3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>15/09/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
66 residue in cursor mode
69 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
70 HTSJDK from 2.12 to 2.23
73 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
74 optimisations and improvements suggested by Bob Hanson and
75 improved compatibility with JalviewJS
78 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
79 alignments from Pfam and Rfam
82 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
83 import (no longer based on .gz extension)
86 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
89 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
90 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
94 <!-- JAL-3667 -->Improved warning messages, debug logging
95 and fixed Retry action when Jalview encounters errors when
96 saving or making backup files.
99 <!-- JAL-3676 -->Enhanced Jalview Java Console:
101 <li>Jalview's logging level can be configured</li>
102 <li>Copy to Clipboard Buttion</li>
106 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
107 when running on Linux (Requires Java 11+)
109 </ul> <em>Launching Jalview</em>
112 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
113 through a system property
116 <!-- JAL-3477 -->Improved built-in documentation and command
117 line help for configuring Jalview's memory
121 <td align="left" valign="top">
124 <!-- JAL-3691 -->Conservation and Quality tracks are shown
125 but not calculated and no protein or DNA score models are
126 available for tree/PCA calculation when launched with
127 Turkish language locale
130 <!-- JAL-3493 -->Escape does not clear highlights on the
131 alignment (Since Jalview 2.10.3)
134 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
135 doesn't slide selected sequences, just sequence under cursor
138 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
139 sequence under the cursor
142 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
143 multiple EMBL gene products shown forĀ a single contig
146 <!-- JAL-3696 -->Errors encountered when processing variants
147 from VCF files yield "Error processing VCF: Format specifier
151 <!-- JAL-3697 -->Count of features not shown can be wrong
152 when there are both local and complementary features mapped
153 to the position under the cursor
156 <!-- JAL-3673 -->Sequence ID for reference sequence is
157 clipped when Right align Sequence IDs enabled
160 <!-- JAL-2983 -->Slider with negative range values not
161 rendered correctly in VAqua4 (Since 2.10.4)
164 <!-- JAL-3685 -->Single quotes not displayed correctly in
165 internationalised text for some messages and log output
168 <!-- JAL-3490 -->Find doesn't report matches that span
169 hidden gapped columns
172 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
173 panels, Alignment viewport and annotation renderer.
176 <!-- JAL-3561 -->Jalview ignores file format parameter
177 specifying output format when exporting an alignment via the
181 <!-- JAL-3667 -->Windows 10: For a minority of users, if
182 backups are not enabled, Jalview sometimes fails to
183 overwrite an existing file and raises a warning dialog. (in
184 2.11.0, and 2.11.1.0, the workaround is to try to save the
185 file again, and if that fails, delete the original file and
188 </ul> <em>Launching Jalview</em>
191 <!-- JAL-3718 -->Jalview application fails when launched the
192 first time for a version that has different jars to the
193 previous launched version.
195 </ul> <em>Developing Jalview</em>
198 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
199 data, causing cloverReport gradle task to fail with an
203 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
204 monitor the release channel
206 </ul> <em>New Known defects</em>
209 <!-- JAL-3576 -->Co-located features exported and re-imported
210 are ordered differently when shown on alignment and in
211 tooltips. (Also affects v2.11.1.0)
214 <!-- JAL-3702 -->Drag and drop of alignment file onto
215 alignment window when in a HiDPI scaled mode in Linux only
216 works for the top left quadrant of the alignment window
219 <!-- JAL-3701 -->Stale build data in jalview standalone jar
220 builds (only affects 2.11.1.1 branch)
223 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
224 when alignment view restored from project (since Jalview 2.11.0)
230 <td width="60" align="center" nowrap><strong><a
231 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
232 <em>22/04/2020</em></strong></td>
233 <td align="left" valign="top">
236 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
237 'virtual' codon features shown on protein (or vice versa)
238 for display in alignments, on structure views (including
239 transfer to UCSF chimera), in feature reports and for
243 <!-- JAL-3121 -->Feature attributes from VCF files can be
244 exported and re-imported as GFF3 files
247 <!-- JAL-3376 -->Capture VCF "fixed column" values
248 POS, ID, QUAL, FILTER as Feature Attributes
251 <!-- JAL-3375 -->More robust VCF numeric data field
252 validation while parsing
255 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
259 <!-- JAL-3535 -->Feature Settings dialog title includes name
263 <!-- JAL-3538 -->Font anti-aliasing in alignment views
267 <!-- JAL-3468 -->Very long feature descriptions truncated in
271 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
272 with no feature types visible
275 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
277 </ul><em>Jalview Installer</em>
280 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
281 in console (may be null when Jalview launched as executable jar or via conda)
284 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
287 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
290 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
292 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
293 </ul> <em>Release processes</em>
296 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
299 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
301 </ul> <em>Build System</em>
304 <!-- JAL-3510 -->Clover updated to 4.4.1
307 <!-- JAL-3513 -->Test code included in Clover coverage
311 <em>Groovy Scripts</em>
314 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
315 to stdout containing the consensus sequence for each
316 alignment in a Jalview session
319 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
320 genomic sequence_variant annotation from CDS as
321 missense_variant or synonymous_variant on protein products.
325 <td align="left" valign="top">
328 <!-- JAL-3581 -->Hidden sequence markers still visible when
329 'Show hidden markers' option is not ticked
332 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
333 PNG output when 'Automatically set ID width' is set in
334 jalview preferences or properties file
337 <!-- JAL-3571 -->Feature Editor dialog can be opened when
338 'Show Sequence Features' option is not ticked
341 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
342 buttons in Feature Settings dialog are clicked when no
346 <!-- JAL-3412 -->ID margins for CDS and Protein views not
347 equal when split frame is first opened
350 <!-- JAL-3296 -->Sequence position numbers in status bar not
351 correct after editing a sequence's start position
354 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
355 with annotation and exceptions thrown when only a few
356 columns shown in wrapped mode
359 <!-- JAL-3386 -->Sequence IDs missing in headless export of
360 wrapped alignment figure with annotations
363 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
364 ID fails with ClassCastException
367 <!-- JAL-3389 -->Chimera session not restored from Jalview
371 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
372 feature settings dialog also selects columns
375 <!-- JAL-3473 -->SpinnerNumberModel causes
376 IllegalArgumentException in some circumstances
379 <!-- JAL-3534 -->Multiple feature settings dialogs can be
383 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
384 alignment window is closed
387 <!-- JAL-3406 -->Credits missing some authors in Jalview
388 help documentation for 2.11.0 release
391 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
392 includes Pfam ID as sequence's accession rather than its
395 </ul> <em>Java 11 Compatibility issues</em>
398 <!-- JAL-2987 -->OSX - Can't view some search results in
399 PDB/Uniprot search panel
401 </ul> <em>Installer</em>
404 <!-- JAL-3447 -->Jalview should not create file associations
405 for 3D structure files (.pdb, .mmcif. .cif)
407 </ul> <em>Repository and Source Release</em>
410 <!-- JAL-3474 -->removed obsolete .cvsignore files from
414 <!-- JAL-3541 -->Clover report generation running out of
417 </ul> <em>New Known Issues</em>
420 <!-- JAL-3523 -->OSX - Current working directory not
421 preserved when Jalview.app launched with parameters from
425 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
426 clipped in headless figure export when Right Align option
430 <!-- JAL-3542 -->Jalview Installation type always reports
431 'Source' in console output
434 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
435 bamboo server but run fine locally.
441 <td width="60" align="center" nowrap>
442 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
443 <em>04/07/2019</em></strong>
445 <td align="left" valign="top">
448 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
449 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
450 source project) rather than InstallAnywhere
453 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
454 settings, receive over the air updates and launch specific
455 versions via (<a href="https://github.com/threerings/getdown">Three
459 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
460 formats supported by Jalview (including .jvp project files)
463 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
464 arguments and switch between different getdown channels
467 <!-- JAL-3141 -->Backup files created when saving Jalview project
472 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
473 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
475 <!-- JAL-2620 -->Alternative genetic code tables for
476 'Translate as cDNA'</li>
478 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
479 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
482 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
483 implementation that allows updates) used for Sequence Feature collections</li>
485 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
486 features can be filtered and shaded according to any
487 associated attributes (e.g. variant attributes from VCF
488 file, or key-value pairs imported from column 9 of GFF
492 <!-- JAL-2879 -->Feature Attributes and shading schemes
493 stored and restored from Jalview Projects
496 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
497 recognise variant features
500 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
501 sequences (also coloured red by default)
504 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
508 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
509 algorithm (Z-sort/transparency and filter aware)
512 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
518 <!-- JAL-3205 -->Symmetric score matrices for faster
519 tree and PCA calculations
521 <li><strong>Principal Components Analysis Viewer</strong>
524 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
525 and Viewer state saved in Jalview Project
527 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
530 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
534 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
539 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
541 <li><strong>Speed and Efficiency</strong>
544 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
545 multiple groups when working with large alignments
548 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
552 <li><strong>User Interface</strong>
555 <!-- JAL-2933 -->Finder panel remembers last position in each
559 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
560 what is shown)<br />Only visible regions of alignment are shown by
561 default (can be changed in user preferences)
564 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
565 to the Overwrite Dialog
568 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
572 <!-- JAL-1244 -->Status bar shows bounds when dragging a
573 selection region, and gap count when inserting or deleting gaps
576 <!-- JAL-3132 -->Status bar updates over sequence and annotation
580 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
584 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
588 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
591 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
595 <!-- JAL-3181 -->Consistent ordering of links in sequence id
599 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
601 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
605 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
606 <li><strong>Java 11 Support (not yet on general release)</strong>
609 <!-- -->OSX GUI integrations for App menu's 'About' entry and
614 <em>Deprecations</em>
616 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
617 capabilities removed from the Jalview Desktop
619 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
620 unmarshalling has been replaced by JAXB for Jalview projects
621 and XML based data retrieval clients</li>
622 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
623 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
624 </ul> <em>Documentation</em>
626 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
627 not supported in EPS figure export
629 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
630 </ul> <em>Development and Release Processes</em>
633 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
636 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
638 <!-- JAL-3225 -->Eclipse project configuration managed with
642 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
643 Bamboo continuous integration for unattended Test Suite
647 <!-- JAL-2864 -->Memory test suite to detect leaks in common
651 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
655 <!-- JAL-3248 -->Developer documentation migrated to
656 markdown (with HTML rendering)
659 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
662 <!-- JAL-3289 -->New URLs for publishing development
667 <td align="left" valign="top">
670 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
673 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
674 superposition in Jmol fail on Windows
677 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
678 structures for sequences with lots of PDB structures
681 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
685 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
686 project involving multiple views
689 <!-- JAL-3164 -->Overview for complementary view in a linked
690 CDS/Protein alignment is not updated when Hide Columns by
691 Annotation dialog hides columns
694 <!-- JAL-3158 -->Selection highlighting in the complement of a
695 CDS/Protein alignment stops working after making a selection in
696 one view, then making another selection in the other view
699 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
703 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
704 Settings and Jalview Preferences panels
707 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
708 overview with large alignments
711 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
712 region if columns were selected by dragging right-to-left and the
713 mouse moved to the left of the first column
716 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
717 hidden column marker via scale popup menu
720 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
721 doesn't tell users the invalid URL
724 <!-- JAL-2816 -->Tooltips displayed for features filtered by
728 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
729 show cross references or Fetch Database References are shown in
733 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
734 peptide sequence (computed variant shown as p.Res.null)
737 <!-- JAL-2060 -->'Graduated colour' option not offered for
738 manually created features (where feature score is Float.NaN)
741 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
742 when columns are hidden
745 <!-- JAL-3082 -->Regular expression error for '(' in Select
746 Columns by Annotation description
749 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
750 out of Scale or Annotation Panel
753 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
757 <!-- JAL-3074 -->Left/right drag in annotation can scroll
761 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
765 <!-- JAL-3002 -->Column display is out by one after Page Down,
766 Page Up in wrapped mode
769 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
772 <!-- JAL-2932 -->Finder searches in minimised alignments
775 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
776 on opening an alignment
779 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
783 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
784 different groups in the alignment are selected
787 <!-- JAL-2717 -->Internationalised colour scheme names not shown
791 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
795 <!-- JAL-3125 -->Value input for graduated feature colour
796 threshold gets 'unrounded'
799 <!-- JAL-2982 -->PCA image export doesn't respect background
803 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
806 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
809 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
813 <!-- JAL-2964 -->Associate Tree with All Views not restored from
817 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
818 shown in complementary view
821 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
822 without normalisation
825 <!-- JAL-3021 -->Sequence Details report should open positioned at top
829 <!-- JAL-914 -->Help page can be opened twice
832 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
834 </ul> <em>Editing</em>
837 <!-- JAL-2822 -->Start and End should be updated when sequence
838 data at beginning or end of alignment added/removed via 'Edit'
842 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
843 relocate sequence features correctly when start of sequence is
844 removed (Known defect since 2.10)
847 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
848 dialog corrupts dataset sequence
851 <!-- JAL-868 -->Structure colours not updated when associated tree
852 repartitions the alignment view (Regression in 2.10.5)
854 </ul> <em>Datamodel</em>
857 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
858 sequence's End is greater than its length
860 </ul> <em>Bugs fixed for Java 11 Support (not yet on
861 general release)</em>
864 <!-- JAL-3288 -->Menus work properly in split-screen
866 </ul> <em>New Known Defects</em>
869 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
872 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
873 regions of protein alignment.
876 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
877 is restored from a Jalview 2.11 project
880 <!-- JAL-3213 -->Alignment panel height can be too small after
884 <!-- JAL-3240 -->Display is incorrect after removing gapped
885 columns within hidden columns
888 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
889 window after dragging left to select columns to left of visible
893 <!-- JAL-2876 -->Features coloured according to their description
894 string and thresholded by score in earlier versions of Jalview are
895 not shown as thresholded features in 2.11. To workaround please
896 create a Score filter instead.
899 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
901 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
904 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
905 alignments with multiple views can close views unexpectedly
908 <em>Java 11 Specific defects</em>
911 <!-- JAL-3235 -->Jalview Properties file is not sorted
912 alphabetically when saved
918 <td width="60" nowrap>
920 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
923 <td><div align="left">
927 <!-- JAL-3101 -->Default memory for Jalview webstart and
928 InstallAnywhere increased to 1G.
931 <!-- JAL-247 -->Hidden sequence markers and representative
932 sequence bolding included when exporting alignment as EPS,
933 SVG, PNG or HTML. <em>Display is configured via the
934 Format menu, or for command-line use via a Jalview
935 properties file.</em>
938 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
939 API and sequence data now imported as JSON.
942 <!-- JAL-3065 -->Change in recommended way of starting
943 Jalview via a Java command line: add jars in lib directory
944 to CLASSPATH, rather than via the deprecated java.ext.dirs
951 <!-- JAL-3047 -->Support added to execute test suite
952 instrumented with <a href="http://openclover.org/">Open
957 <td><div align="left">
961 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
962 row shown in Feredoxin Structure alignment view of example
966 <!-- JAL-2854 -->Annotation obscures sequences if lots of
967 annotation displayed.
970 <!-- JAL-3107 -->Group conservation/consensus not shown
971 for newly created group when 'Apply to all groups'
975 <!-- JAL-3087 -->Corrupted display when switching to
976 wrapped mode when sequence panel's vertical scrollbar is
980 <!-- JAL-3003 -->Alignment is black in exported EPS file
981 when sequences are selected in exported view.</em>
984 <!-- JAL-3059 -->Groups with different coloured borders
985 aren't rendered with correct colour.
988 <!-- JAL-3092 -->Jalview could hang when importing certain
989 types of knotted RNA secondary structure.
992 <!-- JAL-3095 -->Sequence highlight and selection in
993 trimmed VARNA 2D structure is incorrect for sequences that
997 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
998 annotation when columns are inserted into an alignment,
999 and when exporting as Stockholm flatfile.
1002 <!-- JAL-3053 -->Jalview annotation rows containing upper
1003 and lower-case 'E' and 'H' do not automatically get
1004 treated as RNA secondary structure.
1007 <!-- JAL-3106 -->.jvp should be used as default extension
1008 (not .jar) when saving a Jalview project file.
1011 <!-- JAL-3105 -->Mac Users: closing a window correctly
1012 transfers focus to previous window on OSX
1015 <em>Java 10 Issues Resolved</em>
1018 <!-- JAL-2988 -->OSX - Can't save new files via the File
1019 or export menus by typing in a name into the Save dialog
1023 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1024 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1025 'look and feel' which has improved compatibility with the
1026 latest version of OSX.
1033 <td width="60" nowrap>
1034 <div align="center">
1035 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1036 <em>7/06/2018</em></strong>
1039 <td><div align="left">
1043 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1044 annotation retrieved from Uniprot
1047 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1048 onto the Jalview Desktop
1052 <td><div align="left">
1056 <!-- JAL-3017 -->Cannot import features with multiple
1057 variant elements (blocks import of some Uniprot records)
1060 <!-- JAL-2997 -->Clustal files with sequence positions in
1061 right-hand column parsed correctly
1064 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1065 not alignment area in exported graphic
1068 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1069 window has input focus
1072 <!-- JAL-2992 -->Annotation panel set too high when
1073 annotation added to view (Windows)
1076 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1077 network connectivity is poor
1080 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1081 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1082 the currently open URL and links from a page viewed in
1083 Firefox or Chrome on Windows is now fully supported. If
1084 you are using Edge, only links in the page can be
1085 dragged, and with Internet Explorer, only the currently
1086 open URL in the browser can be dropped onto Jalview.</em>
1089 <em>New Known Defects</em>
1091 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1096 <td width="60" nowrap>
1097 <div align="center">
1098 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1101 <td><div align="left">
1105 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1106 for disabling automatic superposition of multiple
1107 structures and open structures in existing views
1110 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1111 ID and annotation area margins can be click-dragged to
1115 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1119 <!-- JAL-2759 -->Improved performance for large alignments
1120 and lots of hidden columns
1123 <!-- JAL-2593 -->Improved performance when rendering lots
1124 of features (particularly when transparency is disabled)
1127 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1128 exchange of Jalview features and Chimera attributes made
1134 <td><div align="left">
1137 <!-- JAL-2899 -->Structure and Overview aren't updated
1138 when Colour By Annotation threshold slider is adjusted
1141 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1142 overlapping alignment panel
1145 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1149 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1150 improved: CDS not handled correctly if transcript has no
1154 <!-- JAL-2321 -->Secondary structure and temperature
1155 factor annotation not added to sequence when local PDB
1156 file associated with it by drag'n'drop or structure
1160 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1161 dialog doesn't import PDB files dropped on an alignment
1164 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1165 scroll bar doesn't work for some CDS/Protein views
1168 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1169 Java 1.8u153 onwards and Java 1.9u4+.
1172 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1173 columns in annotation row
1176 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1177 honored in batch mode
1180 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1181 for structures added to existing Jmol view
1184 <!-- JAL-2223 -->'View Mappings' includes duplicate
1185 entries after importing project with multiple views
1188 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1189 protein sequences via SIFTS from associated PDB entries
1190 with negative residue numbers or missing residues fails
1193 <!-- JAL-2952 -->Exception when shading sequence with negative
1194 Temperature Factor values from annotated PDB files (e.g.
1195 as generated by CONSURF)
1198 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1199 tooltip doesn't include a text description of mutation
1202 <!-- JAL-2922 -->Invert displayed features very slow when
1203 structure and/or overview windows are also shown
1206 <!-- JAL-2954 -->Selecting columns from highlighted regions
1207 very slow for alignments with large numbers of sequences
1210 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1211 with 'StringIndexOutOfBounds'
1214 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1215 platforms running Java 10
1218 <!-- JAL-2960 -->Adding a structure to existing structure
1219 view appears to do nothing because the view is hidden behind the alignment view
1225 <!-- JAL-2926 -->Copy consensus sequence option in applet
1226 should copy the group consensus when popup is opened on it
1232 <!-- JAL-2913 -->Fixed ID width preference is not respected
1235 <em>New Known Defects</em>
1238 <!-- JAL-2973 --> Exceptions occasionally raised when
1239 editing a large alignment and overview is displayed
1242 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1243 repeatedly after a series of edits even when the overview
1244 is no longer reflecting updates
1247 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1248 structures for protein subsequence (if 'Trim Retrieved
1249 Sequences' enabled) or Ensembl isoforms (Workaround in
1250 2.10.4 is to fail back to N&W mapping)
1253 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1254 option gives blank output
1261 <td width="60" nowrap>
1262 <div align="center">
1263 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1266 <td><div align="left">
1267 <ul><li>Updated Certum Codesigning Certificate
1268 (Valid till 30th November 2018)</li></ul></div></td>
1269 <td><div align="left">
1270 <em>Desktop</em><ul>
1272 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1273 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1274 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1275 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1276 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1277 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1278 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1284 <td width="60" nowrap>
1285 <div align="center">
1286 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1289 <td><div align="left">
1293 <!-- JAL-2446 -->Faster and more efficient management and
1294 rendering of sequence features
1297 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1298 429 rate limit request hander
1301 <!-- JAL-2773 -->Structure views don't get updated unless
1302 their colours have changed
1305 <!-- JAL-2495 -->All linked sequences are highlighted for
1306 a structure mousover (Jmol) or selection (Chimera)
1309 <!-- JAL-2790 -->'Cancel' button in progress bar for
1310 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1313 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1314 view from Ensembl locus cross-references
1317 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1321 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1322 feature can be disabled
1325 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1326 PDB easier retrieval of sequences for lists of IDs
1329 <!-- JAL-2758 -->Short names for sequences retrieved from
1335 <li>Groovy interpreter updated to 2.4.12</li>
1336 <li>Example groovy script for generating a matrix of
1337 percent identity scores for current alignment.</li>
1339 <em>Testing and Deployment</em>
1342 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1346 <td><div align="left">
1350 <!-- JAL-2643 -->Pressing tab after updating the colour
1351 threshold text field doesn't trigger an update to the
1355 <!-- JAL-2682 -->Race condition when parsing sequence ID
1359 <!-- JAL-2608 -->Overview windows are also closed when
1360 alignment window is closed
1363 <!-- JAL-2548 -->Export of features doesn't always respect
1367 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1368 takes a long time in Cursor mode
1374 <!-- JAL-2777 -->Structures with whitespace chainCode
1375 cannot be viewed in Chimera
1378 <!-- JAL-2728 -->Protein annotation panel too high in
1382 <!-- JAL-2757 -->Can't edit the query after the server
1383 error warning icon is shown in Uniprot and PDB Free Text
1387 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1390 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1393 <!-- JAL-2739 -->Hidden column marker in last column not
1394 rendered when switching back from Wrapped to normal view
1397 <!-- JAL-2768 -->Annotation display corrupted when
1398 scrolling right in unwapped alignment view
1401 <!-- JAL-2542 -->Existing features on subsequence
1402 incorrectly relocated when full sequence retrieved from
1406 <!-- JAL-2733 -->Last reported memory still shown when
1407 Desktop->Show Memory is unticked (OSX only)
1410 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1411 features of same type and group to be selected for
1415 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1416 alignments when hidden columns are present
1419 <!-- JAL-2392 -->Jalview freezes when loading and
1420 displaying several structures
1423 <!-- JAL-2732 -->Black outlines left after resizing or
1427 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1428 within the Jalview desktop on OSX
1431 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1432 when in wrapped alignment mode
1435 <!-- JAL-2636 -->Scale mark not shown when close to right
1436 hand end of alignment
1439 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1440 each selected sequence do not have correct start/end
1444 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1445 after canceling the Alignment Window's Font dialog
1448 <!-- JAL-2036 -->Show cross-references not enabled after
1449 restoring project until a new view is created
1452 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1453 URL links appears when only default EMBL-EBI link is
1454 configured (since 2.10.2b2)
1457 <!-- JAL-2775 -->Overview redraws whole window when box
1458 position is adjusted
1461 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1462 in a multi-chain structure when viewing alignment
1463 involving more than one chain (since 2.10)
1466 <!-- JAL-2811 -->Double residue highlights in cursor mode
1467 if new selection moves alignment window
1470 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1471 arrow key in cursor mode to pass hidden column marker
1474 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1475 that produces correctly annotated transcripts and products
1478 <!-- JAL-2776 -->Toggling a feature group after first time
1479 doesn't update associated structure view
1482 <em>Applet</em><br />
1485 <!-- JAL-2687 -->Concurrent modification exception when
1486 closing alignment panel
1489 <em>BioJSON</em><br />
1492 <!-- JAL-2546 -->BioJSON export does not preserve
1493 non-positional features
1496 <em>New Known Issues</em>
1499 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1500 sequence features correctly (for many previous versions of
1504 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1505 using cursor in wrapped panel other than top
1508 <!-- JAL-2791 -->Select columns containing feature ignores
1509 graduated colour threshold
1512 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1513 always preserve numbering and sequence features
1516 <em>Known Java 9 Issues</em>
1519 <!-- JAL-2902 -->Groovy Console very slow to open and is
1520 not responsive when entering characters (Webstart, Java
1527 <td width="60" nowrap>
1528 <div align="center">
1529 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1530 <em>2/10/2017</em></strong>
1533 <td><div align="left">
1534 <em>New features in Jalview Desktop</em>
1537 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1539 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1543 <td><div align="left">
1547 <td width="60" nowrap>
1548 <div align="center">
1549 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1550 <em>7/9/2017</em></strong>
1553 <td><div align="left">
1557 <!-- JAL-2588 -->Show gaps in overview window by colouring
1558 in grey (sequences used to be coloured grey, and gaps were
1562 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1566 <!-- JAL-2587 -->Overview updates immediately on increase
1567 in size and progress bar shown as higher resolution
1568 overview is recalculated
1573 <td><div align="left">
1577 <!-- JAL-2664 -->Overview window redraws every hidden
1578 column region row by row
1581 <!-- JAL-2681 -->duplicate protein sequences shown after
1582 retrieving Ensembl crossrefs for sequences from Uniprot
1585 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1586 format setting is unticked
1589 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1590 if group has show boxes format setting unticked
1593 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1594 autoscrolling whilst dragging current selection group to
1595 include sequences and columns not currently displayed
1598 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1599 assemblies are imported via CIF file
1602 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1603 displayed when threshold or conservation colouring is also
1607 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1611 <!-- JAL-2673 -->Jalview continues to scroll after
1612 dragging a selected region off the visible region of the
1616 <!-- JAL-2724 -->Cannot apply annotation based
1617 colourscheme to all groups in a view
1620 <!-- JAL-2511 -->IDs don't line up with sequences
1621 initially after font size change using the Font chooser or
1628 <td width="60" nowrap>
1629 <div align="center">
1630 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1633 <td><div align="left">
1634 <em>Calculations</em>
1638 <!-- JAL-1933 -->Occupancy annotation row shows number of
1639 ungapped positions in each column of the alignment.
1642 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1643 a calculation dialog box
1646 <!-- JAL-2379 -->Revised implementation of PCA for speed
1647 and memory efficiency (~30x faster)
1650 <!-- JAL-2403 -->Revised implementation of sequence
1651 similarity scores as used by Tree, PCA, Shading Consensus
1652 and other calculations
1655 <!-- JAL-2416 -->Score matrices are stored as resource
1656 files within the Jalview codebase
1659 <!-- JAL-2500 -->Trees computed on Sequence Feature
1660 Similarity may have different topology due to increased
1667 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1668 model for alignments and groups
1671 <!-- JAL-384 -->Custom shading schemes created via groovy
1678 <!-- JAL-2526 -->Efficiency improvements for interacting
1679 with alignment and overview windows
1682 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1686 <!-- JAL-2388 -->Hidden columns and sequences can be
1690 <!-- JAL-2611 -->Click-drag in visible area allows fine
1691 adjustment of visible position
1695 <em>Data import/export</em>
1698 <!-- JAL-2535 -->Posterior probability annotation from
1699 Stockholm files imported as sequence associated annotation
1702 <!-- JAL-2507 -->More robust per-sequence positional
1703 annotation input/output via stockholm flatfile
1706 <!-- JAL-2533 -->Sequence names don't include file
1707 extension when importing structure files without embedded
1708 names or PDB accessions
1711 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1712 format sequence substitution matrices
1715 <em>User Interface</em>
1718 <!-- JAL-2447 --> Experimental Features Checkbox in
1719 Desktop's Tools menu to hide or show untested features in
1723 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1724 via Overview or sequence motif search operations
1727 <!-- JAL-2547 -->Amend sequence features dialog box can be
1728 opened by double clicking gaps within sequence feature
1732 <!-- JAL-1476 -->Status bar message shown when not enough
1733 aligned positions were available to create a 3D structure
1737 <em>3D Structure</em>
1740 <!-- JAL-2430 -->Hidden regions in alignment views are not
1741 coloured in linked structure views
1744 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1745 file-based command exchange
1748 <!-- JAL-2375 -->Structure chooser automatically shows
1749 Cached Structures rather than querying the PDBe if
1750 structures are already available for sequences
1753 <!-- JAL-2520 -->Structures imported via URL are cached in
1754 the Jalview project rather than downloaded again when the
1755 project is reopened.
1758 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1759 to transfer Chimera's structure attributes as Jalview
1760 features, and vice-versa (<strong>Experimental
1764 <em>Web Services</em>
1767 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1770 <!-- JAL-2335 -->Filter non-standard amino acids and
1771 nucleotides when submitting to AACon and other MSA
1775 <!-- JAL-2316, -->URLs for viewing database
1776 cross-references provided by identifiers.org and the
1777 EMBL-EBI's MIRIAM DB
1784 <!-- JAL-2344 -->FileFormatI interface for describing and
1785 identifying file formats (instead of String constants)
1788 <!-- JAL-2228 -->FeatureCounter script refactored for
1789 efficiency when counting all displayed features (not
1790 backwards compatible with 2.10.1)
1793 <em>Example files</em>
1796 <!-- JAL-2631 -->Graduated feature colour style example
1797 included in the example feature file
1800 <em>Documentation</em>
1803 <!-- JAL-2339 -->Release notes reformatted for readability
1804 with the built-in Java help viewer
1807 <!-- JAL-1644 -->Find documentation updated with 'search
1808 sequence description' option
1814 <!-- JAL-2485, -->External service integration tests for
1815 Uniprot REST Free Text Search Client
1818 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1821 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1826 <td><div align="left">
1827 <em>Calculations</em>
1830 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1831 matrix - C->R should be '-3'<br />Old matrix restored
1832 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1834 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1835 Jalview's treatment of gaps in PCA and substitution matrix
1836 based Tree calculations.<br /> <br />In earlier versions
1837 of Jalview, gaps matching gaps were penalised, and gaps
1838 matching non-gaps penalised even more. In the PCA
1839 calculation, gaps were actually treated as non-gaps - so
1840 different costs were applied, which meant Jalview's PCAs
1841 were different to those produced by SeqSpace.<br />Jalview
1842 now treats gaps in the same way as SeqSpace (ie it scores
1843 them as 0). <br /> <br />Enter the following in the
1844 Groovy console to restore pre-2.10.2 behaviour:<br />
1845 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1846 // for 2.10.1 mode <br />
1847 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1848 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1849 these settings will affect all subsequent tree and PCA
1850 calculations (not recommended)</em></li>
1852 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1853 scaling of branch lengths for trees computed using
1854 Sequence Feature Similarity.
1857 <!-- JAL-2377 -->PCA calculation could hang when
1858 generating output report when working with highly
1859 redundant alignments
1862 <!-- JAL-2544 --> Sort by features includes features to
1863 right of selected region when gaps present on right-hand
1867 <em>User Interface</em>
1870 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1871 doesn't reselect a specific sequence's associated
1872 annotation after it was used for colouring a view
1875 <!-- JAL-2419 -->Current selection lost if popup menu
1876 opened on a region of alignment without groups
1879 <!-- JAL-2374 -->Popup menu not always shown for regions
1880 of an alignment with overlapping groups
1883 <!-- JAL-2310 -->Finder double counts if both a sequence's
1884 name and description match
1887 <!-- JAL-2370 -->Hiding column selection containing two
1888 hidden regions results in incorrect hidden regions
1891 <!-- JAL-2386 -->'Apply to all groups' setting when
1892 changing colour does not apply Conservation slider value
1896 <!-- JAL-2373 -->Percentage identity and conservation menu
1897 items do not show a tick or allow shading to be disabled
1900 <!-- JAL-2385 -->Conservation shading or PID threshold
1901 lost when base colourscheme changed if slider not visible
1904 <!-- JAL-2547 -->Sequence features shown in tooltip for
1905 gaps before start of features
1908 <!-- JAL-2623 -->Graduated feature colour threshold not
1909 restored to UI when feature colour is edited
1912 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1913 a time when scrolling vertically in wrapped mode.
1916 <!-- JAL-2630 -->Structure and alignment overview update
1917 as graduate feature colour settings are modified via the
1921 <!-- JAL-2034 -->Overview window doesn't always update
1922 when a group defined on the alignment is resized
1925 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1926 wrapped view result in positional status updates
1930 <!-- JAL-2563 -->Status bar doesn't show position for
1931 ambiguous amino acid and nucleotide symbols
1934 <!-- JAL-2602 -->Copy consensus sequence failed if
1935 alignment included gapped columns
1938 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1939 widgets don't permanently disappear
1942 <!-- JAL-2503 -->Cannot select or filter quantitative
1943 annotation that are shown only as column labels (e.g.
1944 T-Coffee column reliability scores)
1947 <!-- JAL-2594 -->Exception thrown if trying to create a
1948 sequence feature on gaps only
1951 <!-- JAL-2504 -->Features created with 'New feature'
1952 button from a Find inherit previously defined feature type
1953 rather than the Find query string
1956 <!-- JAL-2423 -->incorrect title in output window when
1957 exporting tree calculated in Jalview
1960 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1961 and then revealing them reorders sequences on the
1965 <!-- JAL-964 -->Group panel in sequence feature settings
1966 doesn't update to reflect available set of groups after
1967 interactively adding or modifying features
1970 <!-- JAL-2225 -->Sequence Database chooser unusable on
1974 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1975 only excluded gaps in current sequence and ignored
1982 <!-- JAL-2421 -->Overview window visible region moves
1983 erratically when hidden rows or columns are present
1986 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1987 Structure Viewer's colour menu don't correspond to
1991 <!-- JAL-2405 -->Protein specific colours only offered in
1992 colour and group colour menu for protein alignments
1995 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1996 reflect currently selected view or group's shading
2000 <!-- JAL-2624 -->Feature colour thresholds not respected
2001 when rendered on overview and structures when opacity at
2005 <!-- JAL-2589 -->User defined gap colour not shown in
2006 overview when features overlaid on alignment
2009 <!-- JAL-2567 -->Feature settings for different views not
2010 recovered correctly from Jalview project file
2013 <!-- JAL-2256 -->Feature colours in overview when first opened
2014 (automatically via preferences) are different to the main
2018 <em>Data import/export</em>
2021 <!-- JAL-2576 -->Very large alignments take a long time to
2025 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2026 added after a sequence was imported are not written to
2030 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2031 when importing RNA secondary structure via Stockholm
2034 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2035 not shown in correct direction for simple pseudoknots
2038 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2039 with lightGray or darkGray via features file (but can
2043 <!-- JAL-2383 -->Above PID colour threshold not recovered
2044 when alignment view imported from project
2047 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2048 structure and sequences extracted from structure files
2049 imported via URL and viewed in Jmol
2052 <!-- JAL-2520 -->Structures loaded via URL are saved in
2053 Jalview Projects rather than fetched via URL again when
2054 the project is loaded and the structure viewed
2057 <em>Web Services</em>
2060 <!-- JAL-2519 -->EnsemblGenomes example failing after
2061 release of Ensembl v.88
2064 <!-- JAL-2366 -->Proxy server address and port always
2065 appear enabled in Preferences->Connections
2068 <!-- JAL-2461 -->DAS registry not found exceptions
2069 removed from console output
2072 <!-- JAL-2582 -->Cannot retrieve protein products from
2073 Ensembl by Peptide ID
2076 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2077 created from SIFTs, and spurious 'Couldn't open structure
2078 in Chimera' errors raised after April 2017 update (problem
2079 due to 'null' string rather than empty string used for
2080 residues with no corresponding PDB mapping).
2083 <em>Application UI</em>
2086 <!-- JAL-2361 -->User Defined Colours not added to Colour
2090 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2091 case' residues (button in colourscheme editor debugged and
2092 new documentation and tooltips added)
2095 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2096 doesn't restore group-specific text colour thresholds
2099 <!-- JAL-2243 -->Feature settings panel does not update as
2100 new features are added to alignment
2103 <!-- JAL-2532 -->Cancel in feature settings reverts
2104 changes to feature colours via the Amend features dialog
2107 <!-- JAL-2506 -->Null pointer exception when attempting to
2108 edit graduated feature colour via amend features dialog
2112 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2113 selection menu changes colours of alignment views
2116 <!-- JAL-2426 -->Spurious exceptions in console raised
2117 from alignment calculation workers after alignment has
2121 <!-- JAL-1608 -->Typo in selection popup menu - Create
2122 groups now 'Create Group'
2125 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2126 Create/Undefine group doesn't always work
2129 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2130 shown again after pressing 'Cancel'
2133 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2134 adjusts start position in wrap mode
2137 <!-- JAL-2563 -->Status bar doesn't show positions for
2138 ambiguous amino acids
2141 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2142 CDS/Protein view after CDS sequences added for aligned
2146 <!-- JAL-2592 -->User defined colourschemes called 'User
2147 Defined' don't appear in Colours menu
2153 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2154 score models doesn't always result in an updated PCA plot
2157 <!-- JAL-2442 -->Features not rendered as transparent on
2158 overview or linked structure view
2161 <!-- JAL-2372 -->Colour group by conservation doesn't
2165 <!-- JAL-2517 -->Hitting Cancel after applying
2166 user-defined colourscheme doesn't restore original
2173 <!-- JAL-2314 -->Unit test failure:
2174 jalview.ws.jabaws.RNAStructExportImport setup fails
2177 <!-- JAL-2307 -->Unit test failure:
2178 jalview.ws.sifts.SiftsClientTest due to compatibility
2179 problems with deep array comparison equality asserts in
2180 successive versions of TestNG
2183 <!-- JAL-2479 -->Relocated StructureChooserTest and
2184 ParameterUtilsTest Unit tests to Network suite
2187 <em>New Known Issues</em>
2190 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2191 phase after a sequence motif find operation
2194 <!-- JAL-2550 -->Importing annotation file with rows
2195 containing just upper and lower case letters are
2196 interpreted as WUSS RNA secondary structure symbols
2199 <!-- JAL-2590 -->Cannot load and display Newick trees
2200 reliably from eggnog Ortholog database
2203 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2204 containing features of type Highlight' when 'B' is pressed
2205 to mark columns containing highlighted regions.
2208 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2209 doesn't always add secondary structure annotation.
2214 <td width="60" nowrap>
2215 <div align="center">
2216 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2219 <td><div align="left">
2223 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2224 for all consensus calculations
2227 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2230 <li>Updated Jalview's Certum code signing certificate
2233 <em>Application</em>
2236 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2237 set of database cross-references, sorted alphabetically
2240 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2241 from database cross references. Users with custom links
2242 will receive a <a href="webServices/urllinks.html#warning">warning
2243 dialog</a> asking them to update their preferences.
2246 <!-- JAL-2287-->Cancel button and escape listener on
2247 dialog warning user about disconnecting Jalview from a
2251 <!-- JAL-2320-->Jalview's Chimera control window closes if
2252 the Chimera it is connected to is shut down
2255 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2256 columns menu item to mark columns containing highlighted
2257 regions (e.g. from structure selections or results of a
2261 <!-- JAL-2284-->Command line option for batch-generation
2262 of HTML pages rendering alignment data with the BioJS
2272 <!-- JAL-2286 -->Columns with more than one modal residue
2273 are not coloured or thresholded according to percent
2274 identity (first observed in Jalview 2.8.2)
2277 <!-- JAL-2301 -->Threonine incorrectly reported as not
2281 <!-- JAL-2318 -->Updates to documentation pages (above PID
2282 threshold, amino acid properties)
2285 <!-- JAL-2292 -->Lower case residues in sequences are not
2286 reported as mapped to residues in a structure file in the
2290 <!--JAL-2324 -->Identical features with non-numeric scores
2291 could be added multiple times to a sequence
2294 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2295 bond features shown as two highlighted residues rather
2296 than a range in linked structure views, and treated
2297 correctly when selecting and computing trees from features
2300 <!-- JAL-2281-->Custom URL links for database
2301 cross-references are matched to database name regardless
2306 <em>Application</em>
2309 <!-- JAL-2282-->Custom URL links for specific database
2310 names without regular expressions also offer links from
2314 <!-- JAL-2315-->Removing a single configured link in the
2315 URL links pane in Connections preferences doesn't actually
2316 update Jalview configuration
2319 <!-- JAL-2272-->CTRL-Click on a selected region to open
2320 the alignment area popup menu doesn't work on El-Capitan
2323 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2324 files with similarly named sequences if dropped onto the
2328 <!-- JAL-2312 -->Additional mappings are shown for PDB
2329 entries where more chains exist in the PDB accession than
2330 are reported in the SIFTS file
2333 <!-- JAL-2317-->Certain structures do not get mapped to
2334 the structure view when displayed with Chimera
2337 <!-- JAL-2317-->No chains shown in the Chimera view
2338 panel's View->Show Chains submenu
2341 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2342 work for wrapped alignment views
2345 <!--JAL-2197 -->Rename UI components for running JPred
2346 predictions from 'JNet' to 'JPred'
2349 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2350 corrupted when annotation panel vertical scroll is not at
2351 first annotation row
2354 <!--JAL-2332 -->Attempting to view structure for Hen
2355 lysozyme results in a PDB Client error dialog box
2358 <!-- JAL-2319 -->Structure View's mapping report switched
2359 ranges for PDB and sequence for SIFTS
2362 SIFTS 'Not_Observed' residues mapped to non-existant
2366 <!-- <em>New Known Issues</em>
2373 <td width="60" nowrap>
2374 <div align="center">
2375 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2376 <em>25/10/2016</em></strong>
2379 <td><em>Application</em>
2381 <li>3D Structure chooser opens with 'Cached structures'
2382 view if structures already loaded</li>
2383 <li>Progress bar reports models as they are loaded to
2384 structure views</li>
2390 <li>Colour by conservation always enabled and no tick
2391 shown in menu when BLOSUM or PID shading applied</li>
2392 <li>FER1_ARATH and FER2_ARATH labels were switched in
2393 example sequences/projects/trees</li>
2395 <em>Application</em>
2397 <li>Jalview projects with views of local PDB structure
2398 files saved on Windows cannot be opened on OSX</li>
2399 <li>Multiple structure views can be opened and superposed
2400 without timeout for structures with multiple models or
2401 multiple sequences in alignment</li>
2402 <li>Cannot import or associated local PDB files without a
2403 PDB ID HEADER line</li>
2404 <li>RMSD is not output in Jmol console when superposition
2406 <li>Drag and drop of URL from Browser fails for Linux and
2407 OSX versions earlier than El Capitan</li>
2408 <li>ENA client ignores invalid content from ENA server</li>
2409 <li>Exceptions are not raised in console when ENA client
2410 attempts to fetch non-existent IDs via Fetch DB Refs UI
2412 <li>Exceptions are not raised in console when a new view
2413 is created on the alignment</li>
2414 <li>OSX right-click fixed for group selections: CMD-click
2415 to insert/remove gaps in groups and CTRL-click to open group
2418 <em>Build and deployment</em>
2420 <li>URL link checker now copes with multi-line anchor
2423 <em>New Known Issues</em>
2425 <li>Drag and drop from URL links in browsers do not work
2432 <td width="60" nowrap>
2433 <div align="center">
2434 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2437 <td><em>General</em>
2440 <!-- JAL-2124 -->Updated Spanish translations.
2443 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2444 for importing structure data to Jalview. Enables mmCIF and
2448 <!-- JAL-192 --->Alignment ruler shows positions relative to
2452 <!-- JAL-2202 -->Position/residue shown in status bar when
2453 mousing over sequence associated annotation
2456 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2460 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2461 '()', canonical '[]' and invalid '{}' base pair populations
2465 <!-- JAL-2092 -->Feature settings popup menu options for
2466 showing or hiding columns containing a feature
2469 <!-- JAL-1557 -->Edit selected group by double clicking on
2470 group and sequence associated annotation labels
2473 <!-- JAL-2236 -->Sequence name added to annotation label in
2474 select/hide columns by annotation and colour by annotation
2478 </ul> <em>Application</em>
2481 <!-- JAL-2050-->Automatically hide introns when opening a
2482 gene/transcript view
2485 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2489 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2490 structure mappings with the EMBL-EBI PDBe SIFTS database
2493 <!-- JAL-2079 -->Updated download sites used for Rfam and
2494 Pfam sources to xfam.org
2497 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2500 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2501 over sequences in Jalview
2504 <!-- JAL-2027-->Support for reverse-complement coding
2505 regions in ENA and EMBL
2508 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2509 for record retrieval via ENA rest API
2512 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2516 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2517 groovy script execution
2520 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2521 alignment window's Calculate menu
2524 <!-- JAL-1812 -->Allow groovy scripts that call
2525 Jalview.getAlignFrames() to run in headless mode
2528 <!-- JAL-2068 -->Support for creating new alignment
2529 calculation workers from groovy scripts
2532 <!-- JAL-1369 --->Store/restore reference sequence in
2536 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2537 associations are now saved/restored from project
2540 <!-- JAL-1993 -->Database selection dialog always shown
2541 before sequence fetcher is opened
2544 <!-- JAL-2183 -->Double click on an entry in Jalview's
2545 database chooser opens a sequence fetcher
2548 <!-- JAL-1563 -->Free-text search client for UniProt using
2549 the UniProt REST API
2552 <!-- JAL-2168 -->-nonews command line parameter to prevent
2553 the news reader opening
2556 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2557 querying stored in preferences
2560 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2564 <!-- JAL-1977-->Tooltips shown on database chooser
2567 <!-- JAL-391 -->Reverse complement function in calculate
2568 menu for nucleotide sequences
2571 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2572 and feature counts preserves alignment ordering (and
2573 debugged for complex feature sets).
2576 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2577 viewing structures with Jalview 2.10
2580 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2581 genome, transcript CCDS and gene ids via the Ensembl and
2582 Ensembl Genomes REST API
2585 <!-- JAL-2049 -->Protein sequence variant annotation
2586 computed for 'sequence_variant' annotation on CDS regions
2590 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2594 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2595 Ref Fetcher fails to match, or otherwise updates sequence
2596 data from external database records.
2599 <!-- JAL-2154 -->Revised Jalview Project format for
2600 efficient recovery of sequence coding and alignment
2601 annotation relationships.
2603 </ul> <!-- <em>Applet</em>
2614 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2618 <!-- JAL-2018-->Export features in Jalview format (again)
2619 includes graduated colourschemes
2622 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2623 working with big alignments and lots of hidden columns
2626 <!-- JAL-2053-->Hidden column markers not always rendered
2627 at right of alignment window
2630 <!-- JAL-2067 -->Tidied up links in help file table of
2634 <!-- JAL-2072 -->Feature based tree calculation not shown
2638 <!-- JAL-2075 -->Hidden columns ignored during feature
2639 based tree calculation
2642 <!-- JAL-2065 -->Alignment view stops updating when show
2643 unconserved enabled for group on alignment
2646 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2650 <!-- JAL-2146 -->Alignment column in status incorrectly
2651 shown as "Sequence position" when mousing over
2655 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2656 hidden columns present
2659 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2660 user created annotation added to alignment
2663 <!-- JAL-1841 -->RNA Structure consensus only computed for
2664 '()' base pair annotation
2667 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2668 in zero scores for all base pairs in RNA Structure
2672 <!-- JAL-2174-->Extend selection with columns containing
2676 <!-- JAL-2275 -->Pfam format writer puts extra space at
2677 beginning of sequence
2680 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2684 <!-- JAL-2238 -->Cannot create groups on an alignment from
2685 from a tree when t-coffee scores are shown
2688 <!-- JAL-1836,1967 -->Cannot import and view PDB
2689 structures with chains containing negative resnums (4q4h)
2692 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2696 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2697 to Clustal, PIR and PileUp output
2700 <!-- JAL-2008 -->Reordering sequence features that are
2701 not visible causes alignment window to repaint
2704 <!-- JAL-2006 -->Threshold sliders don't work in
2705 graduated colour and colour by annotation row for e-value
2706 scores associated with features and annotation rows
2709 <!-- JAL-1797 -->amino acid physicochemical conservation
2710 calculation should be case independent
2713 <!-- JAL-2173 -->Remove annotation also updates hidden
2717 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2718 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2719 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2722 <!-- JAL-2065 -->Null pointer exceptions and redraw
2723 problems when reference sequence defined and 'show
2724 non-conserved' enabled
2727 <!-- JAL-1306 -->Quality and Conservation are now shown on
2728 load even when Consensus calculation is disabled
2731 <!-- JAL-1932 -->Remove right on penultimate column of
2732 alignment does nothing
2735 <em>Application</em>
2738 <!-- JAL-1552-->URLs and links can't be imported by
2739 drag'n'drop on OSX when launched via webstart (note - not
2740 yet fixed for El Capitan)
2743 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2744 output when running on non-gb/us i18n platforms
2747 <!-- JAL-1944 -->Error thrown when exporting a view with
2748 hidden sequences as flat-file alignment
2751 <!-- JAL-2030-->InstallAnywhere distribution fails when
2755 <!-- JAL-2080-->Jalview very slow to launch via webstart
2756 (also hotfix for 2.9.0b2)
2759 <!-- JAL-2085 -->Cannot save project when view has a
2760 reference sequence defined
2763 <!-- JAL-1011 -->Columns are suddenly selected in other
2764 alignments and views when revealing hidden columns
2767 <!-- JAL-1989 -->Hide columns not mirrored in complement
2768 view in a cDNA/Protein splitframe
2771 <!-- JAL-1369 -->Cannot save/restore representative
2772 sequence from project when only one sequence is
2776 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2777 in Structure Chooser
2780 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2781 structure consensus didn't refresh annotation panel
2784 <!-- JAL-1962 -->View mapping in structure view shows
2785 mappings between sequence and all chains in a PDB file
2788 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2789 dialogs format columns correctly, don't display array
2790 data, sort columns according to type
2793 <!-- JAL-1975 -->Export complete shown after destination
2794 file chooser is cancelled during an image export
2797 <!-- JAL-2025 -->Error when querying PDB Service with
2798 sequence name containing special characters
2801 <!-- JAL-2024 -->Manual PDB structure querying should be
2805 <!-- JAL-2104 -->Large tooltips with broken HTML
2806 formatting don't wrap
2809 <!-- JAL-1128 -->Figures exported from wrapped view are
2810 truncated so L looks like I in consensus annotation
2813 <!-- JAL-2003 -->Export features should only export the
2814 currently displayed features for the current selection or
2818 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2819 after fetching cross-references, and restoring from
2823 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2824 followed in the structure viewer
2827 <!-- JAL-2163 -->Titles for individual alignments in
2828 splitframe not restored from project
2831 <!-- JAL-2145 -->missing autocalculated annotation at
2832 trailing end of protein alignment in transcript/product
2833 splitview when pad-gaps not enabled by default
2836 <!-- JAL-1797 -->amino acid physicochemical conservation
2840 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2841 article has been read (reopened issue due to
2842 internationalisation problems)
2845 <!-- JAL-1960 -->Only offer PDB structures in structure
2846 viewer based on sequence name, PDB and UniProt
2851 <!-- JAL-1976 -->No progress bar shown during export of
2855 <!-- JAL-2213 -->Structures not always superimposed after
2856 multiple structures are shown for one or more sequences.
2859 <!-- JAL-1370 -->Reference sequence characters should not
2860 be replaced with '.' when 'Show unconserved' format option
2864 <!-- JAL-1823 -->Cannot specify chain code when entering
2865 specific PDB id for sequence
2868 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2869 'Export hidden sequences' is enabled, but 'export hidden
2870 columns' is disabled.
2873 <!--JAL-2026-->Best Quality option in structure chooser
2874 selects lowest rather than highest resolution structures
2878 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2879 to sequence mapping in 'View Mappings' report
2882 <!-- JAL-2284 -->Unable to read old Jalview projects that
2883 contain non-XML data added after Jalvew wrote project.
2886 <!-- JAL-2118 -->Newly created annotation row reorders
2887 after clicking on it to create new annotation for a
2891 <!-- JAL-1980 -->Null Pointer Exception raised when
2892 pressing Add on an orphaned cut'n'paste window.
2894 <!-- may exclude, this is an external service stability issue JAL-1941
2895 -- > RNA 3D structure not added via DSSR service</li> -->
2900 <!-- JAL-2151 -->Incorrect columns are selected when
2901 hidden columns present before start of sequence
2904 <!-- JAL-1986 -->Missing dependencies on applet pages
2908 <!-- JAL-1947 -->Overview pixel size changes when
2909 sequences are hidden in applet
2912 <!-- JAL-1996 -->Updated instructions for applet
2913 deployment on examples pages.
2920 <td width="60" nowrap>
2921 <div align="center">
2922 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2923 <em>16/10/2015</em></strong>
2926 <td><em>General</em>
2928 <li>Time stamps for signed Jalview application and applet
2933 <em>Application</em>
2935 <li>Duplicate group consensus and conservation rows
2936 shown when tree is partitioned</li>
2937 <li>Erratic behaviour when tree partitions made with
2938 multiple cDNA/Protein split views</li>
2944 <td width="60" nowrap>
2945 <div align="center">
2946 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2947 <em>8/10/2015</em></strong>
2950 <td><em>General</em>
2952 <li>Updated Spanish translations of localized text for
2954 </ul> <em>Application</em>
2956 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2957 <li>Signed OSX InstallAnywhere installer<br></li>
2958 <li>Support for per-sequence based annotations in BioJSON</li>
2959 </ul> <em>Applet</em>
2961 <li>Split frame example added to applet examples page</li>
2962 </ul> <em>Build and Deployment</em>
2965 <!-- JAL-1888 -->New ant target for running Jalview's test
2973 <li>Mapping of cDNA to protein in split frames
2974 incorrect when sequence start > 1</li>
2975 <li>Broken images in filter column by annotation dialog
2977 <li>Feature colours not parsed from features file</li>
2978 <li>Exceptions and incomplete link URLs recovered when
2979 loading a features file containing HTML tags in feature
2983 <em>Application</em>
2985 <li>Annotations corrupted after BioJS export and
2987 <li>Incorrect sequence limits after Fetch DB References
2988 with 'trim retrieved sequences'</li>
2989 <li>Incorrect warning about deleting all data when
2990 deleting selected columns</li>
2991 <li>Patch to build system for shipping properly signed
2992 JNLP templates for webstart launch</li>
2993 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2994 unreleased structures for download or viewing</li>
2995 <li>Tab/space/return keystroke operation of EMBL-PDBe
2996 fetcher/viewer dialogs works correctly</li>
2997 <li>Disabled 'minimise' button on Jalview windows
2998 running on OSX to workaround redraw hang bug</li>
2999 <li>Split cDNA/Protein view position and geometry not
3000 recovered from jalview project</li>
3001 <li>Initial enabled/disabled state of annotation menu
3002 sorter 'show autocalculated first/last' corresponds to
3004 <li>Restoring of Clustal, RNA Helices and T-Coffee
3005 color schemes from BioJSON</li>
3009 <li>Reorder sequences mirrored in cDNA/Protein split
3011 <li>Applet with Jmol examples not loading correctly</li>
3017 <td><div align="center">
3018 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3020 <td><em>General</em>
3022 <li>Linked visualisation and analysis of DNA and Protein
3025 <li>Translated cDNA alignments shown as split protein
3026 and DNA alignment views</li>
3027 <li>Codon consensus annotation for linked protein and
3028 cDNA alignment views</li>
3029 <li>Link cDNA or Protein product sequences by loading
3030 them onto Protein or cDNA alignments</li>
3031 <li>Reconstruct linked cDNA alignment from aligned
3032 protein sequences</li>
3035 <li>Jmol integration updated to Jmol v14.2.14</li>
3036 <li>Import and export of Jalview alignment views as <a
3037 href="features/bioJsonFormat.html">BioJSON</a></li>
3038 <li>New alignment annotation file statements for
3039 reference sequences and marking hidden columns</li>
3040 <li>Reference sequence based alignment shading to
3041 highlight variation</li>
3042 <li>Select or hide columns according to alignment
3044 <li>Find option for locating sequences by description</li>
3045 <li>Conserved physicochemical properties shown in amino
3046 acid conservation row</li>
3047 <li>Alignments can be sorted by number of RNA helices</li>
3048 </ul> <em>Application</em>
3050 <li>New cDNA/Protein analysis capabilities
3052 <li>Get Cross-References should open a Split Frame
3053 view with cDNA/Protein</li>
3054 <li>Detect when nucleotide sequences and protein
3055 sequences are placed in the same alignment</li>
3056 <li>Split cDNA/Protein views are saved in Jalview
3061 <li>Use REST API to talk to Chimera</li>
3062 <li>Selected regions in Chimera are highlighted in linked
3063 Jalview windows</li>
3065 <li>VARNA RNA viewer updated to v3.93</li>
3066 <li>VARNA views are saved in Jalview Projects</li>
3067 <li>Pseudoknots displayed as Jalview RNA annotation can
3068 be shown in VARNA</li>
3070 <li>Make groups for selection uses marked columns as well
3071 as the active selected region</li>
3073 <li>Calculate UPGMA and NJ trees using sequence feature
3075 <li>New Export options
3077 <li>New Export Settings dialog to control hidden
3078 region export in flat file generation</li>
3080 <li>Export alignment views for display with the <a
3081 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3083 <li>Export scrollable SVG in HTML page</li>
3084 <li>Optional embedding of BioJSON data when exporting
3085 alignment figures to HTML</li>
3087 <li>3D structure retrieval and display
3089 <li>Free text and structured queries with the PDBe
3091 <li>PDBe Search API based discovery and selection of
3092 PDB structures for a sequence set</li>
3096 <li>JPred4 employed for protein secondary structure
3098 <li>Hide Insertions menu option to hide unaligned columns
3099 for one or a group of sequences</li>
3100 <li>Automatically hide insertions in alignments imported
3101 from the JPred4 web server</li>
3102 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3103 system on OSX<br />LGPL libraries courtesy of <a
3104 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3106 <li>changed 'View nucleotide structure' submenu to 'View
3107 VARNA 2D Structure'</li>
3108 <li>change "View protein structure" menu option to "3D
3111 </ul> <em>Applet</em>
3113 <li>New layout for applet example pages</li>
3114 <li>New parameters to enable SplitFrame view
3115 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3116 <li>New example demonstrating linked viewing of cDNA and
3117 Protein alignments</li>
3118 </ul> <em>Development and deployment</em>
3120 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3121 <li>Include installation type and git revision in build
3122 properties and console log output</li>
3123 <li>Jalview Github organisation, and new github site for
3124 storing BioJsMSA Templates</li>
3125 <li>Jalview's unit tests now managed with TestNG</li>
3128 <!-- <em>General</em>
3130 </ul> --> <!-- issues resolved --> <em>Application</em>
3132 <li>Escape should close any open find dialogs</li>
3133 <li>Typo in select-by-features status report</li>
3134 <li>Consensus RNA secondary secondary structure
3135 predictions are not highlighted in amber</li>
3136 <li>Missing gap character in v2.7 example file means
3137 alignment appears unaligned when pad-gaps is not enabled</li>
3138 <li>First switch to RNA Helices colouring doesn't colour
3139 associated structure views</li>
3140 <li>ID width preference option is greyed out when auto
3141 width checkbox not enabled</li>
3142 <li>Stopped a warning dialog from being shown when
3143 creating user defined colours</li>
3144 <li>'View Mapping' in structure viewer shows sequence
3145 mappings for just that viewer's sequences</li>
3146 <li>Workaround for superposing PDB files containing
3147 multiple models in Chimera</li>
3148 <li>Report sequence position in status bar when hovering
3149 over Jmol structure</li>
3150 <li>Cannot output gaps as '.' symbols with Selection ->
3151 output to text box</li>
3152 <li>Flat file exports of alignments with hidden columns
3153 have incorrect sequence start/end</li>
3154 <li>'Aligning' a second chain to a Chimera structure from
3156 <li>Colour schemes applied to structure viewers don't
3157 work for nucleotide</li>
3158 <li>Loading/cut'n'pasting an empty or invalid file leads
3159 to a grey/invisible alignment window</li>
3160 <li>Exported Jpred annotation from a sequence region
3161 imports to different position</li>
3162 <li>Space at beginning of sequence feature tooltips shown
3163 on some platforms</li>
3164 <li>Chimera viewer 'View | Show Chain' menu is not
3166 <li>'New View' fails with a Null Pointer Exception in
3167 console if Chimera has been opened</li>
3168 <li>Mouseover to Chimera not working</li>
3169 <li>Miscellaneous ENA XML feature qualifiers not
3171 <li>NPE in annotation renderer after 'Extract Scores'</li>
3172 <li>If two structures in one Chimera window, mouseover of
3173 either sequence shows on first structure</li>
3174 <li>'Show annotations' options should not make
3175 non-positional annotations visible</li>
3176 <li>Subsequence secondary structure annotation not shown
3177 in right place after 'view flanking regions'</li>
3178 <li>File Save As type unset when current file format is
3180 <li>Save as '.jar' option removed for saving Jalview
3182 <li>Colour by Sequence colouring in Chimera more
3184 <li>Cannot 'add reference annotation' for a sequence in
3185 several views on same alignment</li>
3186 <li>Cannot show linked products for EMBL / ENA records</li>
3187 <li>Jalview's tooltip wraps long texts containing no
3189 </ul> <em>Applet</em>
3191 <li>Jmol to JalviewLite mouseover/link not working</li>
3192 <li>JalviewLite can't import sequences with ID
3193 descriptions containing angle brackets</li>
3194 </ul> <em>General</em>
3196 <li>Cannot export and reimport RNA secondary structure
3197 via jalview annotation file</li>
3198 <li>Random helix colour palette for colour by annotation
3199 with RNA secondary structure</li>
3200 <li>Mouseover to cDNA from STOP residue in protein
3201 translation doesn't work.</li>
3202 <li>hints when using the select by annotation dialog box</li>
3203 <li>Jmol alignment incorrect if PDB file has alternate CA
3205 <li>FontChooser message dialog appears to hang after
3206 choosing 1pt font</li>
3207 <li>Peptide secondary structure incorrectly imported from
3208 annotation file when annotation display text includes 'e' or
3210 <li>Cannot set colour of new feature type whilst creating
3212 <li>cDNA translation alignment should not be sequence
3213 order dependent</li>
3214 <li>'Show unconserved' doesn't work for lower case
3216 <li>Nucleotide ambiguity codes involving R not recognised</li>
3217 </ul> <em>Deployment and Documentation</em>
3219 <li>Applet example pages appear different to the rest of
3220 www.jalview.org</li>
3221 </ul> <em>Application Known issues</em>
3223 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3224 <li>Misleading message appears after trying to delete
3226 <li>Jalview icon not shown in dock after InstallAnywhere
3227 version launches</li>
3228 <li>Fetching EMBL reference for an RNA sequence results
3229 fails with a sequence mismatch</li>
3230 <li>Corrupted or unreadable alignment display when
3231 scrolling alignment to right</li>
3232 <li>ArrayIndexOutOfBoundsException thrown when remove
3233 empty columns called on alignment with ragged gapped ends</li>
3234 <li>auto calculated alignment annotation rows do not get
3235 placed above or below non-autocalculated rows</li>
3236 <li>Jalview dekstop becomes sluggish at full screen in
3237 ultra-high resolution</li>
3238 <li>Cannot disable consensus calculation independently of
3239 quality and conservation</li>
3240 <li>Mouseover highlighting between cDNA and protein can
3241 become sluggish with more than one splitframe shown</li>
3242 </ul> <em>Applet Known Issues</em>
3244 <li>Core PDB parsing code requires Jmol</li>
3245 <li>Sequence canvas panel goes white when alignment
3246 window is being resized</li>
3252 <td><div align="center">
3253 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3255 <td><em>General</em>
3257 <li>Updated Java code signing certificate donated by
3259 <li>Features and annotation preserved when performing
3260 pairwise alignment</li>
3261 <li>RNA pseudoknot annotation can be
3262 imported/exported/displayed</li>
3263 <li>'colour by annotation' can colour by RNA and
3264 protein secondary structure</li>
3265 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3266 post-hoc with 2.9 release</em>)
3269 </ul> <em>Application</em>
3271 <li>Extract and display secondary structure for sequences
3272 with 3D structures</li>
3273 <li>Support for parsing RNAML</li>
3274 <li>Annotations menu for layout
3276 <li>sort sequence annotation rows by alignment</li>
3277 <li>place sequence annotation above/below alignment
3280 <li>Output in Stockholm format</li>
3281 <li>Internationalisation: improved Spanish (es)
3283 <li>Structure viewer preferences tab</li>
3284 <li>Disorder and Secondary Structure annotation tracks
3285 shared between alignments</li>
3286 <li>UCSF Chimera launch and linked highlighting from
3288 <li>Show/hide all sequence associated annotation rows for
3289 all or current selection</li>
3290 <li>disorder and secondary structure predictions
3291 available as dataset annotation</li>
3292 <li>Per-sequence rna helices colouring</li>
3295 <li>Sequence database accessions imported when fetching
3296 alignments from Rfam</li>
3297 <li>update VARNA version to 3.91</li>
3299 <li>New groovy scripts for exporting aligned positions,
3300 conservation values, and calculating sum of pairs scores.</li>
3301 <li>Command line argument to set default JABAWS server</li>
3302 <li>include installation type in build properties and
3303 console log output</li>
3304 <li>Updated Jalview project format to preserve dataset
3308 <!-- issues resolved --> <em>Application</em>
3310 <li>Distinguish alignment and sequence associated RNA
3311 structure in structure->view->VARNA</li>
3312 <li>Raise dialog box if user deletes all sequences in an
3314 <li>Pressing F1 results in documentation opening twice</li>
3315 <li>Sequence feature tooltip is wrapped</li>
3316 <li>Double click on sequence associated annotation
3317 selects only first column</li>
3318 <li>Redundancy removal doesn't result in unlinked
3319 leaves shown in tree</li>
3320 <li>Undos after several redundancy removals don't undo
3322 <li>Hide sequence doesn't hide associated annotation</li>
3323 <li>User defined colours dialog box too big to fit on
3324 screen and buttons not visible</li>
3325 <li>author list isn't updated if already written to
3326 Jalview properties</li>
3327 <li>Popup menu won't open after retrieving sequence
3329 <li>File open window for associate PDB doesn't open</li>
3330 <li>Left-then-right click on a sequence id opens a
3331 browser search window</li>
3332 <li>Cannot open sequence feature shading/sort popup menu
3333 in feature settings dialog</li>
3334 <li>better tooltip placement for some areas of Jalview
3336 <li>Allow addition of JABAWS Server which doesn't
3337 pass validation</li>
3338 <li>Web services parameters dialog box is too large to
3340 <li>Muscle nucleotide alignment preset obscured by
3342 <li>JABAWS preset submenus don't contain newly
3343 defined user preset</li>
3344 <li>MSA web services warns user if they were launched
3345 with invalid input</li>
3346 <li>Jalview cannot contact DAS Registy when running on
3349 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3350 'Superpose with' submenu not shown when new view
3354 </ul> <!-- <em>Applet</em>
3356 </ul> <em>General</em>
3358 </ul>--> <em>Deployment and Documentation</em>
3360 <li>2G and 1G options in launchApp have no effect on
3361 memory allocation</li>
3362 <li>launchApp service doesn't automatically open
3363 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3365 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3366 InstallAnywhere reports cannot find valid JVM when Java
3367 1.7_055 is available
3369 </ul> <em>Application Known issues</em>
3372 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3373 corrupted or unreadable alignment display when scrolling
3377 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3378 retrieval fails but progress bar continues for DAS retrieval
3379 with large number of ID
3382 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3383 flatfile output of visible region has incorrect sequence
3387 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3388 rna structure consensus doesn't update when secondary
3389 structure tracks are rearranged
3392 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3393 invalid rna structure positional highlighting does not
3394 highlight position of invalid base pairs
3397 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3398 out of memory errors are not raised when saving Jalview
3399 project from alignment window file menu
3402 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3403 Switching to RNA Helices colouring doesn't propagate to
3407 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3408 colour by RNA Helices not enabled when user created
3409 annotation added to alignment
3412 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3413 Jalview icon not shown on dock in Mountain Lion/Webstart
3415 </ul> <em>Applet Known Issues</em>
3418 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3419 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3422 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3423 Jalview and Jmol example not compatible with IE9
3426 <li>Sort by annotation score doesn't reverse order
3432 <td><div align="center">
3433 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3436 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3439 <li>Internationalisation of user interface (usually
3440 called i18n support) and translation for Spanish locale</li>
3441 <li>Define/Undefine group on current selection with
3442 Ctrl-G/Shift Ctrl-G</li>
3443 <li>Improved group creation/removal options in
3444 alignment/sequence Popup menu</li>
3445 <li>Sensible precision for symbol distribution
3446 percentages shown in logo tooltip.</li>
3447 <li>Annotation panel height set according to amount of
3448 annotation when alignment first opened</li>
3449 </ul> <em>Application</em>
3451 <li>Interactive consensus RNA secondary structure
3452 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3453 <li>Select columns containing particular features from
3454 Feature Settings dialog</li>
3455 <li>View all 'representative' PDB structures for selected
3457 <li>Update Jalview project format:
3459 <li>New file extension for Jalview projects '.jvp'</li>
3460 <li>Preserve sequence and annotation dataset (to
3461 store secondary structure annotation,etc)</li>
3462 <li>Per group and alignment annotation and RNA helix
3466 <li>New similarity measures for PCA and Tree calculation
3468 <li>Experimental support for retrieval and viewing of
3469 flanking regions for an alignment</li>
3473 <!-- issues resolved --> <em>Application</em>
3475 <li>logo keeps spinning and status remains at queued or
3476 running after job is cancelled</li>
3477 <li>cannot export features from alignments imported from
3478 Jalview/VAMSAS projects</li>
3479 <li>Buggy slider for web service parameters that take
3481 <li>Newly created RNA secondary structure line doesn't
3482 have 'display all symbols' flag set</li>
3483 <li>T-COFFEE alignment score shading scheme and other
3484 annotation shading not saved in Jalview project</li>
3485 <li>Local file cannot be loaded in freshly downloaded
3487 <li>Jalview icon not shown on dock in Mountain
3489 <li>Load file from desktop file browser fails</li>
3490 <li>Occasional NPE thrown when calculating large trees</li>
3491 <li>Cannot reorder or slide sequences after dragging an
3492 alignment onto desktop</li>
3493 <li>Colour by annotation dialog throws NPE after using
3494 'extract scores' function</li>
3495 <li>Loading/cut'n'pasting an empty file leads to a grey
3496 alignment window</li>
3497 <li>Disorder thresholds rendered incorrectly after
3498 performing IUPred disorder prediction</li>
3499 <li>Multiple group annotated consensus rows shown when
3500 changing 'normalise logo' display setting</li>
3501 <li>Find shows blank dialog after 'finished searching' if
3502 nothing matches query</li>
3503 <li>Null Pointer Exceptions raised when sorting by
3504 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3506 <li>Errors in Jmol console when structures in alignment
3507 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3509 <li>Not all working JABAWS services are shown in
3511 <li>JAVAWS version of Jalview fails to launch with
3512 'invalid literal/length code'</li>
3513 <li>Annotation/RNA Helix colourschemes cannot be applied
3514 to alignment with groups (actually fixed in 2.8.0b1)</li>
3515 <li>RNA Helices and T-Coffee Scores available as default
3518 </ul> <em>Applet</em>
3520 <li>Remove group option is shown even when selection is
3522 <li>Apply to all groups ticked but colourscheme changes
3523 don't affect groups</li>
3524 <li>Documented RNA Helices and T-Coffee Scores as valid
3525 colourscheme name</li>
3526 <li>Annotation labels drawn on sequence IDs when
3527 Annotation panel is not displayed</li>
3528 <li>Increased font size for dropdown menus on OSX and
3529 embedded windows</li>
3530 </ul> <em>Other</em>
3532 <li>Consensus sequence for alignments/groups with a
3533 single sequence were not calculated</li>
3534 <li>annotation files that contain only groups imported as
3535 annotation and junk sequences</li>
3536 <li>Fasta files with sequences containing '*' incorrectly
3537 recognised as PFAM or BLC</li>
3538 <li>conservation/PID slider apply all groups option
3539 doesn't affect background (2.8.0b1)
3541 <li>redundancy highlighting is erratic at 0% and 100%</li>
3542 <li>Remove gapped columns fails for sequences with ragged
3544 <li>AMSA annotation row with leading spaces is not
3545 registered correctly on import</li>
3546 <li>Jalview crashes when selecting PCA analysis for
3547 certain alignments</li>
3548 <li>Opening the colour by annotation dialog for an
3549 existing annotation based 'use original colours'
3550 colourscheme loses original colours setting</li>
3555 <td><div align="center">
3556 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3557 <em>30/1/2014</em></strong>
3561 <li>Trusted certificates for JalviewLite applet and
3562 Jalview Desktop application<br />Certificate was donated by
3563 <a href="https://www.certum.eu">Certum</a> to the Jalview
3564 open source project).
3566 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3567 <li>Output in Stockholm format</li>
3568 <li>Allow import of data from gzipped files</li>
3569 <li>Export/import group and sequence associated line
3570 graph thresholds</li>
3571 <li>Nucleotide substitution matrix that supports RNA and
3572 ambiguity codes</li>
3573 <li>Allow disorder predictions to be made on the current
3574 selection (or visible selection) in the same way that JPred
3576 <li>Groovy scripting for headless Jalview operation</li>
3577 </ul> <em>Other improvements</em>
3579 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3580 <li>COMBINE statement uses current SEQUENCE_REF and
3581 GROUP_REF scope to group annotation rows</li>
3582 <li>Support '' style escaping of quotes in Newick
3584 <li>Group options for JABAWS service by command line name</li>
3585 <li>Empty tooltip shown for JABA service options with a
3586 link but no description</li>
3587 <li>Select primary source when selecting authority in
3588 database fetcher GUI</li>
3589 <li>Add .mfa to FASTA file extensions recognised by
3591 <li>Annotation label tooltip text wrap</li>
3596 <li>Slow scrolling when lots of annotation rows are
3598 <li>Lots of NPE (and slowness) after creating RNA
3599 secondary structure annotation line</li>
3600 <li>Sequence database accessions not imported when
3601 fetching alignments from Rfam</li>
3602 <li>Incorrect SHMR submission for sequences with
3604 <li>View all structures does not always superpose
3606 <li>Option widgets in service parameters not updated to
3607 reflect user or preset settings</li>
3608 <li>Null pointer exceptions for some services without
3609 presets or adjustable parameters</li>
3610 <li>Discover PDB IDs entry in structure menu doesn't
3611 discover PDB xRefs</li>
3612 <li>Exception encountered while trying to retrieve
3613 features with DAS</li>
3614 <li>Lowest value in annotation row isn't coloured
3615 when colour by annotation (per sequence) is coloured</li>
3616 <li>Keyboard mode P jumps to start of gapped region when
3617 residue follows a gap</li>
3618 <li>Jalview appears to hang importing an alignment with
3619 Wrap as default or after enabling Wrap</li>
3620 <li>'Right click to add annotations' message
3621 shown in wrap mode when no annotations present</li>
3622 <li>Disorder predictions fail with NPE if no automatic
3623 annotation already exists on alignment</li>
3624 <li>oninit javascript function should be called after
3625 initialisation completes</li>
3626 <li>Remove redundancy after disorder prediction corrupts
3627 alignment window display</li>
3628 <li>Example annotation file in documentation is invalid</li>
3629 <li>Grouped line graph annotation rows are not exported
3630 to annotation file</li>
3631 <li>Multi-harmony analysis cannot be run when only two
3633 <li>Cannot create multiple groups of line graphs with
3634 several 'combine' statements in annotation file</li>
3635 <li>Pressing return several times causes Number Format
3636 exceptions in keyboard mode</li>
3637 <li>Multi-harmony (SHMMR) method doesn't submit
3638 correct partitions for input data</li>
3639 <li>Translation from DNA to Amino Acids fails</li>
3640 <li>Jalview fail to load newick tree with quoted label</li>
3641 <li>--headless flag isn't understood</li>
3642 <li>ClassCastException when generating EPS in headless
3644 <li>Adjusting sequence-associated shading threshold only
3645 changes one row's threshold</li>
3646 <li>Preferences and Feature settings panel panel
3647 doesn't open</li>
3648 <li>hide consensus histogram also hides conservation and
3649 quality histograms</li>
3654 <td><div align="center">
3655 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3657 <td><em>Application</em>
3659 <li>Support for JABAWS 2.0 Services (AACon alignment
3660 conservation, protein disorder and Clustal Omega)</li>
3661 <li>JABAWS server status indicator in Web Services
3663 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3664 in Jalview alignment window</li>
3665 <li>Updated Jalview build and deploy framework for OSX
3666 mountain lion, windows 7, and 8</li>
3667 <li>Nucleotide substitution matrix for PCA that supports
3668 RNA and ambiguity codes</li>
3670 <li>Improved sequence database retrieval GUI</li>
3671 <li>Support fetching and database reference look up
3672 against multiple DAS sources (Fetch all from in 'fetch db
3674 <li>Jalview project improvements
3676 <li>Store and retrieve the 'belowAlignment'
3677 flag for annotation</li>
3678 <li>calcId attribute to group annotation rows on the
3680 <li>Store AACon calculation settings for a view in
3681 Jalview project</li>
3685 <li>horizontal scrolling gesture support</li>
3686 <li>Visual progress indicator when PCA calculation is
3688 <li>Simpler JABA web services menus</li>
3689 <li>visual indication that web service results are still
3690 being retrieved from server</li>
3691 <li>Serialise the dialogs that are shown when Jalview
3692 starts up for first time</li>
3693 <li>Jalview user agent string for interacting with HTTP
3695 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3697 <li>Examples directory and Groovy library included in
3698 InstallAnywhere distribution</li>
3699 </ul> <em>Applet</em>
3701 <li>RNA alignment and secondary structure annotation
3702 visualization applet example</li>
3703 </ul> <em>General</em>
3705 <li>Normalise option for consensus sequence logo</li>
3706 <li>Reset button in PCA window to return dimensions to
3708 <li>Allow seqspace or Jalview variant of alignment PCA
3710 <li>PCA with either nucleic acid and protein substitution
3712 <li>Allow windows containing HTML reports to be exported
3714 <li>Interactive display and editing of RNA secondary
3715 structure contacts</li>
3716 <li>RNA Helix Alignment Colouring</li>
3717 <li>RNA base pair logo consensus</li>
3718 <li>Parse sequence associated secondary structure
3719 information in Stockholm files</li>
3720 <li>HTML Export database accessions and annotation
3721 information presented in tooltip for sequences</li>
3722 <li>Import secondary structure from LOCARNA clustalw
3723 style RNA alignment files</li>
3724 <li>import and visualise T-COFFEE quality scores for an
3726 <li>'colour by annotation' per sequence option to
3727 shade each sequence according to its associated alignment
3729 <li>New Jalview Logo</li>
3730 </ul> <em>Documentation and Development</em>
3732 <li>documentation for score matrices used in Jalview</li>
3733 <li>New Website!</li>
3735 <td><em>Application</em>
3737 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3738 wsdbfetch REST service</li>
3739 <li>Stop windows being moved outside desktop on OSX</li>
3740 <li>Filetype associations not installed for webstart
3742 <li>Jalview does not always retrieve progress of a JABAWS
3743 job execution in full once it is complete</li>
3744 <li>revise SHMR RSBS definition to ensure alignment is
3745 uploaded via ali_file parameter</li>
3746 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3747 <li>View all structures superposed fails with exception</li>
3748 <li>Jnet job queues forever if a very short sequence is
3749 submitted for prediction</li>
3750 <li>Cut and paste menu not opened when mouse clicked on
3752 <li>Putting fractional value into integer text box in
3753 alignment parameter dialog causes Jalview to hang</li>
3754 <li>Structure view highlighting doesn't work on
3756 <li>View all structures fails with exception shown in
3758 <li>Characters in filename associated with PDBEntry not
3759 escaped in a platform independent way</li>
3760 <li>Jalview desktop fails to launch with exception when
3762 <li>Tree calculation reports 'you must have 2 or more
3763 sequences selected' when selection is empty</li>
3764 <li>Jalview desktop fails to launch with jar signature
3765 failure when java web start temporary file caching is
3767 <li>DAS Sequence retrieval with range qualification
3768 results in sequence xref which includes range qualification</li>
3769 <li>Errors during processing of command line arguments
3770 cause progress bar (JAL-898) to be removed</li>
3771 <li>Replace comma for semi-colon option not disabled for
3772 DAS sources in sequence fetcher</li>
3773 <li>Cannot close news reader when JABAWS server warning
3774 dialog is shown</li>
3775 <li>Option widgets not updated to reflect user settings</li>
3776 <li>Edited sequence not submitted to web service</li>
3777 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3778 <li>InstallAnywhere installer doesn't unpack and run
3779 on OSX Mountain Lion</li>
3780 <li>Annotation panel not given a scroll bar when
3781 sequences with alignment annotation are pasted into the
3783 <li>Sequence associated annotation rows not associated
3784 when loaded from Jalview project</li>
3785 <li>Browser launch fails with NPE on java 1.7</li>
3786 <li>JABAWS alignment marked as finished when job was
3787 cancelled or job failed due to invalid input</li>
3788 <li>NPE with v2.7 example when clicking on Tree
3789 associated with all views</li>
3790 <li>Exceptions when copy/paste sequences with grouped
3791 annotation rows to new window</li>
3792 </ul> <em>Applet</em>
3794 <li>Sequence features are momentarily displayed before
3795 they are hidden using hidefeaturegroups applet parameter</li>
3796 <li>loading features via javascript API automatically
3797 enables feature display</li>
3798 <li>scrollToColumnIn javascript API method doesn't
3800 </ul> <em>General</em>
3802 <li>Redundancy removal fails for rna alignment</li>
3803 <li>PCA calculation fails when sequence has been selected
3804 and then deselected</li>
3805 <li>PCA window shows grey box when first opened on OSX</li>
3806 <li>Letters coloured pink in sequence logo when alignment
3807 coloured with clustalx</li>
3808 <li>Choosing fonts without letter symbols defined causes
3809 exceptions and redraw errors</li>
3810 <li>Initial PCA plot view is not same as manually
3811 reconfigured view</li>
3812 <li>Grouped annotation graph label has incorrect line
3814 <li>Grouped annotation graph label display is corrupted
3815 for lots of labels</li>
3820 <div align="center">
3821 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3824 <td><em>Application</em>
3826 <li>Jalview Desktop News Reader</li>
3827 <li>Tweaked default layout of web services menu</li>
3828 <li>View/alignment association menu to enable user to
3829 easily specify which alignment a multi-structure view takes
3830 its colours/correspondences from</li>
3831 <li>Allow properties file location to be specified as URL</li>
3832 <li>Extend Jalview project to preserve associations
3833 between many alignment views and a single Jmol display</li>
3834 <li>Store annotation row height in Jalview project file</li>
3835 <li>Annotation row column label formatting attributes
3836 stored in project file</li>
3837 <li>Annotation row order for auto-calculated annotation
3838 rows preserved in Jalview project file</li>
3839 <li>Visual progress indication when Jalview state is
3840 saved using Desktop window menu</li>
3841 <li>Visual indication that command line arguments are
3842 still being processed</li>
3843 <li>Groovy script execution from URL</li>
3844 <li>Colour by annotation default min and max colours in
3846 <li>Automatically associate PDB files dragged onto an
3847 alignment with sequences that have high similarity and
3849 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3850 <li>'view structures' option to open many
3851 structures in same window</li>
3852 <li>Sort associated views menu option for tree panel</li>
3853 <li>Group all JABA and non-JABA services for a particular
3854 analysis function in its own submenu</li>
3855 </ul> <em>Applet</em>
3857 <li>Userdefined and autogenerated annotation rows for
3859 <li>Adjustment of alignment annotation pane height</li>
3860 <li>Annotation scrollbar for annotation panel</li>
3861 <li>Drag to reorder annotation rows in annotation panel</li>
3862 <li>'automaticScrolling' parameter</li>
3863 <li>Allow sequences with partial ID string matches to be
3864 annotated from GFF/Jalview features files</li>
3865 <li>Sequence logo annotation row in applet</li>
3866 <li>Absolute paths relative to host server in applet
3867 parameters are treated as such</li>
3868 <li>New in the JalviewLite javascript API:
3870 <li>JalviewLite.js javascript library</li>
3871 <li>Javascript callbacks for
3873 <li>Applet initialisation</li>
3874 <li>Sequence/alignment mouse-overs and selections</li>
3877 <li>scrollTo row and column alignment scrolling
3879 <li>Select sequence/alignment regions from javascript</li>
3880 <li>javascript structure viewer harness to pass
3881 messages between Jmol and Jalview when running as
3882 distinct applets</li>
3883 <li>sortBy method</li>
3884 <li>Set of applet and application examples shipped
3885 with documentation</li>
3886 <li>New example to demonstrate JalviewLite and Jmol
3887 javascript message exchange</li>
3889 </ul> <em>General</em>
3891 <li>Enable Jmol displays to be associated with multiple
3892 multiple alignments</li>
3893 <li>Option to automatically sort alignment with new tree</li>
3894 <li>User configurable link to enable redirects to a
3895 www.Jalview.org mirror</li>
3896 <li>Jmol colours option for Jmol displays</li>
3897 <li>Configurable newline string when writing alignment
3898 and other flat files</li>
3899 <li>Allow alignment annotation description lines to
3900 contain html tags</li>
3901 </ul> <em>Documentation and Development</em>
3903 <li>Add groovy test harness for bulk load testing to
3905 <li>Groovy script to load and align a set of sequences
3906 using a web service before displaying the result in the
3907 Jalview desktop</li>
3908 <li>Restructured javascript and applet api documentation</li>
3909 <li>Ant target to publish example html files with applet
3911 <li>Netbeans project for building Jalview from source</li>
3912 <li>ant task to create online javadoc for Jalview source</li>
3914 <td><em>Application</em>
3916 <li>User defined colourscheme throws exception when
3917 current built in colourscheme is saved as new scheme</li>
3918 <li>AlignFrame->Save in application pops up save
3919 dialog for valid filename/format</li>
3920 <li>Cannot view associated structure for UniProt sequence</li>
3921 <li>PDB file association breaks for UniProt sequence
3923 <li>Associate PDB from file dialog does not tell you
3924 which sequence is to be associated with the file</li>
3925 <li>Find All raises null pointer exception when query
3926 only matches sequence IDs</li>
3927 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3928 <li>Jalview project with Jmol views created with Jalview
3929 2.4 cannot be loaded</li>
3930 <li>Filetype associations not installed for webstart
3932 <li>Two or more chains in a single PDB file associated
3933 with sequences in different alignments do not get coloured
3934 by their associated sequence</li>
3935 <li>Visibility status of autocalculated annotation row
3936 not preserved when project is loaded</li>
3937 <li>Annotation row height and visibility attributes not
3938 stored in Jalview project</li>
3939 <li>Tree bootstraps are not preserved when saved as a
3940 Jalview project</li>
3941 <li>Envision2 workflow tooltips are corrupted</li>
3942 <li>Enabling show group conservation also enables colour
3943 by conservation</li>
3944 <li>Duplicate group associated conservation or consensus
3945 created on new view</li>
3946 <li>Annotation scrollbar not displayed after 'show
3947 all hidden annotation rows' option selected</li>
3948 <li>Alignment quality not updated after alignment
3949 annotation row is hidden then shown</li>
3950 <li>Preserve colouring of structures coloured by
3951 sequences in pre Jalview 2.7 projects</li>
3952 <li>Web service job parameter dialog is not laid out
3954 <li>Web services menu not refreshed after 'reset
3955 services' button is pressed in preferences</li>
3956 <li>Annotation off by one in Jalview v2_3 example project</li>
3957 <li>Structures imported from file and saved in project
3958 get name like jalview_pdb1234.txt when reloaded</li>
3959 <li>Jalview does not always retrieve progress of a JABAWS
3960 job execution in full once it is complete</li>
3961 </ul> <em>Applet</em>
3963 <li>Alignment height set incorrectly when lots of
3964 annotation rows are displayed</li>
3965 <li>Relative URLs in feature HTML text not resolved to
3967 <li>View follows highlighting does not work for positions
3969 <li><= shown as = in tooltip</li>
3970 <li>Export features raises exception when no features
3972 <li>Separator string used for serialising lists of IDs
3973 for javascript api is modified when separator string
3974 provided as parameter</li>
3975 <li>Null pointer exception when selecting tree leaves for
3976 alignment with no existing selection</li>
3977 <li>Relative URLs for datasources assumed to be relative
3978 to applet's codebase</li>
3979 <li>Status bar not updated after finished searching and
3980 search wraps around to first result</li>
3981 <li>StructureSelectionManager instance shared between
3982 several Jalview applets causes race conditions and memory
3984 <li>Hover tooltip and mouseover of position on structure
3985 not sent from Jmol in applet</li>
3986 <li>Certain sequences of javascript method calls to
3987 applet API fatally hang browser</li>
3988 </ul> <em>General</em>
3990 <li>View follows structure mouseover scrolls beyond
3991 position with wrapped view and hidden regions</li>
3992 <li>Find sequence position moves to wrong residue
3993 with/without hidden columns</li>
3994 <li>Sequence length given in alignment properties window
3996 <li>InvalidNumberFormat exceptions thrown when trying to
3997 import PDB like structure files</li>
3998 <li>Positional search results are only highlighted
3999 between user-supplied sequence start/end bounds</li>
4000 <li>End attribute of sequence is not validated</li>
4001 <li>Find dialog only finds first sequence containing a
4002 given sequence position</li>
4003 <li>Sequence numbering not preserved in MSF alignment
4005 <li>Jalview PDB file reader does not extract sequence
4006 from nucleotide chains correctly</li>
4007 <li>Structure colours not updated when tree partition
4008 changed in alignment</li>
4009 <li>Sequence associated secondary structure not correctly
4010 parsed in interleaved stockholm</li>
4011 <li>Colour by annotation dialog does not restore current
4013 <li>Hiding (nearly) all sequences doesn't work
4015 <li>Sequences containing lowercase letters are not
4016 properly associated with their pdb files</li>
4017 </ul> <em>Documentation and Development</em>
4019 <li>schemas/JalviewWsParamSet.xsd corrupted by
4020 ApplyCopyright tool</li>
4025 <div align="center">
4026 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4029 <td><em>Application</em>
4031 <li>New warning dialog when the Jalview Desktop cannot
4032 contact web services</li>
4033 <li>JABA service parameters for a preset are shown in
4034 service job window</li>
4035 <li>JABA Service menu entries reworded</li>
4039 <li>Modeller PIR IO broken - cannot correctly import a
4040 pir file emitted by Jalview</li>
4041 <li>Existing feature settings transferred to new
4042 alignment view created from cut'n'paste</li>
4043 <li>Improved test for mixed amino/nucleotide chains when
4044 parsing PDB files</li>
4045 <li>Consensus and conservation annotation rows
4046 occasionally become blank for all new windows</li>
4047 <li>Exception raised when right clicking above sequences
4048 in wrapped view mode</li>
4049 </ul> <em>Application</em>
4051 <li>multiple multiply aligned structure views cause cpu
4052 usage to hit 100% and computer to hang</li>
4053 <li>Web Service parameter layout breaks for long user
4054 parameter names</li>
4055 <li>Jaba service discovery hangs desktop if Jaba server
4062 <div align="center">
4063 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4066 <td><em>Application</em>
4068 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4069 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4072 <li>Web Services preference tab</li>
4073 <li>Analysis parameters dialog box and user defined
4075 <li>Improved speed and layout of Envision2 service menu</li>
4076 <li>Superpose structures using associated sequence
4078 <li>Export coordinates and projection as CSV from PCA
4080 </ul> <em>Applet</em>
4082 <li>enable javascript: execution by the applet via the
4083 link out mechanism</li>
4084 </ul> <em>Other</em>
4086 <li>Updated the Jmol Jalview interface to work with Jmol
4088 <li>The Jalview Desktop and JalviewLite applet now
4089 require Java 1.5</li>
4090 <li>Allow Jalview feature colour specification for GFF
4091 sequence annotation files</li>
4092 <li>New 'colour by label' keword in Jalview feature file
4093 type colour specification</li>
4094 <li>New Jalview Desktop Groovy API method that allows a
4095 script to check if it being run in an interactive session or
4096 in a batch operation from the Jalview command line</li>
4100 <li>clustalx colourscheme colours Ds preferentially when
4101 both D+E are present in over 50% of the column</li>
4102 </ul> <em>Application</em>
4104 <li>typo in AlignmentFrame->View->Hide->all but
4105 selected Regions menu item</li>
4106 <li>sequence fetcher replaces ',' for ';' when the ',' is
4107 part of a valid accession ID</li>
4108 <li>fatal OOM if object retrieved by sequence fetcher
4109 runs out of memory</li>
4110 <li>unhandled Out of Memory Error when viewing pca
4111 analysis results</li>
4112 <li>InstallAnywhere builds fail to launch on OS X java
4113 10.5 update 4 (due to apple Java 1.6 update)</li>
4114 <li>Installanywhere Jalview silently fails to launch</li>
4115 </ul> <em>Applet</em>
4117 <li>Jalview.getFeatureGroups() raises an
4118 ArrayIndexOutOfBoundsException if no feature groups are
4125 <div align="center">
4126 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4132 <li>Alignment prettyprinter doesn't cope with long
4134 <li>clustalx colourscheme colours Ds preferentially when
4135 both D+E are present in over 50% of the column</li>
4136 <li>nucleic acid structures retrieved from PDB do not
4137 import correctly</li>
4138 <li>More columns get selected than were clicked on when a
4139 number of columns are hidden</li>
4140 <li>annotation label popup menu not providing correct
4141 add/hide/show options when rows are hidden or none are
4143 <li>Stockholm format shown in list of readable formats,
4144 and parser copes better with alignments from RFAM.</li>
4145 <li>CSV output of consensus only includes the percentage
4146 of all symbols if sequence logo display is enabled</li>
4148 </ul> <em>Applet</em>
4150 <li>annotation panel disappears when annotation is
4152 </ul> <em>Application</em>
4154 <li>Alignment view not redrawn properly when new
4155 alignment opened where annotation panel is visible but no
4156 annotations are present on alignment</li>
4157 <li>pasted region containing hidden columns is
4158 incorrectly displayed in new alignment window</li>
4159 <li>Jalview slow to complete operations when stdout is
4160 flooded (fix is to close the Jalview console)</li>
4161 <li>typo in AlignmentFrame->View->Hide->all but
4162 selected Rregions menu item.</li>
4163 <li>inconsistent group submenu and Format submenu entry
4164 'Un' or 'Non'conserved</li>
4165 <li>Sequence feature settings are being shared by
4166 multiple distinct alignments</li>
4167 <li>group annotation not recreated when tree partition is
4169 <li>double click on group annotation to select sequences
4170 does not propagate to associated trees</li>
4171 <li>Mac OSX specific issues:
4173 <li>exception raised when mouse clicked on desktop
4174 window background</li>
4175 <li>Desktop menu placed on menu bar and application
4176 name set correctly</li>
4177 <li>sequence feature settings not wide enough for the
4178 save feature colourscheme button</li>
4187 <div align="center">
4188 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4191 <td><em>New Capabilities</em>
4193 <li>URL links generated from description line for
4194 regular-expression based URL links (applet and application)
4196 <li>Non-positional feature URL links are shown in link
4198 <li>Linked viewing of nucleic acid sequences and
4200 <li>Automatic Scrolling option in View menu to display
4201 the currently highlighted region of an alignment.</li>
4202 <li>Order an alignment by sequence length, or using the
4203 average score or total feature count for each sequence.</li>
4204 <li>Shading features by score or associated description</li>
4205 <li>Subdivide alignment and groups based on identity of
4206 selected subsequence (Make Groups from Selection).</li>
4207 <li>New hide/show options including Shift+Control+H to
4208 hide everything but the currently selected region.</li>
4209 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4210 </ul> <em>Application</em>
4212 <li>Fetch DB References capabilities and UI expanded to
4213 support retrieval from DAS sequence sources</li>
4214 <li>Local DAS Sequence sources can be added via the
4215 command line or via the Add local source dialog box.</li>
4216 <li>DAS Dbref and DbxRef feature types are parsed as
4217 database references and protein_name is parsed as
4218 description line (BioSapiens terms).</li>
4219 <li>Enable or disable non-positional feature and database
4220 references in sequence ID tooltip from View menu in
4222 <!-- <li>New hidden columns and rows and representatives capabilities
4223 in annotations file (in progress - not yet fully implemented)</li> -->
4224 <li>Group-associated consensus, sequence logos and
4225 conservation plots</li>
4226 <li>Symbol distributions for each column can be exported
4227 and visualized as sequence logos</li>
4228 <li>Optionally scale multi-character column labels to fit
4229 within each column of annotation row<!-- todo for applet -->
4231 <li>Optional automatic sort of associated alignment view
4232 when a new tree is opened.</li>
4233 <li>Jalview Java Console</li>
4234 <li>Better placement of desktop window when moving
4235 between different screens.</li>
4236 <li>New preference items for sequence ID tooltip and
4237 consensus annotation</li>
4238 <li>Client to submit sequences and IDs to Envision2
4240 <li><em>Vamsas Capabilities</em>
4242 <li>Improved VAMSAS synchronization (Jalview archive
4243 used to preserve views, structures, and tree display
4245 <li>Import of vamsas documents from disk or URL via
4247 <li>Sharing of selected regions between views and
4248 with other VAMSAS applications (Experimental feature!)</li>
4249 <li>Updated API to VAMSAS version 0.2</li>
4251 </ul> <em>Applet</em>
4253 <li>Middle button resizes annotation row height</li>
4256 <li>sortByTree (true/false) - automatically sort the
4257 associated alignment view by the tree when a new tree is
4259 <li>showTreeBootstraps (true/false) - show or hide
4260 branch bootstraps (default is to show them if available)</li>
4261 <li>showTreeDistances (true/false) - show or hide
4262 branch lengths (default is to show them if available)</li>
4263 <li>showUnlinkedTreeNodes (true/false) - indicate if
4264 unassociated nodes should be highlighted in the tree
4266 <li>heightScale and widthScale (1.0 or more) -
4267 increase the height or width of a cell in the alignment
4268 grid relative to the current font size.</li>
4271 <li>Non-positional features displayed in sequence ID
4273 </ul> <em>Other</em>
4275 <li>Features format: graduated colour definitions and
4276 specification of feature scores</li>
4277 <li>Alignment Annotations format: new keywords for group
4278 associated annotation (GROUP_REF) and annotation row display
4279 properties (ROW_PROPERTIES)</li>
4280 <li>XML formats extended to support graduated feature
4281 colourschemes, group associated annotation, and profile
4282 visualization settings.</li></td>
4285 <li>Source field in GFF files parsed as feature source
4286 rather than description</li>
4287 <li>Non-positional features are now included in sequence
4288 feature and gff files (controlled via non-positional feature
4289 visibility in tooltip).</li>
4290 <li>URL links generated for all feature links (bugfix)</li>
4291 <li>Added URL embedding instructions to features file
4293 <li>Codons containing ambiguous nucleotides translated as
4294 'X' in peptide product</li>
4295 <li>Match case switch in find dialog box works for both
4296 sequence ID and sequence string and query strings do not
4297 have to be in upper case to match case-insensitively.</li>
4298 <li>AMSA files only contain first column of
4299 multi-character column annotation labels</li>
4300 <li>Jalview Annotation File generation/parsing consistent
4301 with documentation (e.g. Stockholm annotation can be
4302 exported and re-imported)</li>
4303 <li>PDB files without embedded PDB IDs given a friendly
4305 <li>Find incrementally searches ID string matches as well
4306 as subsequence matches, and correctly reports total number
4310 <li>Better handling of exceptions during sequence
4312 <li>Dasobert generated non-positional feature URL
4313 link text excludes the start_end suffix</li>
4314 <li>DAS feature and source retrieval buttons disabled
4315 when fetch or registry operations in progress.</li>
4316 <li>PDB files retrieved from URLs are cached properly</li>
4317 <li>Sequence description lines properly shared via
4319 <li>Sequence fetcher fetches multiple records for all
4321 <li>Ensured that command line das feature retrieval
4322 completes before alignment figures are generated.</li>
4323 <li>Reduced time taken when opening file browser for
4325 <li>isAligned check prior to calculating tree, PCA or
4326 submitting an MSA to JNet now excludes hidden sequences.</li>
4327 <li>User defined group colours properly recovered
4328 from Jalview projects.</li>
4337 <div align="center">
4338 <strong>2.4.0.b2</strong><br> 28/10/2009
4343 <li>Experimental support for google analytics usage
4345 <li>Jalview privacy settings (user preferences and docs).</li>
4350 <li>Race condition in applet preventing startup in
4352 <li>Exception when feature created from selection beyond
4353 length of sequence.</li>
4354 <li>Allow synthetic PDB files to be imported gracefully</li>
4355 <li>Sequence associated annotation rows associate with
4356 all sequences with a given id</li>
4357 <li>Find function matches case-insensitively for sequence
4358 ID string searches</li>
4359 <li>Non-standard characters do not cause pairwise
4360 alignment to fail with exception</li>
4361 </ul> <em>Application Issues</em>
4363 <li>Sequences are now validated against EMBL database</li>
4364 <li>Sequence fetcher fetches multiple records for all
4366 </ul> <em>InstallAnywhere Issues</em>
4368 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4369 issue with installAnywhere mechanism)</li>
4370 <li>Command line launching of JARs from InstallAnywhere
4371 version (java class versioning error fixed)</li>
4378 <div align="center">
4379 <strong>2.4</strong><br> 27/8/2008
4382 <td><em>User Interface</em>
4384 <li>Linked highlighting of codon and amino acid from
4385 translation and protein products</li>
4386 <li>Linked highlighting of structure associated with
4387 residue mapping to codon position</li>
4388 <li>Sequence Fetcher provides example accession numbers
4389 and 'clear' button</li>
4390 <li>MemoryMonitor added as an option under Desktop's
4392 <li>Extract score function to parse whitespace separated
4393 numeric data in description line</li>
4394 <li>Column labels in alignment annotation can be centred.</li>
4395 <li>Tooltip for sequence associated annotation give name
4397 </ul> <em>Web Services and URL fetching</em>
4399 <li>JPred3 web service</li>
4400 <li>Prototype sequence search client (no public services
4402 <li>Fetch either seed alignment or full alignment from
4404 <li>URL Links created for matching database cross
4405 references as well as sequence ID</li>
4406 <li>URL Links can be created using regular-expressions</li>
4407 </ul> <em>Sequence Database Connectivity</em>
4409 <li>Retrieval of cross-referenced sequences from other
4411 <li>Generalised database reference retrieval and
4412 validation to all fetchable databases</li>
4413 <li>Fetch sequences from DAS sources supporting the
4414 sequence command</li>
4415 </ul> <em>Import and Export</em>
4416 <li>export annotation rows as CSV for spreadsheet import</li>
4417 <li>Jalview projects record alignment dataset associations,
4418 EMBL products, and cDNA sequence mappings</li>
4419 <li>Sequence Group colour can be specified in Annotation
4421 <li>Ad-hoc colouring of group in Annotation File using RGB
4422 triplet as name of colourscheme</li>
4423 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4425 <li>treenode binding for VAMSAS tree exchange</li>
4426 <li>local editing and update of sequences in VAMSAS
4427 alignments (experimental)</li>
4428 <li>Create new or select existing session to join</li>
4429 <li>load and save of vamsas documents</li>
4430 </ul> <em>Application command line</em>
4432 <li>-tree parameter to open trees (introduced for passing
4434 <li>-fetchfrom command line argument to specify nicknames
4435 of DAS servers to query for alignment features</li>
4436 <li>-dasserver command line argument to add new servers
4437 that are also automatically queried for features</li>
4438 <li>-groovy command line argument executes a given groovy
4439 script after all input data has been loaded and parsed</li>
4440 </ul> <em>Applet-Application data exchange</em>
4442 <li>Trees passed as applet parameters can be passed to
4443 application (when using "View in full
4444 application")</li>
4445 </ul> <em>Applet Parameters</em>
4447 <li>feature group display control parameter</li>
4448 <li>debug parameter</li>
4449 <li>showbutton parameter</li>
4450 </ul> <em>Applet API methods</em>
4452 <li>newView public method</li>
4453 <li>Window (current view) specific get/set public methods</li>
4454 <li>Feature display control methods</li>
4455 <li>get list of currently selected sequences</li>
4456 </ul> <em>New Jalview distribution features</em>
4458 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4459 <li>RELEASE file gives build properties for the latest
4460 Jalview release.</li>
4461 <li>Java 1.1 Applet build made easier and donotobfuscate
4462 property controls execution of obfuscator</li>
4463 <li>Build target for generating source distribution</li>
4464 <li>Debug flag for javacc</li>
4465 <li>.jalview_properties file is documented (slightly) in
4466 jalview.bin.Cache</li>
4467 <li>Continuous Build Integration for stable and
4468 development version of Application, Applet and source
4473 <li>selected region output includes visible annotations
4474 (for certain formats)</li>
4475 <li>edit label/displaychar contains existing label/char
4477 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4478 <li>shorter peptide product names from EMBL records</li>
4479 <li>Newick string generator makes compact representations</li>
4480 <li>bootstrap values parsed correctly for tree files with
4482 <li>pathological filechooser bug avoided by not allowing
4483 filenames containing a ':'</li>
4484 <li>Fixed exception when parsing GFF files containing
4485 global sequence features</li>
4486 <li>Alignment datasets are finalized only when number of
4487 references from alignment sequences goes to zero</li>
4488 <li>Close of tree branch colour box without colour
4489 selection causes cascading exceptions</li>
4490 <li>occasional negative imgwidth exceptions</li>
4491 <li>better reporting of non-fatal warnings to user when
4492 file parsing fails.</li>
4493 <li>Save works when Jalview project is default format</li>
4494 <li>Save as dialog opened if current alignment format is
4495 not a valid output format</li>
4496 <li>UniProt canonical names introduced for both das and
4498 <li>Histidine should be midblue (not pink!) in Zappo</li>
4499 <li>error messages passed up and output when data read
4501 <li>edit undo recovers previous dataset sequence when
4502 sequence is edited</li>
4503 <li>allow PDB files without pdb ID HEADER lines (like
4504 those generated by MODELLER) to be read in properly</li>
4505 <li>allow reading of JPred concise files as a normal
4507 <li>Stockholm annotation parsing and alignment properties
4508 import fixed for PFAM records</li>
4509 <li>Structure view windows have correct name in Desktop
4511 <li>annotation consisting of sequence associated scores
4512 can be read and written correctly to annotation file</li>
4513 <li>Aligned cDNA translation to aligned peptide works
4515 <li>Fixed display of hidden sequence markers and
4516 non-italic font for representatives in Applet</li>
4517 <li>Applet Menus are always embedded in applet window on
4519 <li>Newly shown features appear at top of stack (in
4521 <li>Annotations added via parameter not drawn properly
4522 due to null pointer exceptions</li>
4523 <li>Secondary structure lines are drawn starting from
4524 first column of alignment</li>
4525 <li>UniProt XML import updated for new schema release in
4527 <li>Sequence feature to sequence ID match for Features
4528 file is case-insensitive</li>
4529 <li>Sequence features read from Features file appended to
4530 all sequences with matching IDs</li>
4531 <li>PDB structure coloured correctly for associated views
4532 containing a sub-sequence</li>
4533 <li>PDB files can be retrieved by applet from Jar files</li>
4534 <li>feature and annotation file applet parameters
4535 referring to different directories are retrieved correctly</li>
4536 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4537 <li>Fixed application hang whilst waiting for
4538 splash-screen version check to complete</li>
4539 <li>Applet properly URLencodes input parameter values
4540 when passing them to the launchApp service</li>
4541 <li>display name and local features preserved in results
4542 retrieved from web service</li>
4543 <li>Visual delay indication for sequence retrieval and
4544 sequence fetcher initialisation</li>
4545 <li>updated Application to use DAS 1.53e version of
4546 dasobert DAS client</li>
4547 <li>Re-instated Full AMSA support and .amsa file
4549 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4557 <div align="center">
4558 <strong>2.3</strong><br> 9/5/07
4563 <li>Jmol 11.0.2 integration</li>
4564 <li>PDB views stored in Jalview XML files</li>
4565 <li>Slide sequences</li>
4566 <li>Edit sequence in place</li>
4567 <li>EMBL CDS features</li>
4568 <li>DAS Feature mapping</li>
4569 <li>Feature ordering</li>
4570 <li>Alignment Properties</li>
4571 <li>Annotation Scores</li>
4572 <li>Sort by scores</li>
4573 <li>Feature/annotation editing in applet</li>
4578 <li>Headless state operation in 2.2.1</li>
4579 <li>Incorrect and unstable DNA pairwise alignment</li>
4580 <li>Cut and paste of sequences with annotation</li>
4581 <li>Feature group display state in XML</li>
4582 <li>Feature ordering in XML</li>
4583 <li>blc file iteration selection using filename # suffix</li>
4584 <li>Stockholm alignment properties</li>
4585 <li>Stockhom alignment secondary structure annotation</li>
4586 <li>2.2.1 applet had no feature transparency</li>
4587 <li>Number pad keys can be used in cursor mode</li>
4588 <li>Structure Viewer mirror image resolved</li>
4595 <div align="center">
4596 <strong>2.2.1</strong><br> 12/2/07
4601 <li>Non standard characters can be read and displayed
4602 <li>Annotations/Features can be imported/exported to the
4604 <li>Applet allows editing of sequence/annotation/group
4605 name & description
4606 <li>Preference setting to display sequence name in
4608 <li>Annotation file format extended to allow
4609 Sequence_groups to be defined
4610 <li>Default opening of alignment overview panel can be
4611 specified in preferences
4612 <li>PDB residue numbering annotation added to associated
4618 <li>Applet crash under certain Linux OS with Java 1.6
4620 <li>Annotation file export / import bugs fixed
4621 <li>PNG / EPS image output bugs fixed
4627 <div align="center">
4628 <strong>2.2</strong><br> 27/11/06
4633 <li>Multiple views on alignment
4634 <li>Sequence feature editing
4635 <li>"Reload" alignment
4636 <li>"Save" to current filename
4637 <li>Background dependent text colour
4638 <li>Right align sequence ids
4639 <li>User-defined lower case residue colours
4642 <li>Menu item accelerator keys
4643 <li>Control-V pastes to current alignment
4644 <li>Cancel button for DAS Feature Fetching
4645 <li>PCA and PDB Viewers zoom via mouse roller
4646 <li>User-defined sub-tree colours and sub-tree selection
4648 <li>'New Window' button on the 'Output to Text box'
4653 <li>New memory efficient Undo/Redo System
4654 <li>Optimised symbol lookups and conservation/consensus
4656 <li>Region Conservation/Consensus recalculated after
4658 <li>Fixed Remove Empty Columns Bug (empty columns at end
4660 <li>Slowed DAS Feature Fetching for increased robustness.
4662 <li>Made angle brackets in ASCII feature descriptions
4664 <li>Re-instated Zoom function for PCA
4665 <li>Sequence descriptions conserved in web service
4667 <li>UniProt ID discoverer uses any word separated by
4669 <li>WsDbFetch query/result association resolved
4670 <li>Tree leaf to sequence mapping improved
4671 <li>Smooth fonts switch moved to FontChooser dialog box.
4678 <div align="center">
4679 <strong>2.1.1</strong><br> 12/9/06
4684 <li>Copy consensus sequence to clipboard</li>
4689 <li>Image output - rightmost residues are rendered if
4690 sequence id panel has been resized</li>
4691 <li>Image output - all offscreen group boundaries are
4693 <li>Annotation files with sequence references - all
4694 elements in file are relative to sequence position</li>
4695 <li>Mac Applet users can use Alt key for group editing</li>
4701 <div align="center">
4702 <strong>2.1</strong><br> 22/8/06
4707 <li>MAFFT Multiple Alignment in default Web Service list</li>
4708 <li>DAS Feature fetching</li>
4709 <li>Hide sequences and columns</li>
4710 <li>Export Annotations and Features</li>
4711 <li>GFF file reading / writing</li>
4712 <li>Associate structures with sequences from local PDB
4714 <li>Add sequences to exisiting alignment</li>
4715 <li>Recently opened files / URL lists</li>
4716 <li>Applet can launch the full application</li>
4717 <li>Applet has transparency for features (Java 1.2
4719 <li>Applet has user defined colours parameter</li>
4720 <li>Applet can load sequences from parameter
4721 "sequence<em>x</em>"
4727 <li>Redundancy Panel reinstalled in the Applet</li>
4728 <li>Monospaced font - EPS / rescaling bug fixed</li>
4729 <li>Annotation files with sequence references bug fixed</li>
4735 <div align="center">
4736 <strong>2.08.1</strong><br> 2/5/06
4741 <li>Change case of selected region from Popup menu</li>
4742 <li>Choose to match case when searching</li>
4743 <li>Middle mouse button and mouse movement can compress /
4744 expand the visible width and height of the alignment</li>
4749 <li>Annotation Panel displays complete JNet results</li>
4755 <div align="center">
4756 <strong>2.08b</strong><br> 18/4/06
4762 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4763 <li>Righthand label on wrapped alignments shows correct
4770 <div align="center">
4771 <strong>2.08</strong><br> 10/4/06
4776 <li>Editing can be locked to the selection area</li>
4777 <li>Keyboard editing</li>
4778 <li>Create sequence features from searches</li>
4779 <li>Precalculated annotations can be loaded onto
4781 <li>Features file allows grouping of features</li>
4782 <li>Annotation Colouring scheme added</li>
4783 <li>Smooth fonts off by default - Faster rendering</li>
4784 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4789 <li>Drag & Drop fixed on Linux</li>
4790 <li>Jalview Archive file faster to load/save, sequence
4791 descriptions saved.</li>
4797 <div align="center">
4798 <strong>2.07</strong><br> 12/12/05
4803 <li>PDB Structure Viewer enhanced</li>
4804 <li>Sequence Feature retrieval and display enhanced</li>
4805 <li>Choose to output sequence start-end after sequence
4806 name for file output</li>
4807 <li>Sequence Fetcher WSDBFetch@EBI</li>
4808 <li>Applet can read feature files, PDB files and can be
4809 used for HTML form input</li>
4814 <li>HTML output writes groups and features</li>
4815 <li>Group editing is Control and mouse click</li>
4816 <li>File IO bugs</li>
4822 <div align="center">
4823 <strong>2.06</strong><br> 28/9/05
4828 <li>View annotations in wrapped mode</li>
4829 <li>More options for PCA viewer</li>
4834 <li>GUI bugs resolved</li>
4835 <li>Runs with -nodisplay from command line</li>
4841 <div align="center">
4842 <strong>2.05b</strong><br> 15/9/05
4847 <li>Choose EPS export as lineart or text</li>
4848 <li>Jar files are executable</li>
4849 <li>Can read in Uracil - maps to unknown residue</li>
4854 <li>Known OutOfMemory errors give warning message</li>
4855 <li>Overview window calculated more efficiently</li>
4856 <li>Several GUI bugs resolved</li>
4862 <div align="center">
4863 <strong>2.05</strong><br> 30/8/05
4868 <li>Edit and annotate in "Wrapped" view</li>
4873 <li>Several GUI bugs resolved</li>
4879 <div align="center">
4880 <strong>2.04</strong><br> 24/8/05
4885 <li>Hold down mouse wheel & scroll to change font
4891 <li>Improved JPred client reliability</li>
4892 <li>Improved loading of Jalview files</li>
4898 <div align="center">
4899 <strong>2.03</strong><br> 18/8/05
4904 <li>Set Proxy server name and port in preferences</li>
4905 <li>Multiple URL links from sequence ids</li>
4906 <li>User Defined Colours can have a scheme name and added
4908 <li>Choose to ignore gaps in consensus calculation</li>
4909 <li>Unix users can set default web browser</li>
4910 <li>Runs without GUI for batch processing</li>
4911 <li>Dynamically generated Web Service Menus</li>
4916 <li>InstallAnywhere download for Sparc Solaris</li>
4922 <div align="center">
4923 <strong>2.02</strong><br> 18/7/05
4929 <li>Copy & Paste order of sequences maintains
4930 alignment order.</li>
4936 <div align="center">
4937 <strong>2.01</strong><br> 12/7/05
4942 <li>Use delete key for deleting selection.</li>
4943 <li>Use Mouse wheel to scroll sequences.</li>
4944 <li>Help file updated to describe how to add alignment
4946 <li>Version and build date written to build properties
4948 <li>InstallAnywhere installation will check for updates
4949 at launch of Jalview.</li>
4954 <li>Delete gaps bug fixed.</li>
4955 <li>FileChooser sorts columns.</li>
4956 <li>Can remove groups one by one.</li>
4957 <li>Filechooser icons installed.</li>
4958 <li>Finder ignores return character when searching.
4959 Return key will initiate a search.<br>
4966 <div align="center">
4967 <strong>2.0</strong><br> 20/6/05
4972 <li>New codebase</li>