3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>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-3493 -->Escape does not clear highlights on the
126 alignment (Since Jalview 2.10.3)
129 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
130 doesn't slide selected sequences, just sequence under cursor
133 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
134 multiple EMBL gene products shown forĀ a single contig
137 <!-- JAL-3696 -->Errors encountered when processing variants
138 from VCF files yield "Error processing VCF: Format specifier
142 <!-- JAL-3697 -->Count of features not shown can be wrong
143 when there are both local and complementary features mapped
144 to the position under the cursor
147 <!-- JAL-3673 -->Sequence ID for reference sequence is
148 clipped when Right align Sequence IDs enabled
151 <!-- JAL-2983 -->Slider with negative range values not
152 rendered correctly in VAqua4 (Since 2.10.4)
155 <!-- JAL-3685 -->Single quotes not displayed correctly in
156 internationalised text for some messages and log output
159 <!-- JAL-3490 -->Find doesn't report matches that span
160 hidden gapped columns
163 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
164 panels, Alignment viewport and annotation renderer.
166 </ul> <em>Developing Jalview</em>
169 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
170 data, causing cloverReport gradle task to fail with an
173 </ul> <em>New Known defects</em>
176 <!-- JAL-3576 -->Co-located features exported and re-imported
177 are ordered differently when shown on alignment and in
178 tooltips. (Also affects v2.11.1.0)
181 <!-- JAL-3667 -->Windows 10: For a minority of users, if
182 backups are not enabled, Jalview sometimes fails to
183 overwrite an existing file and raises a warning dialog.
184 Workaround is to try to save the file again, and if that
185 fails, delete the original file and save in place.
188 <!-- JAL-3701 -->Stale build data in jalview standalone jar
189 builds (only affects 2.11.1.1 branch)
195 <td width="60" align="center" nowrap><strong><a
196 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
197 <em>22/04/2020</em></strong></td>
198 <td align="left" valign="top">
201 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
202 'virtual' codon features shown on protein (or vice versa)
203 for display in alignments, on structure views (including
204 transfer to UCSF chimera), in feature reports and for
208 <!-- JAL-3121 -->Feature attributes from VCF files can be
209 exported and re-imported as GFF3 files
212 <!-- JAL-3376 -->Capture VCF "fixed column" values
213 POS, ID, QUAL, FILTER as Feature Attributes
216 <!-- JAL-3375 -->More robust VCF numeric data field
217 validation while parsing
220 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
224 <!-- JAL-3535 -->Feature Settings dialog title includes name
228 <!-- JAL-3538 -->Font anti-aliasing in alignment views
232 <!-- JAL-3468 -->Very long feature descriptions truncated in
236 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
237 with no feature types visible
240 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
242 </ul><em>Jalview Installer</em>
245 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
246 in console (may be null when Jalview launched as executable jar or via conda)
249 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
252 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
255 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
257 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
258 </ul> <em>Release processes</em>
261 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
264 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
266 </ul> <em>Build System</em>
269 <!-- JAL-3510 -->Clover updated to 4.4.1
272 <!-- JAL-3513 -->Test code included in Clover coverage
276 <em>Groovy Scripts</em>
279 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
280 to stdout containing the consensus sequence for each
281 alignment in a Jalview session
284 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
285 genomic sequence_variant annotation from CDS as
286 missense_variant or synonymous_variant on protein products.
290 <td align="left" valign="top">
293 <!-- JAL-3581 -->Hidden sequence markers still visible when
294 'Show hidden markers' option is not ticked
297 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
298 PNG output when 'Automatically set ID width' is set in
299 jalview preferences or properties file
302 <!-- JAL-3571 -->Feature Editor dialog can be opened when
303 'Show Sequence Features' option is not ticked
306 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
307 buttons in Feature Settings dialog are clicked when no
311 <!-- JAL-3412 -->ID margins for CDS and Protein views not
312 equal when split frame is first opened
315 <!-- JAL-3296 -->Sequence position numbers in status bar not
316 correct after editing a sequence's start position
319 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
320 with annotation and exceptions thrown when only a few
321 columns shown in wrapped mode
324 <!-- JAL-3386 -->Sequence IDs missing in headless export of
325 wrapped alignment figure with annotations
328 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
329 ID fails with ClassCastException
332 <!-- JAL-3389 -->Chimera session not restored from Jalview
336 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
337 feature settings dialog also selects columns
340 <!-- JAL-3473 -->SpinnerNumberModel causes
341 IllegalArgumentException in some circumstances
344 <!-- JAL-3534 -->Multiple feature settings dialogs can be
348 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
349 alignment window is closed
352 <!-- JAL-3406 -->Credits missing some authors in Jalview
353 help documentation for 2.11.0 release
356 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
357 includes Pfam ID as sequence's accession rather than its
360 </ul> <em>Java 11 Compatibility issues</em>
363 <!-- JAL-2987 -->OSX - Can't view some search results in
364 PDB/Uniprot search panel
366 </ul> <em>Installer</em>
369 <!-- JAL-3447 -->Jalview should not create file associations
370 for 3D structure files (.pdb, .mmcif. .cif)
372 </ul> <em>Repository and Source Release</em>
375 <!-- JAL-3474 -->removed obsolete .cvsignore files from
379 <!-- JAL-3541 -->Clover report generation running out of
382 </ul> <em>New Known Issues</em>
385 <!-- JAL-3523 -->OSX - Current working directory not
386 preserved when Jalview.app launched with parameters from
390 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
391 clipped in headless figure export when Right Align option
395 <!-- JAL-3542 -->Jalview Installation type always reports
396 'Source' in console output
399 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
400 bamboo server but run fine locally.
406 <td width="60" align="center" nowrap>
407 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
408 <em>04/07/2019</em></strong>
410 <td align="left" valign="top">
413 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
414 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
415 source project) rather than InstallAnywhere
418 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
419 settings, receive over the air updates and launch specific
420 versions via (<a href="https://github.com/threerings/getdown">Three
424 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
425 formats supported by Jalview (including .jvp project files)
428 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
429 arguments and switch between different getdown channels
432 <!-- JAL-3141 -->Backup files created when saving Jalview project
437 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
438 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
440 <!-- JAL-2620 -->Alternative genetic code tables for
441 'Translate as cDNA'</li>
443 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
444 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
447 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
448 implementation that allows updates) used for Sequence Feature collections</li>
450 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
451 features can be filtered and shaded according to any
452 associated attributes (e.g. variant attributes from VCF
453 file, or key-value pairs imported from column 9 of GFF
457 <!-- JAL-2879 -->Feature Attributes and shading schemes
458 stored and restored from Jalview Projects
461 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
462 recognise variant features
465 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
466 sequences (also coloured red by default)
469 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
473 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
474 algorithm (Z-sort/transparency and filter aware)
477 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
483 <!-- JAL-3205 -->Symmetric score matrices for faster
484 tree and PCA calculations
486 <li><strong>Principal Components Analysis Viewer</strong>
489 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
490 and Viewer state saved in Jalview Project
492 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
495 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
499 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
504 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
506 <li><strong>Speed and Efficiency</strong>
509 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
510 multiple groups when working with large alignments
513 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
517 <li><strong>User Interface</strong>
520 <!-- JAL-2933 -->Finder panel remembers last position in each
524 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
525 what is shown)<br />Only visible regions of alignment are shown by
526 default (can be changed in user preferences)
529 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
530 to the Overwrite Dialog
533 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
537 <!-- JAL-1244 -->Status bar shows bounds when dragging a
538 selection region, and gap count when inserting or deleting gaps
541 <!-- JAL-3132 -->Status bar updates over sequence and annotation
545 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
549 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
553 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
556 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
560 <!-- JAL-3181 -->Consistent ordering of links in sequence id
564 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
566 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
570 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
571 <li><strong>Java 11 Support (not yet on general release)</strong>
574 <!-- -->OSX GUI integrations for App menu's 'About' entry and
579 <em>Deprecations</em>
581 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
582 capabilities removed from the Jalview Desktop
584 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
585 unmarshalling has been replaced by JAXB for Jalview projects
586 and XML based data retrieval clients</li>
587 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
588 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
589 </ul> <em>Documentation</em>
591 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
592 not supported in EPS figure export
594 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
595 </ul> <em>Development and Release Processes</em>
598 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
601 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
603 <!-- JAL-3225 -->Eclipse project configuration managed with
607 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
608 Bamboo continuous integration for unattended Test Suite
612 <!-- JAL-2864 -->Memory test suite to detect leaks in common
616 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
620 <!-- JAL-3248 -->Developer documentation migrated to
621 markdown (with HTML rendering)
624 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
627 <!-- JAL-3289 -->New URLs for publishing development
632 <td align="left" valign="top">
635 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
638 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
639 superposition in Jmol fail on Windows
642 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
643 structures for sequences with lots of PDB structures
646 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
650 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
651 project involving multiple views
654 <!-- JAL-3164 -->Overview for complementary view in a linked
655 CDS/Protein alignment is not updated when Hide Columns by
656 Annotation dialog hides columns
659 <!-- JAL-3158 -->Selection highlighting in the complement of a
660 CDS/Protein alignment stops working after making a selection in
661 one view, then making another selection in the other view
664 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
668 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
669 Settings and Jalview Preferences panels
672 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
673 overview with large alignments
676 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
677 region if columns were selected by dragging right-to-left and the
678 mouse moved to the left of the first column
681 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
682 hidden column marker via scale popup menu
685 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
686 doesn't tell users the invalid URL
689 <!-- JAL-2816 -->Tooltips displayed for features filtered by
693 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
694 show cross references or Fetch Database References are shown in
698 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
699 peptide sequence (computed variant shown as p.Res.null)
702 <!-- JAL-2060 -->'Graduated colour' option not offered for
703 manually created features (where feature score is Float.NaN)
706 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
707 when columns are hidden
710 <!-- JAL-3082 -->Regular expression error for '(' in Select
711 Columns by Annotation description
714 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
715 out of Scale or Annotation Panel
718 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
722 <!-- JAL-3074 -->Left/right drag in annotation can scroll
726 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
730 <!-- JAL-3002 -->Column display is out by one after Page Down,
731 Page Up in wrapped mode
734 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
737 <!-- JAL-2932 -->Finder searches in minimised alignments
740 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
741 on opening an alignment
744 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
748 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
749 different groups in the alignment are selected
752 <!-- JAL-2717 -->Internationalised colour scheme names not shown
756 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
760 <!-- JAL-3125 -->Value input for graduated feature colour
761 threshold gets 'unrounded'
764 <!-- JAL-2982 -->PCA image export doesn't respect background
768 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
771 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
774 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
778 <!-- JAL-2964 -->Associate Tree with All Views not restored from
782 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
783 shown in complementary view
786 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
787 without normalisation
790 <!-- JAL-3021 -->Sequence Details report should open positioned at top
794 <!-- JAL-914 -->Help page can be opened twice
797 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
799 </ul> <em>Editing</em>
802 <!-- JAL-2822 -->Start and End should be updated when sequence
803 data at beginning or end of alignment added/removed via 'Edit'
807 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
808 relocate sequence features correctly when start of sequence is
809 removed (Known defect since 2.10)
812 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
813 dialog corrupts dataset sequence
816 <!-- JAL-868 -->Structure colours not updated when associated tree
817 repartitions the alignment view (Regression in 2.10.5)
819 </ul> <em>Datamodel</em>
822 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
823 sequence's End is greater than its length
825 </ul> <em>Bugs fixed for Java 11 Support (not yet on
826 general release)</em>
829 <!-- JAL-3288 -->Menus work properly in split-screen
831 </ul> <em>New Known Defects</em>
834 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
837 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
838 regions of protein alignment.
841 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
842 is restored from a Jalview 2.11 project
845 <!-- JAL-3213 -->Alignment panel height can be too small after
849 <!-- JAL-3240 -->Display is incorrect after removing gapped
850 columns within hidden columns
853 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
854 window after dragging left to select columns to left of visible
858 <!-- JAL-2876 -->Features coloured according to their description
859 string and thresholded by score in earlier versions of Jalview are
860 not shown as thresholded features in 2.11. To workaround please
861 create a Score filter instead.
864 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
866 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
869 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
870 alignments with multiple views can close views unexpectedly
873 <em>Java 11 Specific defects</em>
876 <!-- JAL-3235 -->Jalview Properties file is not sorted
877 alphabetically when saved
883 <td width="60" nowrap>
885 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
888 <td><div align="left">
892 <!-- JAL-3101 -->Default memory for Jalview webstart and
893 InstallAnywhere increased to 1G.
896 <!-- JAL-247 -->Hidden sequence markers and representative
897 sequence bolding included when exporting alignment as EPS,
898 SVG, PNG or HTML. <em>Display is configured via the
899 Format menu, or for command-line use via a Jalview
900 properties file.</em>
903 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
904 API and sequence data now imported as JSON.
907 <!-- JAL-3065 -->Change in recommended way of starting
908 Jalview via a Java command line: add jars in lib directory
909 to CLASSPATH, rather than via the deprecated java.ext.dirs
916 <!-- JAL-3047 -->Support added to execute test suite
917 instrumented with <a href="http://openclover.org/">Open
922 <td><div align="left">
926 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
927 row shown in Feredoxin Structure alignment view of example
931 <!-- JAL-2854 -->Annotation obscures sequences if lots of
932 annotation displayed.
935 <!-- JAL-3107 -->Group conservation/consensus not shown
936 for newly created group when 'Apply to all groups'
940 <!-- JAL-3087 -->Corrupted display when switching to
941 wrapped mode when sequence panel's vertical scrollbar is
945 <!-- JAL-3003 -->Alignment is black in exported EPS file
946 when sequences are selected in exported view.</em>
949 <!-- JAL-3059 -->Groups with different coloured borders
950 aren't rendered with correct colour.
953 <!-- JAL-3092 -->Jalview could hang when importing certain
954 types of knotted RNA secondary structure.
957 <!-- JAL-3095 -->Sequence highlight and selection in
958 trimmed VARNA 2D structure is incorrect for sequences that
962 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
963 annotation when columns are inserted into an alignment,
964 and when exporting as Stockholm flatfile.
967 <!-- JAL-3053 -->Jalview annotation rows containing upper
968 and lower-case 'E' and 'H' do not automatically get
969 treated as RNA secondary structure.
972 <!-- JAL-3106 -->.jvp should be used as default extension
973 (not .jar) when saving a Jalview project file.
976 <!-- JAL-3105 -->Mac Users: closing a window correctly
977 transfers focus to previous window on OSX
980 <em>Java 10 Issues Resolved</em>
983 <!-- JAL-2988 -->OSX - Can't save new files via the File
984 or export menus by typing in a name into the Save dialog
988 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
989 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
990 'look and feel' which has improved compatibility with the
991 latest version of OSX.
998 <td width="60" nowrap>
1000 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1001 <em>7/06/2018</em></strong>
1004 <td><div align="left">
1008 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1009 annotation retrieved from Uniprot
1012 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1013 onto the Jalview Desktop
1017 <td><div align="left">
1021 <!-- JAL-3017 -->Cannot import features with multiple
1022 variant elements (blocks import of some Uniprot records)
1025 <!-- JAL-2997 -->Clustal files with sequence positions in
1026 right-hand column parsed correctly
1029 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1030 not alignment area in exported graphic
1033 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1034 window has input focus
1037 <!-- JAL-2992 -->Annotation panel set too high when
1038 annotation added to view (Windows)
1041 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1042 network connectivity is poor
1045 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1046 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1047 the currently open URL and links from a page viewed in
1048 Firefox or Chrome on Windows is now fully supported. If
1049 you are using Edge, only links in the page can be
1050 dragged, and with Internet Explorer, only the currently
1051 open URL in the browser can be dropped onto Jalview.</em>
1054 <em>New Known Defects</em>
1056 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1061 <td width="60" nowrap>
1062 <div align="center">
1063 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1066 <td><div align="left">
1070 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1071 for disabling automatic superposition of multiple
1072 structures and open structures in existing views
1075 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1076 ID and annotation area margins can be click-dragged to
1080 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1084 <!-- JAL-2759 -->Improved performance for large alignments
1085 and lots of hidden columns
1088 <!-- JAL-2593 -->Improved performance when rendering lots
1089 of features (particularly when transparency is disabled)
1092 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1093 exchange of Jalview features and Chimera attributes made
1099 <td><div align="left">
1102 <!-- JAL-2899 -->Structure and Overview aren't updated
1103 when Colour By Annotation threshold slider is adjusted
1106 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1107 overlapping alignment panel
1110 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1114 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1115 improved: CDS not handled correctly if transcript has no
1119 <!-- JAL-2321 -->Secondary structure and temperature
1120 factor annotation not added to sequence when local PDB
1121 file associated with it by drag'n'drop or structure
1125 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1126 dialog doesn't import PDB files dropped on an alignment
1129 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1130 scroll bar doesn't work for some CDS/Protein views
1133 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1134 Java 1.8u153 onwards and Java 1.9u4+.
1137 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1138 columns in annotation row
1141 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1142 honored in batch mode
1145 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1146 for structures added to existing Jmol view
1149 <!-- JAL-2223 -->'View Mappings' includes duplicate
1150 entries after importing project with multiple views
1153 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1154 protein sequences via SIFTS from associated PDB entries
1155 with negative residue numbers or missing residues fails
1158 <!-- JAL-2952 -->Exception when shading sequence with negative
1159 Temperature Factor values from annotated PDB files (e.g.
1160 as generated by CONSURF)
1163 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1164 tooltip doesn't include a text description of mutation
1167 <!-- JAL-2922 -->Invert displayed features very slow when
1168 structure and/or overview windows are also shown
1171 <!-- JAL-2954 -->Selecting columns from highlighted regions
1172 very slow for alignments with large numbers of sequences
1175 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1176 with 'StringIndexOutOfBounds'
1179 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1180 platforms running Java 10
1183 <!-- JAL-2960 -->Adding a structure to existing structure
1184 view appears to do nothing because the view is hidden behind the alignment view
1190 <!-- JAL-2926 -->Copy consensus sequence option in applet
1191 should copy the group consensus when popup is opened on it
1197 <!-- JAL-2913 -->Fixed ID width preference is not respected
1200 <em>New Known Defects</em>
1203 <!-- JAL-2973 --> Exceptions occasionally raised when
1204 editing a large alignment and overview is displayed
1207 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1208 repeatedly after a series of edits even when the overview
1209 is no longer reflecting updates
1212 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1213 structures for protein subsequence (if 'Trim Retrieved
1214 Sequences' enabled) or Ensembl isoforms (Workaround in
1215 2.10.4 is to fail back to N&W mapping)
1218 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1219 option gives blank output
1226 <td width="60" nowrap>
1227 <div align="center">
1228 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1231 <td><div align="left">
1232 <ul><li>Updated Certum Codesigning Certificate
1233 (Valid till 30th November 2018)</li></ul></div></td>
1234 <td><div align="left">
1235 <em>Desktop</em><ul>
1237 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1238 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1239 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1240 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1241 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1242 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1243 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1249 <td width="60" nowrap>
1250 <div align="center">
1251 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1254 <td><div align="left">
1258 <!-- JAL-2446 -->Faster and more efficient management and
1259 rendering of sequence features
1262 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1263 429 rate limit request hander
1266 <!-- JAL-2773 -->Structure views don't get updated unless
1267 their colours have changed
1270 <!-- JAL-2495 -->All linked sequences are highlighted for
1271 a structure mousover (Jmol) or selection (Chimera)
1274 <!-- JAL-2790 -->'Cancel' button in progress bar for
1275 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1278 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1279 view from Ensembl locus cross-references
1282 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1286 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1287 feature can be disabled
1290 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1291 PDB easier retrieval of sequences for lists of IDs
1294 <!-- JAL-2758 -->Short names for sequences retrieved from
1300 <li>Groovy interpreter updated to 2.4.12</li>
1301 <li>Example groovy script for generating a matrix of
1302 percent identity scores for current alignment.</li>
1304 <em>Testing and Deployment</em>
1307 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1311 <td><div align="left">
1315 <!-- JAL-2643 -->Pressing tab after updating the colour
1316 threshold text field doesn't trigger an update to the
1320 <!-- JAL-2682 -->Race condition when parsing sequence ID
1324 <!-- JAL-2608 -->Overview windows are also closed when
1325 alignment window is closed
1328 <!-- JAL-2548 -->Export of features doesn't always respect
1332 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1333 takes a long time in Cursor mode
1339 <!-- JAL-2777 -->Structures with whitespace chainCode
1340 cannot be viewed in Chimera
1343 <!-- JAL-2728 -->Protein annotation panel too high in
1347 <!-- JAL-2757 -->Can't edit the query after the server
1348 error warning icon is shown in Uniprot and PDB Free Text
1352 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1355 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1358 <!-- JAL-2739 -->Hidden column marker in last column not
1359 rendered when switching back from Wrapped to normal view
1362 <!-- JAL-2768 -->Annotation display corrupted when
1363 scrolling right in unwapped alignment view
1366 <!-- JAL-2542 -->Existing features on subsequence
1367 incorrectly relocated when full sequence retrieved from
1371 <!-- JAL-2733 -->Last reported memory still shown when
1372 Desktop->Show Memory is unticked (OSX only)
1375 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1376 features of same type and group to be selected for
1380 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1381 alignments when hidden columns are present
1384 <!-- JAL-2392 -->Jalview freezes when loading and
1385 displaying several structures
1388 <!-- JAL-2732 -->Black outlines left after resizing or
1392 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1393 within the Jalview desktop on OSX
1396 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1397 when in wrapped alignment mode
1400 <!-- JAL-2636 -->Scale mark not shown when close to right
1401 hand end of alignment
1404 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1405 each selected sequence do not have correct start/end
1409 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1410 after canceling the Alignment Window's Font dialog
1413 <!-- JAL-2036 -->Show cross-references not enabled after
1414 restoring project until a new view is created
1417 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1418 URL links appears when only default EMBL-EBI link is
1419 configured (since 2.10.2b2)
1422 <!-- JAL-2775 -->Overview redraws whole window when box
1423 position is adjusted
1426 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1427 in a multi-chain structure when viewing alignment
1428 involving more than one chain (since 2.10)
1431 <!-- JAL-2811 -->Double residue highlights in cursor mode
1432 if new selection moves alignment window
1435 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1436 arrow key in cursor mode to pass hidden column marker
1439 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1440 that produces correctly annotated transcripts and products
1443 <!-- JAL-2776 -->Toggling a feature group after first time
1444 doesn't update associated structure view
1447 <em>Applet</em><br />
1450 <!-- JAL-2687 -->Concurrent modification exception when
1451 closing alignment panel
1454 <em>BioJSON</em><br />
1457 <!-- JAL-2546 -->BioJSON export does not preserve
1458 non-positional features
1461 <em>New Known Issues</em>
1464 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1465 sequence features correctly (for many previous versions of
1469 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1470 using cursor in wrapped panel other than top
1473 <!-- JAL-2791 -->Select columns containing feature ignores
1474 graduated colour threshold
1477 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1478 always preserve numbering and sequence features
1481 <em>Known Java 9 Issues</em>
1484 <!-- JAL-2902 -->Groovy Console very slow to open and is
1485 not responsive when entering characters (Webstart, Java
1492 <td width="60" nowrap>
1493 <div align="center">
1494 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1495 <em>2/10/2017</em></strong>
1498 <td><div align="left">
1499 <em>New features in Jalview Desktop</em>
1502 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1504 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1508 <td><div align="left">
1512 <td width="60" nowrap>
1513 <div align="center">
1514 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1515 <em>7/9/2017</em></strong>
1518 <td><div align="left">
1522 <!-- JAL-2588 -->Show gaps in overview window by colouring
1523 in grey (sequences used to be coloured grey, and gaps were
1527 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1531 <!-- JAL-2587 -->Overview updates immediately on increase
1532 in size and progress bar shown as higher resolution
1533 overview is recalculated
1538 <td><div align="left">
1542 <!-- JAL-2664 -->Overview window redraws every hidden
1543 column region row by row
1546 <!-- JAL-2681 -->duplicate protein sequences shown after
1547 retrieving Ensembl crossrefs for sequences from Uniprot
1550 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1551 format setting is unticked
1554 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1555 if group has show boxes format setting unticked
1558 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1559 autoscrolling whilst dragging current selection group to
1560 include sequences and columns not currently displayed
1563 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1564 assemblies are imported via CIF file
1567 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1568 displayed when threshold or conservation colouring is also
1572 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1576 <!-- JAL-2673 -->Jalview continues to scroll after
1577 dragging a selected region off the visible region of the
1581 <!-- JAL-2724 -->Cannot apply annotation based
1582 colourscheme to all groups in a view
1585 <!-- JAL-2511 -->IDs don't line up with sequences
1586 initially after font size change using the Font chooser or
1593 <td width="60" nowrap>
1594 <div align="center">
1595 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1598 <td><div align="left">
1599 <em>Calculations</em>
1603 <!-- JAL-1933 -->Occupancy annotation row shows number of
1604 ungapped positions in each column of the alignment.
1607 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1608 a calculation dialog box
1611 <!-- JAL-2379 -->Revised implementation of PCA for speed
1612 and memory efficiency (~30x faster)
1615 <!-- JAL-2403 -->Revised implementation of sequence
1616 similarity scores as used by Tree, PCA, Shading Consensus
1617 and other calculations
1620 <!-- JAL-2416 -->Score matrices are stored as resource
1621 files within the Jalview codebase
1624 <!-- JAL-2500 -->Trees computed on Sequence Feature
1625 Similarity may have different topology due to increased
1632 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1633 model for alignments and groups
1636 <!-- JAL-384 -->Custom shading schemes created via groovy
1643 <!-- JAL-2526 -->Efficiency improvements for interacting
1644 with alignment and overview windows
1647 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1651 <!-- JAL-2388 -->Hidden columns and sequences can be
1655 <!-- JAL-2611 -->Click-drag in visible area allows fine
1656 adjustment of visible position
1660 <em>Data import/export</em>
1663 <!-- JAL-2535 -->Posterior probability annotation from
1664 Stockholm files imported as sequence associated annotation
1667 <!-- JAL-2507 -->More robust per-sequence positional
1668 annotation input/output via stockholm flatfile
1671 <!-- JAL-2533 -->Sequence names don't include file
1672 extension when importing structure files without embedded
1673 names or PDB accessions
1676 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1677 format sequence substitution matrices
1680 <em>User Interface</em>
1683 <!-- JAL-2447 --> Experimental Features Checkbox in
1684 Desktop's Tools menu to hide or show untested features in
1688 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1689 via Overview or sequence motif search operations
1692 <!-- JAL-2547 -->Amend sequence features dialog box can be
1693 opened by double clicking gaps within sequence feature
1697 <!-- JAL-1476 -->Status bar message shown when not enough
1698 aligned positions were available to create a 3D structure
1702 <em>3D Structure</em>
1705 <!-- JAL-2430 -->Hidden regions in alignment views are not
1706 coloured in linked structure views
1709 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1710 file-based command exchange
1713 <!-- JAL-2375 -->Structure chooser automatically shows
1714 Cached Structures rather than querying the PDBe if
1715 structures are already available for sequences
1718 <!-- JAL-2520 -->Structures imported via URL are cached in
1719 the Jalview project rather than downloaded again when the
1720 project is reopened.
1723 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1724 to transfer Chimera's structure attributes as Jalview
1725 features, and vice-versa (<strong>Experimental
1729 <em>Web Services</em>
1732 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1735 <!-- JAL-2335 -->Filter non-standard amino acids and
1736 nucleotides when submitting to AACon and other MSA
1740 <!-- JAL-2316, -->URLs for viewing database
1741 cross-references provided by identifiers.org and the
1742 EMBL-EBI's MIRIAM DB
1749 <!-- JAL-2344 -->FileFormatI interface for describing and
1750 identifying file formats (instead of String constants)
1753 <!-- JAL-2228 -->FeatureCounter script refactored for
1754 efficiency when counting all displayed features (not
1755 backwards compatible with 2.10.1)
1758 <em>Example files</em>
1761 <!-- JAL-2631 -->Graduated feature colour style example
1762 included in the example feature file
1765 <em>Documentation</em>
1768 <!-- JAL-2339 -->Release notes reformatted for readability
1769 with the built-in Java help viewer
1772 <!-- JAL-1644 -->Find documentation updated with 'search
1773 sequence description' option
1779 <!-- JAL-2485, -->External service integration tests for
1780 Uniprot REST Free Text Search Client
1783 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1786 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1791 <td><div align="left">
1792 <em>Calculations</em>
1795 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1796 matrix - C->R should be '-3'<br />Old matrix restored
1797 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1799 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1800 Jalview's treatment of gaps in PCA and substitution matrix
1801 based Tree calculations.<br /> <br />In earlier versions
1802 of Jalview, gaps matching gaps were penalised, and gaps
1803 matching non-gaps penalised even more. In the PCA
1804 calculation, gaps were actually treated as non-gaps - so
1805 different costs were applied, which meant Jalview's PCAs
1806 were different to those produced by SeqSpace.<br />Jalview
1807 now treats gaps in the same way as SeqSpace (ie it scores
1808 them as 0). <br /> <br />Enter the following in the
1809 Groovy console to restore pre-2.10.2 behaviour:<br />
1810 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1811 // for 2.10.1 mode <br />
1812 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1813 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1814 these settings will affect all subsequent tree and PCA
1815 calculations (not recommended)</em></li>
1817 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1818 scaling of branch lengths for trees computed using
1819 Sequence Feature Similarity.
1822 <!-- JAL-2377 -->PCA calculation could hang when
1823 generating output report when working with highly
1824 redundant alignments
1827 <!-- JAL-2544 --> Sort by features includes features to
1828 right of selected region when gaps present on right-hand
1832 <em>User Interface</em>
1835 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1836 doesn't reselect a specific sequence's associated
1837 annotation after it was used for colouring a view
1840 <!-- JAL-2419 -->Current selection lost if popup menu
1841 opened on a region of alignment without groups
1844 <!-- JAL-2374 -->Popup menu not always shown for regions
1845 of an alignment with overlapping groups
1848 <!-- JAL-2310 -->Finder double counts if both a sequence's
1849 name and description match
1852 <!-- JAL-2370 -->Hiding column selection containing two
1853 hidden regions results in incorrect hidden regions
1856 <!-- JAL-2386 -->'Apply to all groups' setting when
1857 changing colour does not apply Conservation slider value
1861 <!-- JAL-2373 -->Percentage identity and conservation menu
1862 items do not show a tick or allow shading to be disabled
1865 <!-- JAL-2385 -->Conservation shading or PID threshold
1866 lost when base colourscheme changed if slider not visible
1869 <!-- JAL-2547 -->Sequence features shown in tooltip for
1870 gaps before start of features
1873 <!-- JAL-2623 -->Graduated feature colour threshold not
1874 restored to UI when feature colour is edited
1877 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1878 a time when scrolling vertically in wrapped mode.
1881 <!-- JAL-2630 -->Structure and alignment overview update
1882 as graduate feature colour settings are modified via the
1886 <!-- JAL-2034 -->Overview window doesn't always update
1887 when a group defined on the alignment is resized
1890 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1891 wrapped view result in positional status updates
1895 <!-- JAL-2563 -->Status bar doesn't show position for
1896 ambiguous amino acid and nucleotide symbols
1899 <!-- JAL-2602 -->Copy consensus sequence failed if
1900 alignment included gapped columns
1903 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1904 widgets don't permanently disappear
1907 <!-- JAL-2503 -->Cannot select or filter quantitative
1908 annotation that are shown only as column labels (e.g.
1909 T-Coffee column reliability scores)
1912 <!-- JAL-2594 -->Exception thrown if trying to create a
1913 sequence feature on gaps only
1916 <!-- JAL-2504 -->Features created with 'New feature'
1917 button from a Find inherit previously defined feature type
1918 rather than the Find query string
1921 <!-- JAL-2423 -->incorrect title in output window when
1922 exporting tree calculated in Jalview
1925 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1926 and then revealing them reorders sequences on the
1930 <!-- JAL-964 -->Group panel in sequence feature settings
1931 doesn't update to reflect available set of groups after
1932 interactively adding or modifying features
1935 <!-- JAL-2225 -->Sequence Database chooser unusable on
1939 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1940 only excluded gaps in current sequence and ignored
1947 <!-- JAL-2421 -->Overview window visible region moves
1948 erratically when hidden rows or columns are present
1951 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1952 Structure Viewer's colour menu don't correspond to
1956 <!-- JAL-2405 -->Protein specific colours only offered in
1957 colour and group colour menu for protein alignments
1960 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1961 reflect currently selected view or group's shading
1965 <!-- JAL-2624 -->Feature colour thresholds not respected
1966 when rendered on overview and structures when opacity at
1970 <!-- JAL-2589 -->User defined gap colour not shown in
1971 overview when features overlaid on alignment
1974 <!-- JAL-2567 -->Feature settings for different views not
1975 recovered correctly from Jalview project file
1978 <!-- JAL-2256 -->Feature colours in overview when first opened
1979 (automatically via preferences) are different to the main
1983 <em>Data import/export</em>
1986 <!-- JAL-2576 -->Very large alignments take a long time to
1990 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1991 added after a sequence was imported are not written to
1995 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1996 when importing RNA secondary structure via Stockholm
1999 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2000 not shown in correct direction for simple pseudoknots
2003 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2004 with lightGray or darkGray via features file (but can
2008 <!-- JAL-2383 -->Above PID colour threshold not recovered
2009 when alignment view imported from project
2012 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2013 structure and sequences extracted from structure files
2014 imported via URL and viewed in Jmol
2017 <!-- JAL-2520 -->Structures loaded via URL are saved in
2018 Jalview Projects rather than fetched via URL again when
2019 the project is loaded and the structure viewed
2022 <em>Web Services</em>
2025 <!-- JAL-2519 -->EnsemblGenomes example failing after
2026 release of Ensembl v.88
2029 <!-- JAL-2366 -->Proxy server address and port always
2030 appear enabled in Preferences->Connections
2033 <!-- JAL-2461 -->DAS registry not found exceptions
2034 removed from console output
2037 <!-- JAL-2582 -->Cannot retrieve protein products from
2038 Ensembl by Peptide ID
2041 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2042 created from SIFTs, and spurious 'Couldn't open structure
2043 in Chimera' errors raised after April 2017 update (problem
2044 due to 'null' string rather than empty string used for
2045 residues with no corresponding PDB mapping).
2048 <em>Application UI</em>
2051 <!-- JAL-2361 -->User Defined Colours not added to Colour
2055 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2056 case' residues (button in colourscheme editor debugged and
2057 new documentation and tooltips added)
2060 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2061 doesn't restore group-specific text colour thresholds
2064 <!-- JAL-2243 -->Feature settings panel does not update as
2065 new features are added to alignment
2068 <!-- JAL-2532 -->Cancel in feature settings reverts
2069 changes to feature colours via the Amend features dialog
2072 <!-- JAL-2506 -->Null pointer exception when attempting to
2073 edit graduated feature colour via amend features dialog
2077 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2078 selection menu changes colours of alignment views
2081 <!-- JAL-2426 -->Spurious exceptions in console raised
2082 from alignment calculation workers after alignment has
2086 <!-- JAL-1608 -->Typo in selection popup menu - Create
2087 groups now 'Create Group'
2090 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2091 Create/Undefine group doesn't always work
2094 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2095 shown again after pressing 'Cancel'
2098 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2099 adjusts start position in wrap mode
2102 <!-- JAL-2563 -->Status bar doesn't show positions for
2103 ambiguous amino acids
2106 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2107 CDS/Protein view after CDS sequences added for aligned
2111 <!-- JAL-2592 -->User defined colourschemes called 'User
2112 Defined' don't appear in Colours menu
2118 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2119 score models doesn't always result in an updated PCA plot
2122 <!-- JAL-2442 -->Features not rendered as transparent on
2123 overview or linked structure view
2126 <!-- JAL-2372 -->Colour group by conservation doesn't
2130 <!-- JAL-2517 -->Hitting Cancel after applying
2131 user-defined colourscheme doesn't restore original
2138 <!-- JAL-2314 -->Unit test failure:
2139 jalview.ws.jabaws.RNAStructExportImport setup fails
2142 <!-- JAL-2307 -->Unit test failure:
2143 jalview.ws.sifts.SiftsClientTest due to compatibility
2144 problems with deep array comparison equality asserts in
2145 successive versions of TestNG
2148 <!-- JAL-2479 -->Relocated StructureChooserTest and
2149 ParameterUtilsTest Unit tests to Network suite
2152 <em>New Known Issues</em>
2155 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2156 phase after a sequence motif find operation
2159 <!-- JAL-2550 -->Importing annotation file with rows
2160 containing just upper and lower case letters are
2161 interpreted as WUSS RNA secondary structure symbols
2164 <!-- JAL-2590 -->Cannot load and display Newick trees
2165 reliably from eggnog Ortholog database
2168 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2169 containing features of type Highlight' when 'B' is pressed
2170 to mark columns containing highlighted regions.
2173 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2174 doesn't always add secondary structure annotation.
2179 <td width="60" nowrap>
2180 <div align="center">
2181 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2184 <td><div align="left">
2188 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2189 for all consensus calculations
2192 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2195 <li>Updated Jalview's Certum code signing certificate
2198 <em>Application</em>
2201 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2202 set of database cross-references, sorted alphabetically
2205 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2206 from database cross references. Users with custom links
2207 will receive a <a href="webServices/urllinks.html#warning">warning
2208 dialog</a> asking them to update their preferences.
2211 <!-- JAL-2287-->Cancel button and escape listener on
2212 dialog warning user about disconnecting Jalview from a
2216 <!-- JAL-2320-->Jalview's Chimera control window closes if
2217 the Chimera it is connected to is shut down
2220 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2221 columns menu item to mark columns containing highlighted
2222 regions (e.g. from structure selections or results of a
2226 <!-- JAL-2284-->Command line option for batch-generation
2227 of HTML pages rendering alignment data with the BioJS
2237 <!-- JAL-2286 -->Columns with more than one modal residue
2238 are not coloured or thresholded according to percent
2239 identity (first observed in Jalview 2.8.2)
2242 <!-- JAL-2301 -->Threonine incorrectly reported as not
2246 <!-- JAL-2318 -->Updates to documentation pages (above PID
2247 threshold, amino acid properties)
2250 <!-- JAL-2292 -->Lower case residues in sequences are not
2251 reported as mapped to residues in a structure file in the
2255 <!--JAL-2324 -->Identical features with non-numeric scores
2256 could be added multiple times to a sequence
2259 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2260 bond features shown as two highlighted residues rather
2261 than a range in linked structure views, and treated
2262 correctly when selecting and computing trees from features
2265 <!-- JAL-2281-->Custom URL links for database
2266 cross-references are matched to database name regardless
2271 <em>Application</em>
2274 <!-- JAL-2282-->Custom URL links for specific database
2275 names without regular expressions also offer links from
2279 <!-- JAL-2315-->Removing a single configured link in the
2280 URL links pane in Connections preferences doesn't actually
2281 update Jalview configuration
2284 <!-- JAL-2272-->CTRL-Click on a selected region to open
2285 the alignment area popup menu doesn't work on El-Capitan
2288 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2289 files with similarly named sequences if dropped onto the
2293 <!-- JAL-2312 -->Additional mappings are shown for PDB
2294 entries where more chains exist in the PDB accession than
2295 are reported in the SIFTS file
2298 <!-- JAL-2317-->Certain structures do not get mapped to
2299 the structure view when displayed with Chimera
2302 <!-- JAL-2317-->No chains shown in the Chimera view
2303 panel's View->Show Chains submenu
2306 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2307 work for wrapped alignment views
2310 <!--JAL-2197 -->Rename UI components for running JPred
2311 predictions from 'JNet' to 'JPred'
2314 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2315 corrupted when annotation panel vertical scroll is not at
2316 first annotation row
2319 <!--JAL-2332 -->Attempting to view structure for Hen
2320 lysozyme results in a PDB Client error dialog box
2323 <!-- JAL-2319 -->Structure View's mapping report switched
2324 ranges for PDB and sequence for SIFTS
2327 SIFTS 'Not_Observed' residues mapped to non-existant
2331 <!-- <em>New Known Issues</em>
2338 <td width="60" nowrap>
2339 <div align="center">
2340 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2341 <em>25/10/2016</em></strong>
2344 <td><em>Application</em>
2346 <li>3D Structure chooser opens with 'Cached structures'
2347 view if structures already loaded</li>
2348 <li>Progress bar reports models as they are loaded to
2349 structure views</li>
2355 <li>Colour by conservation always enabled and no tick
2356 shown in menu when BLOSUM or PID shading applied</li>
2357 <li>FER1_ARATH and FER2_ARATH labels were switched in
2358 example sequences/projects/trees</li>
2360 <em>Application</em>
2362 <li>Jalview projects with views of local PDB structure
2363 files saved on Windows cannot be opened on OSX</li>
2364 <li>Multiple structure views can be opened and superposed
2365 without timeout for structures with multiple models or
2366 multiple sequences in alignment</li>
2367 <li>Cannot import or associated local PDB files without a
2368 PDB ID HEADER line</li>
2369 <li>RMSD is not output in Jmol console when superposition
2371 <li>Drag and drop of URL from Browser fails for Linux and
2372 OSX versions earlier than El Capitan</li>
2373 <li>ENA client ignores invalid content from ENA server</li>
2374 <li>Exceptions are not raised in console when ENA client
2375 attempts to fetch non-existent IDs via Fetch DB Refs UI
2377 <li>Exceptions are not raised in console when a new view
2378 is created on the alignment</li>
2379 <li>OSX right-click fixed for group selections: CMD-click
2380 to insert/remove gaps in groups and CTRL-click to open group
2383 <em>Build and deployment</em>
2385 <li>URL link checker now copes with multi-line anchor
2388 <em>New Known Issues</em>
2390 <li>Drag and drop from URL links in browsers do not work
2397 <td width="60" nowrap>
2398 <div align="center">
2399 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2402 <td><em>General</em>
2405 <!-- JAL-2124 -->Updated Spanish translations.
2408 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2409 for importing structure data to Jalview. Enables mmCIF and
2413 <!-- JAL-192 --->Alignment ruler shows positions relative to
2417 <!-- JAL-2202 -->Position/residue shown in status bar when
2418 mousing over sequence associated annotation
2421 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2425 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2426 '()', canonical '[]' and invalid '{}' base pair populations
2430 <!-- JAL-2092 -->Feature settings popup menu options for
2431 showing or hiding columns containing a feature
2434 <!-- JAL-1557 -->Edit selected group by double clicking on
2435 group and sequence associated annotation labels
2438 <!-- JAL-2236 -->Sequence name added to annotation label in
2439 select/hide columns by annotation and colour by annotation
2443 </ul> <em>Application</em>
2446 <!-- JAL-2050-->Automatically hide introns when opening a
2447 gene/transcript view
2450 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2454 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2455 structure mappings with the EMBL-EBI PDBe SIFTS database
2458 <!-- JAL-2079 -->Updated download sites used for Rfam and
2459 Pfam sources to xfam.org
2462 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2465 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2466 over sequences in Jalview
2469 <!-- JAL-2027-->Support for reverse-complement coding
2470 regions in ENA and EMBL
2473 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2474 for record retrieval via ENA rest API
2477 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2481 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2482 groovy script execution
2485 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2486 alignment window's Calculate menu
2489 <!-- JAL-1812 -->Allow groovy scripts that call
2490 Jalview.getAlignFrames() to run in headless mode
2493 <!-- JAL-2068 -->Support for creating new alignment
2494 calculation workers from groovy scripts
2497 <!-- JAL-1369 --->Store/restore reference sequence in
2501 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2502 associations are now saved/restored from project
2505 <!-- JAL-1993 -->Database selection dialog always shown
2506 before sequence fetcher is opened
2509 <!-- JAL-2183 -->Double click on an entry in Jalview's
2510 database chooser opens a sequence fetcher
2513 <!-- JAL-1563 -->Free-text search client for UniProt using
2514 the UniProt REST API
2517 <!-- JAL-2168 -->-nonews command line parameter to prevent
2518 the news reader opening
2521 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2522 querying stored in preferences
2525 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2529 <!-- JAL-1977-->Tooltips shown on database chooser
2532 <!-- JAL-391 -->Reverse complement function in calculate
2533 menu for nucleotide sequences
2536 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2537 and feature counts preserves alignment ordering (and
2538 debugged for complex feature sets).
2541 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2542 viewing structures with Jalview 2.10
2545 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2546 genome, transcript CCDS and gene ids via the Ensembl and
2547 Ensembl Genomes REST API
2550 <!-- JAL-2049 -->Protein sequence variant annotation
2551 computed for 'sequence_variant' annotation on CDS regions
2555 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2559 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2560 Ref Fetcher fails to match, or otherwise updates sequence
2561 data from external database records.
2564 <!-- JAL-2154 -->Revised Jalview Project format for
2565 efficient recovery of sequence coding and alignment
2566 annotation relationships.
2568 </ul> <!-- <em>Applet</em>
2579 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2583 <!-- JAL-2018-->Export features in Jalview format (again)
2584 includes graduated colourschemes
2587 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2588 working with big alignments and lots of hidden columns
2591 <!-- JAL-2053-->Hidden column markers not always rendered
2592 at right of alignment window
2595 <!-- JAL-2067 -->Tidied up links in help file table of
2599 <!-- JAL-2072 -->Feature based tree calculation not shown
2603 <!-- JAL-2075 -->Hidden columns ignored during feature
2604 based tree calculation
2607 <!-- JAL-2065 -->Alignment view stops updating when show
2608 unconserved enabled for group on alignment
2611 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2615 <!-- JAL-2146 -->Alignment column in status incorrectly
2616 shown as "Sequence position" when mousing over
2620 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2621 hidden columns present
2624 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2625 user created annotation added to alignment
2628 <!-- JAL-1841 -->RNA Structure consensus only computed for
2629 '()' base pair annotation
2632 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2633 in zero scores for all base pairs in RNA Structure
2637 <!-- JAL-2174-->Extend selection with columns containing
2641 <!-- JAL-2275 -->Pfam format writer puts extra space at
2642 beginning of sequence
2645 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2649 <!-- JAL-2238 -->Cannot create groups on an alignment from
2650 from a tree when t-coffee scores are shown
2653 <!-- JAL-1836,1967 -->Cannot import and view PDB
2654 structures with chains containing negative resnums (4q4h)
2657 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2661 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2662 to Clustal, PIR and PileUp output
2665 <!-- JAL-2008 -->Reordering sequence features that are
2666 not visible causes alignment window to repaint
2669 <!-- JAL-2006 -->Threshold sliders don't work in
2670 graduated colour and colour by annotation row for e-value
2671 scores associated with features and annotation rows
2674 <!-- JAL-1797 -->amino acid physicochemical conservation
2675 calculation should be case independent
2678 <!-- JAL-2173 -->Remove annotation also updates hidden
2682 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2683 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2684 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2687 <!-- JAL-2065 -->Null pointer exceptions and redraw
2688 problems when reference sequence defined and 'show
2689 non-conserved' enabled
2692 <!-- JAL-1306 -->Quality and Conservation are now shown on
2693 load even when Consensus calculation is disabled
2696 <!-- JAL-1932 -->Remove right on penultimate column of
2697 alignment does nothing
2700 <em>Application</em>
2703 <!-- JAL-1552-->URLs and links can't be imported by
2704 drag'n'drop on OSX when launched via webstart (note - not
2705 yet fixed for El Capitan)
2708 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2709 output when running on non-gb/us i18n platforms
2712 <!-- JAL-1944 -->Error thrown when exporting a view with
2713 hidden sequences as flat-file alignment
2716 <!-- JAL-2030-->InstallAnywhere distribution fails when
2720 <!-- JAL-2080-->Jalview very slow to launch via webstart
2721 (also hotfix for 2.9.0b2)
2724 <!-- JAL-2085 -->Cannot save project when view has a
2725 reference sequence defined
2728 <!-- JAL-1011 -->Columns are suddenly selected in other
2729 alignments and views when revealing hidden columns
2732 <!-- JAL-1989 -->Hide columns not mirrored in complement
2733 view in a cDNA/Protein splitframe
2736 <!-- JAL-1369 -->Cannot save/restore representative
2737 sequence from project when only one sequence is
2741 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2742 in Structure Chooser
2745 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2746 structure consensus didn't refresh annotation panel
2749 <!-- JAL-1962 -->View mapping in structure view shows
2750 mappings between sequence and all chains in a PDB file
2753 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2754 dialogs format columns correctly, don't display array
2755 data, sort columns according to type
2758 <!-- JAL-1975 -->Export complete shown after destination
2759 file chooser is cancelled during an image export
2762 <!-- JAL-2025 -->Error when querying PDB Service with
2763 sequence name containing special characters
2766 <!-- JAL-2024 -->Manual PDB structure querying should be
2770 <!-- JAL-2104 -->Large tooltips with broken HTML
2771 formatting don't wrap
2774 <!-- JAL-1128 -->Figures exported from wrapped view are
2775 truncated so L looks like I in consensus annotation
2778 <!-- JAL-2003 -->Export features should only export the
2779 currently displayed features for the current selection or
2783 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2784 after fetching cross-references, and restoring from
2788 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2789 followed in the structure viewer
2792 <!-- JAL-2163 -->Titles for individual alignments in
2793 splitframe not restored from project
2796 <!-- JAL-2145 -->missing autocalculated annotation at
2797 trailing end of protein alignment in transcript/product
2798 splitview when pad-gaps not enabled by default
2801 <!-- JAL-1797 -->amino acid physicochemical conservation
2805 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2806 article has been read (reopened issue due to
2807 internationalisation problems)
2810 <!-- JAL-1960 -->Only offer PDB structures in structure
2811 viewer based on sequence name, PDB and UniProt
2816 <!-- JAL-1976 -->No progress bar shown during export of
2820 <!-- JAL-2213 -->Structures not always superimposed after
2821 multiple structures are shown for one or more sequences.
2824 <!-- JAL-1370 -->Reference sequence characters should not
2825 be replaced with '.' when 'Show unconserved' format option
2829 <!-- JAL-1823 -->Cannot specify chain code when entering
2830 specific PDB id for sequence
2833 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2834 'Export hidden sequences' is enabled, but 'export hidden
2835 columns' is disabled.
2838 <!--JAL-2026-->Best Quality option in structure chooser
2839 selects lowest rather than highest resolution structures
2843 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2844 to sequence mapping in 'View Mappings' report
2847 <!-- JAL-2284 -->Unable to read old Jalview projects that
2848 contain non-XML data added after Jalvew wrote project.
2851 <!-- JAL-2118 -->Newly created annotation row reorders
2852 after clicking on it to create new annotation for a
2856 <!-- JAL-1980 -->Null Pointer Exception raised when
2857 pressing Add on an orphaned cut'n'paste window.
2859 <!-- may exclude, this is an external service stability issue JAL-1941
2860 -- > RNA 3D structure not added via DSSR service</li> -->
2865 <!-- JAL-2151 -->Incorrect columns are selected when
2866 hidden columns present before start of sequence
2869 <!-- JAL-1986 -->Missing dependencies on applet pages
2873 <!-- JAL-1947 -->Overview pixel size changes when
2874 sequences are hidden in applet
2877 <!-- JAL-1996 -->Updated instructions for applet
2878 deployment on examples pages.
2885 <td width="60" nowrap>
2886 <div align="center">
2887 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2888 <em>16/10/2015</em></strong>
2891 <td><em>General</em>
2893 <li>Time stamps for signed Jalview application and applet
2898 <em>Application</em>
2900 <li>Duplicate group consensus and conservation rows
2901 shown when tree is partitioned</li>
2902 <li>Erratic behaviour when tree partitions made with
2903 multiple cDNA/Protein split views</li>
2909 <td width="60" nowrap>
2910 <div align="center">
2911 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2912 <em>8/10/2015</em></strong>
2915 <td><em>General</em>
2917 <li>Updated Spanish translations of localized text for
2919 </ul> <em>Application</em>
2921 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2922 <li>Signed OSX InstallAnywhere installer<br></li>
2923 <li>Support for per-sequence based annotations in BioJSON</li>
2924 </ul> <em>Applet</em>
2926 <li>Split frame example added to applet examples page</li>
2927 </ul> <em>Build and Deployment</em>
2930 <!-- JAL-1888 -->New ant target for running Jalview's test
2938 <li>Mapping of cDNA to protein in split frames
2939 incorrect when sequence start > 1</li>
2940 <li>Broken images in filter column by annotation dialog
2942 <li>Feature colours not parsed from features file</li>
2943 <li>Exceptions and incomplete link URLs recovered when
2944 loading a features file containing HTML tags in feature
2948 <em>Application</em>
2950 <li>Annotations corrupted after BioJS export and
2952 <li>Incorrect sequence limits after Fetch DB References
2953 with 'trim retrieved sequences'</li>
2954 <li>Incorrect warning about deleting all data when
2955 deleting selected columns</li>
2956 <li>Patch to build system for shipping properly signed
2957 JNLP templates for webstart launch</li>
2958 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2959 unreleased structures for download or viewing</li>
2960 <li>Tab/space/return keystroke operation of EMBL-PDBe
2961 fetcher/viewer dialogs works correctly</li>
2962 <li>Disabled 'minimise' button on Jalview windows
2963 running on OSX to workaround redraw hang bug</li>
2964 <li>Split cDNA/Protein view position and geometry not
2965 recovered from jalview project</li>
2966 <li>Initial enabled/disabled state of annotation menu
2967 sorter 'show autocalculated first/last' corresponds to
2969 <li>Restoring of Clustal, RNA Helices and T-Coffee
2970 color schemes from BioJSON</li>
2974 <li>Reorder sequences mirrored in cDNA/Protein split
2976 <li>Applet with Jmol examples not loading correctly</li>
2982 <td><div align="center">
2983 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2985 <td><em>General</em>
2987 <li>Linked visualisation and analysis of DNA and Protein
2990 <li>Translated cDNA alignments shown as split protein
2991 and DNA alignment views</li>
2992 <li>Codon consensus annotation for linked protein and
2993 cDNA alignment views</li>
2994 <li>Link cDNA or Protein product sequences by loading
2995 them onto Protein or cDNA alignments</li>
2996 <li>Reconstruct linked cDNA alignment from aligned
2997 protein sequences</li>
3000 <li>Jmol integration updated to Jmol v14.2.14</li>
3001 <li>Import and export of Jalview alignment views as <a
3002 href="features/bioJsonFormat.html">BioJSON</a></li>
3003 <li>New alignment annotation file statements for
3004 reference sequences and marking hidden columns</li>
3005 <li>Reference sequence based alignment shading to
3006 highlight variation</li>
3007 <li>Select or hide columns according to alignment
3009 <li>Find option for locating sequences by description</li>
3010 <li>Conserved physicochemical properties shown in amino
3011 acid conservation row</li>
3012 <li>Alignments can be sorted by number of RNA helices</li>
3013 </ul> <em>Application</em>
3015 <li>New cDNA/Protein analysis capabilities
3017 <li>Get Cross-References should open a Split Frame
3018 view with cDNA/Protein</li>
3019 <li>Detect when nucleotide sequences and protein
3020 sequences are placed in the same alignment</li>
3021 <li>Split cDNA/Protein views are saved in Jalview
3026 <li>Use REST API to talk to Chimera</li>
3027 <li>Selected regions in Chimera are highlighted in linked
3028 Jalview windows</li>
3030 <li>VARNA RNA viewer updated to v3.93</li>
3031 <li>VARNA views are saved in Jalview Projects</li>
3032 <li>Pseudoknots displayed as Jalview RNA annotation can
3033 be shown in VARNA</li>
3035 <li>Make groups for selection uses marked columns as well
3036 as the active selected region</li>
3038 <li>Calculate UPGMA and NJ trees using sequence feature
3040 <li>New Export options
3042 <li>New Export Settings dialog to control hidden
3043 region export in flat file generation</li>
3045 <li>Export alignment views for display with the <a
3046 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3048 <li>Export scrollable SVG in HTML page</li>
3049 <li>Optional embedding of BioJSON data when exporting
3050 alignment figures to HTML</li>
3052 <li>3D structure retrieval and display
3054 <li>Free text and structured queries with the PDBe
3056 <li>PDBe Search API based discovery and selection of
3057 PDB structures for a sequence set</li>
3061 <li>JPred4 employed for protein secondary structure
3063 <li>Hide Insertions menu option to hide unaligned columns
3064 for one or a group of sequences</li>
3065 <li>Automatically hide insertions in alignments imported
3066 from the JPred4 web server</li>
3067 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3068 system on OSX<br />LGPL libraries courtesy of <a
3069 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3071 <li>changed 'View nucleotide structure' submenu to 'View
3072 VARNA 2D Structure'</li>
3073 <li>change "View protein structure" menu option to "3D
3076 </ul> <em>Applet</em>
3078 <li>New layout for applet example pages</li>
3079 <li>New parameters to enable SplitFrame view
3080 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3081 <li>New example demonstrating linked viewing of cDNA and
3082 Protein alignments</li>
3083 </ul> <em>Development and deployment</em>
3085 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3086 <li>Include installation type and git revision in build
3087 properties and console log output</li>
3088 <li>Jalview Github organisation, and new github site for
3089 storing BioJsMSA Templates</li>
3090 <li>Jalview's unit tests now managed with TestNG</li>
3093 <!-- <em>General</em>
3095 </ul> --> <!-- issues resolved --> <em>Application</em>
3097 <li>Escape should close any open find dialogs</li>
3098 <li>Typo in select-by-features status report</li>
3099 <li>Consensus RNA secondary secondary structure
3100 predictions are not highlighted in amber</li>
3101 <li>Missing gap character in v2.7 example file means
3102 alignment appears unaligned when pad-gaps is not enabled</li>
3103 <li>First switch to RNA Helices colouring doesn't colour
3104 associated structure views</li>
3105 <li>ID width preference option is greyed out when auto
3106 width checkbox not enabled</li>
3107 <li>Stopped a warning dialog from being shown when
3108 creating user defined colours</li>
3109 <li>'View Mapping' in structure viewer shows sequence
3110 mappings for just that viewer's sequences</li>
3111 <li>Workaround for superposing PDB files containing
3112 multiple models in Chimera</li>
3113 <li>Report sequence position in status bar when hovering
3114 over Jmol structure</li>
3115 <li>Cannot output gaps as '.' symbols with Selection ->
3116 output to text box</li>
3117 <li>Flat file exports of alignments with hidden columns
3118 have incorrect sequence start/end</li>
3119 <li>'Aligning' a second chain to a Chimera structure from
3121 <li>Colour schemes applied to structure viewers don't
3122 work for nucleotide</li>
3123 <li>Loading/cut'n'pasting an empty or invalid file leads
3124 to a grey/invisible alignment window</li>
3125 <li>Exported Jpred annotation from a sequence region
3126 imports to different position</li>
3127 <li>Space at beginning of sequence feature tooltips shown
3128 on some platforms</li>
3129 <li>Chimera viewer 'View | Show Chain' menu is not
3131 <li>'New View' fails with a Null Pointer Exception in
3132 console if Chimera has been opened</li>
3133 <li>Mouseover to Chimera not working</li>
3134 <li>Miscellaneous ENA XML feature qualifiers not
3136 <li>NPE in annotation renderer after 'Extract Scores'</li>
3137 <li>If two structures in one Chimera window, mouseover of
3138 either sequence shows on first structure</li>
3139 <li>'Show annotations' options should not make
3140 non-positional annotations visible</li>
3141 <li>Subsequence secondary structure annotation not shown
3142 in right place after 'view flanking regions'</li>
3143 <li>File Save As type unset when current file format is
3145 <li>Save as '.jar' option removed for saving Jalview
3147 <li>Colour by Sequence colouring in Chimera more
3149 <li>Cannot 'add reference annotation' for a sequence in
3150 several views on same alignment</li>
3151 <li>Cannot show linked products for EMBL / ENA records</li>
3152 <li>Jalview's tooltip wraps long texts containing no
3154 </ul> <em>Applet</em>
3156 <li>Jmol to JalviewLite mouseover/link not working</li>
3157 <li>JalviewLite can't import sequences with ID
3158 descriptions containing angle brackets</li>
3159 </ul> <em>General</em>
3161 <li>Cannot export and reimport RNA secondary structure
3162 via jalview annotation file</li>
3163 <li>Random helix colour palette for colour by annotation
3164 with RNA secondary structure</li>
3165 <li>Mouseover to cDNA from STOP residue in protein
3166 translation doesn't work.</li>
3167 <li>hints when using the select by annotation dialog box</li>
3168 <li>Jmol alignment incorrect if PDB file has alternate CA
3170 <li>FontChooser message dialog appears to hang after
3171 choosing 1pt font</li>
3172 <li>Peptide secondary structure incorrectly imported from
3173 annotation file when annotation display text includes 'e' or
3175 <li>Cannot set colour of new feature type whilst creating
3177 <li>cDNA translation alignment should not be sequence
3178 order dependent</li>
3179 <li>'Show unconserved' doesn't work for lower case
3181 <li>Nucleotide ambiguity codes involving R not recognised</li>
3182 </ul> <em>Deployment and Documentation</em>
3184 <li>Applet example pages appear different to the rest of
3185 www.jalview.org</li>
3186 </ul> <em>Application Known issues</em>
3188 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3189 <li>Misleading message appears after trying to delete
3191 <li>Jalview icon not shown in dock after InstallAnywhere
3192 version launches</li>
3193 <li>Fetching EMBL reference for an RNA sequence results
3194 fails with a sequence mismatch</li>
3195 <li>Corrupted or unreadable alignment display when
3196 scrolling alignment to right</li>
3197 <li>ArrayIndexOutOfBoundsException thrown when remove
3198 empty columns called on alignment with ragged gapped ends</li>
3199 <li>auto calculated alignment annotation rows do not get
3200 placed above or below non-autocalculated rows</li>
3201 <li>Jalview dekstop becomes sluggish at full screen in
3202 ultra-high resolution</li>
3203 <li>Cannot disable consensus calculation independently of
3204 quality and conservation</li>
3205 <li>Mouseover highlighting between cDNA and protein can
3206 become sluggish with more than one splitframe shown</li>
3207 </ul> <em>Applet Known Issues</em>
3209 <li>Core PDB parsing code requires Jmol</li>
3210 <li>Sequence canvas panel goes white when alignment
3211 window is being resized</li>
3217 <td><div align="center">
3218 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3220 <td><em>General</em>
3222 <li>Updated Java code signing certificate donated by
3224 <li>Features and annotation preserved when performing
3225 pairwise alignment</li>
3226 <li>RNA pseudoknot annotation can be
3227 imported/exported/displayed</li>
3228 <li>'colour by annotation' can colour by RNA and
3229 protein secondary structure</li>
3230 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3231 post-hoc with 2.9 release</em>)
3234 </ul> <em>Application</em>
3236 <li>Extract and display secondary structure for sequences
3237 with 3D structures</li>
3238 <li>Support for parsing RNAML</li>
3239 <li>Annotations menu for layout
3241 <li>sort sequence annotation rows by alignment</li>
3242 <li>place sequence annotation above/below alignment
3245 <li>Output in Stockholm format</li>
3246 <li>Internationalisation: improved Spanish (es)
3248 <li>Structure viewer preferences tab</li>
3249 <li>Disorder and Secondary Structure annotation tracks
3250 shared between alignments</li>
3251 <li>UCSF Chimera launch and linked highlighting from
3253 <li>Show/hide all sequence associated annotation rows for
3254 all or current selection</li>
3255 <li>disorder and secondary structure predictions
3256 available as dataset annotation</li>
3257 <li>Per-sequence rna helices colouring</li>
3260 <li>Sequence database accessions imported when fetching
3261 alignments from Rfam</li>
3262 <li>update VARNA version to 3.91</li>
3264 <li>New groovy scripts for exporting aligned positions,
3265 conservation values, and calculating sum of pairs scores.</li>
3266 <li>Command line argument to set default JABAWS server</li>
3267 <li>include installation type in build properties and
3268 console log output</li>
3269 <li>Updated Jalview project format to preserve dataset
3273 <!-- issues resolved --> <em>Application</em>
3275 <li>Distinguish alignment and sequence associated RNA
3276 structure in structure->view->VARNA</li>
3277 <li>Raise dialog box if user deletes all sequences in an
3279 <li>Pressing F1 results in documentation opening twice</li>
3280 <li>Sequence feature tooltip is wrapped</li>
3281 <li>Double click on sequence associated annotation
3282 selects only first column</li>
3283 <li>Redundancy removal doesn't result in unlinked
3284 leaves shown in tree</li>
3285 <li>Undos after several redundancy removals don't undo
3287 <li>Hide sequence doesn't hide associated annotation</li>
3288 <li>User defined colours dialog box too big to fit on
3289 screen and buttons not visible</li>
3290 <li>author list isn't updated if already written to
3291 Jalview properties</li>
3292 <li>Popup menu won't open after retrieving sequence
3294 <li>File open window for associate PDB doesn't open</li>
3295 <li>Left-then-right click on a sequence id opens a
3296 browser search window</li>
3297 <li>Cannot open sequence feature shading/sort popup menu
3298 in feature settings dialog</li>
3299 <li>better tooltip placement for some areas of Jalview
3301 <li>Allow addition of JABAWS Server which doesn't
3302 pass validation</li>
3303 <li>Web services parameters dialog box is too large to
3305 <li>Muscle nucleotide alignment preset obscured by
3307 <li>JABAWS preset submenus don't contain newly
3308 defined user preset</li>
3309 <li>MSA web services warns user if they were launched
3310 with invalid input</li>
3311 <li>Jalview cannot contact DAS Registy when running on
3314 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3315 'Superpose with' submenu not shown when new view
3319 </ul> <!-- <em>Applet</em>
3321 </ul> <em>General</em>
3323 </ul>--> <em>Deployment and Documentation</em>
3325 <li>2G and 1G options in launchApp have no effect on
3326 memory allocation</li>
3327 <li>launchApp service doesn't automatically open
3328 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3330 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3331 InstallAnywhere reports cannot find valid JVM when Java
3332 1.7_055 is available
3334 </ul> <em>Application Known issues</em>
3337 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3338 corrupted or unreadable alignment display when scrolling
3342 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3343 retrieval fails but progress bar continues for DAS retrieval
3344 with large number of ID
3347 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3348 flatfile output of visible region has incorrect sequence
3352 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3353 rna structure consensus doesn't update when secondary
3354 structure tracks are rearranged
3357 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3358 invalid rna structure positional highlighting does not
3359 highlight position of invalid base pairs
3362 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3363 out of memory errors are not raised when saving Jalview
3364 project from alignment window file menu
3367 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3368 Switching to RNA Helices colouring doesn't propagate to
3372 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3373 colour by RNA Helices not enabled when user created
3374 annotation added to alignment
3377 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3378 Jalview icon not shown on dock in Mountain Lion/Webstart
3380 </ul> <em>Applet Known Issues</em>
3383 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3384 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3387 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3388 Jalview and Jmol example not compatible with IE9
3391 <li>Sort by annotation score doesn't reverse order
3397 <td><div align="center">
3398 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3401 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3404 <li>Internationalisation of user interface (usually
3405 called i18n support) and translation for Spanish locale</li>
3406 <li>Define/Undefine group on current selection with
3407 Ctrl-G/Shift Ctrl-G</li>
3408 <li>Improved group creation/removal options in
3409 alignment/sequence Popup menu</li>
3410 <li>Sensible precision for symbol distribution
3411 percentages shown in logo tooltip.</li>
3412 <li>Annotation panel height set according to amount of
3413 annotation when alignment first opened</li>
3414 </ul> <em>Application</em>
3416 <li>Interactive consensus RNA secondary structure
3417 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3418 <li>Select columns containing particular features from
3419 Feature Settings dialog</li>
3420 <li>View all 'representative' PDB structures for selected
3422 <li>Update Jalview project format:
3424 <li>New file extension for Jalview projects '.jvp'</li>
3425 <li>Preserve sequence and annotation dataset (to
3426 store secondary structure annotation,etc)</li>
3427 <li>Per group and alignment annotation and RNA helix
3431 <li>New similarity measures for PCA and Tree calculation
3433 <li>Experimental support for retrieval and viewing of
3434 flanking regions for an alignment</li>
3438 <!-- issues resolved --> <em>Application</em>
3440 <li>logo keeps spinning and status remains at queued or
3441 running after job is cancelled</li>
3442 <li>cannot export features from alignments imported from
3443 Jalview/VAMSAS projects</li>
3444 <li>Buggy slider for web service parameters that take
3446 <li>Newly created RNA secondary structure line doesn't
3447 have 'display all symbols' flag set</li>
3448 <li>T-COFFEE alignment score shading scheme and other
3449 annotation shading not saved in Jalview project</li>
3450 <li>Local file cannot be loaded in freshly downloaded
3452 <li>Jalview icon not shown on dock in Mountain
3454 <li>Load file from desktop file browser fails</li>
3455 <li>Occasional NPE thrown when calculating large trees</li>
3456 <li>Cannot reorder or slide sequences after dragging an
3457 alignment onto desktop</li>
3458 <li>Colour by annotation dialog throws NPE after using
3459 'extract scores' function</li>
3460 <li>Loading/cut'n'pasting an empty file leads to a grey
3461 alignment window</li>
3462 <li>Disorder thresholds rendered incorrectly after
3463 performing IUPred disorder prediction</li>
3464 <li>Multiple group annotated consensus rows shown when
3465 changing 'normalise logo' display setting</li>
3466 <li>Find shows blank dialog after 'finished searching' if
3467 nothing matches query</li>
3468 <li>Null Pointer Exceptions raised when sorting by
3469 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3471 <li>Errors in Jmol console when structures in alignment
3472 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3474 <li>Not all working JABAWS services are shown in
3476 <li>JAVAWS version of Jalview fails to launch with
3477 'invalid literal/length code'</li>
3478 <li>Annotation/RNA Helix colourschemes cannot be applied
3479 to alignment with groups (actually fixed in 2.8.0b1)</li>
3480 <li>RNA Helices and T-Coffee Scores available as default
3483 </ul> <em>Applet</em>
3485 <li>Remove group option is shown even when selection is
3487 <li>Apply to all groups ticked but colourscheme changes
3488 don't affect groups</li>
3489 <li>Documented RNA Helices and T-Coffee Scores as valid
3490 colourscheme name</li>
3491 <li>Annotation labels drawn on sequence IDs when
3492 Annotation panel is not displayed</li>
3493 <li>Increased font size for dropdown menus on OSX and
3494 embedded windows</li>
3495 </ul> <em>Other</em>
3497 <li>Consensus sequence for alignments/groups with a
3498 single sequence were not calculated</li>
3499 <li>annotation files that contain only groups imported as
3500 annotation and junk sequences</li>
3501 <li>Fasta files with sequences containing '*' incorrectly
3502 recognised as PFAM or BLC</li>
3503 <li>conservation/PID slider apply all groups option
3504 doesn't affect background (2.8.0b1)
3506 <li>redundancy highlighting is erratic at 0% and 100%</li>
3507 <li>Remove gapped columns fails for sequences with ragged
3509 <li>AMSA annotation row with leading spaces is not
3510 registered correctly on import</li>
3511 <li>Jalview crashes when selecting PCA analysis for
3512 certain alignments</li>
3513 <li>Opening the colour by annotation dialog for an
3514 existing annotation based 'use original colours'
3515 colourscheme loses original colours setting</li>
3520 <td><div align="center">
3521 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3522 <em>30/1/2014</em></strong>
3526 <li>Trusted certificates for JalviewLite applet and
3527 Jalview Desktop application<br />Certificate was donated by
3528 <a href="https://www.certum.eu">Certum</a> to the Jalview
3529 open source project).
3531 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3532 <li>Output in Stockholm format</li>
3533 <li>Allow import of data from gzipped files</li>
3534 <li>Export/import group and sequence associated line
3535 graph thresholds</li>
3536 <li>Nucleotide substitution matrix that supports RNA and
3537 ambiguity codes</li>
3538 <li>Allow disorder predictions to be made on the current
3539 selection (or visible selection) in the same way that JPred
3541 <li>Groovy scripting for headless Jalview operation</li>
3542 </ul> <em>Other improvements</em>
3544 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3545 <li>COMBINE statement uses current SEQUENCE_REF and
3546 GROUP_REF scope to group annotation rows</li>
3547 <li>Support '' style escaping of quotes in Newick
3549 <li>Group options for JABAWS service by command line name</li>
3550 <li>Empty tooltip shown for JABA service options with a
3551 link but no description</li>
3552 <li>Select primary source when selecting authority in
3553 database fetcher GUI</li>
3554 <li>Add .mfa to FASTA file extensions recognised by
3556 <li>Annotation label tooltip text wrap</li>
3561 <li>Slow scrolling when lots of annotation rows are
3563 <li>Lots of NPE (and slowness) after creating RNA
3564 secondary structure annotation line</li>
3565 <li>Sequence database accessions not imported when
3566 fetching alignments from Rfam</li>
3567 <li>Incorrect SHMR submission for sequences with
3569 <li>View all structures does not always superpose
3571 <li>Option widgets in service parameters not updated to
3572 reflect user or preset settings</li>
3573 <li>Null pointer exceptions for some services without
3574 presets or adjustable parameters</li>
3575 <li>Discover PDB IDs entry in structure menu doesn't
3576 discover PDB xRefs</li>
3577 <li>Exception encountered while trying to retrieve
3578 features with DAS</li>
3579 <li>Lowest value in annotation row isn't coloured
3580 when colour by annotation (per sequence) is coloured</li>
3581 <li>Keyboard mode P jumps to start of gapped region when
3582 residue follows a gap</li>
3583 <li>Jalview appears to hang importing an alignment with
3584 Wrap as default or after enabling Wrap</li>
3585 <li>'Right click to add annotations' message
3586 shown in wrap mode when no annotations present</li>
3587 <li>Disorder predictions fail with NPE if no automatic
3588 annotation already exists on alignment</li>
3589 <li>oninit javascript function should be called after
3590 initialisation completes</li>
3591 <li>Remove redundancy after disorder prediction corrupts
3592 alignment window display</li>
3593 <li>Example annotation file in documentation is invalid</li>
3594 <li>Grouped line graph annotation rows are not exported
3595 to annotation file</li>
3596 <li>Multi-harmony analysis cannot be run when only two
3598 <li>Cannot create multiple groups of line graphs with
3599 several 'combine' statements in annotation file</li>
3600 <li>Pressing return several times causes Number Format
3601 exceptions in keyboard mode</li>
3602 <li>Multi-harmony (SHMMR) method doesn't submit
3603 correct partitions for input data</li>
3604 <li>Translation from DNA to Amino Acids fails</li>
3605 <li>Jalview fail to load newick tree with quoted label</li>
3606 <li>--headless flag isn't understood</li>
3607 <li>ClassCastException when generating EPS in headless
3609 <li>Adjusting sequence-associated shading threshold only
3610 changes one row's threshold</li>
3611 <li>Preferences and Feature settings panel panel
3612 doesn't open</li>
3613 <li>hide consensus histogram also hides conservation and
3614 quality histograms</li>
3619 <td><div align="center">
3620 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3622 <td><em>Application</em>
3624 <li>Support for JABAWS 2.0 Services (AACon alignment
3625 conservation, protein disorder and Clustal Omega)</li>
3626 <li>JABAWS server status indicator in Web Services
3628 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3629 in Jalview alignment window</li>
3630 <li>Updated Jalview build and deploy framework for OSX
3631 mountain lion, windows 7, and 8</li>
3632 <li>Nucleotide substitution matrix for PCA that supports
3633 RNA and ambiguity codes</li>
3635 <li>Improved sequence database retrieval GUI</li>
3636 <li>Support fetching and database reference look up
3637 against multiple DAS sources (Fetch all from in 'fetch db
3639 <li>Jalview project improvements
3641 <li>Store and retrieve the 'belowAlignment'
3642 flag for annotation</li>
3643 <li>calcId attribute to group annotation rows on the
3645 <li>Store AACon calculation settings for a view in
3646 Jalview project</li>
3650 <li>horizontal scrolling gesture support</li>
3651 <li>Visual progress indicator when PCA calculation is
3653 <li>Simpler JABA web services menus</li>
3654 <li>visual indication that web service results are still
3655 being retrieved from server</li>
3656 <li>Serialise the dialogs that are shown when Jalview
3657 starts up for first time</li>
3658 <li>Jalview user agent string for interacting with HTTP
3660 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3662 <li>Examples directory and Groovy library included in
3663 InstallAnywhere distribution</li>
3664 </ul> <em>Applet</em>
3666 <li>RNA alignment and secondary structure annotation
3667 visualization applet example</li>
3668 </ul> <em>General</em>
3670 <li>Normalise option for consensus sequence logo</li>
3671 <li>Reset button in PCA window to return dimensions to
3673 <li>Allow seqspace or Jalview variant of alignment PCA
3675 <li>PCA with either nucleic acid and protein substitution
3677 <li>Allow windows containing HTML reports to be exported
3679 <li>Interactive display and editing of RNA secondary
3680 structure contacts</li>
3681 <li>RNA Helix Alignment Colouring</li>
3682 <li>RNA base pair logo consensus</li>
3683 <li>Parse sequence associated secondary structure
3684 information in Stockholm files</li>
3685 <li>HTML Export database accessions and annotation
3686 information presented in tooltip for sequences</li>
3687 <li>Import secondary structure from LOCARNA clustalw
3688 style RNA alignment files</li>
3689 <li>import and visualise T-COFFEE quality scores for an
3691 <li>'colour by annotation' per sequence option to
3692 shade each sequence according to its associated alignment
3694 <li>New Jalview Logo</li>
3695 </ul> <em>Documentation and Development</em>
3697 <li>documentation for score matrices used in Jalview</li>
3698 <li>New Website!</li>
3700 <td><em>Application</em>
3702 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3703 wsdbfetch REST service</li>
3704 <li>Stop windows being moved outside desktop on OSX</li>
3705 <li>Filetype associations not installed for webstart
3707 <li>Jalview does not always retrieve progress of a JABAWS
3708 job execution in full once it is complete</li>
3709 <li>revise SHMR RSBS definition to ensure alignment is
3710 uploaded via ali_file parameter</li>
3711 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3712 <li>View all structures superposed fails with exception</li>
3713 <li>Jnet job queues forever if a very short sequence is
3714 submitted for prediction</li>
3715 <li>Cut and paste menu not opened when mouse clicked on
3717 <li>Putting fractional value into integer text box in
3718 alignment parameter dialog causes Jalview to hang</li>
3719 <li>Structure view highlighting doesn't work on
3721 <li>View all structures fails with exception shown in
3723 <li>Characters in filename associated with PDBEntry not
3724 escaped in a platform independent way</li>
3725 <li>Jalview desktop fails to launch with exception when
3727 <li>Tree calculation reports 'you must have 2 or more
3728 sequences selected' when selection is empty</li>
3729 <li>Jalview desktop fails to launch with jar signature
3730 failure when java web start temporary file caching is
3732 <li>DAS Sequence retrieval with range qualification
3733 results in sequence xref which includes range qualification</li>
3734 <li>Errors during processing of command line arguments
3735 cause progress bar (JAL-898) to be removed</li>
3736 <li>Replace comma for semi-colon option not disabled for
3737 DAS sources in sequence fetcher</li>
3738 <li>Cannot close news reader when JABAWS server warning
3739 dialog is shown</li>
3740 <li>Option widgets not updated to reflect user settings</li>
3741 <li>Edited sequence not submitted to web service</li>
3742 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3743 <li>InstallAnywhere installer doesn't unpack and run
3744 on OSX Mountain Lion</li>
3745 <li>Annotation panel not given a scroll bar when
3746 sequences with alignment annotation are pasted into the
3748 <li>Sequence associated annotation rows not associated
3749 when loaded from Jalview project</li>
3750 <li>Browser launch fails with NPE on java 1.7</li>
3751 <li>JABAWS alignment marked as finished when job was
3752 cancelled or job failed due to invalid input</li>
3753 <li>NPE with v2.7 example when clicking on Tree
3754 associated with all views</li>
3755 <li>Exceptions when copy/paste sequences with grouped
3756 annotation rows to new window</li>
3757 </ul> <em>Applet</em>
3759 <li>Sequence features are momentarily displayed before
3760 they are hidden using hidefeaturegroups applet parameter</li>
3761 <li>loading features via javascript API automatically
3762 enables feature display</li>
3763 <li>scrollToColumnIn javascript API method doesn't
3765 </ul> <em>General</em>
3767 <li>Redundancy removal fails for rna alignment</li>
3768 <li>PCA calculation fails when sequence has been selected
3769 and then deselected</li>
3770 <li>PCA window shows grey box when first opened on OSX</li>
3771 <li>Letters coloured pink in sequence logo when alignment
3772 coloured with clustalx</li>
3773 <li>Choosing fonts without letter symbols defined causes
3774 exceptions and redraw errors</li>
3775 <li>Initial PCA plot view is not same as manually
3776 reconfigured view</li>
3777 <li>Grouped annotation graph label has incorrect line
3779 <li>Grouped annotation graph label display is corrupted
3780 for lots of labels</li>
3785 <div align="center">
3786 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3789 <td><em>Application</em>
3791 <li>Jalview Desktop News Reader</li>
3792 <li>Tweaked default layout of web services menu</li>
3793 <li>View/alignment association menu to enable user to
3794 easily specify which alignment a multi-structure view takes
3795 its colours/correspondences from</li>
3796 <li>Allow properties file location to be specified as URL</li>
3797 <li>Extend Jalview project to preserve associations
3798 between many alignment views and a single Jmol display</li>
3799 <li>Store annotation row height in Jalview project file</li>
3800 <li>Annotation row column label formatting attributes
3801 stored in project file</li>
3802 <li>Annotation row order for auto-calculated annotation
3803 rows preserved in Jalview project file</li>
3804 <li>Visual progress indication when Jalview state is
3805 saved using Desktop window menu</li>
3806 <li>Visual indication that command line arguments are
3807 still being processed</li>
3808 <li>Groovy script execution from URL</li>
3809 <li>Colour by annotation default min and max colours in
3811 <li>Automatically associate PDB files dragged onto an
3812 alignment with sequences that have high similarity and
3814 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3815 <li>'view structures' option to open many
3816 structures in same window</li>
3817 <li>Sort associated views menu option for tree panel</li>
3818 <li>Group all JABA and non-JABA services for a particular
3819 analysis function in its own submenu</li>
3820 </ul> <em>Applet</em>
3822 <li>Userdefined and autogenerated annotation rows for
3824 <li>Adjustment of alignment annotation pane height</li>
3825 <li>Annotation scrollbar for annotation panel</li>
3826 <li>Drag to reorder annotation rows in annotation panel</li>
3827 <li>'automaticScrolling' parameter</li>
3828 <li>Allow sequences with partial ID string matches to be
3829 annotated from GFF/Jalview features files</li>
3830 <li>Sequence logo annotation row in applet</li>
3831 <li>Absolute paths relative to host server in applet
3832 parameters are treated as such</li>
3833 <li>New in the JalviewLite javascript API:
3835 <li>JalviewLite.js javascript library</li>
3836 <li>Javascript callbacks for
3838 <li>Applet initialisation</li>
3839 <li>Sequence/alignment mouse-overs and selections</li>
3842 <li>scrollTo row and column alignment scrolling
3844 <li>Select sequence/alignment regions from javascript</li>
3845 <li>javascript structure viewer harness to pass
3846 messages between Jmol and Jalview when running as
3847 distinct applets</li>
3848 <li>sortBy method</li>
3849 <li>Set of applet and application examples shipped
3850 with documentation</li>
3851 <li>New example to demonstrate JalviewLite and Jmol
3852 javascript message exchange</li>
3854 </ul> <em>General</em>
3856 <li>Enable Jmol displays to be associated with multiple
3857 multiple alignments</li>
3858 <li>Option to automatically sort alignment with new tree</li>
3859 <li>User configurable link to enable redirects to a
3860 www.Jalview.org mirror</li>
3861 <li>Jmol colours option for Jmol displays</li>
3862 <li>Configurable newline string when writing alignment
3863 and other flat files</li>
3864 <li>Allow alignment annotation description lines to
3865 contain html tags</li>
3866 </ul> <em>Documentation and Development</em>
3868 <li>Add groovy test harness for bulk load testing to
3870 <li>Groovy script to load and align a set of sequences
3871 using a web service before displaying the result in the
3872 Jalview desktop</li>
3873 <li>Restructured javascript and applet api documentation</li>
3874 <li>Ant target to publish example html files with applet
3876 <li>Netbeans project for building Jalview from source</li>
3877 <li>ant task to create online javadoc for Jalview source</li>
3879 <td><em>Application</em>
3881 <li>User defined colourscheme throws exception when
3882 current built in colourscheme is saved as new scheme</li>
3883 <li>AlignFrame->Save in application pops up save
3884 dialog for valid filename/format</li>
3885 <li>Cannot view associated structure for UniProt sequence</li>
3886 <li>PDB file association breaks for UniProt sequence
3888 <li>Associate PDB from file dialog does not tell you
3889 which sequence is to be associated with the file</li>
3890 <li>Find All raises null pointer exception when query
3891 only matches sequence IDs</li>
3892 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3893 <li>Jalview project with Jmol views created with Jalview
3894 2.4 cannot be loaded</li>
3895 <li>Filetype associations not installed for webstart
3897 <li>Two or more chains in a single PDB file associated
3898 with sequences in different alignments do not get coloured
3899 by their associated sequence</li>
3900 <li>Visibility status of autocalculated annotation row
3901 not preserved when project is loaded</li>
3902 <li>Annotation row height and visibility attributes not
3903 stored in Jalview project</li>
3904 <li>Tree bootstraps are not preserved when saved as a
3905 Jalview project</li>
3906 <li>Envision2 workflow tooltips are corrupted</li>
3907 <li>Enabling show group conservation also enables colour
3908 by conservation</li>
3909 <li>Duplicate group associated conservation or consensus
3910 created on new view</li>
3911 <li>Annotation scrollbar not displayed after 'show
3912 all hidden annotation rows' option selected</li>
3913 <li>Alignment quality not updated after alignment
3914 annotation row is hidden then shown</li>
3915 <li>Preserve colouring of structures coloured by
3916 sequences in pre Jalview 2.7 projects</li>
3917 <li>Web service job parameter dialog is not laid out
3919 <li>Web services menu not refreshed after 'reset
3920 services' button is pressed in preferences</li>
3921 <li>Annotation off by one in Jalview v2_3 example project</li>
3922 <li>Structures imported from file and saved in project
3923 get name like jalview_pdb1234.txt when reloaded</li>
3924 <li>Jalview does not always retrieve progress of a JABAWS
3925 job execution in full once it is complete</li>
3926 </ul> <em>Applet</em>
3928 <li>Alignment height set incorrectly when lots of
3929 annotation rows are displayed</li>
3930 <li>Relative URLs in feature HTML text not resolved to
3932 <li>View follows highlighting does not work for positions
3934 <li><= shown as = in tooltip</li>
3935 <li>Export features raises exception when no features
3937 <li>Separator string used for serialising lists of IDs
3938 for javascript api is modified when separator string
3939 provided as parameter</li>
3940 <li>Null pointer exception when selecting tree leaves for
3941 alignment with no existing selection</li>
3942 <li>Relative URLs for datasources assumed to be relative
3943 to applet's codebase</li>
3944 <li>Status bar not updated after finished searching and
3945 search wraps around to first result</li>
3946 <li>StructureSelectionManager instance shared between
3947 several Jalview applets causes race conditions and memory
3949 <li>Hover tooltip and mouseover of position on structure
3950 not sent from Jmol in applet</li>
3951 <li>Certain sequences of javascript method calls to
3952 applet API fatally hang browser</li>
3953 </ul> <em>General</em>
3955 <li>View follows structure mouseover scrolls beyond
3956 position with wrapped view and hidden regions</li>
3957 <li>Find sequence position moves to wrong residue
3958 with/without hidden columns</li>
3959 <li>Sequence length given in alignment properties window
3961 <li>InvalidNumberFormat exceptions thrown when trying to
3962 import PDB like structure files</li>
3963 <li>Positional search results are only highlighted
3964 between user-supplied sequence start/end bounds</li>
3965 <li>End attribute of sequence is not validated</li>
3966 <li>Find dialog only finds first sequence containing a
3967 given sequence position</li>
3968 <li>Sequence numbering not preserved in MSF alignment
3970 <li>Jalview PDB file reader does not extract sequence
3971 from nucleotide chains correctly</li>
3972 <li>Structure colours not updated when tree partition
3973 changed in alignment</li>
3974 <li>Sequence associated secondary structure not correctly
3975 parsed in interleaved stockholm</li>
3976 <li>Colour by annotation dialog does not restore current
3978 <li>Hiding (nearly) all sequences doesn't work
3980 <li>Sequences containing lowercase letters are not
3981 properly associated with their pdb files</li>
3982 </ul> <em>Documentation and Development</em>
3984 <li>schemas/JalviewWsParamSet.xsd corrupted by
3985 ApplyCopyright tool</li>
3990 <div align="center">
3991 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3994 <td><em>Application</em>
3996 <li>New warning dialog when the Jalview Desktop cannot
3997 contact web services</li>
3998 <li>JABA service parameters for a preset are shown in
3999 service job window</li>
4000 <li>JABA Service menu entries reworded</li>
4004 <li>Modeller PIR IO broken - cannot correctly import a
4005 pir file emitted by Jalview</li>
4006 <li>Existing feature settings transferred to new
4007 alignment view created from cut'n'paste</li>
4008 <li>Improved test for mixed amino/nucleotide chains when
4009 parsing PDB files</li>
4010 <li>Consensus and conservation annotation rows
4011 occasionally become blank for all new windows</li>
4012 <li>Exception raised when right clicking above sequences
4013 in wrapped view mode</li>
4014 </ul> <em>Application</em>
4016 <li>multiple multiply aligned structure views cause cpu
4017 usage to hit 100% and computer to hang</li>
4018 <li>Web Service parameter layout breaks for long user
4019 parameter names</li>
4020 <li>Jaba service discovery hangs desktop if Jaba server
4027 <div align="center">
4028 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4031 <td><em>Application</em>
4033 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4034 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4037 <li>Web Services preference tab</li>
4038 <li>Analysis parameters dialog box and user defined
4040 <li>Improved speed and layout of Envision2 service menu</li>
4041 <li>Superpose structures using associated sequence
4043 <li>Export coordinates and projection as CSV from PCA
4045 </ul> <em>Applet</em>
4047 <li>enable javascript: execution by the applet via the
4048 link out mechanism</li>
4049 </ul> <em>Other</em>
4051 <li>Updated the Jmol Jalview interface to work with Jmol
4053 <li>The Jalview Desktop and JalviewLite applet now
4054 require Java 1.5</li>
4055 <li>Allow Jalview feature colour specification for GFF
4056 sequence annotation files</li>
4057 <li>New 'colour by label' keword in Jalview feature file
4058 type colour specification</li>
4059 <li>New Jalview Desktop Groovy API method that allows a
4060 script to check if it being run in an interactive session or
4061 in a batch operation from the Jalview command line</li>
4065 <li>clustalx colourscheme colours Ds preferentially when
4066 both D+E are present in over 50% of the column</li>
4067 </ul> <em>Application</em>
4069 <li>typo in AlignmentFrame->View->Hide->all but
4070 selected Regions menu item</li>
4071 <li>sequence fetcher replaces ',' for ';' when the ',' is
4072 part of a valid accession ID</li>
4073 <li>fatal OOM if object retrieved by sequence fetcher
4074 runs out of memory</li>
4075 <li>unhandled Out of Memory Error when viewing pca
4076 analysis results</li>
4077 <li>InstallAnywhere builds fail to launch on OS X java
4078 10.5 update 4 (due to apple Java 1.6 update)</li>
4079 <li>Installanywhere Jalview silently fails to launch</li>
4080 </ul> <em>Applet</em>
4082 <li>Jalview.getFeatureGroups() raises an
4083 ArrayIndexOutOfBoundsException if no feature groups are
4090 <div align="center">
4091 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4097 <li>Alignment prettyprinter doesn't cope with long
4099 <li>clustalx colourscheme colours Ds preferentially when
4100 both D+E are present in over 50% of the column</li>
4101 <li>nucleic acid structures retrieved from PDB do not
4102 import correctly</li>
4103 <li>More columns get selected than were clicked on when a
4104 number of columns are hidden</li>
4105 <li>annotation label popup menu not providing correct
4106 add/hide/show options when rows are hidden or none are
4108 <li>Stockholm format shown in list of readable formats,
4109 and parser copes better with alignments from RFAM.</li>
4110 <li>CSV output of consensus only includes the percentage
4111 of all symbols if sequence logo display is enabled</li>
4113 </ul> <em>Applet</em>
4115 <li>annotation panel disappears when annotation is
4117 </ul> <em>Application</em>
4119 <li>Alignment view not redrawn properly when new
4120 alignment opened where annotation panel is visible but no
4121 annotations are present on alignment</li>
4122 <li>pasted region containing hidden columns is
4123 incorrectly displayed in new alignment window</li>
4124 <li>Jalview slow to complete operations when stdout is
4125 flooded (fix is to close the Jalview console)</li>
4126 <li>typo in AlignmentFrame->View->Hide->all but
4127 selected Rregions menu item.</li>
4128 <li>inconsistent group submenu and Format submenu entry
4129 'Un' or 'Non'conserved</li>
4130 <li>Sequence feature settings are being shared by
4131 multiple distinct alignments</li>
4132 <li>group annotation not recreated when tree partition is
4134 <li>double click on group annotation to select sequences
4135 does not propagate to associated trees</li>
4136 <li>Mac OSX specific issues:
4138 <li>exception raised when mouse clicked on desktop
4139 window background</li>
4140 <li>Desktop menu placed on menu bar and application
4141 name set correctly</li>
4142 <li>sequence feature settings not wide enough for the
4143 save feature colourscheme button</li>
4152 <div align="center">
4153 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4156 <td><em>New Capabilities</em>
4158 <li>URL links generated from description line for
4159 regular-expression based URL links (applet and application)
4161 <li>Non-positional feature URL links are shown in link
4163 <li>Linked viewing of nucleic acid sequences and
4165 <li>Automatic Scrolling option in View menu to display
4166 the currently highlighted region of an alignment.</li>
4167 <li>Order an alignment by sequence length, or using the
4168 average score or total feature count for each sequence.</li>
4169 <li>Shading features by score or associated description</li>
4170 <li>Subdivide alignment and groups based on identity of
4171 selected subsequence (Make Groups from Selection).</li>
4172 <li>New hide/show options including Shift+Control+H to
4173 hide everything but the currently selected region.</li>
4174 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4175 </ul> <em>Application</em>
4177 <li>Fetch DB References capabilities and UI expanded to
4178 support retrieval from DAS sequence sources</li>
4179 <li>Local DAS Sequence sources can be added via the
4180 command line or via the Add local source dialog box.</li>
4181 <li>DAS Dbref and DbxRef feature types are parsed as
4182 database references and protein_name is parsed as
4183 description line (BioSapiens terms).</li>
4184 <li>Enable or disable non-positional feature and database
4185 references in sequence ID tooltip from View menu in
4187 <!-- <li>New hidden columns and rows and representatives capabilities
4188 in annotations file (in progress - not yet fully implemented)</li> -->
4189 <li>Group-associated consensus, sequence logos and
4190 conservation plots</li>
4191 <li>Symbol distributions for each column can be exported
4192 and visualized as sequence logos</li>
4193 <li>Optionally scale multi-character column labels to fit
4194 within each column of annotation row<!-- todo for applet -->
4196 <li>Optional automatic sort of associated alignment view
4197 when a new tree is opened.</li>
4198 <li>Jalview Java Console</li>
4199 <li>Better placement of desktop window when moving
4200 between different screens.</li>
4201 <li>New preference items for sequence ID tooltip and
4202 consensus annotation</li>
4203 <li>Client to submit sequences and IDs to Envision2
4205 <li><em>Vamsas Capabilities</em>
4207 <li>Improved VAMSAS synchronization (Jalview archive
4208 used to preserve views, structures, and tree display
4210 <li>Import of vamsas documents from disk or URL via
4212 <li>Sharing of selected regions between views and
4213 with other VAMSAS applications (Experimental feature!)</li>
4214 <li>Updated API to VAMSAS version 0.2</li>
4216 </ul> <em>Applet</em>
4218 <li>Middle button resizes annotation row height</li>
4221 <li>sortByTree (true/false) - automatically sort the
4222 associated alignment view by the tree when a new tree is
4224 <li>showTreeBootstraps (true/false) - show or hide
4225 branch bootstraps (default is to show them if available)</li>
4226 <li>showTreeDistances (true/false) - show or hide
4227 branch lengths (default is to show them if available)</li>
4228 <li>showUnlinkedTreeNodes (true/false) - indicate if
4229 unassociated nodes should be highlighted in the tree
4231 <li>heightScale and widthScale (1.0 or more) -
4232 increase the height or width of a cell in the alignment
4233 grid relative to the current font size.</li>
4236 <li>Non-positional features displayed in sequence ID
4238 </ul> <em>Other</em>
4240 <li>Features format: graduated colour definitions and
4241 specification of feature scores</li>
4242 <li>Alignment Annotations format: new keywords for group
4243 associated annotation (GROUP_REF) and annotation row display
4244 properties (ROW_PROPERTIES)</li>
4245 <li>XML formats extended to support graduated feature
4246 colourschemes, group associated annotation, and profile
4247 visualization settings.</li></td>
4250 <li>Source field in GFF files parsed as feature source
4251 rather than description</li>
4252 <li>Non-positional features are now included in sequence
4253 feature and gff files (controlled via non-positional feature
4254 visibility in tooltip).</li>
4255 <li>URL links generated for all feature links (bugfix)</li>
4256 <li>Added URL embedding instructions to features file
4258 <li>Codons containing ambiguous nucleotides translated as
4259 'X' in peptide product</li>
4260 <li>Match case switch in find dialog box works for both
4261 sequence ID and sequence string and query strings do not
4262 have to be in upper case to match case-insensitively.</li>
4263 <li>AMSA files only contain first column of
4264 multi-character column annotation labels</li>
4265 <li>Jalview Annotation File generation/parsing consistent
4266 with documentation (e.g. Stockholm annotation can be
4267 exported and re-imported)</li>
4268 <li>PDB files without embedded PDB IDs given a friendly
4270 <li>Find incrementally searches ID string matches as well
4271 as subsequence matches, and correctly reports total number
4275 <li>Better handling of exceptions during sequence
4277 <li>Dasobert generated non-positional feature URL
4278 link text excludes the start_end suffix</li>
4279 <li>DAS feature and source retrieval buttons disabled
4280 when fetch or registry operations in progress.</li>
4281 <li>PDB files retrieved from URLs are cached properly</li>
4282 <li>Sequence description lines properly shared via
4284 <li>Sequence fetcher fetches multiple records for all
4286 <li>Ensured that command line das feature retrieval
4287 completes before alignment figures are generated.</li>
4288 <li>Reduced time taken when opening file browser for
4290 <li>isAligned check prior to calculating tree, PCA or
4291 submitting an MSA to JNet now excludes hidden sequences.</li>
4292 <li>User defined group colours properly recovered
4293 from Jalview projects.</li>
4302 <div align="center">
4303 <strong>2.4.0.b2</strong><br> 28/10/2009
4308 <li>Experimental support for google analytics usage
4310 <li>Jalview privacy settings (user preferences and docs).</li>
4315 <li>Race condition in applet preventing startup in
4317 <li>Exception when feature created from selection beyond
4318 length of sequence.</li>
4319 <li>Allow synthetic PDB files to be imported gracefully</li>
4320 <li>Sequence associated annotation rows associate with
4321 all sequences with a given id</li>
4322 <li>Find function matches case-insensitively for sequence
4323 ID string searches</li>
4324 <li>Non-standard characters do not cause pairwise
4325 alignment to fail with exception</li>
4326 </ul> <em>Application Issues</em>
4328 <li>Sequences are now validated against EMBL database</li>
4329 <li>Sequence fetcher fetches multiple records for all
4331 </ul> <em>InstallAnywhere Issues</em>
4333 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4334 issue with installAnywhere mechanism)</li>
4335 <li>Command line launching of JARs from InstallAnywhere
4336 version (java class versioning error fixed)</li>
4343 <div align="center">
4344 <strong>2.4</strong><br> 27/8/2008
4347 <td><em>User Interface</em>
4349 <li>Linked highlighting of codon and amino acid from
4350 translation and protein products</li>
4351 <li>Linked highlighting of structure associated with
4352 residue mapping to codon position</li>
4353 <li>Sequence Fetcher provides example accession numbers
4354 and 'clear' button</li>
4355 <li>MemoryMonitor added as an option under Desktop's
4357 <li>Extract score function to parse whitespace separated
4358 numeric data in description line</li>
4359 <li>Column labels in alignment annotation can be centred.</li>
4360 <li>Tooltip for sequence associated annotation give name
4362 </ul> <em>Web Services and URL fetching</em>
4364 <li>JPred3 web service</li>
4365 <li>Prototype sequence search client (no public services
4367 <li>Fetch either seed alignment or full alignment from
4369 <li>URL Links created for matching database cross
4370 references as well as sequence ID</li>
4371 <li>URL Links can be created using regular-expressions</li>
4372 </ul> <em>Sequence Database Connectivity</em>
4374 <li>Retrieval of cross-referenced sequences from other
4376 <li>Generalised database reference retrieval and
4377 validation to all fetchable databases</li>
4378 <li>Fetch sequences from DAS sources supporting the
4379 sequence command</li>
4380 </ul> <em>Import and Export</em>
4381 <li>export annotation rows as CSV for spreadsheet import</li>
4382 <li>Jalview projects record alignment dataset associations,
4383 EMBL products, and cDNA sequence mappings</li>
4384 <li>Sequence Group colour can be specified in Annotation
4386 <li>Ad-hoc colouring of group in Annotation File using RGB
4387 triplet as name of colourscheme</li>
4388 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4390 <li>treenode binding for VAMSAS tree exchange</li>
4391 <li>local editing and update of sequences in VAMSAS
4392 alignments (experimental)</li>
4393 <li>Create new or select existing session to join</li>
4394 <li>load and save of vamsas documents</li>
4395 </ul> <em>Application command line</em>
4397 <li>-tree parameter to open trees (introduced for passing
4399 <li>-fetchfrom command line argument to specify nicknames
4400 of DAS servers to query for alignment features</li>
4401 <li>-dasserver command line argument to add new servers
4402 that are also automatically queried for features</li>
4403 <li>-groovy command line argument executes a given groovy
4404 script after all input data has been loaded and parsed</li>
4405 </ul> <em>Applet-Application data exchange</em>
4407 <li>Trees passed as applet parameters can be passed to
4408 application (when using "View in full
4409 application")</li>
4410 </ul> <em>Applet Parameters</em>
4412 <li>feature group display control parameter</li>
4413 <li>debug parameter</li>
4414 <li>showbutton parameter</li>
4415 </ul> <em>Applet API methods</em>
4417 <li>newView public method</li>
4418 <li>Window (current view) specific get/set public methods</li>
4419 <li>Feature display control methods</li>
4420 <li>get list of currently selected sequences</li>
4421 </ul> <em>New Jalview distribution features</em>
4423 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4424 <li>RELEASE file gives build properties for the latest
4425 Jalview release.</li>
4426 <li>Java 1.1 Applet build made easier and donotobfuscate
4427 property controls execution of obfuscator</li>
4428 <li>Build target for generating source distribution</li>
4429 <li>Debug flag for javacc</li>
4430 <li>.jalview_properties file is documented (slightly) in
4431 jalview.bin.Cache</li>
4432 <li>Continuous Build Integration for stable and
4433 development version of Application, Applet and source
4438 <li>selected region output includes visible annotations
4439 (for certain formats)</li>
4440 <li>edit label/displaychar contains existing label/char
4442 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4443 <li>shorter peptide product names from EMBL records</li>
4444 <li>Newick string generator makes compact representations</li>
4445 <li>bootstrap values parsed correctly for tree files with
4447 <li>pathological filechooser bug avoided by not allowing
4448 filenames containing a ':'</li>
4449 <li>Fixed exception when parsing GFF files containing
4450 global sequence features</li>
4451 <li>Alignment datasets are finalized only when number of
4452 references from alignment sequences goes to zero</li>
4453 <li>Close of tree branch colour box without colour
4454 selection causes cascading exceptions</li>
4455 <li>occasional negative imgwidth exceptions</li>
4456 <li>better reporting of non-fatal warnings to user when
4457 file parsing fails.</li>
4458 <li>Save works when Jalview project is default format</li>
4459 <li>Save as dialog opened if current alignment format is
4460 not a valid output format</li>
4461 <li>UniProt canonical names introduced for both das and
4463 <li>Histidine should be midblue (not pink!) in Zappo</li>
4464 <li>error messages passed up and output when data read
4466 <li>edit undo recovers previous dataset sequence when
4467 sequence is edited</li>
4468 <li>allow PDB files without pdb ID HEADER lines (like
4469 those generated by MODELLER) to be read in properly</li>
4470 <li>allow reading of JPred concise files as a normal
4472 <li>Stockholm annotation parsing and alignment properties
4473 import fixed for PFAM records</li>
4474 <li>Structure view windows have correct name in Desktop
4476 <li>annotation consisting of sequence associated scores
4477 can be read and written correctly to annotation file</li>
4478 <li>Aligned cDNA translation to aligned peptide works
4480 <li>Fixed display of hidden sequence markers and
4481 non-italic font for representatives in Applet</li>
4482 <li>Applet Menus are always embedded in applet window on
4484 <li>Newly shown features appear at top of stack (in
4486 <li>Annotations added via parameter not drawn properly
4487 due to null pointer exceptions</li>
4488 <li>Secondary structure lines are drawn starting from
4489 first column of alignment</li>
4490 <li>UniProt XML import updated for new schema release in
4492 <li>Sequence feature to sequence ID match for Features
4493 file is case-insensitive</li>
4494 <li>Sequence features read from Features file appended to
4495 all sequences with matching IDs</li>
4496 <li>PDB structure coloured correctly for associated views
4497 containing a sub-sequence</li>
4498 <li>PDB files can be retrieved by applet from Jar files</li>
4499 <li>feature and annotation file applet parameters
4500 referring to different directories are retrieved correctly</li>
4501 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4502 <li>Fixed application hang whilst waiting for
4503 splash-screen version check to complete</li>
4504 <li>Applet properly URLencodes input parameter values
4505 when passing them to the launchApp service</li>
4506 <li>display name and local features preserved in results
4507 retrieved from web service</li>
4508 <li>Visual delay indication for sequence retrieval and
4509 sequence fetcher initialisation</li>
4510 <li>updated Application to use DAS 1.53e version of
4511 dasobert DAS client</li>
4512 <li>Re-instated Full AMSA support and .amsa file
4514 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4522 <div align="center">
4523 <strong>2.3</strong><br> 9/5/07
4528 <li>Jmol 11.0.2 integration</li>
4529 <li>PDB views stored in Jalview XML files</li>
4530 <li>Slide sequences</li>
4531 <li>Edit sequence in place</li>
4532 <li>EMBL CDS features</li>
4533 <li>DAS Feature mapping</li>
4534 <li>Feature ordering</li>
4535 <li>Alignment Properties</li>
4536 <li>Annotation Scores</li>
4537 <li>Sort by scores</li>
4538 <li>Feature/annotation editing in applet</li>
4543 <li>Headless state operation in 2.2.1</li>
4544 <li>Incorrect and unstable DNA pairwise alignment</li>
4545 <li>Cut and paste of sequences with annotation</li>
4546 <li>Feature group display state in XML</li>
4547 <li>Feature ordering in XML</li>
4548 <li>blc file iteration selection using filename # suffix</li>
4549 <li>Stockholm alignment properties</li>
4550 <li>Stockhom alignment secondary structure annotation</li>
4551 <li>2.2.1 applet had no feature transparency</li>
4552 <li>Number pad keys can be used in cursor mode</li>
4553 <li>Structure Viewer mirror image resolved</li>
4560 <div align="center">
4561 <strong>2.2.1</strong><br> 12/2/07
4566 <li>Non standard characters can be read and displayed
4567 <li>Annotations/Features can be imported/exported to the
4569 <li>Applet allows editing of sequence/annotation/group
4570 name & description
4571 <li>Preference setting to display sequence name in
4573 <li>Annotation file format extended to allow
4574 Sequence_groups to be defined
4575 <li>Default opening of alignment overview panel can be
4576 specified in preferences
4577 <li>PDB residue numbering annotation added to associated
4583 <li>Applet crash under certain Linux OS with Java 1.6
4585 <li>Annotation file export / import bugs fixed
4586 <li>PNG / EPS image output bugs fixed
4592 <div align="center">
4593 <strong>2.2</strong><br> 27/11/06
4598 <li>Multiple views on alignment
4599 <li>Sequence feature editing
4600 <li>"Reload" alignment
4601 <li>"Save" to current filename
4602 <li>Background dependent text colour
4603 <li>Right align sequence ids
4604 <li>User-defined lower case residue colours
4607 <li>Menu item accelerator keys
4608 <li>Control-V pastes to current alignment
4609 <li>Cancel button for DAS Feature Fetching
4610 <li>PCA and PDB Viewers zoom via mouse roller
4611 <li>User-defined sub-tree colours and sub-tree selection
4613 <li>'New Window' button on the 'Output to Text box'
4618 <li>New memory efficient Undo/Redo System
4619 <li>Optimised symbol lookups and conservation/consensus
4621 <li>Region Conservation/Consensus recalculated after
4623 <li>Fixed Remove Empty Columns Bug (empty columns at end
4625 <li>Slowed DAS Feature Fetching for increased robustness.
4627 <li>Made angle brackets in ASCII feature descriptions
4629 <li>Re-instated Zoom function for PCA
4630 <li>Sequence descriptions conserved in web service
4632 <li>UniProt ID discoverer uses any word separated by
4634 <li>WsDbFetch query/result association resolved
4635 <li>Tree leaf to sequence mapping improved
4636 <li>Smooth fonts switch moved to FontChooser dialog box.
4643 <div align="center">
4644 <strong>2.1.1</strong><br> 12/9/06
4649 <li>Copy consensus sequence to clipboard</li>
4654 <li>Image output - rightmost residues are rendered if
4655 sequence id panel has been resized</li>
4656 <li>Image output - all offscreen group boundaries are
4658 <li>Annotation files with sequence references - all
4659 elements in file are relative to sequence position</li>
4660 <li>Mac Applet users can use Alt key for group editing</li>
4666 <div align="center">
4667 <strong>2.1</strong><br> 22/8/06
4672 <li>MAFFT Multiple Alignment in default Web Service list</li>
4673 <li>DAS Feature fetching</li>
4674 <li>Hide sequences and columns</li>
4675 <li>Export Annotations and Features</li>
4676 <li>GFF file reading / writing</li>
4677 <li>Associate structures with sequences from local PDB
4679 <li>Add sequences to exisiting alignment</li>
4680 <li>Recently opened files / URL lists</li>
4681 <li>Applet can launch the full application</li>
4682 <li>Applet has transparency for features (Java 1.2
4684 <li>Applet has user defined colours parameter</li>
4685 <li>Applet can load sequences from parameter
4686 "sequence<em>x</em>"
4692 <li>Redundancy Panel reinstalled in the Applet</li>
4693 <li>Monospaced font - EPS / rescaling bug fixed</li>
4694 <li>Annotation files with sequence references bug fixed</li>
4700 <div align="center">
4701 <strong>2.08.1</strong><br> 2/5/06
4706 <li>Change case of selected region from Popup menu</li>
4707 <li>Choose to match case when searching</li>
4708 <li>Middle mouse button and mouse movement can compress /
4709 expand the visible width and height of the alignment</li>
4714 <li>Annotation Panel displays complete JNet results</li>
4720 <div align="center">
4721 <strong>2.08b</strong><br> 18/4/06
4727 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4728 <li>Righthand label on wrapped alignments shows correct
4735 <div align="center">
4736 <strong>2.08</strong><br> 10/4/06
4741 <li>Editing can be locked to the selection area</li>
4742 <li>Keyboard editing</li>
4743 <li>Create sequence features from searches</li>
4744 <li>Precalculated annotations can be loaded onto
4746 <li>Features file allows grouping of features</li>
4747 <li>Annotation Colouring scheme added</li>
4748 <li>Smooth fonts off by default - Faster rendering</li>
4749 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4754 <li>Drag & Drop fixed on Linux</li>
4755 <li>Jalview Archive file faster to load/save, sequence
4756 descriptions saved.</li>
4762 <div align="center">
4763 <strong>2.07</strong><br> 12/12/05
4768 <li>PDB Structure Viewer enhanced</li>
4769 <li>Sequence Feature retrieval and display enhanced</li>
4770 <li>Choose to output sequence start-end after sequence
4771 name for file output</li>
4772 <li>Sequence Fetcher WSDBFetch@EBI</li>
4773 <li>Applet can read feature files, PDB files and can be
4774 used for HTML form input</li>
4779 <li>HTML output writes groups and features</li>
4780 <li>Group editing is Control and mouse click</li>
4781 <li>File IO bugs</li>
4787 <div align="center">
4788 <strong>2.06</strong><br> 28/9/05
4793 <li>View annotations in wrapped mode</li>
4794 <li>More options for PCA viewer</li>
4799 <li>GUI bugs resolved</li>
4800 <li>Runs with -nodisplay from command line</li>
4806 <div align="center">
4807 <strong>2.05b</strong><br> 15/9/05
4812 <li>Choose EPS export as lineart or text</li>
4813 <li>Jar files are executable</li>
4814 <li>Can read in Uracil - maps to unknown residue</li>
4819 <li>Known OutOfMemory errors give warning message</li>
4820 <li>Overview window calculated more efficiently</li>
4821 <li>Several GUI bugs resolved</li>
4827 <div align="center">
4828 <strong>2.05</strong><br> 30/8/05
4833 <li>Edit and annotate in "Wrapped" view</li>
4838 <li>Several GUI bugs resolved</li>
4844 <div align="center">
4845 <strong>2.04</strong><br> 24/8/05
4850 <li>Hold down mouse wheel & scroll to change font
4856 <li>Improved JPred client reliability</li>
4857 <li>Improved loading of Jalview files</li>
4863 <div align="center">
4864 <strong>2.03</strong><br> 18/8/05
4869 <li>Set Proxy server name and port in preferences</li>
4870 <li>Multiple URL links from sequence ids</li>
4871 <li>User Defined Colours can have a scheme name and added
4873 <li>Choose to ignore gaps in consensus calculation</li>
4874 <li>Unix users can set default web browser</li>
4875 <li>Runs without GUI for batch processing</li>
4876 <li>Dynamically generated Web Service Menus</li>
4881 <li>InstallAnywhere download for Sparc Solaris</li>
4887 <div align="center">
4888 <strong>2.02</strong><br> 18/7/05
4894 <li>Copy & Paste order of sequences maintains
4895 alignment order.</li>
4901 <div align="center">
4902 <strong>2.01</strong><br> 12/7/05
4907 <li>Use delete key for deleting selection.</li>
4908 <li>Use Mouse wheel to scroll sequences.</li>
4909 <li>Help file updated to describe how to add alignment
4911 <li>Version and build date written to build properties
4913 <li>InstallAnywhere installation will check for updates
4914 at launch of Jalview.</li>
4919 <li>Delete gaps bug fixed.</li>
4920 <li>FileChooser sorts columns.</li>
4921 <li>Can remove groups one by one.</li>
4922 <li>Filechooser icons installed.</li>
4923 <li>Finder ignores return character when searching.
4924 Return key will initiate a search.<br>
4931 <div align="center">
4932 <strong>2.0</strong><br> 20/6/05
4937 <li>New codebase</li>