3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.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 'virtual'
66 codon features shown on protein (or vice versa) for display
67 in alignments, on structure views, in feature reports and for export.
70 <!-- JAL-3121 -->Feature attributes from VCF files can be
71 exported and re-imported as GFF3 files
74 <!-- JAL-3376 -->Capture VCF "fixed column" values
75 POS, ID, QUAL, FILTER as Feature Attributes
78 <!-- JAL-3375 -->More robust VCF numeric data field
79 validation while parsing
82 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
86 <!-- JAL-3535 -->Feature Settings dialog title includes name
90 <!-- JAL-3538 -->Font anti-aliasing in alignment views
94 <!-- JAL-3468 -->Very long feature descriptions truncated in
98 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
99 with no feature types visible
101 </ul><em>Jalview Installer</em>
104 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
105 in console (may be null when Jalview launched as executable jar or via conda)
108 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
111 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
114 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
116 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
117 </ul> <em>Release processes</em>
120 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
123 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
125 </ul> <em>Build System</em>
128 <!-- JAL-3510 -->Clover updated to 4.4.1
131 <!-- JAL-3513 -->Test code included in Clover coverage
135 <em>Groovy Scripts</em>
138 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
139 to stdout containing the consensus sequence for each
140 alignment in a Jalview session
144 <td align="left" valign="top">
147 <!-- JAL-3581 -->Hidden sequence markers still visible when
148 'Show hidden markers' option is not ticked
151 <!-- JAL-3571 -->Feature Editor dialog can be opened when
152 'Show Sequence Features' option is not ticked
155 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
156 buttons in Feature Settings dialog are clicked when no
160 <!-- JAL-3412 -->ID margins for CDS and Protein views not
161 equal when split frame is first opened
164 <!-- JAL-3296 -->Sequence position numbers in status bar not
165 correct after editing a sequence's start position
168 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
169 with annotation and exceptions thrown when only a few
170 columns shown in wrapped mode
173 <!-- JAL-3386 -->Sequence IDs missing in headless export of
174 wrapped alignment figure with annotations
177 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
178 ID fails with ClassCastException
181 <!-- JAL-3389 -->Chimera session not restored from Jalview
185 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
186 feature settings dialog also selects columns
189 <!-- JAL-3473 -->SpinnerNumberModel causes
190 IllegalArgumentException in some circumstances
193 <!-- JAL-3534 -->Multiple feature settings dialogs can be
197 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
198 alignment window is closed
201 <!-- JAL-3406 -->Credits missing some authors in Jalview
202 help documentation for 2.11.0 release
205 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
206 includes Pfam ID as sequence's accession rather than its
209 </ul> <em>Java 11 Compatibility issues</em>
212 <!-- JAL-2987 -->OSX - Can't view some search results in
213 PDB/Uniprot search panel
215 </ul> <em>Installer</em>
218 <!-- JAL-3447 -->Jalview should not create file associations
219 for 3D structure files (.pdb, .mmcif. .cif)
221 </ul> <em>Repository and Source Release</em>
224 <!-- JAL-3474 -->removed obsolete .cvsignore files from
228 <!-- JAL-3541 -->Clover report generation running out of
231 </ul> <em>New Known Issues</em>
234 <!-- JAL-3523 -->OSX - Current working directory not
235 preserved when Jalview.app launched with parameters from
239 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
240 clipped in headless figure export when Right Align option
244 <!-- JAL-3542 -->Jalview Installation type always reports
245 'Source' in console output
248 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
249 bamboo server but run fine locally.
252 <!-- JAL-3574 -->Filtering features by genomic location (POS) is broken by rounding
258 <td width="60" align="center" nowrap>
259 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
260 <em>04/07/2019</em></strong>
262 <td align="left" valign="top">
265 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
266 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
267 source project) rather than InstallAnywhere
270 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
271 settings, receive over the air updates and launch specific
272 versions via (<a href="https://github.com/threerings/getdown">Three
276 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
277 formats supported by Jalview (including .jvp project files)
280 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
281 arguments and switch between different getdown channels
284 <!-- JAL-3141 -->Backup files created when saving Jalview project
289 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
290 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
292 <!-- JAL-2620 -->Alternative genetic code tables for
293 'Translate as cDNA'</li>
295 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
296 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
299 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
300 implementation that allows updates) used for Sequence Feature collections</li>
302 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
303 features can be filtered and shaded according to any
304 associated attributes (e.g. variant attributes from VCF
305 file, or key-value pairs imported from column 9 of GFF
309 <!-- JAL-2879 -->Feature Attributes and shading schemes
310 stored and restored from Jalview Projects
313 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
314 recognise variant features
317 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
318 sequences (also coloured red by default)
321 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
325 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
326 algorithm (Z-sort/transparency and filter aware)
329 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
335 <!-- JAL-3205 -->Symmetric score matrices for faster
336 tree and PCA calculations
338 <li><strong>Principal Components Analysis Viewer</strong>
341 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
342 and Viewer state saved in Jalview Project
344 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
347 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
351 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
356 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
358 <li><strong>Speed and Efficiency</strong>
361 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
362 multiple groups when working with large alignments
365 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
369 <li><strong>User Interface</strong>
372 <!-- JAL-2933 -->Finder panel remembers last position in each
376 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
377 what is shown)<br />Only visible regions of alignment are shown by
378 default (can be changed in user preferences)
381 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
382 to the Overwrite Dialog
385 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
389 <!-- JAL-1244 -->Status bar shows bounds when dragging a
390 selection region, and gap count when inserting or deleting gaps
393 <!-- JAL-3132 -->Status bar updates over sequence and annotation
397 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
401 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
405 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
408 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
412 <!-- JAL-3181 -->Consistent ordering of links in sequence id
416 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
418 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
422 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
423 <li><strong>Java 11 Support (not yet on general release)</strong>
426 <!-- -->OSX GUI integrations for App menu's 'About' entry and
431 <em>Deprecations</em>
433 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
434 capabilities removed from the Jalview Desktop
436 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
437 unmarshalling has been replaced by JAXB for Jalview projects
438 and XML based data retrieval clients</li>
439 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
440 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
441 </ul> <em>Documentation</em>
443 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
444 not supported in EPS figure export
446 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
447 </ul> <em>Development and Release Processes</em>
450 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
453 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
455 <!-- JAL-3225 -->Eclipse project configuration managed with
459 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
460 Bamboo continuous integration for unattended Test Suite
464 <!-- JAL-2864 -->Memory test suite to detect leaks in common
468 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
472 <!-- JAL-3248 -->Developer documentation migrated to
473 markdown (with HTML rendering)
476 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
479 <!-- JAL-3289 -->New URLs for publishing development
484 <td align="left" valign="top">
487 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
490 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
491 superposition in Jmol fail on Windows
494 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
495 structures for sequences with lots of PDB structures
498 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
502 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
503 project involving multiple views
506 <!-- JAL-3164 -->Overview for complementary view in a linked
507 CDS/Protein alignment is not updated when Hide Columns by
508 Annotation dialog hides columns
511 <!-- JAL-3158 -->Selection highlighting in the complement of a
512 CDS/Protein alignment stops working after making a selection in
513 one view, then making another selection in the other view
516 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
520 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
521 Settings and Jalview Preferences panels
524 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
525 overview with large alignments
528 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
529 region if columns were selected by dragging right-to-left and the
530 mouse moved to the left of the first column
533 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
534 hidden column marker via scale popup menu
537 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
538 doesn't tell users the invalid URL
541 <!-- JAL-2816 -->Tooltips displayed for features filtered by
545 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
546 show cross references or Fetch Database References are shown in
550 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
551 peptide sequence (computed variant shown as p.Res.null)
554 <!-- JAL-2060 -->'Graduated colour' option not offered for
555 manually created features (where feature score is Float.NaN)
558 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
559 when columns are hidden
562 <!-- JAL-3082 -->Regular expression error for '(' in Select
563 Columns by Annotation description
566 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
567 out of Scale or Annotation Panel
570 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
574 <!-- JAL-3074 -->Left/right drag in annotation can scroll
578 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
582 <!-- JAL-3002 -->Column display is out by one after Page Down,
583 Page Up in wrapped mode
586 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
589 <!-- JAL-2932 -->Finder searches in minimised alignments
592 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
593 on opening an alignment
596 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
600 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
601 different groups in the alignment are selected
604 <!-- JAL-2717 -->Internationalised colour scheme names not shown
608 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
612 <!-- JAL-3125 -->Value input for graduated feature colour
613 threshold gets 'unrounded'
616 <!-- JAL-2982 -->PCA image export doesn't respect background
620 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
623 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
626 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
630 <!-- JAL-2964 -->Associate Tree with All Views not restored from
634 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
635 shown in complementary view
638 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
639 without normalisation
642 <!-- JAL-3021 -->Sequence Details report should open positioned at top
646 <!-- JAL-914 -->Help page can be opened twice
649 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
651 </ul> <em>Editing</em>
654 <!-- JAL-2822 -->Start and End should be updated when sequence
655 data at beginning or end of alignment added/removed via 'Edit'
659 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
660 relocate sequence features correctly when start of sequence is
661 removed (Known defect since 2.10)
664 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
665 dialog corrupts dataset sequence
668 <!-- JAL-868 -->Structure colours not updated when associated tree
669 repartitions the alignment view (Regression in 2.10.5)
671 </ul> <em>Datamodel</em>
674 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
675 sequence's End is greater than its length
677 </ul> <em>Bugs fixed for Java 11 Support (not yet on
678 general release)</em>
681 <!-- JAL-3288 -->Menus work properly in split-screen
683 </ul> <em>New Known Defects</em>
686 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
689 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
690 regions of protein alignment.
693 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
694 is restored from a Jalview 2.11 project
697 <!-- JAL-3213 -->Alignment panel height can be too small after
701 <!-- JAL-3240 -->Display is incorrect after removing gapped
702 columns within hidden columns
705 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
706 window after dragging left to select columns to left of visible
710 <!-- JAL-2876 -->Features coloured according to their description
711 string and thresholded by score in earlier versions of Jalview are
712 not shown as thresholded features in 2.11. To workaround please
713 create a Score filter instead.
716 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
718 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
721 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
722 alignments with multiple views can close views unexpectedly
725 <em>Java 11 Specific defects</em>
728 <!-- JAL-3235 -->Jalview Properties file is not sorted
729 alphabetically when saved
735 <td width="60" nowrap>
737 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
740 <td><div align="left">
744 <!-- JAL-3101 -->Default memory for Jalview webstart and
745 InstallAnywhere increased to 1G.
748 <!-- JAL-247 -->Hidden sequence markers and representative
749 sequence bolding included when exporting alignment as EPS,
750 SVG, PNG or HTML. <em>Display is configured via the
751 Format menu, or for command-line use via a Jalview
752 properties file.</em>
755 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
756 API and sequence data now imported as JSON.
759 <!-- JAL-3065 -->Change in recommended way of starting
760 Jalview via a Java command line: add jars in lib directory
761 to CLASSPATH, rather than via the deprecated java.ext.dirs
768 <!-- JAL-3047 -->Support added to execute test suite
769 instrumented with <a href="http://openclover.org/">Open
774 <td><div align="left">
778 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
779 row shown in Feredoxin Structure alignment view of example
783 <!-- JAL-2854 -->Annotation obscures sequences if lots of
784 annotation displayed.
787 <!-- JAL-3107 -->Group conservation/consensus not shown
788 for newly created group when 'Apply to all groups'
792 <!-- JAL-3087 -->Corrupted display when switching to
793 wrapped mode when sequence panel's vertical scrollbar is
797 <!-- JAL-3003 -->Alignment is black in exported EPS file
798 when sequences are selected in exported view.</em>
801 <!-- JAL-3059 -->Groups with different coloured borders
802 aren't rendered with correct colour.
805 <!-- JAL-3092 -->Jalview could hang when importing certain
806 types of knotted RNA secondary structure.
809 <!-- JAL-3095 -->Sequence highlight and selection in
810 trimmed VARNA 2D structure is incorrect for sequences that
814 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
815 annotation when columns are inserted into an alignment,
816 and when exporting as Stockholm flatfile.
819 <!-- JAL-3053 -->Jalview annotation rows containing upper
820 and lower-case 'E' and 'H' do not automatically get
821 treated as RNA secondary structure.
824 <!-- JAL-3106 -->.jvp should be used as default extension
825 (not .jar) when saving a Jalview project file.
828 <!-- JAL-3105 -->Mac Users: closing a window correctly
829 transfers focus to previous window on OSX
832 <em>Java 10 Issues Resolved</em>
835 <!-- JAL-2988 -->OSX - Can't save new files via the File
836 or export menus by typing in a name into the Save dialog
840 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
841 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
842 'look and feel' which has improved compatibility with the
843 latest version of OSX.
850 <td width="60" nowrap>
852 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
853 <em>7/06/2018</em></strong>
856 <td><div align="left">
860 <!-- JAL-2920 -->Use HGVS nomenclature for variant
861 annotation retrieved from Uniprot
864 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
865 onto the Jalview Desktop
869 <td><div align="left">
873 <!-- JAL-3017 -->Cannot import features with multiple
874 variant elements (blocks import of some Uniprot records)
877 <!-- JAL-2997 -->Clustal files with sequence positions in
878 right-hand column parsed correctly
881 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
882 not alignment area in exported graphic
885 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
886 window has input focus
889 <!-- JAL-2992 -->Annotation panel set too high when
890 annotation added to view (Windows)
893 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
894 network connectivity is poor
897 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
898 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
899 the currently open URL and links from a page viewed in
900 Firefox or Chrome on Windows is now fully supported. If
901 you are using Edge, only links in the page can be
902 dragged, and with Internet Explorer, only the currently
903 open URL in the browser can be dropped onto Jalview.</em>
906 <em>New Known Defects</em>
908 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
913 <td width="60" nowrap>
915 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
918 <td><div align="left">
922 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
923 for disabling automatic superposition of multiple
924 structures and open structures in existing views
927 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
928 ID and annotation area margins can be click-dragged to
932 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
936 <!-- JAL-2759 -->Improved performance for large alignments
937 and lots of hidden columns
940 <!-- JAL-2593 -->Improved performance when rendering lots
941 of features (particularly when transparency is disabled)
944 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
945 exchange of Jalview features and Chimera attributes made
951 <td><div align="left">
954 <!-- JAL-2899 -->Structure and Overview aren't updated
955 when Colour By Annotation threshold slider is adjusted
958 <!-- JAL-2778 -->Slow redraw when Overview panel shown
959 overlapping alignment panel
962 <!-- JAL-2929 -->Overview doesn't show end of unpadded
966 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
967 improved: CDS not handled correctly if transcript has no
971 <!-- JAL-2321 -->Secondary structure and temperature
972 factor annotation not added to sequence when local PDB
973 file associated with it by drag'n'drop or structure
977 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
978 dialog doesn't import PDB files dropped on an alignment
981 <!-- JAL-2666 -->Linked scrolling via protein horizontal
982 scroll bar doesn't work for some CDS/Protein views
985 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
986 Java 1.8u153 onwards and Java 1.9u4+.
989 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
990 columns in annotation row
993 <!-- JAL-2913 -->Preferences panel's ID Width control is not
994 honored in batch mode
997 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
998 for structures added to existing Jmol view
1001 <!-- JAL-2223 -->'View Mappings' includes duplicate
1002 entries after importing project with multiple views
1005 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1006 protein sequences via SIFTS from associated PDB entries
1007 with negative residue numbers or missing residues fails
1010 <!-- JAL-2952 -->Exception when shading sequence with negative
1011 Temperature Factor values from annotated PDB files (e.g.
1012 as generated by CONSURF)
1015 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1016 tooltip doesn't include a text description of mutation
1019 <!-- JAL-2922 -->Invert displayed features very slow when
1020 structure and/or overview windows are also shown
1023 <!-- JAL-2954 -->Selecting columns from highlighted regions
1024 very slow for alignments with large numbers of sequences
1027 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1028 with 'StringIndexOutOfBounds'
1031 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1032 platforms running Java 10
1035 <!-- JAL-2960 -->Adding a structure to existing structure
1036 view appears to do nothing because the view is hidden behind the alignment view
1042 <!-- JAL-2926 -->Copy consensus sequence option in applet
1043 should copy the group consensus when popup is opened on it
1049 <!-- JAL-2913 -->Fixed ID width preference is not respected
1052 <em>New Known Defects</em>
1055 <!-- JAL-2973 --> Exceptions occasionally raised when
1056 editing a large alignment and overview is displayed
1059 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1060 repeatedly after a series of edits even when the overview
1061 is no longer reflecting updates
1064 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1065 structures for protein subsequence (if 'Trim Retrieved
1066 Sequences' enabled) or Ensembl isoforms (Workaround in
1067 2.10.4 is to fail back to N&W mapping)
1070 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1071 option gives blank output
1078 <td width="60" nowrap>
1079 <div align="center">
1080 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1083 <td><div align="left">
1084 <ul><li>Updated Certum Codesigning Certificate
1085 (Valid till 30th November 2018)</li></ul></div></td>
1086 <td><div align="left">
1087 <em>Desktop</em><ul>
1089 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1090 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1091 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1092 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1093 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1094 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1095 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1101 <td width="60" nowrap>
1102 <div align="center">
1103 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1106 <td><div align="left">
1110 <!-- JAL-2446 -->Faster and more efficient management and
1111 rendering of sequence features
1114 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1115 429 rate limit request hander
1118 <!-- JAL-2773 -->Structure views don't get updated unless
1119 their colours have changed
1122 <!-- JAL-2495 -->All linked sequences are highlighted for
1123 a structure mousover (Jmol) or selection (Chimera)
1126 <!-- JAL-2790 -->'Cancel' button in progress bar for
1127 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1130 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1131 view from Ensembl locus cross-references
1134 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1138 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1139 feature can be disabled
1142 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1143 PDB easier retrieval of sequences for lists of IDs
1146 <!-- JAL-2758 -->Short names for sequences retrieved from
1152 <li>Groovy interpreter updated to 2.4.12</li>
1153 <li>Example groovy script for generating a matrix of
1154 percent identity scores for current alignment.</li>
1156 <em>Testing and Deployment</em>
1159 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1163 <td><div align="left">
1167 <!-- JAL-2643 -->Pressing tab after updating the colour
1168 threshold text field doesn't trigger an update to the
1172 <!-- JAL-2682 -->Race condition when parsing sequence ID
1176 <!-- JAL-2608 -->Overview windows are also closed when
1177 alignment window is closed
1180 <!-- JAL-2548 -->Export of features doesn't always respect
1184 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1185 takes a long time in Cursor mode
1191 <!-- JAL-2777 -->Structures with whitespace chainCode
1192 cannot be viewed in Chimera
1195 <!-- JAL-2728 -->Protein annotation panel too high in
1199 <!-- JAL-2757 -->Can't edit the query after the server
1200 error warning icon is shown in Uniprot and PDB Free Text
1204 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1207 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1210 <!-- JAL-2739 -->Hidden column marker in last column not
1211 rendered when switching back from Wrapped to normal view
1214 <!-- JAL-2768 -->Annotation display corrupted when
1215 scrolling right in unwapped alignment view
1218 <!-- JAL-2542 -->Existing features on subsequence
1219 incorrectly relocated when full sequence retrieved from
1223 <!-- JAL-2733 -->Last reported memory still shown when
1224 Desktop->Show Memory is unticked (OSX only)
1227 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1228 features of same type and group to be selected for
1232 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1233 alignments when hidden columns are present
1236 <!-- JAL-2392 -->Jalview freezes when loading and
1237 displaying several structures
1240 <!-- JAL-2732 -->Black outlines left after resizing or
1244 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1245 within the Jalview desktop on OSX
1248 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1249 when in wrapped alignment mode
1252 <!-- JAL-2636 -->Scale mark not shown when close to right
1253 hand end of alignment
1256 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1257 each selected sequence do not have correct start/end
1261 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1262 after canceling the Alignment Window's Font dialog
1265 <!-- JAL-2036 -->Show cross-references not enabled after
1266 restoring project until a new view is created
1269 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1270 URL links appears when only default EMBL-EBI link is
1271 configured (since 2.10.2b2)
1274 <!-- JAL-2775 -->Overview redraws whole window when box
1275 position is adjusted
1278 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1279 in a multi-chain structure when viewing alignment
1280 involving more than one chain (since 2.10)
1283 <!-- JAL-2811 -->Double residue highlights in cursor mode
1284 if new selection moves alignment window
1287 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1288 arrow key in cursor mode to pass hidden column marker
1291 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1292 that produces correctly annotated transcripts and products
1295 <!-- JAL-2776 -->Toggling a feature group after first time
1296 doesn't update associated structure view
1299 <em>Applet</em><br />
1302 <!-- JAL-2687 -->Concurrent modification exception when
1303 closing alignment panel
1306 <em>BioJSON</em><br />
1309 <!-- JAL-2546 -->BioJSON export does not preserve
1310 non-positional features
1313 <em>New Known Issues</em>
1316 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1317 sequence features correctly (for many previous versions of
1321 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1322 using cursor in wrapped panel other than top
1325 <!-- JAL-2791 -->Select columns containing feature ignores
1326 graduated colour threshold
1329 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1330 always preserve numbering and sequence features
1333 <em>Known Java 9 Issues</em>
1336 <!-- JAL-2902 -->Groovy Console very slow to open and is
1337 not responsive when entering characters (Webstart, Java
1344 <td width="60" nowrap>
1345 <div align="center">
1346 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1347 <em>2/10/2017</em></strong>
1350 <td><div align="left">
1351 <em>New features in Jalview Desktop</em>
1354 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1356 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1360 <td><div align="left">
1364 <td width="60" nowrap>
1365 <div align="center">
1366 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1367 <em>7/9/2017</em></strong>
1370 <td><div align="left">
1374 <!-- JAL-2588 -->Show gaps in overview window by colouring
1375 in grey (sequences used to be coloured grey, and gaps were
1379 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1383 <!-- JAL-2587 -->Overview updates immediately on increase
1384 in size and progress bar shown as higher resolution
1385 overview is recalculated
1390 <td><div align="left">
1394 <!-- JAL-2664 -->Overview window redraws every hidden
1395 column region row by row
1398 <!-- JAL-2681 -->duplicate protein sequences shown after
1399 retrieving Ensembl crossrefs for sequences from Uniprot
1402 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1403 format setting is unticked
1406 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1407 if group has show boxes format setting unticked
1410 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1411 autoscrolling whilst dragging current selection group to
1412 include sequences and columns not currently displayed
1415 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1416 assemblies are imported via CIF file
1419 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1420 displayed when threshold or conservation colouring is also
1424 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1428 <!-- JAL-2673 -->Jalview continues to scroll after
1429 dragging a selected region off the visible region of the
1433 <!-- JAL-2724 -->Cannot apply annotation based
1434 colourscheme to all groups in a view
1437 <!-- JAL-2511 -->IDs don't line up with sequences
1438 initially after font size change using the Font chooser or
1445 <td width="60" nowrap>
1446 <div align="center">
1447 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1450 <td><div align="left">
1451 <em>Calculations</em>
1455 <!-- JAL-1933 -->Occupancy annotation row shows number of
1456 ungapped positions in each column of the alignment.
1459 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1460 a calculation dialog box
1463 <!-- JAL-2379 -->Revised implementation of PCA for speed
1464 and memory efficiency (~30x faster)
1467 <!-- JAL-2403 -->Revised implementation of sequence
1468 similarity scores as used by Tree, PCA, Shading Consensus
1469 and other calculations
1472 <!-- JAL-2416 -->Score matrices are stored as resource
1473 files within the Jalview codebase
1476 <!-- JAL-2500 -->Trees computed on Sequence Feature
1477 Similarity may have different topology due to increased
1484 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1485 model for alignments and groups
1488 <!-- JAL-384 -->Custom shading schemes created via groovy
1495 <!-- JAL-2526 -->Efficiency improvements for interacting
1496 with alignment and overview windows
1499 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1503 <!-- JAL-2388 -->Hidden columns and sequences can be
1507 <!-- JAL-2611 -->Click-drag in visible area allows fine
1508 adjustment of visible position
1512 <em>Data import/export</em>
1515 <!-- JAL-2535 -->Posterior probability annotation from
1516 Stockholm files imported as sequence associated annotation
1519 <!-- JAL-2507 -->More robust per-sequence positional
1520 annotation input/output via stockholm flatfile
1523 <!-- JAL-2533 -->Sequence names don't include file
1524 extension when importing structure files without embedded
1525 names or PDB accessions
1528 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1529 format sequence substitution matrices
1532 <em>User Interface</em>
1535 <!-- JAL-2447 --> Experimental Features Checkbox in
1536 Desktop's Tools menu to hide or show untested features in
1540 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1541 via Overview or sequence motif search operations
1544 <!-- JAL-2547 -->Amend sequence features dialog box can be
1545 opened by double clicking gaps within sequence feature
1549 <!-- JAL-1476 -->Status bar message shown when not enough
1550 aligned positions were available to create a 3D structure
1554 <em>3D Structure</em>
1557 <!-- JAL-2430 -->Hidden regions in alignment views are not
1558 coloured in linked structure views
1561 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1562 file-based command exchange
1565 <!-- JAL-2375 -->Structure chooser automatically shows
1566 Cached Structures rather than querying the PDBe if
1567 structures are already available for sequences
1570 <!-- JAL-2520 -->Structures imported via URL are cached in
1571 the Jalview project rather than downloaded again when the
1572 project is reopened.
1575 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1576 to transfer Chimera's structure attributes as Jalview
1577 features, and vice-versa (<strong>Experimental
1581 <em>Web Services</em>
1584 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1587 <!-- JAL-2335 -->Filter non-standard amino acids and
1588 nucleotides when submitting to AACon and other MSA
1592 <!-- JAL-2316, -->URLs for viewing database
1593 cross-references provided by identifiers.org and the
1594 EMBL-EBI's MIRIAM DB
1601 <!-- JAL-2344 -->FileFormatI interface for describing and
1602 identifying file formats (instead of String constants)
1605 <!-- JAL-2228 -->FeatureCounter script refactored for
1606 efficiency when counting all displayed features (not
1607 backwards compatible with 2.10.1)
1610 <em>Example files</em>
1613 <!-- JAL-2631 -->Graduated feature colour style example
1614 included in the example feature file
1617 <em>Documentation</em>
1620 <!-- JAL-2339 -->Release notes reformatted for readability
1621 with the built-in Java help viewer
1624 <!-- JAL-1644 -->Find documentation updated with 'search
1625 sequence description' option
1631 <!-- JAL-2485, -->External service integration tests for
1632 Uniprot REST Free Text Search Client
1635 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1638 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1643 <td><div align="left">
1644 <em>Calculations</em>
1647 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1648 matrix - C->R should be '-3'<br />Old matrix restored
1649 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1651 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1652 Jalview's treatment of gaps in PCA and substitution matrix
1653 based Tree calculations.<br /> <br />In earlier versions
1654 of Jalview, gaps matching gaps were penalised, and gaps
1655 matching non-gaps penalised even more. In the PCA
1656 calculation, gaps were actually treated as non-gaps - so
1657 different costs were applied, which meant Jalview's PCAs
1658 were different to those produced by SeqSpace.<br />Jalview
1659 now treats gaps in the same way as SeqSpace (ie it scores
1660 them as 0). <br /> <br />Enter the following in the
1661 Groovy console to restore pre-2.10.2 behaviour:<br />
1662 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1663 // for 2.10.1 mode <br />
1664 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1665 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1666 these settings will affect all subsequent tree and PCA
1667 calculations (not recommended)</em></li>
1669 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1670 scaling of branch lengths for trees computed using
1671 Sequence Feature Similarity.
1674 <!-- JAL-2377 -->PCA calculation could hang when
1675 generating output report when working with highly
1676 redundant alignments
1679 <!-- JAL-2544 --> Sort by features includes features to
1680 right of selected region when gaps present on right-hand
1684 <em>User Interface</em>
1687 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1688 doesn't reselect a specific sequence's associated
1689 annotation after it was used for colouring a view
1692 <!-- JAL-2419 -->Current selection lost if popup menu
1693 opened on a region of alignment without groups
1696 <!-- JAL-2374 -->Popup menu not always shown for regions
1697 of an alignment with overlapping groups
1700 <!-- JAL-2310 -->Finder double counts if both a sequence's
1701 name and description match
1704 <!-- JAL-2370 -->Hiding column selection containing two
1705 hidden regions results in incorrect hidden regions
1708 <!-- JAL-2386 -->'Apply to all groups' setting when
1709 changing colour does not apply Conservation slider value
1713 <!-- JAL-2373 -->Percentage identity and conservation menu
1714 items do not show a tick or allow shading to be disabled
1717 <!-- JAL-2385 -->Conservation shading or PID threshold
1718 lost when base colourscheme changed if slider not visible
1721 <!-- JAL-2547 -->Sequence features shown in tooltip for
1722 gaps before start of features
1725 <!-- JAL-2623 -->Graduated feature colour threshold not
1726 restored to UI when feature colour is edited
1729 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1730 a time when scrolling vertically in wrapped mode.
1733 <!-- JAL-2630 -->Structure and alignment overview update
1734 as graduate feature colour settings are modified via the
1738 <!-- JAL-2034 -->Overview window doesn't always update
1739 when a group defined on the alignment is resized
1742 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1743 wrapped view result in positional status updates
1747 <!-- JAL-2563 -->Status bar doesn't show position for
1748 ambiguous amino acid and nucleotide symbols
1751 <!-- JAL-2602 -->Copy consensus sequence failed if
1752 alignment included gapped columns
1755 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1756 widgets don't permanently disappear
1759 <!-- JAL-2503 -->Cannot select or filter quantitative
1760 annotation that are shown only as column labels (e.g.
1761 T-Coffee column reliability scores)
1764 <!-- JAL-2594 -->Exception thrown if trying to create a
1765 sequence feature on gaps only
1768 <!-- JAL-2504 -->Features created with 'New feature'
1769 button from a Find inherit previously defined feature type
1770 rather than the Find query string
1773 <!-- JAL-2423 -->incorrect title in output window when
1774 exporting tree calculated in Jalview
1777 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1778 and then revealing them reorders sequences on the
1782 <!-- JAL-964 -->Group panel in sequence feature settings
1783 doesn't update to reflect available set of groups after
1784 interactively adding or modifying features
1787 <!-- JAL-2225 -->Sequence Database chooser unusable on
1791 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1792 only excluded gaps in current sequence and ignored
1799 <!-- JAL-2421 -->Overview window visible region moves
1800 erratically when hidden rows or columns are present
1803 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1804 Structure Viewer's colour menu don't correspond to
1808 <!-- JAL-2405 -->Protein specific colours only offered in
1809 colour and group colour menu for protein alignments
1812 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1813 reflect currently selected view or group's shading
1817 <!-- JAL-2624 -->Feature colour thresholds not respected
1818 when rendered on overview and structures when opacity at
1822 <!-- JAL-2589 -->User defined gap colour not shown in
1823 overview when features overlaid on alignment
1826 <!-- JAL-2567 -->Feature settings for different views not
1827 recovered correctly from Jalview project file
1830 <!-- JAL-2256 -->Feature colours in overview when first opened
1831 (automatically via preferences) are different to the main
1835 <em>Data import/export</em>
1838 <!-- JAL-2576 -->Very large alignments take a long time to
1842 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1843 added after a sequence was imported are not written to
1847 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1848 when importing RNA secondary structure via Stockholm
1851 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1852 not shown in correct direction for simple pseudoknots
1855 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1856 with lightGray or darkGray via features file (but can
1860 <!-- JAL-2383 -->Above PID colour threshold not recovered
1861 when alignment view imported from project
1864 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1865 structure and sequences extracted from structure files
1866 imported via URL and viewed in Jmol
1869 <!-- JAL-2520 -->Structures loaded via URL are saved in
1870 Jalview Projects rather than fetched via URL again when
1871 the project is loaded and the structure viewed
1874 <em>Web Services</em>
1877 <!-- JAL-2519 -->EnsemblGenomes example failing after
1878 release of Ensembl v.88
1881 <!-- JAL-2366 -->Proxy server address and port always
1882 appear enabled in Preferences->Connections
1885 <!-- JAL-2461 -->DAS registry not found exceptions
1886 removed from console output
1889 <!-- JAL-2582 -->Cannot retrieve protein products from
1890 Ensembl by Peptide ID
1893 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1894 created from SIFTs, and spurious 'Couldn't open structure
1895 in Chimera' errors raised after April 2017 update (problem
1896 due to 'null' string rather than empty string used for
1897 residues with no corresponding PDB mapping).
1900 <em>Application UI</em>
1903 <!-- JAL-2361 -->User Defined Colours not added to Colour
1907 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1908 case' residues (button in colourscheme editor debugged and
1909 new documentation and tooltips added)
1912 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1913 doesn't restore group-specific text colour thresholds
1916 <!-- JAL-2243 -->Feature settings panel does not update as
1917 new features are added to alignment
1920 <!-- JAL-2532 -->Cancel in feature settings reverts
1921 changes to feature colours via the Amend features dialog
1924 <!-- JAL-2506 -->Null pointer exception when attempting to
1925 edit graduated feature colour via amend features dialog
1929 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1930 selection menu changes colours of alignment views
1933 <!-- JAL-2426 -->Spurious exceptions in console raised
1934 from alignment calculation workers after alignment has
1938 <!-- JAL-1608 -->Typo in selection popup menu - Create
1939 groups now 'Create Group'
1942 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1943 Create/Undefine group doesn't always work
1946 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1947 shown again after pressing 'Cancel'
1950 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1951 adjusts start position in wrap mode
1954 <!-- JAL-2563 -->Status bar doesn't show positions for
1955 ambiguous amino acids
1958 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1959 CDS/Protein view after CDS sequences added for aligned
1963 <!-- JAL-2592 -->User defined colourschemes called 'User
1964 Defined' don't appear in Colours menu
1970 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1971 score models doesn't always result in an updated PCA plot
1974 <!-- JAL-2442 -->Features not rendered as transparent on
1975 overview or linked structure view
1978 <!-- JAL-2372 -->Colour group by conservation doesn't
1982 <!-- JAL-2517 -->Hitting Cancel after applying
1983 user-defined colourscheme doesn't restore original
1990 <!-- JAL-2314 -->Unit test failure:
1991 jalview.ws.jabaws.RNAStructExportImport setup fails
1994 <!-- JAL-2307 -->Unit test failure:
1995 jalview.ws.sifts.SiftsClientTest due to compatibility
1996 problems with deep array comparison equality asserts in
1997 successive versions of TestNG
2000 <!-- JAL-2479 -->Relocated StructureChooserTest and
2001 ParameterUtilsTest Unit tests to Network suite
2004 <em>New Known Issues</em>
2007 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2008 phase after a sequence motif find operation
2011 <!-- JAL-2550 -->Importing annotation file with rows
2012 containing just upper and lower case letters are
2013 interpreted as WUSS RNA secondary structure symbols
2016 <!-- JAL-2590 -->Cannot load and display Newick trees
2017 reliably from eggnog Ortholog database
2020 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2021 containing features of type Highlight' when 'B' is pressed
2022 to mark columns containing highlighted regions.
2025 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2026 doesn't always add secondary structure annotation.
2031 <td width="60" nowrap>
2032 <div align="center">
2033 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2036 <td><div align="left">
2040 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2041 for all consensus calculations
2044 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2047 <li>Updated Jalview's Certum code signing certificate
2050 <em>Application</em>
2053 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2054 set of database cross-references, sorted alphabetically
2057 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2058 from database cross references. Users with custom links
2059 will receive a <a href="webServices/urllinks.html#warning">warning
2060 dialog</a> asking them to update their preferences.
2063 <!-- JAL-2287-->Cancel button and escape listener on
2064 dialog warning user about disconnecting Jalview from a
2068 <!-- JAL-2320-->Jalview's Chimera control window closes if
2069 the Chimera it is connected to is shut down
2072 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2073 columns menu item to mark columns containing highlighted
2074 regions (e.g. from structure selections or results of a
2078 <!-- JAL-2284-->Command line option for batch-generation
2079 of HTML pages rendering alignment data with the BioJS
2089 <!-- JAL-2286 -->Columns with more than one modal residue
2090 are not coloured or thresholded according to percent
2091 identity (first observed in Jalview 2.8.2)
2094 <!-- JAL-2301 -->Threonine incorrectly reported as not
2098 <!-- JAL-2318 -->Updates to documentation pages (above PID
2099 threshold, amino acid properties)
2102 <!-- JAL-2292 -->Lower case residues in sequences are not
2103 reported as mapped to residues in a structure file in the
2107 <!--JAL-2324 -->Identical features with non-numeric scores
2108 could be added multiple times to a sequence
2111 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2112 bond features shown as two highlighted residues rather
2113 than a range in linked structure views, and treated
2114 correctly when selecting and computing trees from features
2117 <!-- JAL-2281-->Custom URL links for database
2118 cross-references are matched to database name regardless
2123 <em>Application</em>
2126 <!-- JAL-2282-->Custom URL links for specific database
2127 names without regular expressions also offer links from
2131 <!-- JAL-2315-->Removing a single configured link in the
2132 URL links pane in Connections preferences doesn't actually
2133 update Jalview configuration
2136 <!-- JAL-2272-->CTRL-Click on a selected region to open
2137 the alignment area popup menu doesn't work on El-Capitan
2140 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2141 files with similarly named sequences if dropped onto the
2145 <!-- JAL-2312 -->Additional mappings are shown for PDB
2146 entries where more chains exist in the PDB accession than
2147 are reported in the SIFTS file
2150 <!-- JAL-2317-->Certain structures do not get mapped to
2151 the structure view when displayed with Chimera
2154 <!-- JAL-2317-->No chains shown in the Chimera view
2155 panel's View->Show Chains submenu
2158 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2159 work for wrapped alignment views
2162 <!--JAL-2197 -->Rename UI components for running JPred
2163 predictions from 'JNet' to 'JPred'
2166 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2167 corrupted when annotation panel vertical scroll is not at
2168 first annotation row
2171 <!--JAL-2332 -->Attempting to view structure for Hen
2172 lysozyme results in a PDB Client error dialog box
2175 <!-- JAL-2319 -->Structure View's mapping report switched
2176 ranges for PDB and sequence for SIFTS
2179 SIFTS 'Not_Observed' residues mapped to non-existant
2183 <!-- <em>New Known Issues</em>
2190 <td width="60" nowrap>
2191 <div align="center">
2192 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2193 <em>25/10/2016</em></strong>
2196 <td><em>Application</em>
2198 <li>3D Structure chooser opens with 'Cached structures'
2199 view if structures already loaded</li>
2200 <li>Progress bar reports models as they are loaded to
2201 structure views</li>
2207 <li>Colour by conservation always enabled and no tick
2208 shown in menu when BLOSUM or PID shading applied</li>
2209 <li>FER1_ARATH and FER2_ARATH labels were switched in
2210 example sequences/projects/trees</li>
2212 <em>Application</em>
2214 <li>Jalview projects with views of local PDB structure
2215 files saved on Windows cannot be opened on OSX</li>
2216 <li>Multiple structure views can be opened and superposed
2217 without timeout for structures with multiple models or
2218 multiple sequences in alignment</li>
2219 <li>Cannot import or associated local PDB files without a
2220 PDB ID HEADER line</li>
2221 <li>RMSD is not output in Jmol console when superposition
2223 <li>Drag and drop of URL from Browser fails for Linux and
2224 OSX versions earlier than El Capitan</li>
2225 <li>ENA client ignores invalid content from ENA server</li>
2226 <li>Exceptions are not raised in console when ENA client
2227 attempts to fetch non-existent IDs via Fetch DB Refs UI
2229 <li>Exceptions are not raised in console when a new view
2230 is created on the alignment</li>
2231 <li>OSX right-click fixed for group selections: CMD-click
2232 to insert/remove gaps in groups and CTRL-click to open group
2235 <em>Build and deployment</em>
2237 <li>URL link checker now copes with multi-line anchor
2240 <em>New Known Issues</em>
2242 <li>Drag and drop from URL links in browsers do not work
2249 <td width="60" nowrap>
2250 <div align="center">
2251 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2254 <td><em>General</em>
2257 <!-- JAL-2124 -->Updated Spanish translations.
2260 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2261 for importing structure data to Jalview. Enables mmCIF and
2265 <!-- JAL-192 --->Alignment ruler shows positions relative to
2269 <!-- JAL-2202 -->Position/residue shown in status bar when
2270 mousing over sequence associated annotation
2273 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2277 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2278 '()', canonical '[]' and invalid '{}' base pair populations
2282 <!-- JAL-2092 -->Feature settings popup menu options for
2283 showing or hiding columns containing a feature
2286 <!-- JAL-1557 -->Edit selected group by double clicking on
2287 group and sequence associated annotation labels
2290 <!-- JAL-2236 -->Sequence name added to annotation label in
2291 select/hide columns by annotation and colour by annotation
2295 </ul> <em>Application</em>
2298 <!-- JAL-2050-->Automatically hide introns when opening a
2299 gene/transcript view
2302 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2306 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2307 structure mappings with the EMBL-EBI PDBe SIFTS database
2310 <!-- JAL-2079 -->Updated download sites used for Rfam and
2311 Pfam sources to xfam.org
2314 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2317 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2318 over sequences in Jalview
2321 <!-- JAL-2027-->Support for reverse-complement coding
2322 regions in ENA and EMBL
2325 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2326 for record retrieval via ENA rest API
2329 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2333 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2334 groovy script execution
2337 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2338 alignment window's Calculate menu
2341 <!-- JAL-1812 -->Allow groovy scripts that call
2342 Jalview.getAlignFrames() to run in headless mode
2345 <!-- JAL-2068 -->Support for creating new alignment
2346 calculation workers from groovy scripts
2349 <!-- JAL-1369 --->Store/restore reference sequence in
2353 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2354 associations are now saved/restored from project
2357 <!-- JAL-1993 -->Database selection dialog always shown
2358 before sequence fetcher is opened
2361 <!-- JAL-2183 -->Double click on an entry in Jalview's
2362 database chooser opens a sequence fetcher
2365 <!-- JAL-1563 -->Free-text search client for UniProt using
2366 the UniProt REST API
2369 <!-- JAL-2168 -->-nonews command line parameter to prevent
2370 the news reader opening
2373 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2374 querying stored in preferences
2377 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2381 <!-- JAL-1977-->Tooltips shown on database chooser
2384 <!-- JAL-391 -->Reverse complement function in calculate
2385 menu for nucleotide sequences
2388 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2389 and feature counts preserves alignment ordering (and
2390 debugged for complex feature sets).
2393 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2394 viewing structures with Jalview 2.10
2397 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2398 genome, transcript CCDS and gene ids via the Ensembl and
2399 Ensembl Genomes REST API
2402 <!-- JAL-2049 -->Protein sequence variant annotation
2403 computed for 'sequence_variant' annotation on CDS regions
2407 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2411 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2412 Ref Fetcher fails to match, or otherwise updates sequence
2413 data from external database records.
2416 <!-- JAL-2154 -->Revised Jalview Project format for
2417 efficient recovery of sequence coding and alignment
2418 annotation relationships.
2420 </ul> <!-- <em>Applet</em>
2431 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2435 <!-- JAL-2018-->Export features in Jalview format (again)
2436 includes graduated colourschemes
2439 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2440 working with big alignments and lots of hidden columns
2443 <!-- JAL-2053-->Hidden column markers not always rendered
2444 at right of alignment window
2447 <!-- JAL-2067 -->Tidied up links in help file table of
2451 <!-- JAL-2072 -->Feature based tree calculation not shown
2455 <!-- JAL-2075 -->Hidden columns ignored during feature
2456 based tree calculation
2459 <!-- JAL-2065 -->Alignment view stops updating when show
2460 unconserved enabled for group on alignment
2463 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2467 <!-- JAL-2146 -->Alignment column in status incorrectly
2468 shown as "Sequence position" when mousing over
2472 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2473 hidden columns present
2476 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2477 user created annotation added to alignment
2480 <!-- JAL-1841 -->RNA Structure consensus only computed for
2481 '()' base pair annotation
2484 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2485 in zero scores for all base pairs in RNA Structure
2489 <!-- JAL-2174-->Extend selection with columns containing
2493 <!-- JAL-2275 -->Pfam format writer puts extra space at
2494 beginning of sequence
2497 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2501 <!-- JAL-2238 -->Cannot create groups on an alignment from
2502 from a tree when t-coffee scores are shown
2505 <!-- JAL-1836,1967 -->Cannot import and view PDB
2506 structures with chains containing negative resnums (4q4h)
2509 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2513 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2514 to Clustal, PIR and PileUp output
2517 <!-- JAL-2008 -->Reordering sequence features that are
2518 not visible causes alignment window to repaint
2521 <!-- JAL-2006 -->Threshold sliders don't work in
2522 graduated colour and colour by annotation row for e-value
2523 scores associated with features and annotation rows
2526 <!-- JAL-1797 -->amino acid physicochemical conservation
2527 calculation should be case independent
2530 <!-- JAL-2173 -->Remove annotation also updates hidden
2534 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2535 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2536 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2539 <!-- JAL-2065 -->Null pointer exceptions and redraw
2540 problems when reference sequence defined and 'show
2541 non-conserved' enabled
2544 <!-- JAL-1306 -->Quality and Conservation are now shown on
2545 load even when Consensus calculation is disabled
2548 <!-- JAL-1932 -->Remove right on penultimate column of
2549 alignment does nothing
2552 <em>Application</em>
2555 <!-- JAL-1552-->URLs and links can't be imported by
2556 drag'n'drop on OSX when launched via webstart (note - not
2557 yet fixed for El Capitan)
2560 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2561 output when running on non-gb/us i18n platforms
2564 <!-- JAL-1944 -->Error thrown when exporting a view with
2565 hidden sequences as flat-file alignment
2568 <!-- JAL-2030-->InstallAnywhere distribution fails when
2572 <!-- JAL-2080-->Jalview very slow to launch via webstart
2573 (also hotfix for 2.9.0b2)
2576 <!-- JAL-2085 -->Cannot save project when view has a
2577 reference sequence defined
2580 <!-- JAL-1011 -->Columns are suddenly selected in other
2581 alignments and views when revealing hidden columns
2584 <!-- JAL-1989 -->Hide columns not mirrored in complement
2585 view in a cDNA/Protein splitframe
2588 <!-- JAL-1369 -->Cannot save/restore representative
2589 sequence from project when only one sequence is
2593 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2594 in Structure Chooser
2597 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2598 structure consensus didn't refresh annotation panel
2601 <!-- JAL-1962 -->View mapping in structure view shows
2602 mappings between sequence and all chains in a PDB file
2605 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2606 dialogs format columns correctly, don't display array
2607 data, sort columns according to type
2610 <!-- JAL-1975 -->Export complete shown after destination
2611 file chooser is cancelled during an image export
2614 <!-- JAL-2025 -->Error when querying PDB Service with
2615 sequence name containing special characters
2618 <!-- JAL-2024 -->Manual PDB structure querying should be
2622 <!-- JAL-2104 -->Large tooltips with broken HTML
2623 formatting don't wrap
2626 <!-- JAL-1128 -->Figures exported from wrapped view are
2627 truncated so L looks like I in consensus annotation
2630 <!-- JAL-2003 -->Export features should only export the
2631 currently displayed features for the current selection or
2635 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2636 after fetching cross-references, and restoring from
2640 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2641 followed in the structure viewer
2644 <!-- JAL-2163 -->Titles for individual alignments in
2645 splitframe not restored from project
2648 <!-- JAL-2145 -->missing autocalculated annotation at
2649 trailing end of protein alignment in transcript/product
2650 splitview when pad-gaps not enabled by default
2653 <!-- JAL-1797 -->amino acid physicochemical conservation
2657 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2658 article has been read (reopened issue due to
2659 internationalisation problems)
2662 <!-- JAL-1960 -->Only offer PDB structures in structure
2663 viewer based on sequence name, PDB and UniProt
2668 <!-- JAL-1976 -->No progress bar shown during export of
2672 <!-- JAL-2213 -->Structures not always superimposed after
2673 multiple structures are shown for one or more sequences.
2676 <!-- JAL-1370 -->Reference sequence characters should not
2677 be replaced with '.' when 'Show unconserved' format option
2681 <!-- JAL-1823 -->Cannot specify chain code when entering
2682 specific PDB id for sequence
2685 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2686 'Export hidden sequences' is enabled, but 'export hidden
2687 columns' is disabled.
2690 <!--JAL-2026-->Best Quality option in structure chooser
2691 selects lowest rather than highest resolution structures
2695 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2696 to sequence mapping in 'View Mappings' report
2699 <!-- JAL-2284 -->Unable to read old Jalview projects that
2700 contain non-XML data added after Jalvew wrote project.
2703 <!-- JAL-2118 -->Newly created annotation row reorders
2704 after clicking on it to create new annotation for a
2708 <!-- JAL-1980 -->Null Pointer Exception raised when
2709 pressing Add on an orphaned cut'n'paste window.
2711 <!-- may exclude, this is an external service stability issue JAL-1941
2712 -- > RNA 3D structure not added via DSSR service</li> -->
2717 <!-- JAL-2151 -->Incorrect columns are selected when
2718 hidden columns present before start of sequence
2721 <!-- JAL-1986 -->Missing dependencies on applet pages
2725 <!-- JAL-1947 -->Overview pixel size changes when
2726 sequences are hidden in applet
2729 <!-- JAL-1996 -->Updated instructions for applet
2730 deployment on examples pages.
2737 <td width="60" nowrap>
2738 <div align="center">
2739 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2740 <em>16/10/2015</em></strong>
2743 <td><em>General</em>
2745 <li>Time stamps for signed Jalview application and applet
2750 <em>Application</em>
2752 <li>Duplicate group consensus and conservation rows
2753 shown when tree is partitioned</li>
2754 <li>Erratic behaviour when tree partitions made with
2755 multiple cDNA/Protein split views</li>
2761 <td width="60" nowrap>
2762 <div align="center">
2763 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2764 <em>8/10/2015</em></strong>
2767 <td><em>General</em>
2769 <li>Updated Spanish translations of localized text for
2771 </ul> <em>Application</em>
2773 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2774 <li>Signed OSX InstallAnywhere installer<br></li>
2775 <li>Support for per-sequence based annotations in BioJSON</li>
2776 </ul> <em>Applet</em>
2778 <li>Split frame example added to applet examples page</li>
2779 </ul> <em>Build and Deployment</em>
2782 <!-- JAL-1888 -->New ant target for running Jalview's test
2790 <li>Mapping of cDNA to protein in split frames
2791 incorrect when sequence start > 1</li>
2792 <li>Broken images in filter column by annotation dialog
2794 <li>Feature colours not parsed from features file</li>
2795 <li>Exceptions and incomplete link URLs recovered when
2796 loading a features file containing HTML tags in feature
2800 <em>Application</em>
2802 <li>Annotations corrupted after BioJS export and
2804 <li>Incorrect sequence limits after Fetch DB References
2805 with 'trim retrieved sequences'</li>
2806 <li>Incorrect warning about deleting all data when
2807 deleting selected columns</li>
2808 <li>Patch to build system for shipping properly signed
2809 JNLP templates for webstart launch</li>
2810 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2811 unreleased structures for download or viewing</li>
2812 <li>Tab/space/return keystroke operation of EMBL-PDBe
2813 fetcher/viewer dialogs works correctly</li>
2814 <li>Disabled 'minimise' button on Jalview windows
2815 running on OSX to workaround redraw hang bug</li>
2816 <li>Split cDNA/Protein view position and geometry not
2817 recovered from jalview project</li>
2818 <li>Initial enabled/disabled state of annotation menu
2819 sorter 'show autocalculated first/last' corresponds to
2821 <li>Restoring of Clustal, RNA Helices and T-Coffee
2822 color schemes from BioJSON</li>
2826 <li>Reorder sequences mirrored in cDNA/Protein split
2828 <li>Applet with Jmol examples not loading correctly</li>
2834 <td><div align="center">
2835 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2837 <td><em>General</em>
2839 <li>Linked visualisation and analysis of DNA and Protein
2842 <li>Translated cDNA alignments shown as split protein
2843 and DNA alignment views</li>
2844 <li>Codon consensus annotation for linked protein and
2845 cDNA alignment views</li>
2846 <li>Link cDNA or Protein product sequences by loading
2847 them onto Protein or cDNA alignments</li>
2848 <li>Reconstruct linked cDNA alignment from aligned
2849 protein sequences</li>
2852 <li>Jmol integration updated to Jmol v14.2.14</li>
2853 <li>Import and export of Jalview alignment views as <a
2854 href="features/bioJsonFormat.html">BioJSON</a></li>
2855 <li>New alignment annotation file statements for
2856 reference sequences and marking hidden columns</li>
2857 <li>Reference sequence based alignment shading to
2858 highlight variation</li>
2859 <li>Select or hide columns according to alignment
2861 <li>Find option for locating sequences by description</li>
2862 <li>Conserved physicochemical properties shown in amino
2863 acid conservation row</li>
2864 <li>Alignments can be sorted by number of RNA helices</li>
2865 </ul> <em>Application</em>
2867 <li>New cDNA/Protein analysis capabilities
2869 <li>Get Cross-References should open a Split Frame
2870 view with cDNA/Protein</li>
2871 <li>Detect when nucleotide sequences and protein
2872 sequences are placed in the same alignment</li>
2873 <li>Split cDNA/Protein views are saved in Jalview
2878 <li>Use REST API to talk to Chimera</li>
2879 <li>Selected regions in Chimera are highlighted in linked
2880 Jalview windows</li>
2882 <li>VARNA RNA viewer updated to v3.93</li>
2883 <li>VARNA views are saved in Jalview Projects</li>
2884 <li>Pseudoknots displayed as Jalview RNA annotation can
2885 be shown in VARNA</li>
2887 <li>Make groups for selection uses marked columns as well
2888 as the active selected region</li>
2890 <li>Calculate UPGMA and NJ trees using sequence feature
2892 <li>New Export options
2894 <li>New Export Settings dialog to control hidden
2895 region export in flat file generation</li>
2897 <li>Export alignment views for display with the <a
2898 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2900 <li>Export scrollable SVG in HTML page</li>
2901 <li>Optional embedding of BioJSON data when exporting
2902 alignment figures to HTML</li>
2904 <li>3D structure retrieval and display
2906 <li>Free text and structured queries with the PDBe
2908 <li>PDBe Search API based discovery and selection of
2909 PDB structures for a sequence set</li>
2913 <li>JPred4 employed for protein secondary structure
2915 <li>Hide Insertions menu option to hide unaligned columns
2916 for one or a group of sequences</li>
2917 <li>Automatically hide insertions in alignments imported
2918 from the JPred4 web server</li>
2919 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2920 system on OSX<br />LGPL libraries courtesy of <a
2921 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2923 <li>changed 'View nucleotide structure' submenu to 'View
2924 VARNA 2D Structure'</li>
2925 <li>change "View protein structure" menu option to "3D
2928 </ul> <em>Applet</em>
2930 <li>New layout for applet example pages</li>
2931 <li>New parameters to enable SplitFrame view
2932 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2933 <li>New example demonstrating linked viewing of cDNA and
2934 Protein alignments</li>
2935 </ul> <em>Development and deployment</em>
2937 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2938 <li>Include installation type and git revision in build
2939 properties and console log output</li>
2940 <li>Jalview Github organisation, and new github site for
2941 storing BioJsMSA Templates</li>
2942 <li>Jalview's unit tests now managed with TestNG</li>
2945 <!-- <em>General</em>
2947 </ul> --> <!-- issues resolved --> <em>Application</em>
2949 <li>Escape should close any open find dialogs</li>
2950 <li>Typo in select-by-features status report</li>
2951 <li>Consensus RNA secondary secondary structure
2952 predictions are not highlighted in amber</li>
2953 <li>Missing gap character in v2.7 example file means
2954 alignment appears unaligned when pad-gaps is not enabled</li>
2955 <li>First switch to RNA Helices colouring doesn't colour
2956 associated structure views</li>
2957 <li>ID width preference option is greyed out when auto
2958 width checkbox not enabled</li>
2959 <li>Stopped a warning dialog from being shown when
2960 creating user defined colours</li>
2961 <li>'View Mapping' in structure viewer shows sequence
2962 mappings for just that viewer's sequences</li>
2963 <li>Workaround for superposing PDB files containing
2964 multiple models in Chimera</li>
2965 <li>Report sequence position in status bar when hovering
2966 over Jmol structure</li>
2967 <li>Cannot output gaps as '.' symbols with Selection ->
2968 output to text box</li>
2969 <li>Flat file exports of alignments with hidden columns
2970 have incorrect sequence start/end</li>
2971 <li>'Aligning' a second chain to a Chimera structure from
2973 <li>Colour schemes applied to structure viewers don't
2974 work for nucleotide</li>
2975 <li>Loading/cut'n'pasting an empty or invalid file leads
2976 to a grey/invisible alignment window</li>
2977 <li>Exported Jpred annotation from a sequence region
2978 imports to different position</li>
2979 <li>Space at beginning of sequence feature tooltips shown
2980 on some platforms</li>
2981 <li>Chimera viewer 'View | Show Chain' menu is not
2983 <li>'New View' fails with a Null Pointer Exception in
2984 console if Chimera has been opened</li>
2985 <li>Mouseover to Chimera not working</li>
2986 <li>Miscellaneous ENA XML feature qualifiers not
2988 <li>NPE in annotation renderer after 'Extract Scores'</li>
2989 <li>If two structures in one Chimera window, mouseover of
2990 either sequence shows on first structure</li>
2991 <li>'Show annotations' options should not make
2992 non-positional annotations visible</li>
2993 <li>Subsequence secondary structure annotation not shown
2994 in right place after 'view flanking regions'</li>
2995 <li>File Save As type unset when current file format is
2997 <li>Save as '.jar' option removed for saving Jalview
2999 <li>Colour by Sequence colouring in Chimera more
3001 <li>Cannot 'add reference annotation' for a sequence in
3002 several views on same alignment</li>
3003 <li>Cannot show linked products for EMBL / ENA records</li>
3004 <li>Jalview's tooltip wraps long texts containing no
3006 </ul> <em>Applet</em>
3008 <li>Jmol to JalviewLite mouseover/link not working</li>
3009 <li>JalviewLite can't import sequences with ID
3010 descriptions containing angle brackets</li>
3011 </ul> <em>General</em>
3013 <li>Cannot export and reimport RNA secondary structure
3014 via jalview annotation file</li>
3015 <li>Random helix colour palette for colour by annotation
3016 with RNA secondary structure</li>
3017 <li>Mouseover to cDNA from STOP residue in protein
3018 translation doesn't work.</li>
3019 <li>hints when using the select by annotation dialog box</li>
3020 <li>Jmol alignment incorrect if PDB file has alternate CA
3022 <li>FontChooser message dialog appears to hang after
3023 choosing 1pt font</li>
3024 <li>Peptide secondary structure incorrectly imported from
3025 annotation file when annotation display text includes 'e' or
3027 <li>Cannot set colour of new feature type whilst creating
3029 <li>cDNA translation alignment should not be sequence
3030 order dependent</li>
3031 <li>'Show unconserved' doesn't work for lower case
3033 <li>Nucleotide ambiguity codes involving R not recognised</li>
3034 </ul> <em>Deployment and Documentation</em>
3036 <li>Applet example pages appear different to the rest of
3037 www.jalview.org</li>
3038 </ul> <em>Application Known issues</em>
3040 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3041 <li>Misleading message appears after trying to delete
3043 <li>Jalview icon not shown in dock after InstallAnywhere
3044 version launches</li>
3045 <li>Fetching EMBL reference for an RNA sequence results
3046 fails with a sequence mismatch</li>
3047 <li>Corrupted or unreadable alignment display when
3048 scrolling alignment to right</li>
3049 <li>ArrayIndexOutOfBoundsException thrown when remove
3050 empty columns called on alignment with ragged gapped ends</li>
3051 <li>auto calculated alignment annotation rows do not get
3052 placed above or below non-autocalculated rows</li>
3053 <li>Jalview dekstop becomes sluggish at full screen in
3054 ultra-high resolution</li>
3055 <li>Cannot disable consensus calculation independently of
3056 quality and conservation</li>
3057 <li>Mouseover highlighting between cDNA and protein can
3058 become sluggish with more than one splitframe shown</li>
3059 </ul> <em>Applet Known Issues</em>
3061 <li>Core PDB parsing code requires Jmol</li>
3062 <li>Sequence canvas panel goes white when alignment
3063 window is being resized</li>
3069 <td><div align="center">
3070 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3072 <td><em>General</em>
3074 <li>Updated Java code signing certificate donated by
3076 <li>Features and annotation preserved when performing
3077 pairwise alignment</li>
3078 <li>RNA pseudoknot annotation can be
3079 imported/exported/displayed</li>
3080 <li>'colour by annotation' can colour by RNA and
3081 protein secondary structure</li>
3082 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3083 post-hoc with 2.9 release</em>)
3086 </ul> <em>Application</em>
3088 <li>Extract and display secondary structure for sequences
3089 with 3D structures</li>
3090 <li>Support for parsing RNAML</li>
3091 <li>Annotations menu for layout
3093 <li>sort sequence annotation rows by alignment</li>
3094 <li>place sequence annotation above/below alignment
3097 <li>Output in Stockholm format</li>
3098 <li>Internationalisation: improved Spanish (es)
3100 <li>Structure viewer preferences tab</li>
3101 <li>Disorder and Secondary Structure annotation tracks
3102 shared between alignments</li>
3103 <li>UCSF Chimera launch and linked highlighting from
3105 <li>Show/hide all sequence associated annotation rows for
3106 all or current selection</li>
3107 <li>disorder and secondary structure predictions
3108 available as dataset annotation</li>
3109 <li>Per-sequence rna helices colouring</li>
3112 <li>Sequence database accessions imported when fetching
3113 alignments from Rfam</li>
3114 <li>update VARNA version to 3.91</li>
3116 <li>New groovy scripts for exporting aligned positions,
3117 conservation values, and calculating sum of pairs scores.</li>
3118 <li>Command line argument to set default JABAWS server</li>
3119 <li>include installation type in build properties and
3120 console log output</li>
3121 <li>Updated Jalview project format to preserve dataset
3125 <!-- issues resolved --> <em>Application</em>
3127 <li>Distinguish alignment and sequence associated RNA
3128 structure in structure->view->VARNA</li>
3129 <li>Raise dialog box if user deletes all sequences in an
3131 <li>Pressing F1 results in documentation opening twice</li>
3132 <li>Sequence feature tooltip is wrapped</li>
3133 <li>Double click on sequence associated annotation
3134 selects only first column</li>
3135 <li>Redundancy removal doesn't result in unlinked
3136 leaves shown in tree</li>
3137 <li>Undos after several redundancy removals don't undo
3139 <li>Hide sequence doesn't hide associated annotation</li>
3140 <li>User defined colours dialog box too big to fit on
3141 screen and buttons not visible</li>
3142 <li>author list isn't updated if already written to
3143 Jalview properties</li>
3144 <li>Popup menu won't open after retrieving sequence
3146 <li>File open window for associate PDB doesn't open</li>
3147 <li>Left-then-right click on a sequence id opens a
3148 browser search window</li>
3149 <li>Cannot open sequence feature shading/sort popup menu
3150 in feature settings dialog</li>
3151 <li>better tooltip placement for some areas of Jalview
3153 <li>Allow addition of JABAWS Server which doesn't
3154 pass validation</li>
3155 <li>Web services parameters dialog box is too large to
3157 <li>Muscle nucleotide alignment preset obscured by
3159 <li>JABAWS preset submenus don't contain newly
3160 defined user preset</li>
3161 <li>MSA web services warns user if they were launched
3162 with invalid input</li>
3163 <li>Jalview cannot contact DAS Registy when running on
3166 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3167 'Superpose with' submenu not shown when new view
3171 </ul> <!-- <em>Applet</em>
3173 </ul> <em>General</em>
3175 </ul>--> <em>Deployment and Documentation</em>
3177 <li>2G and 1G options in launchApp have no effect on
3178 memory allocation</li>
3179 <li>launchApp service doesn't automatically open
3180 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3182 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3183 InstallAnywhere reports cannot find valid JVM when Java
3184 1.7_055 is available
3186 </ul> <em>Application Known issues</em>
3189 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3190 corrupted or unreadable alignment display when scrolling
3194 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3195 retrieval fails but progress bar continues for DAS retrieval
3196 with large number of ID
3199 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3200 flatfile output of visible region has incorrect sequence
3204 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3205 rna structure consensus doesn't update when secondary
3206 structure tracks are rearranged
3209 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3210 invalid rna structure positional highlighting does not
3211 highlight position of invalid base pairs
3214 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3215 out of memory errors are not raised when saving Jalview
3216 project from alignment window file menu
3219 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3220 Switching to RNA Helices colouring doesn't propagate to
3224 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3225 colour by RNA Helices not enabled when user created
3226 annotation added to alignment
3229 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3230 Jalview icon not shown on dock in Mountain Lion/Webstart
3232 </ul> <em>Applet Known Issues</em>
3235 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3236 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3239 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3240 Jalview and Jmol example not compatible with IE9
3243 <li>Sort by annotation score doesn't reverse order
3249 <td><div align="center">
3250 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3253 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3256 <li>Internationalisation of user interface (usually
3257 called i18n support) and translation for Spanish locale</li>
3258 <li>Define/Undefine group on current selection with
3259 Ctrl-G/Shift Ctrl-G</li>
3260 <li>Improved group creation/removal options in
3261 alignment/sequence Popup menu</li>
3262 <li>Sensible precision for symbol distribution
3263 percentages shown in logo tooltip.</li>
3264 <li>Annotation panel height set according to amount of
3265 annotation when alignment first opened</li>
3266 </ul> <em>Application</em>
3268 <li>Interactive consensus RNA secondary structure
3269 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3270 <li>Select columns containing particular features from
3271 Feature Settings dialog</li>
3272 <li>View all 'representative' PDB structures for selected
3274 <li>Update Jalview project format:
3276 <li>New file extension for Jalview projects '.jvp'</li>
3277 <li>Preserve sequence and annotation dataset (to
3278 store secondary structure annotation,etc)</li>
3279 <li>Per group and alignment annotation and RNA helix
3283 <li>New similarity measures for PCA and Tree calculation
3285 <li>Experimental support for retrieval and viewing of
3286 flanking regions for an alignment</li>
3290 <!-- issues resolved --> <em>Application</em>
3292 <li>logo keeps spinning and status remains at queued or
3293 running after job is cancelled</li>
3294 <li>cannot export features from alignments imported from
3295 Jalview/VAMSAS projects</li>
3296 <li>Buggy slider for web service parameters that take
3298 <li>Newly created RNA secondary structure line doesn't
3299 have 'display all symbols' flag set</li>
3300 <li>T-COFFEE alignment score shading scheme and other
3301 annotation shading not saved in Jalview project</li>
3302 <li>Local file cannot be loaded in freshly downloaded
3304 <li>Jalview icon not shown on dock in Mountain
3306 <li>Load file from desktop file browser fails</li>
3307 <li>Occasional NPE thrown when calculating large trees</li>
3308 <li>Cannot reorder or slide sequences after dragging an
3309 alignment onto desktop</li>
3310 <li>Colour by annotation dialog throws NPE after using
3311 'extract scores' function</li>
3312 <li>Loading/cut'n'pasting an empty file leads to a grey
3313 alignment window</li>
3314 <li>Disorder thresholds rendered incorrectly after
3315 performing IUPred disorder prediction</li>
3316 <li>Multiple group annotated consensus rows shown when
3317 changing 'normalise logo' display setting</li>
3318 <li>Find shows blank dialog after 'finished searching' if
3319 nothing matches query</li>
3320 <li>Null Pointer Exceptions raised when sorting by
3321 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3323 <li>Errors in Jmol console when structures in alignment
3324 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3326 <li>Not all working JABAWS services are shown in
3328 <li>JAVAWS version of Jalview fails to launch with
3329 'invalid literal/length code'</li>
3330 <li>Annotation/RNA Helix colourschemes cannot be applied
3331 to alignment with groups (actually fixed in 2.8.0b1)</li>
3332 <li>RNA Helices and T-Coffee Scores available as default
3335 </ul> <em>Applet</em>
3337 <li>Remove group option is shown even when selection is
3339 <li>Apply to all groups ticked but colourscheme changes
3340 don't affect groups</li>
3341 <li>Documented RNA Helices and T-Coffee Scores as valid
3342 colourscheme name</li>
3343 <li>Annotation labels drawn on sequence IDs when
3344 Annotation panel is not displayed</li>
3345 <li>Increased font size for dropdown menus on OSX and
3346 embedded windows</li>
3347 </ul> <em>Other</em>
3349 <li>Consensus sequence for alignments/groups with a
3350 single sequence were not calculated</li>
3351 <li>annotation files that contain only groups imported as
3352 annotation and junk sequences</li>
3353 <li>Fasta files with sequences containing '*' incorrectly
3354 recognised as PFAM or BLC</li>
3355 <li>conservation/PID slider apply all groups option
3356 doesn't affect background (2.8.0b1)
3358 <li>redundancy highlighting is erratic at 0% and 100%</li>
3359 <li>Remove gapped columns fails for sequences with ragged
3361 <li>AMSA annotation row with leading spaces is not
3362 registered correctly on import</li>
3363 <li>Jalview crashes when selecting PCA analysis for
3364 certain alignments</li>
3365 <li>Opening the colour by annotation dialog for an
3366 existing annotation based 'use original colours'
3367 colourscheme loses original colours setting</li>
3372 <td><div align="center">
3373 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3374 <em>30/1/2014</em></strong>
3378 <li>Trusted certificates for JalviewLite applet and
3379 Jalview Desktop application<br />Certificate was donated by
3380 <a href="https://www.certum.eu">Certum</a> to the Jalview
3381 open source project).
3383 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3384 <li>Output in Stockholm format</li>
3385 <li>Allow import of data from gzipped files</li>
3386 <li>Export/import group and sequence associated line
3387 graph thresholds</li>
3388 <li>Nucleotide substitution matrix that supports RNA and
3389 ambiguity codes</li>
3390 <li>Allow disorder predictions to be made on the current
3391 selection (or visible selection) in the same way that JPred
3393 <li>Groovy scripting for headless Jalview operation</li>
3394 </ul> <em>Other improvements</em>
3396 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3397 <li>COMBINE statement uses current SEQUENCE_REF and
3398 GROUP_REF scope to group annotation rows</li>
3399 <li>Support '' style escaping of quotes in Newick
3401 <li>Group options for JABAWS service by command line name</li>
3402 <li>Empty tooltip shown for JABA service options with a
3403 link but no description</li>
3404 <li>Select primary source when selecting authority in
3405 database fetcher GUI</li>
3406 <li>Add .mfa to FASTA file extensions recognised by
3408 <li>Annotation label tooltip text wrap</li>
3413 <li>Slow scrolling when lots of annotation rows are
3415 <li>Lots of NPE (and slowness) after creating RNA
3416 secondary structure annotation line</li>
3417 <li>Sequence database accessions not imported when
3418 fetching alignments from Rfam</li>
3419 <li>Incorrect SHMR submission for sequences with
3421 <li>View all structures does not always superpose
3423 <li>Option widgets in service parameters not updated to
3424 reflect user or preset settings</li>
3425 <li>Null pointer exceptions for some services without
3426 presets or adjustable parameters</li>
3427 <li>Discover PDB IDs entry in structure menu doesn't
3428 discover PDB xRefs</li>
3429 <li>Exception encountered while trying to retrieve
3430 features with DAS</li>
3431 <li>Lowest value in annotation row isn't coloured
3432 when colour by annotation (per sequence) is coloured</li>
3433 <li>Keyboard mode P jumps to start of gapped region when
3434 residue follows a gap</li>
3435 <li>Jalview appears to hang importing an alignment with
3436 Wrap as default or after enabling Wrap</li>
3437 <li>'Right click to add annotations' message
3438 shown in wrap mode when no annotations present</li>
3439 <li>Disorder predictions fail with NPE if no automatic
3440 annotation already exists on alignment</li>
3441 <li>oninit javascript function should be called after
3442 initialisation completes</li>
3443 <li>Remove redundancy after disorder prediction corrupts
3444 alignment window display</li>
3445 <li>Example annotation file in documentation is invalid</li>
3446 <li>Grouped line graph annotation rows are not exported
3447 to annotation file</li>
3448 <li>Multi-harmony analysis cannot be run when only two
3450 <li>Cannot create multiple groups of line graphs with
3451 several 'combine' statements in annotation file</li>
3452 <li>Pressing return several times causes Number Format
3453 exceptions in keyboard mode</li>
3454 <li>Multi-harmony (SHMMR) method doesn't submit
3455 correct partitions for input data</li>
3456 <li>Translation from DNA to Amino Acids fails</li>
3457 <li>Jalview fail to load newick tree with quoted label</li>
3458 <li>--headless flag isn't understood</li>
3459 <li>ClassCastException when generating EPS in headless
3461 <li>Adjusting sequence-associated shading threshold only
3462 changes one row's threshold</li>
3463 <li>Preferences and Feature settings panel panel
3464 doesn't open</li>
3465 <li>hide consensus histogram also hides conservation and
3466 quality histograms</li>
3471 <td><div align="center">
3472 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3474 <td><em>Application</em>
3476 <li>Support for JABAWS 2.0 Services (AACon alignment
3477 conservation, protein disorder and Clustal Omega)</li>
3478 <li>JABAWS server status indicator in Web Services
3480 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3481 in Jalview alignment window</li>
3482 <li>Updated Jalview build and deploy framework for OSX
3483 mountain lion, windows 7, and 8</li>
3484 <li>Nucleotide substitution matrix for PCA that supports
3485 RNA and ambiguity codes</li>
3487 <li>Improved sequence database retrieval GUI</li>
3488 <li>Support fetching and database reference look up
3489 against multiple DAS sources (Fetch all from in 'fetch db
3491 <li>Jalview project improvements
3493 <li>Store and retrieve the 'belowAlignment'
3494 flag for annotation</li>
3495 <li>calcId attribute to group annotation rows on the
3497 <li>Store AACon calculation settings for a view in
3498 Jalview project</li>
3502 <li>horizontal scrolling gesture support</li>
3503 <li>Visual progress indicator when PCA calculation is
3505 <li>Simpler JABA web services menus</li>
3506 <li>visual indication that web service results are still
3507 being retrieved from server</li>
3508 <li>Serialise the dialogs that are shown when Jalview
3509 starts up for first time</li>
3510 <li>Jalview user agent string for interacting with HTTP
3512 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3514 <li>Examples directory and Groovy library included in
3515 InstallAnywhere distribution</li>
3516 </ul> <em>Applet</em>
3518 <li>RNA alignment and secondary structure annotation
3519 visualization applet example</li>
3520 </ul> <em>General</em>
3522 <li>Normalise option for consensus sequence logo</li>
3523 <li>Reset button in PCA window to return dimensions to
3525 <li>Allow seqspace or Jalview variant of alignment PCA
3527 <li>PCA with either nucleic acid and protein substitution
3529 <li>Allow windows containing HTML reports to be exported
3531 <li>Interactive display and editing of RNA secondary
3532 structure contacts</li>
3533 <li>RNA Helix Alignment Colouring</li>
3534 <li>RNA base pair logo consensus</li>
3535 <li>Parse sequence associated secondary structure
3536 information in Stockholm files</li>
3537 <li>HTML Export database accessions and annotation
3538 information presented in tooltip for sequences</li>
3539 <li>Import secondary structure from LOCARNA clustalw
3540 style RNA alignment files</li>
3541 <li>import and visualise T-COFFEE quality scores for an
3543 <li>'colour by annotation' per sequence option to
3544 shade each sequence according to its associated alignment
3546 <li>New Jalview Logo</li>
3547 </ul> <em>Documentation and Development</em>
3549 <li>documentation for score matrices used in Jalview</li>
3550 <li>New Website!</li>
3552 <td><em>Application</em>
3554 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3555 wsdbfetch REST service</li>
3556 <li>Stop windows being moved outside desktop on OSX</li>
3557 <li>Filetype associations not installed for webstart
3559 <li>Jalview does not always retrieve progress of a JABAWS
3560 job execution in full once it is complete</li>
3561 <li>revise SHMR RSBS definition to ensure alignment is
3562 uploaded via ali_file parameter</li>
3563 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3564 <li>View all structures superposed fails with exception</li>
3565 <li>Jnet job queues forever if a very short sequence is
3566 submitted for prediction</li>
3567 <li>Cut and paste menu not opened when mouse clicked on
3569 <li>Putting fractional value into integer text box in
3570 alignment parameter dialog causes Jalview to hang</li>
3571 <li>Structure view highlighting doesn't work on
3573 <li>View all structures fails with exception shown in
3575 <li>Characters in filename associated with PDBEntry not
3576 escaped in a platform independent way</li>
3577 <li>Jalview desktop fails to launch with exception when
3579 <li>Tree calculation reports 'you must have 2 or more
3580 sequences selected' when selection is empty</li>
3581 <li>Jalview desktop fails to launch with jar signature
3582 failure when java web start temporary file caching is
3584 <li>DAS Sequence retrieval with range qualification
3585 results in sequence xref which includes range qualification</li>
3586 <li>Errors during processing of command line arguments
3587 cause progress bar (JAL-898) to be removed</li>
3588 <li>Replace comma for semi-colon option not disabled for
3589 DAS sources in sequence fetcher</li>
3590 <li>Cannot close news reader when JABAWS server warning
3591 dialog is shown</li>
3592 <li>Option widgets not updated to reflect user settings</li>
3593 <li>Edited sequence not submitted to web service</li>
3594 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3595 <li>InstallAnywhere installer doesn't unpack and run
3596 on OSX Mountain Lion</li>
3597 <li>Annotation panel not given a scroll bar when
3598 sequences with alignment annotation are pasted into the
3600 <li>Sequence associated annotation rows not associated
3601 when loaded from Jalview project</li>
3602 <li>Browser launch fails with NPE on java 1.7</li>
3603 <li>JABAWS alignment marked as finished when job was
3604 cancelled or job failed due to invalid input</li>
3605 <li>NPE with v2.7 example when clicking on Tree
3606 associated with all views</li>
3607 <li>Exceptions when copy/paste sequences with grouped
3608 annotation rows to new window</li>
3609 </ul> <em>Applet</em>
3611 <li>Sequence features are momentarily displayed before
3612 they are hidden using hidefeaturegroups applet parameter</li>
3613 <li>loading features via javascript API automatically
3614 enables feature display</li>
3615 <li>scrollToColumnIn javascript API method doesn't
3617 </ul> <em>General</em>
3619 <li>Redundancy removal fails for rna alignment</li>
3620 <li>PCA calculation fails when sequence has been selected
3621 and then deselected</li>
3622 <li>PCA window shows grey box when first opened on OSX</li>
3623 <li>Letters coloured pink in sequence logo when alignment
3624 coloured with clustalx</li>
3625 <li>Choosing fonts without letter symbols defined causes
3626 exceptions and redraw errors</li>
3627 <li>Initial PCA plot view is not same as manually
3628 reconfigured view</li>
3629 <li>Grouped annotation graph label has incorrect line
3631 <li>Grouped annotation graph label display is corrupted
3632 for lots of labels</li>
3637 <div align="center">
3638 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3641 <td><em>Application</em>
3643 <li>Jalview Desktop News Reader</li>
3644 <li>Tweaked default layout of web services menu</li>
3645 <li>View/alignment association menu to enable user to
3646 easily specify which alignment a multi-structure view takes
3647 its colours/correspondences from</li>
3648 <li>Allow properties file location to be specified as URL</li>
3649 <li>Extend Jalview project to preserve associations
3650 between many alignment views and a single Jmol display</li>
3651 <li>Store annotation row height in Jalview project file</li>
3652 <li>Annotation row column label formatting attributes
3653 stored in project file</li>
3654 <li>Annotation row order for auto-calculated annotation
3655 rows preserved in Jalview project file</li>
3656 <li>Visual progress indication when Jalview state is
3657 saved using Desktop window menu</li>
3658 <li>Visual indication that command line arguments are
3659 still being processed</li>
3660 <li>Groovy script execution from URL</li>
3661 <li>Colour by annotation default min and max colours in
3663 <li>Automatically associate PDB files dragged onto an
3664 alignment with sequences that have high similarity and
3666 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3667 <li>'view structures' option to open many
3668 structures in same window</li>
3669 <li>Sort associated views menu option for tree panel</li>
3670 <li>Group all JABA and non-JABA services for a particular
3671 analysis function in its own submenu</li>
3672 </ul> <em>Applet</em>
3674 <li>Userdefined and autogenerated annotation rows for
3676 <li>Adjustment of alignment annotation pane height</li>
3677 <li>Annotation scrollbar for annotation panel</li>
3678 <li>Drag to reorder annotation rows in annotation panel</li>
3679 <li>'automaticScrolling' parameter</li>
3680 <li>Allow sequences with partial ID string matches to be
3681 annotated from GFF/Jalview features files</li>
3682 <li>Sequence logo annotation row in applet</li>
3683 <li>Absolute paths relative to host server in applet
3684 parameters are treated as such</li>
3685 <li>New in the JalviewLite javascript API:
3687 <li>JalviewLite.js javascript library</li>
3688 <li>Javascript callbacks for
3690 <li>Applet initialisation</li>
3691 <li>Sequence/alignment mouse-overs and selections</li>
3694 <li>scrollTo row and column alignment scrolling
3696 <li>Select sequence/alignment regions from javascript</li>
3697 <li>javascript structure viewer harness to pass
3698 messages between Jmol and Jalview when running as
3699 distinct applets</li>
3700 <li>sortBy method</li>
3701 <li>Set of applet and application examples shipped
3702 with documentation</li>
3703 <li>New example to demonstrate JalviewLite and Jmol
3704 javascript message exchange</li>
3706 </ul> <em>General</em>
3708 <li>Enable Jmol displays to be associated with multiple
3709 multiple alignments</li>
3710 <li>Option to automatically sort alignment with new tree</li>
3711 <li>User configurable link to enable redirects to a
3712 www.Jalview.org mirror</li>
3713 <li>Jmol colours option for Jmol displays</li>
3714 <li>Configurable newline string when writing alignment
3715 and other flat files</li>
3716 <li>Allow alignment annotation description lines to
3717 contain html tags</li>
3718 </ul> <em>Documentation and Development</em>
3720 <li>Add groovy test harness for bulk load testing to
3722 <li>Groovy script to load and align a set of sequences
3723 using a web service before displaying the result in the
3724 Jalview desktop</li>
3725 <li>Restructured javascript and applet api documentation</li>
3726 <li>Ant target to publish example html files with applet
3728 <li>Netbeans project for building Jalview from source</li>
3729 <li>ant task to create online javadoc for Jalview source</li>
3731 <td><em>Application</em>
3733 <li>User defined colourscheme throws exception when
3734 current built in colourscheme is saved as new scheme</li>
3735 <li>AlignFrame->Save in application pops up save
3736 dialog for valid filename/format</li>
3737 <li>Cannot view associated structure for UniProt sequence</li>
3738 <li>PDB file association breaks for UniProt sequence
3740 <li>Associate PDB from file dialog does not tell you
3741 which sequence is to be associated with the file</li>
3742 <li>Find All raises null pointer exception when query
3743 only matches sequence IDs</li>
3744 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3745 <li>Jalview project with Jmol views created with Jalview
3746 2.4 cannot be loaded</li>
3747 <li>Filetype associations not installed for webstart
3749 <li>Two or more chains in a single PDB file associated
3750 with sequences in different alignments do not get coloured
3751 by their associated sequence</li>
3752 <li>Visibility status of autocalculated annotation row
3753 not preserved when project is loaded</li>
3754 <li>Annotation row height and visibility attributes not
3755 stored in Jalview project</li>
3756 <li>Tree bootstraps are not preserved when saved as a
3757 Jalview project</li>
3758 <li>Envision2 workflow tooltips are corrupted</li>
3759 <li>Enabling show group conservation also enables colour
3760 by conservation</li>
3761 <li>Duplicate group associated conservation or consensus
3762 created on new view</li>
3763 <li>Annotation scrollbar not displayed after 'show
3764 all hidden annotation rows' option selected</li>
3765 <li>Alignment quality not updated after alignment
3766 annotation row is hidden then shown</li>
3767 <li>Preserve colouring of structures coloured by
3768 sequences in pre Jalview 2.7 projects</li>
3769 <li>Web service job parameter dialog is not laid out
3771 <li>Web services menu not refreshed after 'reset
3772 services' button is pressed in preferences</li>
3773 <li>Annotation off by one in Jalview v2_3 example project</li>
3774 <li>Structures imported from file and saved in project
3775 get name like jalview_pdb1234.txt when reloaded</li>
3776 <li>Jalview does not always retrieve progress of a JABAWS
3777 job execution in full once it is complete</li>
3778 </ul> <em>Applet</em>
3780 <li>Alignment height set incorrectly when lots of
3781 annotation rows are displayed</li>
3782 <li>Relative URLs in feature HTML text not resolved to
3784 <li>View follows highlighting does not work for positions
3786 <li><= shown as = in tooltip</li>
3787 <li>Export features raises exception when no features
3789 <li>Separator string used for serialising lists of IDs
3790 for javascript api is modified when separator string
3791 provided as parameter</li>
3792 <li>Null pointer exception when selecting tree leaves for
3793 alignment with no existing selection</li>
3794 <li>Relative URLs for datasources assumed to be relative
3795 to applet's codebase</li>
3796 <li>Status bar not updated after finished searching and
3797 search wraps around to first result</li>
3798 <li>StructureSelectionManager instance shared between
3799 several Jalview applets causes race conditions and memory
3801 <li>Hover tooltip and mouseover of position on structure
3802 not sent from Jmol in applet</li>
3803 <li>Certain sequences of javascript method calls to
3804 applet API fatally hang browser</li>
3805 </ul> <em>General</em>
3807 <li>View follows structure mouseover scrolls beyond
3808 position with wrapped view and hidden regions</li>
3809 <li>Find sequence position moves to wrong residue
3810 with/without hidden columns</li>
3811 <li>Sequence length given in alignment properties window
3813 <li>InvalidNumberFormat exceptions thrown when trying to
3814 import PDB like structure files</li>
3815 <li>Positional search results are only highlighted
3816 between user-supplied sequence start/end bounds</li>
3817 <li>End attribute of sequence is not validated</li>
3818 <li>Find dialog only finds first sequence containing a
3819 given sequence position</li>
3820 <li>Sequence numbering not preserved in MSF alignment
3822 <li>Jalview PDB file reader does not extract sequence
3823 from nucleotide chains correctly</li>
3824 <li>Structure colours not updated when tree partition
3825 changed in alignment</li>
3826 <li>Sequence associated secondary structure not correctly
3827 parsed in interleaved stockholm</li>
3828 <li>Colour by annotation dialog does not restore current
3830 <li>Hiding (nearly) all sequences doesn't work
3832 <li>Sequences containing lowercase letters are not
3833 properly associated with their pdb files</li>
3834 </ul> <em>Documentation and Development</em>
3836 <li>schemas/JalviewWsParamSet.xsd corrupted by
3837 ApplyCopyright tool</li>
3842 <div align="center">
3843 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3846 <td><em>Application</em>
3848 <li>New warning dialog when the Jalview Desktop cannot
3849 contact web services</li>
3850 <li>JABA service parameters for a preset are shown in
3851 service job window</li>
3852 <li>JABA Service menu entries reworded</li>
3856 <li>Modeller PIR IO broken - cannot correctly import a
3857 pir file emitted by Jalview</li>
3858 <li>Existing feature settings transferred to new
3859 alignment view created from cut'n'paste</li>
3860 <li>Improved test for mixed amino/nucleotide chains when
3861 parsing PDB files</li>
3862 <li>Consensus and conservation annotation rows
3863 occasionally become blank for all new windows</li>
3864 <li>Exception raised when right clicking above sequences
3865 in wrapped view mode</li>
3866 </ul> <em>Application</em>
3868 <li>multiple multiply aligned structure views cause cpu
3869 usage to hit 100% and computer to hang</li>
3870 <li>Web Service parameter layout breaks for long user
3871 parameter names</li>
3872 <li>Jaba service discovery hangs desktop if Jaba server
3879 <div align="center">
3880 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3883 <td><em>Application</em>
3885 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3886 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3889 <li>Web Services preference tab</li>
3890 <li>Analysis parameters dialog box and user defined
3892 <li>Improved speed and layout of Envision2 service menu</li>
3893 <li>Superpose structures using associated sequence
3895 <li>Export coordinates and projection as CSV from PCA
3897 </ul> <em>Applet</em>
3899 <li>enable javascript: execution by the applet via the
3900 link out mechanism</li>
3901 </ul> <em>Other</em>
3903 <li>Updated the Jmol Jalview interface to work with Jmol
3905 <li>The Jalview Desktop and JalviewLite applet now
3906 require Java 1.5</li>
3907 <li>Allow Jalview feature colour specification for GFF
3908 sequence annotation files</li>
3909 <li>New 'colour by label' keword in Jalview feature file
3910 type colour specification</li>
3911 <li>New Jalview Desktop Groovy API method that allows a
3912 script to check if it being run in an interactive session or
3913 in a batch operation from the Jalview command line</li>
3917 <li>clustalx colourscheme colours Ds preferentially when
3918 both D+E are present in over 50% of the column</li>
3919 </ul> <em>Application</em>
3921 <li>typo in AlignmentFrame->View->Hide->all but
3922 selected Regions menu item</li>
3923 <li>sequence fetcher replaces ',' for ';' when the ',' is
3924 part of a valid accession ID</li>
3925 <li>fatal OOM if object retrieved by sequence fetcher
3926 runs out of memory</li>
3927 <li>unhandled Out of Memory Error when viewing pca
3928 analysis results</li>
3929 <li>InstallAnywhere builds fail to launch on OS X java
3930 10.5 update 4 (due to apple Java 1.6 update)</li>
3931 <li>Installanywhere Jalview silently fails to launch</li>
3932 </ul> <em>Applet</em>
3934 <li>Jalview.getFeatureGroups() raises an
3935 ArrayIndexOutOfBoundsException if no feature groups are
3942 <div align="center">
3943 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3949 <li>Alignment prettyprinter doesn't cope with long
3951 <li>clustalx colourscheme colours Ds preferentially when
3952 both D+E are present in over 50% of the column</li>
3953 <li>nucleic acid structures retrieved from PDB do not
3954 import correctly</li>
3955 <li>More columns get selected than were clicked on when a
3956 number of columns are hidden</li>
3957 <li>annotation label popup menu not providing correct
3958 add/hide/show options when rows are hidden or none are
3960 <li>Stockholm format shown in list of readable formats,
3961 and parser copes better with alignments from RFAM.</li>
3962 <li>CSV output of consensus only includes the percentage
3963 of all symbols if sequence logo display is enabled</li>
3965 </ul> <em>Applet</em>
3967 <li>annotation panel disappears when annotation is
3969 </ul> <em>Application</em>
3971 <li>Alignment view not redrawn properly when new
3972 alignment opened where annotation panel is visible but no
3973 annotations are present on alignment</li>
3974 <li>pasted region containing hidden columns is
3975 incorrectly displayed in new alignment window</li>
3976 <li>Jalview slow to complete operations when stdout is
3977 flooded (fix is to close the Jalview console)</li>
3978 <li>typo in AlignmentFrame->View->Hide->all but
3979 selected Rregions menu item.</li>
3980 <li>inconsistent group submenu and Format submenu entry
3981 'Un' or 'Non'conserved</li>
3982 <li>Sequence feature settings are being shared by
3983 multiple distinct alignments</li>
3984 <li>group annotation not recreated when tree partition is
3986 <li>double click on group annotation to select sequences
3987 does not propagate to associated trees</li>
3988 <li>Mac OSX specific issues:
3990 <li>exception raised when mouse clicked on desktop
3991 window background</li>
3992 <li>Desktop menu placed on menu bar and application
3993 name set correctly</li>
3994 <li>sequence feature settings not wide enough for the
3995 save feature colourscheme button</li>
4004 <div align="center">
4005 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4008 <td><em>New Capabilities</em>
4010 <li>URL links generated from description line for
4011 regular-expression based URL links (applet and application)
4013 <li>Non-positional feature URL links are shown in link
4015 <li>Linked viewing of nucleic acid sequences and
4017 <li>Automatic Scrolling option in View menu to display
4018 the currently highlighted region of an alignment.</li>
4019 <li>Order an alignment by sequence length, or using the
4020 average score or total feature count for each sequence.</li>
4021 <li>Shading features by score or associated description</li>
4022 <li>Subdivide alignment and groups based on identity of
4023 selected subsequence (Make Groups from Selection).</li>
4024 <li>New hide/show options including Shift+Control+H to
4025 hide everything but the currently selected region.</li>
4026 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4027 </ul> <em>Application</em>
4029 <li>Fetch DB References capabilities and UI expanded to
4030 support retrieval from DAS sequence sources</li>
4031 <li>Local DAS Sequence sources can be added via the
4032 command line or via the Add local source dialog box.</li>
4033 <li>DAS Dbref and DbxRef feature types are parsed as
4034 database references and protein_name is parsed as
4035 description line (BioSapiens terms).</li>
4036 <li>Enable or disable non-positional feature and database
4037 references in sequence ID tooltip from View menu in
4039 <!-- <li>New hidden columns and rows and representatives capabilities
4040 in annotations file (in progress - not yet fully implemented)</li> -->
4041 <li>Group-associated consensus, sequence logos and
4042 conservation plots</li>
4043 <li>Symbol distributions for each column can be exported
4044 and visualized as sequence logos</li>
4045 <li>Optionally scale multi-character column labels to fit
4046 within each column of annotation row<!-- todo for applet -->
4048 <li>Optional automatic sort of associated alignment view
4049 when a new tree is opened.</li>
4050 <li>Jalview Java Console</li>
4051 <li>Better placement of desktop window when moving
4052 between different screens.</li>
4053 <li>New preference items for sequence ID tooltip and
4054 consensus annotation</li>
4055 <li>Client to submit sequences and IDs to Envision2
4057 <li><em>Vamsas Capabilities</em>
4059 <li>Improved VAMSAS synchronization (Jalview archive
4060 used to preserve views, structures, and tree display
4062 <li>Import of vamsas documents from disk or URL via
4064 <li>Sharing of selected regions between views and
4065 with other VAMSAS applications (Experimental feature!)</li>
4066 <li>Updated API to VAMSAS version 0.2</li>
4068 </ul> <em>Applet</em>
4070 <li>Middle button resizes annotation row height</li>
4073 <li>sortByTree (true/false) - automatically sort the
4074 associated alignment view by the tree when a new tree is
4076 <li>showTreeBootstraps (true/false) - show or hide
4077 branch bootstraps (default is to show them if available)</li>
4078 <li>showTreeDistances (true/false) - show or hide
4079 branch lengths (default is to show them if available)</li>
4080 <li>showUnlinkedTreeNodes (true/false) - indicate if
4081 unassociated nodes should be highlighted in the tree
4083 <li>heightScale and widthScale (1.0 or more) -
4084 increase the height or width of a cell in the alignment
4085 grid relative to the current font size.</li>
4088 <li>Non-positional features displayed in sequence ID
4090 </ul> <em>Other</em>
4092 <li>Features format: graduated colour definitions and
4093 specification of feature scores</li>
4094 <li>Alignment Annotations format: new keywords for group
4095 associated annotation (GROUP_REF) and annotation row display
4096 properties (ROW_PROPERTIES)</li>
4097 <li>XML formats extended to support graduated feature
4098 colourschemes, group associated annotation, and profile
4099 visualization settings.</li></td>
4102 <li>Source field in GFF files parsed as feature source
4103 rather than description</li>
4104 <li>Non-positional features are now included in sequence
4105 feature and gff files (controlled via non-positional feature
4106 visibility in tooltip).</li>
4107 <li>URL links generated for all feature links (bugfix)</li>
4108 <li>Added URL embedding instructions to features file
4110 <li>Codons containing ambiguous nucleotides translated as
4111 'X' in peptide product</li>
4112 <li>Match case switch in find dialog box works for both
4113 sequence ID and sequence string and query strings do not
4114 have to be in upper case to match case-insensitively.</li>
4115 <li>AMSA files only contain first column of
4116 multi-character column annotation labels</li>
4117 <li>Jalview Annotation File generation/parsing consistent
4118 with documentation (e.g. Stockholm annotation can be
4119 exported and re-imported)</li>
4120 <li>PDB files without embedded PDB IDs given a friendly
4122 <li>Find incrementally searches ID string matches as well
4123 as subsequence matches, and correctly reports total number
4127 <li>Better handling of exceptions during sequence
4129 <li>Dasobert generated non-positional feature URL
4130 link text excludes the start_end suffix</li>
4131 <li>DAS feature and source retrieval buttons disabled
4132 when fetch or registry operations in progress.</li>
4133 <li>PDB files retrieved from URLs are cached properly</li>
4134 <li>Sequence description lines properly shared via
4136 <li>Sequence fetcher fetches multiple records for all
4138 <li>Ensured that command line das feature retrieval
4139 completes before alignment figures are generated.</li>
4140 <li>Reduced time taken when opening file browser for
4142 <li>isAligned check prior to calculating tree, PCA or
4143 submitting an MSA to JNet now excludes hidden sequences.</li>
4144 <li>User defined group colours properly recovered
4145 from Jalview projects.</li>
4154 <div align="center">
4155 <strong>2.4.0.b2</strong><br> 28/10/2009
4160 <li>Experimental support for google analytics usage
4162 <li>Jalview privacy settings (user preferences and docs).</li>
4167 <li>Race condition in applet preventing startup in
4169 <li>Exception when feature created from selection beyond
4170 length of sequence.</li>
4171 <li>Allow synthetic PDB files to be imported gracefully</li>
4172 <li>Sequence associated annotation rows associate with
4173 all sequences with a given id</li>
4174 <li>Find function matches case-insensitively for sequence
4175 ID string searches</li>
4176 <li>Non-standard characters do not cause pairwise
4177 alignment to fail with exception</li>
4178 </ul> <em>Application Issues</em>
4180 <li>Sequences are now validated against EMBL database</li>
4181 <li>Sequence fetcher fetches multiple records for all
4183 </ul> <em>InstallAnywhere Issues</em>
4185 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4186 issue with installAnywhere mechanism)</li>
4187 <li>Command line launching of JARs from InstallAnywhere
4188 version (java class versioning error fixed)</li>
4195 <div align="center">
4196 <strong>2.4</strong><br> 27/8/2008
4199 <td><em>User Interface</em>
4201 <li>Linked highlighting of codon and amino acid from
4202 translation and protein products</li>
4203 <li>Linked highlighting of structure associated with
4204 residue mapping to codon position</li>
4205 <li>Sequence Fetcher provides example accession numbers
4206 and 'clear' button</li>
4207 <li>MemoryMonitor added as an option under Desktop's
4209 <li>Extract score function to parse whitespace separated
4210 numeric data in description line</li>
4211 <li>Column labels in alignment annotation can be centred.</li>
4212 <li>Tooltip for sequence associated annotation give name
4214 </ul> <em>Web Services and URL fetching</em>
4216 <li>JPred3 web service</li>
4217 <li>Prototype sequence search client (no public services
4219 <li>Fetch either seed alignment or full alignment from
4221 <li>URL Links created for matching database cross
4222 references as well as sequence ID</li>
4223 <li>URL Links can be created using regular-expressions</li>
4224 </ul> <em>Sequence Database Connectivity</em>
4226 <li>Retrieval of cross-referenced sequences from other
4228 <li>Generalised database reference retrieval and
4229 validation to all fetchable databases</li>
4230 <li>Fetch sequences from DAS sources supporting the
4231 sequence command</li>
4232 </ul> <em>Import and Export</em>
4233 <li>export annotation rows as CSV for spreadsheet import</li>
4234 <li>Jalview projects record alignment dataset associations,
4235 EMBL products, and cDNA sequence mappings</li>
4236 <li>Sequence Group colour can be specified in Annotation
4238 <li>Ad-hoc colouring of group in Annotation File using RGB
4239 triplet as name of colourscheme</li>
4240 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4242 <li>treenode binding for VAMSAS tree exchange</li>
4243 <li>local editing and update of sequences in VAMSAS
4244 alignments (experimental)</li>
4245 <li>Create new or select existing session to join</li>
4246 <li>load and save of vamsas documents</li>
4247 </ul> <em>Application command line</em>
4249 <li>-tree parameter to open trees (introduced for passing
4251 <li>-fetchfrom command line argument to specify nicknames
4252 of DAS servers to query for alignment features</li>
4253 <li>-dasserver command line argument to add new servers
4254 that are also automatically queried for features</li>
4255 <li>-groovy command line argument executes a given groovy
4256 script after all input data has been loaded and parsed</li>
4257 </ul> <em>Applet-Application data exchange</em>
4259 <li>Trees passed as applet parameters can be passed to
4260 application (when using "View in full
4261 application")</li>
4262 </ul> <em>Applet Parameters</em>
4264 <li>feature group display control parameter</li>
4265 <li>debug parameter</li>
4266 <li>showbutton parameter</li>
4267 </ul> <em>Applet API methods</em>
4269 <li>newView public method</li>
4270 <li>Window (current view) specific get/set public methods</li>
4271 <li>Feature display control methods</li>
4272 <li>get list of currently selected sequences</li>
4273 </ul> <em>New Jalview distribution features</em>
4275 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4276 <li>RELEASE file gives build properties for the latest
4277 Jalview release.</li>
4278 <li>Java 1.1 Applet build made easier and donotobfuscate
4279 property controls execution of obfuscator</li>
4280 <li>Build target for generating source distribution</li>
4281 <li>Debug flag for javacc</li>
4282 <li>.jalview_properties file is documented (slightly) in
4283 jalview.bin.Cache</li>
4284 <li>Continuous Build Integration for stable and
4285 development version of Application, Applet and source
4290 <li>selected region output includes visible annotations
4291 (for certain formats)</li>
4292 <li>edit label/displaychar contains existing label/char
4294 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4295 <li>shorter peptide product names from EMBL records</li>
4296 <li>Newick string generator makes compact representations</li>
4297 <li>bootstrap values parsed correctly for tree files with
4299 <li>pathological filechooser bug avoided by not allowing
4300 filenames containing a ':'</li>
4301 <li>Fixed exception when parsing GFF files containing
4302 global sequence features</li>
4303 <li>Alignment datasets are finalized only when number of
4304 references from alignment sequences goes to zero</li>
4305 <li>Close of tree branch colour box without colour
4306 selection causes cascading exceptions</li>
4307 <li>occasional negative imgwidth exceptions</li>
4308 <li>better reporting of non-fatal warnings to user when
4309 file parsing fails.</li>
4310 <li>Save works when Jalview project is default format</li>
4311 <li>Save as dialog opened if current alignment format is
4312 not a valid output format</li>
4313 <li>UniProt canonical names introduced for both das and
4315 <li>Histidine should be midblue (not pink!) in Zappo</li>
4316 <li>error messages passed up and output when data read
4318 <li>edit undo recovers previous dataset sequence when
4319 sequence is edited</li>
4320 <li>allow PDB files without pdb ID HEADER lines (like
4321 those generated by MODELLER) to be read in properly</li>
4322 <li>allow reading of JPred concise files as a normal
4324 <li>Stockholm annotation parsing and alignment properties
4325 import fixed for PFAM records</li>
4326 <li>Structure view windows have correct name in Desktop
4328 <li>annotation consisting of sequence associated scores
4329 can be read and written correctly to annotation file</li>
4330 <li>Aligned cDNA translation to aligned peptide works
4332 <li>Fixed display of hidden sequence markers and
4333 non-italic font for representatives in Applet</li>
4334 <li>Applet Menus are always embedded in applet window on
4336 <li>Newly shown features appear at top of stack (in
4338 <li>Annotations added via parameter not drawn properly
4339 due to null pointer exceptions</li>
4340 <li>Secondary structure lines are drawn starting from
4341 first column of alignment</li>
4342 <li>UniProt XML import updated for new schema release in
4344 <li>Sequence feature to sequence ID match for Features
4345 file is case-insensitive</li>
4346 <li>Sequence features read from Features file appended to
4347 all sequences with matching IDs</li>
4348 <li>PDB structure coloured correctly for associated views
4349 containing a sub-sequence</li>
4350 <li>PDB files can be retrieved by applet from Jar files</li>
4351 <li>feature and annotation file applet parameters
4352 referring to different directories are retrieved correctly</li>
4353 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4354 <li>Fixed application hang whilst waiting for
4355 splash-screen version check to complete</li>
4356 <li>Applet properly URLencodes input parameter values
4357 when passing them to the launchApp service</li>
4358 <li>display name and local features preserved in results
4359 retrieved from web service</li>
4360 <li>Visual delay indication for sequence retrieval and
4361 sequence fetcher initialisation</li>
4362 <li>updated Application to use DAS 1.53e version of
4363 dasobert DAS client</li>
4364 <li>Re-instated Full AMSA support and .amsa file
4366 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4374 <div align="center">
4375 <strong>2.3</strong><br> 9/5/07
4380 <li>Jmol 11.0.2 integration</li>
4381 <li>PDB views stored in Jalview XML files</li>
4382 <li>Slide sequences</li>
4383 <li>Edit sequence in place</li>
4384 <li>EMBL CDS features</li>
4385 <li>DAS Feature mapping</li>
4386 <li>Feature ordering</li>
4387 <li>Alignment Properties</li>
4388 <li>Annotation Scores</li>
4389 <li>Sort by scores</li>
4390 <li>Feature/annotation editing in applet</li>
4395 <li>Headless state operation in 2.2.1</li>
4396 <li>Incorrect and unstable DNA pairwise alignment</li>
4397 <li>Cut and paste of sequences with annotation</li>
4398 <li>Feature group display state in XML</li>
4399 <li>Feature ordering in XML</li>
4400 <li>blc file iteration selection using filename # suffix</li>
4401 <li>Stockholm alignment properties</li>
4402 <li>Stockhom alignment secondary structure annotation</li>
4403 <li>2.2.1 applet had no feature transparency</li>
4404 <li>Number pad keys can be used in cursor mode</li>
4405 <li>Structure Viewer mirror image resolved</li>
4412 <div align="center">
4413 <strong>2.2.1</strong><br> 12/2/07
4418 <li>Non standard characters can be read and displayed
4419 <li>Annotations/Features can be imported/exported to the
4421 <li>Applet allows editing of sequence/annotation/group
4422 name & description
4423 <li>Preference setting to display sequence name in
4425 <li>Annotation file format extended to allow
4426 Sequence_groups to be defined
4427 <li>Default opening of alignment overview panel can be
4428 specified in preferences
4429 <li>PDB residue numbering annotation added to associated
4435 <li>Applet crash under certain Linux OS with Java 1.6
4437 <li>Annotation file export / import bugs fixed
4438 <li>PNG / EPS image output bugs fixed
4444 <div align="center">
4445 <strong>2.2</strong><br> 27/11/06
4450 <li>Multiple views on alignment
4451 <li>Sequence feature editing
4452 <li>"Reload" alignment
4453 <li>"Save" to current filename
4454 <li>Background dependent text colour
4455 <li>Right align sequence ids
4456 <li>User-defined lower case residue colours
4459 <li>Menu item accelerator keys
4460 <li>Control-V pastes to current alignment
4461 <li>Cancel button for DAS Feature Fetching
4462 <li>PCA and PDB Viewers zoom via mouse roller
4463 <li>User-defined sub-tree colours and sub-tree selection
4465 <li>'New Window' button on the 'Output to Text box'
4470 <li>New memory efficient Undo/Redo System
4471 <li>Optimised symbol lookups and conservation/consensus
4473 <li>Region Conservation/Consensus recalculated after
4475 <li>Fixed Remove Empty Columns Bug (empty columns at end
4477 <li>Slowed DAS Feature Fetching for increased robustness.
4479 <li>Made angle brackets in ASCII feature descriptions
4481 <li>Re-instated Zoom function for PCA
4482 <li>Sequence descriptions conserved in web service
4484 <li>UniProt ID discoverer uses any word separated by
4486 <li>WsDbFetch query/result association resolved
4487 <li>Tree leaf to sequence mapping improved
4488 <li>Smooth fonts switch moved to FontChooser dialog box.
4495 <div align="center">
4496 <strong>2.1.1</strong><br> 12/9/06
4501 <li>Copy consensus sequence to clipboard</li>
4506 <li>Image output - rightmost residues are rendered if
4507 sequence id panel has been resized</li>
4508 <li>Image output - all offscreen group boundaries are
4510 <li>Annotation files with sequence references - all
4511 elements in file are relative to sequence position</li>
4512 <li>Mac Applet users can use Alt key for group editing</li>
4518 <div align="center">
4519 <strong>2.1</strong><br> 22/8/06
4524 <li>MAFFT Multiple Alignment in default Web Service list</li>
4525 <li>DAS Feature fetching</li>
4526 <li>Hide sequences and columns</li>
4527 <li>Export Annotations and Features</li>
4528 <li>GFF file reading / writing</li>
4529 <li>Associate structures with sequences from local PDB
4531 <li>Add sequences to exisiting alignment</li>
4532 <li>Recently opened files / URL lists</li>
4533 <li>Applet can launch the full application</li>
4534 <li>Applet has transparency for features (Java 1.2
4536 <li>Applet has user defined colours parameter</li>
4537 <li>Applet can load sequences from parameter
4538 "sequence<em>x</em>"
4544 <li>Redundancy Panel reinstalled in the Applet</li>
4545 <li>Monospaced font - EPS / rescaling bug fixed</li>
4546 <li>Annotation files with sequence references bug fixed</li>
4552 <div align="center">
4553 <strong>2.08.1</strong><br> 2/5/06
4558 <li>Change case of selected region from Popup menu</li>
4559 <li>Choose to match case when searching</li>
4560 <li>Middle mouse button and mouse movement can compress /
4561 expand the visible width and height of the alignment</li>
4566 <li>Annotation Panel displays complete JNet results</li>
4572 <div align="center">
4573 <strong>2.08b</strong><br> 18/4/06
4579 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4580 <li>Righthand label on wrapped alignments shows correct
4587 <div align="center">
4588 <strong>2.08</strong><br> 10/4/06
4593 <li>Editing can be locked to the selection area</li>
4594 <li>Keyboard editing</li>
4595 <li>Create sequence features from searches</li>
4596 <li>Precalculated annotations can be loaded onto
4598 <li>Features file allows grouping of features</li>
4599 <li>Annotation Colouring scheme added</li>
4600 <li>Smooth fonts off by default - Faster rendering</li>
4601 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4606 <li>Drag & Drop fixed on Linux</li>
4607 <li>Jalview Archive file faster to load/save, sequence
4608 descriptions saved.</li>
4614 <div align="center">
4615 <strong>2.07</strong><br> 12/12/05
4620 <li>PDB Structure Viewer enhanced</li>
4621 <li>Sequence Feature retrieval and display enhanced</li>
4622 <li>Choose to output sequence start-end after sequence
4623 name for file output</li>
4624 <li>Sequence Fetcher WSDBFetch@EBI</li>
4625 <li>Applet can read feature files, PDB files and can be
4626 used for HTML form input</li>
4631 <li>HTML output writes groups and features</li>
4632 <li>Group editing is Control and mouse click</li>
4633 <li>File IO bugs</li>
4639 <div align="center">
4640 <strong>2.06</strong><br> 28/9/05
4645 <li>View annotations in wrapped mode</li>
4646 <li>More options for PCA viewer</li>
4651 <li>GUI bugs resolved</li>
4652 <li>Runs with -nodisplay from command line</li>
4658 <div align="center">
4659 <strong>2.05b</strong><br> 15/9/05
4664 <li>Choose EPS export as lineart or text</li>
4665 <li>Jar files are executable</li>
4666 <li>Can read in Uracil - maps to unknown residue</li>
4671 <li>Known OutOfMemory errors give warning message</li>
4672 <li>Overview window calculated more efficiently</li>
4673 <li>Several GUI bugs resolved</li>
4679 <div align="center">
4680 <strong>2.05</strong><br> 30/8/05
4685 <li>Edit and annotate in "Wrapped" view</li>
4690 <li>Several GUI bugs resolved</li>
4696 <div align="center">
4697 <strong>2.04</strong><br> 24/8/05
4702 <li>Hold down mouse wheel & scroll to change font
4708 <li>Improved JPred client reliability</li>
4709 <li>Improved loading of Jalview files</li>
4715 <div align="center">
4716 <strong>2.03</strong><br> 18/8/05
4721 <li>Set Proxy server name and port in preferences</li>
4722 <li>Multiple URL links from sequence ids</li>
4723 <li>User Defined Colours can have a scheme name and added
4725 <li>Choose to ignore gaps in consensus calculation</li>
4726 <li>Unix users can set default web browser</li>
4727 <li>Runs without GUI for batch processing</li>
4728 <li>Dynamically generated Web Service Menus</li>
4733 <li>InstallAnywhere download for Sparc Solaris</li>
4739 <div align="center">
4740 <strong>2.02</strong><br> 18/7/05
4746 <li>Copy & Paste order of sequences maintains
4747 alignment order.</li>
4753 <div align="center">
4754 <strong>2.01</strong><br> 12/7/05
4759 <li>Use delete key for deleting selection.</li>
4760 <li>Use Mouse wheel to scroll sequences.</li>
4761 <li>Help file updated to describe how to add alignment
4763 <li>Version and build date written to build properties
4765 <li>InstallAnywhere installation will check for updates
4766 at launch of Jalview.</li>
4771 <li>Delete gaps bug fixed.</li>
4772 <li>FileChooser sorts columns.</li>
4773 <li>Can remove groups one by one.</li>
4774 <li>Filechooser icons installed.</li>
4775 <li>Finder ignores return character when searching.
4776 Return key will initiate a search.<br>
4783 <div align="center">
4784 <strong>2.0</strong><br> 20/6/05
4789 <li>New codebase</li>