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 */
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>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 for 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-3748 -->CDS shown in result of submitting proteins
210 in a CDS/Protein alignment to a web service is wrong when
211 proteins share a common transcript sequence (e.g.
212 genome of RNA viruses)
215 <!-- JAL-3576 -->Co-located features exported and re-imported
216 are ordered differently when shown on alignment and in
217 tooltips. (Also affects v2.11.1.0)
220 <!-- JAL-3702 -->Drag and drop of alignment file onto
221 alignment window when in a HiDPI scaled mode in Linux only
222 works for the top left quadrant of the alignment window
225 <!-- JAL-3701 -->Stale build data in jalview standalone jar
226 builds (only affects 2.11.1.1 branch)
229 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
230 when alignment view restored from project (since Jalview 2.11.0)
236 <td width="60" align="center" nowrap><strong><a
237 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
238 <em>22/04/2020</em></strong></td>
239 <td align="left" valign="top">
242 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
243 'virtual' codon features shown on protein (or vice versa)
244 for display in alignments, on structure views (including
245 transfer to UCSF chimera), in feature reports and for
249 <!-- JAL-3121 -->Feature attributes from VCF files can be
250 exported and re-imported as GFF3 files
253 <!-- JAL-3376 -->Capture VCF "fixed column" values
254 POS, ID, QUAL, FILTER as Feature Attributes
257 <!-- JAL-3375 -->More robust VCF numeric data field
258 validation while parsing
261 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
265 <!-- JAL-3535 -->Feature Settings dialog title includes name
269 <!-- JAL-3538 -->Font anti-aliasing in alignment views
273 <!-- JAL-3468 -->Very long feature descriptions truncated in
277 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
278 with no feature types visible
281 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
283 </ul><em>Jalview Installer</em>
286 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
287 in console (may be null when Jalview launched as executable jar or via conda)
290 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
293 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
296 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
298 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
299 </ul> <em>Release processes</em>
302 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
305 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
307 </ul> <em>Build System</em>
310 <!-- JAL-3510 -->Clover updated to 4.4.1
313 <!-- JAL-3513 -->Test code included in Clover coverage
317 <em>Groovy Scripts</em>
320 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
321 to stdout containing the consensus sequence for each
322 alignment in a Jalview session
325 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
326 genomic sequence_variant annotation from CDS as
327 missense_variant or synonymous_variant on protein products.
331 <td align="left" valign="top">
334 <!-- JAL-3581 -->Hidden sequence markers still visible when
335 'Show hidden markers' option is not ticked
338 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
339 PNG output when 'Automatically set ID width' is set in
340 jalview preferences or properties file
343 <!-- JAL-3571 -->Feature Editor dialog can be opened when
344 'Show Sequence Features' option is not ticked
347 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
348 buttons in Feature Settings dialog are clicked when no
352 <!-- JAL-3412 -->ID margins for CDS and Protein views not
353 equal when split frame is first opened
356 <!-- JAL-3296 -->Sequence position numbers in status bar not
357 correct after editing a sequence's start position
360 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
361 with annotation and exceptions thrown when only a few
362 columns shown in wrapped mode
365 <!-- JAL-3386 -->Sequence IDs missing in headless export of
366 wrapped alignment figure with annotations
369 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
370 ID fails with ClassCastException
373 <!-- JAL-3389 -->Chimera session not restored from Jalview
377 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
378 feature settings dialog also selects columns
381 <!-- JAL-3473 -->SpinnerNumberModel causes
382 IllegalArgumentException in some circumstances
385 <!-- JAL-3534 -->Multiple feature settings dialogs can be
389 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
390 alignment window is closed
393 <!-- JAL-3406 -->Credits missing some authors in Jalview
394 help documentation for 2.11.0 release
397 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
398 includes Pfam ID as sequence's accession rather than its
401 </ul> <em>Java 11 Compatibility issues</em>
404 <!-- JAL-2987 -->OSX - Can't view some search results in
405 PDB/Uniprot search panel
407 </ul> <em>Installer</em>
410 <!-- JAL-3447 -->Jalview should not create file associations
411 for 3D structure files (.pdb, .mmcif. .cif)
413 </ul> <em>Repository and Source Release</em>
416 <!-- JAL-3474 -->removed obsolete .cvsignore files from
420 <!-- JAL-3541 -->Clover report generation running out of
423 </ul> <em>New Known Issues</em>
426 <!-- JAL-3523 -->OSX - Current working directory not
427 preserved when Jalview.app launched with parameters from
431 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
432 clipped in headless figure export when Right Align option
436 <!-- JAL-3542 -->Jalview Installation type always reports
437 'Source' in console output
440 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
441 bamboo server but run fine locally.
447 <td width="60" align="center" nowrap>
448 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
449 <em>04/07/2019</em></strong>
451 <td align="left" valign="top">
454 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
455 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
456 source project) rather than InstallAnywhere
459 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
460 settings, receive over the air updates and launch specific
461 versions via (<a href="https://github.com/threerings/getdown">Three
465 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
466 formats supported by Jalview (including .jvp project files)
469 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
470 arguments and switch between different getdown channels
473 <!-- JAL-3141 -->Backup files created when saving Jalview project
478 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
479 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
481 <!-- JAL-2620 -->Alternative genetic code tables for
482 'Translate as cDNA'</li>
484 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
485 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
488 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
489 implementation that allows updates) used for Sequence Feature collections</li>
491 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
492 features can be filtered and shaded according to any
493 associated attributes (e.g. variant attributes from VCF
494 file, or key-value pairs imported from column 9 of GFF
498 <!-- JAL-2879 -->Feature Attributes and shading schemes
499 stored and restored from Jalview Projects
502 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
503 recognise variant features
506 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
507 sequences (also coloured red by default)
510 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
514 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
515 algorithm (Z-sort/transparency and filter aware)
518 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
524 <!-- JAL-3205 -->Symmetric score matrices for faster
525 tree and PCA calculations
527 <li><strong>Principal Components Analysis Viewer</strong>
530 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
531 and Viewer state saved in Jalview Project
533 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
536 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
540 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
545 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
547 <li><strong>Speed and Efficiency</strong>
550 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
551 multiple groups when working with large alignments
554 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
558 <li><strong>User Interface</strong>
561 <!-- JAL-2933 -->Finder panel remembers last position in each
565 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
566 what is shown)<br />Only visible regions of alignment are shown by
567 default (can be changed in user preferences)
570 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
571 to the Overwrite Dialog
574 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
578 <!-- JAL-1244 -->Status bar shows bounds when dragging a
579 selection region, and gap count when inserting or deleting gaps
582 <!-- JAL-3132 -->Status bar updates over sequence and annotation
586 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
590 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
594 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
597 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
601 <!-- JAL-3181 -->Consistent ordering of links in sequence id
605 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
607 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
611 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
612 <li><strong>Java 11 Support (not yet on general release)</strong>
615 <!-- -->OSX GUI integrations for App menu's 'About' entry and
620 <em>Deprecations</em>
622 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
623 capabilities removed from the Jalview Desktop
625 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
626 unmarshalling has been replaced by JAXB for Jalview projects
627 and XML based data retrieval clients</li>
628 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
629 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
630 </ul> <em>Documentation</em>
632 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
633 not supported in EPS figure export
635 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
636 </ul> <em>Development and Release Processes</em>
639 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
642 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
644 <!-- JAL-3225 -->Eclipse project configuration managed with
648 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
649 Bamboo continuous integration for unattended Test Suite
653 <!-- JAL-2864 -->Memory test suite to detect leaks in common
657 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
661 <!-- JAL-3248 -->Developer documentation migrated to
662 markdown (with HTML rendering)
665 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
668 <!-- JAL-3289 -->New URLs for publishing development
673 <td align="left" valign="top">
676 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
679 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
680 superposition in Jmol fail on Windows
683 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
684 structures for sequences with lots of PDB structures
687 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
691 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
692 project involving multiple views
695 <!-- JAL-3164 -->Overview for complementary view in a linked
696 CDS/Protein alignment is not updated when Hide Columns by
697 Annotation dialog hides columns
700 <!-- JAL-3158 -->Selection highlighting in the complement of a
701 CDS/Protein alignment stops working after making a selection in
702 one view, then making another selection in the other view
705 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
709 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
710 Settings and Jalview Preferences panels
713 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
714 overview with large alignments
717 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
718 region if columns were selected by dragging right-to-left and the
719 mouse moved to the left of the first column
722 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
723 hidden column marker via scale popup menu
726 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
727 doesn't tell users the invalid URL
730 <!-- JAL-2816 -->Tooltips displayed for features filtered by
734 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
735 show cross references or Fetch Database References are shown in
739 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
740 peptide sequence (computed variant shown as p.Res.null)
743 <!-- JAL-2060 -->'Graduated colour' option not offered for
744 manually created features (where feature score is Float.NaN)
747 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
748 when columns are hidden
751 <!-- JAL-3082 -->Regular expression error for '(' in Select
752 Columns by Annotation description
755 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
756 out of Scale or Annotation Panel
759 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
763 <!-- JAL-3074 -->Left/right drag in annotation can scroll
767 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
771 <!-- JAL-3002 -->Column display is out by one after Page Down,
772 Page Up in wrapped mode
775 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
778 <!-- JAL-2932 -->Finder searches in minimised alignments
781 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
782 on opening an alignment
785 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
789 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
790 different groups in the alignment are selected
793 <!-- JAL-2717 -->Internationalised colour scheme names not shown
797 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
801 <!-- JAL-3125 -->Value input for graduated feature colour
802 threshold gets 'unrounded'
805 <!-- JAL-2982 -->PCA image export doesn't respect background
809 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
812 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
815 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
819 <!-- JAL-2964 -->Associate Tree with All Views not restored from
823 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
824 shown in complementary view
827 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
828 without normalisation
831 <!-- JAL-3021 -->Sequence Details report should open positioned at top
835 <!-- JAL-914 -->Help page can be opened twice
838 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
840 </ul> <em>Editing</em>
843 <!-- JAL-2822 -->Start and End should be updated when sequence
844 data at beginning or end of alignment added/removed via 'Edit'
848 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
849 relocate sequence features correctly when start of sequence is
850 removed (Known defect since 2.10)
853 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
854 dialog corrupts dataset sequence
857 <!-- JAL-868 -->Structure colours not updated when associated tree
858 repartitions the alignment view (Regression in 2.10.5)
860 </ul> <em>Datamodel</em>
863 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
864 sequence's End is greater than its length
866 </ul> <em>Bugs fixed for Java 11 Support (not yet on
867 general release)</em>
870 <!-- JAL-3288 -->Menus work properly in split-screen
872 </ul> <em>New Known Defects</em>
875 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
878 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
879 regions of protein alignment.
882 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
883 is restored from a Jalview 2.11 project
886 <!-- JAL-3213 -->Alignment panel height can be too small after
890 <!-- JAL-3240 -->Display is incorrect after removing gapped
891 columns within hidden columns
894 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
895 window after dragging left to select columns to left of visible
899 <!-- JAL-2876 -->Features coloured according to their description
900 string and thresholded by score in earlier versions of Jalview are
901 not shown as thresholded features in 2.11. To workaround please
902 create a Score filter instead.
905 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
907 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
910 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
911 alignments with multiple views can close views unexpectedly
914 <em>Java 11 Specific defects</em>
917 <!-- JAL-3235 -->Jalview Properties file is not sorted
918 alphabetically when saved
924 <td width="60" nowrap>
926 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
929 <td><div align="left">
933 <!-- JAL-3101 -->Default memory for Jalview webstart and
934 InstallAnywhere increased to 1G.
937 <!-- JAL-247 -->Hidden sequence markers and representative
938 sequence bolding included when exporting alignment as EPS,
939 SVG, PNG or HTML. <em>Display is configured via the
940 Format menu, or for command-line use via a Jalview
941 properties file.</em>
944 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
945 API and sequence data now imported as JSON.
948 <!-- JAL-3065 -->Change in recommended way of starting
949 Jalview via a Java command line: add jars in lib directory
950 to CLASSPATH, rather than via the deprecated java.ext.dirs
957 <!-- JAL-3047 -->Support added to execute test suite
958 instrumented with <a href="http://openclover.org/">Open
963 <td><div align="left">
967 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
968 row shown in Feredoxin Structure alignment view of example
972 <!-- JAL-2854 -->Annotation obscures sequences if lots of
973 annotation displayed.
976 <!-- JAL-3107 -->Group conservation/consensus not shown
977 for newly created group when 'Apply to all groups'
981 <!-- JAL-3087 -->Corrupted display when switching to
982 wrapped mode when sequence panel's vertical scrollbar is
986 <!-- JAL-3003 -->Alignment is black in exported EPS file
987 when sequences are selected in exported view.</em>
990 <!-- JAL-3059 -->Groups with different coloured borders
991 aren't rendered with correct colour.
994 <!-- JAL-3092 -->Jalview could hang when importing certain
995 types of knotted RNA secondary structure.
998 <!-- JAL-3095 -->Sequence highlight and selection in
999 trimmed VARNA 2D structure is incorrect for sequences that
1003 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1004 annotation when columns are inserted into an alignment,
1005 and when exporting as Stockholm flatfile.
1008 <!-- JAL-3053 -->Jalview annotation rows containing upper
1009 and lower-case 'E' and 'H' do not automatically get
1010 treated as RNA secondary structure.
1013 <!-- JAL-3106 -->.jvp should be used as default extension
1014 (not .jar) when saving a Jalview project file.
1017 <!-- JAL-3105 -->Mac Users: closing a window correctly
1018 transfers focus to previous window on OSX
1021 <em>Java 10 Issues Resolved</em>
1024 <!-- JAL-2988 -->OSX - Can't save new files via the File
1025 or export menus by typing in a name into the Save dialog
1029 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1030 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1031 'look and feel' which has improved compatibility with the
1032 latest version of OSX.
1039 <td width="60" nowrap>
1040 <div align="center">
1041 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1042 <em>7/06/2018</em></strong>
1045 <td><div align="left">
1049 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1050 annotation retrieved from Uniprot
1053 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1054 onto the Jalview Desktop
1058 <td><div align="left">
1062 <!-- JAL-3017 -->Cannot import features with multiple
1063 variant elements (blocks import of some Uniprot records)
1066 <!-- JAL-2997 -->Clustal files with sequence positions in
1067 right-hand column parsed correctly
1070 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1071 not alignment area in exported graphic
1074 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1075 window has input focus
1078 <!-- JAL-2992 -->Annotation panel set too high when
1079 annotation added to view (Windows)
1082 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1083 network connectivity is poor
1086 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1087 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1088 the currently open URL and links from a page viewed in
1089 Firefox or Chrome on Windows is now fully supported. If
1090 you are using Edge, only links in the page can be
1091 dragged, and with Internet Explorer, only the currently
1092 open URL in the browser can be dropped onto Jalview.</em>
1095 <em>New Known Defects</em>
1097 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1102 <td width="60" nowrap>
1103 <div align="center">
1104 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1107 <td><div align="left">
1111 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1112 for disabling automatic superposition of multiple
1113 structures and open structures in existing views
1116 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1117 ID and annotation area margins can be click-dragged to
1121 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1125 <!-- JAL-2759 -->Improved performance for large alignments
1126 and lots of hidden columns
1129 <!-- JAL-2593 -->Improved performance when rendering lots
1130 of features (particularly when transparency is disabled)
1133 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1134 exchange of Jalview features and Chimera attributes made
1140 <td><div align="left">
1143 <!-- JAL-2899 -->Structure and Overview aren't updated
1144 when Colour By Annotation threshold slider is adjusted
1147 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1148 overlapping alignment panel
1151 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1155 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1156 improved: CDS not handled correctly if transcript has no
1160 <!-- JAL-2321 -->Secondary structure and temperature
1161 factor annotation not added to sequence when local PDB
1162 file associated with it by drag'n'drop or structure
1166 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1167 dialog doesn't import PDB files dropped on an alignment
1170 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1171 scroll bar doesn't work for some CDS/Protein views
1174 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1175 Java 1.8u153 onwards and Java 1.9u4+.
1178 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1179 columns in annotation row
1182 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1183 honored in batch mode
1186 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1187 for structures added to existing Jmol view
1190 <!-- JAL-2223 -->'View Mappings' includes duplicate
1191 entries after importing project with multiple views
1194 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1195 protein sequences via SIFTS from associated PDB entries
1196 with negative residue numbers or missing residues fails
1199 <!-- JAL-2952 -->Exception when shading sequence with negative
1200 Temperature Factor values from annotated PDB files (e.g.
1201 as generated by CONSURF)
1204 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1205 tooltip doesn't include a text description of mutation
1208 <!-- JAL-2922 -->Invert displayed features very slow when
1209 structure and/or overview windows are also shown
1212 <!-- JAL-2954 -->Selecting columns from highlighted regions
1213 very slow for alignments with large numbers of sequences
1216 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1217 with 'StringIndexOutOfBounds'
1220 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1221 platforms running Java 10
1224 <!-- JAL-2960 -->Adding a structure to existing structure
1225 view appears to do nothing because the view is hidden behind the alignment view
1231 <!-- JAL-2926 -->Copy consensus sequence option in applet
1232 should copy the group consensus when popup is opened on it
1238 <!-- JAL-2913 -->Fixed ID width preference is not respected
1241 <em>New Known Defects</em>
1244 <!-- JAL-2973 --> Exceptions occasionally raised when
1245 editing a large alignment and overview is displayed
1248 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1249 repeatedly after a series of edits even when the overview
1250 is no longer reflecting updates
1253 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1254 structures for protein subsequence (if 'Trim Retrieved
1255 Sequences' enabled) or Ensembl isoforms (Workaround in
1256 2.10.4 is to fail back to N&W mapping)
1259 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1260 option gives blank output
1267 <td width="60" nowrap>
1268 <div align="center">
1269 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1272 <td><div align="left">
1273 <ul><li>Updated Certum Codesigning Certificate
1274 (Valid till 30th November 2018)</li></ul></div></td>
1275 <td><div align="left">
1276 <em>Desktop</em><ul>
1278 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1279 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1280 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1281 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1282 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1283 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1284 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1290 <td width="60" nowrap>
1291 <div align="center">
1292 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1295 <td><div align="left">
1299 <!-- JAL-2446 -->Faster and more efficient management and
1300 rendering of sequence features
1303 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1304 429 rate limit request hander
1307 <!-- JAL-2773 -->Structure views don't get updated unless
1308 their colours have changed
1311 <!-- JAL-2495 -->All linked sequences are highlighted for
1312 a structure mousover (Jmol) or selection (Chimera)
1315 <!-- JAL-2790 -->'Cancel' button in progress bar for
1316 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1319 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1320 view from Ensembl locus cross-references
1323 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1327 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1328 feature can be disabled
1331 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1332 PDB easier retrieval of sequences for lists of IDs
1335 <!-- JAL-2758 -->Short names for sequences retrieved from
1341 <li>Groovy interpreter updated to 2.4.12</li>
1342 <li>Example groovy script for generating a matrix of
1343 percent identity scores for current alignment.</li>
1345 <em>Testing and Deployment</em>
1348 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1352 <td><div align="left">
1356 <!-- JAL-2643 -->Pressing tab after updating the colour
1357 threshold text field doesn't trigger an update to the
1361 <!-- JAL-2682 -->Race condition when parsing sequence ID
1365 <!-- JAL-2608 -->Overview windows are also closed when
1366 alignment window is closed
1369 <!-- JAL-2548 -->Export of features doesn't always respect
1373 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1374 takes a long time in Cursor mode
1380 <!-- JAL-2777 -->Structures with whitespace chainCode
1381 cannot be viewed in Chimera
1384 <!-- JAL-2728 -->Protein annotation panel too high in
1388 <!-- JAL-2757 -->Can't edit the query after the server
1389 error warning icon is shown in Uniprot and PDB Free Text
1393 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1396 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1399 <!-- JAL-2739 -->Hidden column marker in last column not
1400 rendered when switching back from Wrapped to normal view
1403 <!-- JAL-2768 -->Annotation display corrupted when
1404 scrolling right in unwapped alignment view
1407 <!-- JAL-2542 -->Existing features on subsequence
1408 incorrectly relocated when full sequence retrieved from
1412 <!-- JAL-2733 -->Last reported memory still shown when
1413 Desktop->Show Memory is unticked (OSX only)
1416 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1417 features of same type and group to be selected for
1421 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1422 alignments when hidden columns are present
1425 <!-- JAL-2392 -->Jalview freezes when loading and
1426 displaying several structures
1429 <!-- JAL-2732 -->Black outlines left after resizing or
1433 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1434 within the Jalview desktop on OSX
1437 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1438 when in wrapped alignment mode
1441 <!-- JAL-2636 -->Scale mark not shown when close to right
1442 hand end of alignment
1445 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1446 each selected sequence do not have correct start/end
1450 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1451 after canceling the Alignment Window's Font dialog
1454 <!-- JAL-2036 -->Show cross-references not enabled after
1455 restoring project until a new view is created
1458 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1459 URL links appears when only default EMBL-EBI link is
1460 configured (since 2.10.2b2)
1463 <!-- JAL-2775 -->Overview redraws whole window when box
1464 position is adjusted
1467 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1468 in a multi-chain structure when viewing alignment
1469 involving more than one chain (since 2.10)
1472 <!-- JAL-2811 -->Double residue highlights in cursor mode
1473 if new selection moves alignment window
1476 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1477 arrow key in cursor mode to pass hidden column marker
1480 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1481 that produces correctly annotated transcripts and products
1484 <!-- JAL-2776 -->Toggling a feature group after first time
1485 doesn't update associated structure view
1488 <em>Applet</em><br />
1491 <!-- JAL-2687 -->Concurrent modification exception when
1492 closing alignment panel
1495 <em>BioJSON</em><br />
1498 <!-- JAL-2546 -->BioJSON export does not preserve
1499 non-positional features
1502 <em>New Known Issues</em>
1505 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1506 sequence features correctly (for many previous versions of
1510 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1511 using cursor in wrapped panel other than top
1514 <!-- JAL-2791 -->Select columns containing feature ignores
1515 graduated colour threshold
1518 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1519 always preserve numbering and sequence features
1522 <em>Known Java 9 Issues</em>
1525 <!-- JAL-2902 -->Groovy Console very slow to open and is
1526 not responsive when entering characters (Webstart, Java
1533 <td width="60" nowrap>
1534 <div align="center">
1535 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1536 <em>2/10/2017</em></strong>
1539 <td><div align="left">
1540 <em>New features in Jalview Desktop</em>
1543 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1545 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1549 <td><div align="left">
1553 <td width="60" nowrap>
1554 <div align="center">
1555 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1556 <em>7/9/2017</em></strong>
1559 <td><div align="left">
1563 <!-- JAL-2588 -->Show gaps in overview window by colouring
1564 in grey (sequences used to be coloured grey, and gaps were
1568 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1572 <!-- JAL-2587 -->Overview updates immediately on increase
1573 in size and progress bar shown as higher resolution
1574 overview is recalculated
1579 <td><div align="left">
1583 <!-- JAL-2664 -->Overview window redraws every hidden
1584 column region row by row
1587 <!-- JAL-2681 -->duplicate protein sequences shown after
1588 retrieving Ensembl crossrefs for sequences from Uniprot
1591 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1592 format setting is unticked
1595 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1596 if group has show boxes format setting unticked
1599 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1600 autoscrolling whilst dragging current selection group to
1601 include sequences and columns not currently displayed
1604 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1605 assemblies are imported via CIF file
1608 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1609 displayed when threshold or conservation colouring is also
1613 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1617 <!-- JAL-2673 -->Jalview continues to scroll after
1618 dragging a selected region off the visible region of the
1622 <!-- JAL-2724 -->Cannot apply annotation based
1623 colourscheme to all groups in a view
1626 <!-- JAL-2511 -->IDs don't line up with sequences
1627 initially after font size change using the Font chooser or
1634 <td width="60" nowrap>
1635 <div align="center">
1636 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1639 <td><div align="left">
1640 <em>Calculations</em>
1644 <!-- JAL-1933 -->Occupancy annotation row shows number of
1645 ungapped positions in each column of the alignment.
1648 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1649 a calculation dialog box
1652 <!-- JAL-2379 -->Revised implementation of PCA for speed
1653 and memory efficiency (~30x faster)
1656 <!-- JAL-2403 -->Revised implementation of sequence
1657 similarity scores as used by Tree, PCA, Shading Consensus
1658 and other calculations
1661 <!-- JAL-2416 -->Score matrices are stored as resource
1662 files within the Jalview codebase
1665 <!-- JAL-2500 -->Trees computed on Sequence Feature
1666 Similarity may have different topology due to increased
1673 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1674 model for alignments and groups
1677 <!-- JAL-384 -->Custom shading schemes created via groovy
1684 <!-- JAL-2526 -->Efficiency improvements for interacting
1685 with alignment and overview windows
1688 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1692 <!-- JAL-2388 -->Hidden columns and sequences can be
1696 <!-- JAL-2611 -->Click-drag in visible area allows fine
1697 adjustment of visible position
1701 <em>Data import/export</em>
1704 <!-- JAL-2535 -->Posterior probability annotation from
1705 Stockholm files imported as sequence associated annotation
1708 <!-- JAL-2507 -->More robust per-sequence positional
1709 annotation input/output via stockholm flatfile
1712 <!-- JAL-2533 -->Sequence names don't include file
1713 extension when importing structure files without embedded
1714 names or PDB accessions
1717 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1718 format sequence substitution matrices
1721 <em>User Interface</em>
1724 <!-- JAL-2447 --> Experimental Features Checkbox in
1725 Desktop's Tools menu to hide or show untested features in
1729 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1730 via Overview or sequence motif search operations
1733 <!-- JAL-2547 -->Amend sequence features dialog box can be
1734 opened by double clicking gaps within sequence feature
1738 <!-- JAL-1476 -->Status bar message shown when not enough
1739 aligned positions were available to create a 3D structure
1743 <em>3D Structure</em>
1746 <!-- JAL-2430 -->Hidden regions in alignment views are not
1747 coloured in linked structure views
1750 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1751 file-based command exchange
1754 <!-- JAL-2375 -->Structure chooser automatically shows
1755 Cached Structures rather than querying the PDBe if
1756 structures are already available for sequences
1759 <!-- JAL-2520 -->Structures imported via URL are cached in
1760 the Jalview project rather than downloaded again when the
1761 project is reopened.
1764 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1765 to transfer Chimera's structure attributes as Jalview
1766 features, and vice-versa (<strong>Experimental
1770 <em>Web Services</em>
1773 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1776 <!-- JAL-2335 -->Filter non-standard amino acids and
1777 nucleotides when submitting to AACon and other MSA
1781 <!-- JAL-2316, -->URLs for viewing database
1782 cross-references provided by identifiers.org and the
1783 EMBL-EBI's MIRIAM DB
1790 <!-- JAL-2344 -->FileFormatI interface for describing and
1791 identifying file formats (instead of String constants)
1794 <!-- JAL-2228 -->FeatureCounter script refactored for
1795 efficiency when counting all displayed features (not
1796 backwards compatible with 2.10.1)
1799 <em>Example files</em>
1802 <!-- JAL-2631 -->Graduated feature colour style example
1803 included in the example feature file
1806 <em>Documentation</em>
1809 <!-- JAL-2339 -->Release notes reformatted for readability
1810 with the built-in Java help viewer
1813 <!-- JAL-1644 -->Find documentation updated with 'search
1814 sequence description' option
1820 <!-- JAL-2485, -->External service integration tests for
1821 Uniprot REST Free Text Search Client
1824 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1827 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1832 <td><div align="left">
1833 <em>Calculations</em>
1836 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1837 matrix - C->R should be '-3'<br />Old matrix restored
1838 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1840 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1841 Jalview's treatment of gaps in PCA and substitution matrix
1842 based Tree calculations.<br /> <br />In earlier versions
1843 of Jalview, gaps matching gaps were penalised, and gaps
1844 matching non-gaps penalised even more. In the PCA
1845 calculation, gaps were actually treated as non-gaps - so
1846 different costs were applied, which meant Jalview's PCAs
1847 were different to those produced by SeqSpace.<br />Jalview
1848 now treats gaps in the same way as SeqSpace (ie it scores
1849 them as 0). <br /> <br />Enter the following in the
1850 Groovy console to restore pre-2.10.2 behaviour:<br />
1851 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1852 // for 2.10.1 mode <br />
1853 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1854 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1855 these settings will affect all subsequent tree and PCA
1856 calculations (not recommended)</em></li>
1858 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1859 scaling of branch lengths for trees computed using
1860 Sequence Feature Similarity.
1863 <!-- JAL-2377 -->PCA calculation could hang when
1864 generating output report when working with highly
1865 redundant alignments
1868 <!-- JAL-2544 --> Sort by features includes features to
1869 right of selected region when gaps present on right-hand
1873 <em>User Interface</em>
1876 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1877 doesn't reselect a specific sequence's associated
1878 annotation after it was used for colouring a view
1881 <!-- JAL-2419 -->Current selection lost if popup menu
1882 opened on a region of alignment without groups
1885 <!-- JAL-2374 -->Popup menu not always shown for regions
1886 of an alignment with overlapping groups
1889 <!-- JAL-2310 -->Finder double counts if both a sequence's
1890 name and description match
1893 <!-- JAL-2370 -->Hiding column selection containing two
1894 hidden regions results in incorrect hidden regions
1897 <!-- JAL-2386 -->'Apply to all groups' setting when
1898 changing colour does not apply Conservation slider value
1902 <!-- JAL-2373 -->Percentage identity and conservation menu
1903 items do not show a tick or allow shading to be disabled
1906 <!-- JAL-2385 -->Conservation shading or PID threshold
1907 lost when base colourscheme changed if slider not visible
1910 <!-- JAL-2547 -->Sequence features shown in tooltip for
1911 gaps before start of features
1914 <!-- JAL-2623 -->Graduated feature colour threshold not
1915 restored to UI when feature colour is edited
1918 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1919 a time when scrolling vertically in wrapped mode.
1922 <!-- JAL-2630 -->Structure and alignment overview update
1923 as graduate feature colour settings are modified via the
1927 <!-- JAL-2034 -->Overview window doesn't always update
1928 when a group defined on the alignment is resized
1931 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1932 wrapped view result in positional status updates
1936 <!-- JAL-2563 -->Status bar doesn't show position for
1937 ambiguous amino acid and nucleotide symbols
1940 <!-- JAL-2602 -->Copy consensus sequence failed if
1941 alignment included gapped columns
1944 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1945 widgets don't permanently disappear
1948 <!-- JAL-2503 -->Cannot select or filter quantitative
1949 annotation that are shown only as column labels (e.g.
1950 T-Coffee column reliability scores)
1953 <!-- JAL-2594 -->Exception thrown if trying to create a
1954 sequence feature on gaps only
1957 <!-- JAL-2504 -->Features created with 'New feature'
1958 button from a Find inherit previously defined feature type
1959 rather than the Find query string
1962 <!-- JAL-2423 -->incorrect title in output window when
1963 exporting tree calculated in Jalview
1966 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1967 and then revealing them reorders sequences on the
1971 <!-- JAL-964 -->Group panel in sequence feature settings
1972 doesn't update to reflect available set of groups after
1973 interactively adding or modifying features
1976 <!-- JAL-2225 -->Sequence Database chooser unusable on
1980 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1981 only excluded gaps in current sequence and ignored
1988 <!-- JAL-2421 -->Overview window visible region moves
1989 erratically when hidden rows or columns are present
1992 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1993 Structure Viewer's colour menu don't correspond to
1997 <!-- JAL-2405 -->Protein specific colours only offered in
1998 colour and group colour menu for protein alignments
2001 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2002 reflect currently selected view or group's shading
2006 <!-- JAL-2624 -->Feature colour thresholds not respected
2007 when rendered on overview and structures when opacity at
2011 <!-- JAL-2589 -->User defined gap colour not shown in
2012 overview when features overlaid on alignment
2015 <!-- JAL-2567 -->Feature settings for different views not
2016 recovered correctly from Jalview project file
2019 <!-- JAL-2256 -->Feature colours in overview when first opened
2020 (automatically via preferences) are different to the main
2024 <em>Data import/export</em>
2027 <!-- JAL-2576 -->Very large alignments take a long time to
2031 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2032 added after a sequence was imported are not written to
2036 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2037 when importing RNA secondary structure via Stockholm
2040 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2041 not shown in correct direction for simple pseudoknots
2044 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2045 with lightGray or darkGray via features file (but can
2049 <!-- JAL-2383 -->Above PID colour threshold not recovered
2050 when alignment view imported from project
2053 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2054 structure and sequences extracted from structure files
2055 imported via URL and viewed in Jmol
2058 <!-- JAL-2520 -->Structures loaded via URL are saved in
2059 Jalview Projects rather than fetched via URL again when
2060 the project is loaded and the structure viewed
2063 <em>Web Services</em>
2066 <!-- JAL-2519 -->EnsemblGenomes example failing after
2067 release of Ensembl v.88
2070 <!-- JAL-2366 -->Proxy server address and port always
2071 appear enabled in Preferences->Connections
2074 <!-- JAL-2461 -->DAS registry not found exceptions
2075 removed from console output
2078 <!-- JAL-2582 -->Cannot retrieve protein products from
2079 Ensembl by Peptide ID
2082 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2083 created from SIFTs, and spurious 'Couldn't open structure
2084 in Chimera' errors raised after April 2017 update (problem
2085 due to 'null' string rather than empty string used for
2086 residues with no corresponding PDB mapping).
2089 <em>Application UI</em>
2092 <!-- JAL-2361 -->User Defined Colours not added to Colour
2096 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2097 case' residues (button in colourscheme editor debugged and
2098 new documentation and tooltips added)
2101 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2102 doesn't restore group-specific text colour thresholds
2105 <!-- JAL-2243 -->Feature settings panel does not update as
2106 new features are added to alignment
2109 <!-- JAL-2532 -->Cancel in feature settings reverts
2110 changes to feature colours via the Amend features dialog
2113 <!-- JAL-2506 -->Null pointer exception when attempting to
2114 edit graduated feature colour via amend features dialog
2118 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2119 selection menu changes colours of alignment views
2122 <!-- JAL-2426 -->Spurious exceptions in console raised
2123 from alignment calculation workers after alignment has
2127 <!-- JAL-1608 -->Typo in selection popup menu - Create
2128 groups now 'Create Group'
2131 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2132 Create/Undefine group doesn't always work
2135 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2136 shown again after pressing 'Cancel'
2139 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2140 adjusts start position in wrap mode
2143 <!-- JAL-2563 -->Status bar doesn't show positions for
2144 ambiguous amino acids
2147 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2148 CDS/Protein view after CDS sequences added for aligned
2152 <!-- JAL-2592 -->User defined colourschemes called 'User
2153 Defined' don't appear in Colours menu
2159 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2160 score models doesn't always result in an updated PCA plot
2163 <!-- JAL-2442 -->Features not rendered as transparent on
2164 overview or linked structure view
2167 <!-- JAL-2372 -->Colour group by conservation doesn't
2171 <!-- JAL-2517 -->Hitting Cancel after applying
2172 user-defined colourscheme doesn't restore original
2179 <!-- JAL-2314 -->Unit test failure:
2180 jalview.ws.jabaws.RNAStructExportImport setup fails
2183 <!-- JAL-2307 -->Unit test failure:
2184 jalview.ws.sifts.SiftsClientTest due to compatibility
2185 problems with deep array comparison equality asserts in
2186 successive versions of TestNG
2189 <!-- JAL-2479 -->Relocated StructureChooserTest and
2190 ParameterUtilsTest Unit tests to Network suite
2193 <em>New Known Issues</em>
2196 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2197 phase after a sequence motif find operation
2200 <!-- JAL-2550 -->Importing annotation file with rows
2201 containing just upper and lower case letters are
2202 interpreted as WUSS RNA secondary structure symbols
2205 <!-- JAL-2590 -->Cannot load and display Newick trees
2206 reliably from eggnog Ortholog database
2209 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2210 containing features of type Highlight' when 'B' is pressed
2211 to mark columns containing highlighted regions.
2214 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2215 doesn't always add secondary structure annotation.
2220 <td width="60" nowrap>
2221 <div align="center">
2222 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2225 <td><div align="left">
2229 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2230 for all consensus calculations
2233 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2236 <li>Updated Jalview's Certum code signing certificate
2239 <em>Application</em>
2242 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2243 set of database cross-references, sorted alphabetically
2246 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2247 from database cross references. Users with custom links
2248 will receive a <a href="webServices/urllinks.html#warning">warning
2249 dialog</a> asking them to update their preferences.
2252 <!-- JAL-2287-->Cancel button and escape listener on
2253 dialog warning user about disconnecting Jalview from a
2257 <!-- JAL-2320-->Jalview's Chimera control window closes if
2258 the Chimera it is connected to is shut down
2261 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2262 columns menu item to mark columns containing highlighted
2263 regions (e.g. from structure selections or results of a
2267 <!-- JAL-2284-->Command line option for batch-generation
2268 of HTML pages rendering alignment data with the BioJS
2278 <!-- JAL-2286 -->Columns with more than one modal residue
2279 are not coloured or thresholded according to percent
2280 identity (first observed in Jalview 2.8.2)
2283 <!-- JAL-2301 -->Threonine incorrectly reported as not
2287 <!-- JAL-2318 -->Updates to documentation pages (above PID
2288 threshold, amino acid properties)
2291 <!-- JAL-2292 -->Lower case residues in sequences are not
2292 reported as mapped to residues in a structure file in the
2296 <!--JAL-2324 -->Identical features with non-numeric scores
2297 could be added multiple times to a sequence
2300 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2301 bond features shown as two highlighted residues rather
2302 than a range in linked structure views, and treated
2303 correctly when selecting and computing trees from features
2306 <!-- JAL-2281-->Custom URL links for database
2307 cross-references are matched to database name regardless
2312 <em>Application</em>
2315 <!-- JAL-2282-->Custom URL links for specific database
2316 names without regular expressions also offer links from
2320 <!-- JAL-2315-->Removing a single configured link in the
2321 URL links pane in Connections preferences doesn't actually
2322 update Jalview configuration
2325 <!-- JAL-2272-->CTRL-Click on a selected region to open
2326 the alignment area popup menu doesn't work on El-Capitan
2329 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2330 files with similarly named sequences if dropped onto the
2334 <!-- JAL-2312 -->Additional mappings are shown for PDB
2335 entries where more chains exist in the PDB accession than
2336 are reported in the SIFTS file
2339 <!-- JAL-2317-->Certain structures do not get mapped to
2340 the structure view when displayed with Chimera
2343 <!-- JAL-2317-->No chains shown in the Chimera view
2344 panel's View->Show Chains submenu
2347 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2348 work for wrapped alignment views
2351 <!--JAL-2197 -->Rename UI components for running JPred
2352 predictions from 'JNet' to 'JPred'
2355 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2356 corrupted when annotation panel vertical scroll is not at
2357 first annotation row
2360 <!--JAL-2332 -->Attempting to view structure for Hen
2361 lysozyme results in a PDB Client error dialog box
2364 <!-- JAL-2319 -->Structure View's mapping report switched
2365 ranges for PDB and sequence for SIFTS
2368 SIFTS 'Not_Observed' residues mapped to non-existant
2372 <!-- <em>New Known Issues</em>
2379 <td width="60" nowrap>
2380 <div align="center">
2381 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2382 <em>25/10/2016</em></strong>
2385 <td><em>Application</em>
2387 <li>3D Structure chooser opens with 'Cached structures'
2388 view if structures already loaded</li>
2389 <li>Progress bar reports models as they are loaded to
2390 structure views</li>
2396 <li>Colour by conservation always enabled and no tick
2397 shown in menu when BLOSUM or PID shading applied</li>
2398 <li>FER1_ARATH and FER2_ARATH labels were switched in
2399 example sequences/projects/trees</li>
2401 <em>Application</em>
2403 <li>Jalview projects with views of local PDB structure
2404 files saved on Windows cannot be opened on OSX</li>
2405 <li>Multiple structure views can be opened and superposed
2406 without timeout for structures with multiple models or
2407 multiple sequences in alignment</li>
2408 <li>Cannot import or associated local PDB files without a
2409 PDB ID HEADER line</li>
2410 <li>RMSD is not output in Jmol console when superposition
2412 <li>Drag and drop of URL from Browser fails for Linux and
2413 OSX versions earlier than El Capitan</li>
2414 <li>ENA client ignores invalid content from ENA server</li>
2415 <li>Exceptions are not raised in console when ENA client
2416 attempts to fetch non-existent IDs via Fetch DB Refs UI
2418 <li>Exceptions are not raised in console when a new view
2419 is created on the alignment</li>
2420 <li>OSX right-click fixed for group selections: CMD-click
2421 to insert/remove gaps in groups and CTRL-click to open group
2424 <em>Build and deployment</em>
2426 <li>URL link checker now copes with multi-line anchor
2429 <em>New Known Issues</em>
2431 <li>Drag and drop from URL links in browsers do not work
2438 <td width="60" nowrap>
2439 <div align="center">
2440 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2443 <td><em>General</em>
2446 <!-- JAL-2124 -->Updated Spanish translations.
2449 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2450 for importing structure data to Jalview. Enables mmCIF and
2454 <!-- JAL-192 --->Alignment ruler shows positions relative to
2458 <!-- JAL-2202 -->Position/residue shown in status bar when
2459 mousing over sequence associated annotation
2462 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2466 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2467 '()', canonical '[]' and invalid '{}' base pair populations
2471 <!-- JAL-2092 -->Feature settings popup menu options for
2472 showing or hiding columns containing a feature
2475 <!-- JAL-1557 -->Edit selected group by double clicking on
2476 group and sequence associated annotation labels
2479 <!-- JAL-2236 -->Sequence name added to annotation label in
2480 select/hide columns by annotation and colour by annotation
2484 </ul> <em>Application</em>
2487 <!-- JAL-2050-->Automatically hide introns when opening a
2488 gene/transcript view
2491 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2495 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2496 structure mappings with the EMBL-EBI PDBe SIFTS database
2499 <!-- JAL-2079 -->Updated download sites used for Rfam and
2500 Pfam sources to xfam.org
2503 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2506 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2507 over sequences in Jalview
2510 <!-- JAL-2027-->Support for reverse-complement coding
2511 regions in ENA and EMBL
2514 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2515 for record retrieval via ENA rest API
2518 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2522 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2523 groovy script execution
2526 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2527 alignment window's Calculate menu
2530 <!-- JAL-1812 -->Allow groovy scripts that call
2531 Jalview.getAlignFrames() to run in headless mode
2534 <!-- JAL-2068 -->Support for creating new alignment
2535 calculation workers from groovy scripts
2538 <!-- JAL-1369 --->Store/restore reference sequence in
2542 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2543 associations are now saved/restored from project
2546 <!-- JAL-1993 -->Database selection dialog always shown
2547 before sequence fetcher is opened
2550 <!-- JAL-2183 -->Double click on an entry in Jalview's
2551 database chooser opens a sequence fetcher
2554 <!-- JAL-1563 -->Free-text search client for UniProt using
2555 the UniProt REST API
2558 <!-- JAL-2168 -->-nonews command line parameter to prevent
2559 the news reader opening
2562 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2563 querying stored in preferences
2566 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2570 <!-- JAL-1977-->Tooltips shown on database chooser
2573 <!-- JAL-391 -->Reverse complement function in calculate
2574 menu for nucleotide sequences
2577 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2578 and feature counts preserves alignment ordering (and
2579 debugged for complex feature sets).
2582 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2583 viewing structures with Jalview 2.10
2586 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2587 genome, transcript CCDS and gene ids via the Ensembl and
2588 Ensembl Genomes REST API
2591 <!-- JAL-2049 -->Protein sequence variant annotation
2592 computed for 'sequence_variant' annotation on CDS regions
2596 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2600 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2601 Ref Fetcher fails to match, or otherwise updates sequence
2602 data from external database records.
2605 <!-- JAL-2154 -->Revised Jalview Project format for
2606 efficient recovery of sequence coding and alignment
2607 annotation relationships.
2609 </ul> <!-- <em>Applet</em>
2620 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2624 <!-- JAL-2018-->Export features in Jalview format (again)
2625 includes graduated colourschemes
2628 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2629 working with big alignments and lots of hidden columns
2632 <!-- JAL-2053-->Hidden column markers not always rendered
2633 at right of alignment window
2636 <!-- JAL-2067 -->Tidied up links in help file table of
2640 <!-- JAL-2072 -->Feature based tree calculation not shown
2644 <!-- JAL-2075 -->Hidden columns ignored during feature
2645 based tree calculation
2648 <!-- JAL-2065 -->Alignment view stops updating when show
2649 unconserved enabled for group on alignment
2652 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2656 <!-- JAL-2146 -->Alignment column in status incorrectly
2657 shown as "Sequence position" when mousing over
2661 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2662 hidden columns present
2665 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2666 user created annotation added to alignment
2669 <!-- JAL-1841 -->RNA Structure consensus only computed for
2670 '()' base pair annotation
2673 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2674 in zero scores for all base pairs in RNA Structure
2678 <!-- JAL-2174-->Extend selection with columns containing
2682 <!-- JAL-2275 -->Pfam format writer puts extra space at
2683 beginning of sequence
2686 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2690 <!-- JAL-2238 -->Cannot create groups on an alignment from
2691 from a tree when t-coffee scores are shown
2694 <!-- JAL-1836,1967 -->Cannot import and view PDB
2695 structures with chains containing negative resnums (4q4h)
2698 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2702 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2703 to Clustal, PIR and PileUp output
2706 <!-- JAL-2008 -->Reordering sequence features that are
2707 not visible causes alignment window to repaint
2710 <!-- JAL-2006 -->Threshold sliders don't work in
2711 graduated colour and colour by annotation row for e-value
2712 scores associated with features and annotation rows
2715 <!-- JAL-1797 -->amino acid physicochemical conservation
2716 calculation should be case independent
2719 <!-- JAL-2173 -->Remove annotation also updates hidden
2723 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2724 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2725 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2728 <!-- JAL-2065 -->Null pointer exceptions and redraw
2729 problems when reference sequence defined and 'show
2730 non-conserved' enabled
2733 <!-- JAL-1306 -->Quality and Conservation are now shown on
2734 load even when Consensus calculation is disabled
2737 <!-- JAL-1932 -->Remove right on penultimate column of
2738 alignment does nothing
2741 <em>Application</em>
2744 <!-- JAL-1552-->URLs and links can't be imported by
2745 drag'n'drop on OSX when launched via webstart (note - not
2746 yet fixed for El Capitan)
2749 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2750 output when running on non-gb/us i18n platforms
2753 <!-- JAL-1944 -->Error thrown when exporting a view with
2754 hidden sequences as flat-file alignment
2757 <!-- JAL-2030-->InstallAnywhere distribution fails when
2761 <!-- JAL-2080-->Jalview very slow to launch via webstart
2762 (also hotfix for 2.9.0b2)
2765 <!-- JAL-2085 -->Cannot save project when view has a
2766 reference sequence defined
2769 <!-- JAL-1011 -->Columns are suddenly selected in other
2770 alignments and views when revealing hidden columns
2773 <!-- JAL-1989 -->Hide columns not mirrored in complement
2774 view in a cDNA/Protein splitframe
2777 <!-- JAL-1369 -->Cannot save/restore representative
2778 sequence from project when only one sequence is
2782 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2783 in Structure Chooser
2786 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2787 structure consensus didn't refresh annotation panel
2790 <!-- JAL-1962 -->View mapping in structure view shows
2791 mappings between sequence and all chains in a PDB file
2794 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2795 dialogs format columns correctly, don't display array
2796 data, sort columns according to type
2799 <!-- JAL-1975 -->Export complete shown after destination
2800 file chooser is cancelled during an image export
2803 <!-- JAL-2025 -->Error when querying PDB Service with
2804 sequence name containing special characters
2807 <!-- JAL-2024 -->Manual PDB structure querying should be
2811 <!-- JAL-2104 -->Large tooltips with broken HTML
2812 formatting don't wrap
2815 <!-- JAL-1128 -->Figures exported from wrapped view are
2816 truncated so L looks like I in consensus annotation
2819 <!-- JAL-2003 -->Export features should only export the
2820 currently displayed features for the current selection or
2824 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2825 after fetching cross-references, and restoring from
2829 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2830 followed in the structure viewer
2833 <!-- JAL-2163 -->Titles for individual alignments in
2834 splitframe not restored from project
2837 <!-- JAL-2145 -->missing autocalculated annotation at
2838 trailing end of protein alignment in transcript/product
2839 splitview when pad-gaps not enabled by default
2842 <!-- JAL-1797 -->amino acid physicochemical conservation
2846 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2847 article has been read (reopened issue due to
2848 internationalisation problems)
2851 <!-- JAL-1960 -->Only offer PDB structures in structure
2852 viewer based on sequence name, PDB and UniProt
2857 <!-- JAL-1976 -->No progress bar shown during export of
2861 <!-- JAL-2213 -->Structures not always superimposed after
2862 multiple structures are shown for one or more sequences.
2865 <!-- JAL-1370 -->Reference sequence characters should not
2866 be replaced with '.' when 'Show unconserved' format option
2870 <!-- JAL-1823 -->Cannot specify chain code when entering
2871 specific PDB id for sequence
2874 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2875 'Export hidden sequences' is enabled, but 'export hidden
2876 columns' is disabled.
2879 <!--JAL-2026-->Best Quality option in structure chooser
2880 selects lowest rather than highest resolution structures
2884 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2885 to sequence mapping in 'View Mappings' report
2888 <!-- JAL-2284 -->Unable to read old Jalview projects that
2889 contain non-XML data added after Jalvew wrote project.
2892 <!-- JAL-2118 -->Newly created annotation row reorders
2893 after clicking on it to create new annotation for a
2897 <!-- JAL-1980 -->Null Pointer Exception raised when
2898 pressing Add on an orphaned cut'n'paste window.
2900 <!-- may exclude, this is an external service stability issue JAL-1941
2901 -- > RNA 3D structure not added via DSSR service</li> -->
2906 <!-- JAL-2151 -->Incorrect columns are selected when
2907 hidden columns present before start of sequence
2910 <!-- JAL-1986 -->Missing dependencies on applet pages
2914 <!-- JAL-1947 -->Overview pixel size changes when
2915 sequences are hidden in applet
2918 <!-- JAL-1996 -->Updated instructions for applet
2919 deployment on examples pages.
2926 <td width="60" nowrap>
2927 <div align="center">
2928 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2929 <em>16/10/2015</em></strong>
2932 <td><em>General</em>
2934 <li>Time stamps for signed Jalview application and applet
2939 <em>Application</em>
2941 <li>Duplicate group consensus and conservation rows
2942 shown when tree is partitioned</li>
2943 <li>Erratic behaviour when tree partitions made with
2944 multiple cDNA/Protein split views</li>
2950 <td width="60" nowrap>
2951 <div align="center">
2952 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2953 <em>8/10/2015</em></strong>
2956 <td><em>General</em>
2958 <li>Updated Spanish translations of localized text for
2960 </ul> <em>Application</em>
2962 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2963 <li>Signed OSX InstallAnywhere installer<br></li>
2964 <li>Support for per-sequence based annotations in BioJSON</li>
2965 </ul> <em>Applet</em>
2967 <li>Split frame example added to applet examples page</li>
2968 </ul> <em>Build and Deployment</em>
2971 <!-- JAL-1888 -->New ant target for running Jalview's test
2979 <li>Mapping of cDNA to protein in split frames
2980 incorrect when sequence start > 1</li>
2981 <li>Broken images in filter column by annotation dialog
2983 <li>Feature colours not parsed from features file</li>
2984 <li>Exceptions and incomplete link URLs recovered when
2985 loading a features file containing HTML tags in feature
2989 <em>Application</em>
2991 <li>Annotations corrupted after BioJS export and
2993 <li>Incorrect sequence limits after Fetch DB References
2994 with 'trim retrieved sequences'</li>
2995 <li>Incorrect warning about deleting all data when
2996 deleting selected columns</li>
2997 <li>Patch to build system for shipping properly signed
2998 JNLP templates for webstart launch</li>
2999 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3000 unreleased structures for download or viewing</li>
3001 <li>Tab/space/return keystroke operation of EMBL-PDBe
3002 fetcher/viewer dialogs works correctly</li>
3003 <li>Disabled 'minimise' button on Jalview windows
3004 running on OSX to workaround redraw hang bug</li>
3005 <li>Split cDNA/Protein view position and geometry not
3006 recovered from jalview project</li>
3007 <li>Initial enabled/disabled state of annotation menu
3008 sorter 'show autocalculated first/last' corresponds to
3010 <li>Restoring of Clustal, RNA Helices and T-Coffee
3011 color schemes from BioJSON</li>
3015 <li>Reorder sequences mirrored in cDNA/Protein split
3017 <li>Applet with Jmol examples not loading correctly</li>
3023 <td><div align="center">
3024 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3026 <td><em>General</em>
3028 <li>Linked visualisation and analysis of DNA and Protein
3031 <li>Translated cDNA alignments shown as split protein
3032 and DNA alignment views</li>
3033 <li>Codon consensus annotation for linked protein and
3034 cDNA alignment views</li>
3035 <li>Link cDNA or Protein product sequences by loading
3036 them onto Protein or cDNA alignments</li>
3037 <li>Reconstruct linked cDNA alignment from aligned
3038 protein sequences</li>
3041 <li>Jmol integration updated to Jmol v14.2.14</li>
3042 <li>Import and export of Jalview alignment views as <a
3043 href="features/bioJsonFormat.html">BioJSON</a></li>
3044 <li>New alignment annotation file statements for
3045 reference sequences and marking hidden columns</li>
3046 <li>Reference sequence based alignment shading to
3047 highlight variation</li>
3048 <li>Select or hide columns according to alignment
3050 <li>Find option for locating sequences by description</li>
3051 <li>Conserved physicochemical properties shown in amino
3052 acid conservation row</li>
3053 <li>Alignments can be sorted by number of RNA helices</li>
3054 </ul> <em>Application</em>
3056 <li>New cDNA/Protein analysis capabilities
3058 <li>Get Cross-References should open a Split Frame
3059 view with cDNA/Protein</li>
3060 <li>Detect when nucleotide sequences and protein
3061 sequences are placed in the same alignment</li>
3062 <li>Split cDNA/Protein views are saved in Jalview
3067 <li>Use REST API to talk to Chimera</li>
3068 <li>Selected regions in Chimera are highlighted in linked
3069 Jalview windows</li>
3071 <li>VARNA RNA viewer updated to v3.93</li>
3072 <li>VARNA views are saved in Jalview Projects</li>
3073 <li>Pseudoknots displayed as Jalview RNA annotation can
3074 be shown in VARNA</li>
3076 <li>Make groups for selection uses marked columns as well
3077 as the active selected region</li>
3079 <li>Calculate UPGMA and NJ trees using sequence feature
3081 <li>New Export options
3083 <li>New Export Settings dialog to control hidden
3084 region export in flat file generation</li>
3086 <li>Export alignment views for display with the <a
3087 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3089 <li>Export scrollable SVG in HTML page</li>
3090 <li>Optional embedding of BioJSON data when exporting
3091 alignment figures to HTML</li>
3093 <li>3D structure retrieval and display
3095 <li>Free text and structured queries with the PDBe
3097 <li>PDBe Search API based discovery and selection of
3098 PDB structures for a sequence set</li>
3102 <li>JPred4 employed for protein secondary structure
3104 <li>Hide Insertions menu option to hide unaligned columns
3105 for one or a group of sequences</li>
3106 <li>Automatically hide insertions in alignments imported
3107 from the JPred4 web server</li>
3108 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3109 system on OSX<br />LGPL libraries courtesy of <a
3110 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3112 <li>changed 'View nucleotide structure' submenu to 'View
3113 VARNA 2D Structure'</li>
3114 <li>change "View protein structure" menu option to "3D
3117 </ul> <em>Applet</em>
3119 <li>New layout for applet example pages</li>
3120 <li>New parameters to enable SplitFrame view
3121 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3122 <li>New example demonstrating linked viewing of cDNA and
3123 Protein alignments</li>
3124 </ul> <em>Development and deployment</em>
3126 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3127 <li>Include installation type and git revision in build
3128 properties and console log output</li>
3129 <li>Jalview Github organisation, and new github site for
3130 storing BioJsMSA Templates</li>
3131 <li>Jalview's unit tests now managed with TestNG</li>
3134 <!-- <em>General</em>
3136 </ul> --> <!-- issues resolved --> <em>Application</em>
3138 <li>Escape should close any open find dialogs</li>
3139 <li>Typo in select-by-features status report</li>
3140 <li>Consensus RNA secondary secondary structure
3141 predictions are not highlighted in amber</li>
3142 <li>Missing gap character in v2.7 example file means
3143 alignment appears unaligned when pad-gaps is not enabled</li>
3144 <li>First switch to RNA Helices colouring doesn't colour
3145 associated structure views</li>
3146 <li>ID width preference option is greyed out when auto
3147 width checkbox not enabled</li>
3148 <li>Stopped a warning dialog from being shown when
3149 creating user defined colours</li>
3150 <li>'View Mapping' in structure viewer shows sequence
3151 mappings for just that viewer's sequences</li>
3152 <li>Workaround for superposing PDB files containing
3153 multiple models in Chimera</li>
3154 <li>Report sequence position in status bar when hovering
3155 over Jmol structure</li>
3156 <li>Cannot output gaps as '.' symbols with Selection ->
3157 output to text box</li>
3158 <li>Flat file exports of alignments with hidden columns
3159 have incorrect sequence start/end</li>
3160 <li>'Aligning' a second chain to a Chimera structure from
3162 <li>Colour schemes applied to structure viewers don't
3163 work for nucleotide</li>
3164 <li>Loading/cut'n'pasting an empty or invalid file leads
3165 to a grey/invisible alignment window</li>
3166 <li>Exported Jpred annotation from a sequence region
3167 imports to different position</li>
3168 <li>Space at beginning of sequence feature tooltips shown
3169 on some platforms</li>
3170 <li>Chimera viewer 'View | Show Chain' menu is not
3172 <li>'New View' fails with a Null Pointer Exception in
3173 console if Chimera has been opened</li>
3174 <li>Mouseover to Chimera not working</li>
3175 <li>Miscellaneous ENA XML feature qualifiers not
3177 <li>NPE in annotation renderer after 'Extract Scores'</li>
3178 <li>If two structures in one Chimera window, mouseover of
3179 either sequence shows on first structure</li>
3180 <li>'Show annotations' options should not make
3181 non-positional annotations visible</li>
3182 <li>Subsequence secondary structure annotation not shown
3183 in right place after 'view flanking regions'</li>
3184 <li>File Save As type unset when current file format is
3186 <li>Save as '.jar' option removed for saving Jalview
3188 <li>Colour by Sequence colouring in Chimera more
3190 <li>Cannot 'add reference annotation' for a sequence in
3191 several views on same alignment</li>
3192 <li>Cannot show linked products for EMBL / ENA records</li>
3193 <li>Jalview's tooltip wraps long texts containing no
3195 </ul> <em>Applet</em>
3197 <li>Jmol to JalviewLite mouseover/link not working</li>
3198 <li>JalviewLite can't import sequences with ID
3199 descriptions containing angle brackets</li>
3200 </ul> <em>General</em>
3202 <li>Cannot export and reimport RNA secondary structure
3203 via jalview annotation file</li>
3204 <li>Random helix colour palette for colour by annotation
3205 with RNA secondary structure</li>
3206 <li>Mouseover to cDNA from STOP residue in protein
3207 translation doesn't work.</li>
3208 <li>hints when using the select by annotation dialog box</li>
3209 <li>Jmol alignment incorrect if PDB file has alternate CA
3211 <li>FontChooser message dialog appears to hang after
3212 choosing 1pt font</li>
3213 <li>Peptide secondary structure incorrectly imported from
3214 annotation file when annotation display text includes 'e' or
3216 <li>Cannot set colour of new feature type whilst creating
3218 <li>cDNA translation alignment should not be sequence
3219 order dependent</li>
3220 <li>'Show unconserved' doesn't work for lower case
3222 <li>Nucleotide ambiguity codes involving R not recognised</li>
3223 </ul> <em>Deployment and Documentation</em>
3225 <li>Applet example pages appear different to the rest of
3226 www.jalview.org</li>
3227 </ul> <em>Application Known issues</em>
3229 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3230 <li>Misleading message appears after trying to delete
3232 <li>Jalview icon not shown in dock after InstallAnywhere
3233 version launches</li>
3234 <li>Fetching EMBL reference for an RNA sequence results
3235 fails with a sequence mismatch</li>
3236 <li>Corrupted or unreadable alignment display when
3237 scrolling alignment to right</li>
3238 <li>ArrayIndexOutOfBoundsException thrown when remove
3239 empty columns called on alignment with ragged gapped ends</li>
3240 <li>auto calculated alignment annotation rows do not get
3241 placed above or below non-autocalculated rows</li>
3242 <li>Jalview dekstop becomes sluggish at full screen in
3243 ultra-high resolution</li>
3244 <li>Cannot disable consensus calculation independently of
3245 quality and conservation</li>
3246 <li>Mouseover highlighting between cDNA and protein can
3247 become sluggish with more than one splitframe shown</li>
3248 </ul> <em>Applet Known Issues</em>
3250 <li>Core PDB parsing code requires Jmol</li>
3251 <li>Sequence canvas panel goes white when alignment
3252 window is being resized</li>
3258 <td><div align="center">
3259 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3261 <td><em>General</em>
3263 <li>Updated Java code signing certificate donated by
3265 <li>Features and annotation preserved when performing
3266 pairwise alignment</li>
3267 <li>RNA pseudoknot annotation can be
3268 imported/exported/displayed</li>
3269 <li>'colour by annotation' can colour by RNA and
3270 protein secondary structure</li>
3271 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3272 post-hoc with 2.9 release</em>)
3275 </ul> <em>Application</em>
3277 <li>Extract and display secondary structure for sequences
3278 with 3D structures</li>
3279 <li>Support for parsing RNAML</li>
3280 <li>Annotations menu for layout
3282 <li>sort sequence annotation rows by alignment</li>
3283 <li>place sequence annotation above/below alignment
3286 <li>Output in Stockholm format</li>
3287 <li>Internationalisation: improved Spanish (es)
3289 <li>Structure viewer preferences tab</li>
3290 <li>Disorder and Secondary Structure annotation tracks
3291 shared between alignments</li>
3292 <li>UCSF Chimera launch and linked highlighting from
3294 <li>Show/hide all sequence associated annotation rows for
3295 all or current selection</li>
3296 <li>disorder and secondary structure predictions
3297 available as dataset annotation</li>
3298 <li>Per-sequence rna helices colouring</li>
3301 <li>Sequence database accessions imported when fetching
3302 alignments from Rfam</li>
3303 <li>update VARNA version to 3.91</li>
3305 <li>New groovy scripts for exporting aligned positions,
3306 conservation values, and calculating sum of pairs scores.</li>
3307 <li>Command line argument to set default JABAWS server</li>
3308 <li>include installation type in build properties and
3309 console log output</li>
3310 <li>Updated Jalview project format to preserve dataset
3314 <!-- issues resolved --> <em>Application</em>
3316 <li>Distinguish alignment and sequence associated RNA
3317 structure in structure->view->VARNA</li>
3318 <li>Raise dialog box if user deletes all sequences in an
3320 <li>Pressing F1 results in documentation opening twice</li>
3321 <li>Sequence feature tooltip is wrapped</li>
3322 <li>Double click on sequence associated annotation
3323 selects only first column</li>
3324 <li>Redundancy removal doesn't result in unlinked
3325 leaves shown in tree</li>
3326 <li>Undos after several redundancy removals don't undo
3328 <li>Hide sequence doesn't hide associated annotation</li>
3329 <li>User defined colours dialog box too big to fit on
3330 screen and buttons not visible</li>
3331 <li>author list isn't updated if already written to
3332 Jalview properties</li>
3333 <li>Popup menu won't open after retrieving sequence
3335 <li>File open window for associate PDB doesn't open</li>
3336 <li>Left-then-right click on a sequence id opens a
3337 browser search window</li>
3338 <li>Cannot open sequence feature shading/sort popup menu
3339 in feature settings dialog</li>
3340 <li>better tooltip placement for some areas of Jalview
3342 <li>Allow addition of JABAWS Server which doesn't
3343 pass validation</li>
3344 <li>Web services parameters dialog box is too large to
3346 <li>Muscle nucleotide alignment preset obscured by
3348 <li>JABAWS preset submenus don't contain newly
3349 defined user preset</li>
3350 <li>MSA web services warns user if they were launched
3351 with invalid input</li>
3352 <li>Jalview cannot contact DAS Registy when running on
3355 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3356 'Superpose with' submenu not shown when new view
3360 </ul> <!-- <em>Applet</em>
3362 </ul> <em>General</em>
3364 </ul>--> <em>Deployment and Documentation</em>
3366 <li>2G and 1G options in launchApp have no effect on
3367 memory allocation</li>
3368 <li>launchApp service doesn't automatically open
3369 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3371 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3372 InstallAnywhere reports cannot find valid JVM when Java
3373 1.7_055 is available
3375 </ul> <em>Application Known issues</em>
3378 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3379 corrupted or unreadable alignment display when scrolling
3383 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3384 retrieval fails but progress bar continues for DAS retrieval
3385 with large number of ID
3388 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3389 flatfile output of visible region has incorrect sequence
3393 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3394 rna structure consensus doesn't update when secondary
3395 structure tracks are rearranged
3398 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3399 invalid rna structure positional highlighting does not
3400 highlight position of invalid base pairs
3403 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3404 out of memory errors are not raised when saving Jalview
3405 project from alignment window file menu
3408 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3409 Switching to RNA Helices colouring doesn't propagate to
3413 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3414 colour by RNA Helices not enabled when user created
3415 annotation added to alignment
3418 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3419 Jalview icon not shown on dock in Mountain Lion/Webstart
3421 </ul> <em>Applet Known Issues</em>
3424 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3425 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3428 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3429 Jalview and Jmol example not compatible with IE9
3432 <li>Sort by annotation score doesn't reverse order
3438 <td><div align="center">
3439 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3442 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3445 <li>Internationalisation of user interface (usually
3446 called i18n support) and translation for Spanish locale</li>
3447 <li>Define/Undefine group on current selection with
3448 Ctrl-G/Shift Ctrl-G</li>
3449 <li>Improved group creation/removal options in
3450 alignment/sequence Popup menu</li>
3451 <li>Sensible precision for symbol distribution
3452 percentages shown in logo tooltip.</li>
3453 <li>Annotation panel height set according to amount of
3454 annotation when alignment first opened</li>
3455 </ul> <em>Application</em>
3457 <li>Interactive consensus RNA secondary structure
3458 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3459 <li>Select columns containing particular features from
3460 Feature Settings dialog</li>
3461 <li>View all 'representative' PDB structures for selected
3463 <li>Update Jalview project format:
3465 <li>New file extension for Jalview projects '.jvp'</li>
3466 <li>Preserve sequence and annotation dataset (to
3467 store secondary structure annotation,etc)</li>
3468 <li>Per group and alignment annotation and RNA helix
3472 <li>New similarity measures for PCA and Tree calculation
3474 <li>Experimental support for retrieval and viewing of
3475 flanking regions for an alignment</li>
3479 <!-- issues resolved --> <em>Application</em>
3481 <li>logo keeps spinning and status remains at queued or
3482 running after job is cancelled</li>
3483 <li>cannot export features from alignments imported from
3484 Jalview/VAMSAS projects</li>
3485 <li>Buggy slider for web service parameters that take
3487 <li>Newly created RNA secondary structure line doesn't
3488 have 'display all symbols' flag set</li>
3489 <li>T-COFFEE alignment score shading scheme and other
3490 annotation shading not saved in Jalview project</li>
3491 <li>Local file cannot be loaded in freshly downloaded
3493 <li>Jalview icon not shown on dock in Mountain
3495 <li>Load file from desktop file browser fails</li>
3496 <li>Occasional NPE thrown when calculating large trees</li>
3497 <li>Cannot reorder or slide sequences after dragging an
3498 alignment onto desktop</li>
3499 <li>Colour by annotation dialog throws NPE after using
3500 'extract scores' function</li>
3501 <li>Loading/cut'n'pasting an empty file leads to a grey
3502 alignment window</li>
3503 <li>Disorder thresholds rendered incorrectly after
3504 performing IUPred disorder prediction</li>
3505 <li>Multiple group annotated consensus rows shown when
3506 changing 'normalise logo' display setting</li>
3507 <li>Find shows blank dialog after 'finished searching' if
3508 nothing matches query</li>
3509 <li>Null Pointer Exceptions raised when sorting by
3510 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3512 <li>Errors in Jmol console when structures in alignment
3513 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3515 <li>Not all working JABAWS services are shown in
3517 <li>JAVAWS version of Jalview fails to launch with
3518 'invalid literal/length code'</li>
3519 <li>Annotation/RNA Helix colourschemes cannot be applied
3520 to alignment with groups (actually fixed in 2.8.0b1)</li>
3521 <li>RNA Helices and T-Coffee Scores available as default
3524 </ul> <em>Applet</em>
3526 <li>Remove group option is shown even when selection is
3528 <li>Apply to all groups ticked but colourscheme changes
3529 don't affect groups</li>
3530 <li>Documented RNA Helices and T-Coffee Scores as valid
3531 colourscheme name</li>
3532 <li>Annotation labels drawn on sequence IDs when
3533 Annotation panel is not displayed</li>
3534 <li>Increased font size for dropdown menus on OSX and
3535 embedded windows</li>
3536 </ul> <em>Other</em>
3538 <li>Consensus sequence for alignments/groups with a
3539 single sequence were not calculated</li>
3540 <li>annotation files that contain only groups imported as
3541 annotation and junk sequences</li>
3542 <li>Fasta files with sequences containing '*' incorrectly
3543 recognised as PFAM or BLC</li>
3544 <li>conservation/PID slider apply all groups option
3545 doesn't affect background (2.8.0b1)
3547 <li>redundancy highlighting is erratic at 0% and 100%</li>
3548 <li>Remove gapped columns fails for sequences with ragged
3550 <li>AMSA annotation row with leading spaces is not
3551 registered correctly on import</li>
3552 <li>Jalview crashes when selecting PCA analysis for
3553 certain alignments</li>
3554 <li>Opening the colour by annotation dialog for an
3555 existing annotation based 'use original colours'
3556 colourscheme loses original colours setting</li>
3561 <td><div align="center">
3562 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3563 <em>30/1/2014</em></strong>
3567 <li>Trusted certificates for JalviewLite applet and
3568 Jalview Desktop application<br />Certificate was donated by
3569 <a href="https://www.certum.eu">Certum</a> to the Jalview
3570 open source project).
3572 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3573 <li>Output in Stockholm format</li>
3574 <li>Allow import of data from gzipped files</li>
3575 <li>Export/import group and sequence associated line
3576 graph thresholds</li>
3577 <li>Nucleotide substitution matrix that supports RNA and
3578 ambiguity codes</li>
3579 <li>Allow disorder predictions to be made on the current
3580 selection (or visible selection) in the same way that JPred
3582 <li>Groovy scripting for headless Jalview operation</li>
3583 </ul> <em>Other improvements</em>
3585 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3586 <li>COMBINE statement uses current SEQUENCE_REF and
3587 GROUP_REF scope to group annotation rows</li>
3588 <li>Support '' style escaping of quotes in Newick
3590 <li>Group options for JABAWS service by command line name</li>
3591 <li>Empty tooltip shown for JABA service options with a
3592 link but no description</li>
3593 <li>Select primary source when selecting authority in
3594 database fetcher GUI</li>
3595 <li>Add .mfa to FASTA file extensions recognised by
3597 <li>Annotation label tooltip text wrap</li>
3602 <li>Slow scrolling when lots of annotation rows are
3604 <li>Lots of NPE (and slowness) after creating RNA
3605 secondary structure annotation line</li>
3606 <li>Sequence database accessions not imported when
3607 fetching alignments from Rfam</li>
3608 <li>Incorrect SHMR submission for sequences with
3610 <li>View all structures does not always superpose
3612 <li>Option widgets in service parameters not updated to
3613 reflect user or preset settings</li>
3614 <li>Null pointer exceptions for some services without
3615 presets or adjustable parameters</li>
3616 <li>Discover PDB IDs entry in structure menu doesn't
3617 discover PDB xRefs</li>
3618 <li>Exception encountered while trying to retrieve
3619 features with DAS</li>
3620 <li>Lowest value in annotation row isn't coloured
3621 when colour by annotation (per sequence) is coloured</li>
3622 <li>Keyboard mode P jumps to start of gapped region when
3623 residue follows a gap</li>
3624 <li>Jalview appears to hang importing an alignment with
3625 Wrap as default or after enabling Wrap</li>
3626 <li>'Right click to add annotations' message
3627 shown in wrap mode when no annotations present</li>
3628 <li>Disorder predictions fail with NPE if no automatic
3629 annotation already exists on alignment</li>
3630 <li>oninit javascript function should be called after
3631 initialisation completes</li>
3632 <li>Remove redundancy after disorder prediction corrupts
3633 alignment window display</li>
3634 <li>Example annotation file in documentation is invalid</li>
3635 <li>Grouped line graph annotation rows are not exported
3636 to annotation file</li>
3637 <li>Multi-harmony analysis cannot be run when only two
3639 <li>Cannot create multiple groups of line graphs with
3640 several 'combine' statements in annotation file</li>
3641 <li>Pressing return several times causes Number Format
3642 exceptions in keyboard mode</li>
3643 <li>Multi-harmony (SHMMR) method doesn't submit
3644 correct partitions for input data</li>
3645 <li>Translation from DNA to Amino Acids fails</li>
3646 <li>Jalview fail to load newick tree with quoted label</li>
3647 <li>--headless flag isn't understood</li>
3648 <li>ClassCastException when generating EPS in headless
3650 <li>Adjusting sequence-associated shading threshold only
3651 changes one row's threshold</li>
3652 <li>Preferences and Feature settings panel panel
3653 doesn't open</li>
3654 <li>hide consensus histogram also hides conservation and
3655 quality histograms</li>
3660 <td><div align="center">
3661 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3663 <td><em>Application</em>
3665 <li>Support for JABAWS 2.0 Services (AACon alignment
3666 conservation, protein disorder and Clustal Omega)</li>
3667 <li>JABAWS server status indicator in Web Services
3669 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3670 in Jalview alignment window</li>
3671 <li>Updated Jalview build and deploy framework for OSX
3672 mountain lion, windows 7, and 8</li>
3673 <li>Nucleotide substitution matrix for PCA that supports
3674 RNA and ambiguity codes</li>
3676 <li>Improved sequence database retrieval GUI</li>
3677 <li>Support fetching and database reference look up
3678 against multiple DAS sources (Fetch all from in 'fetch db
3680 <li>Jalview project improvements
3682 <li>Store and retrieve the 'belowAlignment'
3683 flag for annotation</li>
3684 <li>calcId attribute to group annotation rows on the
3686 <li>Store AACon calculation settings for a view in
3687 Jalview project</li>
3691 <li>horizontal scrolling gesture support</li>
3692 <li>Visual progress indicator when PCA calculation is
3694 <li>Simpler JABA web services menus</li>
3695 <li>visual indication that web service results are still
3696 being retrieved from server</li>
3697 <li>Serialise the dialogs that are shown when Jalview
3698 starts up for first time</li>
3699 <li>Jalview user agent string for interacting with HTTP
3701 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3703 <li>Examples directory and Groovy library included in
3704 InstallAnywhere distribution</li>
3705 </ul> <em>Applet</em>
3707 <li>RNA alignment and secondary structure annotation
3708 visualization applet example</li>
3709 </ul> <em>General</em>
3711 <li>Normalise option for consensus sequence logo</li>
3712 <li>Reset button in PCA window to return dimensions to
3714 <li>Allow seqspace or Jalview variant of alignment PCA
3716 <li>PCA with either nucleic acid and protein substitution
3718 <li>Allow windows containing HTML reports to be exported
3720 <li>Interactive display and editing of RNA secondary
3721 structure contacts</li>
3722 <li>RNA Helix Alignment Colouring</li>
3723 <li>RNA base pair logo consensus</li>
3724 <li>Parse sequence associated secondary structure
3725 information in Stockholm files</li>
3726 <li>HTML Export database accessions and annotation
3727 information presented in tooltip for sequences</li>
3728 <li>Import secondary structure from LOCARNA clustalw
3729 style RNA alignment files</li>
3730 <li>import and visualise T-COFFEE quality scores for an
3732 <li>'colour by annotation' per sequence option to
3733 shade each sequence according to its associated alignment
3735 <li>New Jalview Logo</li>
3736 </ul> <em>Documentation and Development</em>
3738 <li>documentation for score matrices used in Jalview</li>
3739 <li>New Website!</li>
3741 <td><em>Application</em>
3743 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3744 wsdbfetch REST service</li>
3745 <li>Stop windows being moved outside desktop on OSX</li>
3746 <li>Filetype associations not installed for webstart
3748 <li>Jalview does not always retrieve progress of a JABAWS
3749 job execution in full once it is complete</li>
3750 <li>revise SHMR RSBS definition to ensure alignment is
3751 uploaded via ali_file parameter</li>
3752 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3753 <li>View all structures superposed fails with exception</li>
3754 <li>Jnet job queues forever if a very short sequence is
3755 submitted for prediction</li>
3756 <li>Cut and paste menu not opened when mouse clicked on
3758 <li>Putting fractional value into integer text box in
3759 alignment parameter dialog causes Jalview to hang</li>
3760 <li>Structure view highlighting doesn't work on
3762 <li>View all structures fails with exception shown in
3764 <li>Characters in filename associated with PDBEntry not
3765 escaped in a platform independent way</li>
3766 <li>Jalview desktop fails to launch with exception when
3768 <li>Tree calculation reports 'you must have 2 or more
3769 sequences selected' when selection is empty</li>
3770 <li>Jalview desktop fails to launch with jar signature
3771 failure when java web start temporary file caching is
3773 <li>DAS Sequence retrieval with range qualification
3774 results in sequence xref which includes range qualification</li>
3775 <li>Errors during processing of command line arguments
3776 cause progress bar (JAL-898) to be removed</li>
3777 <li>Replace comma for semi-colon option not disabled for
3778 DAS sources in sequence fetcher</li>
3779 <li>Cannot close news reader when JABAWS server warning
3780 dialog is shown</li>
3781 <li>Option widgets not updated to reflect user settings</li>
3782 <li>Edited sequence not submitted to web service</li>
3783 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3784 <li>InstallAnywhere installer doesn't unpack and run
3785 on OSX Mountain Lion</li>
3786 <li>Annotation panel not given a scroll bar when
3787 sequences with alignment annotation are pasted into the
3789 <li>Sequence associated annotation rows not associated
3790 when loaded from Jalview project</li>
3791 <li>Browser launch fails with NPE on java 1.7</li>
3792 <li>JABAWS alignment marked as finished when job was
3793 cancelled or job failed due to invalid input</li>
3794 <li>NPE with v2.7 example when clicking on Tree
3795 associated with all views</li>
3796 <li>Exceptions when copy/paste sequences with grouped
3797 annotation rows to new window</li>
3798 </ul> <em>Applet</em>
3800 <li>Sequence features are momentarily displayed before
3801 they are hidden using hidefeaturegroups applet parameter</li>
3802 <li>loading features via javascript API automatically
3803 enables feature display</li>
3804 <li>scrollToColumnIn javascript API method doesn't
3806 </ul> <em>General</em>
3808 <li>Redundancy removal fails for rna alignment</li>
3809 <li>PCA calculation fails when sequence has been selected
3810 and then deselected</li>
3811 <li>PCA window shows grey box when first opened on OSX</li>
3812 <li>Letters coloured pink in sequence logo when alignment
3813 coloured with clustalx</li>
3814 <li>Choosing fonts without letter symbols defined causes
3815 exceptions and redraw errors</li>
3816 <li>Initial PCA plot view is not same as manually
3817 reconfigured view</li>
3818 <li>Grouped annotation graph label has incorrect line
3820 <li>Grouped annotation graph label display is corrupted
3821 for lots of labels</li>
3826 <div align="center">
3827 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3830 <td><em>Application</em>
3832 <li>Jalview Desktop News Reader</li>
3833 <li>Tweaked default layout of web services menu</li>
3834 <li>View/alignment association menu to enable user to
3835 easily specify which alignment a multi-structure view takes
3836 its colours/correspondences from</li>
3837 <li>Allow properties file location to be specified as URL</li>
3838 <li>Extend Jalview project to preserve associations
3839 between many alignment views and a single Jmol display</li>
3840 <li>Store annotation row height in Jalview project file</li>
3841 <li>Annotation row column label formatting attributes
3842 stored in project file</li>
3843 <li>Annotation row order for auto-calculated annotation
3844 rows preserved in Jalview project file</li>
3845 <li>Visual progress indication when Jalview state is
3846 saved using Desktop window menu</li>
3847 <li>Visual indication that command line arguments are
3848 still being processed</li>
3849 <li>Groovy script execution from URL</li>
3850 <li>Colour by annotation default min and max colours in
3852 <li>Automatically associate PDB files dragged onto an
3853 alignment with sequences that have high similarity and
3855 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3856 <li>'view structures' option to open many
3857 structures in same window</li>
3858 <li>Sort associated views menu option for tree panel</li>
3859 <li>Group all JABA and non-JABA services for a particular
3860 analysis function in its own submenu</li>
3861 </ul> <em>Applet</em>
3863 <li>Userdefined and autogenerated annotation rows for
3865 <li>Adjustment of alignment annotation pane height</li>
3866 <li>Annotation scrollbar for annotation panel</li>
3867 <li>Drag to reorder annotation rows in annotation panel</li>
3868 <li>'automaticScrolling' parameter</li>
3869 <li>Allow sequences with partial ID string matches to be
3870 annotated from GFF/Jalview features files</li>
3871 <li>Sequence logo annotation row in applet</li>
3872 <li>Absolute paths relative to host server in applet
3873 parameters are treated as such</li>
3874 <li>New in the JalviewLite javascript API:
3876 <li>JalviewLite.js javascript library</li>
3877 <li>Javascript callbacks for
3879 <li>Applet initialisation</li>
3880 <li>Sequence/alignment mouse-overs and selections</li>
3883 <li>scrollTo row and column alignment scrolling
3885 <li>Select sequence/alignment regions from javascript</li>
3886 <li>javascript structure viewer harness to pass
3887 messages between Jmol and Jalview when running as
3888 distinct applets</li>
3889 <li>sortBy method</li>
3890 <li>Set of applet and application examples shipped
3891 with documentation</li>
3892 <li>New example to demonstrate JalviewLite and Jmol
3893 javascript message exchange</li>
3895 </ul> <em>General</em>
3897 <li>Enable Jmol displays to be associated with multiple
3898 multiple alignments</li>
3899 <li>Option to automatically sort alignment with new tree</li>
3900 <li>User configurable link to enable redirects to a
3901 www.Jalview.org mirror</li>
3902 <li>Jmol colours option for Jmol displays</li>
3903 <li>Configurable newline string when writing alignment
3904 and other flat files</li>
3905 <li>Allow alignment annotation description lines to
3906 contain html tags</li>
3907 </ul> <em>Documentation and Development</em>
3909 <li>Add groovy test harness for bulk load testing to
3911 <li>Groovy script to load and align a set of sequences
3912 using a web service before displaying the result in the
3913 Jalview desktop</li>
3914 <li>Restructured javascript and applet api documentation</li>
3915 <li>Ant target to publish example html files with applet
3917 <li>Netbeans project for building Jalview from source</li>
3918 <li>ant task to create online javadoc for Jalview source</li>
3920 <td><em>Application</em>
3922 <li>User defined colourscheme throws exception when
3923 current built in colourscheme is saved as new scheme</li>
3924 <li>AlignFrame->Save in application pops up save
3925 dialog for valid filename/format</li>
3926 <li>Cannot view associated structure for UniProt sequence</li>
3927 <li>PDB file association breaks for UniProt sequence
3929 <li>Associate PDB from file dialog does not tell you
3930 which sequence is to be associated with the file</li>
3931 <li>Find All raises null pointer exception when query
3932 only matches sequence IDs</li>
3933 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3934 <li>Jalview project with Jmol views created with Jalview
3935 2.4 cannot be loaded</li>
3936 <li>Filetype associations not installed for webstart
3938 <li>Two or more chains in a single PDB file associated
3939 with sequences in different alignments do not get coloured
3940 by their associated sequence</li>
3941 <li>Visibility status of autocalculated annotation row
3942 not preserved when project is loaded</li>
3943 <li>Annotation row height and visibility attributes not
3944 stored in Jalview project</li>
3945 <li>Tree bootstraps are not preserved when saved as a
3946 Jalview project</li>
3947 <li>Envision2 workflow tooltips are corrupted</li>
3948 <li>Enabling show group conservation also enables colour
3949 by conservation</li>
3950 <li>Duplicate group associated conservation or consensus
3951 created on new view</li>
3952 <li>Annotation scrollbar not displayed after 'show
3953 all hidden annotation rows' option selected</li>
3954 <li>Alignment quality not updated after alignment
3955 annotation row is hidden then shown</li>
3956 <li>Preserve colouring of structures coloured by
3957 sequences in pre Jalview 2.7 projects</li>
3958 <li>Web service job parameter dialog is not laid out
3960 <li>Web services menu not refreshed after 'reset
3961 services' button is pressed in preferences</li>
3962 <li>Annotation off by one in Jalview v2_3 example project</li>
3963 <li>Structures imported from file and saved in project
3964 get name like jalview_pdb1234.txt when reloaded</li>
3965 <li>Jalview does not always retrieve progress of a JABAWS
3966 job execution in full once it is complete</li>
3967 </ul> <em>Applet</em>
3969 <li>Alignment height set incorrectly when lots of
3970 annotation rows are displayed</li>
3971 <li>Relative URLs in feature HTML text not resolved to
3973 <li>View follows highlighting does not work for positions
3975 <li><= shown as = in tooltip</li>
3976 <li>Export features raises exception when no features
3978 <li>Separator string used for serialising lists of IDs
3979 for javascript api is modified when separator string
3980 provided as parameter</li>
3981 <li>Null pointer exception when selecting tree leaves for
3982 alignment with no existing selection</li>
3983 <li>Relative URLs for datasources assumed to be relative
3984 to applet's codebase</li>
3985 <li>Status bar not updated after finished searching and
3986 search wraps around to first result</li>
3987 <li>StructureSelectionManager instance shared between
3988 several Jalview applets causes race conditions and memory
3990 <li>Hover tooltip and mouseover of position on structure
3991 not sent from Jmol in applet</li>
3992 <li>Certain sequences of javascript method calls to
3993 applet API fatally hang browser</li>
3994 </ul> <em>General</em>
3996 <li>View follows structure mouseover scrolls beyond
3997 position with wrapped view and hidden regions</li>
3998 <li>Find sequence position moves to wrong residue
3999 with/without hidden columns</li>
4000 <li>Sequence length given in alignment properties window
4002 <li>InvalidNumberFormat exceptions thrown when trying to
4003 import PDB like structure files</li>
4004 <li>Positional search results are only highlighted
4005 between user-supplied sequence start/end bounds</li>
4006 <li>End attribute of sequence is not validated</li>
4007 <li>Find dialog only finds first sequence containing a
4008 given sequence position</li>
4009 <li>Sequence numbering not preserved in MSF alignment
4011 <li>Jalview PDB file reader does not extract sequence
4012 from nucleotide chains correctly</li>
4013 <li>Structure colours not updated when tree partition
4014 changed in alignment</li>
4015 <li>Sequence associated secondary structure not correctly
4016 parsed in interleaved stockholm</li>
4017 <li>Colour by annotation dialog does not restore current
4019 <li>Hiding (nearly) all sequences doesn't work
4021 <li>Sequences containing lowercase letters are not
4022 properly associated with their pdb files</li>
4023 </ul> <em>Documentation and Development</em>
4025 <li>schemas/JalviewWsParamSet.xsd corrupted by
4026 ApplyCopyright tool</li>
4031 <div align="center">
4032 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4035 <td><em>Application</em>
4037 <li>New warning dialog when the Jalview Desktop cannot
4038 contact web services</li>
4039 <li>JABA service parameters for a preset are shown in
4040 service job window</li>
4041 <li>JABA Service menu entries reworded</li>
4045 <li>Modeller PIR IO broken - cannot correctly import a
4046 pir file emitted by Jalview</li>
4047 <li>Existing feature settings transferred to new
4048 alignment view created from cut'n'paste</li>
4049 <li>Improved test for mixed amino/nucleotide chains when
4050 parsing PDB files</li>
4051 <li>Consensus and conservation annotation rows
4052 occasionally become blank for all new windows</li>
4053 <li>Exception raised when right clicking above sequences
4054 in wrapped view mode</li>
4055 </ul> <em>Application</em>
4057 <li>multiple multiply aligned structure views cause cpu
4058 usage to hit 100% and computer to hang</li>
4059 <li>Web Service parameter layout breaks for long user
4060 parameter names</li>
4061 <li>Jaba service discovery hangs desktop if Jaba server
4068 <div align="center">
4069 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4072 <td><em>Application</em>
4074 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4075 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4078 <li>Web Services preference tab</li>
4079 <li>Analysis parameters dialog box and user defined
4081 <li>Improved speed and layout of Envision2 service menu</li>
4082 <li>Superpose structures using associated sequence
4084 <li>Export coordinates and projection as CSV from PCA
4086 </ul> <em>Applet</em>
4088 <li>enable javascript: execution by the applet via the
4089 link out mechanism</li>
4090 </ul> <em>Other</em>
4092 <li>Updated the Jmol Jalview interface to work with Jmol
4094 <li>The Jalview Desktop and JalviewLite applet now
4095 require Java 1.5</li>
4096 <li>Allow Jalview feature colour specification for GFF
4097 sequence annotation files</li>
4098 <li>New 'colour by label' keword in Jalview feature file
4099 type colour specification</li>
4100 <li>New Jalview Desktop Groovy API method that allows a
4101 script to check if it being run in an interactive session or
4102 in a batch operation from the Jalview command line</li>
4106 <li>clustalx colourscheme colours Ds preferentially when
4107 both D+E are present in over 50% of the column</li>
4108 </ul> <em>Application</em>
4110 <li>typo in AlignmentFrame->View->Hide->all but
4111 selected Regions menu item</li>
4112 <li>sequence fetcher replaces ',' for ';' when the ',' is
4113 part of a valid accession ID</li>
4114 <li>fatal OOM if object retrieved by sequence fetcher
4115 runs out of memory</li>
4116 <li>unhandled Out of Memory Error when viewing pca
4117 analysis results</li>
4118 <li>InstallAnywhere builds fail to launch on OS X java
4119 10.5 update 4 (due to apple Java 1.6 update)</li>
4120 <li>Installanywhere Jalview silently fails to launch</li>
4121 </ul> <em>Applet</em>
4123 <li>Jalview.getFeatureGroups() raises an
4124 ArrayIndexOutOfBoundsException if no feature groups are
4131 <div align="center">
4132 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4138 <li>Alignment prettyprinter doesn't cope with long
4140 <li>clustalx colourscheme colours Ds preferentially when
4141 both D+E are present in over 50% of the column</li>
4142 <li>nucleic acid structures retrieved from PDB do not
4143 import correctly</li>
4144 <li>More columns get selected than were clicked on when a
4145 number of columns are hidden</li>
4146 <li>annotation label popup menu not providing correct
4147 add/hide/show options when rows are hidden or none are
4149 <li>Stockholm format shown in list of readable formats,
4150 and parser copes better with alignments from RFAM.</li>
4151 <li>CSV output of consensus only includes the percentage
4152 of all symbols if sequence logo display is enabled</li>
4154 </ul> <em>Applet</em>
4156 <li>annotation panel disappears when annotation is
4158 </ul> <em>Application</em>
4160 <li>Alignment view not redrawn properly when new
4161 alignment opened where annotation panel is visible but no
4162 annotations are present on alignment</li>
4163 <li>pasted region containing hidden columns is
4164 incorrectly displayed in new alignment window</li>
4165 <li>Jalview slow to complete operations when stdout is
4166 flooded (fix is to close the Jalview console)</li>
4167 <li>typo in AlignmentFrame->View->Hide->all but
4168 selected Rregions menu item.</li>
4169 <li>inconsistent group submenu and Format submenu entry
4170 'Un' or 'Non'conserved</li>
4171 <li>Sequence feature settings are being shared by
4172 multiple distinct alignments</li>
4173 <li>group annotation not recreated when tree partition is
4175 <li>double click on group annotation to select sequences
4176 does not propagate to associated trees</li>
4177 <li>Mac OSX specific issues:
4179 <li>exception raised when mouse clicked on desktop
4180 window background</li>
4181 <li>Desktop menu placed on menu bar and application
4182 name set correctly</li>
4183 <li>sequence feature settings not wide enough for the
4184 save feature colourscheme button</li>
4193 <div align="center">
4194 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4197 <td><em>New Capabilities</em>
4199 <li>URL links generated from description line for
4200 regular-expression based URL links (applet and application)
4202 <li>Non-positional feature URL links are shown in link
4204 <li>Linked viewing of nucleic acid sequences and
4206 <li>Automatic Scrolling option in View menu to display
4207 the currently highlighted region of an alignment.</li>
4208 <li>Order an alignment by sequence length, or using the
4209 average score or total feature count for each sequence.</li>
4210 <li>Shading features by score or associated description</li>
4211 <li>Subdivide alignment and groups based on identity of
4212 selected subsequence (Make Groups from Selection).</li>
4213 <li>New hide/show options including Shift+Control+H to
4214 hide everything but the currently selected region.</li>
4215 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4216 </ul> <em>Application</em>
4218 <li>Fetch DB References capabilities and UI expanded to
4219 support retrieval from DAS sequence sources</li>
4220 <li>Local DAS Sequence sources can be added via the
4221 command line or via the Add local source dialog box.</li>
4222 <li>DAS Dbref and DbxRef feature types are parsed as
4223 database references and protein_name is parsed as
4224 description line (BioSapiens terms).</li>
4225 <li>Enable or disable non-positional feature and database
4226 references in sequence ID tooltip from View menu in
4228 <!-- <li>New hidden columns and rows and representatives capabilities
4229 in annotations file (in progress - not yet fully implemented)</li> -->
4230 <li>Group-associated consensus, sequence logos and
4231 conservation plots</li>
4232 <li>Symbol distributions for each column can be exported
4233 and visualized as sequence logos</li>
4234 <li>Optionally scale multi-character column labels to fit
4235 within each column of annotation row<!-- todo for applet -->
4237 <li>Optional automatic sort of associated alignment view
4238 when a new tree is opened.</li>
4239 <li>Jalview Java Console</li>
4240 <li>Better placement of desktop window when moving
4241 between different screens.</li>
4242 <li>New preference items for sequence ID tooltip and
4243 consensus annotation</li>
4244 <li>Client to submit sequences and IDs to Envision2
4246 <li><em>Vamsas Capabilities</em>
4248 <li>Improved VAMSAS synchronization (Jalview archive
4249 used to preserve views, structures, and tree display
4251 <li>Import of vamsas documents from disk or URL via
4253 <li>Sharing of selected regions between views and
4254 with other VAMSAS applications (Experimental feature!)</li>
4255 <li>Updated API to VAMSAS version 0.2</li>
4257 </ul> <em>Applet</em>
4259 <li>Middle button resizes annotation row height</li>
4262 <li>sortByTree (true/false) - automatically sort the
4263 associated alignment view by the tree when a new tree is
4265 <li>showTreeBootstraps (true/false) - show or hide
4266 branch bootstraps (default is to show them if available)</li>
4267 <li>showTreeDistances (true/false) - show or hide
4268 branch lengths (default is to show them if available)</li>
4269 <li>showUnlinkedTreeNodes (true/false) - indicate if
4270 unassociated nodes should be highlighted in the tree
4272 <li>heightScale and widthScale (1.0 or more) -
4273 increase the height or width of a cell in the alignment
4274 grid relative to the current font size.</li>
4277 <li>Non-positional features displayed in sequence ID
4279 </ul> <em>Other</em>
4281 <li>Features format: graduated colour definitions and
4282 specification of feature scores</li>
4283 <li>Alignment Annotations format: new keywords for group
4284 associated annotation (GROUP_REF) and annotation row display
4285 properties (ROW_PROPERTIES)</li>
4286 <li>XML formats extended to support graduated feature
4287 colourschemes, group associated annotation, and profile
4288 visualization settings.</li></td>
4291 <li>Source field in GFF files parsed as feature source
4292 rather than description</li>
4293 <li>Non-positional features are now included in sequence
4294 feature and gff files (controlled via non-positional feature
4295 visibility in tooltip).</li>
4296 <li>URL links generated for all feature links (bugfix)</li>
4297 <li>Added URL embedding instructions to features file
4299 <li>Codons containing ambiguous nucleotides translated as
4300 'X' in peptide product</li>
4301 <li>Match case switch in find dialog box works for both
4302 sequence ID and sequence string and query strings do not
4303 have to be in upper case to match case-insensitively.</li>
4304 <li>AMSA files only contain first column of
4305 multi-character column annotation labels</li>
4306 <li>Jalview Annotation File generation/parsing consistent
4307 with documentation (e.g. Stockholm annotation can be
4308 exported and re-imported)</li>
4309 <li>PDB files without embedded PDB IDs given a friendly
4311 <li>Find incrementally searches ID string matches as well
4312 as subsequence matches, and correctly reports total number
4316 <li>Better handling of exceptions during sequence
4318 <li>Dasobert generated non-positional feature URL
4319 link text excludes the start_end suffix</li>
4320 <li>DAS feature and source retrieval buttons disabled
4321 when fetch or registry operations in progress.</li>
4322 <li>PDB files retrieved from URLs are cached properly</li>
4323 <li>Sequence description lines properly shared via
4325 <li>Sequence fetcher fetches multiple records for all
4327 <li>Ensured that command line das feature retrieval
4328 completes before alignment figures are generated.</li>
4329 <li>Reduced time taken when opening file browser for
4331 <li>isAligned check prior to calculating tree, PCA or
4332 submitting an MSA to JNet now excludes hidden sequences.</li>
4333 <li>User defined group colours properly recovered
4334 from Jalview projects.</li>
4343 <div align="center">
4344 <strong>2.4.0.b2</strong><br> 28/10/2009
4349 <li>Experimental support for google analytics usage
4351 <li>Jalview privacy settings (user preferences and docs).</li>
4356 <li>Race condition in applet preventing startup in
4358 <li>Exception when feature created from selection beyond
4359 length of sequence.</li>
4360 <li>Allow synthetic PDB files to be imported gracefully</li>
4361 <li>Sequence associated annotation rows associate with
4362 all sequences with a given id</li>
4363 <li>Find function matches case-insensitively for sequence
4364 ID string searches</li>
4365 <li>Non-standard characters do not cause pairwise
4366 alignment to fail with exception</li>
4367 </ul> <em>Application Issues</em>
4369 <li>Sequences are now validated against EMBL database</li>
4370 <li>Sequence fetcher fetches multiple records for all
4372 </ul> <em>InstallAnywhere Issues</em>
4374 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4375 issue with installAnywhere mechanism)</li>
4376 <li>Command line launching of JARs from InstallAnywhere
4377 version (java class versioning error fixed)</li>
4384 <div align="center">
4385 <strong>2.4</strong><br> 27/8/2008
4388 <td><em>User Interface</em>
4390 <li>Linked highlighting of codon and amino acid from
4391 translation and protein products</li>
4392 <li>Linked highlighting of structure associated with
4393 residue mapping to codon position</li>
4394 <li>Sequence Fetcher provides example accession numbers
4395 and 'clear' button</li>
4396 <li>MemoryMonitor added as an option under Desktop's
4398 <li>Extract score function to parse whitespace separated
4399 numeric data in description line</li>
4400 <li>Column labels in alignment annotation can be centred.</li>
4401 <li>Tooltip for sequence associated annotation give name
4403 </ul> <em>Web Services and URL fetching</em>
4405 <li>JPred3 web service</li>
4406 <li>Prototype sequence search client (no public services
4408 <li>Fetch either seed alignment or full alignment from
4410 <li>URL Links created for matching database cross
4411 references as well as sequence ID</li>
4412 <li>URL Links can be created using regular-expressions</li>
4413 </ul> <em>Sequence Database Connectivity</em>
4415 <li>Retrieval of cross-referenced sequences from other
4417 <li>Generalised database reference retrieval and
4418 validation to all fetchable databases</li>
4419 <li>Fetch sequences from DAS sources supporting the
4420 sequence command</li>
4421 </ul> <em>Import and Export</em>
4422 <li>export annotation rows as CSV for spreadsheet import</li>
4423 <li>Jalview projects record alignment dataset associations,
4424 EMBL products, and cDNA sequence mappings</li>
4425 <li>Sequence Group colour can be specified in Annotation
4427 <li>Ad-hoc colouring of group in Annotation File using RGB
4428 triplet as name of colourscheme</li>
4429 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4431 <li>treenode binding for VAMSAS tree exchange</li>
4432 <li>local editing and update of sequences in VAMSAS
4433 alignments (experimental)</li>
4434 <li>Create new or select existing session to join</li>
4435 <li>load and save of vamsas documents</li>
4436 </ul> <em>Application command line</em>
4438 <li>-tree parameter to open trees (introduced for passing
4440 <li>-fetchfrom command line argument to specify nicknames
4441 of DAS servers to query for alignment features</li>
4442 <li>-dasserver command line argument to add new servers
4443 that are also automatically queried for features</li>
4444 <li>-groovy command line argument executes a given groovy
4445 script after all input data has been loaded and parsed</li>
4446 </ul> <em>Applet-Application data exchange</em>
4448 <li>Trees passed as applet parameters can be passed to
4449 application (when using "View in full
4450 application")</li>
4451 </ul> <em>Applet Parameters</em>
4453 <li>feature group display control parameter</li>
4454 <li>debug parameter</li>
4455 <li>showbutton parameter</li>
4456 </ul> <em>Applet API methods</em>
4458 <li>newView public method</li>
4459 <li>Window (current view) specific get/set public methods</li>
4460 <li>Feature display control methods</li>
4461 <li>get list of currently selected sequences</li>
4462 </ul> <em>New Jalview distribution features</em>
4464 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4465 <li>RELEASE file gives build properties for the latest
4466 Jalview release.</li>
4467 <li>Java 1.1 Applet build made easier and donotobfuscate
4468 property controls execution of obfuscator</li>
4469 <li>Build target for generating source distribution</li>
4470 <li>Debug flag for javacc</li>
4471 <li>.jalview_properties file is documented (slightly) in
4472 jalview.bin.Cache</li>
4473 <li>Continuous Build Integration for stable and
4474 development version of Application, Applet and source
4479 <li>selected region output includes visible annotations
4480 (for certain formats)</li>
4481 <li>edit label/displaychar contains existing label/char
4483 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4484 <li>shorter peptide product names from EMBL records</li>
4485 <li>Newick string generator makes compact representations</li>
4486 <li>bootstrap values parsed correctly for tree files with
4488 <li>pathological filechooser bug avoided by not allowing
4489 filenames containing a ':'</li>
4490 <li>Fixed exception when parsing GFF files containing
4491 global sequence features</li>
4492 <li>Alignment datasets are finalized only when number of
4493 references from alignment sequences goes to zero</li>
4494 <li>Close of tree branch colour box without colour
4495 selection causes cascading exceptions</li>
4496 <li>occasional negative imgwidth exceptions</li>
4497 <li>better reporting of non-fatal warnings to user when
4498 file parsing fails.</li>
4499 <li>Save works when Jalview project is default format</li>
4500 <li>Save as dialog opened if current alignment format is
4501 not a valid output format</li>
4502 <li>UniProt canonical names introduced for both das and
4504 <li>Histidine should be midblue (not pink!) in Zappo</li>
4505 <li>error messages passed up and output when data read
4507 <li>edit undo recovers previous dataset sequence when
4508 sequence is edited</li>
4509 <li>allow PDB files without pdb ID HEADER lines (like
4510 those generated by MODELLER) to be read in properly</li>
4511 <li>allow reading of JPred concise files as a normal
4513 <li>Stockholm annotation parsing and alignment properties
4514 import fixed for PFAM records</li>
4515 <li>Structure view windows have correct name in Desktop
4517 <li>annotation consisting of sequence associated scores
4518 can be read and written correctly to annotation file</li>
4519 <li>Aligned cDNA translation to aligned peptide works
4521 <li>Fixed display of hidden sequence markers and
4522 non-italic font for representatives in Applet</li>
4523 <li>Applet Menus are always embedded in applet window on
4525 <li>Newly shown features appear at top of stack (in
4527 <li>Annotations added via parameter not drawn properly
4528 due to null pointer exceptions</li>
4529 <li>Secondary structure lines are drawn starting from
4530 first column of alignment</li>
4531 <li>UniProt XML import updated for new schema release in
4533 <li>Sequence feature to sequence ID match for Features
4534 file is case-insensitive</li>
4535 <li>Sequence features read from Features file appended to
4536 all sequences with matching IDs</li>
4537 <li>PDB structure coloured correctly for associated views
4538 containing a sub-sequence</li>
4539 <li>PDB files can be retrieved by applet from Jar files</li>
4540 <li>feature and annotation file applet parameters
4541 referring to different directories are retrieved correctly</li>
4542 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4543 <li>Fixed application hang whilst waiting for
4544 splash-screen version check to complete</li>
4545 <li>Applet properly URLencodes input parameter values
4546 when passing them to the launchApp service</li>
4547 <li>display name and local features preserved in results
4548 retrieved from web service</li>
4549 <li>Visual delay indication for sequence retrieval and
4550 sequence fetcher initialisation</li>
4551 <li>updated Application to use DAS 1.53e version of
4552 dasobert DAS client</li>
4553 <li>Re-instated Full AMSA support and .amsa file
4555 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4563 <div align="center">
4564 <strong>2.3</strong><br> 9/5/07
4569 <li>Jmol 11.0.2 integration</li>
4570 <li>PDB views stored in Jalview XML files</li>
4571 <li>Slide sequences</li>
4572 <li>Edit sequence in place</li>
4573 <li>EMBL CDS features</li>
4574 <li>DAS Feature mapping</li>
4575 <li>Feature ordering</li>
4576 <li>Alignment Properties</li>
4577 <li>Annotation Scores</li>
4578 <li>Sort by scores</li>
4579 <li>Feature/annotation editing in applet</li>
4584 <li>Headless state operation in 2.2.1</li>
4585 <li>Incorrect and unstable DNA pairwise alignment</li>
4586 <li>Cut and paste of sequences with annotation</li>
4587 <li>Feature group display state in XML</li>
4588 <li>Feature ordering in XML</li>
4589 <li>blc file iteration selection using filename # suffix</li>
4590 <li>Stockholm alignment properties</li>
4591 <li>Stockhom alignment secondary structure annotation</li>
4592 <li>2.2.1 applet had no feature transparency</li>
4593 <li>Number pad keys can be used in cursor mode</li>
4594 <li>Structure Viewer mirror image resolved</li>
4601 <div align="center">
4602 <strong>2.2.1</strong><br> 12/2/07
4607 <li>Non standard characters can be read and displayed
4608 <li>Annotations/Features can be imported/exported to the
4610 <li>Applet allows editing of sequence/annotation/group
4611 name & description
4612 <li>Preference setting to display sequence name in
4614 <li>Annotation file format extended to allow
4615 Sequence_groups to be defined
4616 <li>Default opening of alignment overview panel can be
4617 specified in preferences
4618 <li>PDB residue numbering annotation added to associated
4624 <li>Applet crash under certain Linux OS with Java 1.6
4626 <li>Annotation file export / import bugs fixed
4627 <li>PNG / EPS image output bugs fixed
4633 <div align="center">
4634 <strong>2.2</strong><br> 27/11/06
4639 <li>Multiple views on alignment
4640 <li>Sequence feature editing
4641 <li>"Reload" alignment
4642 <li>"Save" to current filename
4643 <li>Background dependent text colour
4644 <li>Right align sequence ids
4645 <li>User-defined lower case residue colours
4648 <li>Menu item accelerator keys
4649 <li>Control-V pastes to current alignment
4650 <li>Cancel button for DAS Feature Fetching
4651 <li>PCA and PDB Viewers zoom via mouse roller
4652 <li>User-defined sub-tree colours and sub-tree selection
4654 <li>'New Window' button on the 'Output to Text box'
4659 <li>New memory efficient Undo/Redo System
4660 <li>Optimised symbol lookups and conservation/consensus
4662 <li>Region Conservation/Consensus recalculated after
4664 <li>Fixed Remove Empty Columns Bug (empty columns at end
4666 <li>Slowed DAS Feature Fetching for increased robustness.
4668 <li>Made angle brackets in ASCII feature descriptions
4670 <li>Re-instated Zoom function for PCA
4671 <li>Sequence descriptions conserved in web service
4673 <li>UniProt ID discoverer uses any word separated by
4675 <li>WsDbFetch query/result association resolved
4676 <li>Tree leaf to sequence mapping improved
4677 <li>Smooth fonts switch moved to FontChooser dialog box.
4684 <div align="center">
4685 <strong>2.1.1</strong><br> 12/9/06
4690 <li>Copy consensus sequence to clipboard</li>
4695 <li>Image output - rightmost residues are rendered if
4696 sequence id panel has been resized</li>
4697 <li>Image output - all offscreen group boundaries are
4699 <li>Annotation files with sequence references - all
4700 elements in file are relative to sequence position</li>
4701 <li>Mac Applet users can use Alt key for group editing</li>
4707 <div align="center">
4708 <strong>2.1</strong><br> 22/8/06
4713 <li>MAFFT Multiple Alignment in default Web Service list</li>
4714 <li>DAS Feature fetching</li>
4715 <li>Hide sequences and columns</li>
4716 <li>Export Annotations and Features</li>
4717 <li>GFF file reading / writing</li>
4718 <li>Associate structures with sequences from local PDB
4720 <li>Add sequences to exisiting alignment</li>
4721 <li>Recently opened files / URL lists</li>
4722 <li>Applet can launch the full application</li>
4723 <li>Applet has transparency for features (Java 1.2
4725 <li>Applet has user defined colours parameter</li>
4726 <li>Applet can load sequences from parameter
4727 "sequence<em>x</em>"
4733 <li>Redundancy Panel reinstalled in the Applet</li>
4734 <li>Monospaced font - EPS / rescaling bug fixed</li>
4735 <li>Annotation files with sequence references bug fixed</li>
4741 <div align="center">
4742 <strong>2.08.1</strong><br> 2/5/06
4747 <li>Change case of selected region from Popup menu</li>
4748 <li>Choose to match case when searching</li>
4749 <li>Middle mouse button and mouse movement can compress /
4750 expand the visible width and height of the alignment</li>
4755 <li>Annotation Panel displays complete JNet results</li>
4761 <div align="center">
4762 <strong>2.08b</strong><br> 18/4/06
4768 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4769 <li>Righthand label on wrapped alignments shows correct
4776 <div align="center">
4777 <strong>2.08</strong><br> 10/4/06
4782 <li>Editing can be locked to the selection area</li>
4783 <li>Keyboard editing</li>
4784 <li>Create sequence features from searches</li>
4785 <li>Precalculated annotations can be loaded onto
4787 <li>Features file allows grouping of features</li>
4788 <li>Annotation Colouring scheme added</li>
4789 <li>Smooth fonts off by default - Faster rendering</li>
4790 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4795 <li>Drag & Drop fixed on Linux</li>
4796 <li>Jalview Archive file faster to load/save, sequence
4797 descriptions saved.</li>
4803 <div align="center">
4804 <strong>2.07</strong><br> 12/12/05
4809 <li>PDB Structure Viewer enhanced</li>
4810 <li>Sequence Feature retrieval and display enhanced</li>
4811 <li>Choose to output sequence start-end after sequence
4812 name for file output</li>
4813 <li>Sequence Fetcher WSDBFetch@EBI</li>
4814 <li>Applet can read feature files, PDB files and can be
4815 used for HTML form input</li>
4820 <li>HTML output writes groups and features</li>
4821 <li>Group editing is Control and mouse click</li>
4822 <li>File IO bugs</li>
4828 <div align="center">
4829 <strong>2.06</strong><br> 28/9/05
4834 <li>View annotations in wrapped mode</li>
4835 <li>More options for PCA viewer</li>
4840 <li>GUI bugs resolved</li>
4841 <li>Runs with -nodisplay from command line</li>
4847 <div align="center">
4848 <strong>2.05b</strong><br> 15/9/05
4853 <li>Choose EPS export as lineart or text</li>
4854 <li>Jar files are executable</li>
4855 <li>Can read in Uracil - maps to unknown residue</li>
4860 <li>Known OutOfMemory errors give warning message</li>
4861 <li>Overview window calculated more efficiently</li>
4862 <li>Several GUI bugs resolved</li>
4868 <div align="center">
4869 <strong>2.05</strong><br> 30/8/05
4874 <li>Edit and annotate in "Wrapped" view</li>
4879 <li>Several GUI bugs resolved</li>
4885 <div align="center">
4886 <strong>2.04</strong><br> 24/8/05
4891 <li>Hold down mouse wheel & scroll to change font
4897 <li>Improved JPred client reliability</li>
4898 <li>Improved loading of Jalview files</li>
4904 <div align="center">
4905 <strong>2.03</strong><br> 18/8/05
4910 <li>Set Proxy server name and port in preferences</li>
4911 <li>Multiple URL links from sequence ids</li>
4912 <li>User Defined Colours can have a scheme name and added
4914 <li>Choose to ignore gaps in consensus calculation</li>
4915 <li>Unix users can set default web browser</li>
4916 <li>Runs without GUI for batch processing</li>
4917 <li>Dynamically generated Web Service Menus</li>
4922 <li>InstallAnywhere download for Sparc Solaris</li>
4928 <div align="center">
4929 <strong>2.02</strong><br> 18/7/05
4935 <li>Copy & Paste order of sequences maintains
4936 alignment order.</li>
4942 <div align="center">
4943 <strong>2.01</strong><br> 12/7/05
4948 <li>Use delete key for deleting selection.</li>
4949 <li>Use Mouse wheel to scroll sequences.</li>
4950 <li>Help file updated to describe how to add alignment
4952 <li>Version and build date written to build properties
4954 <li>InstallAnywhere installation will check for updates
4955 at launch of Jalview.</li>
4960 <li>Delete gaps bug fixed.</li>
4961 <li>FileChooser sorts columns.</li>
4962 <li>Can remove groups one by one.</li>
4963 <li>Filechooser icons installed.</li>
4964 <li>Finder ignores return character when searching.
4965 Return key will initiate a search.<br>
4972 <div align="center">
4973 <strong>2.0</strong><br> 20/6/05
4978 <li>New codebase</li>