validation to all fetchable databases</li>
4361 <li>Fetch sequences from DAS sources supporting the
4362 sequence command</li>
4363 </ul> <em>Import and Export</em>
4364 <li>export annotation rows as CSV for spreadsheet import</li>
4365 <li>Jalview projects record alignment dataset associations,
4366 EMBL products, and cDNA sequence mappings</li>
4367 <li>Sequence Group colour can be specified in Annotation
4369 <li>Ad-hoc colouring of group in Annotation File using RGB
4370 triplet as name of colourscheme</li>
4371 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4373 <li>treenode binding for VAMSAS tree exchange</li>
4374 <li>local editing and update of sequences in VAMSAS
4375 alignments (experimental)</li>
4376 <li>Create new or select existing session to join</li>
4377 <li>load and save of vamsas documents</li>
4378 </ul> <em>Application command line</em>
4380 <li>-tree parameter to open trees (introduced for passing
4382 <li>-fetchfrom command line argument to specify nicknames
4383 of DAS servers to query for alignment features</li>
4384 <li>-dasserver command line argument to add new servers
4385 that are also automatically queried for features</li>
4386 <li>-groovy command line argument executes a given groovy
4387 script after all input data has been loaded and parsed</li>
4388 </ul> <em>Applet-Application data exchange</em>
4390 <li>Trees passed as applet parameters can be passed to
4391 application (when using "View in full
4392 application")</li>
4393 </ul> <em>Applet Parameters</em>
4395 <li>feature group display control parameter</li>
4396 <li>debug parameter</li>
4397 <li>showbutton parameter</li>
4398 </ul> <em>Applet API methods</em>
4400 <li>newView public method</li>
4401 <li>Window (current view) specific get/set public methods</li>
4402 <li>Feature display control methods</li>
4403 <li>get list of currently selected sequences</li>
4404 </ul> <em>New Jalview distribution features</em>
4406 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4407 <li>RELEASE file gives build properties for the latest
4408 Jalview release.</li>
4409 <li>Java 1.1 Applet build made easier and donotobfuscate
4410 property controls execution of obfuscator</li>
4411 <li>Build target for generating source distribution</li>
4412 <li>Debug flag for javacc</li>
4413 <li>.jalview_properties file is documented (slightly) in
4414 jalview.bin.Cache</li>
4415 <li>Continuous Build Integration for stable and
4416 development version of Application, Applet and source
4421 <li>selected region output includes visible annotations
4422 (for certain formats)</li>
4423 <li>edit label/displaychar contains existing label/char
4425 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4426 <li>shorter peptide product names from EMBL records</li>
4427 <li>Newick string generator makes compact representations</li>
4428 <li>bootstrap values parsed correctly for tree files with
4430 <li>pathological filechooser bug avoided by not allowing
4431 filenames containing a ':'</li>
4432 <li>Fixed exception when parsing GFF files containing
4433 global sequence features</li>
4434 <li>Alignment datasets are finalized only when number of
4435 references from alignment sequences goes to zero</li>
4436 <li>Close of tree branch colour box without colour
4437 selection causes cascading exceptions</li>
4438 <li>occasional negative imgwidth exceptions</li>
4439 <li>better reporting of non-fatal warnings to user when
4440 file parsing fails.</li>
4441 <li>Save works when Jalview project is default format</li>
4442 <li>Save as dialog opened if current alignment format is
4443 not a valid output format</li>
4444 <li>UniProt canonical names introduced for both das and
4446 <li>Histidine should be midblue (not pink!) in Zappo</li>
4447 <li>error messages passed up and output when data read
4449 <li>edit undo recovers previous dataset sequence when
4450 sequence is edited</li>
4451 <li>allow PDB files without pdb ID HEADER lines (like
4452 those generated by MODELLER) to be read in properly</li>
4453 <li>allow reading of JPred concise files as a normal
4455 <li>Stockholm annotation parsing and alignment properties
4456 import fixed for PFAM records</li>
4457 <li>Structure view windows have correct name in Desktop
4459 <li>annotation consisting of sequence associated scores
4460 can be read and written correctly to annotation file</li>
4461 <li>Aligned cDNA translation to aligned peptide works
4463 <li>Fixed display of hidden sequence markers and
4464 non-italic font for representatives in Applet</li>
4465 <li>Applet Menus are always embedded in applet window on
4467 <li>Newly shown features appear at top of stack (in
4469 <li>Annotations added via parameter not drawn properly
4470 due to null pointer exceptions</li>
4471 <li>Secondary structure lines are drawn starting from
4472 first column of alignment</li>
4473 <li>UniProt XML import updated for new schema release in
4475 <li>Sequence feature to sequence ID match for Features
4476 file is case-insensitive</li>
4477 <li>Sequence features read from Features file appended to
4478 all sequences with matching IDs</li>
4479 <li>PDB structure coloured correctly for associated views
4480 containing a sub-sequence</li>
4481 <li>PDB files can be retrieved by applet from Jar files</li>
4482 <li>feature and annotation file applet parameters
4483 referring to different directories are retrieved correctly</li>
4484 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4485 <li>Fixed application hang whilst waiting for
4486 splash-screen version check to complete</li>
4487 <li>Applet properly URLencodes input parameter values
4488 when passing them to the launchApp service</li>
4489 <li>display name and local features preserved in results
4490 retrieved from web service</li>
4491 <li>Visual delay indication for sequence retrieval and
4492 sequence fetcher initialisation</li>
4493 <li>updated Application to use DAS 1.53e version of
4494 dasobert DAS client</li>
4495 <li>Re-instated Full AMSA support and .amsa file
4497 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4505 <div align="center">
4506 <strong>2.3</strong><br> 9/5/07
4511 <li>Jmol 11.0.2 integration</li>
4512 <li>PDB views stored in Jalview XML files</li>
4513 <li>Slide sequences</li>
4514 <li>Edit sequence in place</li>
4515 <li>EMBL CDS features</li>
4516 <li>DAS Feature mapping</li>
4517 <li>Feature ordering</li>
4518 <li>Alignment Properties</li>
4519 <li>Annotation Scores</li>
4520 <li>Sort by scores</li>
4521 <li>Feature/annotation editing in applet</li>
4526 <li>Headless state operation in 2.2.1</li>
4527 <li>Incorrect and unstable DNA pairwise alignment</li>
4528 <li>Cut and paste of sequences with annotation</li>
4529 <li>Feature group display state in XML</li>
4530 <li>Feature ordering in XML</li>
4531 <li>blc file iteration selection using filename # suffix</li>
4532 <li>Stockholm alignment properties</li>
4533 <li>Stockhom alignment secondary structure annotation</li>
4534 <li>2.2.1 applet had no feature transparency</li>
4535 <li>Number pad keys can be used in cursor mode</li>
4536 <li>Structure Viewer mirror image resolved</li>
4543 <div align="center">
4544 <strong>2.2.1</strong><br> 12/2/07
4549 <li>Non standard characters can be read and displayed
4550 <li>Annotations/Features can be imported/exported to the
4552 <li>Applet allows editing of sequence/annotation/group
4553 name & description
4554 <li>Preference setting to display sequence name in
4556 <li>Annotation file format extended to allow
4557 Sequence_groups to be defined
4558 <li>Default opening of alignment overview panel can be
4559 specified in preferences
4560 <li>PDB residue numbering annotation added to associated
4566 <li>Applet crash under certain Linux OS with Java 1.6
4568 <li>Annotation file export / import bugs fixed
4569 <li>PNG / EPS image output bugs fixed
4575 <div align="center">
4576 <strong>2.2</strong><br> 27/11/06
4581 <li>Multiple views on alignment
4582 <li>Sequence feature editing
4583 <li>"Reload" alignment
4584 <li>"Save" to current filename
4585 <li>Background dependent text colour
4586 <li>Right align sequence ids
4587 <li>User-defined lower case residue colours
4590 <li>Menu item accelerator keys
4591 <li>Control-V pastes to current alignment
4592 <li>Cancel button for DAS Feature Fetching
4593 <li>PCA and PDB Viewers zoom via mouse roller
4594 <li>User-defined sub-tree colours and sub-tree selection
4596 <li>'New Window' button on the 'Output to Text box'
4601 <li>New memory efficient Undo/Redo System
4602 <li>Optimised symbol lookups and conservation/consensus
4604 <li>Region Conservation/Consensus recalculated after
4606 <li>Fixed Remove Empty Columns Bug (empty columns at end
4608 <li>Slowed DAS Feature Fetching for increased robustness.
4610 <li>Made angle brackets in ASCII feature descriptions
4612 <li>Re-instated Zoom function for PCA
4613 <li>Sequence descriptions conserved in web service
4615 <li>UniProt ID discoverer uses any word separated by
4617 <li>WsDbFetch query/result association resolved
4618 <li>Tree leaf to sequence mapping improved
4619 <li>Smooth fonts switch moved to FontChooser dialog box.
4626 <div align="center">
4627 <strong>2.1.1</strong><br> 12/9/06
4632 <li>Copy consensus sequence to clipboard</li>
4637 <li>Image output - rightmost residues are rendered if
4638 sequence id panel has been resized</li>
4639 <li>Image output - all offscreen group boundaries are
4641 <li>Annotation files with sequence references - all
4642 elements in file are relative to sequence position</li>
4643 <li>Mac Applet users can use Alt key for group editing</li>
4649 <div align="center">
4650 <strong>2.1</strong><br> 22/8/06
4655 <li>MAFFT Multiple Alignment in default Web Service list</li>
4656 <li>DAS Feature fetching</li>
4657 <li>Hide sequences and columns</li>
4658 <li>Export Annotations and Features</li>
4659 <li>GFF file reading / writing</li>
4660 <li>Associate structures with sequences from local PDB
4662 <li>Add sequences to exisiting alignment</li>
4663 <li>Recently opened files / URL lists</li>
4664 <li>Applet can launch the full application</li>
4665 <li>Applet has transparency for features (Java 1.2
4667 <li>Applet has user defined colours parameter</li>
4668 <li>Applet can load sequences from parameter
4669 "sequence<em>x</em>"
4675 <li>Redundancy Panel reinstalled in the Applet</li>
4676 <li>Monospaced font - EPS / rescaling bug fixed</li>
4677 <li>Annotation files with sequence references bug fixed</li>
4683 <div align="center">
4684 <strong>2.08.1</strong><br> 2/5/06
4689 <li>Change case of selected region from Popup menu</li>
4690 <li>Choose to match case when searching</li>
4691 <li>Middle mouse button and mouse movement can compress /
4692 expand the visible width and height of the alignment</li>
4697 <li>Annotation Panel displays complete JNet results</li>
4703 <div align="center">
4704 <strong>2.08b</strong><br> 18/4/06
4710 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4711 <li>Righthand label on wrapped alignments shows correct
4718 <div align="center">
4719 <strong>2.08</strong><br> 10/4/06
4724 <li>Editing can be locked to the selection area</li>
4725 <li>Keyboard editing</li>
4726 <li>Create sequence features from searches</li>
4727 <li>Precalculated annotations can be loaded onto
4729 <li>Features file allows grouping of features</li>
4730 <li>Annotation Colouring scheme added</li>
4731 <li>Smooth fonts off by default - Faster rendering</li>
4732 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4737 <li>Drag & Drop fixed on Linux</li>
4738 <li>Jalview Archive file faster to load/save, sequence
4739 descriptions saved.</li>
4745 <div align="center">
4746 <strong>2.07</strong><br> 12/12/05
4751 <li>PDB Structure Viewer enhanced</li>
4752 <li>Sequence Feature retrieval and display enhanced</li>
4753 <li>Choose to output sequence start-end after sequence
4754 name for file output</li>
4755 <li>Sequence Fetcher WSDBFetch@EBI</li>
4756 <li>Applet can read feature files, PDB files and can be
4757 used for HTML form input</li>
4762 <li>HTML output writes groups and features</li>
4763 <li>Group editing is Control and mouse click</li>
4764 <li>File IO bugs</li>
4770 <div align="center">
4771 <strong>2.06</strong><br> 28/9/05
4776 <li>View annotations in wrapped mode</li>
4777 <li>More options for PCA viewer</li>
4782 <li>GUI bugs resolved</li>
4783 <li>Runs with -nodisplay from command line</li>
4789 <div align="center">
4790 <strong>2.05b</strong><br> 15/9/05
4795 <li>Choose EPS export as lineart or text</li>
4796 <li>Jar files are executable</li>
4797 <li>Can read in Uracil - maps to unknown residue</li>
4802 <li>Known OutOfMemory errors give warning message</li>
4803 <li>Overview window calculated more efficiently</li>
4804 <li>Several GUI bugs resolved</li>
4810 <div align="center">
4811 <strong>2.05</strong><br> 30/8/05
4816 <li>Edit and annotate in "Wrapped" view</li>
4821 <li>Several GUI bugs resolved</li>
4827 <div align="center">
4828 <strong>2.04</strong><br> 24/8/05
4833 <li>Hold down mouse wheel & scroll to change font
4839 <li>Improved JPred client reliability</li>
4840 <li>Improved loading of Jalview files</li>
4846 <div align="center">
4847 <strong>2.03</strong><br> 18/8/05
4852 <li>Set Proxy server name and port in preferences</li>
4853 <li>Multiple URL links from sequence ids</li>
4854 <li>User Defined Colours can have a scheme name and added
4856 <li>Choose to ignore gaps in consensus calculation</li>
4857 <li>Unix users can set default web browser</li>
4858 <li>Runs without GUI for batch processing</li>
4859 <li>Dynamically generated Web Service Menus</li>
4864 <li>InstallAnywhere download for Sparc Solaris</li>
4870 <div align="center">
4871 <strong>2.02</strong><br> 18/7/05
4877 <li>Copy & Paste order of sequences maintains
4878 alignment order.</li>
4884 <div align="center">
4885 <strong>2.01</strong><br> 12/7/05
4890 <li>Use delete key for deleting selection.</li>
4891 <li>Use Mouse wheel to scroll sequences.</li>
4892 <li>Help file updated to describe how to add alignment
4894 <li>Version and build date written to build properties
4896 <li>InstallAnywhere installation will check for updates
4897 at launch of Jalview.</li>
4902 <li>Delete gaps bug fixed.</li>
4903 <li>FileChooser sorts columns.</li>
4904 <li>Can remove groups one by one.</li>
4905 <li>Filechooser icons installed.</li>
4906 <li>Finder ignores return character when searching.
4907 Return key will initiate a search.<br>
4914 <div align="center">
4915 <strong>2.0</strong><br> 20/6/05
4920 <li>New codebase</li>