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;
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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.2.11.1.0">.0</a><br />
61 <em>22/04/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
66 'virtual' codon features shown on protein (or vice versa)
67 for display in alignments, on structure views (including
68 transfer to UCSF chimera), in feature reports and for
72 <!-- JAL-3121 -->Feature attributes from VCF files can be
73 exported and re-imported as GFF3 files
76 <!-- JAL-3376 -->Capture VCF "fixed column" values
77 POS, ID, QUAL, FILTER as Feature Attributes
80 <!-- JAL-3375 -->More robust VCF numeric data field
81 validation while parsing
84 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
88 <!-- JAL-3535 -->Feature Settings dialog title includes name
92 <!-- JAL-3538 -->Font anti-aliasing in alignment views
96 <!-- JAL-3468 -->Very long feature descriptions truncated in
100 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
101 with no feature types visible
104 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
106 </ul><em>Jalview Installer</em>
109 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
110 in console (may be null when Jalview launched as executable jar or via conda)
113 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
116 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
119 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
121 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
122 </ul> <em>Release processes</em>
125 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
128 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
130 </ul> <em>Build System</em>
133 <!-- JAL-3510 -->Clover updated to 4.4.1
136 <!-- JAL-3513 -->Test code included in Clover coverage
140 <em>Groovy Scripts</em>
143 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
144 to stdout containing the consensus sequence for each
145 alignment in a Jalview session
148 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
149 genomic sequence_variant annotation from CDS as
150 missense_variant or synonymous_variant on protein products.
154 <td align="left" valign="top">
157 <!-- JAL-3581 -->Hidden sequence markers still visible when
158 'Show hidden markers' option is not ticked
161 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
162 PNG output when 'Automatically set ID width' is set in
163 jalview preferences or properties file
166 <!-- JAL-3571 -->Feature Editor dialog can be opened when
167 'Show Sequence Features' option is not ticked
170 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
171 buttons in Feature Settings dialog are clicked when no
175 <!-- JAL-3412 -->ID margins for CDS and Protein views not
176 equal when split frame is first opened
179 <!-- JAL-3296 -->Sequence position numbers in status bar not
180 correct after editing a sequence's start position
183 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
184 with annotation and exceptions thrown when only a few
185 columns shown in wrapped mode
188 <!-- JAL-3386 -->Sequence IDs missing in headless export of
189 wrapped alignment figure with annotations
192 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
193 ID fails with ClassCastException
196 <!-- JAL-3389 -->Chimera session not restored from Jalview
200 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
201 feature settings dialog also selects columns
204 <!-- JAL-3473 -->SpinnerNumberModel causes
205 IllegalArgumentException in some circumstances
208 <!-- JAL-3534 -->Multiple feature settings dialogs can be
212 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
213 alignment window is closed
216 <!-- JAL-3406 -->Credits missing some authors in Jalview
217 help documentation for 2.11.0 release
220 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
221 includes Pfam ID as sequence's accession rather than its
224 </ul> <em>Java 11 Compatibility issues</em>
227 <!-- JAL-2987 -->OSX - Can't view some search results in
228 PDB/Uniprot search panel
230 </ul> <em>Installer</em>
233 <!-- JAL-3447 -->Jalview should not create file associations
234 for 3D structure files (.pdb, .mmcif. .cif)
236 </ul> <em>Repository and Source Release</em>
239 <!-- JAL-3474 -->removed obsolete .cvsignore files from
243 <!-- JAL-3541 -->Clover report generation running out of
246 </ul> <em>New Known Issues</em>
249 <!-- JAL-3523 -->OSX - Current working directory not
250 preserved when Jalview.app launched with parameters from
254 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
255 clipped in headless figure export when Right Align option
259 <!-- JAL-3542 -->Jalview Installation type always reports
260 'Source' in console output
263 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
264 bamboo server but run fine locally.
270 <td width="60" align="center" nowrap>
271 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
272 <em>04/07/2019</em></strong>
274 <td align="left" valign="top">
277 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
278 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
279 source project) rather than InstallAnywhere
282 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
283 settings, receive over the air updates and launch specific
284 versions via (<a href="https://github.com/threerings/getdown">Three
288 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
289 formats supported by Jalview (including .jvp project files)
292 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
293 arguments and switch between different getdown channels
296 <!-- JAL-3141 -->Backup files created when saving Jalview project
301 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
302 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
304 <!-- JAL-2620 -->Alternative genetic code tables for
305 'Translate as cDNA'</li>
307 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
308 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
311 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
312 implementation that allows updates) used for Sequence Feature collections</li>
314 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
315 features can be filtered and shaded according to any
316 associated attributes (e.g. variant attributes from VCF
317 file, or key-value pairs imported from column 9 of GFF
321 <!-- JAL-2879 -->Feature Attributes and shading schemes
322 stored and restored from Jalview Projects
325 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
326 recognise variant features
329 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
330 sequences (also coloured red by default)
333 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
337 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
338 algorithm (Z-sort/transparency and filter aware)
341 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
347 <!-- JAL-3205 -->Symmetric score matrices for faster
348 tree and PCA calculations
350 <li><strong>Principal Components Analysis Viewer</strong>
353 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
354 and Viewer state saved in Jalview Project
356 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
359 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
363 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
368 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
370 <li><strong>Speed and Efficiency</strong>
373 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
374 multiple groups when working with large alignments
377 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
381 <li><strong>User Interface</strong>
384 <!-- JAL-2933 -->Finder panel remembers last position in each
388 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
389 what is shown)<br />Only visible regions of alignment are shown by
390 default (can be changed in user preferences)
393 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
394 to the Overwrite Dialog
397 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
401 <!-- JAL-1244 -->Status bar shows bounds when dragging a
402 selection region, and gap count when inserting or deleting gaps
405 <!-- JAL-3132 -->Status bar updates over sequence and annotation
409 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
413 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
417 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
420 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
424 <!-- JAL-3181 -->Consistent ordering of links in sequence id
428 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
430 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
434 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
435 <li><strong>Java 11 Support (not yet on general release)</strong>
438 <!-- -->OSX GUI integrations for App menu's 'About' entry and
443 <em>Deprecations</em>
445 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
446 capabilities removed from the Jalview Desktop
448 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
449 unmarshalling has been replaced by JAXB for Jalview projects
450 and XML based data retrieval clients</li>
451 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
452 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
453 </ul> <em>Documentation</em>
455 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
456 not supported in EPS figure export
458 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
459 </ul> <em>Development and Release Processes</em>
462 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
465 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
467 <!-- JAL-3225 -->Eclipse project configuration managed with
471 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
472 Bamboo continuous integration for unattended Test Suite
476 <!-- JAL-2864 -->Memory test suite to detect leaks in common
480 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
484 <!-- JAL-3248 -->Developer documentation migrated to
485 markdown (with HTML rendering)
488 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
491 <!-- JAL-3289 -->New URLs for publishing development
496 <td align="left" valign="top">
499 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
502 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
503 superposition in Jmol fail on Windows
506 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
507 structures for sequences with lots of PDB structures
510 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
514 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
515 project involving multiple views
518 <!-- JAL-3164 -->Overview for complementary view in a linked
519 CDS/Protein alignment is not updated when Hide Columns by
520 Annotation dialog hides columns
523 <!-- JAL-3158 -->Selection highlighting in the complement of a
524 CDS/Protein alignment stops working after making a selection in
525 one view, then making another selection in the other view
528 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
532 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
533 Settings and Jalview Preferences panels
536 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
537 overview with large alignments
540 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
541 region if columns were selected by dragging right-to-left and the
542 mouse moved to the left of the first column
545 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
546 hidden column marker via scale popup menu
549 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
550 doesn't tell users the invalid URL
553 <!-- JAL-2816 -->Tooltips displayed for features filtered by
557 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
558 show cross references or Fetch Database References are shown in
562 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
563 peptide sequence (computed variant shown as p.Res.null)
566 <!-- JAL-2060 -->'Graduated colour' option not offered for
567 manually created features (where feature score is Float.NaN)
570 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
571 when columns are hidden
574 <!-- JAL-3082 -->Regular expression error for '(' in Select
575 Columns by Annotation description
578 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
579 out of Scale or Annotation Panel
582 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
586 <!-- JAL-3074 -->Left/right drag in annotation can scroll
590 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
594 <!-- JAL-3002 -->Column display is out by one after Page Down,
595 Page Up in wrapped mode
598 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
601 <!-- JAL-2932 -->Finder searches in minimised alignments
604 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
605 on opening an alignment
608 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
612 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
613 different groups in the alignment are selected
616 <!-- JAL-2717 -->Internationalised colour scheme names not shown
620 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
624 <!-- JAL-3125 -->Value input for graduated feature colour
625 threshold gets 'unrounded'
628 <!-- JAL-2982 -->PCA image export doesn't respect background
632 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
635 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
638 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
642 <!-- JAL-2964 -->Associate Tree with All Views not restored from
646 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
647 shown in complementary view
650 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
651 without normalisation
654 <!-- JAL-3021 -->Sequence Details report should open positioned at top
658 <!-- JAL-914 -->Help page can be opened twice
661 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
663 </ul> <em>Editing</em>
666 <!-- JAL-2822 -->Start and End should be updated when sequence
667 data at beginning or end of alignment added/removed via 'Edit'
671 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
672 relocate sequence features correctly when start of sequence is
673 removed (Known defect since 2.10)
676 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
677 dialog corrupts dataset sequence
680 <!-- JAL-868 -->Structure colours not updated when associated tree
681 repartitions the alignment view (Regression in 2.10.5)
683 </ul> <em>Datamodel</em>
686 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
687 sequence's End is greater than its length
689 </ul> <em>Bugs fixed for Java 11 Support (not yet on
690 general release)</em>
693 <!-- JAL-3288 -->Menus work properly in split-screen
695 </ul> <em>New Known Defects</em>
698 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
701 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
702 regions of protein alignment.
705 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
706 is restored from a Jalview 2.11 project
709 <!-- JAL-3213 -->Alignment panel height can be too small after
713 <!-- JAL-3240 -->Display is incorrect after removing gapped
714 columns within hidden columns
717 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
718 window after dragging left to select columns to left of visible
722 <!-- JAL-2876 -->Features coloured according to their description
723 string and thresholded by score in earlier versions of Jalview are
724 not shown as thresholded features in 2.11. To workaround please
725 create a Score filter instead.
728 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
730 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
733 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
734 alignments with multiple views can close views unexpectedly
737 <em>Java 11 Specific defects</em>
740 <!-- JAL-3235 -->Jalview Properties file is not sorted
741 alphabetically when saved
747 <td width="60" nowrap>
749 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
752 <td><div align="left">
756 <!-- JAL-3101 -->Default memory for Jalview webstart and
757 InstallAnywhere increased to 1G.
760 <!-- JAL-247 -->Hidden sequence markers and representative
761 sequence bolding included when exporting alignment as EPS,
762 SVG, PNG or HTML. <em>Display is configured via the
763 Format menu, or for command-line use via a Jalview
764 properties file.</em>
767 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
768 API and sequence data now imported as JSON.
771 <!-- JAL-3065 -->Change in recommended way of starting
772 Jalview via a Java command line: add jars in lib directory
773 to CLASSPATH, rather than via the deprecated java.ext.dirs
780 <!-- JAL-3047 -->Support added to execute test suite
781 instrumented with <a href="http://openclover.org/">Open
786 <td><div align="left">
790 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
791 row shown in Feredoxin Structure alignment view of example
795 <!-- JAL-2854 -->Annotation obscures sequences if lots of
796 annotation displayed.
799 <!-- JAL-3107 -->Group conservation/consensus not shown
800 for newly created group when 'Apply to all groups'
804 <!-- JAL-3087 -->Corrupted display when switching to
805 wrapped mode when sequence panel's vertical scrollbar is
809 <!-- JAL-3003 -->Alignment is black in exported EPS file
810 when sequences are selected in exported view.</em>
813 <!-- JAL-3059 -->Groups with different coloured borders
814 aren't rendered with correct colour.
817 <!-- JAL-3092 -->Jalview could hang when importing certain
818 types of knotted RNA secondary structure.
821 <!-- JAL-3095 -->Sequence highlight and selection in
822 trimmed VARNA 2D structure is incorrect for sequences that
826 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
827 annotation when columns are inserted into an alignment,
828 and when exporting as Stockholm flatfile.
831 <!-- JAL-3053 -->Jalview annotation rows containing upper
832 and lower-case 'E' and 'H' do not automatically get
833 treated as RNA secondary structure.
836 <!-- JAL-3106 -->.jvp should be used as default extension
837 (not .jar) when saving a Jalview project file.
840 <!-- JAL-3105 -->Mac Users: closing a window correctly
841 transfers focus to previous window on OSX
844 <em>Java 10 Issues Resolved</em>
847 <!-- JAL-2988 -->OSX - Can't save new files via the File
848 or export menus by typing in a name into the Save dialog
852 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
853 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
854 'look and feel' which has improved compatibility with the
855 latest version of OSX.
862 <td width="60" nowrap>
864 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
865 <em>7/06/2018</em></strong>
868 <td><div align="left">
872 <!-- JAL-2920 -->Use HGVS nomenclature for variant
873 annotation retrieved from Uniprot
876 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
877 onto the Jalview Desktop
881 <td><div align="left">
885 <!-- JAL-3017 -->Cannot import features with multiple
886 variant elements (blocks import of some Uniprot records)
889 <!-- JAL-2997 -->Clustal files with sequence positions in
890 right-hand column parsed correctly
893 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
894 not alignment area in exported graphic
897 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
898 window has input focus
901 <!-- JAL-2992 -->Annotation panel set too high when
902 annotation added to view (Windows)
905 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
906 network connectivity is poor
909 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
910 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
911 the currently open URL and links from a page viewed in
912 Firefox or Chrome on Windows is now fully supported. If
913 you are using Edge, only links in the page can be
914 dragged, and with Internet Explorer, only the currently
915 open URL in the browser can be dropped onto Jalview.</em>
918 <em>New Known Defects</em>
920 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
925 <td width="60" nowrap>
927 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
930 <td><div align="left">
934 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
935 for disabling automatic superposition of multiple
936 structures and open structures in existing views
939 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
940 ID and annotation area margins can be click-dragged to
944 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
948 <!-- JAL-2759 -->Improved performance for large alignments
949 and lots of hidden columns
952 <!-- JAL-2593 -->Improved performance when rendering lots
953 of features (particularly when transparency is disabled)
956 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
957 exchange of Jalview features and Chimera attributes made
963 <td><div align="left">
966 <!-- JAL-2899 -->Structure and Overview aren't updated
967 when Colour By Annotation threshold slider is adjusted
970 <!-- JAL-2778 -->Slow redraw when Overview panel shown
971 overlapping alignment panel
974 <!-- JAL-2929 -->Overview doesn't show end of unpadded
978 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
979 improved: CDS not handled correctly if transcript has no
983 <!-- JAL-2321 -->Secondary structure and temperature
984 factor annotation not added to sequence when local PDB
985 file associated with it by drag'n'drop or structure
989 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
990 dialog doesn't import PDB files dropped on an alignment
993 <!-- JAL-2666 -->Linked scrolling via protein horizontal
994 scroll bar doesn't work for some CDS/Protein views
997 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
998 Java 1.8u153 onwards and Java 1.9u4+.
1001 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1002 columns in annotation row
1005 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1006 honored in batch mode
1009 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1010 for structures added to existing Jmol view
1013 <!-- JAL-2223 -->'View Mappings' includes duplicate
1014 entries after importing project with multiple views
1017 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1018 protein sequences via SIFTS from associated PDB entries
1019 with negative residue numbers or missing residues fails
1022 <!-- JAL-2952 -->Exception when shading sequence with negative
1023 Temperature Factor values from annotated PDB files (e.g.
1024 as generated by CONSURF)
1027 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1028 tooltip doesn't include a text description of mutation
1031 <!-- JAL-2922 -->Invert displayed features very slow when
1032 structure and/or overview windows are also shown
1035 <!-- JAL-2954 -->Selecting columns from highlighted regions
1036 very slow for alignments with large numbers of sequences
1039 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1040 with 'StringIndexOutOfBounds'
1043 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1044 platforms running Java 10
1047 <!-- JAL-2960 -->Adding a structure to existing structure
1048 view appears to do nothing because the view is hidden behind the alignment view
1054 <!-- JAL-2926 -->Copy consensus sequence option in applet
1055 should copy the group consensus when popup is opened on it
1061 <!-- JAL-2913 -->Fixed ID width preference is not respected
1064 <em>New Known Defects</em>
1067 <!-- JAL-2973 --> Exceptions occasionally raised when
1068 editing a large alignment and overview is displayed
1071 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1072 repeatedly after a series of edits even when the overview
1073 is no longer reflecting updates
1076 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1077 structures for protein subsequence (if 'Trim Retrieved
1078 Sequences' enabled) or Ensembl isoforms (Workaround in
1079 2.10.4 is to fail back to N&W mapping)
1082 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1083 option gives blank output
1090 <td width="60" nowrap>
1091 <div align="center">
1092 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1095 <td><div align="left">
1096 <ul><li>Updated Certum Codesigning Certificate
1097 (Valid till 30th November 2018)</li></ul></div></td>
1098 <td><div align="left">
1099 <em>Desktop</em><ul>
1101 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1102 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1103 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1104 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1105 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1106 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1107 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1113 <td width="60" nowrap>
1114 <div align="center">
1115 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1118 <td><div align="left">
1122 <!-- JAL-2446 -->Faster and more efficient management and
1123 rendering of sequence features
1126 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1127 429 rate limit request hander
1130 <!-- JAL-2773 -->Structure views don't get updated unless
1131 their colours have changed
1134 <!-- JAL-2495 -->All linked sequences are highlighted for
1135 a structure mousover (Jmol) or selection (Chimera)
1138 <!-- JAL-2790 -->'Cancel' button in progress bar for
1139 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1142 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1143 view from Ensembl locus cross-references
1146 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1150 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1151 feature can be disabled
1154 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1155 PDB easier retrieval of sequences for lists of IDs
1158 <!-- JAL-2758 -->Short names for sequences retrieved from
1164 <li>Groovy interpreter updated to 2.4.12</li>
1165 <li>Example groovy script for generating a matrix of
1166 percent identity scores for current alignment.</li>
1168 <em>Testing and Deployment</em>
1171 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1175 <td><div align="left">
1179 <!-- JAL-2643 -->Pressing tab after updating the colour
1180 threshold text field doesn't trigger an update to the
1184 <!-- JAL-2682 -->Race condition when parsing sequence ID
1188 <!-- JAL-2608 -->Overview windows are also closed when
1189 alignment window is closed
1192 <!-- JAL-2548 -->Export of features doesn't always respect
1196 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1197 takes a long time in Cursor mode
1203 <!-- JAL-2777 -->Structures with whitespace chainCode
1204 cannot be viewed in Chimera
1207 <!-- JAL-2728 -->Protein annotation panel too high in
1211 <!-- JAL-2757 -->Can't edit the query after the server
1212 error warning icon is shown in Uniprot and PDB Free Text
1216 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1219 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1222 <!-- JAL-2739 -->Hidden column marker in last column not
1223 rendered when switching back from Wrapped to normal view
1226 <!-- JAL-2768 -->Annotation display corrupted when
1227 scrolling right in unwapped alignment view
1230 <!-- JAL-2542 -->Existing features on subsequence
1231 incorrectly relocated when full sequence retrieved from
1235 <!-- JAL-2733 -->Last reported memory still shown when
1236 Desktop->Show Memory is unticked (OSX only)
1239 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1240 features of same type and group to be selected for
1244 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1245 alignments when hidden columns are present
1248 <!-- JAL-2392 -->Jalview freezes when loading and
1249 displaying several structures
1252 <!-- JAL-2732 -->Black outlines left after resizing or
1256 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1257 within the Jalview desktop on OSX
1260 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1261 when in wrapped alignment mode
1264 <!-- JAL-2636 -->Scale mark not shown when close to right
1265 hand end of alignment
1268 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1269 each selected sequence do not have correct start/end
1273 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1274 after canceling the Alignment Window's Font dialog
1277 <!-- JAL-2036 -->Show cross-references not enabled after
1278 restoring project until a new view is created
1281 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1282 URL links appears when only default EMBL-EBI link is
1283 configured (since 2.10.2b2)
1286 <!-- JAL-2775 -->Overview redraws whole window when box
1287 position is adjusted
1290 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1291 in a multi-chain structure when viewing alignment
1292 involving more than one chain (since 2.10)
1295 <!-- JAL-2811 -->Double residue highlights in cursor mode
1296 if new selection moves alignment window
1299 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1300 arrow key in cursor mode to pass hidden column marker
1303 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1304 that produces correctly annotated transcripts and products
1307 <!-- JAL-2776 -->Toggling a feature group after first time
1308 doesn't update associated structure view
1311 <em>Applet</em><br />
1314 <!-- JAL-2687 -->Concurrent modification exception when
1315 closing alignment panel
1318 <em>BioJSON</em><br />
1321 <!-- JAL-2546 -->BioJSON export does not preserve
1322 non-positional features
1325 <em>New Known Issues</em>
1328 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1329 sequence features correctly (for many previous versions of
1333 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1334 using cursor in wrapped panel other than top
1337 <!-- JAL-2791 -->Select columns containing feature ignores
1338 graduated colour threshold
1341 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1342 always preserve numbering and sequence features
1345 <em>Known Java 9 Issues</em>
1348 <!-- JAL-2902 -->Groovy Console very slow to open and is
1349 not responsive when entering characters (Webstart, Java
1356 <td width="60" nowrap>
1357 <div align="center">
1358 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1359 <em>2/10/2017</em></strong>
1362 <td><div align="left">
1363 <em>New features in Jalview Desktop</em>
1366 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1368 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1372 <td><div align="left">
1376 <td width="60" nowrap>
1377 <div align="center">
1378 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1379 <em>7/9/2017</em></strong>
1382 <td><div align="left">
1386 <!-- JAL-2588 -->Show gaps in overview window by colouring
1387 in grey (sequences used to be coloured grey, and gaps were
1391 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1395 <!-- JAL-2587 -->Overview updates immediately on increase
1396 in size and progress bar shown as higher resolution
1397 overview is recalculated
1402 <td><div align="left">
1406 <!-- JAL-2664 -->Overview window redraws every hidden
1407 column region row by row
1410 <!-- JAL-2681 -->duplicate protein sequences shown after
1411 retrieving Ensembl crossrefs for sequences from Uniprot
1414 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1415 format setting is unticked
1418 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1419 if group has show boxes format setting unticked
1422 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1423 autoscrolling whilst dragging current selection group to
1424 include sequences and columns not currently displayed
1427 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1428 assemblies are imported via CIF file
1431 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1432 displayed when threshold or conservation colouring is also
1436 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1440 <!-- JAL-2673 -->Jalview continues to scroll after
1441 dragging a selected region off the visible region of the
1445 <!-- JAL-2724 -->Cannot apply annotation based
1446 colourscheme to all groups in a view
1449 <!-- JAL-2511 -->IDs don't line up with sequences
1450 initially after font size change using the Font chooser or
1457 <td width="60" nowrap>
1458 <div align="center">
1459 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1462 <td><div align="left">
1463 <em>Calculations</em>
1467 <!-- JAL-1933 -->Occupancy annotation row shows number of
1468 ungapped positions in each column of the alignment.
1471 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1472 a calculation dialog box
1475 <!-- JAL-2379 -->Revised implementation of PCA for speed
1476 and memory efficiency (~30x faster)
1479 <!-- JAL-2403 -->Revised implementation of sequence
1480 similarity scores as used by Tree, PCA, Shading Consensus
1481 and other calculations
1484 <!-- JAL-2416 -->Score matrices are stored as resource
1485 files within the Jalview codebase
1488 <!-- JAL-2500 -->Trees computed on Sequence Feature
1489 Similarity may have different topology due to increased
1496 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1497 model for alignments and groups
1500 <!-- JAL-384 -->Custom shading schemes created via groovy
1507 <!-- JAL-2526 -->Efficiency improvements for interacting
1508 with alignment and overview windows
1511 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1515 <!-- JAL-2388 -->Hidden columns and sequences can be
1519 <!-- JAL-2611 -->Click-drag in visible area allows fine
1520 adjustment of visible position
1524 <em>Data import/export</em>
1527 <!-- JAL-2535 -->Posterior probability annotation from
1528 Stockholm files imported as sequence associated annotation
1531 <!-- JAL-2507 -->More robust per-sequence positional
1532 annotation input/output via stockholm flatfile
1535 <!-- JAL-2533 -->Sequence names don't include file
1536 extension when importing structure files without embedded
1537 names or PDB accessions
1540 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1541 format sequence substitution matrices
1544 <em>User Interface</em>
1547 <!-- JAL-2447 --> Experimental Features Checkbox in
1548 Desktop's Tools menu to hide or show untested features in
1552 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1553 via Overview or sequence motif search operations
1556 <!-- JAL-2547 -->Amend sequence features dialog box can be
1557 opened by double clicking gaps within sequence feature
1561 <!-- JAL-1476 -->Status bar message shown when not enough
1562 aligned positions were available to create a 3D structure
1566 <em>3D Structure</em>
1569 <!-- JAL-2430 -->Hidden regions in alignment views are not
1570 coloured in linked structure views
1573 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1574 file-based command exchange
1577 <!-- JAL-2375 -->Structure chooser automatically shows
1578 Cached Structures rather than querying the PDBe if
1579 structures are already available for sequences
1582 <!-- JAL-2520 -->Structures imported via URL are cached in
1583 the Jalview project rather than downloaded again when the
1584 project is reopened.
1587 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1588 to transfer Chimera's structure attributes as Jalview
1589 features, and vice-versa (<strong>Experimental
1593 <em>Web Services</em>
1596 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1599 <!-- JAL-2335 -->Filter non-standard amino acids and
1600 nucleotides when submitting to AACon and other MSA
1604 <!-- JAL-2316, -->URLs for viewing database
1605 cross-references provided by identifiers.org and the
1606 EMBL-EBI's MIRIAM DB
1613 <!-- JAL-2344 -->FileFormatI interface for describing and
1614 identifying file formats (instead of String constants)
1617 <!-- JAL-2228 -->FeatureCounter script refactored for
1618 efficiency when counting all displayed features (not
1619 backwards compatible with 2.10.1)
1622 <em>Example files</em>
1625 <!-- JAL-2631 -->Graduated feature colour style example
1626 included in the example feature file
1629 <em>Documentation</em>
1632 <!-- JAL-2339 -->Release notes reformatted for readability
1633 with the built-in Java help viewer
1636 <!-- JAL-1644 -->Find documentation updated with 'search
1637 sequence description' option
1643 <!-- JAL-2485, -->External service integration tests for
1644 Uniprot REST Free Text Search Client
1647 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1650 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1655 <td><div align="left">
1656 <em>Calculations</em>
1659 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1660 matrix - C->R should be '-3'<br />Old matrix restored
1661 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1663 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1664 Jalview's treatment of gaps in PCA and substitution matrix
1665 based Tree calculations.<br /> <br />In earlier versions
1666 of Jalview, gaps matching gaps were penalised, and gaps
1667 matching non-gaps penalised even more. In the PCA
1668 calculation, gaps were actually treated as non-gaps - so
1669 different costs were applied, which meant Jalview's PCAs
1670 were different to those produced by SeqSpace.<br />Jalview
1671 now treats gaps in the same way as SeqSpace (ie it scores
1672 them as 0). <br /> <br />Enter the following in the
1673 Groovy console to restore pre-2.10.2 behaviour:<br />
1674 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1675 // for 2.10.1 mode <br />
1676 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1677 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1678 these settings will affect all subsequent tree and PCA
1679 calculations (not recommended)</em></li>
1681 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1682 scaling of branch lengths for trees computed using
1683 Sequence Feature Similarity.
1686 <!-- JAL-2377 -->PCA calculation could hang when
1687 generating output report when working with highly
1688 redundant alignments
1691 <!-- JAL-2544 --> Sort by features includes features to
1692 right of selected region when gaps present on right-hand
1696 <em>User Interface</em>
1699 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1700 doesn't reselect a specific sequence's associated
1701 annotation after it was used for colouring a view
1704 <!-- JAL-2419 -->Current selection lost if popup menu
1705 opened on a region of alignment without groups
1708 <!-- JAL-2374 -->Popup menu not always shown for regions
1709 of an alignment with overlapping groups
1712 <!-- JAL-2310 -->Finder double counts if both a sequence's
1713 name and description match
1716 <!-- JAL-2370 -->Hiding column selection containing two
1717 hidden regions results in incorrect hidden regions
1720 <!-- JAL-2386 -->'Apply to all groups' setting when
1721 changing colour does not apply Conservation slider value
1725 <!-- JAL-2373 -->Percentage identity and conservation menu
1726 items do not show a tick or allow shading to be disabled
1729 <!-- JAL-2385 -->Conservation shading or PID threshold
1730 lost when base colourscheme changed if slider not visible
1733 <!-- JAL-2547 -->Sequence features shown in tooltip for
1734 gaps before start of features
1737 <!-- JAL-2623 -->Graduated feature colour threshold not
1738 restored to UI when feature colour is edited
1741 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1742 a time when scrolling vertically in wrapped mode.
1745 <!-- JAL-2630 -->Structure and alignment overview update
1746 as graduate feature colour settings are modified via the
1750 <!-- JAL-2034 -->Overview window doesn't always update
1751 when a group defined on the alignment is resized
1754 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1755 wrapped view result in positional status updates
1759 <!-- JAL-2563 -->Status bar doesn't show position for
1760 ambiguous amino acid and nucleotide symbols
1763 <!-- JAL-2602 -->Copy consensus sequence failed if
1764 alignment included gapped columns
1767 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1768 widgets don't permanently disappear
1771 <!-- JAL-2503 -->Cannot select or filter quantitative
1772 annotation that are shown only as column labels (e.g.
1773 T-Coffee column reliability scores)
1776 <!-- JAL-2594 -->Exception thrown if trying to create a
1777 sequence feature on gaps only
1780 <!-- JAL-2504 -->Features created with 'New feature'
1781 button from a Find inherit previously defined feature type
1782 rather than the Find query string
1785 <!-- JAL-2423 -->incorrect title in output window when
1786 exporting tree calculated in Jalview
1789 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1790 and then revealing them reorders sequences on the
1794 <!-- JAL-964 -->Group panel in sequence feature settings
1795 doesn't update to reflect available set of groups after
1796 interactively adding or modifying features
1799 <!-- JAL-2225 -->Sequence Database chooser unusable on
1803 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1804 only excluded gaps in current sequence and ignored
1811 <!-- JAL-2421 -->Overview window visible region moves
1812 erratically when hidden rows or columns are present
1815 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1816 Structure Viewer's colour menu don't correspond to
1820 <!-- JAL-2405 -->Protein specific colours only offered in
1821 colour and group colour menu for protein alignments
1824 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1825 reflect currently selected view or group's shading
1829 <!-- JAL-2624 -->Feature colour thresholds not respected
1830 when rendered on overview and structures when opacity at
1834 <!-- JAL-2589 -->User defined gap colour not shown in
1835 overview when features overlaid on alignment
1838 <!-- JAL-2567 -->Feature settings for different views not
1839 recovered correctly from Jalview project file
1842 <!-- JAL-2256 -->Feature colours in overview when first opened
1843 (automatically via preferences) are different to the main
1847 <em>Data import/export</em>
1850 <!-- JAL-2576 -->Very large alignments take a long time to
1854 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1855 added after a sequence was imported are not written to
1859 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1860 when importing RNA secondary structure via Stockholm
1863 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1864 not shown in correct direction for simple pseudoknots
1867 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1868 with lightGray or darkGray via features file (but can
1872 <!-- JAL-2383 -->Above PID colour threshold not recovered
1873 when alignment view imported from project
1876 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1877 structure and sequences extracted from structure files
1878 imported via URL and viewed in Jmol
1881 <!-- JAL-2520 -->Structures loaded via URL are saved in
1882 Jalview Projects rather than fetched via URL again when
1883 the project is loaded and the structure viewed
1886 <em>Web Services</em>
1889 <!-- JAL-2519 -->EnsemblGenomes example failing after
1890 release of Ensembl v.88
1893 <!-- JAL-2366 -->Proxy server address and port always
1894 appear enabled in Preferences->Connections
1897 <!-- JAL-2461 -->DAS registry not found exceptions
1898 removed from console output
1901 <!-- JAL-2582 -->Cannot retrieve protein products from
1902 Ensembl by Peptide ID
1905 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1906 created from SIFTs, and spurious 'Couldn't open structure
1907 in Chimera' errors raised after April 2017 update (problem
1908 due to 'null' string rather than empty string used for
1909 residues with no corresponding PDB mapping).
1912 <em>Application UI</em>
1915 <!-- JAL-2361 -->User Defined Colours not added to Colour
1919 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1920 case' residues (button in colourscheme editor debugged and
1921 new documentation and tooltips added)
1924 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1925 doesn't restore group-specific text colour thresholds
1928 <!-- JAL-2243 -->Feature settings panel does not update as
1929 new features are added to alignment
1932 <!-- JAL-2532 -->Cancel in feature settings reverts
1933 changes to feature colours via the Amend features dialog
1936 <!-- JAL-2506 -->Null pointer exception when attempting to
1937 edit graduated feature colour via amend features dialog
1941 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1942 selection menu changes colours of alignment views
1945 <!-- JAL-2426 -->Spurious exceptions in console raised
1946 from alignment calculation workers after alignment has
1950 <!-- JAL-1608 -->Typo in selection popup menu - Create
1951 groups now 'Create Group'
1954 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1955 Create/Undefine group doesn't always work
1958 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1959 shown again after pressing 'Cancel'
1962 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1963 adjusts start position in wrap mode
1966 <!-- JAL-2563 -->Status bar doesn't show positions for
1967 ambiguous amino acids
1970 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1971 CDS/Protein view after CDS sequences added for aligned
1975 <!-- JAL-2592 -->User defined colourschemes called 'User
1976 Defined' don't appear in Colours menu
1982 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1983 score models doesn't always result in an updated PCA plot
1986 <!-- JAL-2442 -->Features not rendered as transparent on
1987 overview or linked structure view
1990 <!-- JAL-2372 -->Colour group by conservation doesn't
1994 <!-- JAL-2517 -->Hitting Cancel after applying
1995 user-defined colourscheme doesn't restore original
2002 <!-- JAL-2314 -->Unit test failure:
2003 jalview.ws.jabaws.RNAStructExportImport setup fails
2006 <!-- JAL-2307 -->Unit test failure:
2007 jalview.ws.sifts.SiftsClientTest due to compatibility
2008 problems with deep array comparison equality asserts in
2009 successive versions of TestNG
2012 <!-- JAL-2479 -->Relocated StructureChooserTest and
2013 ParameterUtilsTest Unit tests to Network suite
2016 <em>New Known Issues</em>
2019 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2020 phase after a sequence motif find operation
2023 <!-- JAL-2550 -->Importing annotation file with rows
2024 containing just upper and lower case letters are
2025 interpreted as WUSS RNA secondary structure symbols
2028 <!-- JAL-2590 -->Cannot load and display Newick trees
2029 reliably from eggnog Ortholog database
2032 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2033 containing features of type Highlight' when 'B' is pressed
2034 to mark columns containing highlighted regions.
2037 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2038 doesn't always add secondary structure annotation.
2043 <td width="60" nowrap>
2044 <div align="center">
2045 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2048 <td><div align="left">
2052 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2053 for all consensus calculations
2056 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2059 <li>Updated Jalview's Certum code signing certificate
2062 <em>Application</em>
2065 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2066 set of database cross-references, sorted alphabetically
2069 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2070 from database cross references. Users with custom links
2071 will receive a <a href="webServices/urllinks.html#warning">warning
2072 dialog</a> asking them to update their preferences.
2075 <!-- JAL-2287-->Cancel button and escape listener on
2076 dialog warning user about disconnecting Jalview from a
2080 <!-- JAL-2320-->Jalview's Chimera control window closes if
2081 the Chimera it is connected to is shut down
2084 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2085 columns menu item to mark columns containing highlighted
2086 regions (e.g. from structure selections or results of a
2090 <!-- JAL-2284-->Command line option for batch-generation
2091 of HTML pages rendering alignment data with the BioJS
2101 <!-- JAL-2286 -->Columns with more than one modal residue
2102 are not coloured or thresholded according to percent
2103 identity (first observed in Jalview 2.8.2)
2106 <!-- JAL-2301 -->Threonine incorrectly reported as not
2110 <!-- JAL-2318 -->Updates to documentation pages (above PID
2111 threshold, amino acid properties)
2114 <!-- JAL-2292 -->Lower case residues in sequences are not
2115 reported as mapped to residues in a structure file in the
2119 <!--JAL-2324 -->Identical features with non-numeric scores
2120 could be added multiple times to a sequence
2123 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2124 bond features shown as two highlighted residues rather
2125 than a range in linked structure views, and treated
2126 correctly when selecting and computing trees from features
2129 <!-- JAL-2281-->Custom URL links for database
2130 cross-references are matched to database name regardless
2135 <em>Application</em>
2138 <!-- JAL-2282-->Custom URL links for specific database
2139 names without regular expressions also offer links from
2143 <!-- JAL-2315-->Removing a single configured link in the
2144 URL links pane in Connections preferences doesn't actually
2145 update Jalview configuration
2148 <!-- JAL-2272-->CTRL-Click on a selected region to open
2149 the alignment area popup menu doesn't work on El-Capitan
2152 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2153 files with similarly named sequences if dropped onto the
2157 <!-- JAL-2312 -->Additional mappings are shown for PDB
2158 entries where more chains exist in the PDB accession than
2159 are reported in the SIFTS file
2162 <!-- JAL-2317-->Certain structures do not get mapped to
2163 the structure view when displayed with Chimera
2166 <!-- JAL-2317-->No chains shown in the Chimera view
2167 panel's View->Show Chains submenu
2170 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2171 work for wrapped alignment views
2174 <!--JAL-2197 -->Rename UI components for running JPred
2175 predictions from 'JNet' to 'JPred'
2178 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2179 corrupted when annotation panel vertical scroll is not at
2180 first annotation row
2183 <!--JAL-2332 -->Attempting to view structure for Hen
2184 lysozyme results in a PDB Client error dialog box
2187 <!-- JAL-2319 -->Structure View's mapping report switched
2188 ranges for PDB and sequence for SIFTS
2191 SIFTS 'Not_Observed' residues mapped to non-existant
2195 <!-- <em>New Known Issues</em>
2202 <td width="60" nowrap>
2203 <div align="center">
2204 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2205 <em>25/10/2016</em></strong>
2208 <td><em>Application</em>
2210 <li>3D Structure chooser opens with 'Cached structures'
2211 view if structures already loaded</li>
2212 <li>Progress bar reports models as they are loaded to
2213 structure views</li>
2219 <li>Colour by conservation always enabled and no tick
2220 shown in menu when BLOSUM or PID shading applied</li>
2221 <li>FER1_ARATH and FER2_ARATH labels were switched in
2222 example sequences/projects/trees</li>
2224 <em>Application</em>
2226 <li>Jalview projects with views of local PDB structure
2227 files saved on Windows cannot be opened on OSX</li>
2228 <li>Multiple structure views can be opened and superposed
2229 without timeout for structures with multiple models or
2230 multiple sequences in alignment</li>
2231 <li>Cannot import or associated local PDB files without a
2232 PDB ID HEADER line</li>
2233 <li>RMSD is not output in Jmol console when superposition
2235 <li>Drag and drop of URL from Browser fails for Linux and
2236 OSX versions earlier than El Capitan</li>
2237 <li>ENA client ignores invalid content from ENA server</li>
2238 <li>Exceptions are not raised in console when ENA client
2239 attempts to fetch non-existent IDs via Fetch DB Refs UI
2241 <li>Exceptions are not raised in console when a new view
2242 is created on the alignment</li>
2243 <li>OSX right-click fixed for group selections: CMD-click
2244 to insert/remove gaps in groups and CTRL-click to open group
2247 <em>Build and deployment</em>
2249 <li>URL link checker now copes with multi-line anchor
2252 <em>New Known Issues</em>
2254 <li>Drag and drop from URL links in browsers do not work
2261 <td width="60" nowrap>
2262 <div align="center">
2263 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2266 <td><em>General</em>
2269 <!-- JAL-2124 -->Updated Spanish translations.
2272 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2273 for importing structure data to Jalview. Enables mmCIF and
2277 <!-- JAL-192 --->Alignment ruler shows positions relative to
2281 <!-- JAL-2202 -->Position/residue shown in status bar when
2282 mousing over sequence associated annotation
2285 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2289 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2290 '()', canonical '[]' and invalid '{}' base pair populations
2294 <!-- JAL-2092 -->Feature settings popup menu options for
2295 showing or hiding columns containing a feature
2298 <!-- JAL-1557 -->Edit selected group by double clicking on
2299 group and sequence associated annotation labels
2302 <!-- JAL-2236 -->Sequence name added to annotation label in
2303 select/hide columns by annotation and colour by annotation
2307 </ul> <em>Application</em>
2310 <!-- JAL-2050-->Automatically hide introns when opening a
2311 gene/transcript view
2314 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2318 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2319 structure mappings with the EMBL-EBI PDBe SIFTS database
2322 <!-- JAL-2079 -->Updated download sites used for Rfam and
2323 Pfam sources to xfam.org
2326 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2329 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2330 over sequences in Jalview
2333 <!-- JAL-2027-->Support for reverse-complement coding
2334 regions in ENA and EMBL
2337 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2338 for record retrieval via ENA rest API
2341 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2345 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2346 groovy script execution
2349 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2350 alignment window's Calculate menu
2353 <!-- JAL-1812 -->Allow groovy scripts that call
2354 Jalview.getAlignFrames() to run in headless mode
2357 <!-- JAL-2068 -->Support for creating new alignment
2358 calculation workers from groovy scripts
2361 <!-- JAL-1369 --->Store/restore reference sequence in
2365 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2366 associations are now saved/restored from project
2369 <!-- JAL-1993 -->Database selection dialog always shown
2370 before sequence fetcher is opened
2373 <!-- JAL-2183 -->Double click on an entry in Jalview's
2374 database chooser opens a sequence fetcher
2377 <!-- JAL-1563 -->Free-text search client for UniProt using
2378 the UniProt REST API
2381 <!-- JAL-2168 -->-nonews command line parameter to prevent
2382 the news reader opening
2385 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2386 querying stored in preferences
2389 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2393 <!-- JAL-1977-->Tooltips shown on database chooser
2396 <!-- JAL-391 -->Reverse complement function in calculate
2397 menu for nucleotide sequences
2400 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2401 and feature counts preserves alignment ordering (and
2402 debugged for complex feature sets).
2405 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2406 viewing structures with Jalview 2.10
2409 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2410 genome, transcript CCDS and gene ids via the Ensembl and
2411 Ensembl Genomes REST API
2414 <!-- JAL-2049 -->Protein sequence variant annotation
2415 computed for 'sequence_variant' annotation on CDS regions
2419 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2423 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2424 Ref Fetcher fails to match, or otherwise updates sequence
2425 data from external database records.
2428 <!-- JAL-2154 -->Revised Jalview Project format for
2429 efficient recovery of sequence coding and alignment
2430 annotation relationships.
2432 </ul> <!-- <em>Applet</em>
2443 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2447 <!-- JAL-2018-->Export features in Jalview format (again)
2448 includes graduated colourschemes
2451 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2452 working with big alignments and lots of hidden columns
2455 <!-- JAL-2053-->Hidden column markers not always rendered
2456 at right of alignment window
2459 <!-- JAL-2067 -->Tidied up links in help file table of
2463 <!-- JAL-2072 -->Feature based tree calculation not shown
2467 <!-- JAL-2075 -->Hidden columns ignored during feature
2468 based tree calculation
2471 <!-- JAL-2065 -->Alignment view stops updating when show
2472 unconserved enabled for group on alignment
2475 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2479 <!-- JAL-2146 -->Alignment column in status incorrectly
2480 shown as "Sequence position" when mousing over
2484 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2485 hidden columns present
2488 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2489 user created annotation added to alignment
2492 <!-- JAL-1841 -->RNA Structure consensus only computed for
2493 '()' base pair annotation
2496 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2497 in zero scores for all base pairs in RNA Structure
2501 <!-- JAL-2174-->Extend selection with columns containing
2505 <!-- JAL-2275 -->Pfam format writer puts extra space at
2506 beginning of sequence
2509 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2513 <!-- JAL-2238 -->Cannot create groups on an alignment from
2514 from a tree when t-coffee scores are shown
2517 <!-- JAL-1836,1967 -->Cannot import and view PDB
2518 structures with chains containing negative resnums (4q4h)
2521 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2525 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2526 to Clustal, PIR and PileUp output
2529 <!-- JAL-2008 -->Reordering sequence features that are
2530 not visible causes alignment window to repaint
2533 <!-- JAL-2006 -->Threshold sliders don't work in
2534 graduated colour and colour by annotation row for e-value
2535 scores associated with features and annotation rows
2538 <!-- JAL-1797 -->amino acid physicochemical conservation
2539 calculation should be case independent
2542 <!-- JAL-2173 -->Remove annotation also updates hidden
2546 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2547 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2548 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2551 <!-- JAL-2065 -->Null pointer exceptions and redraw
2552 problems when reference sequence defined and 'show
2553 non-conserved' enabled
2556 <!-- JAL-1306 -->Quality and Conservation are now shown on
2557 load even when Consensus calculation is disabled
2560 <!-- JAL-1932 -->Remove right on penultimate column of
2561 alignment does nothing
2564 <em>Application</em>
2567 <!-- JAL-1552-->URLs and links can't be imported by
2568 drag'n'drop on OSX when launched via webstart (note - not
2569 yet fixed for El Capitan)
2572 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2573 output when running on non-gb/us i18n platforms
2576 <!-- JAL-1944 -->Error thrown when exporting a view with
2577 hidden sequences as flat-file alignment
2580 <!-- JAL-2030-->InstallAnywhere distribution fails when
2584 <!-- JAL-2080-->Jalview very slow to launch via webstart
2585 (also hotfix for 2.9.0b2)
2588 <!-- JAL-2085 -->Cannot save project when view has a
2589 reference sequence defined
2592 <!-- JAL-1011 -->Columns are suddenly selected in other
2593 alignments and views when revealing hidden columns
2596 <!-- JAL-1989 -->Hide columns not mirrored in complement
2597 view in a cDNA/Protein splitframe
2600 <!-- JAL-1369 -->Cannot save/restore representative
2601 sequence from project when only one sequence is
2605 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2606 in Structure Chooser
2609 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2610 structure consensus didn't refresh annotation panel
2613 <!-- JAL-1962 -->View mapping in structure view shows
2614 mappings between sequence and all chains in a PDB file
2617 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2618 dialogs format columns correctly, don't display array
2619 data, sort columns according to type
2622 <!-- JAL-1975 -->Export complete shown after destination
2623 file chooser is cancelled during an image export
2626 <!-- JAL-2025 -->Error when querying PDB Service with
2627 sequence name containing special characters
2630 <!-- JAL-2024 -->Manual PDB structure querying should be
2634 <!-- JAL-2104 -->Large tooltips with broken HTML
2635 formatting don't wrap
2638 <!-- JAL-1128 -->Figures exported from wrapped view are
2639 truncated so L looks like I in consensus annotation
2642 <!-- JAL-2003 -->Export features should only export the
2643 currently displayed features for the current selection or
2647 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2648 after fetching cross-references, and restoring from
2652 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2653 followed in the structure viewer
2656 <!-- JAL-2163 -->Titles for individual alignments in
2657 splitframe not restored from project
2660 <!-- JAL-2145 -->missing autocalculated annotation at
2661 trailing end of protein alignment in transcript/product
2662 splitview when pad-gaps not enabled by default
2665 <!-- JAL-1797 -->amino acid physicochemical conservation
2669 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2670 article has been read (reopened issue due to
2671 internationalisation problems)
2674 <!-- JAL-1960 -->Only offer PDB structures in structure
2675 viewer based on sequence name, PDB and UniProt
2680 <!-- JAL-1976 -->No progress bar shown during export of
2684 <!-- JAL-2213 -->Structures not always superimposed after
2685 multiple structures are shown for one or more sequences.
2688 <!-- JAL-1370 -->Reference sequence characters should not
2689 be replaced with '.' when 'Show unconserved' format option
2693 <!-- JAL-1823 -->Cannot specify chain code when entering
2694 specific PDB id for sequence
2697 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2698 'Export hidden sequences' is enabled, but 'export hidden
2699 columns' is disabled.
2702 <!--JAL-2026-->Best Quality option in structure chooser
2703 selects lowest rather than highest resolution structures
2707 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2708 to sequence mapping in 'View Mappings' report
2711 <!-- JAL-2284 -->Unable to read old Jalview projects that
2712 contain non-XML data added after Jalvew wrote project.
2715 <!-- JAL-2118 -->Newly created annotation row reorders
2716 after clicking on it to create new annotation for a
2720 <!-- JAL-1980 -->Null Pointer Exception raised when
2721 pressing Add on an orphaned cut'n'paste window.
2723 <!-- may exclude, this is an external service stability issue JAL-1941
2724 -- > RNA 3D structure not added via DSSR service</li> -->
2729 <!-- JAL-2151 -->Incorrect columns are selected when
2730 hidden columns present before start of sequence
2733 <!-- JAL-1986 -->Missing dependencies on applet pages
2737 <!-- JAL-1947 -->Overview pixel size changes when
2738 sequences are hidden in applet
2741 <!-- JAL-1996 -->Updated instructions for applet
2742 deployment on examples pages.
2749 <td width="60" nowrap>
2750 <div align="center">
2751 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2752 <em>16/10/2015</em></strong>
2755 <td><em>General</em>
2757 <li>Time stamps for signed Jalview application and applet
2762 <em>Application</em>
2764 <li>Duplicate group consensus and conservation rows
2765 shown when tree is partitioned</li>
2766 <li>Erratic behaviour when tree partitions made with
2767 multiple cDNA/Protein split views</li>
2773 <td width="60" nowrap>
2774 <div align="center">
2775 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2776 <em>8/10/2015</em></strong>
2779 <td><em>General</em>
2781 <li>Updated Spanish translations of localized text for
2783 </ul> <em>Application</em>
2785 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2786 <li>Signed OSX InstallAnywhere installer<br></li>
2787 <li>Support for per-sequence based annotations in BioJSON</li>
2788 </ul> <em>Applet</em>
2790 <li>Split frame example added to applet examples page</li>
2791 </ul> <em>Build and Deployment</em>
2794 <!-- JAL-1888 -->New ant target for running Jalview's test
2802 <li>Mapping of cDNA to protein in split frames
2803 incorrect when sequence start > 1</li>
2804 <li>Broken images in filter column by annotation dialog
2806 <li>Feature colours not parsed from features file</li>
2807 <li>Exceptions and incomplete link URLs recovered when
2808 loading a features file containing HTML tags in feature
2812 <em>Application</em>
2814 <li>Annotations corrupted after BioJS export and
2816 <li>Incorrect sequence limits after Fetch DB References
2817 with 'trim retrieved sequences'</li>
2818 <li>Incorrect warning about deleting all data when
2819 deleting selected columns</li>
2820 <li>Patch to build system for shipping properly signed
2821 JNLP templates for webstart launch</li>
2822 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2823 unreleased structures for download or viewing</li>
2824 <li>Tab/space/return keystroke operation of EMBL-PDBe
2825 fetcher/viewer dialogs works correctly</li>
2826 <li>Disabled 'minimise' button on Jalview windows
2827 running on OSX to workaround redraw hang bug</li>
2828 <li>Split cDNA/Protein view position and geometry not
2829 recovered from jalview project</li>
2830 <li>Initial enabled/disabled state of annotation menu
2831 sorter 'show autocalculated first/last' corresponds to
2833 <li>Restoring of Clustal, RNA Helices and T-Coffee
2834 color schemes from BioJSON</li>
2838 <li>Reorder sequences mirrored in cDNA/Protein split
2840 <li>Applet with Jmol examples not loading correctly</li>
2846 <td><div align="center">
2847 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2849 <td><em>General</em>
2851 <li>Linked visualisation and analysis of DNA and Protein
2854 <li>Translated cDNA alignments shown as split protein
2855 and DNA alignment views</li>
2856 <li>Codon consensus annotation for linked protein and
2857 cDNA alignment views</li>
2858 <li>Link cDNA or Protein product sequences by loading
2859 them onto Protein or cDNA alignments</li>
2860 <li>Reconstruct linked cDNA alignment from aligned
2861 protein sequences</li>
2864 <li>Jmol integration updated to Jmol v14.2.14</li>
2865 <li>Import and export of Jalview alignment views as <a
2866 href="features/bioJsonFormat.html">BioJSON</a></li>
2867 <li>New alignment annotation file statements for
2868 reference sequences and marking hidden columns</li>
2869 <li>Reference sequence based alignment shading to
2870 highlight variation</li>
2871 <li>Select or hide columns according to alignment
2873 <li>Find option for locating sequences by description</li>
2874 <li>Conserved physicochemical properties shown in amino
2875 acid conservation row</li>
2876 <li>Alignments can be sorted by number of RNA helices</li>
2877 </ul> <em>Application</em>
2879 <li>New cDNA/Protein analysis capabilities
2881 <li>Get Cross-References should open a Split Frame
2882 view with cDNA/Protein</li>
2883 <li>Detect when nucleotide sequences and protein
2884 sequences are placed in the same alignment</li>
2885 <li>Split cDNA/Protein views are saved in Jalview
2890 <li>Use REST API to talk to Chimera</li>
2891 <li>Selected regions in Chimera are highlighted in linked
2892 Jalview windows</li>
2894 <li>VARNA RNA viewer updated to v3.93</li>
2895 <li>VARNA views are saved in Jalview Projects</li>
2896 <li>Pseudoknots displayed as Jalview RNA annotation can
2897 be shown in VARNA</li>
2899 <li>Make groups for selection uses marked columns as well
2900 as the active selected region</li>
2902 <li>Calculate UPGMA and NJ trees using sequence feature
2904 <li>New Export options
2906 <li>New Export Settings dialog to control hidden
2907 region export in flat file generation</li>
2909 <li>Export alignment views for display with the <a
2910 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2912 <li>Export scrollable SVG in HTML page</li>
2913 <li>Optional embedding of BioJSON data when exporting
2914 alignment figures to HTML</li>
2916 <li>3D structure retrieval and display
2918 <li>Free text and structured queries with the PDBe
2920 <li>PDBe Search API based discovery and selection of
2921 PDB structures for a sequence set</li>
2925 <li>JPred4 employed for protein secondary structure
2927 <li>Hide Insertions menu option to hide unaligned columns
2928 for one or a group of sequences</li>
2929 <li>Automatically hide insertions in alignments imported
2930 from the JPred4 web server</li>
2931 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2932 system on OSX<br />LGPL libraries courtesy of <a
2933 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2935 <li>changed 'View nucleotide structure' submenu to 'View
2936 VARNA 2D Structure'</li>
2937 <li>change "View protein structure" menu option to "3D
2940 </ul> <em>Applet</em>
2942 <li>New layout for applet example pages</li>
2943 <li>New parameters to enable SplitFrame view
2944 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2945 <li>New example demonstrating linked viewing of cDNA and
2946 Protein alignments</li>
2947 </ul> <em>Development and deployment</em>
2949 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2950 <li>Include installation type and git revision in build
2951 properties and console log output</li>
2952 <li>Jalview Github organisation, and new github site for
2953 storing BioJsMSA Templates</li>
2954 <li>Jalview's unit tests now managed with TestNG</li>
2957 <!-- <em>General</em>
2959 </ul> --> <!-- issues resolved --> <em>Application</em>
2961 <li>Escape should close any open find dialogs</li>
2962 <li>Typo in select-by-features status report</li>
2963 <li>Consensus RNA secondary secondary structure
2964 predictions are not highlighted in amber</li>
2965 <li>Missing gap character in v2.7 example file means
2966 alignment appears unaligned when pad-gaps is not enabled</li>
2967 <li>First switch to RNA Helices colouring doesn't colour
2968 associated structure views</li>
2969 <li>ID width preference option is greyed out when auto
2970 width checkbox not enabled</li>
2971 <li>Stopped a warning dialog from being shown when
2972 creating user defined colours</li>
2973 <li>'View Mapping' in structure viewer shows sequence
2974 mappings for just that viewer's sequences</li>
2975 <li>Workaround for superposing PDB files containing
2976 multiple models in Chimera</li>
2977 <li>Report sequence position in status bar when hovering
2978 over Jmol structure</li>
2979 <li>Cannot output gaps as '.' symbols with Selection ->
2980 output to text box</li>
2981 <li>Flat file exports of alignments with hidden columns
2982 have incorrect sequence start/end</li>
2983 <li>'Aligning' a second chain to a Chimera structure from
2985 <li>Colour schemes applied to structure viewers don't
2986 work for nucleotide</li>
2987 <li>Loading/cut'n'pasting an empty or invalid file leads
2988 to a grey/invisible alignment window</li>
2989 <li>Exported Jpred annotation from a sequence region
2990 imports to different position</li>
2991 <li>Space at beginning of sequence feature tooltips shown
2992 on some platforms</li>
2993 <li>Chimera viewer 'View | Show Chain' menu is not
2995 <li>'New View' fails with a Null Pointer Exception in
2996 console if Chimera has been opened</li>
2997 <li>Mouseover to Chimera not working</li>
2998 <li>Miscellaneous ENA XML feature qualifiers not
3000 <li>NPE in annotation renderer after 'Extract Scores'</li>
3001 <li>If two structures in one Chimera window, mouseover of
3002 either sequence shows on first structure</li>
3003 <li>'Show annotations' options should not make
3004 non-positional annotations visible</li>
3005 <li>Subsequence secondary structure annotation not shown
3006 in right place after 'view flanking regions'</li>
3007 <li>File Save As type unset when current file format is
3009 <li>Save as '.jar' option removed for saving Jalview
3011 <li>Colour by Sequence colouring in Chimera more
3013 <li>Cannot 'add reference annotation' for a sequence in
3014 several views on same alignment</li>
3015 <li>Cannot show linked products for EMBL / ENA records</li>
3016 <li>Jalview's tooltip wraps long texts containing no
3018 </ul> <em>Applet</em>
3020 <li>Jmol to JalviewLite mouseover/link not working</li>
3021 <li>JalviewLite can't import sequences with ID
3022 descriptions containing angle brackets</li>
3023 </ul> <em>General</em>
3025 <li>Cannot export and reimport RNA secondary structure
3026 via jalview annotation file</li>
3027 <li>Random helix colour palette for colour by annotation
3028 with RNA secondary structure</li>
3029 <li>Mouseover to cDNA from STOP residue in protein
3030 translation doesn't work.</li>
3031 <li>hints when using the select by annotation dialog box</li>
3032 <li>Jmol alignment incorrect if PDB file has alternate CA
3034 <li>FontChooser message dialog appears to hang after
3035 choosing 1pt font</li>
3036 <li>Peptide secondary structure incorrectly imported from
3037 annotation file when annotation display text includes 'e' or
3039 <li>Cannot set colour of new feature type whilst creating
3041 <li>cDNA translation alignment should not be sequence
3042 order dependent</li>
3043 <li>'Show unconserved' doesn't work for lower case
3045 <li>Nucleotide ambiguity codes involving R not recognised</li>
3046 </ul> <em>Deployment and Documentation</em>
3048 <li>Applet example pages appear different to the rest of
3049 www.jalview.org</li>
3050 </ul> <em>Application Known issues</em>
3052 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3053 <li>Misleading message appears after trying to delete
3055 <li>Jalview icon not shown in dock after InstallAnywhere
3056 version launches</li>
3057 <li>Fetching EMBL reference for an RNA sequence results
3058 fails with a sequence mismatch</li>
3059 <li>Corrupted or unreadable alignment display when
3060 scrolling alignment to right</li>
3061 <li>ArrayIndexOutOfBoundsException thrown when remove
3062 empty columns called on alignment with ragged gapped ends</li>
3063 <li>auto calculated alignment annotation rows do not get
3064 placed above or below non-autocalculated rows</li>
3065 <li>Jalview dekstop becomes sluggish at full screen in
3066 ultra-high resolution</li>
3067 <li>Cannot disable consensus calculation independently of
3068 quality and conservation</li>
3069 <li>Mouseover highlighting between cDNA and protein can
3070 become sluggish with more than one splitframe shown</li>
3071 </ul> <em>Applet Known Issues</em>
3073 <li>Core PDB parsing code requires Jmol</li>
3074 <li>Sequence canvas panel goes white when alignment
3075 window is being resized</li>
3081 <td><div align="center">
3082 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3084 <td><em>General</em>
3086 <li>Updated Java code signing certificate donated by
3088 <li>Features and annotation preserved when performing
3089 pairwise alignment</li>
3090 <li>RNA pseudoknot annotation can be
3091 imported/exported/displayed</li>
3092 <li>'colour by annotation' can colour by RNA and
3093 protein secondary structure</li>
3094 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3095 post-hoc with 2.9 release</em>)
3098 </ul> <em>Application</em>
3100 <li>Extract and display secondary structure for sequences
3101 with 3D structures</li>
3102 <li>Support for parsing RNAML</li>
3103 <li>Annotations menu for layout
3105 <li>sort sequence annotation rows by alignment</li>
3106 <li>place sequence annotation above/below alignment
3109 <li>Output in Stockholm format</li>
3110 <li>Internationalisation: improved Spanish (es)
3112 <li>Structure viewer preferences tab</li>
3113 <li>Disorder and Secondary Structure annotation tracks
3114 shared between alignments</li>
3115 <li>UCSF Chimera launch and linked highlighting from
3117 <li>Show/hide all sequence associated annotation rows for
3118 all or current selection</li>
3119 <li>disorder and secondary structure predictions
3120 available as dataset annotation</li>
3121 <li>Per-sequence rna helices colouring</li>
3124 <li>Sequence database accessions imported when fetching
3125 alignments from Rfam</li>
3126 <li>update VARNA version to 3.91</li>
3128 <li>New groovy scripts for exporting aligned positions,
3129 conservation values, and calculating sum of pairs scores.</li>
3130 <li>Command line argument to set default JABAWS server</li>
3131 <li>include installation type in build properties and
3132 console log output</li>
3133 <li>Updated Jalview project format to preserve dataset
3137 <!-- issues resolved --> <em>Application</em>
3139 <li>Distinguish alignment and sequence associated RNA
3140 structure in structure->view->VARNA</li>
3141 <li>Raise dialog box if user deletes all sequences in an
3143 <li>Pressing F1 results in documentation opening twice</li>
3144 <li>Sequence feature tooltip is wrapped</li>
3145 <li>Double click on sequence associated annotation
3146 selects only first column</li>
3147 <li>Redundancy removal doesn't result in unlinked
3148 leaves shown in tree</li>
3149 <li>Undos after several redundancy removals don't undo
3151 <li>Hide sequence doesn't hide associated annotation</li>
3152 <li>User defined colours dialog box too big to fit on
3153 screen and buttons not visible</li>
3154 <li>author list isn't updated if already written to
3155 Jalview properties</li>
3156 <li>Popup menu won't open after retrieving sequence
3158 <li>File open window for associate PDB doesn't open</li>
3159 <li>Left-then-right click on a sequence id opens a
3160 browser search window</li>
3161 <li>Cannot open sequence feature shading/sort popup menu
3162 in feature settings dialog</li>
3163 <li>better tooltip placement for some areas of Jalview
3165 <li>Allow addition of JABAWS Server which doesn't
3166 pass validation</li>
3167 <li>Web services parameters dialog box is too large to
3169 <li>Muscle nucleotide alignment preset obscured by
3171 <li>JABAWS preset submenus don't contain newly
3172 defined user preset</li>
3173 <li>MSA web services warns user if they were launched
3174 with invalid input</li>
3175 <li>Jalview cannot contact DAS Registy when running on
3178 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3179 'Superpose with' submenu not shown when new view
3183 </ul> <!-- <em>Applet</em>
3185 </ul> <em>General</em>
3187 </ul>--> <em>Deployment and Documentation</em>
3189 <li>2G and 1G options in launchApp have no effect on
3190 memory allocation</li>
3191 <li>launchApp service doesn't automatically open
3192 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3194 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3195 InstallAnywhere reports cannot find valid JVM when Java
3196 1.7_055 is available
3198 </ul> <em>Application Known issues</em>
3201 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3202 corrupted or unreadable alignment display when scrolling
3206 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3207 retrieval fails but progress bar continues for DAS retrieval
3208 with large number of ID
3211 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3212 flatfile output of visible region has incorrect sequence
3216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3217 rna structure consensus doesn't update when secondary
3218 structure tracks are rearranged
3221 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3222 invalid rna structure positional highlighting does not
3223 highlight position of invalid base pairs
3226 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3227 out of memory errors are not raised when saving Jalview
3228 project from alignment window file menu
3231 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3232 Switching to RNA Helices colouring doesn't propagate to
3236 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3237 colour by RNA Helices not enabled when user created
3238 annotation added to alignment
3241 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3242 Jalview icon not shown on dock in Mountain Lion/Webstart
3244 </ul> <em>Applet Known Issues</em>
3247 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3248 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3252 Jalview and Jmol example not compatible with IE9
3255 <li>Sort by annotation score doesn't reverse order
3261 <td><div align="center">
3262 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3265 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3268 <li>Internationalisation of user interface (usually
3269 called i18n support) and translation for Spanish locale</li>
3270 <li>Define/Undefine group on current selection with
3271 Ctrl-G/Shift Ctrl-G</li>
3272 <li>Improved group creation/removal options in
3273 alignment/sequence Popup menu</li>
3274 <li>Sensible precision for symbol distribution
3275 percentages shown in logo tooltip.</li>
3276 <li>Annotation panel height set according to amount of
3277 annotation when alignment first opened</li>
3278 </ul> <em>Application</em>
3280 <li>Interactive consensus RNA secondary structure
3281 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3282 <li>Select columns containing particular features from
3283 Feature Settings dialog</li>
3284 <li>View all 'representative' PDB structures for selected
3286 <li>Update Jalview project format:
3288 <li>New file extension for Jalview projects '.jvp'</li>
3289 <li>Preserve sequence and annotation dataset (to
3290 store secondary structure annotation,etc)</li>
3291 <li>Per group and alignment annotation and RNA helix
3295 <li>New similarity measures for PCA and Tree calculation
3297 <li>Experimental support for retrieval and viewing of
3298 flanking regions for an alignment</li>
3302 <!-- issues resolved --> <em>Application</em>
3304 <li>logo keeps spinning and status remains at queued or
3305 running after job is cancelled</li>
3306 <li>cannot export features from alignments imported from
3307 Jalview/VAMSAS projects</li>
3308 <li>Buggy slider for web service parameters that take
3310 <li>Newly created RNA secondary structure line doesn't
3311 have 'display all symbols' flag set</li>
3312 <li>T-COFFEE alignment score shading scheme and other
3313 annotation shading not saved in Jalview project</li>
3314 <li>Local file cannot be loaded in freshly downloaded
3316 <li>Jalview icon not shown on dock in Mountain
3318 <li>Load file from desktop file browser fails</li>
3319 <li>Occasional NPE thrown when calculating large trees</li>
3320 <li>Cannot reorder or slide sequences after dragging an
3321 alignment onto desktop</li>
3322 <li>Colour by annotation dialog throws NPE after using
3323 'extract scores' function</li>
3324 <li>Loading/cut'n'pasting an empty file leads to a grey
3325 alignment window</li>
3326 <li>Disorder thresholds rendered incorrectly after
3327 performing IUPred disorder prediction</li>
3328 <li>Multiple group annotated consensus rows shown when
3329 changing 'normalise logo' display setting</li>
3330 <li>Find shows blank dialog after 'finished searching' if
3331 nothing matches query</li>
3332 <li>Null Pointer Exceptions raised when sorting by
3333 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3335 <li>Errors in Jmol console when structures in alignment
3336 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3338 <li>Not all working JABAWS services are shown in
3340 <li>JAVAWS version of Jalview fails to launch with
3341 'invalid literal/length code'</li>
3342 <li>Annotation/RNA Helix colourschemes cannot be applied
3343 to alignment with groups (actually fixed in 2.8.0b1)</li>
3344 <li>RNA Helices and T-Coffee Scores available as default
3347 </ul> <em>Applet</em>
3349 <li>Remove group option is shown even when selection is
3351 <li>Apply to all groups ticked but colourscheme changes
3352 don't affect groups</li>
3353 <li>Documented RNA Helices and T-Coffee Scores as valid
3354 colourscheme name</li>
3355 <li>Annotation labels drawn on sequence IDs when
3356 Annotation panel is not displayed</li>
3357 <li>Increased font size for dropdown menus on OSX and
3358 embedded windows</li>
3359 </ul> <em>Other</em>
3361 <li>Consensus sequence for alignments/groups with a
3362 single sequence were not calculated</li>
3363 <li>annotation files that contain only groups imported as
3364 annotation and junk sequences</li>
3365 <li>Fasta files with sequences containing '*' incorrectly
3366 recognised as PFAM or BLC</li>
3367 <li>conservation/PID slider apply all groups option
3368 doesn't affect background (2.8.0b1)
3370 <li>redundancy highlighting is erratic at 0% and 100%</li>
3371 <li>Remove gapped columns fails for sequences with ragged
3373 <li>AMSA annotation row with leading spaces is not
3374 registered correctly on import</li>
3375 <li>Jalview crashes when selecting PCA analysis for
3376 certain alignments</li>
3377 <li>Opening the colour by annotation dialog for an
3378 existing annotation based 'use original colours'
3379 colourscheme loses original colours setting</li>
3384 <td><div align="center">
3385 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3386 <em>30/1/2014</em></strong>
3390 <li>Trusted certificates for JalviewLite applet and
3391 Jalview Desktop application<br />Certificate was donated by
3392 <a href="https://www.certum.eu">Certum</a> to the Jalview
3393 open source project).
3395 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3396 <li>Output in Stockholm format</li>
3397 <li>Allow import of data from gzipped files</li>
3398 <li>Export/import group and sequence associated line
3399 graph thresholds</li>
3400 <li>Nucleotide substitution matrix that supports RNA and
3401 ambiguity codes</li>
3402 <li>Allow disorder predictions to be made on the current
3403 selection (or visible selection) in the same way that JPred
3405 <li>Groovy scripting for headless Jalview operation</li>
3406 </ul> <em>Other improvements</em>
3408 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3409 <li>COMBINE statement uses current SEQUENCE_REF and
3410 GROUP_REF scope to group annotation rows</li>
3411 <li>Support '' style escaping of quotes in Newick
3413 <li>Group options for JABAWS service by command line name</li>
3414 <li>Empty tooltip shown for JABA service options with a
3415 link but no description</li>
3416 <li>Select primary source when selecting authority in
3417 database fetcher GUI</li>
3418 <li>Add .mfa to FASTA file extensions recognised by
3420 <li>Annotation label tooltip text wrap</li>
3425 <li>Slow scrolling when lots of annotation rows are
3427 <li>Lots of NPE (and slowness) after creating RNA
3428 secondary structure annotation line</li>
3429 <li>Sequence database accessions not imported when
3430 fetching alignments from Rfam</li>
3431 <li>Incorrect SHMR submission for sequences with
3433 <li>View all structures does not always superpose
3435 <li>Option widgets in service parameters not updated to
3436 reflect user or preset settings</li>
3437 <li>Null pointer exceptions for some services without
3438 presets or adjustable parameters</li>
3439 <li>Discover PDB IDs entry in structure menu doesn't
3440 discover PDB xRefs</li>
3441 <li>Exception encountered while trying to retrieve
3442 features with DAS</li>
3443 <li>Lowest value in annotation row isn't coloured
3444 when colour by annotation (per sequence) is coloured</li>
3445 <li>Keyboard mode P jumps to start of gapped region when
3446 residue follows a gap</li>
3447 <li>Jalview appears to hang importing an alignment with
3448 Wrap as default or after enabling Wrap</li>
3449 <li>'Right click to add annotations' message
3450 shown in wrap mode when no annotations present</li>
3451 <li>Disorder predictions fail with NPE if no automatic
3452 annotation already exists on alignment</li>
3453 <li>oninit javascript function should be called after
3454 initialisation completes</li>
3455 <li>Remove redundancy after disorder prediction corrupts
3456 alignment window display</li>
3457 <li>Example annotation file in documentation is invalid</li>
3458 <li>Grouped line graph annotation rows are not exported
3459 to annotation file</li>
3460 <li>Multi-harmony analysis cannot be run when only two
3462 <li>Cannot create multiple groups of line graphs with
3463 several 'combine' statements in annotation file</li>
3464 <li>Pressing return several times causes Number Format
3465 exceptions in keyboard mode</li>
3466 <li>Multi-harmony (SHMMR) method doesn't submit
3467 correct partitions for input data</li>
3468 <li>Translation from DNA to Amino Acids fails</li>
3469 <li>Jalview fail to load newick tree with quoted label</li>
3470 <li>--headless flag isn't understood</li>
3471 <li>ClassCastException when generating EPS in headless
3473 <li>Adjusting sequence-associated shading threshold only
3474 changes one row's threshold</li>
3475 <li>Preferences and Feature settings panel panel
3476 doesn't open</li>
3477 <li>hide consensus histogram also hides conservation and
3478 quality histograms</li>
3483 <td><div align="center">
3484 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3486 <td><em>Application</em>
3488 <li>Support for JABAWS 2.0 Services (AACon alignment
3489 conservation, protein disorder and Clustal Omega)</li>
3490 <li>JABAWS server status indicator in Web Services
3492 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3493 in Jalview alignment window</li>
3494 <li>Updated Jalview build and deploy framework for OSX
3495 mountain lion, windows 7, and 8</li>
3496 <li>Nucleotide substitution matrix for PCA that supports
3497 RNA and ambiguity codes</li>
3499 <li>Improved sequence database retrieval GUI</li>
3500 <li>Support fetching and database reference look up
3501 against multiple DAS sources (Fetch all from in 'fetch db
3503 <li>Jalview project improvements
3505 <li>Store and retrieve the 'belowAlignment'
3506 flag for annotation</li>
3507 <li>calcId attribute to group annotation rows on the
3509 <li>Store AACon calculation settings for a view in
3510 Jalview project</li>
3514 <li>horizontal scrolling gesture support</li>
3515 <li>Visual progress indicator when PCA calculation is
3517 <li>Simpler JABA web services menus</li>
3518 <li>visual indication that web service results are still
3519 being retrieved from server</li>
3520 <li>Serialise the dialogs that are shown when Jalview
3521 starts up for first time</li>
3522 <li>Jalview user agent string for interacting with HTTP
3524 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3526 <li>Examples directory and Groovy library included in
3527 InstallAnywhere distribution</li>
3528 </ul> <em>Applet</em>
3530 <li>RNA alignment and secondary structure annotation
3531 visualization applet example</li>
3532 </ul> <em>General</em>
3534 <li>Normalise option for consensus sequence logo</li>
3535 <li>Reset button in PCA window to return dimensions to
3537 <li>Allow seqspace or Jalview variant of alignment PCA
3539 <li>PCA with either nucleic acid and protein substitution
3541 <li>Allow windows containing HTML reports to be exported
3543 <li>Interactive display and editing of RNA secondary
3544 structure contacts</li>
3545 <li>RNA Helix Alignment Colouring</li>
3546 <li>RNA base pair logo consensus</li>
3547 <li>Parse sequence associated secondary structure
3548 information in Stockholm files</li>
3549 <li>HTML Export database accessions and annotation
3550 information presented in tooltip for sequences</li>
3551 <li>Import secondary structure from LOCARNA clustalw
3552 style RNA alignment files</li>
3553 <li>import and visualise T-COFFEE quality scores for an
3555 <li>'colour by annotation' per sequence option to
3556 shade each sequence according to its associated alignment
3558 <li>New Jalview Logo</li>
3559 </ul> <em>Documentation and Development</em>
3561 <li>documentation for score matrices used in Jalview</li>
3562 <li>New Website!</li>
3564 <td><em>Application</em>
3566 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3567 wsdbfetch REST service</li>
3568 <li>Stop windows being moved outside desktop on OSX</li>
3569 <li>Filetype associations not installed for webstart
3571 <li>Jalview does not always retrieve progress of a JABAWS
3572 job execution in full once it is complete</li>
3573 <li>revise SHMR RSBS definition to ensure alignment is
3574 uploaded via ali_file parameter</li>
3575 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3576 <li>View all structures superposed fails with exception</li>
3577 <li>Jnet job queues forever if a very short sequence is
3578 submitted for prediction</li>
3579 <li>Cut and paste menu not opened when mouse clicked on
3581 <li>Putting fractional value into integer text box in
3582 alignment parameter dialog causes Jalview to hang</li>
3583 <li>Structure view highlighting doesn't work on
3585 <li>View all structures fails with exception shown in
3587 <li>Characters in filename associated with PDBEntry not
3588 escaped in a platform independent way</li>
3589 <li>Jalview desktop fails to launch with exception when
3591 <li>Tree calculation reports 'you must have 2 or more
3592 sequences selected' when selection is empty</li>
3593 <li>Jalview desktop fails to launch with jar signature
3594 failure when java web start temporary file caching is
3596 <li>DAS Sequence retrieval with range qualification
3597 results in sequence xref which includes range qualification</li>
3598 <li>Errors during processing of command line arguments
3599 cause progress bar (JAL-898) to be removed</li>
3600 <li>Replace comma for semi-colon option not disabled for
3601 DAS sources in sequence fetcher</li>
3602 <li>Cannot close news reader when JABAWS server warning
3603 dialog is shown</li>
3604 <li>Option widgets not updated to reflect user settings</li>
3605 <li>Edited sequence not submitted to web service</li>
3606 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3607 <li>InstallAnywhere installer doesn't unpack and run
3608 on OSX Mountain Lion</li>
3609 <li>Annotation panel not given a scroll bar when
3610 sequences with alignment annotation are pasted into the
3612 <li>Sequence associated annotation rows not associated
3613 when loaded from Jalview project</li>
3614 <li>Browser launch fails with NPE on java 1.7</li>
3615 <li>JABAWS alignment marked as finished when job was
3616 cancelled or job failed due to invalid input</li>
3617 <li>NPE with v2.7 example when clicking on Tree
3618 associated with all views</li>
3619 <li>Exceptions when copy/paste sequences with grouped
3620 annotation rows to new window</li>
3621 </ul> <em>Applet</em>
3623 <li>Sequence features are momentarily displayed before
3624 they are hidden using hidefeaturegroups applet parameter</li>
3625 <li>loading features via javascript API automatically
3626 enables feature display</li>
3627 <li>scrollToColumnIn javascript API method doesn't
3629 </ul> <em>General</em>
3631 <li>Redundancy removal fails for rna alignment</li>
3632 <li>PCA calculation fails when sequence has been selected
3633 and then deselected</li>
3634 <li>PCA window shows grey box when first opened on OSX</li>
3635 <li>Letters coloured pink in sequence logo when alignment
3636 coloured with clustalx</li>
3637 <li>Choosing fonts without letter symbols defined causes
3638 exceptions and redraw errors</li>
3639 <li>Initial PCA plot view is not same as manually
3640 reconfigured view</li>
3641 <li>Grouped annotation graph label has incorrect line
3643 <li>Grouped annotation graph label display is corrupted
3644 for lots of labels</li>
3649 <div align="center">
3650 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3653 <td><em>Application</em>
3655 <li>Jalview Desktop News Reader</li>
3656 <li>Tweaked default layout of web services menu</li>
3657 <li>View/alignment association menu to enable user to
3658 easily specify which alignment a multi-structure view takes
3659 its colours/correspondences from</li>
3660 <li>Allow properties file location to be specified as URL</li>
3661 <li>Extend Jalview project to preserve associations
3662 between many alignment views and a single Jmol display</li>
3663 <li>Store annotation row height in Jalview project file</li>
3664 <li>Annotation row column label formatting attributes
3665 stored in project file</li>
3666 <li>Annotation row order for auto-calculated annotation
3667 rows preserved in Jalview project file</li>
3668 <li>Visual progress indication when Jalview state is
3669 saved using Desktop window menu</li>
3670 <li>Visual indication that command line arguments are
3671 still being processed</li>
3672 <li>Groovy script execution from URL</li>
3673 <li>Colour by annotation default min and max colours in
3675 <li>Automatically associate PDB files dragged onto an
3676 alignment with sequences that have high similarity and
3678 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3679 <li>'view structures' option to open many
3680 structures in same window</li>
3681 <li>Sort associated views menu option for tree panel</li>
3682 <li>Group all JABA and non-JABA services for a particular
3683 analysis function in its own submenu</li>
3684 </ul> <em>Applet</em>
3686 <li>Userdefined and autogenerated annotation rows for
3688 <li>Adjustment of alignment annotation pane height</li>
3689 <li>Annotation scrollbar for annotation panel</li>
3690 <li>Drag to reorder annotation rows in annotation panel</li>
3691 <li>'automaticScrolling' parameter</li>
3692 <li>Allow sequences with partial ID string matches to be
3693 annotated from GFF/Jalview features files</li>
3694 <li>Sequence logo annotation row in applet</li>
3695 <li>Absolute paths relative to host server in applet
3696 parameters are treated as such</li>
3697 <li>New in the JalviewLite javascript API:
3699 <li>JalviewLite.js javascript library</li>
3700 <li>Javascript callbacks for
3702 <li>Applet initialisation</li>
3703 <li>Sequence/alignment mouse-overs and selections</li>
3706 <li>scrollTo row and column alignment scrolling
3708 <li>Select sequence/alignment regions from javascript</li>
3709 <li>javascript structure viewer harness to pass
3710 messages between Jmol and Jalview when running as
3711 distinct applets</li>
3712 <li>sortBy method</li>
3713 <li>Set of applet and application examples shipped
3714 with documentation</li>
3715 <li>New example to demonstrate JalviewLite and Jmol
3716 javascript message exchange</li>
3718 </ul> <em>General</em>
3720 <li>Enable Jmol displays to be associated with multiple
3721 multiple alignments</li>
3722 <li>Option to automatically sort alignment with new tree</li>
3723 <li>User configurable link to enable redirects to a
3724 www.Jalview.org mirror</li>
3725 <li>Jmol colours option for Jmol displays</li>
3726 <li>Configurable newline string when writing alignment
3727 and other flat files</li>
3728 <li>Allow alignment annotation description lines to
3729 contain html tags</li>
3730 </ul> <em>Documentation and Development</em>
3732 <li>Add groovy test harness for bulk load testing to
3734 <li>Groovy script to load and align a set of sequences
3735 using a web service before displaying the result in the
3736 Jalview desktop</li>
3737 <li>Restructured javascript and applet api documentation</li>
3738 <li>Ant target to publish example html files with applet
3740 <li>Netbeans project for building Jalview from source</li>
3741 <li>ant task to create online javadoc for Jalview source</li>
3743 <td><em>Application</em>
3745 <li>User defined colourscheme throws exception when
3746 current built in colourscheme is saved as new scheme</li>
3747 <li>AlignFrame->Save in application pops up save
3748 dialog for valid filename/format</li>
3749 <li>Cannot view associated structure for UniProt sequence</li>
3750 <li>PDB file association breaks for UniProt sequence
3752 <li>Associate PDB from file dialog does not tell you
3753 which sequence is to be associated with the file</li>
3754 <li>Find All raises null pointer exception when query
3755 only matches sequence IDs</li>
3756 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3757 <li>Jalview project with Jmol views created with Jalview
3758 2.4 cannot be loaded</li>
3759 <li>Filetype associations not installed for webstart
3761 <li>Two or more chains in a single PDB file associated
3762 with sequences in different alignments do not get coloured
3763 by their associated sequence</li>
3764 <li>Visibility status of autocalculated annotation row
3765 not preserved when project is loaded</li>
3766 <li>Annotation row height and visibility attributes not
3767 stored in Jalview project</li>
3768 <li>Tree bootstraps are not preserved when saved as a
3769 Jalview project</li>
3770 <li>Envision2 workflow tooltips are corrupted</li>
3771 <li>Enabling show group conservation also enables colour
3772 by conservation</li>
3773 <li>Duplicate group associated conservation or consensus
3774 created on new view</li>
3775 <li>Annotation scrollbar not displayed after 'show
3776 all hidden annotation rows' option selected</li>
3777 <li>Alignment quality not updated after alignment
3778 annotation row is hidden then shown</li>
3779 <li>Preserve colouring of structures coloured by
3780 sequences in pre Jalview 2.7 projects</li>
3781 <li>Web service job parameter dialog is not laid out
3783 <li>Web services menu not refreshed after 'reset
3784 services' button is pressed in preferences</li>
3785 <li>Annotation off by one in Jalview v2_3 example project</li>
3786 <li>Structures imported from file and saved in project
3787 get name like jalview_pdb1234.txt when reloaded</li>
3788 <li>Jalview does not always retrieve progress of a JABAWS
3789 job execution in full once it is complete</li>
3790 </ul> <em>Applet</em>
3792 <li>Alignment height set incorrectly when lots of
3793 annotation rows are displayed</li>
3794 <li>Relative URLs in feature HTML text not resolved to
3796 <li>View follows highlighting does not work for positions
3798 <li><= shown as = in tooltip</li>
3799 <li>Export features raises exception when no features
3801 <li>Separator string used for serialising lists of IDs
3802 for javascript api is modified when separator string
3803 provided as parameter</li>
3804 <li>Null pointer exception when selecting tree leaves for
3805 alignment with no existing selection</li>
3806 <li>Relative URLs for datasources assumed to be relative
3807 to applet's codebase</li>
3808 <li>Status bar not updated after finished searching and
3809 search wraps around to first result</li>
3810 <li>StructureSelectionManager instance shared between
3811 several Jalview applets causes race conditions and memory
3813 <li>Hover tooltip and mouseover of position on structure
3814 not sent from Jmol in applet</li>
3815 <li>Certain sequences of javascript method calls to
3816 applet API fatally hang browser</li>
3817 </ul> <em>General</em>
3819 <li>View follows structure mouseover scrolls beyond
3820 position with wrapped view and hidden regions</li>
3821 <li>Find sequence position moves to wrong residue
3822 with/without hidden columns</li>
3823 <li>Sequence length given in alignment properties window
3825 <li>InvalidNumberFormat exceptions thrown when trying to
3826 import PDB like structure files</li>
3827 <li>Positional search results are only highlighted
3828 between user-supplied sequence start/end bounds</li>
3829 <li>End attribute of sequence is not validated</li>
3830 <li>Find dialog only finds first sequence containing a
3831 given sequence position</li>
3832 <li>Sequence numbering not preserved in MSF alignment
3834 <li>Jalview PDB file reader does not extract sequence
3835 from nucleotide chains correctly</li>
3836 <li>Structure colours not updated when tree partition
3837 changed in alignment</li>
3838 <li>Sequence associated secondary structure not correctly
3839 parsed in interleaved stockholm</li>
3840 <li>Colour by annotation dialog does not restore current
3842 <li>Hiding (nearly) all sequences doesn't work
3844 <li>Sequences containing lowercase letters are not
3845 properly associated with their pdb files</li>
3846 </ul> <em>Documentation and Development</em>
3848 <li>schemas/JalviewWsParamSet.xsd corrupted by
3849 ApplyCopyright tool</li>
3854 <div align="center">
3855 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3858 <td><em>Application</em>
3860 <li>New warning dialog when the Jalview Desktop cannot
3861 contact web services</li>
3862 <li>JABA service parameters for a preset are shown in
3863 service job window</li>
3864 <li>JABA Service menu entries reworded</li>
3868 <li>Modeller PIR IO broken - cannot correctly import a
3869 pir file emitted by Jalview</li>
3870 <li>Existing feature settings transferred to new
3871 alignment view created from cut'n'paste</li>
3872 <li>Improved test for mixed amino/nucleotide chains when
3873 parsing PDB files</li>
3874 <li>Consensus and conservation annotation rows
3875 occasionally become blank for all new windows</li>
3876 <li>Exception raised when right clicking above sequences
3877 in wrapped view mode</li>
3878 </ul> <em>Application</em>
3880 <li>multiple multiply aligned structure views cause cpu
3881 usage to hit 100% and computer to hang</li>
3882 <li>Web Service parameter layout breaks for long user
3883 parameter names</li>
3884 <li>Jaba service discovery hangs desktop if Jaba server
3891 <div align="center">
3892 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3895 <td><em>Application</em>
3897 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3898 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3901 <li>Web Services preference tab</li>
3902 <li>Analysis parameters dialog box and user defined
3904 <li>Improved speed and layout of Envision2 service menu</li>
3905 <li>Superpose structures using associated sequence
3907 <li>Export coordinates and projection as CSV from PCA
3909 </ul> <em>Applet</em>
3911 <li>enable javascript: execution by the applet via the
3912 link out mechanism</li>
3913 </ul> <em>Other</em>
3915 <li>Updated the Jmol Jalview interface to work with Jmol
3917 <li>The Jalview Desktop and JalviewLite applet now
3918 require Java 1.5</li>
3919 <li>Allow Jalview feature colour specification for GFF
3920 sequence annotation files</li>
3921 <li>New 'colour by label' keword in Jalview feature file
3922 type colour specification</li>
3923 <li>New Jalview Desktop Groovy API method that allows a
3924 script to check if it being run in an interactive session or
3925 in a batch operation from the Jalview command line</li>
3929 <li>clustalx colourscheme colours Ds preferentially when
3930 both D+E are present in over 50% of the column</li>
3931 </ul> <em>Application</em>
3933 <li>typo in AlignmentFrame->View->Hide->all but
3934 selected Regions menu item</li>
3935 <li>sequence fetcher replaces ',' for ';' when the ',' is
3936 part of a valid accession ID</li>
3937 <li>fatal OOM if object retrieved by sequence fetcher
3938 runs out of memory</li>
3939 <li>unhandled Out of Memory Error when viewing pca
3940 analysis results</li>
3941 <li>InstallAnywhere builds fail to launch on OS X java
3942 10.5 update 4 (due to apple Java 1.6 update)</li>
3943 <li>Installanywhere Jalview silently fails to launch</li>
3944 </ul> <em>Applet</em>
3946 <li>Jalview.getFeatureGroups() raises an
3947 ArrayIndexOutOfBoundsException if no feature groups are
3954 <div align="center">
3955 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3961 <li>Alignment prettyprinter doesn't cope with long
3963 <li>clustalx colourscheme colours Ds preferentially when
3964 both D+E are present in over 50% of the column</li>
3965 <li>nucleic acid structures retrieved from PDB do not
3966 import correctly</li>
3967 <li>More columns get selected than were clicked on when a
3968 number of columns are hidden</li>
3969 <li>annotation label popup menu not providing correct
3970 add/hide/show options when rows are hidden or none are
3972 <li>Stockholm format shown in list of readable formats,
3973 and parser copes better with alignments from RFAM.</li>
3974 <li>CSV output of consensus only includes the percentage
3975 of all symbols if sequence logo display is enabled</li>
3977 </ul> <em>Applet</em>
3979 <li>annotation panel disappears when annotation is
3981 </ul> <em>Application</em>
3983 <li>Alignment view not redrawn properly when new
3984 alignment opened where annotation panel is visible but no
3985 annotations are present on alignment</li>
3986 <li>pasted region containing hidden columns is
3987 incorrectly displayed in new alignment window</li>
3988 <li>Jalview slow to complete operations when stdout is
3989 flooded (fix is to close the Jalview console)</li>
3990 <li>typo in AlignmentFrame->View->Hide->all but
3991 selected Rregions menu item.</li>
3992 <li>inconsistent group submenu and Format submenu entry
3993 'Un' or 'Non'conserved</li>
3994 <li>Sequence feature settings are being shared by
3995 multiple distinct alignments</li>
3996 <li>group annotation not recreated when tree partition is
3998 <li>double click on group annotation to select sequences
3999 does not propagate to associated trees</li>
4000 <li>Mac OSX specific issues:
4002 <li>exception raised when mouse clicked on desktop
4003 window background</li>
4004 <li>Desktop menu placed on menu bar and application
4005 name set correctly</li>
4006 <li>sequence feature settings not wide enough for the
4007 save feature colourscheme button</li>
4016 <div align="center">
4017 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4020 <td><em>New Capabilities</em>
4022 <li>URL links generated from description line for
4023 regular-expression based URL links (applet and application)
4025 <li>Non-positional feature URL links are shown in link
4027 <li>Linked viewing of nucleic acid sequences and
4029 <li>Automatic Scrolling option in View menu to display
4030 the currently highlighted region of an alignment.</li>
4031 <li>Order an alignment by sequence length, or using the
4032 average score or total feature count for each sequence.</li>
4033 <li>Shading features by score or associated description</li>
4034 <li>Subdivide alignment and groups based on identity of
4035 selected subsequence (Make Groups from Selection).</li>
4036 <li>New hide/show options including Shift+Control+H to
4037 hide everything but the currently selected region.</li>
4038 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4039 </ul> <em>Application</em>
4041 <li>Fetch DB References capabilities and UI expanded to
4042 support retrieval from DAS sequence sources</li>
4043 <li>Local DAS Sequence sources can be added via the
4044 command line or via the Add local source dialog box.</li>
4045 <li>DAS Dbref and DbxRef feature types are parsed as
4046 database references and protein_name is parsed as
4047 description line (BioSapiens terms).</li>
4048 <li>Enable or disable non-positional feature and database
4049 references in sequence ID tooltip from View menu in
4051 <!-- <li>New hidden columns and rows and representatives capabilities
4052 in annotations file (in progress - not yet fully implemented)</li> -->
4053 <li>Group-associated consensus, sequence logos and
4054 conservation plots</li>
4055 <li>Symbol distributions for each column can be exported
4056 and visualized as sequence logos</li>
4057 <li>Optionally scale multi-character column labels to fit
4058 within each column of annotation row<!-- todo for applet -->
4060 <li>Optional automatic sort of associated alignment view
4061 when a new tree is opened.</li>
4062 <li>Jalview Java Console</li>
4063 <li>Better placement of desktop window when moving
4064 between different screens.</li>
4065 <li>New preference items for sequence ID tooltip and
4066 consensus annotation</li>
4067 <li>Client to submit sequences and IDs to Envision2
4069 <li><em>Vamsas Capabilities</em>
4071 <li>Improved VAMSAS synchronization (Jalview archive
4072 used to preserve views, structures, and tree display
4074 <li>Import of vamsas documents from disk or URL via
4076 <li>Sharing of selected regions between views and
4077 with other VAMSAS applications (Experimental feature!)</li>
4078 <li>Updated API to VAMSAS version 0.2</li>
4080 </ul> <em>Applet</em>
4082 <li>Middle button resizes annotation row height</li>
4085 <li>sortByTree (true/false) - automatically sort the
4086 associated alignment view by the tree when a new tree is
4088 <li>showTreeBootstraps (true/false) - show or hide
4089 branch bootstraps (default is to show them if available)</li>
4090 <li>showTreeDistances (true/false) - show or hide
4091 branch lengths (default is to show them if available)</li>
4092 <li>showUnlinkedTreeNodes (true/false) - indicate if
4093 unassociated nodes should be highlighted in the tree
4095 <li>heightScale and widthScale (1.0 or more) -
4096 increase the height or width of a cell in the alignment
4097 grid relative to the current font size.</li>
4100 <li>Non-positional features displayed in sequence ID
4102 </ul> <em>Other</em>
4104 <li>Features format: graduated colour definitions and
4105 specification of feature scores</li>
4106 <li>Alignment Annotations format: new keywords for group
4107 associated annotation (GROUP_REF) and annotation row display
4108 properties (ROW_PROPERTIES)</li>
4109 <li>XML formats extended to support graduated feature
4110 colourschemes, group associated annotation, and profile
4111 visualization settings.</li></td>
4114 <li>Source field in GFF files parsed as feature source
4115 rather than description</li>
4116 <li>Non-positional features are now included in sequence
4117 feature and gff files (controlled via non-positional feature
4118 visibility in tooltip).</li>
4119 <li>URL links generated for all feature links (bugfix)</li>
4120 <li>Added URL embedding instructions to features file
4122 <li>Codons containing ambiguous nucleotides translated as
4123 'X' in peptide product</li>
4124 <li>Match case switch in find dialog box works for both
4125 sequence ID and sequence string and query strings do not
4126 have to be in upper case to match case-insensitively.</li>
4127 <li>AMSA files only contain first column of
4128 multi-character column annotation labels</li>
4129 <li>Jalview Annotation File generation/parsing consistent
4130 with documentation (e.g. Stockholm annotation can be
4131 exported and re-imported)</li>
4132 <li>PDB files without embedded PDB IDs given a friendly
4134 <li>Find incrementally searches ID string matches as well
4135 as subsequence matches, and correctly reports total number
4139 <li>Better handling of exceptions during sequence
4141 <li>Dasobert generated non-positional feature URL
4142 link text excludes the start_end suffix</li>
4143 <li>DAS feature and source retrieval buttons disabled
4144 when fetch or registry operations in progress.</li>
4145 <li>PDB files retrieved from URLs are cached properly</li>
4146 <li>Sequence description lines properly shared via
4148 <li>Sequence fetcher fetches multiple records for all
4150 <li>Ensured that command line das feature retrieval
4151 completes before alignment figures are generated.</li>
4152 <li>Reduced time taken when opening file browser for
4154 <li>isAligned check prior to calculating tree, PCA or
4155 submitting an MSA to JNet now excludes hidden sequences.</li>
4156 <li>User defined group colours properly recovered
4157 from Jalview projects.</li>
4166 <div align="center">
4167 <strong>2.4.0.b2</strong><br> 28/10/2009
4172 <li>Experimental support for google analytics usage
4174 <li>Jalview privacy settings (user preferences and docs).</li>
4179 <li>Race condition in applet preventing startup in
4181 <li>Exception when feature created from selection beyond
4182 length of sequence.</li>
4183 <li>Allow synthetic PDB files to be imported gracefully</li>
4184 <li>Sequence associated annotation rows associate with
4185 all sequences with a given id</li>
4186 <li>Find function matches case-insensitively for sequence
4187 ID string searches</li>
4188 <li>Non-standard characters do not cause pairwise
4189 alignment to fail with exception</li>
4190 </ul> <em>Application Issues</em>
4192 <li>Sequences are now validated against EMBL database</li>
4193 <li>Sequence fetcher fetches multiple records for all
4195 </ul> <em>InstallAnywhere Issues</em>
4197 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4198 issue with installAnywhere mechanism)</li>
4199 <li>Command line launching of JARs from InstallAnywhere
4200 version (java class versioning error fixed)</li>
4207 <div align="center">
4208 <strong>2.4</strong><br> 27/8/2008
4211 <td><em>User Interface</em>
4213 <li>Linked highlighting of codon and amino acid from
4214 translation and protein products</li>
4215 <li>Linked highlighting of structure associated with
4216 residue mapping to codon position</li>
4217 <li>Sequence Fetcher provides example accession numbers
4218 and 'clear' button</li>
4219 <li>MemoryMonitor added as an option under Desktop's
4221 <li>Extract score function to parse whitespace separated
4222 numeric data in description line</li>
4223 <li>Column labels in alignment annotation can be centred.</li>
4224 <li>Tooltip for sequence associated annotation give name
4226 </ul> <em>Web Services and URL fetching</em>
4228 <li>JPred3 web service</li>
4229 <li>Prototype sequence search client (no public services
4231 <li>Fetch either seed alignment or full alignment from
4233 <li>URL Links created for matching database cross
4234 references as well as sequence ID</li>
4235 <li>URL Links can be created using regular-expressions</li>
4236 </ul> <em>Sequence Database Connectivity</em>
4238 <li>Retrieval of cross-referenced sequences from other
4240 <li>Generalised database reference retrieval and
4241 validation to all fetchable databases</li>
4242 <li>Fetch sequences from DAS sources supporting the
4243 sequence command</li>
4244 </ul> <em>Import and Export</em>
4245 <li>export annotation rows as CSV for spreadsheet import</li>
4246 <li>Jalview projects record alignment dataset associations,
4247 EMBL products, and cDNA sequence mappings</li>
4248 <li>Sequence Group colour can be specified in Annotation
4250 <li>Ad-hoc colouring of group in Annotation File using RGB
4251 triplet as name of colourscheme</li>
4252 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4254 <li>treenode binding for VAMSAS tree exchange</li>
4255 <li>local editing and update of sequences in VAMSAS
4256 alignments (experimental)</li>
4257 <li>Create new or select existing session to join</li>
4258 <li>load and save of vamsas documents</li>
4259 </ul> <em>Application command line</em>
4261 <li>-tree parameter to open trees (introduced for passing
4263 <li>-fetchfrom command line argument to specify nicknames
4264 of DAS servers to query for alignment features</li>
4265 <li>-dasserver command line argument to add new servers
4266 that are also automatically queried for features</li>
4267 <li>-groovy command line argument executes a given groovy
4268 script after all input data has been loaded and parsed</li>
4269 </ul> <em>Applet-Application data exchange</em>
4271 <li>Trees passed as applet parameters can be passed to
4272 application (when using "View in full
4273 application")</li>
4274 </ul> <em>Applet Parameters</em>
4276 <li>feature group display control parameter</li>
4277 <li>debug parameter</li>
4278 <li>showbutton parameter</li>
4279 </ul> <em>Applet API methods</em>
4281 <li>newView public method</li>
4282 <li>Window (current view) specific get/set public methods</li>
4283 <li>Feature display control methods</li>
4284 <li>get list of currently selected sequences</li>
4285 </ul> <em>New Jalview distribution features</em>
4287 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4288 <li>RELEASE file gives build properties for the latest
4289 Jalview release.</li>
4290 <li>Java 1.1 Applet build made easier and donotobfuscate
4291 property controls execution of obfuscator</li>
4292 <li>Build target for generating source distribution</li>
4293 <li>Debug flag for javacc</li>
4294 <li>.jalview_properties file is documented (slightly) in
4295 jalview.bin.Cache</li>
4296 <li>Continuous Build Integration for stable and
4297 development version of Application, Applet and source
4302 <li>selected region output includes visible annotations
4303 (for certain formats)</li>
4304 <li>edit label/displaychar contains existing label/char
4306 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4307 <li>shorter peptide product names from EMBL records</li>
4308 <li>Newick string generator makes compact representations</li>
4309 <li>bootstrap values parsed correctly for tree files with
4311 <li>pathological filechooser bug avoided by not allowing
4312 filenames containing a ':'</li>
4313 <li>Fixed exception when parsing GFF files containing
4314 global sequence features</li>
4315 <li>Alignment datasets are finalized only when number of
4316 references from alignment sequences goes to zero</li>
4317 <li>Close of tree branch colour box without colour
4318 selection causes cascading exceptions</li>
4319 <li>occasional negative imgwidth exceptions</li>
4320 <li>better reporting of non-fatal warnings to user when
4321 file parsing fails.</li>
4322 <li>Save works when Jalview project is default format</li>
4323 <li>Save as dialog opened if current alignment format is
4324 not a valid output format</li>
4325 <li>UniProt canonical names introduced for both das and
4327 <li>Histidine should be midblue (not pink!) in Zappo</li>
4328 <li>error messages passed up and output when data read
4330 <li>edit undo recovers previous dataset sequence when
4331 sequence is edited</li>
4332 <li>allow PDB files without pdb ID HEADER lines (like
4333 those generated by MODELLER) to be read in properly</li>
4334 <li>allow reading of JPred concise files as a normal
4336 <li>Stockholm annotation parsing and alignment properties
4337 import fixed for PFAM records</li>
4338 <li>Structure view windows have correct name in Desktop
4340 <li>annotation consisting of sequence associated scores
4341 can be read and written correctly to annotation file</li>
4342 <li>Aligned cDNA translation to aligned peptide works
4344 <li>Fixed display of hidden sequence markers and
4345 non-italic font for representatives in Applet</li>
4346 <li>Applet Menus are always embedded in applet window on
4348 <li>Newly shown features appear at top of stack (in
4350 <li>Annotations added via parameter not drawn properly
4351 due to null pointer exceptions</li>
4352 <li>Secondary structure lines are drawn starting from
4353 first column of alignment</li>
4354 <li>UniProt XML import updated for new schema release in
4356 <li>Sequence feature to sequence ID match for Features
4357 file is case-insensitive</li>
4358 <li>Sequence features read from Features file appended to
4359 all sequences with matching IDs</li>
4360 <li>PDB structure coloured correctly for associated views
4361 containing a sub-sequence</li>
4362 <li>PDB files can be retrieved by applet from Jar files</li>
4363 <li>feature and annotation file applet parameters
4364 referring to different directories are retrieved correctly</li>
4365 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4366 <li>Fixed application hang whilst waiting for
4367 splash-screen version check to complete</li>
4368 <li>Applet properly URLencodes input parameter values
4369 when passing them to the launchApp service</li>
4370 <li>display name and local features preserved in results
4371 retrieved from web service</li>
4372 <li>Visual delay indication for sequence retrieval and
4373 sequence fetcher initialisation</li>
4374 <li>updated Application to use DAS 1.53e version of
4375 dasobert DAS client</li>
4376 <li>Re-instated Full AMSA support and .amsa file
4378 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4386 <div align="center">
4387 <strong>2.3</strong><br> 9/5/07
4392 <li>Jmol 11.0.2 integration</li>
4393 <li>PDB views stored in Jalview XML files</li>
4394 <li>Slide sequences</li>
4395 <li>Edit sequence in place</li>
4396 <li>EMBL CDS features</li>
4397 <li>DAS Feature mapping</li>
4398 <li>Feature ordering</li>
4399 <li>Alignment Properties</li>
4400 <li>Annotation Scores</li>
4401 <li>Sort by scores</li>
4402 <li>Feature/annotation editing in applet</li>
4407 <li>Headless state operation in 2.2.1</li>
4408 <li>Incorrect and unstable DNA pairwise alignment</li>
4409 <li>Cut and paste of sequences with annotation</li>
4410 <li>Feature group display state in XML</li>
4411 <li>Feature ordering in XML</li>
4412 <li>blc file iteration selection using filename # suffix</li>
4413 <li>Stockholm alignment properties</li>
4414 <li>Stockhom alignment secondary structure annotation</li>
4415 <li>2.2.1 applet had no feature transparency</li>
4416 <li>Number pad keys can be used in cursor mode</li>
4417 <li>Structure Viewer mirror image resolved</li>
4424 <div align="center">
4425 <strong>2.2.1</strong><br> 12/2/07
4430 <li>Non standard characters can be read and displayed
4431 <li>Annotations/Features can be imported/exported to the
4433 <li>Applet allows editing of sequence/annotation/group
4434 name & description
4435 <li>Preference setting to display sequence name in
4437 <li>Annotation file format extended to allow
4438 Sequence_groups to be defined
4439 <li>Default opening of alignment overview panel can be
4440 specified in preferences
4441 <li>PDB residue numbering annotation added to associated
4447 <li>Applet crash under certain Linux OS with Java 1.6
4449 <li>Annotation file export / import bugs fixed
4450 <li>PNG / EPS image output bugs fixed
4456 <div align="center">
4457 <strong>2.2</strong><br> 27/11/06
4462 <li>Multiple views on alignment
4463 <li>Sequence feature editing
4464 <li>"Reload" alignment
4465 <li>"Save" to current filename
4466 <li>Background dependent text colour
4467 <li>Right align sequence ids
4468 <li>User-defined lower case residue colours
4471 <li>Menu item accelerator keys
4472 <li>Control-V pastes to current alignment
4473 <li>Cancel button for DAS Feature Fetching
4474 <li>PCA and PDB Viewers zoom via mouse roller
4475 <li>User-defined sub-tree colours and sub-tree selection
4477 <li>'New Window' button on the 'Output to Text box'
4482 <li>New memory efficient Undo/Redo System
4483 <li>Optimised symbol lookups and conservation/consensus
4485 <li>Region Conservation/Consensus recalculated after
4487 <li>Fixed Remove Empty Columns Bug (empty columns at end
4489 <li>Slowed DAS Feature Fetching for increased robustness.
4491 <li>Made angle brackets in ASCII feature descriptions
4493 <li>Re-instated Zoom function for PCA
4494 <li>Sequence descriptions conserved in web service
4496 <li>UniProt ID discoverer uses any word separated by
4498 <li>WsDbFetch query/result association resolved
4499 <li>Tree leaf to sequence mapping improved
4500 <li>Smooth fonts switch moved to FontChooser dialog box.
4507 <div align="center">
4508 <strong>2.1.1</strong><br> 12/9/06
4513 <li>Copy consensus sequence to clipboard</li>
4518 <li>Image output - rightmost residues are rendered if
4519 sequence id panel has been resized</li>
4520 <li>Image output - all offscreen group boundaries are
4522 <li>Annotation files with sequence references - all
4523 elements in file are relative to sequence position</li>
4524 <li>Mac Applet users can use Alt key for group editing</li>
4530 <div align="center">
4531 <strong>2.1</strong><br> 22/8/06
4536 <li>MAFFT Multiple Alignment in default Web Service list</li>
4537 <li>DAS Feature fetching</li>
4538 <li>Hide sequences and columns</li>
4539 <li>Export Annotations and Features</li>
4540 <li>GFF file reading / writing</li>
4541 <li>Associate structures with sequences from local PDB
4543 <li>Add sequences to exisiting alignment</li>
4544 <li>Recently opened files / URL lists</li>
4545 <li>Applet can launch the full application</li>
4546 <li>Applet has transparency for features (Java 1.2
4548 <li>Applet has user defined colours parameter</li>
4549 <li>Applet can load sequences from parameter
4550 "sequence<em>x</em>"
4556 <li>Redundancy Panel reinstalled in the Applet</li>
4557 <li>Monospaced font - EPS / rescaling bug fixed</li>
4558 <li>Annotation files with sequence references bug fixed</li>
4564 <div align="center">
4565 <strong>2.08.1</strong><br> 2/5/06
4570 <li>Change case of selected region from Popup menu</li>
4571 <li>Choose to match case when searching</li>
4572 <li>Middle mouse button and mouse movement can compress /
4573 expand the visible width and height of the alignment</li>
4578 <li>Annotation Panel displays complete JNet results</li>
4584 <div align="center">
4585 <strong>2.08b</strong><br> 18/4/06
4591 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4592 <li>Righthand label on wrapped alignments shows correct
4599 <div align="center">
4600 <strong>2.08</strong><br> 10/4/06
4605 <li>Editing can be locked to the selection area</li>
4606 <li>Keyboard editing</li>
4607 <li>Create sequence features from searches</li>
4608 <li>Precalculated annotations can be loaded onto
4610 <li>Features file allows grouping of features</li>
4611 <li>Annotation Colouring scheme added</li>
4612 <li>Smooth fonts off by default - Faster rendering</li>
4613 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4618 <li>Drag & Drop fixed on Linux</li>
4619 <li>Jalview Archive file faster to load/save, sequence
4620 descriptions saved.</li>
4626 <div align="center">
4627 <strong>2.07</strong><br> 12/12/05
4632 <li>PDB Structure Viewer enhanced</li>
4633 <li>Sequence Feature retrieval and display enhanced</li>
4634 <li>Choose to output sequence start-end after sequence
4635 name for file output</li>
4636 <li>Sequence Fetcher WSDBFetch@EBI</li>
4637 <li>Applet can read feature files, PDB files and can be
4638 used for HTML form input</li>
4643 <li>HTML output writes groups and features</li>
4644 <li>Group editing is Control and mouse click</li>
4645 <li>File IO bugs</li>
4651 <div align="center">
4652 <strong>2.06</strong><br> 28/9/05
4657 <li>View annotations in wrapped mode</li>
4658 <li>More options for PCA viewer</li>
4663 <li>GUI bugs resolved</li>
4664 <li>Runs with -nodisplay from command line</li>
4670 <div align="center">
4671 <strong>2.05b</strong><br> 15/9/05
4676 <li>Choose EPS export as lineart or text</li>
4677 <li>Jar files are executable</li>
4678 <li>Can read in Uracil - maps to unknown residue</li>
4683 <li>Known OutOfMemory errors give warning message</li>
4684 <li>Overview window calculated more efficiently</li>
4685 <li>Several GUI bugs resolved</li>
4691 <div align="center">
4692 <strong>2.05</strong><br> 30/8/05
4697 <li>Edit and annotate in "Wrapped" view</li>
4702 <li>Several GUI bugs resolved</li>
4708 <div align="center">
4709 <strong>2.04</strong><br> 24/8/05
4714 <li>Hold down mouse wheel & scroll to change font
4720 <li>Improved JPred client reliability</li>
4721 <li>Improved loading of Jalview files</li>
4727 <div align="center">
4728 <strong>2.03</strong><br> 18/8/05
4733 <li>Set Proxy server name and port in preferences</li>
4734 <li>Multiple URL links from sequence ids</li>
4735 <li>User Defined Colours can have a scheme name and added
4737 <li>Choose to ignore gaps in consensus calculation</li>
4738 <li>Unix users can set default web browser</li>
4739 <li>Runs without GUI for batch processing</li>
4740 <li>Dynamically generated Web Service Menus</li>
4745 <li>InstallAnywhere download for Sparc Solaris</li>
4751 <div align="center">
4752 <strong>2.02</strong><br> 18/7/05
4758 <li>Copy & Paste order of sequences maintains
4759 alignment order.</li>
4765 <div align="center">
4766 <strong>2.01</strong><br> 12/7/05
4771 <li>Use delete key for deleting selection.</li>
4772 <li>Use Mouse wheel to scroll sequences.</li>
4773 <li>Help file updated to describe how to add alignment
4775 <li>Version and build date written to build properties
4777 <li>InstallAnywhere installation will check for updates
4778 at launch of Jalview.</li>
4783 <li>Delete gaps bug fixed.</li>
4784 <li>FileChooser sorts columns.</li>
4785 <li>Can remove groups one by one.</li>
4786 <li>Filechooser icons installed.</li>
4787 <li>Finder ignores return character when searching.
4788 Return key will initiate a search.<br>
4795 <div align="center">
4796 <strong>2.0</strong><br> 20/6/05
4801 <li>New codebase</li>