3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
61 <em>24/09/2020</em></strong></td>
62 <td align="left" valign="top">
66 <td align="left" valign="top">
69 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
70 "Encountered problems opening
71 https://www.jalview.org/examples/exampleFile_2_7.jvp"
77 <td width="60" align="center" nowrap><strong><a
78 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
79 <em>17/09/2020</em></strong></td>
80 <td align="left" valign="top">
83 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
84 residue in cursor mode
87 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
88 HTSJDK from 2.12 to 2.23
91 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
92 optimisations and improvements suggested by Bob Hanson and
93 improved compatibility with JalviewJS
96 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
97 alignments from Pfam and Rfam
100 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
101 import (no longer based on .gz extension)
104 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
107 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
108 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
112 <!-- JAL-3667 -->Improved warning messages, debug logging
113 and fixed Retry action when Jalview encounters errors when
114 saving or making backup files.
117 <!-- JAL-3676 -->Enhanced Jalview Java Console:
119 <li>Jalview's logging level can be configured</li>
120 <li>Copy to Clipboard Buttion</li>
124 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
125 when running on Linux (Requires Java 11+)
127 </ul> <em>Launching Jalview</em>
130 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
131 through a system property
134 <!-- JAL-3477 -->Improved built-in documentation and command
135 line help for configuring Jalview's memory
139 <td align="left" valign="top">
142 <!-- JAL-3691 -->Conservation and Quality tracks are shown
143 but not calculated and no protein or DNA score models are
144 available for tree/PCA calculation when launched with
145 Turkish language locale
148 <!-- JAL-3493 -->Escape does not clear highlights on the
149 alignment (Since Jalview 2.10.3)
152 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
153 doesn't slide selected sequences, just sequence under cursor
156 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
157 sequence under the cursor
160 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
161 multiple EMBL gene products shown forĀ a single contig
164 <!-- JAL-3696 -->Errors encountered when processing variants
165 from VCF files yield "Error processing VCF: Format specifier
169 <!-- JAL-3697 -->Count of features not shown can be wrong
170 when there are both local and complementary features mapped
171 to the position under the cursor
174 <!-- JAL-3673 -->Sequence ID for reference sequence is
175 clipped when Right align Sequence IDs enabled
178 <!-- JAL-2983 -->Slider with negative range values not
179 rendered correctly in VAqua4 (Since 2.10.4)
182 <!-- JAL-3685 -->Single quotes not displayed correctly in
183 internationalised text for some messages and log output
186 <!-- JAL-3490 -->Find doesn't report matches that span
187 hidden gapped columns
190 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
191 panels, Alignment viewport and annotation renderer.
194 <!-- JAL-3561 -->Jalview ignores file format parameter
195 specifying output format when exporting an alignment via the
199 <!-- JAL-3667 -->Windows 10: For a minority of users, if
200 backups are not enabled, Jalview sometimes fails to
201 overwrite an existing file and raises a warning dialog. (in
202 2.11.0, and 2.11.1.0, the workaround is to try to save the
203 file again, and if that fails, delete the original file and
207 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
211 <!-- JAL-3741 -->References to http://www.jalview.org in
212 program and documentation
214 </ul> <em>Launching Jalview</em>
217 <!-- JAL-3718 -->Jalview application fails when launched the
218 first time for a version that has different jars to the
219 previous launched version.
221 </ul> <em>Developing Jalview</em>
224 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
225 data, causing cloverReport gradle task to fail with an
229 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
230 monitor the release channel
232 </ul> <em>New Known defects</em>
235 <!-- JAL-3748 -->CDS shown in result of submitting proteins
236 in a CDS/Protein alignment to a web service is wrong when
237 proteins share a common transcript sequence (e.g.
238 genome of RNA viruses)
241 <!-- JAL-3576 -->Co-located features exported and re-imported
242 are ordered differently when shown on alignment and in
243 tooltips. (Also affects v2.11.1.0)
246 <!-- JAL-3702 -->Drag and drop of alignment file onto
247 alignment window when in a HiDPI scaled mode in Linux only
248 works for the top left quadrant of the alignment window
251 <!-- JAL-3701 -->Stale build data in jalview standalone jar
252 builds (only affects 2.11.1.1 branch)
255 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
256 when alignment view restored from project (since Jalview 2.11.0)
262 <td width="60" align="center" nowrap><strong><a
263 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
264 <em>22/04/2020</em></strong></td>
265 <td align="left" valign="top">
268 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
269 'virtual' codon features shown on protein (or vice versa)
270 for display in alignments, on structure views (including
271 transfer to UCSF chimera), in feature reports and for
275 <!-- JAL-3121 -->Feature attributes from VCF files can be
276 exported and re-imported as GFF3 files
279 <!-- JAL-3376 -->Capture VCF "fixed column" values
280 POS, ID, QUAL, FILTER as Feature Attributes
283 <!-- JAL-3375 -->More robust VCF numeric data field
284 validation while parsing
287 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
291 <!-- JAL-3535 -->Feature Settings dialog title includes name
295 <!-- JAL-3538 -->Font anti-aliasing in alignment views
299 <!-- JAL-3468 -->Very long feature descriptions truncated in
303 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
304 with no feature types visible
307 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
309 </ul><em>Jalview Installer</em>
312 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
313 in console (may be null when Jalview launched as executable jar or via conda)
316 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
319 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
322 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
324 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
325 </ul> <em>Release processes</em>
328 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
331 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
333 </ul> <em>Build System</em>
336 <!-- JAL-3510 -->Clover updated to 4.4.1
339 <!-- JAL-3513 -->Test code included in Clover coverage
343 <em>Groovy Scripts</em>
346 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
347 to stdout containing the consensus sequence for each
348 alignment in a Jalview session
351 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
352 genomic sequence_variant annotation from CDS as
353 missense_variant or synonymous_variant on protein products.
357 <td align="left" valign="top">
360 <!-- JAL-3581 -->Hidden sequence markers still visible when
361 'Show hidden markers' option is not ticked
364 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
365 PNG output when 'Automatically set ID width' is set in
366 jalview preferences or properties file
369 <!-- JAL-3571 -->Feature Editor dialog can be opened when
370 'Show Sequence Features' option is not ticked
373 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
374 buttons in Feature Settings dialog are clicked when no
378 <!-- JAL-3412 -->ID margins for CDS and Protein views not
379 equal when split frame is first opened
382 <!-- JAL-3296 -->Sequence position numbers in status bar not
383 correct after editing a sequence's start position
386 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
387 with annotation and exceptions thrown when only a few
388 columns shown in wrapped mode
391 <!-- JAL-3386 -->Sequence IDs missing in headless export of
392 wrapped alignment figure with annotations
395 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
396 ID fails with ClassCastException
399 <!-- JAL-3389 -->Chimera session not restored from Jalview
403 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
404 feature settings dialog also selects columns
407 <!-- JAL-3473 -->SpinnerNumberModel causes
408 IllegalArgumentException in some circumstances
411 <!-- JAL-3534 -->Multiple feature settings dialogs can be
415 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
416 alignment window is closed
419 <!-- JAL-3406 -->Credits missing some authors in Jalview
420 help documentation for 2.11.0 release
423 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
424 includes Pfam ID as sequence's accession rather than its
427 </ul> <em>Java 11 Compatibility issues</em>
430 <!-- JAL-2987 -->OSX - Can't view some search results in
431 PDB/Uniprot search panel
433 </ul> <em>Installer</em>
436 <!-- JAL-3447 -->Jalview should not create file associations
437 for 3D structure files (.pdb, .mmcif. .cif)
439 </ul> <em>Repository and Source Release</em>
442 <!-- JAL-3474 -->removed obsolete .cvsignore files from
446 <!-- JAL-3541 -->Clover report generation running out of
449 </ul> <em>New Known Issues</em>
452 <!-- JAL-3523 -->OSX - Current working directory not
453 preserved when Jalview.app launched with parameters from
457 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
458 clipped in headless figure export when Right Align option
462 <!-- JAL-3542 -->Jalview Installation type always reports
463 'Source' in console output
466 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
467 bamboo server but run fine locally.
473 <td width="60" align="center" nowrap>
474 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
475 <em>04/07/2019</em></strong>
477 <td align="left" valign="top">
480 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
481 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
482 source project) rather than InstallAnywhere
485 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
486 settings, receive over the air updates and launch specific
487 versions via (<a href="https://github.com/threerings/getdown">Three
491 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
492 formats supported by Jalview (including .jvp project files)
495 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
496 arguments and switch between different getdown channels
499 <!-- JAL-3141 -->Backup files created when saving Jalview project
504 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
505 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
507 <!-- JAL-2620 -->Alternative genetic code tables for
508 'Translate as cDNA'</li>
510 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
511 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
514 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
515 implementation that allows updates) used for Sequence Feature collections</li>
517 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
518 features can be filtered and shaded according to any
519 associated attributes (e.g. variant attributes from VCF
520 file, or key-value pairs imported from column 9 of GFF
524 <!-- JAL-2879 -->Feature Attributes and shading schemes
525 stored and restored from Jalview Projects
528 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
529 recognise variant features
532 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
533 sequences (also coloured red by default)
536 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
540 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
541 algorithm (Z-sort/transparency and filter aware)
544 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
550 <!-- JAL-3205 -->Symmetric score matrices for faster
551 tree and PCA calculations
553 <li><strong>Principal Components Analysis Viewer</strong>
556 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
557 and Viewer state saved in Jalview Project
559 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
562 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
566 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
571 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
573 <li><strong>Speed and Efficiency</strong>
576 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
577 multiple groups when working with large alignments
580 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
584 <li><strong>User Interface</strong>
587 <!-- JAL-2933 -->Finder panel remembers last position in each
591 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
592 what is shown)<br />Only visible regions of alignment are shown by
593 default (can be changed in user preferences)
596 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
597 to the Overwrite Dialog
600 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
604 <!-- JAL-1244 -->Status bar shows bounds when dragging a
605 selection region, and gap count when inserting or deleting gaps
608 <!-- JAL-3132 -->Status bar updates over sequence and annotation
612 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
616 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
620 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
623 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
627 <!-- JAL-3181 -->Consistent ordering of links in sequence id
631 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
633 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
637 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
638 <li><strong>Java 11 Support (not yet on general release)</strong>
641 <!-- -->OSX GUI integrations for App menu's 'About' entry and
646 <em>Deprecations</em>
648 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
649 capabilities removed from the Jalview Desktop
651 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
652 unmarshalling has been replaced by JAXB for Jalview projects
653 and XML based data retrieval clients</li>
654 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
655 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
656 </ul> <em>Documentation</em>
658 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
659 not supported in EPS figure export
661 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
662 </ul> <em>Development and Release Processes</em>
665 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
668 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
670 <!-- JAL-3225 -->Eclipse project configuration managed with
674 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
675 Bamboo continuous integration for unattended Test Suite
679 <!-- JAL-2864 -->Memory test suite to detect leaks in common
683 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
687 <!-- JAL-3248 -->Developer documentation migrated to
688 markdown (with HTML rendering)
691 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
694 <!-- JAL-3289 -->New URLs for publishing development
699 <td align="left" valign="top">
702 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
705 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
706 superposition in Jmol fail on Windows
709 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
710 structures for sequences with lots of PDB structures
713 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
717 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
718 project involving multiple views
721 <!-- JAL-3164 -->Overview for complementary view in a linked
722 CDS/Protein alignment is not updated when Hide Columns by
723 Annotation dialog hides columns
726 <!-- JAL-3158 -->Selection highlighting in the complement of a
727 CDS/Protein alignment stops working after making a selection in
728 one view, then making another selection in the other view
731 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
735 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
736 Settings and Jalview Preferences panels
739 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
740 overview with large alignments
743 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
744 region if columns were selected by dragging right-to-left and the
745 mouse moved to the left of the first column
748 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
749 hidden column marker via scale popup menu
752 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
753 doesn't tell users the invalid URL
756 <!-- JAL-2816 -->Tooltips displayed for features filtered by
760 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
761 show cross references or Fetch Database References are shown in
765 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
766 peptide sequence (computed variant shown as p.Res.null)
769 <!-- JAL-2060 -->'Graduated colour' option not offered for
770 manually created features (where feature score is Float.NaN)
773 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
774 when columns are hidden
777 <!-- JAL-3082 -->Regular expression error for '(' in Select
778 Columns by Annotation description
781 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
782 out of Scale or Annotation Panel
785 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
789 <!-- JAL-3074 -->Left/right drag in annotation can scroll
793 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
797 <!-- JAL-3002 -->Column display is out by one after Page Down,
798 Page Up in wrapped mode
801 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
804 <!-- JAL-2932 -->Finder searches in minimised alignments
807 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
808 on opening an alignment
811 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
815 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
816 different groups in the alignment are selected
819 <!-- JAL-2717 -->Internationalised colour scheme names not shown
823 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
827 <!-- JAL-3125 -->Value input for graduated feature colour
828 threshold gets 'unrounded'
831 <!-- JAL-2982 -->PCA image export doesn't respect background
835 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
838 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
841 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
845 <!-- JAL-2964 -->Associate Tree with All Views not restored from
849 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
850 shown in complementary view
853 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
854 without normalisation
857 <!-- JAL-3021 -->Sequence Details report should open positioned at top
861 <!-- JAL-914 -->Help page can be opened twice
864 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
866 </ul> <em>Editing</em>
869 <!-- JAL-2822 -->Start and End should be updated when sequence
870 data at beginning or end of alignment added/removed via 'Edit'
874 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
875 relocate sequence features correctly when start of sequence is
876 removed (Known defect since 2.10)
879 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
880 dialog corrupts dataset sequence
883 <!-- JAL-868 -->Structure colours not updated when associated tree
884 repartitions the alignment view (Regression in 2.10.5)
886 </ul> <em>Datamodel</em>
889 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
890 sequence's End is greater than its length
892 </ul> <em>Bugs fixed for Java 11 Support (not yet on
893 general release)</em>
896 <!-- JAL-3288 -->Menus work properly in split-screen
898 </ul> <em>New Known Defects</em>
901 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
904 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
905 regions of protein alignment.
908 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
909 is restored from a Jalview 2.11 project
912 <!-- JAL-3213 -->Alignment panel height can be too small after
916 <!-- JAL-3240 -->Display is incorrect after removing gapped
917 columns within hidden columns
920 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
921 window after dragging left to select columns to left of visible
925 <!-- JAL-2876 -->Features coloured according to their description
926 string and thresholded by score in earlier versions of Jalview are
927 not shown as thresholded features in 2.11. To workaround please
928 create a Score filter instead.
931 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
933 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
936 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
937 alignments with multiple views can close views unexpectedly
940 <em>Java 11 Specific defects</em>
943 <!-- JAL-3235 -->Jalview Properties file is not sorted
944 alphabetically when saved
950 <td width="60" nowrap>
952 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
955 <td><div align="left">
959 <!-- JAL-3101 -->Default memory for Jalview webstart and
960 InstallAnywhere increased to 1G.
963 <!-- JAL-247 -->Hidden sequence markers and representative
964 sequence bolding included when exporting alignment as EPS,
965 SVG, PNG or HTML. <em>Display is configured via the
966 Format menu, or for command-line use via a Jalview
967 properties file.</em>
970 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
971 API and sequence data now imported as JSON.
974 <!-- JAL-3065 -->Change in recommended way of starting
975 Jalview via a Java command line: add jars in lib directory
976 to CLASSPATH, rather than via the deprecated java.ext.dirs
983 <!-- JAL-3047 -->Support added to execute test suite
984 instrumented with <a href="http://openclover.org/">Open
989 <td><div align="left">
993 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
994 row shown in Feredoxin Structure alignment view of example
998 <!-- JAL-2854 -->Annotation obscures sequences if lots of
999 annotation displayed.
1002 <!-- JAL-3107 -->Group conservation/consensus not shown
1003 for newly created group when 'Apply to all groups'
1007 <!-- JAL-3087 -->Corrupted display when switching to
1008 wrapped mode when sequence panel's vertical scrollbar is
1012 <!-- JAL-3003 -->Alignment is black in exported EPS file
1013 when sequences are selected in exported view.</em>
1016 <!-- JAL-3059 -->Groups with different coloured borders
1017 aren't rendered with correct colour.
1020 <!-- JAL-3092 -->Jalview could hang when importing certain
1021 types of knotted RNA secondary structure.
1024 <!-- JAL-3095 -->Sequence highlight and selection in
1025 trimmed VARNA 2D structure is incorrect for sequences that
1029 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1030 annotation when columns are inserted into an alignment,
1031 and when exporting as Stockholm flatfile.
1034 <!-- JAL-3053 -->Jalview annotation rows containing upper
1035 and lower-case 'E' and 'H' do not automatically get
1036 treated as RNA secondary structure.
1039 <!-- JAL-3106 -->.jvp should be used as default extension
1040 (not .jar) when saving a Jalview project file.
1043 <!-- JAL-3105 -->Mac Users: closing a window correctly
1044 transfers focus to previous window on OSX
1047 <em>Java 10 Issues Resolved</em>
1050 <!-- JAL-2988 -->OSX - Can't save new files via the File
1051 or export menus by typing in a name into the Save dialog
1055 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1056 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1057 'look and feel' which has improved compatibility with the
1058 latest version of OSX.
1065 <td width="60" nowrap>
1066 <div align="center">
1067 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1068 <em>7/06/2018</em></strong>
1071 <td><div align="left">
1075 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1076 annotation retrieved from Uniprot
1079 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1080 onto the Jalview Desktop
1084 <td><div align="left">
1088 <!-- JAL-3017 -->Cannot import features with multiple
1089 variant elements (blocks import of some Uniprot records)
1092 <!-- JAL-2997 -->Clustal files with sequence positions in
1093 right-hand column parsed correctly
1096 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1097 not alignment area in exported graphic
1100 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1101 window has input focus
1104 <!-- JAL-2992 -->Annotation panel set too high when
1105 annotation added to view (Windows)
1108 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1109 network connectivity is poor
1112 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1113 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1114 the currently open URL and links from a page viewed in
1115 Firefox or Chrome on Windows is now fully supported. If
1116 you are using Edge, only links in the page can be
1117 dragged, and with Internet Explorer, only the currently
1118 open URL in the browser can be dropped onto Jalview.</em>
1121 <em>New Known Defects</em>
1123 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1128 <td width="60" nowrap>
1129 <div align="center">
1130 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1133 <td><div align="left">
1137 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1138 for disabling automatic superposition of multiple
1139 structures and open structures in existing views
1142 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1143 ID and annotation area margins can be click-dragged to
1147 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1151 <!-- JAL-2759 -->Improved performance for large alignments
1152 and lots of hidden columns
1155 <!-- JAL-2593 -->Improved performance when rendering lots
1156 of features (particularly when transparency is disabled)
1159 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1160 exchange of Jalview features and Chimera attributes made
1166 <td><div align="left">
1169 <!-- JAL-2899 -->Structure and Overview aren't updated
1170 when Colour By Annotation threshold slider is adjusted
1173 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1174 overlapping alignment panel
1177 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1181 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1182 improved: CDS not handled correctly if transcript has no
1186 <!-- JAL-2321 -->Secondary structure and temperature
1187 factor annotation not added to sequence when local PDB
1188 file associated with it by drag'n'drop or structure
1192 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1193 dialog doesn't import PDB files dropped on an alignment
1196 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1197 scroll bar doesn't work for some CDS/Protein views
1200 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1201 Java 1.8u153 onwards and Java 1.9u4+.
1204 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1205 columns in annotation row
1208 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1209 honored in batch mode
1212 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1213 for structures added to existing Jmol view
1216 <!-- JAL-2223 -->'View Mappings' includes duplicate
1217 entries after importing project with multiple views
1220 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1221 protein sequences via SIFTS from associated PDB entries
1222 with negative residue numbers or missing residues fails
1225 <!-- JAL-2952 -->Exception when shading sequence with negative
1226 Temperature Factor values from annotated PDB files (e.g.
1227 as generated by CONSURF)
1230 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1231 tooltip doesn't include a text description of mutation
1234 <!-- JAL-2922 -->Invert displayed features very slow when
1235 structure and/or overview windows are also shown
1238 <!-- JAL-2954 -->Selecting columns from highlighted regions
1239 very slow for alignments with large numbers of sequences
1242 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1243 with 'StringIndexOutOfBounds'
1246 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1247 platforms running Java 10
1250 <!-- JAL-2960 -->Adding a structure to existing structure
1251 view appears to do nothing because the view is hidden behind the alignment view
1257 <!-- JAL-2926 -->Copy consensus sequence option in applet
1258 should copy the group consensus when popup is opened on it
1264 <!-- JAL-2913 -->Fixed ID width preference is not respected
1267 <em>New Known Defects</em>
1270 <!-- JAL-2973 --> Exceptions occasionally raised when
1271 editing a large alignment and overview is displayed
1274 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1275 repeatedly after a series of edits even when the overview
1276 is no longer reflecting updates
1279 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1280 structures for protein subsequence (if 'Trim Retrieved
1281 Sequences' enabled) or Ensembl isoforms (Workaround in
1282 2.10.4 is to fail back to N&W mapping)
1285 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1286 option gives blank output
1293 <td width="60" nowrap>
1294 <div align="center">
1295 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1298 <td><div align="left">
1299 <ul><li>Updated Certum Codesigning Certificate
1300 (Valid till 30th November 2018)</li></ul></div></td>
1301 <td><div align="left">
1302 <em>Desktop</em><ul>
1304 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1305 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1306 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1307 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1308 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1309 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1310 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1316 <td width="60" nowrap>
1317 <div align="center">
1318 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1321 <td><div align="left">
1325 <!-- JAL-2446 -->Faster and more efficient management and
1326 rendering of sequence features
1329 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1330 429 rate limit request hander
1333 <!-- JAL-2773 -->Structure views don't get updated unless
1334 their colours have changed
1337 <!-- JAL-2495 -->All linked sequences are highlighted for
1338 a structure mousover (Jmol) or selection (Chimera)
1341 <!-- JAL-2790 -->'Cancel' button in progress bar for
1342 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1345 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1346 view from Ensembl locus cross-references
1349 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1353 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1354 feature can be disabled
1357 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1358 PDB easier retrieval of sequences for lists of IDs
1361 <!-- JAL-2758 -->Short names for sequences retrieved from
1367 <li>Groovy interpreter updated to 2.4.12</li>
1368 <li>Example groovy script for generating a matrix of
1369 percent identity scores for current alignment.</li>
1371 <em>Testing and Deployment</em>
1374 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1378 <td><div align="left">
1382 <!-- JAL-2643 -->Pressing tab after updating the colour
1383 threshold text field doesn't trigger an update to the
1387 <!-- JAL-2682 -->Race condition when parsing sequence ID
1391 <!-- JAL-2608 -->Overview windows are also closed when
1392 alignment window is closed
1395 <!-- JAL-2548 -->Export of features doesn't always respect
1399 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1400 takes a long time in Cursor mode
1406 <!-- JAL-2777 -->Structures with whitespace chainCode
1407 cannot be viewed in Chimera
1410 <!-- JAL-2728 -->Protein annotation panel too high in
1414 <!-- JAL-2757 -->Can't edit the query after the server
1415 error warning icon is shown in Uniprot and PDB Free Text
1419 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1422 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1425 <!-- JAL-2739 -->Hidden column marker in last column not
1426 rendered when switching back from Wrapped to normal view
1429 <!-- JAL-2768 -->Annotation display corrupted when
1430 scrolling right in unwapped alignment view
1433 <!-- JAL-2542 -->Existing features on subsequence
1434 incorrectly relocated when full sequence retrieved from
1438 <!-- JAL-2733 -->Last reported memory still shown when
1439 Desktop->Show Memory is unticked (OSX only)
1442 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1443 features of same type and group to be selected for
1447 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1448 alignments when hidden columns are present
1451 <!-- JAL-2392 -->Jalview freezes when loading and
1452 displaying several structures
1455 <!-- JAL-2732 -->Black outlines left after resizing or
1459 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1460 within the Jalview desktop on OSX
1463 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1464 when in wrapped alignment mode
1467 <!-- JAL-2636 -->Scale mark not shown when close to right
1468 hand end of alignment
1471 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1472 each selected sequence do not have correct start/end
1476 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1477 after canceling the Alignment Window's Font dialog
1480 <!-- JAL-2036 -->Show cross-references not enabled after
1481 restoring project until a new view is created
1484 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1485 URL links appears when only default EMBL-EBI link is
1486 configured (since 2.10.2b2)
1489 <!-- JAL-2775 -->Overview redraws whole window when box
1490 position is adjusted
1493 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1494 in a multi-chain structure when viewing alignment
1495 involving more than one chain (since 2.10)
1498 <!-- JAL-2811 -->Double residue highlights in cursor mode
1499 if new selection moves alignment window
1502 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1503 arrow key in cursor mode to pass hidden column marker
1506 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1507 that produces correctly annotated transcripts and products
1510 <!-- JAL-2776 -->Toggling a feature group after first time
1511 doesn't update associated structure view
1514 <em>Applet</em><br />
1517 <!-- JAL-2687 -->Concurrent modification exception when
1518 closing alignment panel
1521 <em>BioJSON</em><br />
1524 <!-- JAL-2546 -->BioJSON export does not preserve
1525 non-positional features
1528 <em>New Known Issues</em>
1531 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1532 sequence features correctly (for many previous versions of
1536 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1537 using cursor in wrapped panel other than top
1540 <!-- JAL-2791 -->Select columns containing feature ignores
1541 graduated colour threshold
1544 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1545 always preserve numbering and sequence features
1548 <em>Known Java 9 Issues</em>
1551 <!-- JAL-2902 -->Groovy Console very slow to open and is
1552 not responsive when entering characters (Webstart, Java
1559 <td width="60" nowrap>
1560 <div align="center">
1561 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1562 <em>2/10/2017</em></strong>
1565 <td><div align="left">
1566 <em>New features in Jalview Desktop</em>
1569 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1571 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1575 <td><div align="left">
1579 <td width="60" nowrap>
1580 <div align="center">
1581 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1582 <em>7/9/2017</em></strong>
1585 <td><div align="left">
1589 <!-- JAL-2588 -->Show gaps in overview window by colouring
1590 in grey (sequences used to be coloured grey, and gaps were
1594 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1598 <!-- JAL-2587 -->Overview updates immediately on increase
1599 in size and progress bar shown as higher resolution
1600 overview is recalculated
1605 <td><div align="left">
1609 <!-- JAL-2664 -->Overview window redraws every hidden
1610 column region row by row
1613 <!-- JAL-2681 -->duplicate protein sequences shown after
1614 retrieving Ensembl crossrefs for sequences from Uniprot
1617 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1618 format setting is unticked
1621 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1622 if group has show boxes format setting unticked
1625 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1626 autoscrolling whilst dragging current selection group to
1627 include sequences and columns not currently displayed
1630 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1631 assemblies are imported via CIF file
1634 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1635 displayed when threshold or conservation colouring is also
1639 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1643 <!-- JAL-2673 -->Jalview continues to scroll after
1644 dragging a selected region off the visible region of the
1648 <!-- JAL-2724 -->Cannot apply annotation based
1649 colourscheme to all groups in a view
1652 <!-- JAL-2511 -->IDs don't line up with sequences
1653 initially after font size change using the Font chooser or
1660 <td width="60" nowrap>
1661 <div align="center">
1662 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1665 <td><div align="left">
1666 <em>Calculations</em>
1670 <!-- JAL-1933 -->Occupancy annotation row shows number of
1671 ungapped positions in each column of the alignment.
1674 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1675 a calculation dialog box
1678 <!-- JAL-2379 -->Revised implementation of PCA for speed
1679 and memory efficiency (~30x faster)
1682 <!-- JAL-2403 -->Revised implementation of sequence
1683 similarity scores as used by Tree, PCA, Shading Consensus
1684 and other calculations
1687 <!-- JAL-2416 -->Score matrices are stored as resource
1688 files within the Jalview codebase
1691 <!-- JAL-2500 -->Trees computed on Sequence Feature
1692 Similarity may have different topology due to increased
1699 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1700 model for alignments and groups
1703 <!-- JAL-384 -->Custom shading schemes created via groovy
1710 <!-- JAL-2526 -->Efficiency improvements for interacting
1711 with alignment and overview windows
1714 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1718 <!-- JAL-2388 -->Hidden columns and sequences can be
1722 <!-- JAL-2611 -->Click-drag in visible area allows fine
1723 adjustment of visible position
1727 <em>Data import/export</em>
1730 <!-- JAL-2535 -->Posterior probability annotation from
1731 Stockholm files imported as sequence associated annotation
1734 <!-- JAL-2507 -->More robust per-sequence positional
1735 annotation input/output via stockholm flatfile
1738 <!-- JAL-2533 -->Sequence names don't include file
1739 extension when importing structure files without embedded
1740 names or PDB accessions
1743 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1744 format sequence substitution matrices
1747 <em>User Interface</em>
1750 <!-- JAL-2447 --> Experimental Features Checkbox in
1751 Desktop's Tools menu to hide or show untested features in
1755 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1756 via Overview or sequence motif search operations
1759 <!-- JAL-2547 -->Amend sequence features dialog box can be
1760 opened by double clicking gaps within sequence feature
1764 <!-- JAL-1476 -->Status bar message shown when not enough
1765 aligned positions were available to create a 3D structure
1769 <em>3D Structure</em>
1772 <!-- JAL-2430 -->Hidden regions in alignment views are not
1773 coloured in linked structure views
1776 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1777 file-based command exchange
1780 <!-- JAL-2375 -->Structure chooser automatically shows
1781 Cached Structures rather than querying the PDBe if
1782 structures are already available for sequences
1785 <!-- JAL-2520 -->Structures imported via URL are cached in
1786 the Jalview project rather than downloaded again when the
1787 project is reopened.
1790 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1791 to transfer Chimera's structure attributes as Jalview
1792 features, and vice-versa (<strong>Experimental
1796 <em>Web Services</em>
1799 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1802 <!-- JAL-2335 -->Filter non-standard amino acids and
1803 nucleotides when submitting to AACon and other MSA
1807 <!-- JAL-2316, -->URLs for viewing database
1808 cross-references provided by identifiers.org and the
1809 EMBL-EBI's MIRIAM DB
1816 <!-- JAL-2344 -->FileFormatI interface for describing and
1817 identifying file formats (instead of String constants)
1820 <!-- JAL-2228 -->FeatureCounter script refactored for
1821 efficiency when counting all displayed features (not
1822 backwards compatible with 2.10.1)
1825 <em>Example files</em>
1828 <!-- JAL-2631 -->Graduated feature colour style example
1829 included in the example feature file
1832 <em>Documentation</em>
1835 <!-- JAL-2339 -->Release notes reformatted for readability
1836 with the built-in Java help viewer
1839 <!-- JAL-1644 -->Find documentation updated with 'search
1840 sequence description' option
1846 <!-- JAL-2485, -->External service integration tests for
1847 Uniprot REST Free Text Search Client
1850 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1853 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1858 <td><div align="left">
1859 <em>Calculations</em>
1862 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1863 matrix - C->R should be '-3'<br />Old matrix restored
1864 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1866 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1867 Jalview's treatment of gaps in PCA and substitution matrix
1868 based Tree calculations.<br /> <br />In earlier versions
1869 of Jalview, gaps matching gaps were penalised, and gaps
1870 matching non-gaps penalised even more. In the PCA
1871 calculation, gaps were actually treated as non-gaps - so
1872 different costs were applied, which meant Jalview's PCAs
1873 were different to those produced by SeqSpace.<br />Jalview
1874 now treats gaps in the same way as SeqSpace (ie it scores
1875 them as 0). <br /> <br />Enter the following in the
1876 Groovy console to restore pre-2.10.2 behaviour:<br />
1877 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1878 // for 2.10.1 mode <br />
1879 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1880 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1881 these settings will affect all subsequent tree and PCA
1882 calculations (not recommended)</em></li>
1884 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1885 scaling of branch lengths for trees computed using
1886 Sequence Feature Similarity.
1889 <!-- JAL-2377 -->PCA calculation could hang when
1890 generating output report when working with highly
1891 redundant alignments
1894 <!-- JAL-2544 --> Sort by features includes features to
1895 right of selected region when gaps present on right-hand
1899 <em>User Interface</em>
1902 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1903 doesn't reselect a specific sequence's associated
1904 annotation after it was used for colouring a view
1907 <!-- JAL-2419 -->Current selection lost if popup menu
1908 opened on a region of alignment without groups
1911 <!-- JAL-2374 -->Popup menu not always shown for regions
1912 of an alignment with overlapping groups
1915 <!-- JAL-2310 -->Finder double counts if both a sequence's
1916 name and description match
1919 <!-- JAL-2370 -->Hiding column selection containing two
1920 hidden regions results in incorrect hidden regions
1923 <!-- JAL-2386 -->'Apply to all groups' setting when
1924 changing colour does not apply Conservation slider value
1928 <!-- JAL-2373 -->Percentage identity and conservation menu
1929 items do not show a tick or allow shading to be disabled
1932 <!-- JAL-2385 -->Conservation shading or PID threshold
1933 lost when base colourscheme changed if slider not visible
1936 <!-- JAL-2547 -->Sequence features shown in tooltip for
1937 gaps before start of features
1940 <!-- JAL-2623 -->Graduated feature colour threshold not
1941 restored to UI when feature colour is edited
1944 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1945 a time when scrolling vertically in wrapped mode.
1948 <!-- JAL-2630 -->Structure and alignment overview update
1949 as graduate feature colour settings are modified via the
1953 <!-- JAL-2034 -->Overview window doesn't always update
1954 when a group defined on the alignment is resized
1957 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1958 wrapped view result in positional status updates
1962 <!-- JAL-2563 -->Status bar doesn't show position for
1963 ambiguous amino acid and nucleotide symbols
1966 <!-- JAL-2602 -->Copy consensus sequence failed if
1967 alignment included gapped columns
1970 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1971 widgets don't permanently disappear
1974 <!-- JAL-2503 -->Cannot select or filter quantitative
1975 annotation that are shown only as column labels (e.g.
1976 T-Coffee column reliability scores)
1979 <!-- JAL-2594 -->Exception thrown if trying to create a
1980 sequence feature on gaps only
1983 <!-- JAL-2504 -->Features created with 'New feature'
1984 button from a Find inherit previously defined feature type
1985 rather than the Find query string
1988 <!-- JAL-2423 -->incorrect title in output window when
1989 exporting tree calculated in Jalview
1992 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1993 and then revealing them reorders sequences on the
1997 <!-- JAL-964 -->Group panel in sequence feature settings
1998 doesn't update to reflect available set of groups after
1999 interactively adding or modifying features
2002 <!-- JAL-2225 -->Sequence Database chooser unusable on
2006 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2007 only excluded gaps in current sequence and ignored
2014 <!-- JAL-2421 -->Overview window visible region moves
2015 erratically when hidden rows or columns are present
2018 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2019 Structure Viewer's colour menu don't correspond to
2023 <!-- JAL-2405 -->Protein specific colours only offered in
2024 colour and group colour menu for protein alignments
2027 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2028 reflect currently selected view or group's shading
2032 <!-- JAL-2624 -->Feature colour thresholds not respected
2033 when rendered on overview and structures when opacity at
2037 <!-- JAL-2589 -->User defined gap colour not shown in
2038 overview when features overlaid on alignment
2041 <!-- JAL-2567 -->Feature settings for different views not
2042 recovered correctly from Jalview project file
2045 <!-- JAL-2256 -->Feature colours in overview when first opened
2046 (automatically via preferences) are different to the main
2050 <em>Data import/export</em>
2053 <!-- JAL-2576 -->Very large alignments take a long time to
2057 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2058 added after a sequence was imported are not written to
2062 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2063 when importing RNA secondary structure via Stockholm
2066 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2067 not shown in correct direction for simple pseudoknots
2070 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2071 with lightGray or darkGray via features file (but can
2075 <!-- JAL-2383 -->Above PID colour threshold not recovered
2076 when alignment view imported from project
2079 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2080 structure and sequences extracted from structure files
2081 imported via URL and viewed in Jmol
2084 <!-- JAL-2520 -->Structures loaded via URL are saved in
2085 Jalview Projects rather than fetched via URL again when
2086 the project is loaded and the structure viewed
2089 <em>Web Services</em>
2092 <!-- JAL-2519 -->EnsemblGenomes example failing after
2093 release of Ensembl v.88
2096 <!-- JAL-2366 -->Proxy server address and port always
2097 appear enabled in Preferences->Connections
2100 <!-- JAL-2461 -->DAS registry not found exceptions
2101 removed from console output
2104 <!-- JAL-2582 -->Cannot retrieve protein products from
2105 Ensembl by Peptide ID
2108 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2109 created from SIFTs, and spurious 'Couldn't open structure
2110 in Chimera' errors raised after April 2017 update (problem
2111 due to 'null' string rather than empty string used for
2112 residues with no corresponding PDB mapping).
2115 <em>Application UI</em>
2118 <!-- JAL-2361 -->User Defined Colours not added to Colour
2122 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2123 case' residues (button in colourscheme editor debugged and
2124 new documentation and tooltips added)
2127 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2128 doesn't restore group-specific text colour thresholds
2131 <!-- JAL-2243 -->Feature settings panel does not update as
2132 new features are added to alignment
2135 <!-- JAL-2532 -->Cancel in feature settings reverts
2136 changes to feature colours via the Amend features dialog
2139 <!-- JAL-2506 -->Null pointer exception when attempting to
2140 edit graduated feature colour via amend features dialog
2144 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2145 selection menu changes colours of alignment views
2148 <!-- JAL-2426 -->Spurious exceptions in console raised
2149 from alignment calculation workers after alignment has
2153 <!-- JAL-1608 -->Typo in selection popup menu - Create
2154 groups now 'Create Group'
2157 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2158 Create/Undefine group doesn't always work
2161 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2162 shown again after pressing 'Cancel'
2165 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2166 adjusts start position in wrap mode
2169 <!-- JAL-2563 -->Status bar doesn't show positions for
2170 ambiguous amino acids
2173 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2174 CDS/Protein view after CDS sequences added for aligned
2178 <!-- JAL-2592 -->User defined colourschemes called 'User
2179 Defined' don't appear in Colours menu
2185 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2186 score models doesn't always result in an updated PCA plot
2189 <!-- JAL-2442 -->Features not rendered as transparent on
2190 overview or linked structure view
2193 <!-- JAL-2372 -->Colour group by conservation doesn't
2197 <!-- JAL-2517 -->Hitting Cancel after applying
2198 user-defined colourscheme doesn't restore original
2205 <!-- JAL-2314 -->Unit test failure:
2206 jalview.ws.jabaws.RNAStructExportImport setup fails
2209 <!-- JAL-2307 -->Unit test failure:
2210 jalview.ws.sifts.SiftsClientTest due to compatibility
2211 problems with deep array comparison equality asserts in
2212 successive versions of TestNG
2215 <!-- JAL-2479 -->Relocated StructureChooserTest and
2216 ParameterUtilsTest Unit tests to Network suite
2219 <em>New Known Issues</em>
2222 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2223 phase after a sequence motif find operation
2226 <!-- JAL-2550 -->Importing annotation file with rows
2227 containing just upper and lower case letters are
2228 interpreted as WUSS RNA secondary structure symbols
2231 <!-- JAL-2590 -->Cannot load and display Newick trees
2232 reliably from eggnog Ortholog database
2235 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2236 containing features of type Highlight' when 'B' is pressed
2237 to mark columns containing highlighted regions.
2240 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2241 doesn't always add secondary structure annotation.
2246 <td width="60" nowrap>
2247 <div align="center">
2248 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2251 <td><div align="left">
2255 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2256 for all consensus calculations
2259 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2262 <li>Updated Jalview's Certum code signing certificate
2265 <em>Application</em>
2268 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2269 set of database cross-references, sorted alphabetically
2272 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2273 from database cross references. Users with custom links
2274 will receive a <a href="webServices/urllinks.html#warning">warning
2275 dialog</a> asking them to update their preferences.
2278 <!-- JAL-2287-->Cancel button and escape listener on
2279 dialog warning user about disconnecting Jalview from a
2283 <!-- JAL-2320-->Jalview's Chimera control window closes if
2284 the Chimera it is connected to is shut down
2287 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2288 columns menu item to mark columns containing highlighted
2289 regions (e.g. from structure selections or results of a
2293 <!-- JAL-2284-->Command line option for batch-generation
2294 of HTML pages rendering alignment data with the BioJS
2304 <!-- JAL-2286 -->Columns with more than one modal residue
2305 are not coloured or thresholded according to percent
2306 identity (first observed in Jalview 2.8.2)
2309 <!-- JAL-2301 -->Threonine incorrectly reported as not
2313 <!-- JAL-2318 -->Updates to documentation pages (above PID
2314 threshold, amino acid properties)
2317 <!-- JAL-2292 -->Lower case residues in sequences are not
2318 reported as mapped to residues in a structure file in the
2322 <!--JAL-2324 -->Identical features with non-numeric scores
2323 could be added multiple times to a sequence
2326 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2327 bond features shown as two highlighted residues rather
2328 than a range in linked structure views, and treated
2329 correctly when selecting and computing trees from features
2332 <!-- JAL-2281-->Custom URL links for database
2333 cross-references are matched to database name regardless
2338 <em>Application</em>
2341 <!-- JAL-2282-->Custom URL links for specific database
2342 names without regular expressions also offer links from
2346 <!-- JAL-2315-->Removing a single configured link in the
2347 URL links pane in Connections preferences doesn't actually
2348 update Jalview configuration
2351 <!-- JAL-2272-->CTRL-Click on a selected region to open
2352 the alignment area popup menu doesn't work on El-Capitan
2355 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2356 files with similarly named sequences if dropped onto the
2360 <!-- JAL-2312 -->Additional mappings are shown for PDB
2361 entries where more chains exist in the PDB accession than
2362 are reported in the SIFTS file
2365 <!-- JAL-2317-->Certain structures do not get mapped to
2366 the structure view when displayed with Chimera
2369 <!-- JAL-2317-->No chains shown in the Chimera view
2370 panel's View->Show Chains submenu
2373 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2374 work for wrapped alignment views
2377 <!--JAL-2197 -->Rename UI components for running JPred
2378 predictions from 'JNet' to 'JPred'
2381 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2382 corrupted when annotation panel vertical scroll is not at
2383 first annotation row
2386 <!--JAL-2332 -->Attempting to view structure for Hen
2387 lysozyme results in a PDB Client error dialog box
2390 <!-- JAL-2319 -->Structure View's mapping report switched
2391 ranges for PDB and sequence for SIFTS
2394 SIFTS 'Not_Observed' residues mapped to non-existant
2398 <!-- <em>New Known Issues</em>
2405 <td width="60" nowrap>
2406 <div align="center">
2407 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2408 <em>25/10/2016</em></strong>
2411 <td><em>Application</em>
2413 <li>3D Structure chooser opens with 'Cached structures'
2414 view if structures already loaded</li>
2415 <li>Progress bar reports models as they are loaded to
2416 structure views</li>
2422 <li>Colour by conservation always enabled and no tick
2423 shown in menu when BLOSUM or PID shading applied</li>
2424 <li>FER1_ARATH and FER2_ARATH labels were switched in
2425 example sequences/projects/trees</li>
2427 <em>Application</em>
2429 <li>Jalview projects with views of local PDB structure
2430 files saved on Windows cannot be opened on OSX</li>
2431 <li>Multiple structure views can be opened and superposed
2432 without timeout for structures with multiple models or
2433 multiple sequences in alignment</li>
2434 <li>Cannot import or associated local PDB files without a
2435 PDB ID HEADER line</li>
2436 <li>RMSD is not output in Jmol console when superposition
2438 <li>Drag and drop of URL from Browser fails for Linux and
2439 OSX versions earlier than El Capitan</li>
2440 <li>ENA client ignores invalid content from ENA server</li>
2441 <li>Exceptions are not raised in console when ENA client
2442 attempts to fetch non-existent IDs via Fetch DB Refs UI
2444 <li>Exceptions are not raised in console when a new view
2445 is created on the alignment</li>
2446 <li>OSX right-click fixed for group selections: CMD-click
2447 to insert/remove gaps in groups and CTRL-click to open group
2450 <em>Build and deployment</em>
2452 <li>URL link checker now copes with multi-line anchor
2455 <em>New Known Issues</em>
2457 <li>Drag and drop from URL links in browsers do not work
2464 <td width="60" nowrap>
2465 <div align="center">
2466 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2469 <td><em>General</em>
2472 <!-- JAL-2124 -->Updated Spanish translations.
2475 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2476 for importing structure data to Jalview. Enables mmCIF and
2480 <!-- JAL-192 --->Alignment ruler shows positions relative to
2484 <!-- JAL-2202 -->Position/residue shown in status bar when
2485 mousing over sequence associated annotation
2488 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2492 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2493 '()', canonical '[]' and invalid '{}' base pair populations
2497 <!-- JAL-2092 -->Feature settings popup menu options for
2498 showing or hiding columns containing a feature
2501 <!-- JAL-1557 -->Edit selected group by double clicking on
2502 group and sequence associated annotation labels
2505 <!-- JAL-2236 -->Sequence name added to annotation label in
2506 select/hide columns by annotation and colour by annotation
2510 </ul> <em>Application</em>
2513 <!-- JAL-2050-->Automatically hide introns when opening a
2514 gene/transcript view
2517 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2521 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2522 structure mappings with the EMBL-EBI PDBe SIFTS database
2525 <!-- JAL-2079 -->Updated download sites used for Rfam and
2526 Pfam sources to xfam.org
2529 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2532 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2533 over sequences in Jalview
2536 <!-- JAL-2027-->Support for reverse-complement coding
2537 regions in ENA and EMBL
2540 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2541 for record retrieval via ENA rest API
2544 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2548 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2549 groovy script execution
2552 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2553 alignment window's Calculate menu
2556 <!-- JAL-1812 -->Allow groovy scripts that call
2557 Jalview.getAlignFrames() to run in headless mode
2560 <!-- JAL-2068 -->Support for creating new alignment
2561 calculation workers from groovy scripts
2564 <!-- JAL-1369 --->Store/restore reference sequence in
2568 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2569 associations are now saved/restored from project
2572 <!-- JAL-1993 -->Database selection dialog always shown
2573 before sequence fetcher is opened
2576 <!-- JAL-2183 -->Double click on an entry in Jalview's
2577 database chooser opens a sequence fetcher
2580 <!-- JAL-1563 -->Free-text search client for UniProt using
2581 the UniProt REST API
2584 <!-- JAL-2168 -->-nonews command line parameter to prevent
2585 the news reader opening
2588 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2589 querying stored in preferences
2592 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2596 <!-- JAL-1977-->Tooltips shown on database chooser
2599 <!-- JAL-391 -->Reverse complement function in calculate
2600 menu for nucleotide sequences
2603 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2604 and feature counts preserves alignment ordering (and
2605 debugged for complex feature sets).
2608 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2609 viewing structures with Jalview 2.10
2612 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2613 genome, transcript CCDS and gene ids via the Ensembl and
2614 Ensembl Genomes REST API
2617 <!-- JAL-2049 -->Protein sequence variant annotation
2618 computed for 'sequence_variant' annotation on CDS regions
2622 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2626 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2627 Ref Fetcher fails to match, or otherwise updates sequence
2628 data from external database records.
2631 <!-- JAL-2154 -->Revised Jalview Project format for
2632 efficient recovery of sequence coding and alignment
2633 annotation relationships.
2635 </ul> <!-- <em>Applet</em>
2646 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2650 <!-- JAL-2018-->Export features in Jalview format (again)
2651 includes graduated colourschemes
2654 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2655 working with big alignments and lots of hidden columns
2658 <!-- JAL-2053-->Hidden column markers not always rendered
2659 at right of alignment window
2662 <!-- JAL-2067 -->Tidied up links in help file table of
2666 <!-- JAL-2072 -->Feature based tree calculation not shown
2670 <!-- JAL-2075 -->Hidden columns ignored during feature
2671 based tree calculation
2674 <!-- JAL-2065 -->Alignment view stops updating when show
2675 unconserved enabled for group on alignment
2678 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2682 <!-- JAL-2146 -->Alignment column in status incorrectly
2683 shown as "Sequence position" when mousing over
2687 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2688 hidden columns present
2691 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2692 user created annotation added to alignment
2695 <!-- JAL-1841 -->RNA Structure consensus only computed for
2696 '()' base pair annotation
2699 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2700 in zero scores for all base pairs in RNA Structure
2704 <!-- JAL-2174-->Extend selection with columns containing
2708 <!-- JAL-2275 -->Pfam format writer puts extra space at
2709 beginning of sequence
2712 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2716 <!-- JAL-2238 -->Cannot create groups on an alignment from
2717 from a tree when t-coffee scores are shown
2720 <!-- JAL-1836,1967 -->Cannot import and view PDB
2721 structures with chains containing negative resnums (4q4h)
2724 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2728 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2729 to Clustal, PIR and PileUp output
2732 <!-- JAL-2008 -->Reordering sequence features that are
2733 not visible causes alignment window to repaint
2736 <!-- JAL-2006 -->Threshold sliders don't work in
2737 graduated colour and colour by annotation row for e-value
2738 scores associated with features and annotation rows
2741 <!-- JAL-1797 -->amino acid physicochemical conservation
2742 calculation should be case independent
2745 <!-- JAL-2173 -->Remove annotation also updates hidden
2749 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2750 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2751 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2754 <!-- JAL-2065 -->Null pointer exceptions and redraw
2755 problems when reference sequence defined and 'show
2756 non-conserved' enabled
2759 <!-- JAL-1306 -->Quality and Conservation are now shown on
2760 load even when Consensus calculation is disabled
2763 <!-- JAL-1932 -->Remove right on penultimate column of
2764 alignment does nothing
2767 <em>Application</em>
2770 <!-- JAL-1552-->URLs and links can't be imported by
2771 drag'n'drop on OSX when launched via webstart (note - not
2772 yet fixed for El Capitan)
2775 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2776 output when running on non-gb/us i18n platforms
2779 <!-- JAL-1944 -->Error thrown when exporting a view with
2780 hidden sequences as flat-file alignment
2783 <!-- JAL-2030-->InstallAnywhere distribution fails when
2787 <!-- JAL-2080-->Jalview very slow to launch via webstart
2788 (also hotfix for 2.9.0b2)
2791 <!-- JAL-2085 -->Cannot save project when view has a
2792 reference sequence defined
2795 <!-- JAL-1011 -->Columns are suddenly selected in other
2796 alignments and views when revealing hidden columns
2799 <!-- JAL-1989 -->Hide columns not mirrored in complement
2800 view in a cDNA/Protein splitframe
2803 <!-- JAL-1369 -->Cannot save/restore representative
2804 sequence from project when only one sequence is
2808 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2809 in Structure Chooser
2812 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2813 structure consensus didn't refresh annotation panel
2816 <!-- JAL-1962 -->View mapping in structure view shows
2817 mappings between sequence and all chains in a PDB file
2820 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2821 dialogs format columns correctly, don't display array
2822 data, sort columns according to type
2825 <!-- JAL-1975 -->Export complete shown after destination
2826 file chooser is cancelled during an image export
2829 <!-- JAL-2025 -->Error when querying PDB Service with
2830 sequence name containing special characters
2833 <!-- JAL-2024 -->Manual PDB structure querying should be
2837 <!-- JAL-2104 -->Large tooltips with broken HTML
2838 formatting don't wrap
2841 <!-- JAL-1128 -->Figures exported from wrapped view are
2842 truncated so L looks like I in consensus annotation
2845 <!-- JAL-2003 -->Export features should only export the
2846 currently displayed features for the current selection or
2850 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2851 after fetching cross-references, and restoring from
2855 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2856 followed in the structure viewer
2859 <!-- JAL-2163 -->Titles for individual alignments in
2860 splitframe not restored from project
2863 <!-- JAL-2145 -->missing autocalculated annotation at
2864 trailing end of protein alignment in transcript/product
2865 splitview when pad-gaps not enabled by default
2868 <!-- JAL-1797 -->amino acid physicochemical conservation
2872 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2873 article has been read (reopened issue due to
2874 internationalisation problems)
2877 <!-- JAL-1960 -->Only offer PDB structures in structure
2878 viewer based on sequence name, PDB and UniProt
2883 <!-- JAL-1976 -->No progress bar shown during export of
2887 <!-- JAL-2213 -->Structures not always superimposed after
2888 multiple structures are shown for one or more sequences.
2891 <!-- JAL-1370 -->Reference sequence characters should not
2892 be replaced with '.' when 'Show unconserved' format option
2896 <!-- JAL-1823 -->Cannot specify chain code when entering
2897 specific PDB id for sequence
2900 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2901 'Export hidden sequences' is enabled, but 'export hidden
2902 columns' is disabled.
2905 <!--JAL-2026-->Best Quality option in structure chooser
2906 selects lowest rather than highest resolution structures
2910 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2911 to sequence mapping in 'View Mappings' report
2914 <!-- JAL-2284 -->Unable to read old Jalview projects that
2915 contain non-XML data added after Jalvew wrote project.
2918 <!-- JAL-2118 -->Newly created annotation row reorders
2919 after clicking on it to create new annotation for a
2923 <!-- JAL-1980 -->Null Pointer Exception raised when
2924 pressing Add on an orphaned cut'n'paste window.
2926 <!-- may exclude, this is an external service stability issue JAL-1941
2927 -- > RNA 3D structure not added via DSSR service</li> -->
2932 <!-- JAL-2151 -->Incorrect columns are selected when
2933 hidden columns present before start of sequence
2936 <!-- JAL-1986 -->Missing dependencies on applet pages
2940 <!-- JAL-1947 -->Overview pixel size changes when
2941 sequences are hidden in applet
2944 <!-- JAL-1996 -->Updated instructions for applet
2945 deployment on examples pages.
2952 <td width="60" nowrap>
2953 <div align="center">
2954 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2955 <em>16/10/2015</em></strong>
2958 <td><em>General</em>
2960 <li>Time stamps for signed Jalview application and applet
2965 <em>Application</em>
2967 <li>Duplicate group consensus and conservation rows
2968 shown when tree is partitioned</li>
2969 <li>Erratic behaviour when tree partitions made with
2970 multiple cDNA/Protein split views</li>
2976 <td width="60" nowrap>
2977 <div align="center">
2978 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2979 <em>8/10/2015</em></strong>
2982 <td><em>General</em>
2984 <li>Updated Spanish translations of localized text for
2986 </ul> <em>Application</em>
2988 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2989 <li>Signed OSX InstallAnywhere installer<br></li>
2990 <li>Support for per-sequence based annotations in BioJSON</li>
2991 </ul> <em>Applet</em>
2993 <li>Split frame example added to applet examples page</li>
2994 </ul> <em>Build and Deployment</em>
2997 <!-- JAL-1888 -->New ant target for running Jalview's test
3005 <li>Mapping of cDNA to protein in split frames
3006 incorrect when sequence start > 1</li>
3007 <li>Broken images in filter column by annotation dialog
3009 <li>Feature colours not parsed from features file</li>
3010 <li>Exceptions and incomplete link URLs recovered when
3011 loading a features file containing HTML tags in feature
3015 <em>Application</em>
3017 <li>Annotations corrupted after BioJS export and
3019 <li>Incorrect sequence limits after Fetch DB References
3020 with 'trim retrieved sequences'</li>
3021 <li>Incorrect warning about deleting all data when
3022 deleting selected columns</li>
3023 <li>Patch to build system for shipping properly signed
3024 JNLP templates for webstart launch</li>
3025 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3026 unreleased structures for download or viewing</li>
3027 <li>Tab/space/return keystroke operation of EMBL-PDBe
3028 fetcher/viewer dialogs works correctly</li>
3029 <li>Disabled 'minimise' button on Jalview windows
3030 running on OSX to workaround redraw hang bug</li>
3031 <li>Split cDNA/Protein view position and geometry not
3032 recovered from jalview project</li>
3033 <li>Initial enabled/disabled state of annotation menu
3034 sorter 'show autocalculated first/last' corresponds to
3036 <li>Restoring of Clustal, RNA Helices and T-Coffee
3037 color schemes from BioJSON</li>
3041 <li>Reorder sequences mirrored in cDNA/Protein split
3043 <li>Applet with Jmol examples not loading correctly</li>
3049 <td><div align="center">
3050 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3052 <td><em>General</em>
3054 <li>Linked visualisation and analysis of DNA and Protein
3057 <li>Translated cDNA alignments shown as split protein
3058 and DNA alignment views</li>
3059 <li>Codon consensus annotation for linked protein and
3060 cDNA alignment views</li>
3061 <li>Link cDNA or Protein product sequences by loading
3062 them onto Protein or cDNA alignments</li>
3063 <li>Reconstruct linked cDNA alignment from aligned
3064 protein sequences</li>
3067 <li>Jmol integration updated to Jmol v14.2.14</li>
3068 <li>Import and export of Jalview alignment views as <a
3069 href="features/bioJsonFormat.html">BioJSON</a></li>
3070 <li>New alignment annotation file statements for
3071 reference sequences and marking hidden columns</li>
3072 <li>Reference sequence based alignment shading to
3073 highlight variation</li>
3074 <li>Select or hide columns according to alignment
3076 <li>Find option for locating sequences by description</li>
3077 <li>Conserved physicochemical properties shown in amino
3078 acid conservation row</li>
3079 <li>Alignments can be sorted by number of RNA helices</li>
3080 </ul> <em>Application</em>
3082 <li>New cDNA/Protein analysis capabilities
3084 <li>Get Cross-References should open a Split Frame
3085 view with cDNA/Protein</li>
3086 <li>Detect when nucleotide sequences and protein
3087 sequences are placed in the same alignment</li>
3088 <li>Split cDNA/Protein views are saved in Jalview
3093 <li>Use REST API to talk to Chimera</li>
3094 <li>Selected regions in Chimera are highlighted in linked
3095 Jalview windows</li>
3097 <li>VARNA RNA viewer updated to v3.93</li>
3098 <li>VARNA views are saved in Jalview Projects</li>
3099 <li>Pseudoknots displayed as Jalview RNA annotation can
3100 be shown in VARNA</li>
3102 <li>Make groups for selection uses marked columns as well
3103 as the active selected region</li>
3105 <li>Calculate UPGMA and NJ trees using sequence feature
3107 <li>New Export options
3109 <li>New Export Settings dialog to control hidden
3110 region export in flat file generation</li>
3112 <li>Export alignment views for display with the <a
3113 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3115 <li>Export scrollable SVG in HTML page</li>
3116 <li>Optional embedding of BioJSON data when exporting
3117 alignment figures to HTML</li>
3119 <li>3D structure retrieval and display
3121 <li>Free text and structured queries with the PDBe
3123 <li>PDBe Search API based discovery and selection of
3124 PDB structures for a sequence set</li>
3128 <li>JPred4 employed for protein secondary structure
3130 <li>Hide Insertions menu option to hide unaligned columns
3131 for one or a group of sequences</li>
3132 <li>Automatically hide insertions in alignments imported
3133 from the JPred4 web server</li>
3134 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3135 system on OSX<br />LGPL libraries courtesy of <a
3136 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3138 <li>changed 'View nucleotide structure' submenu to 'View
3139 VARNA 2D Structure'</li>
3140 <li>change "View protein structure" menu option to "3D
3143 </ul> <em>Applet</em>
3145 <li>New layout for applet example pages</li>
3146 <li>New parameters to enable SplitFrame view
3147 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3148 <li>New example demonstrating linked viewing of cDNA and
3149 Protein alignments</li>
3150 </ul> <em>Development and deployment</em>
3152 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3153 <li>Include installation type and git revision in build
3154 properties and console log output</li>
3155 <li>Jalview Github organisation, and new github site for
3156 storing BioJsMSA Templates</li>
3157 <li>Jalview's unit tests now managed with TestNG</li>
3160 <!-- <em>General</em>
3162 </ul> --> <!-- issues resolved --> <em>Application</em>
3164 <li>Escape should close any open find dialogs</li>
3165 <li>Typo in select-by-features status report</li>
3166 <li>Consensus RNA secondary secondary structure
3167 predictions are not highlighted in amber</li>
3168 <li>Missing gap character in v2.7 example file means
3169 alignment appears unaligned when pad-gaps is not enabled</li>
3170 <li>First switch to RNA Helices colouring doesn't colour
3171 associated structure views</li>
3172 <li>ID width preference option is greyed out when auto
3173 width checkbox not enabled</li>
3174 <li>Stopped a warning dialog from being shown when
3175 creating user defined colours</li>
3176 <li>'View Mapping' in structure viewer shows sequence
3177 mappings for just that viewer's sequences</li>
3178 <li>Workaround for superposing PDB files containing
3179 multiple models in Chimera</li>
3180 <li>Report sequence position in status bar when hovering
3181 over Jmol structure</li>
3182 <li>Cannot output gaps as '.' symbols with Selection ->
3183 output to text box</li>
3184 <li>Flat file exports of alignments with hidden columns
3185 have incorrect sequence start/end</li>
3186 <li>'Aligning' a second chain to a Chimera structure from
3188 <li>Colour schemes applied to structure viewers don't
3189 work for nucleotide</li>
3190 <li>Loading/cut'n'pasting an empty or invalid file leads
3191 to a grey/invisible alignment window</li>
3192 <li>Exported Jpred annotation from a sequence region
3193 imports to different position</li>
3194 <li>Space at beginning of sequence feature tooltips shown
3195 on some platforms</li>
3196 <li>Chimera viewer 'View | Show Chain' menu is not
3198 <li>'New View' fails with a Null Pointer Exception in
3199 console if Chimera has been opened</li>
3200 <li>Mouseover to Chimera not working</li>
3201 <li>Miscellaneous ENA XML feature qualifiers not
3203 <li>NPE in annotation renderer after 'Extract Scores'</li>
3204 <li>If two structures in one Chimera window, mouseover of
3205 either sequence shows on first structure</li>
3206 <li>'Show annotations' options should not make
3207 non-positional annotations visible</li>
3208 <li>Subsequence secondary structure annotation not shown
3209 in right place after 'view flanking regions'</li>
3210 <li>File Save As type unset when current file format is
3212 <li>Save as '.jar' option removed for saving Jalview
3214 <li>Colour by Sequence colouring in Chimera more
3216 <li>Cannot 'add reference annotation' for a sequence in
3217 several views on same alignment</li>
3218 <li>Cannot show linked products for EMBL / ENA records</li>
3219 <li>Jalview's tooltip wraps long texts containing no
3221 </ul> <em>Applet</em>
3223 <li>Jmol to JalviewLite mouseover/link not working</li>
3224 <li>JalviewLite can't import sequences with ID
3225 descriptions containing angle brackets</li>
3226 </ul> <em>General</em>
3228 <li>Cannot export and reimport RNA secondary structure
3229 via jalview annotation file</li>
3230 <li>Random helix colour palette for colour by annotation
3231 with RNA secondary structure</li>
3232 <li>Mouseover to cDNA from STOP residue in protein
3233 translation doesn't work.</li>
3234 <li>hints when using the select by annotation dialog box</li>
3235 <li>Jmol alignment incorrect if PDB file has alternate CA
3237 <li>FontChooser message dialog appears to hang after
3238 choosing 1pt font</li>
3239 <li>Peptide secondary structure incorrectly imported from
3240 annotation file when annotation display text includes 'e' or
3242 <li>Cannot set colour of new feature type whilst creating
3244 <li>cDNA translation alignment should not be sequence
3245 order dependent</li>
3246 <li>'Show unconserved' doesn't work for lower case
3248 <li>Nucleotide ambiguity codes involving R not recognised</li>
3249 </ul> <em>Deployment and Documentation</em>
3251 <li>Applet example pages appear different to the rest of
3252 www.jalview.org</li>
3253 </ul> <em>Application Known issues</em>
3255 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3256 <li>Misleading message appears after trying to delete
3258 <li>Jalview icon not shown in dock after InstallAnywhere
3259 version launches</li>
3260 <li>Fetching EMBL reference for an RNA sequence results
3261 fails with a sequence mismatch</li>
3262 <li>Corrupted or unreadable alignment display when
3263 scrolling alignment to right</li>
3264 <li>ArrayIndexOutOfBoundsException thrown when remove
3265 empty columns called on alignment with ragged gapped ends</li>
3266 <li>auto calculated alignment annotation rows do not get
3267 placed above or below non-autocalculated rows</li>
3268 <li>Jalview dekstop becomes sluggish at full screen in
3269 ultra-high resolution</li>
3270 <li>Cannot disable consensus calculation independently of
3271 quality and conservation</li>
3272 <li>Mouseover highlighting between cDNA and protein can
3273 become sluggish with more than one splitframe shown</li>
3274 </ul> <em>Applet Known Issues</em>
3276 <li>Core PDB parsing code requires Jmol</li>
3277 <li>Sequence canvas panel goes white when alignment
3278 window is being resized</li>
3284 <td><div align="center">
3285 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3287 <td><em>General</em>
3289 <li>Updated Java code signing certificate donated by
3291 <li>Features and annotation preserved when performing
3292 pairwise alignment</li>
3293 <li>RNA pseudoknot annotation can be
3294 imported/exported/displayed</li>
3295 <li>'colour by annotation' can colour by RNA and
3296 protein secondary structure</li>
3297 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3298 post-hoc with 2.9 release</em>)
3301 </ul> <em>Application</em>
3303 <li>Extract and display secondary structure for sequences
3304 with 3D structures</li>
3305 <li>Support for parsing RNAML</li>
3306 <li>Annotations menu for layout
3308 <li>sort sequence annotation rows by alignment</li>
3309 <li>place sequence annotation above/below alignment
3312 <li>Output in Stockholm format</li>
3313 <li>Internationalisation: improved Spanish (es)
3315 <li>Structure viewer preferences tab</li>
3316 <li>Disorder and Secondary Structure annotation tracks
3317 shared between alignments</li>
3318 <li>UCSF Chimera launch and linked highlighting from
3320 <li>Show/hide all sequence associated annotation rows for
3321 all or current selection</li>
3322 <li>disorder and secondary structure predictions
3323 available as dataset annotation</li>
3324 <li>Per-sequence rna helices colouring</li>
3327 <li>Sequence database accessions imported when fetching
3328 alignments from Rfam</li>
3329 <li>update VARNA version to 3.91</li>
3331 <li>New groovy scripts for exporting aligned positions,
3332 conservation values, and calculating sum of pairs scores.</li>
3333 <li>Command line argument to set default JABAWS server</li>
3334 <li>include installation type in build properties and
3335 console log output</li>
3336 <li>Updated Jalview project format to preserve dataset
3340 <!-- issues resolved --> <em>Application</em>
3342 <li>Distinguish alignment and sequence associated RNA
3343 structure in structure->view->VARNA</li>
3344 <li>Raise dialog box if user deletes all sequences in an
3346 <li>Pressing F1 results in documentation opening twice</li>
3347 <li>Sequence feature tooltip is wrapped</li>
3348 <li>Double click on sequence associated annotation
3349 selects only first column</li>
3350 <li>Redundancy removal doesn't result in unlinked
3351 leaves shown in tree</li>
3352 <li>Undos after several redundancy removals don't undo
3354 <li>Hide sequence doesn't hide associated annotation</li>
3355 <li>User defined colours dialog box too big to fit on
3356 screen and buttons not visible</li>
3357 <li>author list isn't updated if already written to
3358 Jalview properties</li>
3359 <li>Popup menu won't open after retrieving sequence
3361 <li>File open window for associate PDB doesn't open</li>
3362 <li>Left-then-right click on a sequence id opens a
3363 browser search window</li>
3364 <li>Cannot open sequence feature shading/sort popup menu
3365 in feature settings dialog</li>
3366 <li>better tooltip placement for some areas of Jalview
3368 <li>Allow addition of JABAWS Server which doesn't
3369 pass validation</li>
3370 <li>Web services parameters dialog box is too large to
3372 <li>Muscle nucleotide alignment preset obscured by
3374 <li>JABAWS preset submenus don't contain newly
3375 defined user preset</li>
3376 <li>MSA web services warns user if they were launched
3377 with invalid input</li>
3378 <li>Jalview cannot contact DAS Registy when running on
3381 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3382 'Superpose with' submenu not shown when new view
3386 </ul> <!-- <em>Applet</em>
3388 </ul> <em>General</em>
3390 </ul>--> <em>Deployment and Documentation</em>
3392 <li>2G and 1G options in launchApp have no effect on
3393 memory allocation</li>
3394 <li>launchApp service doesn't automatically open
3395 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3397 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3398 InstallAnywhere reports cannot find valid JVM when Java
3399 1.7_055 is available
3401 </ul> <em>Application Known issues</em>
3404 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3405 corrupted or unreadable alignment display when scrolling
3409 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3410 retrieval fails but progress bar continues for DAS retrieval
3411 with large number of ID
3414 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3415 flatfile output of visible region has incorrect sequence
3419 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3420 rna structure consensus doesn't update when secondary
3421 structure tracks are rearranged
3424 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3425 invalid rna structure positional highlighting does not
3426 highlight position of invalid base pairs
3429 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3430 out of memory errors are not raised when saving Jalview
3431 project from alignment window file menu
3434 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3435 Switching to RNA Helices colouring doesn't propagate to
3439 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3440 colour by RNA Helices not enabled when user created
3441 annotation added to alignment
3444 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3445 Jalview icon not shown on dock in Mountain Lion/Webstart
3447 </ul> <em>Applet Known Issues</em>
3450 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3451 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3454 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3455 Jalview and Jmol example not compatible with IE9
3458 <li>Sort by annotation score doesn't reverse order
3464 <td><div align="center">
3465 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3468 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3471 <li>Internationalisation of user interface (usually
3472 called i18n support) and translation for Spanish locale</li>
3473 <li>Define/Undefine group on current selection with
3474 Ctrl-G/Shift Ctrl-G</li>
3475 <li>Improved group creation/removal options in
3476 alignment/sequence Popup menu</li>
3477 <li>Sensible precision for symbol distribution
3478 percentages shown in logo tooltip.</li>
3479 <li>Annotation panel height set according to amount of
3480 annotation when alignment first opened</li>
3481 </ul> <em>Application</em>
3483 <li>Interactive consensus RNA secondary structure
3484 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3485 <li>Select columns containing particular features from
3486 Feature Settings dialog</li>
3487 <li>View all 'representative' PDB structures for selected
3489 <li>Update Jalview project format:
3491 <li>New file extension for Jalview projects '.jvp'</li>
3492 <li>Preserve sequence and annotation dataset (to
3493 store secondary structure annotation,etc)</li>
3494 <li>Per group and alignment annotation and RNA helix
3498 <li>New similarity measures for PCA and Tree calculation
3500 <li>Experimental support for retrieval and viewing of
3501 flanking regions for an alignment</li>
3505 <!-- issues resolved --> <em>Application</em>
3507 <li>logo keeps spinning and status remains at queued or
3508 running after job is cancelled</li>
3509 <li>cannot export features from alignments imported from
3510 Jalview/VAMSAS projects</li>
3511 <li>Buggy slider for web service parameters that take
3513 <li>Newly created RNA secondary structure line doesn't
3514 have 'display all symbols' flag set</li>
3515 <li>T-COFFEE alignment score shading scheme and other
3516 annotation shading not saved in Jalview project</li>
3517 <li>Local file cannot be loaded in freshly downloaded
3519 <li>Jalview icon not shown on dock in Mountain
3521 <li>Load file from desktop file browser fails</li>
3522 <li>Occasional NPE thrown when calculating large trees</li>
3523 <li>Cannot reorder or slide sequences after dragging an
3524 alignment onto desktop</li>
3525 <li>Colour by annotation dialog throws NPE after using
3526 'extract scores' function</li>
3527 <li>Loading/cut'n'pasting an empty file leads to a grey
3528 alignment window</li>
3529 <li>Disorder thresholds rendered incorrectly after
3530 performing IUPred disorder prediction</li>
3531 <li>Multiple group annotated consensus rows shown when
3532 changing 'normalise logo' display setting</li>
3533 <li>Find shows blank dialog after 'finished searching' if
3534 nothing matches query</li>
3535 <li>Null Pointer Exceptions raised when sorting by
3536 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3538 <li>Errors in Jmol console when structures in alignment
3539 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3541 <li>Not all working JABAWS services are shown in
3543 <li>JAVAWS version of Jalview fails to launch with
3544 'invalid literal/length code'</li>
3545 <li>Annotation/RNA Helix colourschemes cannot be applied
3546 to alignment with groups (actually fixed in 2.8.0b1)</li>
3547 <li>RNA Helices and T-Coffee Scores available as default
3550 </ul> <em>Applet</em>
3552 <li>Remove group option is shown even when selection is
3554 <li>Apply to all groups ticked but colourscheme changes
3555 don't affect groups</li>
3556 <li>Documented RNA Helices and T-Coffee Scores as valid
3557 colourscheme name</li>
3558 <li>Annotation labels drawn on sequence IDs when
3559 Annotation panel is not displayed</li>
3560 <li>Increased font size for dropdown menus on OSX and
3561 embedded windows</li>
3562 </ul> <em>Other</em>
3564 <li>Consensus sequence for alignments/groups with a
3565 single sequence were not calculated</li>
3566 <li>annotation files that contain only groups imported as
3567 annotation and junk sequences</li>
3568 <li>Fasta files with sequences containing '*' incorrectly
3569 recognised as PFAM or BLC</li>
3570 <li>conservation/PID slider apply all groups option
3571 doesn't affect background (2.8.0b1)
3573 <li>redundancy highlighting is erratic at 0% and 100%</li>
3574 <li>Remove gapped columns fails for sequences with ragged
3576 <li>AMSA annotation row with leading spaces is not
3577 registered correctly on import</li>
3578 <li>Jalview crashes when selecting PCA analysis for
3579 certain alignments</li>
3580 <li>Opening the colour by annotation dialog for an
3581 existing annotation based 'use original colours'
3582 colourscheme loses original colours setting</li>
3587 <td><div align="center">
3588 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3589 <em>30/1/2014</em></strong>
3593 <li>Trusted certificates for JalviewLite applet and
3594 Jalview Desktop application<br />Certificate was donated by
3595 <a href="https://www.certum.eu">Certum</a> to the Jalview
3596 open source project).
3598 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3599 <li>Output in Stockholm format</li>
3600 <li>Allow import of data from gzipped files</li>
3601 <li>Export/import group and sequence associated line
3602 graph thresholds</li>
3603 <li>Nucleotide substitution matrix that supports RNA and
3604 ambiguity codes</li>
3605 <li>Allow disorder predictions to be made on the current
3606 selection (or visible selection) in the same way that JPred
3608 <li>Groovy scripting for headless Jalview operation</li>
3609 </ul> <em>Other improvements</em>
3611 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3612 <li>COMBINE statement uses current SEQUENCE_REF and
3613 GROUP_REF scope to group annotation rows</li>
3614 <li>Support '' style escaping of quotes in Newick
3616 <li>Group options for JABAWS service by command line name</li>
3617 <li>Empty tooltip shown for JABA service options with a
3618 link but no description</li>
3619 <li>Select primary source when selecting authority in
3620 database fetcher GUI</li>
3621 <li>Add .mfa to FASTA file extensions recognised by
3623 <li>Annotation label tooltip text wrap</li>
3628 <li>Slow scrolling when lots of annotation rows are
3630 <li>Lots of NPE (and slowness) after creating RNA
3631 secondary structure annotation line</li>
3632 <li>Sequence database accessions not imported when
3633 fetching alignments from Rfam</li>
3634 <li>Incorrect SHMR submission for sequences with
3636 <li>View all structures does not always superpose
3638 <li>Option widgets in service parameters not updated to
3639 reflect user or preset settings</li>
3640 <li>Null pointer exceptions for some services without
3641 presets or adjustable parameters</li>
3642 <li>Discover PDB IDs entry in structure menu doesn't
3643 discover PDB xRefs</li>
3644 <li>Exception encountered while trying to retrieve
3645 features with DAS</li>
3646 <li>Lowest value in annotation row isn't coloured
3647 when colour by annotation (per sequence) is coloured</li>
3648 <li>Keyboard mode P jumps to start of gapped region when
3649 residue follows a gap</li>
3650 <li>Jalview appears to hang importing an alignment with
3651 Wrap as default or after enabling Wrap</li>
3652 <li>'Right click to add annotations' message
3653 shown in wrap mode when no annotations present</li>
3654 <li>Disorder predictions fail with NPE if no automatic
3655 annotation already exists on alignment</li>
3656 <li>oninit javascript function should be called after
3657 initialisation completes</li>
3658 <li>Remove redundancy after disorder prediction corrupts
3659 alignment window display</li>
3660 <li>Example annotation file in documentation is invalid</li>
3661 <li>Grouped line graph annotation rows are not exported
3662 to annotation file</li>
3663 <li>Multi-harmony analysis cannot be run when only two
3665 <li>Cannot create multiple groups of line graphs with
3666 several 'combine' statements in annotation file</li>
3667 <li>Pressing return several times causes Number Format
3668 exceptions in keyboard mode</li>
3669 <li>Multi-harmony (SHMMR) method doesn't submit
3670 correct partitions for input data</li>
3671 <li>Translation from DNA to Amino Acids fails</li>
3672 <li>Jalview fail to load newick tree with quoted label</li>
3673 <li>--headless flag isn't understood</li>
3674 <li>ClassCastException when generating EPS in headless
3676 <li>Adjusting sequence-associated shading threshold only
3677 changes one row's threshold</li>
3678 <li>Preferences and Feature settings panel panel
3679 doesn't open</li>
3680 <li>hide consensus histogram also hides conservation and
3681 quality histograms</li>
3686 <td><div align="center">
3687 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3689 <td><em>Application</em>
3691 <li>Support for JABAWS 2.0 Services (AACon alignment
3692 conservation, protein disorder and Clustal Omega)</li>
3693 <li>JABAWS server status indicator in Web Services
3695 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3696 in Jalview alignment window</li>
3697 <li>Updated Jalview build and deploy framework for OSX
3698 mountain lion, windows 7, and 8</li>
3699 <li>Nucleotide substitution matrix for PCA that supports
3700 RNA and ambiguity codes</li>
3702 <li>Improved sequence database retrieval GUI</li>
3703 <li>Support fetching and database reference look up
3704 against multiple DAS sources (Fetch all from in 'fetch db
3706 <li>Jalview project improvements
3708 <li>Store and retrieve the 'belowAlignment'
3709 flag for annotation</li>
3710 <li>calcId attribute to group annotation rows on the
3712 <li>Store AACon calculation settings for a view in
3713 Jalview project</li>
3717 <li>horizontal scrolling gesture support</li>
3718 <li>Visual progress indicator when PCA calculation is
3720 <li>Simpler JABA web services menus</li>
3721 <li>visual indication that web service results are still
3722 being retrieved from server</li>
3723 <li>Serialise the dialogs that are shown when Jalview
3724 starts up for first time</li>
3725 <li>Jalview user agent string for interacting with HTTP
3727 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3729 <li>Examples directory and Groovy library included in
3730 InstallAnywhere distribution</li>
3731 </ul> <em>Applet</em>
3733 <li>RNA alignment and secondary structure annotation
3734 visualization applet example</li>
3735 </ul> <em>General</em>
3737 <li>Normalise option for consensus sequence logo</li>
3738 <li>Reset button in PCA window to return dimensions to
3740 <li>Allow seqspace or Jalview variant of alignment PCA
3742 <li>PCA with either nucleic acid and protein substitution
3744 <li>Allow windows containing HTML reports to be exported
3746 <li>Interactive display and editing of RNA secondary
3747 structure contacts</li>
3748 <li>RNA Helix Alignment Colouring</li>
3749 <li>RNA base pair logo consensus</li>
3750 <li>Parse sequence associated secondary structure
3751 information in Stockholm files</li>
3752 <li>HTML Export database accessions and annotation
3753 information presented in tooltip for sequences</li>
3754 <li>Import secondary structure from LOCARNA clustalw
3755 style RNA alignment files</li>
3756 <li>import and visualise T-COFFEE quality scores for an
3758 <li>'colour by annotation' per sequence option to
3759 shade each sequence according to its associated alignment
3761 <li>New Jalview Logo</li>
3762 </ul> <em>Documentation and Development</em>
3764 <li>documentation for score matrices used in Jalview</li>
3765 <li>New Website!</li>
3767 <td><em>Application</em>
3769 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3770 wsdbfetch REST service</li>
3771 <li>Stop windows being moved outside desktop on OSX</li>
3772 <li>Filetype associations not installed for webstart
3774 <li>Jalview does not always retrieve progress of a JABAWS
3775 job execution in full once it is complete</li>
3776 <li>revise SHMR RSBS definition to ensure alignment is
3777 uploaded via ali_file parameter</li>
3778 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3779 <li>View all structures superposed fails with exception</li>
3780 <li>Jnet job queues forever if a very short sequence is
3781 submitted for prediction</li>
3782 <li>Cut and paste menu not opened when mouse clicked on
3784 <li>Putting fractional value into integer text box in
3785 alignment parameter dialog causes Jalview to hang</li>
3786 <li>Structure view highlighting doesn't work on
3788 <li>View all structures fails with exception shown in
3790 <li>Characters in filename associated with PDBEntry not
3791 escaped in a platform independent way</li>
3792 <li>Jalview desktop fails to launch with exception when
3794 <li>Tree calculation reports 'you must have 2 or more
3795 sequences selected' when selection is empty</li>
3796 <li>Jalview desktop fails to launch with jar signature
3797 failure when java web start temporary file caching is
3799 <li>DAS Sequence retrieval with range qualification
3800 results in sequence xref which includes range qualification</li>
3801 <li>Errors during processing of command line arguments
3802 cause progress bar (JAL-898) to be removed</li>
3803 <li>Replace comma for semi-colon option not disabled for
3804 DAS sources in sequence fetcher</li>
3805 <li>Cannot close news reader when JABAWS server warning
3806 dialog is shown</li>
3807 <li>Option widgets not updated to reflect user settings</li>
3808 <li>Edited sequence not submitted to web service</li>
3809 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3810 <li>InstallAnywhere installer doesn't unpack and run
3811 on OSX Mountain Lion</li>
3812 <li>Annotation panel not given a scroll bar when
3813 sequences with alignment annotation are pasted into the
3815 <li>Sequence associated annotation rows not associated
3816 when loaded from Jalview project</li>
3817 <li>Browser launch fails with NPE on java 1.7</li>
3818 <li>JABAWS alignment marked as finished when job was
3819 cancelled or job failed due to invalid input</li>
3820 <li>NPE with v2.7 example when clicking on Tree
3821 associated with all views</li>
3822 <li>Exceptions when copy/paste sequences with grouped
3823 annotation rows to new window</li>
3824 </ul> <em>Applet</em>
3826 <li>Sequence features are momentarily displayed before
3827 they are hidden using hidefeaturegroups applet parameter</li>
3828 <li>loading features via javascript API automatically
3829 enables feature display</li>
3830 <li>scrollToColumnIn javascript API method doesn't
3832 </ul> <em>General</em>
3834 <li>Redundancy removal fails for rna alignment</li>
3835 <li>PCA calculation fails when sequence has been selected
3836 and then deselected</li>
3837 <li>PCA window shows grey box when first opened on OSX</li>
3838 <li>Letters coloured pink in sequence logo when alignment
3839 coloured with clustalx</li>
3840 <li>Choosing fonts without letter symbols defined causes
3841 exceptions and redraw errors</li>
3842 <li>Initial PCA plot view is not same as manually
3843 reconfigured view</li>
3844 <li>Grouped annotation graph label has incorrect line
3846 <li>Grouped annotation graph label display is corrupted
3847 for lots of labels</li>
3852 <div align="center">
3853 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3856 <td><em>Application</em>
3858 <li>Jalview Desktop News Reader</li>
3859 <li>Tweaked default layout of web services menu</li>
3860 <li>View/alignment association menu to enable user to
3861 easily specify which alignment a multi-structure view takes
3862 its colours/correspondences from</li>
3863 <li>Allow properties file location to be specified as URL</li>
3864 <li>Extend Jalview project to preserve associations
3865 between many alignment views and a single Jmol display</li>
3866 <li>Store annotation row height in Jalview project file</li>
3867 <li>Annotation row column label formatting attributes
3868 stored in project file</li>
3869 <li>Annotation row order for auto-calculated annotation
3870 rows preserved in Jalview project file</li>
3871 <li>Visual progress indication when Jalview state is
3872 saved using Desktop window menu</li>
3873 <li>Visual indication that command line arguments are
3874 still being processed</li>
3875 <li>Groovy script execution from URL</li>
3876 <li>Colour by annotation default min and max colours in
3878 <li>Automatically associate PDB files dragged onto an
3879 alignment with sequences that have high similarity and
3881 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3882 <li>'view structures' option to open many
3883 structures in same window</li>
3884 <li>Sort associated views menu option for tree panel</li>
3885 <li>Group all JABA and non-JABA services for a particular
3886 analysis function in its own submenu</li>
3887 </ul> <em>Applet</em>
3889 <li>Userdefined and autogenerated annotation rows for
3891 <li>Adjustment of alignment annotation pane height</li>
3892 <li>Annotation scrollbar for annotation panel</li>
3893 <li>Drag to reorder annotation rows in annotation panel</li>
3894 <li>'automaticScrolling' parameter</li>
3895 <li>Allow sequences with partial ID string matches to be
3896 annotated from GFF/Jalview features files</li>
3897 <li>Sequence logo annotation row in applet</li>
3898 <li>Absolute paths relative to host server in applet
3899 parameters are treated as such</li>
3900 <li>New in the JalviewLite javascript API:
3902 <li>JalviewLite.js javascript library</li>
3903 <li>Javascript callbacks for
3905 <li>Applet initialisation</li>
3906 <li>Sequence/alignment mouse-overs and selections</li>
3909 <li>scrollTo row and column alignment scrolling
3911 <li>Select sequence/alignment regions from javascript</li>
3912 <li>javascript structure viewer harness to pass
3913 messages between Jmol and Jalview when running as
3914 distinct applets</li>
3915 <li>sortBy method</li>
3916 <li>Set of applet and application examples shipped
3917 with documentation</li>
3918 <li>New example to demonstrate JalviewLite and Jmol
3919 javascript message exchange</li>
3921 </ul> <em>General</em>
3923 <li>Enable Jmol displays to be associated with multiple
3924 multiple alignments</li>
3925 <li>Option to automatically sort alignment with new tree</li>
3926 <li>User configurable link to enable redirects to a
3927 www.Jalview.org mirror</li>
3928 <li>Jmol colours option for Jmol displays</li>
3929 <li>Configurable newline string when writing alignment
3930 and other flat files</li>
3931 <li>Allow alignment annotation description lines to
3932 contain html tags</li>
3933 </ul> <em>Documentation and Development</em>
3935 <li>Add groovy test harness for bulk load testing to
3937 <li>Groovy script to load and align a set of sequences
3938 using a web service before displaying the result in the
3939 Jalview desktop</li>
3940 <li>Restructured javascript and applet api documentation</li>
3941 <li>Ant target to publish example html files with applet
3943 <li>Netbeans project for building Jalview from source</li>
3944 <li>ant task to create online javadoc for Jalview source</li>
3946 <td><em>Application</em>
3948 <li>User defined colourscheme throws exception when
3949 current built in colourscheme is saved as new scheme</li>
3950 <li>AlignFrame->Save in application pops up save
3951 dialog for valid filename/format</li>
3952 <li>Cannot view associated structure for UniProt sequence</li>
3953 <li>PDB file association breaks for UniProt sequence
3955 <li>Associate PDB from file dialog does not tell you
3956 which sequence is to be associated with the file</li>
3957 <li>Find All raises null pointer exception when query
3958 only matches sequence IDs</li>
3959 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3960 <li>Jalview project with Jmol views created with Jalview
3961 2.4 cannot be loaded</li>
3962 <li>Filetype associations not installed for webstart
3964 <li>Two or more chains in a single PDB file associated
3965 with sequences in different alignments do not get coloured
3966 by their associated sequence</li>
3967 <li>Visibility status of autocalculated annotation row
3968 not preserved when project is loaded</li>
3969 <li>Annotation row height and visibility attributes not
3970 stored in Jalview project</li>
3971 <li>Tree bootstraps are not preserved when saved as a
3972 Jalview project</li>
3973 <li>Envision2 workflow tooltips are corrupted</li>
3974 <li>Enabling show group conservation also enables colour
3975 by conservation</li>
3976 <li>Duplicate group associated conservation or consensus
3977 created on new view</li>
3978 <li>Annotation scrollbar not displayed after 'show
3979 all hidden annotation rows' option selected</li>
3980 <li>Alignment quality not updated after alignment
3981 annotation row is hidden then shown</li>
3982 <li>Preserve colouring of structures coloured by
3983 sequences in pre Jalview 2.7 projects</li>
3984 <li>Web service job parameter dialog is not laid out
3986 <li>Web services menu not refreshed after 'reset
3987 services' button is pressed in preferences</li>
3988 <li>Annotation off by one in Jalview v2_3 example project</li>
3989 <li>Structures imported from file and saved in project
3990 get name like jalview_pdb1234.txt when reloaded</li>
3991 <li>Jalview does not always retrieve progress of a JABAWS
3992 job execution in full once it is complete</li>
3993 </ul> <em>Applet</em>
3995 <li>Alignment height set incorrectly when lots of
3996 annotation rows are displayed</li>
3997 <li>Relative URLs in feature HTML text not resolved to
3999 <li>View follows highlighting does not work for positions
4001 <li><= shown as = in tooltip</li>
4002 <li>Export features raises exception when no features
4004 <li>Separator string used for serialising lists of IDs
4005 for javascript api is modified when separator string
4006 provided as parameter</li>
4007 <li>Null pointer exception when selecting tree leaves for
4008 alignment with no existing selection</li>
4009 <li>Relative URLs for datasources assumed to be relative
4010 to applet's codebase</li>
4011 <li>Status bar not updated after finished searching and
4012 search wraps around to first result</li>
4013 <li>StructureSelectionManager instance shared between
4014 several Jalview applets causes race conditions and memory
4016 <li>Hover tooltip and mouseover of position on structure
4017 not sent from Jmol in applet</li>
4018 <li>Certain sequences of javascript method calls to
4019 applet API fatally hang browser</li>
4020 </ul> <em>General</em>
4022 <li>View follows structure mouseover scrolls beyond
4023 position with wrapped view and hidden regions</li>
4024 <li>Find sequence position moves to wrong residue
4025 with/without hidden columns</li>
4026 <li>Sequence length given in alignment properties window
4028 <li>InvalidNumberFormat exceptions thrown when trying to
4029 import PDB like structure files</li>
4030 <li>Positional search results are only highlighted
4031 between user-supplied sequence start/end bounds</li>
4032 <li>End attribute of sequence is not validated</li>
4033 <li>Find dialog only finds first sequence containing a
4034 given sequence position</li>
4035 <li>Sequence numbering not preserved in MSF alignment
4037 <li>Jalview PDB file reader does not extract sequence
4038 from nucleotide chains correctly</li>
4039 <li>Structure colours not updated when tree partition
4040 changed in alignment</li>
4041 <li>Sequence associated secondary structure not correctly
4042 parsed in interleaved stockholm</li>
4043 <li>Colour by annotation dialog does not restore current
4045 <li>Hiding (nearly) all sequences doesn't work
4047 <li>Sequences containing lowercase letters are not
4048 properly associated with their pdb files</li>
4049 </ul> <em>Documentation and Development</em>
4051 <li>schemas/JalviewWsParamSet.xsd corrupted by
4052 ApplyCopyright tool</li>
4057 <div align="center">
4058 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4061 <td><em>Application</em>
4063 <li>New warning dialog when the Jalview Desktop cannot
4064 contact web services</li>
4065 <li>JABA service parameters for a preset are shown in
4066 service job window</li>
4067 <li>JABA Service menu entries reworded</li>
4071 <li>Modeller PIR IO broken - cannot correctly import a
4072 pir file emitted by Jalview</li>
4073 <li>Existing feature settings transferred to new
4074 alignment view created from cut'n'paste</li>
4075 <li>Improved test for mixed amino/nucleotide chains when
4076 parsing PDB files</li>
4077 <li>Consensus and conservation annotation rows
4078 occasionally become blank for all new windows</li>
4079 <li>Exception raised when right clicking above sequences
4080 in wrapped view mode</li>
4081 </ul> <em>Application</em>
4083 <li>multiple multiply aligned structure views cause cpu
4084 usage to hit 100% and computer to hang</li>
4085 <li>Web Service parameter layout breaks for long user
4086 parameter names</li>
4087 <li>Jaba service discovery hangs desktop if Jaba server
4094 <div align="center">
4095 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4098 <td><em>Application</em>
4100 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4101 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4104 <li>Web Services preference tab</li>
4105 <li>Analysis parameters dialog box and user defined
4107 <li>Improved speed and layout of Envision2 service menu</li>
4108 <li>Superpose structures using associated sequence
4110 <li>Export coordinates and projection as CSV from PCA
4112 </ul> <em>Applet</em>
4114 <li>enable javascript: execution by the applet via the
4115 link out mechanism</li>
4116 </ul> <em>Other</em>
4118 <li>Updated the Jmol Jalview interface to work with Jmol
4120 <li>The Jalview Desktop and JalviewLite applet now
4121 require Java 1.5</li>
4122 <li>Allow Jalview feature colour specification for GFF
4123 sequence annotation files</li>
4124 <li>New 'colour by label' keword in Jalview feature file
4125 type colour specification</li>
4126 <li>New Jalview Desktop Groovy API method that allows a
4127 script to check if it being run in an interactive session or
4128 in a batch operation from the Jalview command line</li>
4132 <li>clustalx colourscheme colours Ds preferentially when
4133 both D+E are present in over 50% of the column</li>
4134 </ul> <em>Application</em>
4136 <li>typo in AlignmentFrame->View->Hide->all but
4137 selected Regions menu item</li>
4138 <li>sequence fetcher replaces ',' for ';' when the ',' is
4139 part of a valid accession ID</li>
4140 <li>fatal OOM if object retrieved by sequence fetcher
4141 runs out of memory</li>
4142 <li>unhandled Out of Memory Error when viewing pca
4143 analysis results</li>
4144 <li>InstallAnywhere builds fail to launch on OS X java
4145 10.5 update 4 (due to apple Java 1.6 update)</li>
4146 <li>Installanywhere Jalview silently fails to launch</li>
4147 </ul> <em>Applet</em>
4149 <li>Jalview.getFeatureGroups() raises an
4150 ArrayIndexOutOfBoundsException if no feature groups are
4157 <div align="center">
4158 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4164 <li>Alignment prettyprinter doesn't cope with long
4166 <li>clustalx colourscheme colours Ds preferentially when
4167 both D+E are present in over 50% of the column</li>
4168 <li>nucleic acid structures retrieved from PDB do not
4169 import correctly</li>
4170 <li>More columns get selected than were clicked on when a
4171 number of columns are hidden</li>
4172 <li>annotation label popup menu not providing correct
4173 add/hide/show options when rows are hidden or none are
4175 <li>Stockholm format shown in list of readable formats,
4176 and parser copes better with alignments from RFAM.</li>
4177 <li>CSV output of consensus only includes the percentage
4178 of all symbols if sequence logo display is enabled</li>
4180 </ul> <em>Applet</em>
4182 <li>annotation panel disappears when annotation is
4184 </ul> <em>Application</em>
4186 <li>Alignment view not redrawn properly when new
4187 alignment opened where annotation panel is visible but no
4188 annotations are present on alignment</li>
4189 <li>pasted region containing hidden columns is
4190 incorrectly displayed in new alignment window</li>
4191 <li>Jalview slow to complete operations when stdout is
4192 flooded (fix is to close the Jalview console)</li>
4193 <li>typo in AlignmentFrame->View->Hide->all but
4194 selected Rregions menu item.</li>
4195 <li>inconsistent group submenu and Format submenu entry
4196 'Un' or 'Non'conserved</li>
4197 <li>Sequence feature settings are being shared by
4198 multiple distinct alignments</li>
4199 <li>group annotation not recreated when tree partition is
4201 <li>double click on group annotation to select sequences
4202 does not propagate to associated trees</li>
4203 <li>Mac OSX specific issues:
4205 <li>exception raised when mouse clicked on desktop
4206 window background</li>
4207 <li>Desktop menu placed on menu bar and application
4208 name set correctly</li>
4209 <li>sequence feature settings not wide enough for the
4210 save feature colourscheme button</li>
4219 <div align="center">
4220 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4223 <td><em>New Capabilities</em>
4225 <li>URL links generated from description line for
4226 regular-expression based URL links (applet and application)
4228 <li>Non-positional feature URL links are shown in link
4230 <li>Linked viewing of nucleic acid sequences and
4232 <li>Automatic Scrolling option in View menu to display
4233 the currently highlighted region of an alignment.</li>
4234 <li>Order an alignment by sequence length, or using the
4235 average score or total feature count for each sequence.</li>
4236 <li>Shading features by score or associated description</li>
4237 <li>Subdivide alignment and groups based on identity of
4238 selected subsequence (Make Groups from Selection).</li>
4239 <li>New hide/show options including Shift+Control+H to
4240 hide everything but the currently selected region.</li>
4241 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4242 </ul> <em>Application</em>
4244 <li>Fetch DB References capabilities and UI expanded to
4245 support retrieval from DAS sequence sources</li>
4246 <li>Local DAS Sequence sources can be added via the
4247 command line or via the Add local source dialog box.</li>
4248 <li>DAS Dbref and DbxRef feature types are parsed as
4249 database references and protein_name is parsed as
4250 description line (BioSapiens terms).</li>
4251 <li>Enable or disable non-positional feature and database
4252 references in sequence ID tooltip from View menu in
4254 <!-- <li>New hidden columns and rows and representatives capabilities
4255 in annotations file (in progress - not yet fully implemented)</li> -->
4256 <li>Group-associated consensus, sequence logos and
4257 conservation plots</li>
4258 <li>Symbol distributions for each column can be exported
4259 and visualized as sequence logos</li>
4260 <li>Optionally scale multi-character column labels to fit
4261 within each column of annotation row<!-- todo for applet -->
4263 <li>Optional automatic sort of associated alignment view
4264 when a new tree is opened.</li>
4265 <li>Jalview Java Console</li>
4266 <li>Better placement of desktop window when moving
4267 between different screens.</li>
4268 <li>New preference items for sequence ID tooltip and
4269 consensus annotation</li>
4270 <li>Client to submit sequences and IDs to Envision2
4272 <li><em>Vamsas Capabilities</em>
4274 <li>Improved VAMSAS synchronization (Jalview archive
4275 used to preserve views, structures, and tree display
4277 <li>Import of vamsas documents from disk or URL via
4279 <li>Sharing of selected regions between views and
4280 with other VAMSAS applications (Experimental feature!)</li>
4281 <li>Updated API to VAMSAS version 0.2</li>
4283 </ul> <em>Applet</em>
4285 <li>Middle button resizes annotation row height</li>
4288 <li>sortByTree (true/false) - automatically sort the
4289 associated alignment view by the tree when a new tree is
4291 <li>showTreeBootstraps (true/false) - show or hide
4292 branch bootstraps (default is to show them if available)</li>
4293 <li>showTreeDistances (true/false) - show or hide
4294 branch lengths (default is to show them if available)</li>
4295 <li>showUnlinkedTreeNodes (true/false) - indicate if
4296 unassociated nodes should be highlighted in the tree
4298 <li>heightScale and widthScale (1.0 or more) -
4299 increase the height or width of a cell in the alignment
4300 grid relative to the current font size.</li>
4303 <li>Non-positional features displayed in sequence ID
4305 </ul> <em>Other</em>
4307 <li>Features format: graduated colour definitions and
4308 specification of feature scores</li>
4309 <li>Alignment Annotations format: new keywords for group
4310 associated annotation (GROUP_REF) and annotation row display
4311 properties (ROW_PROPERTIES)</li>
4312 <li>XML formats extended to support graduated feature
4313 colourschemes, group associated annotation, and profile
4314 visualization settings.</li></td>
4317 <li>Source field in GFF files parsed as feature source
4318 rather than description</li>
4319 <li>Non-positional features are now included in sequence
4320 feature and gff files (controlled via non-positional feature
4321 visibility in tooltip).</li>
4322 <li>URL links generated for all feature links (bugfix)</li>
4323 <li>Added URL embedding instructions to features file
4325 <li>Codons containing ambiguous nucleotides translated as
4326 'X' in peptide product</li>
4327 <li>Match case switch in find dialog box works for both
4328 sequence ID and sequence string and query strings do not
4329 have to be in upper case to match case-insensitively.</li>
4330 <li>AMSA files only contain first column of
4331 multi-character column annotation labels</li>
4332 <li>Jalview Annotation File generation/parsing consistent
4333 with documentation (e.g. Stockholm annotation can be
4334 exported and re-imported)</li>
4335 <li>PDB files without embedded PDB IDs given a friendly
4337 <li>Find incrementally searches ID string matches as well
4338 as subsequence matches, and correctly reports total number
4342 <li>Better handling of exceptions during sequence
4344 <li>Dasobert generated non-positional feature URL
4345 link text excludes the start_end suffix</li>
4346 <li>DAS feature and source retrieval buttons disabled
4347 when fetch or registry operations in progress.</li>
4348 <li>PDB files retrieved from URLs are cached properly</li>
4349 <li>Sequence description lines properly shared via
4351 <li>Sequence fetcher fetches multiple records for all
4353 <li>Ensured that command line das feature retrieval
4354 completes before alignment figures are generated.</li>
4355 <li>Reduced time taken when opening file browser for
4357 <li>isAligned check prior to calculating tree, PCA or
4358 submitting an MSA to JNet now excludes hidden sequences.</li>
4359 <li>User defined group colours properly recovered
4360 from Jalview projects.</li>
4369 <div align="center">
4370 <strong>2.4.0.b2</strong><br> 28/10/2009
4375 <li>Experimental support for google analytics usage
4377 <li>Jalview privacy settings (user preferences and docs).</li>
4382 <li>Race condition in applet preventing startup in
4384 <li>Exception when feature created from selection beyond
4385 length of sequence.</li>
4386 <li>Allow synthetic PDB files to be imported gracefully</li>
4387 <li>Sequence associated annotation rows associate with
4388 all sequences with a given id</li>
4389 <li>Find function matches case-insensitively for sequence
4390 ID string searches</li>
4391 <li>Non-standard characters do not cause pairwise
4392 alignment to fail with exception</li>
4393 </ul> <em>Application Issues</em>
4395 <li>Sequences are now validated against EMBL database</li>
4396 <li>Sequence fetcher fetches multiple records for all
4398 </ul> <em>InstallAnywhere Issues</em>
4400 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4401 issue with installAnywhere mechanism)</li>
4402 <li>Command line launching of JARs from InstallAnywhere
4403 version (java class versioning error fixed)</li>
4410 <div align="center">
4411 <strong>2.4</strong><br> 27/8/2008
4414 <td><em>User Interface</em>
4416 <li>Linked highlighting of codon and amino acid from
4417 translation and protein products</li>
4418 <li>Linked highlighting of structure associated with
4419 residue mapping to codon position</li>
4420 <li>Sequence Fetcher provides example accession numbers
4421 and 'clear' button</li>
4422 <li>MemoryMonitor added as an option under Desktop's
4424 <li>Extract score function to parse whitespace separated
4425 numeric data in description line</li>
4426 <li>Column labels in alignment annotation can be centred.</li>
4427 <li>Tooltip for sequence associated annotation give name
4429 </ul> <em>Web Services and URL fetching</em>
4431 <li>JPred3 web service</li>
4432 <li>Prototype sequence search client (no public services
4434 <li>Fetch either seed alignment or full alignment from
4436 <li>URL Links created for matching database cross
4437 references as well as sequence ID</li>
4438 <li>URL Links can be created using regular-expressions</li>
4439 </ul> <em>Sequence Database Connectivity</em>
4441 <li>Retrieval of cross-referenced sequences from other
4443 <li>Generalised database reference retrieval and
4444 validation to all fetchable databases</li>
4445 <li>Fetch sequences from DAS sources supporting the
4446 sequence command</li>
4447 </ul> <em>Import and Export</em>
4448 <li>export annotation rows as CSV for spreadsheet import</li>
4449 <li>Jalview projects record alignment dataset associations,
4450 EMBL products, and cDNA sequence mappings</li>
4451 <li>Sequence Group colour can be specified in Annotation
4453 <li>Ad-hoc colouring of group in Annotation File using RGB
4454 triplet as name of colourscheme</li>
4455 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4457 <li>treenode binding for VAMSAS tree exchange</li>
4458 <li>local editing and update of sequences in VAMSAS
4459 alignments (experimental)</li>
4460 <li>Create new or select existing session to join</li>
4461 <li>load and save of vamsas documents</li>
4462 </ul> <em>Application command line</em>
4464 <li>-tree parameter to open trees (introduced for passing
4466 <li>-fetchfrom command line argument to specify nicknames
4467 of DAS servers to query for alignment features</li>
4468 <li>-dasserver command line argument to add new servers
4469 that are also automatically queried for features</li>
4470 <li>-groovy command line argument executes a given groovy
4471 script after all input data has been loaded and parsed</li>
4472 </ul> <em>Applet-Application data exchange</em>
4474 <li>Trees passed as applet parameters can be passed to
4475 application (when using "View in full
4476 application")</li>
4477 </ul> <em>Applet Parameters</em>
4479 <li>feature group display control parameter</li>
4480 <li>debug parameter</li>
4481 <li>showbutton parameter</li>
4482 </ul> <em>Applet API methods</em>
4484 <li>newView public method</li>
4485 <li>Window (current view) specific get/set public methods</li>
4486 <li>Feature display control methods</li>
4487 <li>get list of currently selected sequences</li>
4488 </ul> <em>New Jalview distribution features</em>
4490 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4491 <li>RELEASE file gives build properties for the latest
4492 Jalview release.</li>
4493 <li>Java 1.1 Applet build made easier and donotobfuscate
4494 property controls execution of obfuscator</li>
4495 <li>Build target for generating source distribution</li>
4496 <li>Debug flag for javacc</li>
4497 <li>.jalview_properties file is documented (slightly) in
4498 jalview.bin.Cache</li>
4499 <li>Continuous Build Integration for stable and
4500 development version of Application, Applet and source
4505 <li>selected region output includes visible annotations
4506 (for certain formats)</li>
4507 <li>edit label/displaychar contains existing label/char
4509 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4510 <li>shorter peptide product names from EMBL records</li>
4511 <li>Newick string generator makes compact representations</li>
4512 <li>bootstrap values parsed correctly for tree files with
4514 <li>pathological filechooser bug avoided by not allowing
4515 filenames containing a ':'</li>
4516 <li>Fixed exception when parsing GFF files containing
4517 global sequence features</li>
4518 <li>Alignment datasets are finalized only when number of
4519 references from alignment sequences goes to zero</li>
4520 <li>Close of tree branch colour box without colour
4521 selection causes cascading exceptions</li>
4522 <li>occasional negative imgwidth exceptions</li>
4523 <li>better reporting of non-fatal warnings to user when
4524 file parsing fails.</li>
4525 <li>Save works when Jalview project is default format</li>
4526 <li>Save as dialog opened if current alignment format is
4527 not a valid output format</li>
4528 <li>UniProt canonical names introduced for both das and
4530 <li>Histidine should be midblue (not pink!) in Zappo</li>
4531 <li>error messages passed up and output when data read
4533 <li>edit undo recovers previous dataset sequence when
4534 sequence is edited</li>
4535 <li>allow PDB files without pdb ID HEADER lines (like
4536 those generated by MODELLER) to be read in properly</li>
4537 <li>allow reading of JPred concise files as a normal
4539 <li>Stockholm annotation parsing and alignment properties
4540 import fixed for PFAM records</li>
4541 <li>Structure view windows have correct name in Desktop
4543 <li>annotation consisting of sequence associated scores
4544 can be read and written correctly to annotation file</li>
4545 <li>Aligned cDNA translation to aligned peptide works
4547 <li>Fixed display of hidden sequence markers and
4548 non-italic font for representatives in Applet</li>
4549 <li>Applet Menus are always embedded in applet window on
4551 <li>Newly shown features appear at top of stack (in
4553 <li>Annotations added via parameter not drawn properly
4554 due to null pointer exceptions</li>
4555 <li>Secondary structure lines are drawn starting from
4556 first column of alignment</li>
4557 <li>UniProt XML import updated for new schema release in
4559 <li>Sequence feature to sequence ID match for Features
4560 file is case-insensitive</li>
4561 <li>Sequence features read from Features file appended to
4562 all sequences with matching IDs</li>
4563 <li>PDB structure coloured correctly for associated views
4564 containing a sub-sequence</li>
4565 <li>PDB files can be retrieved by applet from Jar files</li>
4566 <li>feature and annotation file applet parameters
4567 referring to different directories are retrieved correctly</li>
4568 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4569 <li>Fixed application hang whilst waiting for
4570 splash-screen version check to complete</li>
4571 <li>Applet properly URLencodes input parameter values
4572 when passing them to the launchApp service</li>
4573 <li>display name and local features preserved in results
4574 retrieved from web service</li>
4575 <li>Visual delay indication for sequence retrieval and
4576 sequence fetcher initialisation</li>
4577 <li>updated Application to use DAS 1.53e version of
4578 dasobert DAS client</li>
4579 <li>Re-instated Full AMSA support and .amsa file
4581 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4589 <div align="center">
4590 <strong>2.3</strong><br> 9/5/07
4595 <li>Jmol 11.0.2 integration</li>
4596 <li>PDB views stored in Jalview XML files</li>
4597 <li>Slide sequences</li>
4598 <li>Edit sequence in place</li>
4599 <li>EMBL CDS features</li>
4600 <li>DAS Feature mapping</li>
4601 <li>Feature ordering</li>
4602 <li>Alignment Properties</li>
4603 <li>Annotation Scores</li>
4604 <li>Sort by scores</li>
4605 <li>Feature/annotation editing in applet</li>
4610 <li>Headless state operation in 2.2.1</li>
4611 <li>Incorrect and unstable DNA pairwise alignment</li>
4612 <li>Cut and paste of sequences with annotation</li>
4613 <li>Feature group display state in XML</li>
4614 <li>Feature ordering in XML</li>
4615 <li>blc file iteration selection using filename # suffix</li>
4616 <li>Stockholm alignment properties</li>
4617 <li>Stockhom alignment secondary structure annotation</li>
4618 <li>2.2.1 applet had no feature transparency</li>
4619 <li>Number pad keys can be used in cursor mode</li>
4620 <li>Structure Viewer mirror image resolved</li>
4627 <div align="center">
4628 <strong>2.2.1</strong><br> 12/2/07
4633 <li>Non standard characters can be read and displayed
4634 <li>Annotations/Features can be imported/exported to the
4636 <li>Applet allows editing of sequence/annotation/group
4637 name & description
4638 <li>Preference setting to display sequence name in
4640 <li>Annotation file format extended to allow
4641 Sequence_groups to be defined
4642 <li>Default opening of alignment overview panel can be
4643 specified in preferences
4644 <li>PDB residue numbering annotation added to associated
4650 <li>Applet crash under certain Linux OS with Java 1.6
4652 <li>Annotation file export / import bugs fixed
4653 <li>PNG / EPS image output bugs fixed
4659 <div align="center">
4660 <strong>2.2</strong><br> 27/11/06
4665 <li>Multiple views on alignment
4666 <li>Sequence feature editing
4667 <li>"Reload" alignment
4668 <li>"Save" to current filename
4669 <li>Background dependent text colour
4670 <li>Right align sequence ids
4671 <li>User-defined lower case residue colours
4674 <li>Menu item accelerator keys
4675 <li>Control-V pastes to current alignment
4676 <li>Cancel button for DAS Feature Fetching
4677 <li>PCA and PDB Viewers zoom via mouse roller
4678 <li>User-defined sub-tree colours and sub-tree selection
4680 <li>'New Window' button on the 'Output to Text box'
4685 <li>New memory efficient Undo/Redo System
4686 <li>Optimised symbol lookups and conservation/consensus
4688 <li>Region Conservation/Consensus recalculated after
4690 <li>Fixed Remove Empty Columns Bug (empty columns at end
4692 <li>Slowed DAS Feature Fetching for increased robustness.
4694 <li>Made angle brackets in ASCII feature descriptions
4696 <li>Re-instated Zoom function for PCA
4697 <li>Sequence descriptions conserved in web service
4699 <li>UniProt ID discoverer uses any word separated by
4701 <li>WsDbFetch query/result association resolved
4702 <li>Tree leaf to sequence mapping improved
4703 <li>Smooth fonts switch moved to FontChooser dialog box.
4710 <div align="center">
4711 <strong>2.1.1</strong><br> 12/9/06
4716 <li>Copy consensus sequence to clipboard</li>
4721 <li>Image output - rightmost residues are rendered if
4722 sequence id panel has been resized</li>
4723 <li>Image output - all offscreen group boundaries are
4725 <li>Annotation files with sequence references - all
4726 elements in file are relative to sequence position</li>
4727 <li>Mac Applet users can use Alt key for group editing</li>
4733 <div align="center">
4734 <strong>2.1</strong><br> 22/8/06
4739 <li>MAFFT Multiple Alignment in default Web Service list</li>
4740 <li>DAS Feature fetching</li>
4741 <li>Hide sequences and columns</li>
4742 <li>Export Annotations and Features</li>
4743 <li>GFF file reading / writing</li>
4744 <li>Associate structures with sequences from local PDB
4746 <li>Add sequences to exisiting alignment</li>
4747 <li>Recently opened files / URL lists</li>
4748 <li>Applet can launch the full application</li>
4749 <li>Applet has transparency for features (Java 1.2
4751 <li>Applet has user defined colours parameter</li>
4752 <li>Applet can load sequences from parameter
4753 "sequence<em>x</em>"
4759 <li>Redundancy Panel reinstalled in the Applet</li>
4760 <li>Monospaced font - EPS / rescaling bug fixed</li>
4761 <li>Annotation files with sequence references bug fixed</li>
4767 <div align="center">
4768 <strong>2.08.1</strong><br> 2/5/06
4773 <li>Change case of selected region from Popup menu</li>
4774 <li>Choose to match case when searching</li>
4775 <li>Middle mouse button and mouse movement can compress /
4776 expand the visible width and height of the alignment</li>
4781 <li>Annotation Panel displays complete JNet results</li>
4787 <div align="center">
4788 <strong>2.08b</strong><br> 18/4/06
4794 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4795 <li>Righthand label on wrapped alignments shows correct
4802 <div align="center">
4803 <strong>2.08</strong><br> 10/4/06
4808 <li>Editing can be locked to the selection area</li>
4809 <li>Keyboard editing</li>
4810 <li>Create sequence features from searches</li>
4811 <li>Precalculated annotations can be loaded onto
4813 <li>Features file allows grouping of features</li>
4814 <li>Annotation Colouring scheme added</li>
4815 <li>Smooth fonts off by default - Faster rendering</li>
4816 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4821 <li>Drag & Drop fixed on Linux</li>
4822 <li>Jalview Archive file faster to load/save, sequence
4823 descriptions saved.</li>
4829 <div align="center">
4830 <strong>2.07</strong><br> 12/12/05
4835 <li>PDB Structure Viewer enhanced</li>
4836 <li>Sequence Feature retrieval and display enhanced</li>
4837 <li>Choose to output sequence start-end after sequence
4838 name for file output</li>
4839 <li>Sequence Fetcher WSDBFetch@EBI</li>
4840 <li>Applet can read feature files, PDB files and can be
4841 used for HTML form input</li>
4846 <li>HTML output writes groups and features</li>
4847 <li>Group editing is Control and mouse click</li>
4848 <li>File IO bugs</li>
4854 <div align="center">
4855 <strong>2.06</strong><br> 28/9/05
4860 <li>View annotations in wrapped mode</li>
4861 <li>More options for PCA viewer</li>
4866 <li>GUI bugs resolved</li>
4867 <li>Runs with -nodisplay from command line</li>
4873 <div align="center">
4874 <strong>2.05b</strong><br> 15/9/05
4879 <li>Choose EPS export as lineart or text</li>
4880 <li>Jar files are executable</li>
4881 <li>Can read in Uracil - maps to unknown residue</li>
4886 <li>Known OutOfMemory errors give warning message</li>
4887 <li>Overview window calculated more efficiently</li>
4888 <li>Several GUI bugs resolved</li>
4894 <div align="center">
4895 <strong>2.05</strong><br> 30/8/05
4900 <li>Edit and annotate in "Wrapped" view</li>
4905 <li>Several GUI bugs resolved</li>
4911 <div align="center">
4912 <strong>2.04</strong><br> 24/8/05
4917 <li>Hold down mouse wheel & scroll to change font
4923 <li>Improved JPred client reliability</li>
4924 <li>Improved loading of Jalview files</li>
4930 <div align="center">
4931 <strong>2.03</strong><br> 18/8/05
4936 <li>Set Proxy server name and port in preferences</li>
4937 <li>Multiple URL links from sequence ids</li>
4938 <li>User Defined Colours can have a scheme name and added
4940 <li>Choose to ignore gaps in consensus calculation</li>
4941 <li>Unix users can set default web browser</li>
4942 <li>Runs without GUI for batch processing</li>
4943 <li>Dynamically generated Web Service Menus</li>
4948 <li>InstallAnywhere download for Sparc Solaris</li>
4954 <div align="center">
4955 <strong>2.02</strong><br> 18/7/05
4961 <li>Copy & Paste order of sequences maintains
4962 alignment order.</li>
4968 <div align="center">
4969 <strong>2.01</strong><br> 12/7/05
4974 <li>Use delete key for deleting selection.</li>
4975 <li>Use Mouse wheel to scroll sequences.</li>
4976 <li>Help file updated to describe how to add alignment
4978 <li>Version and build date written to build properties
4980 <li>InstallAnywhere installation will check for updates
4981 at launch of Jalview.</li>
4986 <li>Delete gaps bug fixed.</li>
4987 <li>FileChooser sorts columns.</li>
4988 <li>Can remove groups one by one.</li>
4989 <li>Filechooser icons installed.</li>
4990 <li>Finder ignores return character when searching.
4991 Return key will initiate a search.<br>
4998 <div align="center">
4999 <strong>2.0</strong><br> 20/6/05
5004 <li>New codebase</li>