3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>11/08/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
71 HTSJDK from 2.12 to 2.23
74 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
75 optimisations and improvements suggested by Bob Hanson and
76 improved compatibility with JalviewJS
79 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
80 alignments from Pfam and Rfam
83 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
84 import (no longer based on .gz extension)
87 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
90 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
91 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
95 <!-- JAL-3667 -->Improved warning messages, debug logging
96 and fixed Retry action when Jalview encounters errors when
97 saving or making backup files.
100 <!-- JAL-3676 -->Enhanced Jalview Java Console:
102 <li>Jalview's logging level can be configured</li>
103 <li>Copy to Clipboard Buttion</li>
107 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
108 when running on Linux (Requires Java 11+)
110 </ul> <em>Launching Jalview</em>
113 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
114 through a system property
117 <!-- JAL-3477 -->Improved built-in documentation and command
118 line help for configuring Jalview's memory
122 <td align="left" valign="top">
125 <!-- JAL-3691 -->Conservation and Quality tracks are shown
126 but not calculated and no protein or DNA score models are
127 available for tree/PCA calculation when launched with
128 Turkish language locale
131 <!-- JAL-3493 -->Escape does not clear highlights on the
132 alignment (Since Jalview 2.10.3)
135 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
136 doesn't slide selected sequences, just sequence under cursor
139 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
140 multiple EMBL gene products shown forĀ a single contig
143 <!-- JAL-3696 -->Errors encountered when processing variants
144 from VCF files yield "Error processing VCF: Format specifier
148 <!-- JAL-3697 -->Count of features not shown can be wrong
149 when there are both local and complementary features mapped
150 to the position under the cursor
153 <!-- JAL-3673 -->Sequence ID for reference sequence is
154 clipped when Right align Sequence IDs enabled
157 <!-- JAL-2983 -->Slider with negative range values not
158 rendered correctly in VAqua4 (Since 2.10.4)
161 <!-- JAL-3685 -->Single quotes not displayed correctly in
162 internationalised text for some messages and log output
165 <!-- JAL-3490 -->Find doesn't report matches that span
166 hidden gapped columns
169 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
170 panels, Alignment viewport and annotation renderer.
173 <!-- JAL-3561 -->Jalview ignores file format parameter
174 specifying output format when exporting an alignment via the
177 </ul> <em>Developing Jalview</em>
180 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
181 data, causing cloverReport gradle task to fail with an
184 </ul> <em>New Known defects</em>
187 <!-- JAL-3576 -->Co-located features exported and re-imported
188 are ordered differently when shown on alignment and in
189 tooltips. (Also affects v2.11.1.0)
192 <!-- JAL-3667 -->Windows 10: For a minority of users, if
193 backups are not enabled, Jalview sometimes fails to
194 overwrite an existing file and raises a warning dialog.
195 Workaround is to try to save the file again, and if that
196 fails, delete the original file and save in place.
199 <!-- JAL-3702 -->Drag and drop of alignment file onto
200 alignment window not working correctly when in a HiDPI
204 <!-- JAL-3701 -->Stale build data in jalview standalone jar
205 builds (only affects 2.11.1.1 branch)
211 <td width="60" align="center" nowrap><strong><a
212 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
213 <em>22/04/2020</em></strong></td>
214 <td align="left" valign="top">
217 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
218 'virtual' codon features shown on protein (or vice versa)
219 for display in alignments, on structure views (including
220 transfer to UCSF chimera), in feature reports and for
224 <!-- JAL-3121 -->Feature attributes from VCF files can be
225 exported and re-imported as GFF3 files
228 <!-- JAL-3376 -->Capture VCF "fixed column" values
229 POS, ID, QUAL, FILTER as Feature Attributes
232 <!-- JAL-3375 -->More robust VCF numeric data field
233 validation while parsing
236 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
240 <!-- JAL-3535 -->Feature Settings dialog title includes name
244 <!-- JAL-3538 -->Font anti-aliasing in alignment views
248 <!-- JAL-3468 -->Very long feature descriptions truncated in
252 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
253 with no feature types visible
256 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
258 </ul><em>Jalview Installer</em>
261 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
262 in console (may be null when Jalview launched as executable jar or via conda)
265 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
268 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
271 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
273 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
274 </ul> <em>Release processes</em>
277 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
280 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
282 </ul> <em>Build System</em>
285 <!-- JAL-3510 -->Clover updated to 4.4.1
288 <!-- JAL-3513 -->Test code included in Clover coverage
292 <em>Groovy Scripts</em>
295 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
296 to stdout containing the consensus sequence for each
297 alignment in a Jalview session
300 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
301 genomic sequence_variant annotation from CDS as
302 missense_variant or synonymous_variant on protein products.
306 <td align="left" valign="top">
309 <!-- JAL-3581 -->Hidden sequence markers still visible when
310 'Show hidden markers' option is not ticked
313 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
314 PNG output when 'Automatically set ID width' is set in
315 jalview preferences or properties file
318 <!-- JAL-3571 -->Feature Editor dialog can be opened when
319 'Show Sequence Features' option is not ticked
322 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
323 buttons in Feature Settings dialog are clicked when no
327 <!-- JAL-3412 -->ID margins for CDS and Protein views not
328 equal when split frame is first opened
331 <!-- JAL-3296 -->Sequence position numbers in status bar not
332 correct after editing a sequence's start position
335 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
336 with annotation and exceptions thrown when only a few
337 columns shown in wrapped mode
340 <!-- JAL-3386 -->Sequence IDs missing in headless export of
341 wrapped alignment figure with annotations
344 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
345 ID fails with ClassCastException
348 <!-- JAL-3389 -->Chimera session not restored from Jalview
352 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
353 feature settings dialog also selects columns
356 <!-- JAL-3473 -->SpinnerNumberModel causes
357 IllegalArgumentException in some circumstances
360 <!-- JAL-3534 -->Multiple feature settings dialogs can be
364 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
365 alignment window is closed
368 <!-- JAL-3406 -->Credits missing some authors in Jalview
369 help documentation for 2.11.0 release
372 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
373 includes Pfam ID as sequence's accession rather than its
376 </ul> <em>Java 11 Compatibility issues</em>
379 <!-- JAL-2987 -->OSX - Can't view some search results in
380 PDB/Uniprot search panel
382 </ul> <em>Installer</em>
385 <!-- JAL-3447 -->Jalview should not create file associations
386 for 3D structure files (.pdb, .mmcif. .cif)
388 </ul> <em>Repository and Source Release</em>
391 <!-- JAL-3474 -->removed obsolete .cvsignore files from
395 <!-- JAL-3541 -->Clover report generation running out of
398 </ul> <em>New Known Issues</em>
401 <!-- JAL-3523 -->OSX - Current working directory not
402 preserved when Jalview.app launched with parameters from
406 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
407 clipped in headless figure export when Right Align option
411 <!-- JAL-3542 -->Jalview Installation type always reports
412 'Source' in console output
415 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
416 bamboo server but run fine locally.
422 <td width="60" align="center" nowrap>
423 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
424 <em>04/07/2019</em></strong>
426 <td align="left" valign="top">
429 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
430 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
431 source project) rather than InstallAnywhere
434 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
435 settings, receive over the air updates and launch specific
436 versions via (<a href="https://github.com/threerings/getdown">Three
440 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
441 formats supported by Jalview (including .jvp project files)
444 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
445 arguments and switch between different getdown channels
448 <!-- JAL-3141 -->Backup files created when saving Jalview project
453 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
454 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
456 <!-- JAL-2620 -->Alternative genetic code tables for
457 'Translate as cDNA'</li>
459 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
460 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
463 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
464 implementation that allows updates) used for Sequence Feature collections</li>
466 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
467 features can be filtered and shaded according to any
468 associated attributes (e.g. variant attributes from VCF
469 file, or key-value pairs imported from column 9 of GFF
473 <!-- JAL-2879 -->Feature Attributes and shading schemes
474 stored and restored from Jalview Projects
477 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
478 recognise variant features
481 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
482 sequences (also coloured red by default)
485 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
489 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
490 algorithm (Z-sort/transparency and filter aware)
493 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
499 <!-- JAL-3205 -->Symmetric score matrices for faster
500 tree and PCA calculations
502 <li><strong>Principal Components Analysis Viewer</strong>
505 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
506 and Viewer state saved in Jalview Project
508 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
511 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
515 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
520 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
522 <li><strong>Speed and Efficiency</strong>
525 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
526 multiple groups when working with large alignments
529 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
533 <li><strong>User Interface</strong>
536 <!-- JAL-2933 -->Finder panel remembers last position in each
540 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
541 what is shown)<br />Only visible regions of alignment are shown by
542 default (can be changed in user preferences)
545 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
546 to the Overwrite Dialog
549 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
553 <!-- JAL-1244 -->Status bar shows bounds when dragging a
554 selection region, and gap count when inserting or deleting gaps
557 <!-- JAL-3132 -->Status bar updates over sequence and annotation
561 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
565 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
569 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
572 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
576 <!-- JAL-3181 -->Consistent ordering of links in sequence id
580 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
582 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
586 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
587 <li><strong>Java 11 Support (not yet on general release)</strong>
590 <!-- -->OSX GUI integrations for App menu's 'About' entry and
595 <em>Deprecations</em>
597 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
598 capabilities removed from the Jalview Desktop
600 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
601 unmarshalling has been replaced by JAXB for Jalview projects
602 and XML based data retrieval clients</li>
603 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
604 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
605 </ul> <em>Documentation</em>
607 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
608 not supported in EPS figure export
610 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
611 </ul> <em>Development and Release Processes</em>
614 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
617 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
619 <!-- JAL-3225 -->Eclipse project configuration managed with
623 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
624 Bamboo continuous integration for unattended Test Suite
628 <!-- JAL-2864 -->Memory test suite to detect leaks in common
632 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
636 <!-- JAL-3248 -->Developer documentation migrated to
637 markdown (with HTML rendering)
640 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
643 <!-- JAL-3289 -->New URLs for publishing development
648 <td align="left" valign="top">
651 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
654 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
655 superposition in Jmol fail on Windows
658 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
659 structures for sequences with lots of PDB structures
662 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
666 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
667 project involving multiple views
670 <!-- JAL-3164 -->Overview for complementary view in a linked
671 CDS/Protein alignment is not updated when Hide Columns by
672 Annotation dialog hides columns
675 <!-- JAL-3158 -->Selection highlighting in the complement of a
676 CDS/Protein alignment stops working after making a selection in
677 one view, then making another selection in the other view
680 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
684 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
685 Settings and Jalview Preferences panels
688 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
689 overview with large alignments
692 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
693 region if columns were selected by dragging right-to-left and the
694 mouse moved to the left of the first column
697 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
698 hidden column marker via scale popup menu
701 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
702 doesn't tell users the invalid URL
705 <!-- JAL-2816 -->Tooltips displayed for features filtered by
709 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
710 show cross references or Fetch Database References are shown in
714 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
715 peptide sequence (computed variant shown as p.Res.null)
718 <!-- JAL-2060 -->'Graduated colour' option not offered for
719 manually created features (where feature score is Float.NaN)
722 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
723 when columns are hidden
726 <!-- JAL-3082 -->Regular expression error for '(' in Select
727 Columns by Annotation description
730 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
731 out of Scale or Annotation Panel
734 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
738 <!-- JAL-3074 -->Left/right drag in annotation can scroll
742 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
746 <!-- JAL-3002 -->Column display is out by one after Page Down,
747 Page Up in wrapped mode
750 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
753 <!-- JAL-2932 -->Finder searches in minimised alignments
756 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
757 on opening an alignment
760 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
764 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
765 different groups in the alignment are selected
768 <!-- JAL-2717 -->Internationalised colour scheme names not shown
772 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
776 <!-- JAL-3125 -->Value input for graduated feature colour
777 threshold gets 'unrounded'
780 <!-- JAL-2982 -->PCA image export doesn't respect background
784 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
787 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
790 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
794 <!-- JAL-2964 -->Associate Tree with All Views not restored from
798 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
799 shown in complementary view
802 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
803 without normalisation
806 <!-- JAL-3021 -->Sequence Details report should open positioned at top
810 <!-- JAL-914 -->Help page can be opened twice
813 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
815 </ul> <em>Editing</em>
818 <!-- JAL-2822 -->Start and End should be updated when sequence
819 data at beginning or end of alignment added/removed via 'Edit'
823 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
824 relocate sequence features correctly when start of sequence is
825 removed (Known defect since 2.10)
828 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
829 dialog corrupts dataset sequence
832 <!-- JAL-868 -->Structure colours not updated when associated tree
833 repartitions the alignment view (Regression in 2.10.5)
835 </ul> <em>Datamodel</em>
838 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
839 sequence's End is greater than its length
841 </ul> <em>Bugs fixed for Java 11 Support (not yet on
842 general release)</em>
845 <!-- JAL-3288 -->Menus work properly in split-screen
847 </ul> <em>New Known Defects</em>
850 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
853 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
854 regions of protein alignment.
857 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
858 is restored from a Jalview 2.11 project
861 <!-- JAL-3213 -->Alignment panel height can be too small after
865 <!-- JAL-3240 -->Display is incorrect after removing gapped
866 columns within hidden columns
869 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
870 window after dragging left to select columns to left of visible
874 <!-- JAL-2876 -->Features coloured according to their description
875 string and thresholded by score in earlier versions of Jalview are
876 not shown as thresholded features in 2.11. To workaround please
877 create a Score filter instead.
880 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
882 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
885 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
886 alignments with multiple views can close views unexpectedly
889 <em>Java 11 Specific defects</em>
892 <!-- JAL-3235 -->Jalview Properties file is not sorted
893 alphabetically when saved
899 <td width="60" nowrap>
901 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
904 <td><div align="left">
908 <!-- JAL-3101 -->Default memory for Jalview webstart and
909 InstallAnywhere increased to 1G.
912 <!-- JAL-247 -->Hidden sequence markers and representative
913 sequence bolding included when exporting alignment as EPS,
914 SVG, PNG or HTML. <em>Display is configured via the
915 Format menu, or for command-line use via a Jalview
916 properties file.</em>
919 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
920 API and sequence data now imported as JSON.
923 <!-- JAL-3065 -->Change in recommended way of starting
924 Jalview via a Java command line: add jars in lib directory
925 to CLASSPATH, rather than via the deprecated java.ext.dirs
932 <!-- JAL-3047 -->Support added to execute test suite
933 instrumented with <a href="http://openclover.org/">Open
938 <td><div align="left">
942 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
943 row shown in Feredoxin Structure alignment view of example
947 <!-- JAL-2854 -->Annotation obscures sequences if lots of
948 annotation displayed.
951 <!-- JAL-3107 -->Group conservation/consensus not shown
952 for newly created group when 'Apply to all groups'
956 <!-- JAL-3087 -->Corrupted display when switching to
957 wrapped mode when sequence panel's vertical scrollbar is
961 <!-- JAL-3003 -->Alignment is black in exported EPS file
962 when sequences are selected in exported view.</em>
965 <!-- JAL-3059 -->Groups with different coloured borders
966 aren't rendered with correct colour.
969 <!-- JAL-3092 -->Jalview could hang when importing certain
970 types of knotted RNA secondary structure.
973 <!-- JAL-3095 -->Sequence highlight and selection in
974 trimmed VARNA 2D structure is incorrect for sequences that
978 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
979 annotation when columns are inserted into an alignment,
980 and when exporting as Stockholm flatfile.
983 <!-- JAL-3053 -->Jalview annotation rows containing upper
984 and lower-case 'E' and 'H' do not automatically get
985 treated as RNA secondary structure.
988 <!-- JAL-3106 -->.jvp should be used as default extension
989 (not .jar) when saving a Jalview project file.
992 <!-- JAL-3105 -->Mac Users: closing a window correctly
993 transfers focus to previous window on OSX
996 <em>Java 10 Issues Resolved</em>
999 <!-- JAL-2988 -->OSX - Can't save new files via the File
1000 or export menus by typing in a name into the Save dialog
1004 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1005 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1006 'look and feel' which has improved compatibility with the
1007 latest version of OSX.
1014 <td width="60" nowrap>
1015 <div align="center">
1016 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1017 <em>7/06/2018</em></strong>
1020 <td><div align="left">
1024 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1025 annotation retrieved from Uniprot
1028 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1029 onto the Jalview Desktop
1033 <td><div align="left">
1037 <!-- JAL-3017 -->Cannot import features with multiple
1038 variant elements (blocks import of some Uniprot records)
1041 <!-- JAL-2997 -->Clustal files with sequence positions in
1042 right-hand column parsed correctly
1045 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1046 not alignment area in exported graphic
1049 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1050 window has input focus
1053 <!-- JAL-2992 -->Annotation panel set too high when
1054 annotation added to view (Windows)
1057 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1058 network connectivity is poor
1061 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1062 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1063 the currently open URL and links from a page viewed in
1064 Firefox or Chrome on Windows is now fully supported. If
1065 you are using Edge, only links in the page can be
1066 dragged, and with Internet Explorer, only the currently
1067 open URL in the browser can be dropped onto Jalview.</em>
1070 <em>New Known Defects</em>
1072 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1077 <td width="60" nowrap>
1078 <div align="center">
1079 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1082 <td><div align="left">
1086 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1087 for disabling automatic superposition of multiple
1088 structures and open structures in existing views
1091 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1092 ID and annotation area margins can be click-dragged to
1096 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1100 <!-- JAL-2759 -->Improved performance for large alignments
1101 and lots of hidden columns
1104 <!-- JAL-2593 -->Improved performance when rendering lots
1105 of features (particularly when transparency is disabled)
1108 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1109 exchange of Jalview features and Chimera attributes made
1115 <td><div align="left">
1118 <!-- JAL-2899 -->Structure and Overview aren't updated
1119 when Colour By Annotation threshold slider is adjusted
1122 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1123 overlapping alignment panel
1126 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1130 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1131 improved: CDS not handled correctly if transcript has no
1135 <!-- JAL-2321 -->Secondary structure and temperature
1136 factor annotation not added to sequence when local PDB
1137 file associated with it by drag'n'drop or structure
1141 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1142 dialog doesn't import PDB files dropped on an alignment
1145 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1146 scroll bar doesn't work for some CDS/Protein views
1149 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1150 Java 1.8u153 onwards and Java 1.9u4+.
1153 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1154 columns in annotation row
1157 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1158 honored in batch mode
1161 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1162 for structures added to existing Jmol view
1165 <!-- JAL-2223 -->'View Mappings' includes duplicate
1166 entries after importing project with multiple views
1169 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1170 protein sequences via SIFTS from associated PDB entries
1171 with negative residue numbers or missing residues fails
1174 <!-- JAL-2952 -->Exception when shading sequence with negative
1175 Temperature Factor values from annotated PDB files (e.g.
1176 as generated by CONSURF)
1179 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1180 tooltip doesn't include a text description of mutation
1183 <!-- JAL-2922 -->Invert displayed features very slow when
1184 structure and/or overview windows are also shown
1187 <!-- JAL-2954 -->Selecting columns from highlighted regions
1188 very slow for alignments with large numbers of sequences
1191 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1192 with 'StringIndexOutOfBounds'
1195 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1196 platforms running Java 10
1199 <!-- JAL-2960 -->Adding a structure to existing structure
1200 view appears to do nothing because the view is hidden behind the alignment view
1206 <!-- JAL-2926 -->Copy consensus sequence option in applet
1207 should copy the group consensus when popup is opened on it
1213 <!-- JAL-2913 -->Fixed ID width preference is not respected
1216 <em>New Known Defects</em>
1219 <!-- JAL-2973 --> Exceptions occasionally raised when
1220 editing a large alignment and overview is displayed
1223 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1224 repeatedly after a series of edits even when the overview
1225 is no longer reflecting updates
1228 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1229 structures for protein subsequence (if 'Trim Retrieved
1230 Sequences' enabled) or Ensembl isoforms (Workaround in
1231 2.10.4 is to fail back to N&W mapping)
1234 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1235 option gives blank output
1242 <td width="60" nowrap>
1243 <div align="center">
1244 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1247 <td><div align="left">
1248 <ul><li>Updated Certum Codesigning Certificate
1249 (Valid till 30th November 2018)</li></ul></div></td>
1250 <td><div align="left">
1251 <em>Desktop</em><ul>
1253 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1254 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1255 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1256 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1257 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1258 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1259 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1265 <td width="60" nowrap>
1266 <div align="center">
1267 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1270 <td><div align="left">
1274 <!-- JAL-2446 -->Faster and more efficient management and
1275 rendering of sequence features
1278 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1279 429 rate limit request hander
1282 <!-- JAL-2773 -->Structure views don't get updated unless
1283 their colours have changed
1286 <!-- JAL-2495 -->All linked sequences are highlighted for
1287 a structure mousover (Jmol) or selection (Chimera)
1290 <!-- JAL-2790 -->'Cancel' button in progress bar for
1291 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1294 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1295 view from Ensembl locus cross-references
1298 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1302 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1303 feature can be disabled
1306 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1307 PDB easier retrieval of sequences for lists of IDs
1310 <!-- JAL-2758 -->Short names for sequences retrieved from
1316 <li>Groovy interpreter updated to 2.4.12</li>
1317 <li>Example groovy script for generating a matrix of
1318 percent identity scores for current alignment.</li>
1320 <em>Testing and Deployment</em>
1323 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1327 <td><div align="left">
1331 <!-- JAL-2643 -->Pressing tab after updating the colour
1332 threshold text field doesn't trigger an update to the
1336 <!-- JAL-2682 -->Race condition when parsing sequence ID
1340 <!-- JAL-2608 -->Overview windows are also closed when
1341 alignment window is closed
1344 <!-- JAL-2548 -->Export of features doesn't always respect
1348 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1349 takes a long time in Cursor mode
1355 <!-- JAL-2777 -->Structures with whitespace chainCode
1356 cannot be viewed in Chimera
1359 <!-- JAL-2728 -->Protein annotation panel too high in
1363 <!-- JAL-2757 -->Can't edit the query after the server
1364 error warning icon is shown in Uniprot and PDB Free Text
1368 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1371 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1374 <!-- JAL-2739 -->Hidden column marker in last column not
1375 rendered when switching back from Wrapped to normal view
1378 <!-- JAL-2768 -->Annotation display corrupted when
1379 scrolling right in unwapped alignment view
1382 <!-- JAL-2542 -->Existing features on subsequence
1383 incorrectly relocated when full sequence retrieved from
1387 <!-- JAL-2733 -->Last reported memory still shown when
1388 Desktop->Show Memory is unticked (OSX only)
1391 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1392 features of same type and group to be selected for
1396 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1397 alignments when hidden columns are present
1400 <!-- JAL-2392 -->Jalview freezes when loading and
1401 displaying several structures
1404 <!-- JAL-2732 -->Black outlines left after resizing or
1408 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1409 within the Jalview desktop on OSX
1412 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1413 when in wrapped alignment mode
1416 <!-- JAL-2636 -->Scale mark not shown when close to right
1417 hand end of alignment
1420 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1421 each selected sequence do not have correct start/end
1425 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1426 after canceling the Alignment Window's Font dialog
1429 <!-- JAL-2036 -->Show cross-references not enabled after
1430 restoring project until a new view is created
1433 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1434 URL links appears when only default EMBL-EBI link is
1435 configured (since 2.10.2b2)
1438 <!-- JAL-2775 -->Overview redraws whole window when box
1439 position is adjusted
1442 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1443 in a multi-chain structure when viewing alignment
1444 involving more than one chain (since 2.10)
1447 <!-- JAL-2811 -->Double residue highlights in cursor mode
1448 if new selection moves alignment window
1451 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1452 arrow key in cursor mode to pass hidden column marker
1455 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1456 that produces correctly annotated transcripts and products
1459 <!-- JAL-2776 -->Toggling a feature group after first time
1460 doesn't update associated structure view
1463 <em>Applet</em><br />
1466 <!-- JAL-2687 -->Concurrent modification exception when
1467 closing alignment panel
1470 <em>BioJSON</em><br />
1473 <!-- JAL-2546 -->BioJSON export does not preserve
1474 non-positional features
1477 <em>New Known Issues</em>
1480 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1481 sequence features correctly (for many previous versions of
1485 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1486 using cursor in wrapped panel other than top
1489 <!-- JAL-2791 -->Select columns containing feature ignores
1490 graduated colour threshold
1493 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1494 always preserve numbering and sequence features
1497 <em>Known Java 9 Issues</em>
1500 <!-- JAL-2902 -->Groovy Console very slow to open and is
1501 not responsive when entering characters (Webstart, Java
1508 <td width="60" nowrap>
1509 <div align="center">
1510 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1511 <em>2/10/2017</em></strong>
1514 <td><div align="left">
1515 <em>New features in Jalview Desktop</em>
1518 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1520 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1524 <td><div align="left">
1528 <td width="60" nowrap>
1529 <div align="center">
1530 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1531 <em>7/9/2017</em></strong>
1534 <td><div align="left">
1538 <!-- JAL-2588 -->Show gaps in overview window by colouring
1539 in grey (sequences used to be coloured grey, and gaps were
1543 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1547 <!-- JAL-2587 -->Overview updates immediately on increase
1548 in size and progress bar shown as higher resolution
1549 overview is recalculated
1554 <td><div align="left">
1558 <!-- JAL-2664 -->Overview window redraws every hidden
1559 column region row by row
1562 <!-- JAL-2681 -->duplicate protein sequences shown after
1563 retrieving Ensembl crossrefs for sequences from Uniprot
1566 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1567 format setting is unticked
1570 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1571 if group has show boxes format setting unticked
1574 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1575 autoscrolling whilst dragging current selection group to
1576 include sequences and columns not currently displayed
1579 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1580 assemblies are imported via CIF file
1583 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1584 displayed when threshold or conservation colouring is also
1588 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1592 <!-- JAL-2673 -->Jalview continues to scroll after
1593 dragging a selected region off the visible region of the
1597 <!-- JAL-2724 -->Cannot apply annotation based
1598 colourscheme to all groups in a view
1601 <!-- JAL-2511 -->IDs don't line up with sequences
1602 initially after font size change using the Font chooser or
1609 <td width="60" nowrap>
1610 <div align="center">
1611 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1614 <td><div align="left">
1615 <em>Calculations</em>
1619 <!-- JAL-1933 -->Occupancy annotation row shows number of
1620 ungapped positions in each column of the alignment.
1623 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1624 a calculation dialog box
1627 <!-- JAL-2379 -->Revised implementation of PCA for speed
1628 and memory efficiency (~30x faster)
1631 <!-- JAL-2403 -->Revised implementation of sequence
1632 similarity scores as used by Tree, PCA, Shading Consensus
1633 and other calculations
1636 <!-- JAL-2416 -->Score matrices are stored as resource
1637 files within the Jalview codebase
1640 <!-- JAL-2500 -->Trees computed on Sequence Feature
1641 Similarity may have different topology due to increased
1648 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1649 model for alignments and groups
1652 <!-- JAL-384 -->Custom shading schemes created via groovy
1659 <!-- JAL-2526 -->Efficiency improvements for interacting
1660 with alignment and overview windows
1663 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1667 <!-- JAL-2388 -->Hidden columns and sequences can be
1671 <!-- JAL-2611 -->Click-drag in visible area allows fine
1672 adjustment of visible position
1676 <em>Data import/export</em>
1679 <!-- JAL-2535 -->Posterior probability annotation from
1680 Stockholm files imported as sequence associated annotation
1683 <!-- JAL-2507 -->More robust per-sequence positional
1684 annotation input/output via stockholm flatfile
1687 <!-- JAL-2533 -->Sequence names don't include file
1688 extension when importing structure files without embedded
1689 names or PDB accessions
1692 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1693 format sequence substitution matrices
1696 <em>User Interface</em>
1699 <!-- JAL-2447 --> Experimental Features Checkbox in
1700 Desktop's Tools menu to hide or show untested features in
1704 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1705 via Overview or sequence motif search operations
1708 <!-- JAL-2547 -->Amend sequence features dialog box can be
1709 opened by double clicking gaps within sequence feature
1713 <!-- JAL-1476 -->Status bar message shown when not enough
1714 aligned positions were available to create a 3D structure
1718 <em>3D Structure</em>
1721 <!-- JAL-2430 -->Hidden regions in alignment views are not
1722 coloured in linked structure views
1725 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1726 file-based command exchange
1729 <!-- JAL-2375 -->Structure chooser automatically shows
1730 Cached Structures rather than querying the PDBe if
1731 structures are already available for sequences
1734 <!-- JAL-2520 -->Structures imported via URL are cached in
1735 the Jalview project rather than downloaded again when the
1736 project is reopened.
1739 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1740 to transfer Chimera's structure attributes as Jalview
1741 features, and vice-versa (<strong>Experimental
1745 <em>Web Services</em>
1748 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1751 <!-- JAL-2335 -->Filter non-standard amino acids and
1752 nucleotides when submitting to AACon and other MSA
1756 <!-- JAL-2316, -->URLs for viewing database
1757 cross-references provided by identifiers.org and the
1758 EMBL-EBI's MIRIAM DB
1765 <!-- JAL-2344 -->FileFormatI interface for describing and
1766 identifying file formats (instead of String constants)
1769 <!-- JAL-2228 -->FeatureCounter script refactored for
1770 efficiency when counting all displayed features (not
1771 backwards compatible with 2.10.1)
1774 <em>Example files</em>
1777 <!-- JAL-2631 -->Graduated feature colour style example
1778 included in the example feature file
1781 <em>Documentation</em>
1784 <!-- JAL-2339 -->Release notes reformatted for readability
1785 with the built-in Java help viewer
1788 <!-- JAL-1644 -->Find documentation updated with 'search
1789 sequence description' option
1795 <!-- JAL-2485, -->External service integration tests for
1796 Uniprot REST Free Text Search Client
1799 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1802 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1807 <td><div align="left">
1808 <em>Calculations</em>
1811 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1812 matrix - C->R should be '-3'<br />Old matrix restored
1813 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1815 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1816 Jalview's treatment of gaps in PCA and substitution matrix
1817 based Tree calculations.<br /> <br />In earlier versions
1818 of Jalview, gaps matching gaps were penalised, and gaps
1819 matching non-gaps penalised even more. In the PCA
1820 calculation, gaps were actually treated as non-gaps - so
1821 different costs were applied, which meant Jalview's PCAs
1822 were different to those produced by SeqSpace.<br />Jalview
1823 now treats gaps in the same way as SeqSpace (ie it scores
1824 them as 0). <br /> <br />Enter the following in the
1825 Groovy console to restore pre-2.10.2 behaviour:<br />
1826 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1827 // for 2.10.1 mode <br />
1828 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1829 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1830 these settings will affect all subsequent tree and PCA
1831 calculations (not recommended)</em></li>
1833 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1834 scaling of branch lengths for trees computed using
1835 Sequence Feature Similarity.
1838 <!-- JAL-2377 -->PCA calculation could hang when
1839 generating output report when working with highly
1840 redundant alignments
1843 <!-- JAL-2544 --> Sort by features includes features to
1844 right of selected region when gaps present on right-hand
1848 <em>User Interface</em>
1851 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1852 doesn't reselect a specific sequence's associated
1853 annotation after it was used for colouring a view
1856 <!-- JAL-2419 -->Current selection lost if popup menu
1857 opened on a region of alignment without groups
1860 <!-- JAL-2374 -->Popup menu not always shown for regions
1861 of an alignment with overlapping groups
1864 <!-- JAL-2310 -->Finder double counts if both a sequence's
1865 name and description match
1868 <!-- JAL-2370 -->Hiding column selection containing two
1869 hidden regions results in incorrect hidden regions
1872 <!-- JAL-2386 -->'Apply to all groups' setting when
1873 changing colour does not apply Conservation slider value
1877 <!-- JAL-2373 -->Percentage identity and conservation menu
1878 items do not show a tick or allow shading to be disabled
1881 <!-- JAL-2385 -->Conservation shading or PID threshold
1882 lost when base colourscheme changed if slider not visible
1885 <!-- JAL-2547 -->Sequence features shown in tooltip for
1886 gaps before start of features
1889 <!-- JAL-2623 -->Graduated feature colour threshold not
1890 restored to UI when feature colour is edited
1893 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1894 a time when scrolling vertically in wrapped mode.
1897 <!-- JAL-2630 -->Structure and alignment overview update
1898 as graduate feature colour settings are modified via the
1902 <!-- JAL-2034 -->Overview window doesn't always update
1903 when a group defined on the alignment is resized
1906 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1907 wrapped view result in positional status updates
1911 <!-- JAL-2563 -->Status bar doesn't show position for
1912 ambiguous amino acid and nucleotide symbols
1915 <!-- JAL-2602 -->Copy consensus sequence failed if
1916 alignment included gapped columns
1919 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1920 widgets don't permanently disappear
1923 <!-- JAL-2503 -->Cannot select or filter quantitative
1924 annotation that are shown only as column labels (e.g.
1925 T-Coffee column reliability scores)
1928 <!-- JAL-2594 -->Exception thrown if trying to create a
1929 sequence feature on gaps only
1932 <!-- JAL-2504 -->Features created with 'New feature'
1933 button from a Find inherit previously defined feature type
1934 rather than the Find query string
1937 <!-- JAL-2423 -->incorrect title in output window when
1938 exporting tree calculated in Jalview
1941 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1942 and then revealing them reorders sequences on the
1946 <!-- JAL-964 -->Group panel in sequence feature settings
1947 doesn't update to reflect available set of groups after
1948 interactively adding or modifying features
1951 <!-- JAL-2225 -->Sequence Database chooser unusable on
1955 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1956 only excluded gaps in current sequence and ignored
1963 <!-- JAL-2421 -->Overview window visible region moves
1964 erratically when hidden rows or columns are present
1967 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1968 Structure Viewer's colour menu don't correspond to
1972 <!-- JAL-2405 -->Protein specific colours only offered in
1973 colour and group colour menu for protein alignments
1976 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1977 reflect currently selected view or group's shading
1981 <!-- JAL-2624 -->Feature colour thresholds not respected
1982 when rendered on overview and structures when opacity at
1986 <!-- JAL-2589 -->User defined gap colour not shown in
1987 overview when features overlaid on alignment
1990 <!-- JAL-2567 -->Feature settings for different views not
1991 recovered correctly from Jalview project file
1994 <!-- JAL-2256 -->Feature colours in overview when first opened
1995 (automatically via preferences) are different to the main
1999 <em>Data import/export</em>
2002 <!-- JAL-2576 -->Very large alignments take a long time to
2006 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2007 added after a sequence was imported are not written to
2011 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2012 when importing RNA secondary structure via Stockholm
2015 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2016 not shown in correct direction for simple pseudoknots
2019 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2020 with lightGray or darkGray via features file (but can
2024 <!-- JAL-2383 -->Above PID colour threshold not recovered
2025 when alignment view imported from project
2028 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2029 structure and sequences extracted from structure files
2030 imported via URL and viewed in Jmol
2033 <!-- JAL-2520 -->Structures loaded via URL are saved in
2034 Jalview Projects rather than fetched via URL again when
2035 the project is loaded and the structure viewed
2038 <em>Web Services</em>
2041 <!-- JAL-2519 -->EnsemblGenomes example failing after
2042 release of Ensembl v.88
2045 <!-- JAL-2366 -->Proxy server address and port always
2046 appear enabled in Preferences->Connections
2049 <!-- JAL-2461 -->DAS registry not found exceptions
2050 removed from console output
2053 <!-- JAL-2582 -->Cannot retrieve protein products from
2054 Ensembl by Peptide ID
2057 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2058 created from SIFTs, and spurious 'Couldn't open structure
2059 in Chimera' errors raised after April 2017 update (problem
2060 due to 'null' string rather than empty string used for
2061 residues with no corresponding PDB mapping).
2064 <em>Application UI</em>
2067 <!-- JAL-2361 -->User Defined Colours not added to Colour
2071 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2072 case' residues (button in colourscheme editor debugged and
2073 new documentation and tooltips added)
2076 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2077 doesn't restore group-specific text colour thresholds
2080 <!-- JAL-2243 -->Feature settings panel does not update as
2081 new features are added to alignment
2084 <!-- JAL-2532 -->Cancel in feature settings reverts
2085 changes to feature colours via the Amend features dialog
2088 <!-- JAL-2506 -->Null pointer exception when attempting to
2089 edit graduated feature colour via amend features dialog
2093 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2094 selection menu changes colours of alignment views
2097 <!-- JAL-2426 -->Spurious exceptions in console raised
2098 from alignment calculation workers after alignment has
2102 <!-- JAL-1608 -->Typo in selection popup menu - Create
2103 groups now 'Create Group'
2106 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2107 Create/Undefine group doesn't always work
2110 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2111 shown again after pressing 'Cancel'
2114 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2115 adjusts start position in wrap mode
2118 <!-- JAL-2563 -->Status bar doesn't show positions for
2119 ambiguous amino acids
2122 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2123 CDS/Protein view after CDS sequences added for aligned
2127 <!-- JAL-2592 -->User defined colourschemes called 'User
2128 Defined' don't appear in Colours menu
2134 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2135 score models doesn't always result in an updated PCA plot
2138 <!-- JAL-2442 -->Features not rendered as transparent on
2139 overview or linked structure view
2142 <!-- JAL-2372 -->Colour group by conservation doesn't
2146 <!-- JAL-2517 -->Hitting Cancel after applying
2147 user-defined colourscheme doesn't restore original
2154 <!-- JAL-2314 -->Unit test failure:
2155 jalview.ws.jabaws.RNAStructExportImport setup fails
2158 <!-- JAL-2307 -->Unit test failure:
2159 jalview.ws.sifts.SiftsClientTest due to compatibility
2160 problems with deep array comparison equality asserts in
2161 successive versions of TestNG
2164 <!-- JAL-2479 -->Relocated StructureChooserTest and
2165 ParameterUtilsTest Unit tests to Network suite
2168 <em>New Known Issues</em>
2171 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2172 phase after a sequence motif find operation
2175 <!-- JAL-2550 -->Importing annotation file with rows
2176 containing just upper and lower case letters are
2177 interpreted as WUSS RNA secondary structure symbols
2180 <!-- JAL-2590 -->Cannot load and display Newick trees
2181 reliably from eggnog Ortholog database
2184 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2185 containing features of type Highlight' when 'B' is pressed
2186 to mark columns containing highlighted regions.
2189 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2190 doesn't always add secondary structure annotation.
2195 <td width="60" nowrap>
2196 <div align="center">
2197 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2200 <td><div align="left">
2204 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2205 for all consensus calculations
2208 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2211 <li>Updated Jalview's Certum code signing certificate
2214 <em>Application</em>
2217 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2218 set of database cross-references, sorted alphabetically
2221 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2222 from database cross references. Users with custom links
2223 will receive a <a href="webServices/urllinks.html#warning">warning
2224 dialog</a> asking them to update their preferences.
2227 <!-- JAL-2287-->Cancel button and escape listener on
2228 dialog warning user about disconnecting Jalview from a
2232 <!-- JAL-2320-->Jalview's Chimera control window closes if
2233 the Chimera it is connected to is shut down
2236 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2237 columns menu item to mark columns containing highlighted
2238 regions (e.g. from structure selections or results of a
2242 <!-- JAL-2284-->Command line option for batch-generation
2243 of HTML pages rendering alignment data with the BioJS
2253 <!-- JAL-2286 -->Columns with more than one modal residue
2254 are not coloured or thresholded according to percent
2255 identity (first observed in Jalview 2.8.2)
2258 <!-- JAL-2301 -->Threonine incorrectly reported as not
2262 <!-- JAL-2318 -->Updates to documentation pages (above PID
2263 threshold, amino acid properties)
2266 <!-- JAL-2292 -->Lower case residues in sequences are not
2267 reported as mapped to residues in a structure file in the
2271 <!--JAL-2324 -->Identical features with non-numeric scores
2272 could be added multiple times to a sequence
2275 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2276 bond features shown as two highlighted residues rather
2277 than a range in linked structure views, and treated
2278 correctly when selecting and computing trees from features
2281 <!-- JAL-2281-->Custom URL links for database
2282 cross-references are matched to database name regardless
2287 <em>Application</em>
2290 <!-- JAL-2282-->Custom URL links for specific database
2291 names without regular expressions also offer links from
2295 <!-- JAL-2315-->Removing a single configured link in the
2296 URL links pane in Connections preferences doesn't actually
2297 update Jalview configuration
2300 <!-- JAL-2272-->CTRL-Click on a selected region to open
2301 the alignment area popup menu doesn't work on El-Capitan
2304 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2305 files with similarly named sequences if dropped onto the
2309 <!-- JAL-2312 -->Additional mappings are shown for PDB
2310 entries where more chains exist in the PDB accession than
2311 are reported in the SIFTS file
2314 <!-- JAL-2317-->Certain structures do not get mapped to
2315 the structure view when displayed with Chimera
2318 <!-- JAL-2317-->No chains shown in the Chimera view
2319 panel's View->Show Chains submenu
2322 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2323 work for wrapped alignment views
2326 <!--JAL-2197 -->Rename UI components for running JPred
2327 predictions from 'JNet' to 'JPred'
2330 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2331 corrupted when annotation panel vertical scroll is not at
2332 first annotation row
2335 <!--JAL-2332 -->Attempting to view structure for Hen
2336 lysozyme results in a PDB Client error dialog box
2339 <!-- JAL-2319 -->Structure View's mapping report switched
2340 ranges for PDB and sequence for SIFTS
2343 SIFTS 'Not_Observed' residues mapped to non-existant
2347 <!-- <em>New Known Issues</em>
2354 <td width="60" nowrap>
2355 <div align="center">
2356 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2357 <em>25/10/2016</em></strong>
2360 <td><em>Application</em>
2362 <li>3D Structure chooser opens with 'Cached structures'
2363 view if structures already loaded</li>
2364 <li>Progress bar reports models as they are loaded to
2365 structure views</li>
2371 <li>Colour by conservation always enabled and no tick
2372 shown in menu when BLOSUM or PID shading applied</li>
2373 <li>FER1_ARATH and FER2_ARATH labels were switched in
2374 example sequences/projects/trees</li>
2376 <em>Application</em>
2378 <li>Jalview projects with views of local PDB structure
2379 files saved on Windows cannot be opened on OSX</li>
2380 <li>Multiple structure views can be opened and superposed
2381 without timeout for structures with multiple models or
2382 multiple sequences in alignment</li>
2383 <li>Cannot import or associated local PDB files without a
2384 PDB ID HEADER line</li>
2385 <li>RMSD is not output in Jmol console when superposition
2387 <li>Drag and drop of URL from Browser fails for Linux and
2388 OSX versions earlier than El Capitan</li>
2389 <li>ENA client ignores invalid content from ENA server</li>
2390 <li>Exceptions are not raised in console when ENA client
2391 attempts to fetch non-existent IDs via Fetch DB Refs UI
2393 <li>Exceptions are not raised in console when a new view
2394 is created on the alignment</li>
2395 <li>OSX right-click fixed for group selections: CMD-click
2396 to insert/remove gaps in groups and CTRL-click to open group
2399 <em>Build and deployment</em>
2401 <li>URL link checker now copes with multi-line anchor
2404 <em>New Known Issues</em>
2406 <li>Drag and drop from URL links in browsers do not work
2413 <td width="60" nowrap>
2414 <div align="center">
2415 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2418 <td><em>General</em>
2421 <!-- JAL-2124 -->Updated Spanish translations.
2424 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2425 for importing structure data to Jalview. Enables mmCIF and
2429 <!-- JAL-192 --->Alignment ruler shows positions relative to
2433 <!-- JAL-2202 -->Position/residue shown in status bar when
2434 mousing over sequence associated annotation
2437 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2441 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2442 '()', canonical '[]' and invalid '{}' base pair populations
2446 <!-- JAL-2092 -->Feature settings popup menu options for
2447 showing or hiding columns containing a feature
2450 <!-- JAL-1557 -->Edit selected group by double clicking on
2451 group and sequence associated annotation labels
2454 <!-- JAL-2236 -->Sequence name added to annotation label in
2455 select/hide columns by annotation and colour by annotation
2459 </ul> <em>Application</em>
2462 <!-- JAL-2050-->Automatically hide introns when opening a
2463 gene/transcript view
2466 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2470 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2471 structure mappings with the EMBL-EBI PDBe SIFTS database
2474 <!-- JAL-2079 -->Updated download sites used for Rfam and
2475 Pfam sources to xfam.org
2478 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2481 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2482 over sequences in Jalview
2485 <!-- JAL-2027-->Support for reverse-complement coding
2486 regions in ENA and EMBL
2489 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2490 for record retrieval via ENA rest API
2493 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2497 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2498 groovy script execution
2501 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2502 alignment window's Calculate menu
2505 <!-- JAL-1812 -->Allow groovy scripts that call
2506 Jalview.getAlignFrames() to run in headless mode
2509 <!-- JAL-2068 -->Support for creating new alignment
2510 calculation workers from groovy scripts
2513 <!-- JAL-1369 --->Store/restore reference sequence in
2517 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2518 associations are now saved/restored from project
2521 <!-- JAL-1993 -->Database selection dialog always shown
2522 before sequence fetcher is opened
2525 <!-- JAL-2183 -->Double click on an entry in Jalview's
2526 database chooser opens a sequence fetcher
2529 <!-- JAL-1563 -->Free-text search client for UniProt using
2530 the UniProt REST API
2533 <!-- JAL-2168 -->-nonews command line parameter to prevent
2534 the news reader opening
2537 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2538 querying stored in preferences
2541 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2545 <!-- JAL-1977-->Tooltips shown on database chooser
2548 <!-- JAL-391 -->Reverse complement function in calculate
2549 menu for nucleotide sequences
2552 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2553 and feature counts preserves alignment ordering (and
2554 debugged for complex feature sets).
2557 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2558 viewing structures with Jalview 2.10
2561 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2562 genome, transcript CCDS and gene ids via the Ensembl and
2563 Ensembl Genomes REST API
2566 <!-- JAL-2049 -->Protein sequence variant annotation
2567 computed for 'sequence_variant' annotation on CDS regions
2571 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2575 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2576 Ref Fetcher fails to match, or otherwise updates sequence
2577 data from external database records.
2580 <!-- JAL-2154 -->Revised Jalview Project format for
2581 efficient recovery of sequence coding and alignment
2582 annotation relationships.
2584 </ul> <!-- <em>Applet</em>
2595 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2599 <!-- JAL-2018-->Export features in Jalview format (again)
2600 includes graduated colourschemes
2603 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2604 working with big alignments and lots of hidden columns
2607 <!-- JAL-2053-->Hidden column markers not always rendered
2608 at right of alignment window
2611 <!-- JAL-2067 -->Tidied up links in help file table of
2615 <!-- JAL-2072 -->Feature based tree calculation not shown
2619 <!-- JAL-2075 -->Hidden columns ignored during feature
2620 based tree calculation
2623 <!-- JAL-2065 -->Alignment view stops updating when show
2624 unconserved enabled for group on alignment
2627 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2631 <!-- JAL-2146 -->Alignment column in status incorrectly
2632 shown as "Sequence position" when mousing over
2636 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2637 hidden columns present
2640 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2641 user created annotation added to alignment
2644 <!-- JAL-1841 -->RNA Structure consensus only computed for
2645 '()' base pair annotation
2648 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2649 in zero scores for all base pairs in RNA Structure
2653 <!-- JAL-2174-->Extend selection with columns containing
2657 <!-- JAL-2275 -->Pfam format writer puts extra space at
2658 beginning of sequence
2661 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2665 <!-- JAL-2238 -->Cannot create groups on an alignment from
2666 from a tree when t-coffee scores are shown
2669 <!-- JAL-1836,1967 -->Cannot import and view PDB
2670 structures with chains containing negative resnums (4q4h)
2673 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2677 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2678 to Clustal, PIR and PileUp output
2681 <!-- JAL-2008 -->Reordering sequence features that are
2682 not visible causes alignment window to repaint
2685 <!-- JAL-2006 -->Threshold sliders don't work in
2686 graduated colour and colour by annotation row for e-value
2687 scores associated with features and annotation rows
2690 <!-- JAL-1797 -->amino acid physicochemical conservation
2691 calculation should be case independent
2694 <!-- JAL-2173 -->Remove annotation also updates hidden
2698 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2699 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2700 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2703 <!-- JAL-2065 -->Null pointer exceptions and redraw
2704 problems when reference sequence defined and 'show
2705 non-conserved' enabled
2708 <!-- JAL-1306 -->Quality and Conservation are now shown on
2709 load even when Consensus calculation is disabled
2712 <!-- JAL-1932 -->Remove right on penultimate column of
2713 alignment does nothing
2716 <em>Application</em>
2719 <!-- JAL-1552-->URLs and links can't be imported by
2720 drag'n'drop on OSX when launched via webstart (note - not
2721 yet fixed for El Capitan)
2724 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2725 output when running on non-gb/us i18n platforms
2728 <!-- JAL-1944 -->Error thrown when exporting a view with
2729 hidden sequences as flat-file alignment
2732 <!-- JAL-2030-->InstallAnywhere distribution fails when
2736 <!-- JAL-2080-->Jalview very slow to launch via webstart
2737 (also hotfix for 2.9.0b2)
2740 <!-- JAL-2085 -->Cannot save project when view has a
2741 reference sequence defined
2744 <!-- JAL-1011 -->Columns are suddenly selected in other
2745 alignments and views when revealing hidden columns
2748 <!-- JAL-1989 -->Hide columns not mirrored in complement
2749 view in a cDNA/Protein splitframe
2752 <!-- JAL-1369 -->Cannot save/restore representative
2753 sequence from project when only one sequence is
2757 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2758 in Structure Chooser
2761 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2762 structure consensus didn't refresh annotation panel
2765 <!-- JAL-1962 -->View mapping in structure view shows
2766 mappings between sequence and all chains in a PDB file
2769 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2770 dialogs format columns correctly, don't display array
2771 data, sort columns according to type
2774 <!-- JAL-1975 -->Export complete shown after destination
2775 file chooser is cancelled during an image export
2778 <!-- JAL-2025 -->Error when querying PDB Service with
2779 sequence name containing special characters
2782 <!-- JAL-2024 -->Manual PDB structure querying should be
2786 <!-- JAL-2104 -->Large tooltips with broken HTML
2787 formatting don't wrap
2790 <!-- JAL-1128 -->Figures exported from wrapped view are
2791 truncated so L looks like I in consensus annotation
2794 <!-- JAL-2003 -->Export features should only export the
2795 currently displayed features for the current selection or
2799 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2800 after fetching cross-references, and restoring from
2804 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2805 followed in the structure viewer
2808 <!-- JAL-2163 -->Titles for individual alignments in
2809 splitframe not restored from project
2812 <!-- JAL-2145 -->missing autocalculated annotation at
2813 trailing end of protein alignment in transcript/product
2814 splitview when pad-gaps not enabled by default
2817 <!-- JAL-1797 -->amino acid physicochemical conservation
2821 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2822 article has been read (reopened issue due to
2823 internationalisation problems)
2826 <!-- JAL-1960 -->Only offer PDB structures in structure
2827 viewer based on sequence name, PDB and UniProt
2832 <!-- JAL-1976 -->No progress bar shown during export of
2836 <!-- JAL-2213 -->Structures not always superimposed after
2837 multiple structures are shown for one or more sequences.
2840 <!-- JAL-1370 -->Reference sequence characters should not
2841 be replaced with '.' when 'Show unconserved' format option
2845 <!-- JAL-1823 -->Cannot specify chain code when entering
2846 specific PDB id for sequence
2849 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2850 'Export hidden sequences' is enabled, but 'export hidden
2851 columns' is disabled.
2854 <!--JAL-2026-->Best Quality option in structure chooser
2855 selects lowest rather than highest resolution structures
2859 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2860 to sequence mapping in 'View Mappings' report
2863 <!-- JAL-2284 -->Unable to read old Jalview projects that
2864 contain non-XML data added after Jalvew wrote project.
2867 <!-- JAL-2118 -->Newly created annotation row reorders
2868 after clicking on it to create new annotation for a
2872 <!-- JAL-1980 -->Null Pointer Exception raised when
2873 pressing Add on an orphaned cut'n'paste window.
2875 <!-- may exclude, this is an external service stability issue JAL-1941
2876 -- > RNA 3D structure not added via DSSR service</li> -->
2881 <!-- JAL-2151 -->Incorrect columns are selected when
2882 hidden columns present before start of sequence
2885 <!-- JAL-1986 -->Missing dependencies on applet pages
2889 <!-- JAL-1947 -->Overview pixel size changes when
2890 sequences are hidden in applet
2893 <!-- JAL-1996 -->Updated instructions for applet
2894 deployment on examples pages.
2901 <td width="60" nowrap>
2902 <div align="center">
2903 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2904 <em>16/10/2015</em></strong>
2907 <td><em>General</em>
2909 <li>Time stamps for signed Jalview application and applet
2914 <em>Application</em>
2916 <li>Duplicate group consensus and conservation rows
2917 shown when tree is partitioned</li>
2918 <li>Erratic behaviour when tree partitions made with
2919 multiple cDNA/Protein split views</li>
2925 <td width="60" nowrap>
2926 <div align="center">
2927 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2928 <em>8/10/2015</em></strong>
2931 <td><em>General</em>
2933 <li>Updated Spanish translations of localized text for
2935 </ul> <em>Application</em>
2937 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2938 <li>Signed OSX InstallAnywhere installer<br></li>
2939 <li>Support for per-sequence based annotations in BioJSON</li>
2940 </ul> <em>Applet</em>
2942 <li>Split frame example added to applet examples page</li>
2943 </ul> <em>Build and Deployment</em>
2946 <!-- JAL-1888 -->New ant target for running Jalview's test
2954 <li>Mapping of cDNA to protein in split frames
2955 incorrect when sequence start > 1</li>
2956 <li>Broken images in filter column by annotation dialog
2958 <li>Feature colours not parsed from features file</li>
2959 <li>Exceptions and incomplete link URLs recovered when
2960 loading a features file containing HTML tags in feature
2964 <em>Application</em>
2966 <li>Annotations corrupted after BioJS export and
2968 <li>Incorrect sequence limits after Fetch DB References
2969 with 'trim retrieved sequences'</li>
2970 <li>Incorrect warning about deleting all data when
2971 deleting selected columns</li>
2972 <li>Patch to build system for shipping properly signed
2973 JNLP templates for webstart launch</li>
2974 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2975 unreleased structures for download or viewing</li>
2976 <li>Tab/space/return keystroke operation of EMBL-PDBe
2977 fetcher/viewer dialogs works correctly</li>
2978 <li>Disabled 'minimise' button on Jalview windows
2979 running on OSX to workaround redraw hang bug</li>
2980 <li>Split cDNA/Protein view position and geometry not
2981 recovered from jalview project</li>
2982 <li>Initial enabled/disabled state of annotation menu
2983 sorter 'show autocalculated first/last' corresponds to
2985 <li>Restoring of Clustal, RNA Helices and T-Coffee
2986 color schemes from BioJSON</li>
2990 <li>Reorder sequences mirrored in cDNA/Protein split
2992 <li>Applet with Jmol examples not loading correctly</li>
2998 <td><div align="center">
2999 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3001 <td><em>General</em>
3003 <li>Linked visualisation and analysis of DNA and Protein
3006 <li>Translated cDNA alignments shown as split protein
3007 and DNA alignment views</li>
3008 <li>Codon consensus annotation for linked protein and
3009 cDNA alignment views</li>
3010 <li>Link cDNA or Protein product sequences by loading
3011 them onto Protein or cDNA alignments</li>
3012 <li>Reconstruct linked cDNA alignment from aligned
3013 protein sequences</li>
3016 <li>Jmol integration updated to Jmol v14.2.14</li>
3017 <li>Import and export of Jalview alignment views as <a
3018 href="features/bioJsonFormat.html">BioJSON</a></li>
3019 <li>New alignment annotation file statements for
3020 reference sequences and marking hidden columns</li>
3021 <li>Reference sequence based alignment shading to
3022 highlight variation</li>
3023 <li>Select or hide columns according to alignment
3025 <li>Find option for locating sequences by description</li>
3026 <li>Conserved physicochemical properties shown in amino
3027 acid conservation row</li>
3028 <li>Alignments can be sorted by number of RNA helices</li>
3029 </ul> <em>Application</em>
3031 <li>New cDNA/Protein analysis capabilities
3033 <li>Get Cross-References should open a Split Frame
3034 view with cDNA/Protein</li>
3035 <li>Detect when nucleotide sequences and protein
3036 sequences are placed in the same alignment</li>
3037 <li>Split cDNA/Protein views are saved in Jalview
3042 <li>Use REST API to talk to Chimera</li>
3043 <li>Selected regions in Chimera are highlighted in linked
3044 Jalview windows</li>
3046 <li>VARNA RNA viewer updated to v3.93</li>
3047 <li>VARNA views are saved in Jalview Projects</li>
3048 <li>Pseudoknots displayed as Jalview RNA annotation can
3049 be shown in VARNA</li>
3051 <li>Make groups for selection uses marked columns as well
3052 as the active selected region</li>
3054 <li>Calculate UPGMA and NJ trees using sequence feature
3056 <li>New Export options
3058 <li>New Export Settings dialog to control hidden
3059 region export in flat file generation</li>
3061 <li>Export alignment views for display with the <a
3062 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3064 <li>Export scrollable SVG in HTML page</li>
3065 <li>Optional embedding of BioJSON data when exporting
3066 alignment figures to HTML</li>
3068 <li>3D structure retrieval and display
3070 <li>Free text and structured queries with the PDBe
3072 <li>PDBe Search API based discovery and selection of
3073 PDB structures for a sequence set</li>
3077 <li>JPred4 employed for protein secondary structure
3079 <li>Hide Insertions menu option to hide unaligned columns
3080 for one or a group of sequences</li>
3081 <li>Automatically hide insertions in alignments imported
3082 from the JPred4 web server</li>
3083 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3084 system on OSX<br />LGPL libraries courtesy of <a
3085 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3087 <li>changed 'View nucleotide structure' submenu to 'View
3088 VARNA 2D Structure'</li>
3089 <li>change "View protein structure" menu option to "3D
3092 </ul> <em>Applet</em>
3094 <li>New layout for applet example pages</li>
3095 <li>New parameters to enable SplitFrame view
3096 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3097 <li>New example demonstrating linked viewing of cDNA and
3098 Protein alignments</li>
3099 </ul> <em>Development and deployment</em>
3101 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3102 <li>Include installation type and git revision in build
3103 properties and console log output</li>
3104 <li>Jalview Github organisation, and new github site for
3105 storing BioJsMSA Templates</li>
3106 <li>Jalview's unit tests now managed with TestNG</li>
3109 <!-- <em>General</em>
3111 </ul> --> <!-- issues resolved --> <em>Application</em>
3113 <li>Escape should close any open find dialogs</li>
3114 <li>Typo in select-by-features status report</li>
3115 <li>Consensus RNA secondary secondary structure
3116 predictions are not highlighted in amber</li>
3117 <li>Missing gap character in v2.7 example file means
3118 alignment appears unaligned when pad-gaps is not enabled</li>
3119 <li>First switch to RNA Helices colouring doesn't colour
3120 associated structure views</li>
3121 <li>ID width preference option is greyed out when auto
3122 width checkbox not enabled</li>
3123 <li>Stopped a warning dialog from being shown when
3124 creating user defined colours</li>
3125 <li>'View Mapping' in structure viewer shows sequence
3126 mappings for just that viewer's sequences</li>
3127 <li>Workaround for superposing PDB files containing
3128 multiple models in Chimera</li>
3129 <li>Report sequence position in status bar when hovering
3130 over Jmol structure</li>
3131 <li>Cannot output gaps as '.' symbols with Selection ->
3132 output to text box</li>
3133 <li>Flat file exports of alignments with hidden columns
3134 have incorrect sequence start/end</li>
3135 <li>'Aligning' a second chain to a Chimera structure from
3137 <li>Colour schemes applied to structure viewers don't
3138 work for nucleotide</li>
3139 <li>Loading/cut'n'pasting an empty or invalid file leads
3140 to a grey/invisible alignment window</li>
3141 <li>Exported Jpred annotation from a sequence region
3142 imports to different position</li>
3143 <li>Space at beginning of sequence feature tooltips shown
3144 on some platforms</li>
3145 <li>Chimera viewer 'View | Show Chain' menu is not
3147 <li>'New View' fails with a Null Pointer Exception in
3148 console if Chimera has been opened</li>
3149 <li>Mouseover to Chimera not working</li>
3150 <li>Miscellaneous ENA XML feature qualifiers not
3152 <li>NPE in annotation renderer after 'Extract Scores'</li>
3153 <li>If two structures in one Chimera window, mouseover of
3154 either sequence shows on first structure</li>
3155 <li>'Show annotations' options should not make
3156 non-positional annotations visible</li>
3157 <li>Subsequence secondary structure annotation not shown
3158 in right place after 'view flanking regions'</li>
3159 <li>File Save As type unset when current file format is
3161 <li>Save as '.jar' option removed for saving Jalview
3163 <li>Colour by Sequence colouring in Chimera more
3165 <li>Cannot 'add reference annotation' for a sequence in
3166 several views on same alignment</li>
3167 <li>Cannot show linked products for EMBL / ENA records</li>
3168 <li>Jalview's tooltip wraps long texts containing no
3170 </ul> <em>Applet</em>
3172 <li>Jmol to JalviewLite mouseover/link not working</li>
3173 <li>JalviewLite can't import sequences with ID
3174 descriptions containing angle brackets</li>
3175 </ul> <em>General</em>
3177 <li>Cannot export and reimport RNA secondary structure
3178 via jalview annotation file</li>
3179 <li>Random helix colour palette for colour by annotation
3180 with RNA secondary structure</li>
3181 <li>Mouseover to cDNA from STOP residue in protein
3182 translation doesn't work.</li>
3183 <li>hints when using the select by annotation dialog box</li>
3184 <li>Jmol alignment incorrect if PDB file has alternate CA
3186 <li>FontChooser message dialog appears to hang after
3187 choosing 1pt font</li>
3188 <li>Peptide secondary structure incorrectly imported from
3189 annotation file when annotation display text includes 'e' or
3191 <li>Cannot set colour of new feature type whilst creating
3193 <li>cDNA translation alignment should not be sequence
3194 order dependent</li>
3195 <li>'Show unconserved' doesn't work for lower case
3197 <li>Nucleotide ambiguity codes involving R not recognised</li>
3198 </ul> <em>Deployment and Documentation</em>
3200 <li>Applet example pages appear different to the rest of
3201 www.jalview.org</li>
3202 </ul> <em>Application Known issues</em>
3204 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3205 <li>Misleading message appears after trying to delete
3207 <li>Jalview icon not shown in dock after InstallAnywhere
3208 version launches</li>
3209 <li>Fetching EMBL reference for an RNA sequence results
3210 fails with a sequence mismatch</li>
3211 <li>Corrupted or unreadable alignment display when
3212 scrolling alignment to right</li>
3213 <li>ArrayIndexOutOfBoundsException thrown when remove
3214 empty columns called on alignment with ragged gapped ends</li>
3215 <li>auto calculated alignment annotation rows do not get
3216 placed above or below non-autocalculated rows</li>
3217 <li>Jalview dekstop becomes sluggish at full screen in
3218 ultra-high resolution</li>
3219 <li>Cannot disable consensus calculation independently of
3220 quality and conservation</li>
3221 <li>Mouseover highlighting between cDNA and protein can
3222 become sluggish with more than one splitframe shown</li>
3223 </ul> <em>Applet Known Issues</em>
3225 <li>Core PDB parsing code requires Jmol</li>
3226 <li>Sequence canvas panel goes white when alignment
3227 window is being resized</li>
3233 <td><div align="center">
3234 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3236 <td><em>General</em>
3238 <li>Updated Java code signing certificate donated by
3240 <li>Features and annotation preserved when performing
3241 pairwise alignment</li>
3242 <li>RNA pseudoknot annotation can be
3243 imported/exported/displayed</li>
3244 <li>'colour by annotation' can colour by RNA and
3245 protein secondary structure</li>
3246 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3247 post-hoc with 2.9 release</em>)
3250 </ul> <em>Application</em>
3252 <li>Extract and display secondary structure for sequences
3253 with 3D structures</li>
3254 <li>Support for parsing RNAML</li>
3255 <li>Annotations menu for layout
3257 <li>sort sequence annotation rows by alignment</li>
3258 <li>place sequence annotation above/below alignment
3261 <li>Output in Stockholm format</li>
3262 <li>Internationalisation: improved Spanish (es)
3264 <li>Structure viewer preferences tab</li>
3265 <li>Disorder and Secondary Structure annotation tracks
3266 shared between alignments</li>
3267 <li>UCSF Chimera launch and linked highlighting from
3269 <li>Show/hide all sequence associated annotation rows for
3270 all or current selection</li>
3271 <li>disorder and secondary structure predictions
3272 available as dataset annotation</li>
3273 <li>Per-sequence rna helices colouring</li>
3276 <li>Sequence database accessions imported when fetching
3277 alignments from Rfam</li>
3278 <li>update VARNA version to 3.91</li>
3280 <li>New groovy scripts for exporting aligned positions,
3281 conservation values, and calculating sum of pairs scores.</li>
3282 <li>Command line argument to set default JABAWS server</li>
3283 <li>include installation type in build properties and
3284 console log output</li>
3285 <li>Updated Jalview project format to preserve dataset
3289 <!-- issues resolved --> <em>Application</em>
3291 <li>Distinguish alignment and sequence associated RNA
3292 structure in structure->view->VARNA</li>
3293 <li>Raise dialog box if user deletes all sequences in an
3295 <li>Pressing F1 results in documentation opening twice</li>
3296 <li>Sequence feature tooltip is wrapped</li>
3297 <li>Double click on sequence associated annotation
3298 selects only first column</li>
3299 <li>Redundancy removal doesn't result in unlinked
3300 leaves shown in tree</li>
3301 <li>Undos after several redundancy removals don't undo
3303 <li>Hide sequence doesn't hide associated annotation</li>
3304 <li>User defined colours dialog box too big to fit on
3305 screen and buttons not visible</li>
3306 <li>author list isn't updated if already written to
3307 Jalview properties</li>
3308 <li>Popup menu won't open after retrieving sequence
3310 <li>File open window for associate PDB doesn't open</li>
3311 <li>Left-then-right click on a sequence id opens a
3312 browser search window</li>
3313 <li>Cannot open sequence feature shading/sort popup menu
3314 in feature settings dialog</li>
3315 <li>better tooltip placement for some areas of Jalview
3317 <li>Allow addition of JABAWS Server which doesn't
3318 pass validation</li>
3319 <li>Web services parameters dialog box is too large to
3321 <li>Muscle nucleotide alignment preset obscured by
3323 <li>JABAWS preset submenus don't contain newly
3324 defined user preset</li>
3325 <li>MSA web services warns user if they were launched
3326 with invalid input</li>
3327 <li>Jalview cannot contact DAS Registy when running on
3330 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3331 'Superpose with' submenu not shown when new view
3335 </ul> <!-- <em>Applet</em>
3337 </ul> <em>General</em>
3339 </ul>--> <em>Deployment and Documentation</em>
3341 <li>2G and 1G options in launchApp have no effect on
3342 memory allocation</li>
3343 <li>launchApp service doesn't automatically open
3344 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3346 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3347 InstallAnywhere reports cannot find valid JVM when Java
3348 1.7_055 is available
3350 </ul> <em>Application Known issues</em>
3353 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3354 corrupted or unreadable alignment display when scrolling
3358 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3359 retrieval fails but progress bar continues for DAS retrieval
3360 with large number of ID
3363 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3364 flatfile output of visible region has incorrect sequence
3368 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3369 rna structure consensus doesn't update when secondary
3370 structure tracks are rearranged
3373 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3374 invalid rna structure positional highlighting does not
3375 highlight position of invalid base pairs
3378 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3379 out of memory errors are not raised when saving Jalview
3380 project from alignment window file menu
3383 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3384 Switching to RNA Helices colouring doesn't propagate to
3388 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3389 colour by RNA Helices not enabled when user created
3390 annotation added to alignment
3393 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3394 Jalview icon not shown on dock in Mountain Lion/Webstart
3396 </ul> <em>Applet Known Issues</em>
3399 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3400 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3403 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3404 Jalview and Jmol example not compatible with IE9
3407 <li>Sort by annotation score doesn't reverse order
3413 <td><div align="center">
3414 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3417 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3420 <li>Internationalisation of user interface (usually
3421 called i18n support) and translation for Spanish locale</li>
3422 <li>Define/Undefine group on current selection with
3423 Ctrl-G/Shift Ctrl-G</li>
3424 <li>Improved group creation/removal options in
3425 alignment/sequence Popup menu</li>
3426 <li>Sensible precision for symbol distribution
3427 percentages shown in logo tooltip.</li>
3428 <li>Annotation panel height set according to amount of
3429 annotation when alignment first opened</li>
3430 </ul> <em>Application</em>
3432 <li>Interactive consensus RNA secondary structure
3433 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3434 <li>Select columns containing particular features from
3435 Feature Settings dialog</li>
3436 <li>View all 'representative' PDB structures for selected
3438 <li>Update Jalview project format:
3440 <li>New file extension for Jalview projects '.jvp'</li>
3441 <li>Preserve sequence and annotation dataset (to
3442 store secondary structure annotation,etc)</li>
3443 <li>Per group and alignment annotation and RNA helix
3447 <li>New similarity measures for PCA and Tree calculation
3449 <li>Experimental support for retrieval and viewing of
3450 flanking regions for an alignment</li>
3454 <!-- issues resolved --> <em>Application</em>
3456 <li>logo keeps spinning and status remains at queued or
3457 running after job is cancelled</li>
3458 <li>cannot export features from alignments imported from
3459 Jalview/VAMSAS projects</li>
3460 <li>Buggy slider for web service parameters that take
3462 <li>Newly created RNA secondary structure line doesn't
3463 have 'display all symbols' flag set</li>
3464 <li>T-COFFEE alignment score shading scheme and other
3465 annotation shading not saved in Jalview project</li>
3466 <li>Local file cannot be loaded in freshly downloaded
3468 <li>Jalview icon not shown on dock in Mountain
3470 <li>Load file from desktop file browser fails</li>
3471 <li>Occasional NPE thrown when calculating large trees</li>
3472 <li>Cannot reorder or slide sequences after dragging an
3473 alignment onto desktop</li>
3474 <li>Colour by annotation dialog throws NPE after using
3475 'extract scores' function</li>
3476 <li>Loading/cut'n'pasting an empty file leads to a grey
3477 alignment window</li>
3478 <li>Disorder thresholds rendered incorrectly after
3479 performing IUPred disorder prediction</li>
3480 <li>Multiple group annotated consensus rows shown when
3481 changing 'normalise logo' display setting</li>
3482 <li>Find shows blank dialog after 'finished searching' if
3483 nothing matches query</li>
3484 <li>Null Pointer Exceptions raised when sorting by
3485 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3487 <li>Errors in Jmol console when structures in alignment
3488 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3490 <li>Not all working JABAWS services are shown in
3492 <li>JAVAWS version of Jalview fails to launch with
3493 'invalid literal/length code'</li>
3494 <li>Annotation/RNA Helix colourschemes cannot be applied
3495 to alignment with groups (actually fixed in 2.8.0b1)</li>
3496 <li>RNA Helices and T-Coffee Scores available as default
3499 </ul> <em>Applet</em>
3501 <li>Remove group option is shown even when selection is
3503 <li>Apply to all groups ticked but colourscheme changes
3504 don't affect groups</li>
3505 <li>Documented RNA Helices and T-Coffee Scores as valid
3506 colourscheme name</li>
3507 <li>Annotation labels drawn on sequence IDs when
3508 Annotation panel is not displayed</li>
3509 <li>Increased font size for dropdown menus on OSX and
3510 embedded windows</li>
3511 </ul> <em>Other</em>
3513 <li>Consensus sequence for alignments/groups with a
3514 single sequence were not calculated</li>
3515 <li>annotation files that contain only groups imported as
3516 annotation and junk sequences</li>
3517 <li>Fasta files with sequences containing '*' incorrectly
3518 recognised as PFAM or BLC</li>
3519 <li>conservation/PID slider apply all groups option
3520 doesn't affect background (2.8.0b1)
3522 <li>redundancy highlighting is erratic at 0% and 100%</li>
3523 <li>Remove gapped columns fails for sequences with ragged
3525 <li>AMSA annotation row with leading spaces is not
3526 registered correctly on import</li>
3527 <li>Jalview crashes when selecting PCA analysis for
3528 certain alignments</li>
3529 <li>Opening the colour by annotation dialog for an
3530 existing annotation based 'use original colours'
3531 colourscheme loses original colours setting</li>
3536 <td><div align="center">
3537 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3538 <em>30/1/2014</em></strong>
3542 <li>Trusted certificates for JalviewLite applet and
3543 Jalview Desktop application<br />Certificate was donated by
3544 <a href="https://www.certum.eu">Certum</a> to the Jalview
3545 open source project).
3547 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3548 <li>Output in Stockholm format</li>
3549 <li>Allow import of data from gzipped files</li>
3550 <li>Export/import group and sequence associated line
3551 graph thresholds</li>
3552 <li>Nucleotide substitution matrix that supports RNA and
3553 ambiguity codes</li>
3554 <li>Allow disorder predictions to be made on the current
3555 selection (or visible selection) in the same way that JPred
3557 <li>Groovy scripting for headless Jalview operation</li>
3558 </ul> <em>Other improvements</em>
3560 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3561 <li>COMBINE statement uses current SEQUENCE_REF and
3562 GROUP_REF scope to group annotation rows</li>
3563 <li>Support '' style escaping of quotes in Newick
3565 <li>Group options for JABAWS service by command line name</li>
3566 <li>Empty tooltip shown for JABA service options with a
3567 link but no description</li>
3568 <li>Select primary source when selecting authority in
3569 database fetcher GUI</li>
3570 <li>Add .mfa to FASTA file extensions recognised by
3572 <li>Annotation label tooltip text wrap</li>
3577 <li>Slow scrolling when lots of annotation rows are
3579 <li>Lots of NPE (and slowness) after creating RNA
3580 secondary structure annotation line</li>
3581 <li>Sequence database accessions not imported when
3582 fetching alignments from Rfam</li>
3583 <li>Incorrect SHMR submission for sequences with
3585 <li>View all structures does not always superpose
3587 <li>Option widgets in service parameters not updated to
3588 reflect user or preset settings</li>
3589 <li>Null pointer exceptions for some services without
3590 presets or adjustable parameters</li>
3591 <li>Discover PDB IDs entry in structure menu doesn't
3592 discover PDB xRefs</li>
3593 <li>Exception encountered while trying to retrieve
3594 features with DAS</li>
3595 <li>Lowest value in annotation row isn't coloured
3596 when colour by annotation (per sequence) is coloured</li>
3597 <li>Keyboard mode P jumps to start of gapped region when
3598 residue follows a gap</li>
3599 <li>Jalview appears to hang importing an alignment with
3600 Wrap as default or after enabling Wrap</li>
3601 <li>'Right click to add annotations' message
3602 shown in wrap mode when no annotations present</li>
3603 <li>Disorder predictions fail with NPE if no automatic
3604 annotation already exists on alignment</li>
3605 <li>oninit javascript function should be called after
3606 initialisation completes</li>
3607 <li>Remove redundancy after disorder prediction corrupts
3608 alignment window display</li>
3609 <li>Example annotation file in documentation is invalid</li>
3610 <li>Grouped line graph annotation rows are not exported
3611 to annotation file</li>
3612 <li>Multi-harmony analysis cannot be run when only two
3614 <li>Cannot create multiple groups of line graphs with
3615 several 'combine' statements in annotation file</li>
3616 <li>Pressing return several times causes Number Format
3617 exceptions in keyboard mode</li>
3618 <li>Multi-harmony (SHMMR) method doesn't submit
3619 correct partitions for input data</li>
3620 <li>Translation from DNA to Amino Acids fails</li>
3621 <li>Jalview fail to load newick tree with quoted label</li>
3622 <li>--headless flag isn't understood</li>
3623 <li>ClassCastException when generating EPS in headless
3625 <li>Adjusting sequence-associated shading threshold only
3626 changes one row's threshold</li>
3627 <li>Preferences and Feature settings panel panel
3628 doesn't open</li>
3629 <li>hide consensus histogram also hides conservation and
3630 quality histograms</li>
3635 <td><div align="center">
3636 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3638 <td><em>Application</em>
3640 <li>Support for JABAWS 2.0 Services (AACon alignment
3641 conservation, protein disorder and Clustal Omega)</li>
3642 <li>JABAWS server status indicator in Web Services
3644 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3645 in Jalview alignment window</li>
3646 <li>Updated Jalview build and deploy framework for OSX
3647 mountain lion, windows 7, and 8</li>
3648 <li>Nucleotide substitution matrix for PCA that supports
3649 RNA and ambiguity codes</li>
3651 <li>Improved sequence database retrieval GUI</li>
3652 <li>Support fetching and database reference look up
3653 against multiple DAS sources (Fetch all from in 'fetch db
3655 <li>Jalview project improvements
3657 <li>Store and retrieve the 'belowAlignment'
3658 flag for annotation</li>
3659 <li>calcId attribute to group annotation rows on the
3661 <li>Store AACon calculation settings for a view in
3662 Jalview project</li>
3666 <li>horizontal scrolling gesture support</li>
3667 <li>Visual progress indicator when PCA calculation is
3669 <li>Simpler JABA web services menus</li>
3670 <li>visual indication that web service results are still
3671 being retrieved from server</li>
3672 <li>Serialise the dialogs that are shown when Jalview
3673 starts up for first time</li>
3674 <li>Jalview user agent string for interacting with HTTP
3676 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3678 <li>Examples directory and Groovy library included in
3679 InstallAnywhere distribution</li>
3680 </ul> <em>Applet</em>
3682 <li>RNA alignment and secondary structure annotation
3683 visualization applet example</li>
3684 </ul> <em>General</em>
3686 <li>Normalise option for consensus sequence logo</li>
3687 <li>Reset button in PCA window to return dimensions to
3689 <li>Allow seqspace or Jalview variant of alignment PCA
3691 <li>PCA with either nucleic acid and protein substitution
3693 <li>Allow windows containing HTML reports to be exported
3695 <li>Interactive display and editing of RNA secondary
3696 structure contacts</li>
3697 <li>RNA Helix Alignment Colouring</li>
3698 <li>RNA base pair logo consensus</li>
3699 <li>Parse sequence associated secondary structure
3700 information in Stockholm files</li>
3701 <li>HTML Export database accessions and annotation
3702 information presented in tooltip for sequences</li>
3703 <li>Import secondary structure from LOCARNA clustalw
3704 style RNA alignment files</li>
3705 <li>import and visualise T-COFFEE quality scores for an
3707 <li>'colour by annotation' per sequence option to
3708 shade each sequence according to its associated alignment
3710 <li>New Jalview Logo</li>
3711 </ul> <em>Documentation and Development</em>
3713 <li>documentation for score matrices used in Jalview</li>
3714 <li>New Website!</li>
3716 <td><em>Application</em>
3718 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3719 wsdbfetch REST service</li>
3720 <li>Stop windows being moved outside desktop on OSX</li>
3721 <li>Filetype associations not installed for webstart
3723 <li>Jalview does not always retrieve progress of a JABAWS
3724 job execution in full once it is complete</li>
3725 <li>revise SHMR RSBS definition to ensure alignment is
3726 uploaded via ali_file parameter</li>
3727 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3728 <li>View all structures superposed fails with exception</li>
3729 <li>Jnet job queues forever if a very short sequence is
3730 submitted for prediction</li>
3731 <li>Cut and paste menu not opened when mouse clicked on
3733 <li>Putting fractional value into integer text box in
3734 alignment parameter dialog causes Jalview to hang</li>
3735 <li>Structure view highlighting doesn't work on
3737 <li>View all structures fails with exception shown in
3739 <li>Characters in filename associated with PDBEntry not
3740 escaped in a platform independent way</li>
3741 <li>Jalview desktop fails to launch with exception when
3743 <li>Tree calculation reports 'you must have 2 or more
3744 sequences selected' when selection is empty</li>
3745 <li>Jalview desktop fails to launch with jar signature
3746 failure when java web start temporary file caching is
3748 <li>DAS Sequence retrieval with range qualification
3749 results in sequence xref which includes range qualification</li>
3750 <li>Errors during processing of command line arguments
3751 cause progress bar (JAL-898) to be removed</li>
3752 <li>Replace comma for semi-colon option not disabled for
3753 DAS sources in sequence fetcher</li>
3754 <li>Cannot close news reader when JABAWS server warning
3755 dialog is shown</li>
3756 <li>Option widgets not updated to reflect user settings</li>
3757 <li>Edited sequence not submitted to web service</li>
3758 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3759 <li>InstallAnywhere installer doesn't unpack and run
3760 on OSX Mountain Lion</li>
3761 <li>Annotation panel not given a scroll bar when
3762 sequences with alignment annotation are pasted into the
3764 <li>Sequence associated annotation rows not associated
3765 when loaded from Jalview project</li>
3766 <li>Browser launch fails with NPE on java 1.7</li>
3767 <li>JABAWS alignment marked as finished when job was
3768 cancelled or job failed due to invalid input</li>
3769 <li>NPE with v2.7 example when clicking on Tree
3770 associated with all views</li>
3771 <li>Exceptions when copy/paste sequences with grouped
3772 annotation rows to new window</li>
3773 </ul> <em>Applet</em>
3775 <li>Sequence features are momentarily displayed before
3776 they are hidden using hidefeaturegroups applet parameter</li>
3777 <li>loading features via javascript API automatically
3778 enables feature display</li>
3779 <li>scrollToColumnIn javascript API method doesn't
3781 </ul> <em>General</em>
3783 <li>Redundancy removal fails for rna alignment</li>
3784 <li>PCA calculation fails when sequence has been selected
3785 and then deselected</li>
3786 <li>PCA window shows grey box when first opened on OSX</li>
3787 <li>Letters coloured pink in sequence logo when alignment
3788 coloured with clustalx</li>
3789 <li>Choosing fonts without letter symbols defined causes
3790 exceptions and redraw errors</li>
3791 <li>Initial PCA plot view is not same as manually
3792 reconfigured view</li>
3793 <li>Grouped annotation graph label has incorrect line
3795 <li>Grouped annotation graph label display is corrupted
3796 for lots of labels</li>
3801 <div align="center">
3802 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3805 <td><em>Application</em>
3807 <li>Jalview Desktop News Reader</li>
3808 <li>Tweaked default layout of web services menu</li>
3809 <li>View/alignment association menu to enable user to
3810 easily specify which alignment a multi-structure view takes
3811 its colours/correspondences from</li>
3812 <li>Allow properties file location to be specified as URL</li>
3813 <li>Extend Jalview project to preserve associations
3814 between many alignment views and a single Jmol display</li>
3815 <li>Store annotation row height in Jalview project file</li>
3816 <li>Annotation row column label formatting attributes
3817 stored in project file</li>
3818 <li>Annotation row order for auto-calculated annotation
3819 rows preserved in Jalview project file</li>
3820 <li>Visual progress indication when Jalview state is
3821 saved using Desktop window menu</li>
3822 <li>Visual indication that command line arguments are
3823 still being processed</li>
3824 <li>Groovy script execution from URL</li>
3825 <li>Colour by annotation default min and max colours in
3827 <li>Automatically associate PDB files dragged onto an
3828 alignment with sequences that have high similarity and
3830 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3831 <li>'view structures' option to open many
3832 structures in same window</li>
3833 <li>Sort associated views menu option for tree panel</li>
3834 <li>Group all JABA and non-JABA services for a particular
3835 analysis function in its own submenu</li>
3836 </ul> <em>Applet</em>
3838 <li>Userdefined and autogenerated annotation rows for
3840 <li>Adjustment of alignment annotation pane height</li>
3841 <li>Annotation scrollbar for annotation panel</li>
3842 <li>Drag to reorder annotation rows in annotation panel</li>
3843 <li>'automaticScrolling' parameter</li>
3844 <li>Allow sequences with partial ID string matches to be
3845 annotated from GFF/Jalview features files</li>
3846 <li>Sequence logo annotation row in applet</li>
3847 <li>Absolute paths relative to host server in applet
3848 parameters are treated as such</li>
3849 <li>New in the JalviewLite javascript API:
3851 <li>JalviewLite.js javascript library</li>
3852 <li>Javascript callbacks for
3854 <li>Applet initialisation</li>
3855 <li>Sequence/alignment mouse-overs and selections</li>
3858 <li>scrollTo row and column alignment scrolling
3860 <li>Select sequence/alignment regions from javascript</li>
3861 <li>javascript structure viewer harness to pass
3862 messages between Jmol and Jalview when running as
3863 distinct applets</li>
3864 <li>sortBy method</li>
3865 <li>Set of applet and application examples shipped
3866 with documentation</li>
3867 <li>New example to demonstrate JalviewLite and Jmol
3868 javascript message exchange</li>
3870 </ul> <em>General</em>
3872 <li>Enable Jmol displays to be associated with multiple
3873 multiple alignments</li>
3874 <li>Option to automatically sort alignment with new tree</li>
3875 <li>User configurable link to enable redirects to a
3876 www.Jalview.org mirror</li>
3877 <li>Jmol colours option for Jmol displays</li>
3878 <li>Configurable newline string when writing alignment
3879 and other flat files</li>
3880 <li>Allow alignment annotation description lines to
3881 contain html tags</li>
3882 </ul> <em>Documentation and Development</em>
3884 <li>Add groovy test harness for bulk load testing to
3886 <li>Groovy script to load and align a set of sequences
3887 using a web service before displaying the result in the
3888 Jalview desktop</li>
3889 <li>Restructured javascript and applet api documentation</li>
3890 <li>Ant target to publish example html files with applet
3892 <li>Netbeans project for building Jalview from source</li>
3893 <li>ant task to create online javadoc for Jalview source</li>
3895 <td><em>Application</em>
3897 <li>User defined colourscheme throws exception when
3898 current built in colourscheme is saved as new scheme</li>
3899 <li>AlignFrame->Save in application pops up save
3900 dialog for valid filename/format</li>
3901 <li>Cannot view associated structure for UniProt sequence</li>
3902 <li>PDB file association breaks for UniProt sequence
3904 <li>Associate PDB from file dialog does not tell you
3905 which sequence is to be associated with the file</li>
3906 <li>Find All raises null pointer exception when query
3907 only matches sequence IDs</li>
3908 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3909 <li>Jalview project with Jmol views created with Jalview
3910 2.4 cannot be loaded</li>
3911 <li>Filetype associations not installed for webstart
3913 <li>Two or more chains in a single PDB file associated
3914 with sequences in different alignments do not get coloured
3915 by their associated sequence</li>
3916 <li>Visibility status of autocalculated annotation row
3917 not preserved when project is loaded</li>
3918 <li>Annotation row height and visibility attributes not
3919 stored in Jalview project</li>
3920 <li>Tree bootstraps are not preserved when saved as a
3921 Jalview project</li>
3922 <li>Envision2 workflow tooltips are corrupted</li>
3923 <li>Enabling show group conservation also enables colour
3924 by conservation</li>
3925 <li>Duplicate group associated conservation or consensus
3926 created on new view</li>
3927 <li>Annotation scrollbar not displayed after 'show
3928 all hidden annotation rows' option selected</li>
3929 <li>Alignment quality not updated after alignment
3930 annotation row is hidden then shown</li>
3931 <li>Preserve colouring of structures coloured by
3932 sequences in pre Jalview 2.7 projects</li>
3933 <li>Web service job parameter dialog is not laid out
3935 <li>Web services menu not refreshed after 'reset
3936 services' button is pressed in preferences</li>
3937 <li>Annotation off by one in Jalview v2_3 example project</li>
3938 <li>Structures imported from file and saved in project
3939 get name like jalview_pdb1234.txt when reloaded</li>
3940 <li>Jalview does not always retrieve progress of a JABAWS
3941 job execution in full once it is complete</li>
3942 </ul> <em>Applet</em>
3944 <li>Alignment height set incorrectly when lots of
3945 annotation rows are displayed</li>
3946 <li>Relative URLs in feature HTML text not resolved to
3948 <li>View follows highlighting does not work for positions
3950 <li><= shown as = in tooltip</li>
3951 <li>Export features raises exception when no features
3953 <li>Separator string used for serialising lists of IDs
3954 for javascript api is modified when separator string
3955 provided as parameter</li>
3956 <li>Null pointer exception when selecting tree leaves for
3957 alignment with no existing selection</li>
3958 <li>Relative URLs for datasources assumed to be relative
3959 to applet's codebase</li>
3960 <li>Status bar not updated after finished searching and
3961 search wraps around to first result</li>
3962 <li>StructureSelectionManager instance shared between
3963 several Jalview applets causes race conditions and memory
3965 <li>Hover tooltip and mouseover of position on structure
3966 not sent from Jmol in applet</li>
3967 <li>Certain sequences of javascript method calls to
3968 applet API fatally hang browser</li>
3969 </ul> <em>General</em>
3971 <li>View follows structure mouseover scrolls beyond
3972 position with wrapped view and hidden regions</li>
3973 <li>Find sequence position moves to wrong residue
3974 with/without hidden columns</li>
3975 <li>Sequence length given in alignment properties window
3977 <li>InvalidNumberFormat exceptions thrown when trying to
3978 import PDB like structure files</li>
3979 <li>Positional search results are only highlighted
3980 between user-supplied sequence start/end bounds</li>
3981 <li>End attribute of sequence is not validated</li>
3982 <li>Find dialog only finds first sequence containing a
3983 given sequence position</li>
3984 <li>Sequence numbering not preserved in MSF alignment
3986 <li>Jalview PDB file reader does not extract sequence
3987 from nucleotide chains correctly</li>
3988 <li>Structure colours not updated when tree partition
3989 changed in alignment</li>
3990 <li>Sequence associated secondary structure not correctly
3991 parsed in interleaved stockholm</li>
3992 <li>Colour by annotation dialog does not restore current
3994 <li>Hiding (nearly) all sequences doesn't work
3996 <li>Sequences containing lowercase letters are not
3997 properly associated with their pdb files</li>
3998 </ul> <em>Documentation and Development</em>
4000 <li>schemas/JalviewWsParamSet.xsd corrupted by
4001 ApplyCopyright tool</li>
4006 <div align="center">
4007 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4010 <td><em>Application</em>
4012 <li>New warning dialog when the Jalview Desktop cannot
4013 contact web services</li>
4014 <li>JABA service parameters for a preset are shown in
4015 service job window</li>
4016 <li>JABA Service menu entries reworded</li>
4020 <li>Modeller PIR IO broken - cannot correctly import a
4021 pir file emitted by Jalview</li>
4022 <li>Existing feature settings transferred to new
4023 alignment view created from cut'n'paste</li>
4024 <li>Improved test for mixed amino/nucleotide chains when
4025 parsing PDB files</li>
4026 <li>Consensus and conservation annotation rows
4027 occasionally become blank for all new windows</li>
4028 <li>Exception raised when right clicking above sequences
4029 in wrapped view mode</li>
4030 </ul> <em>Application</em>
4032 <li>multiple multiply aligned structure views cause cpu
4033 usage to hit 100% and computer to hang</li>
4034 <li>Web Service parameter layout breaks for long user
4035 parameter names</li>
4036 <li>Jaba service discovery hangs desktop if Jaba server
4043 <div align="center">
4044 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4047 <td><em>Application</em>
4049 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4050 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4053 <li>Web Services preference tab</li>
4054 <li>Analysis parameters dialog box and user defined
4056 <li>Improved speed and layout of Envision2 service menu</li>
4057 <li>Superpose structures using associated sequence
4059 <li>Export coordinates and projection as CSV from PCA
4061 </ul> <em>Applet</em>
4063 <li>enable javascript: execution by the applet via the
4064 link out mechanism</li>
4065 </ul> <em>Other</em>
4067 <li>Updated the Jmol Jalview interface to work with Jmol
4069 <li>The Jalview Desktop and JalviewLite applet now
4070 require Java 1.5</li>
4071 <li>Allow Jalview feature colour specification for GFF
4072 sequence annotation files</li>
4073 <li>New 'colour by label' keword in Jalview feature file
4074 type colour specification</li>
4075 <li>New Jalview Desktop Groovy API method that allows a
4076 script to check if it being run in an interactive session or
4077 in a batch operation from the Jalview command line</li>
4081 <li>clustalx colourscheme colours Ds preferentially when
4082 both D+E are present in over 50% of the column</li>
4083 </ul> <em>Application</em>
4085 <li>typo in AlignmentFrame->View->Hide->all but
4086 selected Regions menu item</li>
4087 <li>sequence fetcher replaces ',' for ';' when the ',' is
4088 part of a valid accession ID</li>
4089 <li>fatal OOM if object retrieved by sequence fetcher
4090 runs out of memory</li>
4091 <li>unhandled Out of Memory Error when viewing pca
4092 analysis results</li>
4093 <li>InstallAnywhere builds fail to launch on OS X java
4094 10.5 update 4 (due to apple Java 1.6 update)</li>
4095 <li>Installanywhere Jalview silently fails to launch</li>
4096 </ul> <em>Applet</em>
4098 <li>Jalview.getFeatureGroups() raises an
4099 ArrayIndexOutOfBoundsException if no feature groups are
4106 <div align="center">
4107 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4113 <li>Alignment prettyprinter doesn't cope with long
4115 <li>clustalx colourscheme colours Ds preferentially when
4116 both D+E are present in over 50% of the column</li>
4117 <li>nucleic acid structures retrieved from PDB do not
4118 import correctly</li>
4119 <li>More columns get selected than were clicked on when a
4120 number of columns are hidden</li>
4121 <li>annotation label popup menu not providing correct
4122 add/hide/show options when rows are hidden or none are
4124 <li>Stockholm format shown in list of readable formats,
4125 and parser copes better with alignments from RFAM.</li>
4126 <li>CSV output of consensus only includes the percentage
4127 of all symbols if sequence logo display is enabled</li>
4129 </ul> <em>Applet</em>
4131 <li>annotation panel disappears when annotation is
4133 </ul> <em>Application</em>
4135 <li>Alignment view not redrawn properly when new
4136 alignment opened where annotation panel is visible but no
4137 annotations are present on alignment</li>
4138 <li>pasted region containing hidden columns is
4139 incorrectly displayed in new alignment window</li>
4140 <li>Jalview slow to complete operations when stdout is
4141 flooded (fix is to close the Jalview console)</li>
4142 <li>typo in AlignmentFrame->View->Hide->all but
4143 selected Rregions menu item.</li>
4144 <li>inconsistent group submenu and Format submenu entry
4145 'Un' or 'Non'conserved</li>
4146 <li>Sequence feature settings are being shared by
4147 multiple distinct alignments</li>
4148 <li>group annotation not recreated when tree partition is
4150 <li>double click on group annotation to select sequences
4151 does not propagate to associated trees</li>
4152 <li>Mac OSX specific issues:
4154 <li>exception raised when mouse clicked on desktop
4155 window background</li>
4156 <li>Desktop menu placed on menu bar and application
4157 name set correctly</li>
4158 <li>sequence feature settings not wide enough for the
4159 save feature colourscheme button</li>
4168 <div align="center">
4169 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4172 <td><em>New Capabilities</em>
4174 <li>URL links generated from description line for
4175 regular-expression based URL links (applet and application)
4177 <li>Non-positional feature URL links are shown in link
4179 <li>Linked viewing of nucleic acid sequences and
4181 <li>Automatic Scrolling option in View menu to display
4182 the currently highlighted region of an alignment.</li>
4183 <li>Order an alignment by sequence length, or using the
4184 average score or total feature count for each sequence.</li>
4185 <li>Shading features by score or associated description</li>
4186 <li>Subdivide alignment and groups based on identity of
4187 selected subsequence (Make Groups from Selection).</li>
4188 <li>New hide/show options including Shift+Control+H to
4189 hide everything but the currently selected region.</li>
4190 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4191 </ul> <em>Application</em>
4193 <li>Fetch DB References capabilities and UI expanded to
4194 support retrieval from DAS sequence sources</li>
4195 <li>Local DAS Sequence sources can be added via the
4196 command line or via the Add local source dialog box.</li>
4197 <li>DAS Dbref and DbxRef feature types are parsed as
4198 database references and protein_name is parsed as
4199 description line (BioSapiens terms).</li>
4200 <li>Enable or disable non-positional feature and database
4201 references in sequence ID tooltip from View menu in
4203 <!-- <li>New hidden columns and rows and representatives capabilities
4204 in annotations file (in progress - not yet fully implemented)</li> -->
4205 <li>Group-associated consensus, sequence logos and
4206 conservation plots</li>
4207 <li>Symbol distributions for each column can be exported
4208 and visualized as sequence logos</li>
4209 <li>Optionally scale multi-character column labels to fit
4210 within each column of annotation row<!-- todo for applet -->
4212 <li>Optional automatic sort of associated alignment view
4213 when a new tree is opened.</li>
4214 <li>Jalview Java Console</li>
4215 <li>Better placement of desktop window when moving
4216 between different screens.</li>
4217 <li>New preference items for sequence ID tooltip and
4218 consensus annotation</li>
4219 <li>Client to submit sequences and IDs to Envision2
4221 <li><em>Vamsas Capabilities</em>
4223 <li>Improved VAMSAS synchronization (Jalview archive
4224 used to preserve views, structures, and tree display
4226 <li>Import of vamsas documents from disk or URL via
4228 <li>Sharing of selected regions between views and
4229 with other VAMSAS applications (Experimental feature!)</li>
4230 <li>Updated API to VAMSAS version 0.2</li>
4232 </ul> <em>Applet</em>
4234 <li>Middle button resizes annotation row height</li>
4237 <li>sortByTree (true/false) - automatically sort the
4238 associated alignment view by the tree when a new tree is
4240 <li>showTreeBootstraps (true/false) - show or hide
4241 branch bootstraps (default is to show them if available)</li>
4242 <li>showTreeDistances (true/false) - show or hide
4243 branch lengths (default is to show them if available)</li>
4244 <li>showUnlinkedTreeNodes (true/false) - indicate if
4245 unassociated nodes should be highlighted in the tree
4247 <li>heightScale and widthScale (1.0 or more) -
4248 increase the height or width of a cell in the alignment
4249 grid relative to the current font size.</li>
4252 <li>Non-positional features displayed in sequence ID
4254 </ul> <em>Other</em>
4256 <li>Features format: graduated colour definitions and
4257 specification of feature scores</li>
4258 <li>Alignment Annotations format: new keywords for group
4259 associated annotation (GROUP_REF) and annotation row display
4260 properties (ROW_PROPERTIES)</li>
4261 <li>XML formats extended to support graduated feature
4262 colourschemes, group associated annotation, and profile
4263 visualization settings.</li></td>
4266 <li>Source field in GFF files parsed as feature source
4267 rather than description</li>
4268 <li>Non-positional features are now included in sequence
4269 feature and gff files (controlled via non-positional feature
4270 visibility in tooltip).</li>
4271 <li>URL links generated for all feature links (bugfix)</li>
4272 <li>Added URL embedding instructions to features file
4274 <li>Codons containing ambiguous nucleotides translated as
4275 'X' in peptide product</li>
4276 <li>Match case switch in find dialog box works for both
4277 sequence ID and sequence string and query strings do not
4278 have to be in upper case to match case-insensitively.</li>
4279 <li>AMSA files only contain first column of
4280 multi-character column annotation labels</li>
4281 <li>Jalview Annotation File generation/parsing consistent
4282 with documentation (e.g. Stockholm annotation can be
4283 exported and re-imported)</li>
4284 <li>PDB files without embedded PDB IDs given a friendly
4286 <li>Find incrementally searches ID string matches as well
4287 as subsequence matches, and correctly reports total number
4291 <li>Better handling of exceptions during sequence
4293 <li>Dasobert generated non-positional feature URL
4294 link text excludes the start_end suffix</li>
4295 <li>DAS feature and source retrieval buttons disabled
4296 when fetch or registry operations in progress.</li>
4297 <li>PDB files retrieved from URLs are cached properly</li>
4298 <li>Sequence description lines properly shared via
4300 <li>Sequence fetcher fetches multiple records for all
4302 <li>Ensured that command line das feature retrieval
4303 completes before alignment figures are generated.</li>
4304 <li>Reduced time taken when opening file browser for
4306 <li>isAligned check prior to calculating tree, PCA or
4307 submitting an MSA to JNet now excludes hidden sequences.</li>
4308 <li>User defined group colours properly recovered
4309 from Jalview projects.</li>
4318 <div align="center">
4319 <strong>2.4.0.b2</strong><br> 28/10/2009
4324 <li>Experimental support for google analytics usage
4326 <li>Jalview privacy settings (user preferences and docs).</li>
4331 <li>Race condition in applet preventing startup in
4333 <li>Exception when feature created from selection beyond
4334 length of sequence.</li>
4335 <li>Allow synthetic PDB files to be imported gracefully</li>
4336 <li>Sequence associated annotation rows associate with
4337 all sequences with a given id</li>
4338 <li>Find function matches case-insensitively for sequence
4339 ID string searches</li>
4340 <li>Non-standard characters do not cause pairwise
4341 alignment to fail with exception</li>
4342 </ul> <em>Application Issues</em>
4344 <li>Sequences are now validated against EMBL database</li>
4345 <li>Sequence fetcher fetches multiple records for all
4347 </ul> <em>InstallAnywhere Issues</em>
4349 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4350 issue with installAnywhere mechanism)</li>
4351 <li>Command line launching of JARs from InstallAnywhere
4352 version (java class versioning error fixed)</li>
4359 <div align="center">
4360 <strong>2.4</strong><br> 27/8/2008
4363 <td><em>User Interface</em>
4365 <li>Linked highlighting of codon and amino acid from
4366 translation and protein products</li>
4367 <li>Linked highlighting of structure associated with
4368 residue mapping to codon position</li>
4369 <li>Sequence Fetcher provides example accession numbers
4370 and 'clear' button</li>
4371 <li>MemoryMonitor added as an option under Desktop's
4373 <li>Extract score function to parse whitespace separated
4374 numeric data in description line</li>
4375 <li>Column labels in alignment annotation can be centred.</li>
4376 <li>Tooltip for sequence associated annotation give name
4378 </ul> <em>Web Services and URL fetching</em>
4380 <li>JPred3 web service</li>
4381 <li>Prototype sequence search client (no public services
4383 <li>Fetch either seed alignment or full alignment from
4385 <li>URL Links created for matching database cross
4386 references as well as sequence ID</li>
4387 <li>URL Links can be created using regular-expressions</li>
4388 </ul> <em>Sequence Database Connectivity</em>
4390 <li>Retrieval of cross-referenced sequences from other
4392 <li>Generalised database reference retrieval and
4393 validation to all fetchable databases</li>
4394 <li>Fetch sequences from DAS sources supporting the
4395 sequence command</li>
4396 </ul> <em>Import and Export</em>
4397 <li>export annotation rows as CSV for spreadsheet import</li>
4398 <li>Jalview projects record alignment dataset associations,
4399 EMBL products, and cDNA sequence mappings</li>
4400 <li>Sequence Group colour can be specified in Annotation
4402 <li>Ad-hoc colouring of group in Annotation File using RGB
4403 triplet as name of colourscheme</li>
4404 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4406 <li>treenode binding for VAMSAS tree exchange</li>
4407 <li>local editing and update of sequences in VAMSAS
4408 alignments (experimental)</li>
4409 <li>Create new or select existing session to join</li>
4410 <li>load and save of vamsas documents</li>
4411 </ul> <em>Application command line</em>
4413 <li>-tree parameter to open trees (introduced for passing
4415 <li>-fetchfrom command line argument to specify nicknames
4416 of DAS servers to query for alignment features</li>
4417 <li>-dasserver command line argument to add new servers
4418 that are also automatically queried for features</li>
4419 <li>-groovy command line argument executes a given groovy
4420 script after all input data has been loaded and parsed</li>
4421 </ul> <em>Applet-Application data exchange</em>
4423 <li>Trees passed as applet parameters can be passed to
4424 application (when using "View in full
4425 application")</li>
4426 </ul> <em>Applet Parameters</em>
4428 <li>feature group display control parameter</li>
4429 <li>debug parameter</li>
4430 <li>showbutton parameter</li>
4431 </ul> <em>Applet API methods</em>
4433 <li>newView public method</li>
4434 <li>Window (current view) specific get/set public methods</li>
4435 <li>Feature display control methods</li>
4436 <li>get list of currently selected sequences</li>
4437 </ul> <em>New Jalview distribution features</em>
4439 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4440 <li>RELEASE file gives build properties for the latest
4441 Jalview release.</li>
4442 <li>Java 1.1 Applet build made easier and donotobfuscate
4443 property controls execution of obfuscator</li>
4444 <li>Build target for generating source distribution</li>
4445 <li>Debug flag for javacc</li>
4446 <li>.jalview_properties file is documented (slightly) in
4447 jalview.bin.Cache</li>
4448 <li>Continuous Build Integration for stable and
4449 development version of Application, Applet and source
4454 <li>selected region output includes visible annotations
4455 (for certain formats)</li>
4456 <li>edit label/displaychar contains existing label/char
4458 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4459 <li>shorter peptide product names from EMBL records</li>
4460 <li>Newick string generator makes compact representations</li>
4461 <li>bootstrap values parsed correctly for tree files with
4463 <li>pathological filechooser bug avoided by not allowing
4464 filenames containing a ':'</li>
4465 <li>Fixed exception when parsing GFF files containing
4466 global sequence features</li>
4467 <li>Alignment datasets are finalized only when number of
4468 references from alignment sequences goes to zero</li>
4469 <li>Close of tree branch colour box without colour
4470 selection causes cascading exceptions</li>
4471 <li>occasional negative imgwidth exceptions</li>
4472 <li>better reporting of non-fatal warnings to user when
4473 file parsing fails.</li>
4474 <li>Save works when Jalview project is default format</li>
4475 <li>Save as dialog opened if current alignment format is
4476 not a valid output format</li>
4477 <li>UniProt canonical names introduced for both das and
4479 <li>Histidine should be midblue (not pink!) in Zappo</li>
4480 <li>error messages passed up and output when data read
4482 <li>edit undo recovers previous dataset sequence when
4483 sequence is edited</li>
4484 <li>allow PDB files without pdb ID HEADER lines (like
4485 those generated by MODELLER) to be read in properly</li>
4486 <li>allow reading of JPred concise files as a normal
4488 <li>Stockholm annotation parsing and alignment properties
4489 import fixed for PFAM records</li>
4490 <li>Structure view windows have correct name in Desktop
4492 <li>annotation consisting of sequence associated scores
4493 can be read and written correctly to annotation file</li>
4494 <li>Aligned cDNA translation to aligned peptide works
4496 <li>Fixed display of hidden sequence markers and
4497 non-italic font for representatives in Applet</li>
4498 <li>Applet Menus are always embedded in applet window on
4500 <li>Newly shown features appear at top of stack (in
4502 <li>Annotations added via parameter not drawn properly
4503 due to null pointer exceptions</li>
4504 <li>Secondary structure lines are drawn starting from
4505 first column of alignment</li>
4506 <li>UniProt XML import updated for new schema release in
4508 <li>Sequence feature to sequence ID match for Features
4509 file is case-insensitive</li>
4510 <li>Sequence features read from Features file appended to
4511 all sequences with matching IDs</li>
4512 <li>PDB structure coloured correctly for associated views
4513 containing a sub-sequence</li>
4514 <li>PDB files can be retrieved by applet from Jar files</li>
4515 <li>feature and annotation file applet parameters
4516 referring to different directories are retrieved correctly</li>
4517 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4518 <li>Fixed application hang whilst waiting for
4519 splash-screen version check to complete</li>
4520 <li>Applet properly URLencodes input parameter values
4521 when passing them to the launchApp service</li>
4522 <li>display name and local features preserved in results
4523 retrieved from web service</li>
4524 <li>Visual delay indication for sequence retrieval and
4525 sequence fetcher initialisation</li>
4526 <li>updated Application to use DAS 1.53e version of
4527 dasobert DAS client</li>
4528 <li>Re-instated Full AMSA support and .amsa file
4530 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4538 <div align="center">
4539 <strong>2.3</strong><br> 9/5/07
4544 <li>Jmol 11.0.2 integration</li>
4545 <li>PDB views stored in Jalview XML files</li>
4546 <li>Slide sequences</li>
4547 <li>Edit sequence in place</li>
4548 <li>EMBL CDS features</li>
4549 <li>DAS Feature mapping</li>
4550 <li>Feature ordering</li>
4551 <li>Alignment Properties</li>
4552 <li>Annotation Scores</li>
4553 <li>Sort by scores</li>
4554 <li>Feature/annotation editing in applet</li>
4559 <li>Headless state operation in 2.2.1</li>
4560 <li>Incorrect and unstable DNA pairwise alignment</li>
4561 <li>Cut and paste of sequences with annotation</li>
4562 <li>Feature group display state in XML</li>
4563 <li>Feature ordering in XML</li>
4564 <li>blc file iteration selection using filename # suffix</li>
4565 <li>Stockholm alignment properties</li>
4566 <li>Stockhom alignment secondary structure annotation</li>
4567 <li>2.2.1 applet had no feature transparency</li>
4568 <li>Number pad keys can be used in cursor mode</li>
4569 <li>Structure Viewer mirror image resolved</li>
4576 <div align="center">
4577 <strong>2.2.1</strong><br> 12/2/07
4582 <li>Non standard characters can be read and displayed
4583 <li>Annotations/Features can be imported/exported to the
4585 <li>Applet allows editing of sequence/annotation/group
4586 name & description
4587 <li>Preference setting to display sequence name in
4589 <li>Annotation file format extended to allow
4590 Sequence_groups to be defined
4591 <li>Default opening of alignment overview panel can be
4592 specified in preferences
4593 <li>PDB residue numbering annotation added to associated
4599 <li>Applet crash under certain Linux OS with Java 1.6
4601 <li>Annotation file export / import bugs fixed
4602 <li>PNG / EPS image output bugs fixed
4608 <div align="center">
4609 <strong>2.2</strong><br> 27/11/06
4614 <li>Multiple views on alignment
4615 <li>Sequence feature editing
4616 <li>"Reload" alignment
4617 <li>"Save" to current filename
4618 <li>Background dependent text colour
4619 <li>Right align sequence ids
4620 <li>User-defined lower case residue colours
4623 <li>Menu item accelerator keys
4624 <li>Control-V pastes to current alignment
4625 <li>Cancel button for DAS Feature Fetching
4626 <li>PCA and PDB Viewers zoom via mouse roller
4627 <li>User-defined sub-tree colours and sub-tree selection
4629 <li>'New Window' button on the 'Output to Text box'
4634 <li>New memory efficient Undo/Redo System
4635 <li>Optimised symbol lookups and conservation/consensus
4637 <li>Region Conservation/Consensus recalculated after
4639 <li>Fixed Remove Empty Columns Bug (empty columns at end
4641 <li>Slowed DAS Feature Fetching for increased robustness.
4643 <li>Made angle brackets in ASCII feature descriptions
4645 <li>Re-instated Zoom function for PCA
4646 <li>Sequence descriptions conserved in web service
4648 <li>UniProt ID discoverer uses any word separated by
4650 <li>WsDbFetch query/result association resolved
4651 <li>Tree leaf to sequence mapping improved
4652 <li>Smooth fonts switch moved to FontChooser dialog box.
4659 <div align="center">
4660 <strong>2.1.1</strong><br> 12/9/06
4665 <li>Copy consensus sequence to clipboard</li>
4670 <li>Image output - rightmost residues are rendered if
4671 sequence id panel has been resized</li>
4672 <li>Image output - all offscreen group boundaries are
4674 <li>Annotation files with sequence references - all
4675 elements in file are relative to sequence position</li>
4676 <li>Mac Applet users can use Alt key for group editing</li>
4682 <div align="center">
4683 <strong>2.1</strong><br> 22/8/06
4688 <li>MAFFT Multiple Alignment in default Web Service list</li>
4689 <li>DAS Feature fetching</li>
4690 <li>Hide sequences and columns</li>
4691 <li>Export Annotations and Features</li>
4692 <li>GFF file reading / writing</li>
4693 <li>Associate structures with sequences from local PDB
4695 <li>Add sequences to exisiting alignment</li>
4696 <li>Recently opened files / URL lists</li>
4697 <li>Applet can launch the full application</li>
4698 <li>Applet has transparency for features (Java 1.2
4700 <li>Applet has user defined colours parameter</li>
4701 <li>Applet can load sequences from parameter
4702 "sequence<em>x</em>"
4708 <li>Redundancy Panel reinstalled in the Applet</li>
4709 <li>Monospaced font - EPS / rescaling bug fixed</li>
4710 <li>Annotation files with sequence references bug fixed</li>
4716 <div align="center">
4717 <strong>2.08.1</strong><br> 2/5/06
4722 <li>Change case of selected region from Popup menu</li>
4723 <li>Choose to match case when searching</li>
4724 <li>Middle mouse button and mouse movement can compress /
4725 expand the visible width and height of the alignment</li>
4730 <li>Annotation Panel displays complete JNet results</li>
4736 <div align="center">
4737 <strong>2.08b</strong><br> 18/4/06
4743 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4744 <li>Righthand label on wrapped alignments shows correct
4751 <div align="center">
4752 <strong>2.08</strong><br> 10/4/06
4757 <li>Editing can be locked to the selection area</li>
4758 <li>Keyboard editing</li>
4759 <li>Create sequence features from searches</li>
4760 <li>Precalculated annotations can be loaded onto
4762 <li>Features file allows grouping of features</li>
4763 <li>Annotation Colouring scheme added</li>
4764 <li>Smooth fonts off by default - Faster rendering</li>
4765 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4770 <li>Drag & Drop fixed on Linux</li>
4771 <li>Jalview Archive file faster to load/save, sequence
4772 descriptions saved.</li>
4778 <div align="center">
4779 <strong>2.07</strong><br> 12/12/05
4784 <li>PDB Structure Viewer enhanced</li>
4785 <li>Sequence Feature retrieval and display enhanced</li>
4786 <li>Choose to output sequence start-end after sequence
4787 name for file output</li>
4788 <li>Sequence Fetcher WSDBFetch@EBI</li>
4789 <li>Applet can read feature files, PDB files and can be
4790 used for HTML form input</li>
4795 <li>HTML output writes groups and features</li>
4796 <li>Group editing is Control and mouse click</li>
4797 <li>File IO bugs</li>
4803 <div align="center">
4804 <strong>2.06</strong><br> 28/9/05
4809 <li>View annotations in wrapped mode</li>
4810 <li>More options for PCA viewer</li>
4815 <li>GUI bugs resolved</li>
4816 <li>Runs with -nodisplay from command line</li>
4822 <div align="center">
4823 <strong>2.05b</strong><br> 15/9/05
4828 <li>Choose EPS export as lineart or text</li>
4829 <li>Jar files are executable</li>
4830 <li>Can read in Uracil - maps to unknown residue</li>
4835 <li>Known OutOfMemory errors give warning message</li>
4836 <li>Overview window calculated more efficiently</li>
4837 <li>Several GUI bugs resolved</li>
4843 <div align="center">
4844 <strong>2.05</strong><br> 30/8/05
4849 <li>Edit and annotate in "Wrapped" view</li>
4854 <li>Several GUI bugs resolved</li>
4860 <div align="center">
4861 <strong>2.04</strong><br> 24/8/05
4866 <li>Hold down mouse wheel & scroll to change font
4872 <li>Improved JPred client reliability</li>
4873 <li>Improved loading of Jalview files</li>
4879 <div align="center">
4880 <strong>2.03</strong><br> 18/8/05
4885 <li>Set Proxy server name and port in preferences</li>
4886 <li>Multiple URL links from sequence ids</li>
4887 <li>User Defined Colours can have a scheme name and added
4889 <li>Choose to ignore gaps in consensus calculation</li>
4890 <li>Unix users can set default web browser</li>
4891 <li>Runs without GUI for batch processing</li>
4892 <li>Dynamically generated Web Service Menus</li>
4897 <li>InstallAnywhere download for Sparc Solaris</li>
4903 <div align="center">
4904 <strong>2.02</strong><br> 18/7/05
4910 <li>Copy & Paste order of sequences maintains
4911 alignment order.</li>
4917 <div align="center">
4918 <strong>2.01</strong><br> 12/7/05
4923 <li>Use delete key for deleting selection.</li>
4924 <li>Use Mouse wheel to scroll sequences.</li>
4925 <li>Help file updated to describe how to add alignment
4927 <li>Version and build date written to build properties
4929 <li>InstallAnywhere installation will check for updates
4930 at launch of Jalview.</li>
4935 <li>Delete gaps bug fixed.</li>
4936 <li>FileChooser sorts columns.</li>
4937 <li>Can remove groups one by one.</li>
4938 <li>Filechooser icons installed.</li>
4939 <li>Finder ignores return character when searching.
4940 Return key will initiate a search.<br>
4947 <div align="center">
4948 <strong>2.0</strong><br> 20/6/05
4953 <li>New codebase</li>