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>2/04/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302 -->Map 'virtual'
66 codon features shown on protein (or vice versa) for display
67 in alignments, on structure views 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
122 </ul> <em>Build System</em>
125 <!-- JAL-3510 -->Clover updated to 4.4.1
128 <!-- JAL-3513 -->Test code included in Clover coverage
132 <em>Groovy Scripts</em>
135 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
136 to stdout containing the consensus sequence for each
137 alignment in a Jalview session
141 <td align="left" valign="top">
144 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
145 buttons in Feature Settings dialog are clicked when no
149 <!-- JAL-3412 -->ID margins for CDS and Protein views not
150 equal when split frame is first opened
153 <!-- JAL-3296 -->Sequence position numbers in status bar not
154 correct after editing a sequence's start position
157 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
158 with annotation and exceptions thrown when only a few
159 columns shown in wrapped mode
162 <!-- JAL-3386 -->Sequence IDs missing in headless export of
163 wrapped alignment figure with annotations
166 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
167 ID fails with ClassCastException
170 <!-- JAL-3389 -->Chimera session not restored from Jalview
174 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
175 feature settings dialog also selects columns
178 <!-- JAL-3473 -->SpinnerNumberModel causes
179 IllegalArgumentException in some circumstances
182 <!-- JAL-3534 -->Multiple feature settings dialogs can be
186 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
187 alignment window is closed
190 <!-- JAL-3406 -->Credits missing some authors in Jalview
191 help documentation for 2.11.0 release
193 </ul> <em>Java 11 Compatibility issues</em>
196 <!-- JAL-2987 -->OSX - Can't view some search results in
197 PDB/Uniprot search panel
199 </ul> <em>Installer</em>
202 <!-- JAL-3447 -->Jalview should not create file associations
203 for 3D structure files (.pdb, .mmcif. .cif)
205 </ul> <em>Repository and Source Release</em>
208 <!-- JAL-3474 -->removed obsolete .cvsignore files from
212 <!-- JAL-3541 -->Clover report generation running out of
215 </ul> <em>New Known Issues</em>
218 <!-- JAL-3523 -->OSX - Current working directory not
219 preserved when Jalview.app launched with parameters from
223 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
224 clipped in headless figure export when Right Align option
228 <!-- JAL-3542 -->Jalview Installation type always reports
229 'Source' in console output
232 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
233 bamboo server but run fine locally.
239 <td width="60" align="center" nowrap>
240 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
241 <em>04/07/2019</em></strong>
243 <td align="left" valign="top">
246 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
247 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
248 source project) rather than InstallAnywhere
251 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
252 settings, receive over the air updates and launch specific
253 versions via (<a href="https://github.com/threerings/getdown">Three
257 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
258 formats supported by Jalview (including .jvp project files)
261 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
262 arguments and switch between different getdown channels
265 <!-- JAL-3141 -->Backup files created when saving Jalview project
270 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
271 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
273 <!-- JAL-2620 -->Alternative genetic code tables for
274 'Translate as cDNA'</li>
276 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
277 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
280 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
281 implementation that allows updates) used for Sequence Feature collections</li>
283 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
284 features can be filtered and shaded according to any
285 associated attributes (e.g. variant attributes from VCF
286 file, or key-value pairs imported from column 9 of GFF
290 <!-- JAL-2879 -->Feature Attributes and shading schemes
291 stored and restored from Jalview Projects
294 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
295 recognise variant features
298 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
299 sequences (also coloured red by default)
302 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
306 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
307 algorithm (Z-sort/transparency and filter aware)
310 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
316 <!-- JAL-3205 -->Symmetric score matrices for faster
317 tree and PCA calculations
319 <li><strong>Principal Components Analysis Viewer</strong>
322 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
323 and Viewer state saved in Jalview Project
325 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
328 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
332 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
337 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
339 <li><strong>Speed and Efficiency</strong>
342 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
343 multiple groups when working with large alignments
346 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
350 <li><strong>User Interface</strong>
353 <!-- JAL-2933 -->Finder panel remembers last position in each
357 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
358 what is shown)<br />Only visible regions of alignment are shown by
359 default (can be changed in user preferences)
362 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
363 to the Overwrite Dialog
366 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
370 <!-- JAL-1244 -->Status bar shows bounds when dragging a
371 selection region, and gap count when inserting or deleting gaps
374 <!-- JAL-3132 -->Status bar updates over sequence and annotation
378 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
382 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
386 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
389 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
393 <!-- JAL-3181 -->Consistent ordering of links in sequence id
397 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
399 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
403 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
404 <li><strong>Java 11 Support (not yet on general release)</strong>
407 <!-- -->OSX GUI integrations for App menu's 'About' entry and
412 <em>Deprecations</em>
414 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
415 capabilities removed from the Jalview Desktop
417 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
418 unmarshalling has been replaced by JAXB for Jalview projects
419 and XML based data retrieval clients</li>
420 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
421 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
422 </ul> <em>Documentation</em>
424 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
425 not supported in EPS figure export
427 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
428 </ul> <em>Development and Release Processes</em>
431 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
434 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
436 <!-- JAL-3225 -->Eclipse project configuration managed with
440 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
441 Bamboo continuous integration for unattended Test Suite
445 <!-- JAL-2864 -->Memory test suite to detect leaks in common
449 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
453 <!-- JAL-3248 -->Developer documentation migrated to
454 markdown (with HTML rendering)
457 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
460 <!-- JAL-3289 -->New URLs for publishing development
465 <td align="left" valign="top">
468 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
471 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
472 superposition in Jmol fail on Windows
475 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
476 structures for sequences with lots of PDB structures
479 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
483 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
484 project involving multiple views
487 <!-- JAL-3164 -->Overview for complementary view in a linked
488 CDS/Protein alignment is not updated when Hide Columns by
489 Annotation dialog hides columns
492 <!-- JAL-3158 -->Selection highlighting in the complement of a
493 CDS/Protein alignment stops working after making a selection in
494 one view, then making another selection in the other view
497 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
501 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
502 Settings and Jalview Preferences panels
505 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
506 overview with large alignments
509 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
510 region if columns were selected by dragging right-to-left and the
511 mouse moved to the left of the first column
514 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
515 hidden column marker via scale popup menu
518 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
519 doesn't tell users the invalid URL
522 <!-- JAL-2816 -->Tooltips displayed for features filtered by
526 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
527 show cross references or Fetch Database References are shown in
531 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
532 peptide sequence (computed variant shown as p.Res.null)
535 <!-- JAL-2060 -->'Graduated colour' option not offered for
536 manually created features (where feature score is Float.NaN)
539 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
540 when columns are hidden
543 <!-- JAL-3082 -->Regular expression error for '(' in Select
544 Columns by Annotation description
547 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
548 out of Scale or Annotation Panel
551 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
555 <!-- JAL-3074 -->Left/right drag in annotation can scroll
559 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
563 <!-- JAL-3002 -->Column display is out by one after Page Down,
564 Page Up in wrapped mode
567 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
570 <!-- JAL-2932 -->Finder searches in minimised alignments
573 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
574 on opening an alignment
577 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
581 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
582 different groups in the alignment are selected
585 <!-- JAL-2717 -->Internationalised colour scheme names not shown
589 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
593 <!-- JAL-3125 -->Value input for graduated feature colour
594 threshold gets 'unrounded'
597 <!-- JAL-2982 -->PCA image export doesn't respect background
601 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
604 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
607 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
611 <!-- JAL-2964 -->Associate Tree with All Views not restored from
615 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
616 shown in complementary view
619 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
620 without normalisation
623 <!-- JAL-3021 -->Sequence Details report should open positioned at top
627 <!-- JAL-914 -->Help page can be opened twice
630 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
632 </ul> <em>Editing</em>
635 <!-- JAL-2822 -->Start and End should be updated when sequence
636 data at beginning or end of alignment added/removed via 'Edit'
640 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
641 relocate sequence features correctly when start of sequence is
642 removed (Known defect since 2.10)
645 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
646 dialog corrupts dataset sequence
649 <!-- JAL-868 -->Structure colours not updated when associated tree
650 repartitions the alignment view (Regression in 2.10.5)
652 </ul> <em>Datamodel</em>
655 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
656 sequence's End is greater than its length
658 </ul> <em>Bugs fixed for Java 11 Support (not yet on
659 general release)</em>
662 <!-- JAL-3288 -->Menus work properly in split-screen
664 </ul> <em>New Known Defects</em>
667 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
670 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
671 regions of protein alignment.
674 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
675 is restored from a Jalview 2.11 project
678 <!-- JAL-3213 -->Alignment panel height can be too small after
682 <!-- JAL-3240 -->Display is incorrect after removing gapped
683 columns within hidden columns
686 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
687 window after dragging left to select columns to left of visible
691 <!-- JAL-2876 -->Features coloured according to their description
692 string and thresholded by score in earlier versions of Jalview are
693 not shown as thresholded features in 2.11. To workaround please
694 create a Score filter instead.
697 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
699 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
702 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
703 alignments with multiple views can close views unexpectedly
706 <em>Java 11 Specific defects</em>
709 <!-- JAL-3235 -->Jalview Properties file is not sorted
710 alphabetically when saved
716 <td width="60" nowrap>
718 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
721 <td><div align="left">
725 <!-- JAL-3101 -->Default memory for Jalview webstart and
726 InstallAnywhere increased to 1G.
729 <!-- JAL-247 -->Hidden sequence markers and representative
730 sequence bolding included when exporting alignment as EPS,
731 SVG, PNG or HTML. <em>Display is configured via the
732 Format menu, or for command-line use via a Jalview
733 properties file.</em>
736 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
737 API and sequence data now imported as JSON.
740 <!-- JAL-3065 -->Change in recommended way of starting
741 Jalview via a Java command line: add jars in lib directory
742 to CLASSPATH, rather than via the deprecated java.ext.dirs
749 <!-- JAL-3047 -->Support added to execute test suite
750 instrumented with <a href="http://openclover.org/">Open
755 <td><div align="left">
759 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
760 row shown in Feredoxin Structure alignment view of example
764 <!-- JAL-2854 -->Annotation obscures sequences if lots of
765 annotation displayed.
768 <!-- JAL-3107 -->Group conservation/consensus not shown
769 for newly created group when 'Apply to all groups'
773 <!-- JAL-3087 -->Corrupted display when switching to
774 wrapped mode when sequence panel's vertical scrollbar is
778 <!-- JAL-3003 -->Alignment is black in exported EPS file
779 when sequences are selected in exported view.</em>
782 <!-- JAL-3059 -->Groups with different coloured borders
783 aren't rendered with correct colour.
786 <!-- JAL-3092 -->Jalview could hang when importing certain
787 types of knotted RNA secondary structure.
790 <!-- JAL-3095 -->Sequence highlight and selection in
791 trimmed VARNA 2D structure is incorrect for sequences that
795 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
796 annotation when columns are inserted into an alignment,
797 and when exporting as Stockholm flatfile.
800 <!-- JAL-3053 -->Jalview annotation rows containing upper
801 and lower-case 'E' and 'H' do not automatically get
802 treated as RNA secondary structure.
805 <!-- JAL-3106 -->.jvp should be used as default extension
806 (not .jar) when saving a Jalview project file.
809 <!-- JAL-3105 -->Mac Users: closing a window correctly
810 transfers focus to previous window on OSX
813 <em>Java 10 Issues Resolved</em>
816 <!-- JAL-2988 -->OSX - Can't save new files via the File
817 or export menus by typing in a name into the Save dialog
821 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
822 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
823 'look and feel' which has improved compatibility with the
824 latest version of OSX.
831 <td width="60" nowrap>
833 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
834 <em>7/06/2018</em></strong>
837 <td><div align="left">
841 <!-- JAL-2920 -->Use HGVS nomenclature for variant
842 annotation retrieved from Uniprot
845 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
846 onto the Jalview Desktop
850 <td><div align="left">
854 <!-- JAL-3017 -->Cannot import features with multiple
855 variant elements (blocks import of some Uniprot records)
858 <!-- JAL-2997 -->Clustal files with sequence positions in
859 right-hand column parsed correctly
862 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
863 not alignment area in exported graphic
866 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
867 window has input focus
870 <!-- JAL-2992 -->Annotation panel set too high when
871 annotation added to view (Windows)
874 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
875 network connectivity is poor
878 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
879 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
880 the currently open URL and links from a page viewed in
881 Firefox or Chrome on Windows is now fully supported. If
882 you are using Edge, only links in the page can be
883 dragged, and with Internet Explorer, only the currently
884 open URL in the browser can be dropped onto Jalview.</em>
887 <em>New Known Defects</em>
889 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
894 <td width="60" nowrap>
896 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
899 <td><div align="left">
903 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
904 for disabling automatic superposition of multiple
905 structures and open structures in existing views
908 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
909 ID and annotation area margins can be click-dragged to
913 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
917 <!-- JAL-2759 -->Improved performance for large alignments
918 and lots of hidden columns
921 <!-- JAL-2593 -->Improved performance when rendering lots
922 of features (particularly when transparency is disabled)
925 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
926 exchange of Jalview features and Chimera attributes made
932 <td><div align="left">
935 <!-- JAL-2899 -->Structure and Overview aren't updated
936 when Colour By Annotation threshold slider is adjusted
939 <!-- JAL-2778 -->Slow redraw when Overview panel shown
940 overlapping alignment panel
943 <!-- JAL-2929 -->Overview doesn't show end of unpadded
947 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
948 improved: CDS not handled correctly if transcript has no
952 <!-- JAL-2321 -->Secondary structure and temperature
953 factor annotation not added to sequence when local PDB
954 file associated with it by drag'n'drop or structure
958 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
959 dialog doesn't import PDB files dropped on an alignment
962 <!-- JAL-2666 -->Linked scrolling via protein horizontal
963 scroll bar doesn't work for some CDS/Protein views
966 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
967 Java 1.8u153 onwards and Java 1.9u4+.
970 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
971 columns in annotation row
974 <!-- JAL-2913 -->Preferences panel's ID Width control is not
975 honored in batch mode
978 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
979 for structures added to existing Jmol view
982 <!-- JAL-2223 -->'View Mappings' includes duplicate
983 entries after importing project with multiple views
986 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
987 protein sequences via SIFTS from associated PDB entries
988 with negative residue numbers or missing residues fails
991 <!-- JAL-2952 -->Exception when shading sequence with negative
992 Temperature Factor values from annotated PDB files (e.g.
993 as generated by CONSURF)
996 <!-- JAL-2920 -->Uniprot 'sequence variant' features
997 tooltip doesn't include a text description of mutation
1000 <!-- JAL-2922 -->Invert displayed features very slow when
1001 structure and/or overview windows are also shown
1004 <!-- JAL-2954 -->Selecting columns from highlighted regions
1005 very slow for alignments with large numbers of sequences
1008 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1009 with 'StringIndexOutOfBounds'
1012 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1013 platforms running Java 10
1016 <!-- JAL-2960 -->Adding a structure to existing structure
1017 view appears to do nothing because the view is hidden behind the alignment view
1023 <!-- JAL-2926 -->Copy consensus sequence option in applet
1024 should copy the group consensus when popup is opened on it
1030 <!-- JAL-2913 -->Fixed ID width preference is not respected
1033 <em>New Known Defects</em>
1036 <!-- JAL-2973 --> Exceptions occasionally raised when
1037 editing a large alignment and overview is displayed
1040 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1041 repeatedly after a series of edits even when the overview
1042 is no longer reflecting updates
1045 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1046 structures for protein subsequence (if 'Trim Retrieved
1047 Sequences' enabled) or Ensembl isoforms (Workaround in
1048 2.10.4 is to fail back to N&W mapping)
1051 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1052 option gives blank output
1059 <td width="60" nowrap>
1060 <div align="center">
1061 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1064 <td><div align="left">
1065 <ul><li>Updated Certum Codesigning Certificate
1066 (Valid till 30th November 2018)</li></ul></div></td>
1067 <td><div align="left">
1068 <em>Desktop</em><ul>
1070 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1071 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1072 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1073 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1074 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1075 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1076 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1082 <td width="60" nowrap>
1083 <div align="center">
1084 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1087 <td><div align="left">
1091 <!-- JAL-2446 -->Faster and more efficient management and
1092 rendering of sequence features
1095 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1096 429 rate limit request hander
1099 <!-- JAL-2773 -->Structure views don't get updated unless
1100 their colours have changed
1103 <!-- JAL-2495 -->All linked sequences are highlighted for
1104 a structure mousover (Jmol) or selection (Chimera)
1107 <!-- JAL-2790 -->'Cancel' button in progress bar for
1108 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1111 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1112 view from Ensembl locus cross-references
1115 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1119 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1120 feature can be disabled
1123 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1124 PDB easier retrieval of sequences for lists of IDs
1127 <!-- JAL-2758 -->Short names for sequences retrieved from
1133 <li>Groovy interpreter updated to 2.4.12</li>
1134 <li>Example groovy script for generating a matrix of
1135 percent identity scores for current alignment.</li>
1137 <em>Testing and Deployment</em>
1140 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1144 <td><div align="left">
1148 <!-- JAL-2643 -->Pressing tab after updating the colour
1149 threshold text field doesn't trigger an update to the
1153 <!-- JAL-2682 -->Race condition when parsing sequence ID
1157 <!-- JAL-2608 -->Overview windows are also closed when
1158 alignment window is closed
1161 <!-- JAL-2548 -->Export of features doesn't always respect
1165 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1166 takes a long time in Cursor mode
1172 <!-- JAL-2777 -->Structures with whitespace chainCode
1173 cannot be viewed in Chimera
1176 <!-- JAL-2728 -->Protein annotation panel too high in
1180 <!-- JAL-2757 -->Can't edit the query after the server
1181 error warning icon is shown in Uniprot and PDB Free Text
1185 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1188 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1191 <!-- JAL-2739 -->Hidden column marker in last column not
1192 rendered when switching back from Wrapped to normal view
1195 <!-- JAL-2768 -->Annotation display corrupted when
1196 scrolling right in unwapped alignment view
1199 <!-- JAL-2542 -->Existing features on subsequence
1200 incorrectly relocated when full sequence retrieved from
1204 <!-- JAL-2733 -->Last reported memory still shown when
1205 Desktop->Show Memory is unticked (OSX only)
1208 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1209 features of same type and group to be selected for
1213 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1214 alignments when hidden columns are present
1217 <!-- JAL-2392 -->Jalview freezes when loading and
1218 displaying several structures
1221 <!-- JAL-2732 -->Black outlines left after resizing or
1225 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1226 within the Jalview desktop on OSX
1229 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1230 when in wrapped alignment mode
1233 <!-- JAL-2636 -->Scale mark not shown when close to right
1234 hand end of alignment
1237 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1238 each selected sequence do not have correct start/end
1242 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1243 after canceling the Alignment Window's Font dialog
1246 <!-- JAL-2036 -->Show cross-references not enabled after
1247 restoring project until a new view is created
1250 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1251 URL links appears when only default EMBL-EBI link is
1252 configured (since 2.10.2b2)
1255 <!-- JAL-2775 -->Overview redraws whole window when box
1256 position is adjusted
1259 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1260 in a multi-chain structure when viewing alignment
1261 involving more than one chain (since 2.10)
1264 <!-- JAL-2811 -->Double residue highlights in cursor mode
1265 if new selection moves alignment window
1268 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1269 arrow key in cursor mode to pass hidden column marker
1272 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1273 that produces correctly annotated transcripts and products
1276 <!-- JAL-2776 -->Toggling a feature group after first time
1277 doesn't update associated structure view
1280 <em>Applet</em><br />
1283 <!-- JAL-2687 -->Concurrent modification exception when
1284 closing alignment panel
1287 <em>BioJSON</em><br />
1290 <!-- JAL-2546 -->BioJSON export does not preserve
1291 non-positional features
1294 <em>New Known Issues</em>
1297 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1298 sequence features correctly (for many previous versions of
1302 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1303 using cursor in wrapped panel other than top
1306 <!-- JAL-2791 -->Select columns containing feature ignores
1307 graduated colour threshold
1310 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1311 always preserve numbering and sequence features
1314 <em>Known Java 9 Issues</em>
1317 <!-- JAL-2902 -->Groovy Console very slow to open and is
1318 not responsive when entering characters (Webstart, Java
1325 <td width="60" nowrap>
1326 <div align="center">
1327 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1328 <em>2/10/2017</em></strong>
1331 <td><div align="left">
1332 <em>New features in Jalview Desktop</em>
1335 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1337 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1341 <td><div align="left">
1345 <td width="60" nowrap>
1346 <div align="center">
1347 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1348 <em>7/9/2017</em></strong>
1351 <td><div align="left">
1355 <!-- JAL-2588 -->Show gaps in overview window by colouring
1356 in grey (sequences used to be coloured grey, and gaps were
1360 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1364 <!-- JAL-2587 -->Overview updates immediately on increase
1365 in size and progress bar shown as higher resolution
1366 overview is recalculated
1371 <td><div align="left">
1375 <!-- JAL-2664 -->Overview window redraws every hidden
1376 column region row by row
1379 <!-- JAL-2681 -->duplicate protein sequences shown after
1380 retrieving Ensembl crossrefs for sequences from Uniprot
1383 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1384 format setting is unticked
1387 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1388 if group has show boxes format setting unticked
1391 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1392 autoscrolling whilst dragging current selection group to
1393 include sequences and columns not currently displayed
1396 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1397 assemblies are imported via CIF file
1400 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1401 displayed when threshold or conservation colouring is also
1405 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1409 <!-- JAL-2673 -->Jalview continues to scroll after
1410 dragging a selected region off the visible region of the
1414 <!-- JAL-2724 -->Cannot apply annotation based
1415 colourscheme to all groups in a view
1418 <!-- JAL-2511 -->IDs don't line up with sequences
1419 initially after font size change using the Font chooser or
1426 <td width="60" nowrap>
1427 <div align="center">
1428 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1431 <td><div align="left">
1432 <em>Calculations</em>
1436 <!-- JAL-1933 -->Occupancy annotation row shows number of
1437 ungapped positions in each column of the alignment.
1440 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1441 a calculation dialog box
1444 <!-- JAL-2379 -->Revised implementation of PCA for speed
1445 and memory efficiency (~30x faster)
1448 <!-- JAL-2403 -->Revised implementation of sequence
1449 similarity scores as used by Tree, PCA, Shading Consensus
1450 and other calculations
1453 <!-- JAL-2416 -->Score matrices are stored as resource
1454 files within the Jalview codebase
1457 <!-- JAL-2500 -->Trees computed on Sequence Feature
1458 Similarity may have different topology due to increased
1465 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1466 model for alignments and groups
1469 <!-- JAL-384 -->Custom shading schemes created via groovy
1476 <!-- JAL-2526 -->Efficiency improvements for interacting
1477 with alignment and overview windows
1480 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1484 <!-- JAL-2388 -->Hidden columns and sequences can be
1488 <!-- JAL-2611 -->Click-drag in visible area allows fine
1489 adjustment of visible position
1493 <em>Data import/export</em>
1496 <!-- JAL-2535 -->Posterior probability annotation from
1497 Stockholm files imported as sequence associated annotation
1500 <!-- JAL-2507 -->More robust per-sequence positional
1501 annotation input/output via stockholm flatfile
1504 <!-- JAL-2533 -->Sequence names don't include file
1505 extension when importing structure files without embedded
1506 names or PDB accessions
1509 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1510 format sequence substitution matrices
1513 <em>User Interface</em>
1516 <!-- JAL-2447 --> Experimental Features Checkbox in
1517 Desktop's Tools menu to hide or show untested features in
1521 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1522 via Overview or sequence motif search operations
1525 <!-- JAL-2547 -->Amend sequence features dialog box can be
1526 opened by double clicking gaps within sequence feature
1530 <!-- JAL-1476 -->Status bar message shown when not enough
1531 aligned positions were available to create a 3D structure
1535 <em>3D Structure</em>
1538 <!-- JAL-2430 -->Hidden regions in alignment views are not
1539 coloured in linked structure views
1542 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1543 file-based command exchange
1546 <!-- JAL-2375 -->Structure chooser automatically shows
1547 Cached Structures rather than querying the PDBe if
1548 structures are already available for sequences
1551 <!-- JAL-2520 -->Structures imported via URL are cached in
1552 the Jalview project rather than downloaded again when the
1553 project is reopened.
1556 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1557 to transfer Chimera's structure attributes as Jalview
1558 features, and vice-versa (<strong>Experimental
1562 <em>Web Services</em>
1565 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1568 <!-- JAL-2335 -->Filter non-standard amino acids and
1569 nucleotides when submitting to AACon and other MSA
1573 <!-- JAL-2316, -->URLs for viewing database
1574 cross-references provided by identifiers.org and the
1575 EMBL-EBI's MIRIAM DB
1582 <!-- JAL-2344 -->FileFormatI interface for describing and
1583 identifying file formats (instead of String constants)
1586 <!-- JAL-2228 -->FeatureCounter script refactored for
1587 efficiency when counting all displayed features (not
1588 backwards compatible with 2.10.1)
1591 <em>Example files</em>
1594 <!-- JAL-2631 -->Graduated feature colour style example
1595 included in the example feature file
1598 <em>Documentation</em>
1601 <!-- JAL-2339 -->Release notes reformatted for readability
1602 with the built-in Java help viewer
1605 <!-- JAL-1644 -->Find documentation updated with 'search
1606 sequence description' option
1612 <!-- JAL-2485, -->External service integration tests for
1613 Uniprot REST Free Text Search Client
1616 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1619 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1624 <td><div align="left">
1625 <em>Calculations</em>
1628 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1629 matrix - C->R should be '-3'<br />Old matrix restored
1630 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1632 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1633 Jalview's treatment of gaps in PCA and substitution matrix
1634 based Tree calculations.<br /> <br />In earlier versions
1635 of Jalview, gaps matching gaps were penalised, and gaps
1636 matching non-gaps penalised even more. In the PCA
1637 calculation, gaps were actually treated as non-gaps - so
1638 different costs were applied, which meant Jalview's PCAs
1639 were different to those produced by SeqSpace.<br />Jalview
1640 now treats gaps in the same way as SeqSpace (ie it scores
1641 them as 0). <br /> <br />Enter the following in the
1642 Groovy console to restore pre-2.10.2 behaviour:<br />
1643 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1644 // for 2.10.1 mode <br />
1645 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1646 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1647 these settings will affect all subsequent tree and PCA
1648 calculations (not recommended)</em></li>
1650 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1651 scaling of branch lengths for trees computed using
1652 Sequence Feature Similarity.
1655 <!-- JAL-2377 -->PCA calculation could hang when
1656 generating output report when working with highly
1657 redundant alignments
1660 <!-- JAL-2544 --> Sort by features includes features to
1661 right of selected region when gaps present on right-hand
1665 <em>User Interface</em>
1668 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1669 doesn't reselect a specific sequence's associated
1670 annotation after it was used for colouring a view
1673 <!-- JAL-2419 -->Current selection lost if popup menu
1674 opened on a region of alignment without groups
1677 <!-- JAL-2374 -->Popup menu not always shown for regions
1678 of an alignment with overlapping groups
1681 <!-- JAL-2310 -->Finder double counts if both a sequence's
1682 name and description match
1685 <!-- JAL-2370 -->Hiding column selection containing two
1686 hidden regions results in incorrect hidden regions
1689 <!-- JAL-2386 -->'Apply to all groups' setting when
1690 changing colour does not apply Conservation slider value
1694 <!-- JAL-2373 -->Percentage identity and conservation menu
1695 items do not show a tick or allow shading to be disabled
1698 <!-- JAL-2385 -->Conservation shading or PID threshold
1699 lost when base colourscheme changed if slider not visible
1702 <!-- JAL-2547 -->Sequence features shown in tooltip for
1703 gaps before start of features
1706 <!-- JAL-2623 -->Graduated feature colour threshold not
1707 restored to UI when feature colour is edited
1710 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1711 a time when scrolling vertically in wrapped mode.
1714 <!-- JAL-2630 -->Structure and alignment overview update
1715 as graduate feature colour settings are modified via the
1719 <!-- JAL-2034 -->Overview window doesn't always update
1720 when a group defined on the alignment is resized
1723 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1724 wrapped view result in positional status updates
1728 <!-- JAL-2563 -->Status bar doesn't show position for
1729 ambiguous amino acid and nucleotide symbols
1732 <!-- JAL-2602 -->Copy consensus sequence failed if
1733 alignment included gapped columns
1736 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1737 widgets don't permanently disappear
1740 <!-- JAL-2503 -->Cannot select or filter quantitative
1741 annotation that are shown only as column labels (e.g.
1742 T-Coffee column reliability scores)
1745 <!-- JAL-2594 -->Exception thrown if trying to create a
1746 sequence feature on gaps only
1749 <!-- JAL-2504 -->Features created with 'New feature'
1750 button from a Find inherit previously defined feature type
1751 rather than the Find query string
1754 <!-- JAL-2423 -->incorrect title in output window when
1755 exporting tree calculated in Jalview
1758 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1759 and then revealing them reorders sequences on the
1763 <!-- JAL-964 -->Group panel in sequence feature settings
1764 doesn't update to reflect available set of groups after
1765 interactively adding or modifying features
1768 <!-- JAL-2225 -->Sequence Database chooser unusable on
1772 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1773 only excluded gaps in current sequence and ignored
1780 <!-- JAL-2421 -->Overview window visible region moves
1781 erratically when hidden rows or columns are present
1784 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1785 Structure Viewer's colour menu don't correspond to
1789 <!-- JAL-2405 -->Protein specific colours only offered in
1790 colour and group colour menu for protein alignments
1793 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1794 reflect currently selected view or group's shading
1798 <!-- JAL-2624 -->Feature colour thresholds not respected
1799 when rendered on overview and structures when opacity at
1803 <!-- JAL-2589 -->User defined gap colour not shown in
1804 overview when features overlaid on alignment
1807 <!-- JAL-2567 -->Feature settings for different views not
1808 recovered correctly from Jalview project file
1811 <!-- JAL-2256 -->Feature colours in overview when first opened
1812 (automatically via preferences) are different to the main
1816 <em>Data import/export</em>
1819 <!-- JAL-2576 -->Very large alignments take a long time to
1823 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1824 added after a sequence was imported are not written to
1828 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1829 when importing RNA secondary structure via Stockholm
1832 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1833 not shown in correct direction for simple pseudoknots
1836 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1837 with lightGray or darkGray via features file (but can
1841 <!-- JAL-2383 -->Above PID colour threshold not recovered
1842 when alignment view imported from project
1845 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1846 structure and sequences extracted from structure files
1847 imported via URL and viewed in Jmol
1850 <!-- JAL-2520 -->Structures loaded via URL are saved in
1851 Jalview Projects rather than fetched via URL again when
1852 the project is loaded and the structure viewed
1855 <em>Web Services</em>
1858 <!-- JAL-2519 -->EnsemblGenomes example failing after
1859 release of Ensembl v.88
1862 <!-- JAL-2366 -->Proxy server address and port always
1863 appear enabled in Preferences->Connections
1866 <!-- JAL-2461 -->DAS registry not found exceptions
1867 removed from console output
1870 <!-- JAL-2582 -->Cannot retrieve protein products from
1871 Ensembl by Peptide ID
1874 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1875 created from SIFTs, and spurious 'Couldn't open structure
1876 in Chimera' errors raised after April 2017 update (problem
1877 due to 'null' string rather than empty string used for
1878 residues with no corresponding PDB mapping).
1881 <em>Application UI</em>
1884 <!-- JAL-2361 -->User Defined Colours not added to Colour
1888 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1889 case' residues (button in colourscheme editor debugged and
1890 new documentation and tooltips added)
1893 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1894 doesn't restore group-specific text colour thresholds
1897 <!-- JAL-2243 -->Feature settings panel does not update as
1898 new features are added to alignment
1901 <!-- JAL-2532 -->Cancel in feature settings reverts
1902 changes to feature colours via the Amend features dialog
1905 <!-- JAL-2506 -->Null pointer exception when attempting to
1906 edit graduated feature colour via amend features dialog
1910 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1911 selection menu changes colours of alignment views
1914 <!-- JAL-2426 -->Spurious exceptions in console raised
1915 from alignment calculation workers after alignment has
1919 <!-- JAL-1608 -->Typo in selection popup menu - Create
1920 groups now 'Create Group'
1923 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1924 Create/Undefine group doesn't always work
1927 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1928 shown again after pressing 'Cancel'
1931 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1932 adjusts start position in wrap mode
1935 <!-- JAL-2563 -->Status bar doesn't show positions for
1936 ambiguous amino acids
1939 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1940 CDS/Protein view after CDS sequences added for aligned
1944 <!-- JAL-2592 -->User defined colourschemes called 'User
1945 Defined' don't appear in Colours menu
1951 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1952 score models doesn't always result in an updated PCA plot
1955 <!-- JAL-2442 -->Features not rendered as transparent on
1956 overview or linked structure view
1959 <!-- JAL-2372 -->Colour group by conservation doesn't
1963 <!-- JAL-2517 -->Hitting Cancel after applying
1964 user-defined colourscheme doesn't restore original
1971 <!-- JAL-2314 -->Unit test failure:
1972 jalview.ws.jabaws.RNAStructExportImport setup fails
1975 <!-- JAL-2307 -->Unit test failure:
1976 jalview.ws.sifts.SiftsClientTest due to compatibility
1977 problems with deep array comparison equality asserts in
1978 successive versions of TestNG
1981 <!-- JAL-2479 -->Relocated StructureChooserTest and
1982 ParameterUtilsTest Unit tests to Network suite
1985 <em>New Known Issues</em>
1988 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1989 phase after a sequence motif find operation
1992 <!-- JAL-2550 -->Importing annotation file with rows
1993 containing just upper and lower case letters are
1994 interpreted as WUSS RNA secondary structure symbols
1997 <!-- JAL-2590 -->Cannot load and display Newick trees
1998 reliably from eggnog Ortholog database
2001 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2002 containing features of type Highlight' when 'B' is pressed
2003 to mark columns containing highlighted regions.
2006 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2007 doesn't always add secondary structure annotation.
2012 <td width="60" nowrap>
2013 <div align="center">
2014 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2017 <td><div align="left">
2021 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2022 for all consensus calculations
2025 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2028 <li>Updated Jalview's Certum code signing certificate
2031 <em>Application</em>
2034 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2035 set of database cross-references, sorted alphabetically
2038 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2039 from database cross references. Users with custom links
2040 will receive a <a href="webServices/urllinks.html#warning">warning
2041 dialog</a> asking them to update their preferences.
2044 <!-- JAL-2287-->Cancel button and escape listener on
2045 dialog warning user about disconnecting Jalview from a
2049 <!-- JAL-2320-->Jalview's Chimera control window closes if
2050 the Chimera it is connected to is shut down
2053 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2054 columns menu item to mark columns containing highlighted
2055 regions (e.g. from structure selections or results of a
2059 <!-- JAL-2284-->Command line option for batch-generation
2060 of HTML pages rendering alignment data with the BioJS
2070 <!-- JAL-2286 -->Columns with more than one modal residue
2071 are not coloured or thresholded according to percent
2072 identity (first observed in Jalview 2.8.2)
2075 <!-- JAL-2301 -->Threonine incorrectly reported as not
2079 <!-- JAL-2318 -->Updates to documentation pages (above PID
2080 threshold, amino acid properties)
2083 <!-- JAL-2292 -->Lower case residues in sequences are not
2084 reported as mapped to residues in a structure file in the
2088 <!--JAL-2324 -->Identical features with non-numeric scores
2089 could be added multiple times to a sequence
2092 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2093 bond features shown as two highlighted residues rather
2094 than a range in linked structure views, and treated
2095 correctly when selecting and computing trees from features
2098 <!-- JAL-2281-->Custom URL links for database
2099 cross-references are matched to database name regardless
2104 <em>Application</em>
2107 <!-- JAL-2282-->Custom URL links for specific database
2108 names without regular expressions also offer links from
2112 <!-- JAL-2315-->Removing a single configured link in the
2113 URL links pane in Connections preferences doesn't actually
2114 update Jalview configuration
2117 <!-- JAL-2272-->CTRL-Click on a selected region to open
2118 the alignment area popup menu doesn't work on El-Capitan
2121 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2122 files with similarly named sequences if dropped onto the
2126 <!-- JAL-2312 -->Additional mappings are shown for PDB
2127 entries where more chains exist in the PDB accession than
2128 are reported in the SIFTS file
2131 <!-- JAL-2317-->Certain structures do not get mapped to
2132 the structure view when displayed with Chimera
2135 <!-- JAL-2317-->No chains shown in the Chimera view
2136 panel's View->Show Chains submenu
2139 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2140 work for wrapped alignment views
2143 <!--JAL-2197 -->Rename UI components for running JPred
2144 predictions from 'JNet' to 'JPred'
2147 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2148 corrupted when annotation panel vertical scroll is not at
2149 first annotation row
2152 <!--JAL-2332 -->Attempting to view structure for Hen
2153 lysozyme results in a PDB Client error dialog box
2156 <!-- JAL-2319 -->Structure View's mapping report switched
2157 ranges for PDB and sequence for SIFTS
2160 SIFTS 'Not_Observed' residues mapped to non-existant
2164 <!-- <em>New Known Issues</em>
2171 <td width="60" nowrap>
2172 <div align="center">
2173 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2174 <em>25/10/2016</em></strong>
2177 <td><em>Application</em>
2179 <li>3D Structure chooser opens with 'Cached structures'
2180 view if structures already loaded</li>
2181 <li>Progress bar reports models as they are loaded to
2182 structure views</li>
2188 <li>Colour by conservation always enabled and no tick
2189 shown in menu when BLOSUM or PID shading applied</li>
2190 <li>FER1_ARATH and FER2_ARATH labels were switched in
2191 example sequences/projects/trees</li>
2193 <em>Application</em>
2195 <li>Jalview projects with views of local PDB structure
2196 files saved on Windows cannot be opened on OSX</li>
2197 <li>Multiple structure views can be opened and superposed
2198 without timeout for structures with multiple models or
2199 multiple sequences in alignment</li>
2200 <li>Cannot import or associated local PDB files without a
2201 PDB ID HEADER line</li>
2202 <li>RMSD is not output in Jmol console when superposition
2204 <li>Drag and drop of URL from Browser fails for Linux and
2205 OSX versions earlier than El Capitan</li>
2206 <li>ENA client ignores invalid content from ENA server</li>
2207 <li>Exceptions are not raised in console when ENA client
2208 attempts to fetch non-existent IDs via Fetch DB Refs UI
2210 <li>Exceptions are not raised in console when a new view
2211 is created on the alignment</li>
2212 <li>OSX right-click fixed for group selections: CMD-click
2213 to insert/remove gaps in groups and CTRL-click to open group
2216 <em>Build and deployment</em>
2218 <li>URL link checker now copes with multi-line anchor
2221 <em>New Known Issues</em>
2223 <li>Drag and drop from URL links in browsers do not work
2230 <td width="60" nowrap>
2231 <div align="center">
2232 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2235 <td><em>General</em>
2238 <!-- JAL-2124 -->Updated Spanish translations.
2241 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2242 for importing structure data to Jalview. Enables mmCIF and
2246 <!-- JAL-192 --->Alignment ruler shows positions relative to
2250 <!-- JAL-2202 -->Position/residue shown in status bar when
2251 mousing over sequence associated annotation
2254 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2258 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2259 '()', canonical '[]' and invalid '{}' base pair populations
2263 <!-- JAL-2092 -->Feature settings popup menu options for
2264 showing or hiding columns containing a feature
2267 <!-- JAL-1557 -->Edit selected group by double clicking on
2268 group and sequence associated annotation labels
2271 <!-- JAL-2236 -->Sequence name added to annotation label in
2272 select/hide columns by annotation and colour by annotation
2276 </ul> <em>Application</em>
2279 <!-- JAL-2050-->Automatically hide introns when opening a
2280 gene/transcript view
2283 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2287 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2288 structure mappings with the EMBL-EBI PDBe SIFTS database
2291 <!-- JAL-2079 -->Updated download sites used for Rfam and
2292 Pfam sources to xfam.org
2295 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2298 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2299 over sequences in Jalview
2302 <!-- JAL-2027-->Support for reverse-complement coding
2303 regions in ENA and EMBL
2306 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2307 for record retrieval via ENA rest API
2310 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2314 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2315 groovy script execution
2318 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2319 alignment window's Calculate menu
2322 <!-- JAL-1812 -->Allow groovy scripts that call
2323 Jalview.getAlignFrames() to run in headless mode
2326 <!-- JAL-2068 -->Support for creating new alignment
2327 calculation workers from groovy scripts
2330 <!-- JAL-1369 --->Store/restore reference sequence in
2334 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2335 associations are now saved/restored from project
2338 <!-- JAL-1993 -->Database selection dialog always shown
2339 before sequence fetcher is opened
2342 <!-- JAL-2183 -->Double click on an entry in Jalview's
2343 database chooser opens a sequence fetcher
2346 <!-- JAL-1563 -->Free-text search client for UniProt using
2347 the UniProt REST API
2350 <!-- JAL-2168 -->-nonews command line parameter to prevent
2351 the news reader opening
2354 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2355 querying stored in preferences
2358 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2362 <!-- JAL-1977-->Tooltips shown on database chooser
2365 <!-- JAL-391 -->Reverse complement function in calculate
2366 menu for nucleotide sequences
2369 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2370 and feature counts preserves alignment ordering (and
2371 debugged for complex feature sets).
2374 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2375 viewing structures with Jalview 2.10
2378 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2379 genome, transcript CCDS and gene ids via the Ensembl and
2380 Ensembl Genomes REST API
2383 <!-- JAL-2049 -->Protein sequence variant annotation
2384 computed for 'sequence_variant' annotation on CDS regions
2388 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2392 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2393 Ref Fetcher fails to match, or otherwise updates sequence
2394 data from external database records.
2397 <!-- JAL-2154 -->Revised Jalview Project format for
2398 efficient recovery of sequence coding and alignment
2399 annotation relationships.
2401 </ul> <!-- <em>Applet</em>
2412 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2416 <!-- JAL-2018-->Export features in Jalview format (again)
2417 includes graduated colourschemes
2420 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2421 working with big alignments and lots of hidden columns
2424 <!-- JAL-2053-->Hidden column markers not always rendered
2425 at right of alignment window
2428 <!-- JAL-2067 -->Tidied up links in help file table of
2432 <!-- JAL-2072 -->Feature based tree calculation not shown
2436 <!-- JAL-2075 -->Hidden columns ignored during feature
2437 based tree calculation
2440 <!-- JAL-2065 -->Alignment view stops updating when show
2441 unconserved enabled for group on alignment
2444 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2448 <!-- JAL-2146 -->Alignment column in status incorrectly
2449 shown as "Sequence position" when mousing over
2453 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2454 hidden columns present
2457 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2458 user created annotation added to alignment
2461 <!-- JAL-1841 -->RNA Structure consensus only computed for
2462 '()' base pair annotation
2465 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2466 in zero scores for all base pairs in RNA Structure
2470 <!-- JAL-2174-->Extend selection with columns containing
2474 <!-- JAL-2275 -->Pfam format writer puts extra space at
2475 beginning of sequence
2478 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2482 <!-- JAL-2238 -->Cannot create groups on an alignment from
2483 from a tree when t-coffee scores are shown
2486 <!-- JAL-1836,1967 -->Cannot import and view PDB
2487 structures with chains containing negative resnums (4q4h)
2490 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2494 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2495 to Clustal, PIR and PileUp output
2498 <!-- JAL-2008 -->Reordering sequence features that are
2499 not visible causes alignment window to repaint
2502 <!-- JAL-2006 -->Threshold sliders don't work in
2503 graduated colour and colour by annotation row for e-value
2504 scores associated with features and annotation rows
2507 <!-- JAL-1797 -->amino acid physicochemical conservation
2508 calculation should be case independent
2511 <!-- JAL-2173 -->Remove annotation also updates hidden
2515 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2516 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2517 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2520 <!-- JAL-2065 -->Null pointer exceptions and redraw
2521 problems when reference sequence defined and 'show
2522 non-conserved' enabled
2525 <!-- JAL-1306 -->Quality and Conservation are now shown on
2526 load even when Consensus calculation is disabled
2529 <!-- JAL-1932 -->Remove right on penultimate column of
2530 alignment does nothing
2533 <em>Application</em>
2536 <!-- JAL-1552-->URLs and links can't be imported by
2537 drag'n'drop on OSX when launched via webstart (note - not
2538 yet fixed for El Capitan)
2541 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2542 output when running on non-gb/us i18n platforms
2545 <!-- JAL-1944 -->Error thrown when exporting a view with
2546 hidden sequences as flat-file alignment
2549 <!-- JAL-2030-->InstallAnywhere distribution fails when
2553 <!-- JAL-2080-->Jalview very slow to launch via webstart
2554 (also hotfix for 2.9.0b2)
2557 <!-- JAL-2085 -->Cannot save project when view has a
2558 reference sequence defined
2561 <!-- JAL-1011 -->Columns are suddenly selected in other
2562 alignments and views when revealing hidden columns
2565 <!-- JAL-1989 -->Hide columns not mirrored in complement
2566 view in a cDNA/Protein splitframe
2569 <!-- JAL-1369 -->Cannot save/restore representative
2570 sequence from project when only one sequence is
2574 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2575 in Structure Chooser
2578 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2579 structure consensus didn't refresh annotation panel
2582 <!-- JAL-1962 -->View mapping in structure view shows
2583 mappings between sequence and all chains in a PDB file
2586 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2587 dialogs format columns correctly, don't display array
2588 data, sort columns according to type
2591 <!-- JAL-1975 -->Export complete shown after destination
2592 file chooser is cancelled during an image export
2595 <!-- JAL-2025 -->Error when querying PDB Service with
2596 sequence name containing special characters
2599 <!-- JAL-2024 -->Manual PDB structure querying should be
2603 <!-- JAL-2104 -->Large tooltips with broken HTML
2604 formatting don't wrap
2607 <!-- JAL-1128 -->Figures exported from wrapped view are
2608 truncated so L looks like I in consensus annotation
2611 <!-- JAL-2003 -->Export features should only export the
2612 currently displayed features for the current selection or
2616 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2617 after fetching cross-references, and restoring from
2621 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2622 followed in the structure viewer
2625 <!-- JAL-2163 -->Titles for individual alignments in
2626 splitframe not restored from project
2629 <!-- JAL-2145 -->missing autocalculated annotation at
2630 trailing end of protein alignment in transcript/product
2631 splitview when pad-gaps not enabled by default
2634 <!-- JAL-1797 -->amino acid physicochemical conservation
2638 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2639 article has been read (reopened issue due to
2640 internationalisation problems)
2643 <!-- JAL-1960 -->Only offer PDB structures in structure
2644 viewer based on sequence name, PDB and UniProt
2649 <!-- JAL-1976 -->No progress bar shown during export of
2653 <!-- JAL-2213 -->Structures not always superimposed after
2654 multiple structures are shown for one or more sequences.
2657 <!-- JAL-1370 -->Reference sequence characters should not
2658 be replaced with '.' when 'Show unconserved' format option
2662 <!-- JAL-1823 -->Cannot specify chain code when entering
2663 specific PDB id for sequence
2666 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2667 'Export hidden sequences' is enabled, but 'export hidden
2668 columns' is disabled.
2671 <!--JAL-2026-->Best Quality option in structure chooser
2672 selects lowest rather than highest resolution structures
2676 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2677 to sequence mapping in 'View Mappings' report
2680 <!-- JAL-2284 -->Unable to read old Jalview projects that
2681 contain non-XML data added after Jalvew wrote project.
2684 <!-- JAL-2118 -->Newly created annotation row reorders
2685 after clicking on it to create new annotation for a
2689 <!-- JAL-1980 -->Null Pointer Exception raised when
2690 pressing Add on an orphaned cut'n'paste window.
2692 <!-- may exclude, this is an external service stability issue JAL-1941
2693 -- > RNA 3D structure not added via DSSR service</li> -->
2698 <!-- JAL-2151 -->Incorrect columns are selected when
2699 hidden columns present before start of sequence
2702 <!-- JAL-1986 -->Missing dependencies on applet pages
2706 <!-- JAL-1947 -->Overview pixel size changes when
2707 sequences are hidden in applet
2710 <!-- JAL-1996 -->Updated instructions for applet
2711 deployment on examples pages.
2718 <td width="60" nowrap>
2719 <div align="center">
2720 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2721 <em>16/10/2015</em></strong>
2724 <td><em>General</em>
2726 <li>Time stamps for signed Jalview application and applet
2731 <em>Application</em>
2733 <li>Duplicate group consensus and conservation rows
2734 shown when tree is partitioned</li>
2735 <li>Erratic behaviour when tree partitions made with
2736 multiple cDNA/Protein split views</li>
2742 <td width="60" nowrap>
2743 <div align="center">
2744 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2745 <em>8/10/2015</em></strong>
2748 <td><em>General</em>
2750 <li>Updated Spanish translations of localized text for
2752 </ul> <em>Application</em>
2754 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2755 <li>Signed OSX InstallAnywhere installer<br></li>
2756 <li>Support for per-sequence based annotations in BioJSON</li>
2757 </ul> <em>Applet</em>
2759 <li>Split frame example added to applet examples page</li>
2760 </ul> <em>Build and Deployment</em>
2763 <!-- JAL-1888 -->New ant target for running Jalview's test
2771 <li>Mapping of cDNA to protein in split frames
2772 incorrect when sequence start > 1</li>
2773 <li>Broken images in filter column by annotation dialog
2775 <li>Feature colours not parsed from features file</li>
2776 <li>Exceptions and incomplete link URLs recovered when
2777 loading a features file containing HTML tags in feature
2781 <em>Application</em>
2783 <li>Annotations corrupted after BioJS export and
2785 <li>Incorrect sequence limits after Fetch DB References
2786 with 'trim retrieved sequences'</li>
2787 <li>Incorrect warning about deleting all data when
2788 deleting selected columns</li>
2789 <li>Patch to build system for shipping properly signed
2790 JNLP templates for webstart launch</li>
2791 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2792 unreleased structures for download or viewing</li>
2793 <li>Tab/space/return keystroke operation of EMBL-PDBe
2794 fetcher/viewer dialogs works correctly</li>
2795 <li>Disabled 'minimise' button on Jalview windows
2796 running on OSX to workaround redraw hang bug</li>
2797 <li>Split cDNA/Protein view position and geometry not
2798 recovered from jalview project</li>
2799 <li>Initial enabled/disabled state of annotation menu
2800 sorter 'show autocalculated first/last' corresponds to
2802 <li>Restoring of Clustal, RNA Helices and T-Coffee
2803 color schemes from BioJSON</li>
2807 <li>Reorder sequences mirrored in cDNA/Protein split
2809 <li>Applet with Jmol examples not loading correctly</li>
2815 <td><div align="center">
2816 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2818 <td><em>General</em>
2820 <li>Linked visualisation and analysis of DNA and Protein
2823 <li>Translated cDNA alignments shown as split protein
2824 and DNA alignment views</li>
2825 <li>Codon consensus annotation for linked protein and
2826 cDNA alignment views</li>
2827 <li>Link cDNA or Protein product sequences by loading
2828 them onto Protein or cDNA alignments</li>
2829 <li>Reconstruct linked cDNA alignment from aligned
2830 protein sequences</li>
2833 <li>Jmol integration updated to Jmol v14.2.14</li>
2834 <li>Import and export of Jalview alignment views as <a
2835 href="features/bioJsonFormat.html">BioJSON</a></li>
2836 <li>New alignment annotation file statements for
2837 reference sequences and marking hidden columns</li>
2838 <li>Reference sequence based alignment shading to
2839 highlight variation</li>
2840 <li>Select or hide columns according to alignment
2842 <li>Find option for locating sequences by description</li>
2843 <li>Conserved physicochemical properties shown in amino
2844 acid conservation row</li>
2845 <li>Alignments can be sorted by number of RNA helices</li>
2846 </ul> <em>Application</em>
2848 <li>New cDNA/Protein analysis capabilities
2850 <li>Get Cross-References should open a Split Frame
2851 view with cDNA/Protein</li>
2852 <li>Detect when nucleotide sequences and protein
2853 sequences are placed in the same alignment</li>
2854 <li>Split cDNA/Protein views are saved in Jalview
2859 <li>Use REST API to talk to Chimera</li>
2860 <li>Selected regions in Chimera are highlighted in linked
2861 Jalview windows</li>
2863 <li>VARNA RNA viewer updated to v3.93</li>
2864 <li>VARNA views are saved in Jalview Projects</li>
2865 <li>Pseudoknots displayed as Jalview RNA annotation can
2866 be shown in VARNA</li>
2868 <li>Make groups for selection uses marked columns as well
2869 as the active selected region</li>
2871 <li>Calculate UPGMA and NJ trees using sequence feature
2873 <li>New Export options
2875 <li>New Export Settings dialog to control hidden
2876 region export in flat file generation</li>
2878 <li>Export alignment views for display with the <a
2879 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2881 <li>Export scrollable SVG in HTML page</li>
2882 <li>Optional embedding of BioJSON data when exporting
2883 alignment figures to HTML</li>
2885 <li>3D structure retrieval and display
2887 <li>Free text and structured queries with the PDBe
2889 <li>PDBe Search API based discovery and selection of
2890 PDB structures for a sequence set</li>
2894 <li>JPred4 employed for protein secondary structure
2896 <li>Hide Insertions menu option to hide unaligned columns
2897 for one or a group of sequences</li>
2898 <li>Automatically hide insertions in alignments imported
2899 from the JPred4 web server</li>
2900 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2901 system on OSX<br />LGPL libraries courtesy of <a
2902 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2904 <li>changed 'View nucleotide structure' submenu to 'View
2905 VARNA 2D Structure'</li>
2906 <li>change "View protein structure" menu option to "3D
2909 </ul> <em>Applet</em>
2911 <li>New layout for applet example pages</li>
2912 <li>New parameters to enable SplitFrame view
2913 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2914 <li>New example demonstrating linked viewing of cDNA and
2915 Protein alignments</li>
2916 </ul> <em>Development and deployment</em>
2918 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2919 <li>Include installation type and git revision in build
2920 properties and console log output</li>
2921 <li>Jalview Github organisation, and new github site for
2922 storing BioJsMSA Templates</li>
2923 <li>Jalview's unit tests now managed with TestNG</li>
2926 <!-- <em>General</em>
2928 </ul> --> <!-- issues resolved --> <em>Application</em>
2930 <li>Escape should close any open find dialogs</li>
2931 <li>Typo in select-by-features status report</li>
2932 <li>Consensus RNA secondary secondary structure
2933 predictions are not highlighted in amber</li>
2934 <li>Missing gap character in v2.7 example file means
2935 alignment appears unaligned when pad-gaps is not enabled</li>
2936 <li>First switch to RNA Helices colouring doesn't colour
2937 associated structure views</li>
2938 <li>ID width preference option is greyed out when auto
2939 width checkbox not enabled</li>
2940 <li>Stopped a warning dialog from being shown when
2941 creating user defined colours</li>
2942 <li>'View Mapping' in structure viewer shows sequence
2943 mappings for just that viewer's sequences</li>
2944 <li>Workaround for superposing PDB files containing
2945 multiple models in Chimera</li>
2946 <li>Report sequence position in status bar when hovering
2947 over Jmol structure</li>
2948 <li>Cannot output gaps as '.' symbols with Selection ->
2949 output to text box</li>
2950 <li>Flat file exports of alignments with hidden columns
2951 have incorrect sequence start/end</li>
2952 <li>'Aligning' a second chain to a Chimera structure from
2954 <li>Colour schemes applied to structure viewers don't
2955 work for nucleotide</li>
2956 <li>Loading/cut'n'pasting an empty or invalid file leads
2957 to a grey/invisible alignment window</li>
2958 <li>Exported Jpred annotation from a sequence region
2959 imports to different position</li>
2960 <li>Space at beginning of sequence feature tooltips shown
2961 on some platforms</li>
2962 <li>Chimera viewer 'View | Show Chain' menu is not
2964 <li>'New View' fails with a Null Pointer Exception in
2965 console if Chimera has been opened</li>
2966 <li>Mouseover to Chimera not working</li>
2967 <li>Miscellaneous ENA XML feature qualifiers not
2969 <li>NPE in annotation renderer after 'Extract Scores'</li>
2970 <li>If two structures in one Chimera window, mouseover of
2971 either sequence shows on first structure</li>
2972 <li>'Show annotations' options should not make
2973 non-positional annotations visible</li>
2974 <li>Subsequence secondary structure annotation not shown
2975 in right place after 'view flanking regions'</li>
2976 <li>File Save As type unset when current file format is
2978 <li>Save as '.jar' option removed for saving Jalview
2980 <li>Colour by Sequence colouring in Chimera more
2982 <li>Cannot 'add reference annotation' for a sequence in
2983 several views on same alignment</li>
2984 <li>Cannot show linked products for EMBL / ENA records</li>
2985 <li>Jalview's tooltip wraps long texts containing no
2987 </ul> <em>Applet</em>
2989 <li>Jmol to JalviewLite mouseover/link not working</li>
2990 <li>JalviewLite can't import sequences with ID
2991 descriptions containing angle brackets</li>
2992 </ul> <em>General</em>
2994 <li>Cannot export and reimport RNA secondary structure
2995 via jalview annotation file</li>
2996 <li>Random helix colour palette for colour by annotation
2997 with RNA secondary structure</li>
2998 <li>Mouseover to cDNA from STOP residue in protein
2999 translation doesn't work.</li>
3000 <li>hints when using the select by annotation dialog box</li>
3001 <li>Jmol alignment incorrect if PDB file has alternate CA
3003 <li>FontChooser message dialog appears to hang after
3004 choosing 1pt font</li>
3005 <li>Peptide secondary structure incorrectly imported from
3006 annotation file when annotation display text includes 'e' or
3008 <li>Cannot set colour of new feature type whilst creating
3010 <li>cDNA translation alignment should not be sequence
3011 order dependent</li>
3012 <li>'Show unconserved' doesn't work for lower case
3014 <li>Nucleotide ambiguity codes involving R not recognised</li>
3015 </ul> <em>Deployment and Documentation</em>
3017 <li>Applet example pages appear different to the rest of
3018 www.jalview.org</li>
3019 </ul> <em>Application Known issues</em>
3021 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3022 <li>Misleading message appears after trying to delete
3024 <li>Jalview icon not shown in dock after InstallAnywhere
3025 version launches</li>
3026 <li>Fetching EMBL reference for an RNA sequence results
3027 fails with a sequence mismatch</li>
3028 <li>Corrupted or unreadable alignment display when
3029 scrolling alignment to right</li>
3030 <li>ArrayIndexOutOfBoundsException thrown when remove
3031 empty columns called on alignment with ragged gapped ends</li>
3032 <li>auto calculated alignment annotation rows do not get
3033 placed above or below non-autocalculated rows</li>
3034 <li>Jalview dekstop becomes sluggish at full screen in
3035 ultra-high resolution</li>
3036 <li>Cannot disable consensus calculation independently of
3037 quality and conservation</li>
3038 <li>Mouseover highlighting between cDNA and protein can
3039 become sluggish with more than one splitframe shown</li>
3040 </ul> <em>Applet Known Issues</em>
3042 <li>Core PDB parsing code requires Jmol</li>
3043 <li>Sequence canvas panel goes white when alignment
3044 window is being resized</li>
3050 <td><div align="center">
3051 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3053 <td><em>General</em>
3055 <li>Updated Java code signing certificate donated by
3057 <li>Features and annotation preserved when performing
3058 pairwise alignment</li>
3059 <li>RNA pseudoknot annotation can be
3060 imported/exported/displayed</li>
3061 <li>'colour by annotation' can colour by RNA and
3062 protein secondary structure</li>
3063 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3064 post-hoc with 2.9 release</em>)
3067 </ul> <em>Application</em>
3069 <li>Extract and display secondary structure for sequences
3070 with 3D structures</li>
3071 <li>Support for parsing RNAML</li>
3072 <li>Annotations menu for layout
3074 <li>sort sequence annotation rows by alignment</li>
3075 <li>place sequence annotation above/below alignment
3078 <li>Output in Stockholm format</li>
3079 <li>Internationalisation: improved Spanish (es)
3081 <li>Structure viewer preferences tab</li>
3082 <li>Disorder and Secondary Structure annotation tracks
3083 shared between alignments</li>
3084 <li>UCSF Chimera launch and linked highlighting from
3086 <li>Show/hide all sequence associated annotation rows for
3087 all or current selection</li>
3088 <li>disorder and secondary structure predictions
3089 available as dataset annotation</li>
3090 <li>Per-sequence rna helices colouring</li>
3093 <li>Sequence database accessions imported when fetching
3094 alignments from Rfam</li>
3095 <li>update VARNA version to 3.91</li>
3097 <li>New groovy scripts for exporting aligned positions,
3098 conservation values, and calculating sum of pairs scores.</li>
3099 <li>Command line argument to set default JABAWS server</li>
3100 <li>include installation type in build properties and
3101 console log output</li>
3102 <li>Updated Jalview project format to preserve dataset
3106 <!-- issues resolved --> <em>Application</em>
3108 <li>Distinguish alignment and sequence associated RNA
3109 structure in structure->view->VARNA</li>
3110 <li>Raise dialog box if user deletes all sequences in an
3112 <li>Pressing F1 results in documentation opening twice</li>
3113 <li>Sequence feature tooltip is wrapped</li>
3114 <li>Double click on sequence associated annotation
3115 selects only first column</li>
3116 <li>Redundancy removal doesn't result in unlinked
3117 leaves shown in tree</li>
3118 <li>Undos after several redundancy removals don't undo
3120 <li>Hide sequence doesn't hide associated annotation</li>
3121 <li>User defined colours dialog box too big to fit on
3122 screen and buttons not visible</li>
3123 <li>author list isn't updated if already written to
3124 Jalview properties</li>
3125 <li>Popup menu won't open after retrieving sequence
3127 <li>File open window for associate PDB doesn't open</li>
3128 <li>Left-then-right click on a sequence id opens a
3129 browser search window</li>
3130 <li>Cannot open sequence feature shading/sort popup menu
3131 in feature settings dialog</li>
3132 <li>better tooltip placement for some areas of Jalview
3134 <li>Allow addition of JABAWS Server which doesn't
3135 pass validation</li>
3136 <li>Web services parameters dialog box is too large to
3138 <li>Muscle nucleotide alignment preset obscured by
3140 <li>JABAWS preset submenus don't contain newly
3141 defined user preset</li>
3142 <li>MSA web services warns user if they were launched
3143 with invalid input</li>
3144 <li>Jalview cannot contact DAS Registy when running on
3147 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3148 'Superpose with' submenu not shown when new view
3152 </ul> <!-- <em>Applet</em>
3154 </ul> <em>General</em>
3156 </ul>--> <em>Deployment and Documentation</em>
3158 <li>2G and 1G options in launchApp have no effect on
3159 memory allocation</li>
3160 <li>launchApp service doesn't automatically open
3161 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3163 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3164 InstallAnywhere reports cannot find valid JVM when Java
3165 1.7_055 is available
3167 </ul> <em>Application Known issues</em>
3170 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3171 corrupted or unreadable alignment display when scrolling
3175 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3176 retrieval fails but progress bar continues for DAS retrieval
3177 with large number of ID
3180 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3181 flatfile output of visible region has incorrect sequence
3185 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3186 rna structure consensus doesn't update when secondary
3187 structure tracks are rearranged
3190 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3191 invalid rna structure positional highlighting does not
3192 highlight position of invalid base pairs
3195 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3196 out of memory errors are not raised when saving Jalview
3197 project from alignment window file menu
3200 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3201 Switching to RNA Helices colouring doesn't propagate to
3205 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3206 colour by RNA Helices not enabled when user created
3207 annotation added to alignment
3210 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3211 Jalview icon not shown on dock in Mountain Lion/Webstart
3213 </ul> <em>Applet Known Issues</em>
3216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3217 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3220 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3221 Jalview and Jmol example not compatible with IE9
3224 <li>Sort by annotation score doesn't reverse order
3230 <td><div align="center">
3231 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3234 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3237 <li>Internationalisation of user interface (usually
3238 called i18n support) and translation for Spanish locale</li>
3239 <li>Define/Undefine group on current selection with
3240 Ctrl-G/Shift Ctrl-G</li>
3241 <li>Improved group creation/removal options in
3242 alignment/sequence Popup menu</li>
3243 <li>Sensible precision for symbol distribution
3244 percentages shown in logo tooltip.</li>
3245 <li>Annotation panel height set according to amount of
3246 annotation when alignment first opened</li>
3247 </ul> <em>Application</em>
3249 <li>Interactive consensus RNA secondary structure
3250 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3251 <li>Select columns containing particular features from
3252 Feature Settings dialog</li>
3253 <li>View all 'representative' PDB structures for selected
3255 <li>Update Jalview project format:
3257 <li>New file extension for Jalview projects '.jvp'</li>
3258 <li>Preserve sequence and annotation dataset (to
3259 store secondary structure annotation,etc)</li>
3260 <li>Per group and alignment annotation and RNA helix
3264 <li>New similarity measures for PCA and Tree calculation
3266 <li>Experimental support for retrieval and viewing of
3267 flanking regions for an alignment</li>
3271 <!-- issues resolved --> <em>Application</em>
3273 <li>logo keeps spinning and status remains at queued or
3274 running after job is cancelled</li>
3275 <li>cannot export features from alignments imported from
3276 Jalview/VAMSAS projects</li>
3277 <li>Buggy slider for web service parameters that take
3279 <li>Newly created RNA secondary structure line doesn't
3280 have 'display all symbols' flag set</li>
3281 <li>T-COFFEE alignment score shading scheme and other
3282 annotation shading not saved in Jalview project</li>
3283 <li>Local file cannot be loaded in freshly downloaded
3285 <li>Jalview icon not shown on dock in Mountain
3287 <li>Load file from desktop file browser fails</li>
3288 <li>Occasional NPE thrown when calculating large trees</li>
3289 <li>Cannot reorder or slide sequences after dragging an
3290 alignment onto desktop</li>
3291 <li>Colour by annotation dialog throws NPE after using
3292 'extract scores' function</li>
3293 <li>Loading/cut'n'pasting an empty file leads to a grey
3294 alignment window</li>
3295 <li>Disorder thresholds rendered incorrectly after
3296 performing IUPred disorder prediction</li>
3297 <li>Multiple group annotated consensus rows shown when
3298 changing 'normalise logo' display setting</li>
3299 <li>Find shows blank dialog after 'finished searching' if
3300 nothing matches query</li>
3301 <li>Null Pointer Exceptions raised when sorting by
3302 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3304 <li>Errors in Jmol console when structures in alignment
3305 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3307 <li>Not all working JABAWS services are shown in
3309 <li>JAVAWS version of Jalview fails to launch with
3310 'invalid literal/length code'</li>
3311 <li>Annotation/RNA Helix colourschemes cannot be applied
3312 to alignment with groups (actually fixed in 2.8.0b1)</li>
3313 <li>RNA Helices and T-Coffee Scores available as default
3316 </ul> <em>Applet</em>
3318 <li>Remove group option is shown even when selection is
3320 <li>Apply to all groups ticked but colourscheme changes
3321 don't affect groups</li>
3322 <li>Documented RNA Helices and T-Coffee Scores as valid
3323 colourscheme name</li>
3324 <li>Annotation labels drawn on sequence IDs when
3325 Annotation panel is not displayed</li>
3326 <li>Increased font size for dropdown menus on OSX and
3327 embedded windows</li>
3328 </ul> <em>Other</em>
3330 <li>Consensus sequence for alignments/groups with a
3331 single sequence were not calculated</li>
3332 <li>annotation files that contain only groups imported as
3333 annotation and junk sequences</li>
3334 <li>Fasta files with sequences containing '*' incorrectly
3335 recognised as PFAM or BLC</li>
3336 <li>conservation/PID slider apply all groups option
3337 doesn't affect background (2.8.0b1)
3339 <li>redundancy highlighting is erratic at 0% and 100%</li>
3340 <li>Remove gapped columns fails for sequences with ragged
3342 <li>AMSA annotation row with leading spaces is not
3343 registered correctly on import</li>
3344 <li>Jalview crashes when selecting PCA analysis for
3345 certain alignments</li>
3346 <li>Opening the colour by annotation dialog for an
3347 existing annotation based 'use original colours'
3348 colourscheme loses original colours setting</li>
3353 <td><div align="center">
3354 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3355 <em>30/1/2014</em></strong>
3359 <li>Trusted certificates for JalviewLite applet and
3360 Jalview Desktop application<br />Certificate was donated by
3361 <a href="https://www.certum.eu">Certum</a> to the Jalview
3362 open source project).
3364 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3365 <li>Output in Stockholm format</li>
3366 <li>Allow import of data from gzipped files</li>
3367 <li>Export/import group and sequence associated line
3368 graph thresholds</li>
3369 <li>Nucleotide substitution matrix that supports RNA and
3370 ambiguity codes</li>
3371 <li>Allow disorder predictions to be made on the current
3372 selection (or visible selection) in the same way that JPred
3374 <li>Groovy scripting for headless Jalview operation</li>
3375 </ul> <em>Other improvements</em>
3377 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3378 <li>COMBINE statement uses current SEQUENCE_REF and
3379 GROUP_REF scope to group annotation rows</li>
3380 <li>Support '' style escaping of quotes in Newick
3382 <li>Group options for JABAWS service by command line name</li>
3383 <li>Empty tooltip shown for JABA service options with a
3384 link but no description</li>
3385 <li>Select primary source when selecting authority in
3386 database fetcher GUI</li>
3387 <li>Add .mfa to FASTA file extensions recognised by
3389 <li>Annotation label tooltip text wrap</li>
3394 <li>Slow scrolling when lots of annotation rows are
3396 <li>Lots of NPE (and slowness) after creating RNA
3397 secondary structure annotation line</li>
3398 <li>Sequence database accessions not imported when
3399 fetching alignments from Rfam</li>
3400 <li>Incorrect SHMR submission for sequences with
3402 <li>View all structures does not always superpose
3404 <li>Option widgets in service parameters not updated to
3405 reflect user or preset settings</li>
3406 <li>Null pointer exceptions for some services without
3407 presets or adjustable parameters</li>
3408 <li>Discover PDB IDs entry in structure menu doesn't
3409 discover PDB xRefs</li>
3410 <li>Exception encountered while trying to retrieve
3411 features with DAS</li>
3412 <li>Lowest value in annotation row isn't coloured
3413 when colour by annotation (per sequence) is coloured</li>
3414 <li>Keyboard mode P jumps to start of gapped region when
3415 residue follows a gap</li>
3416 <li>Jalview appears to hang importing an alignment with
3417 Wrap as default or after enabling Wrap</li>
3418 <li>'Right click to add annotations' message
3419 shown in wrap mode when no annotations present</li>
3420 <li>Disorder predictions fail with NPE if no automatic
3421 annotation already exists on alignment</li>
3422 <li>oninit javascript function should be called after
3423 initialisation completes</li>
3424 <li>Remove redundancy after disorder prediction corrupts
3425 alignment window display</li>
3426 <li>Example annotation file in documentation is invalid</li>
3427 <li>Grouped line graph annotation rows are not exported
3428 to annotation file</li>
3429 <li>Multi-harmony analysis cannot be run when only two
3431 <li>Cannot create multiple groups of line graphs with
3432 several 'combine' statements in annotation file</li>
3433 <li>Pressing return several times causes Number Format
3434 exceptions in keyboard mode</li>
3435 <li>Multi-harmony (SHMMR) method doesn't submit
3436 correct partitions for input data</li>
3437 <li>Translation from DNA to Amino Acids fails</li>
3438 <li>Jalview fail to load newick tree with quoted label</li>
3439 <li>--headless flag isn't understood</li>
3440 <li>ClassCastException when generating EPS in headless
3442 <li>Adjusting sequence-associated shading threshold only
3443 changes one row's threshold</li>
3444 <li>Preferences and Feature settings panel panel
3445 doesn't open</li>
3446 <li>hide consensus histogram also hides conservation and
3447 quality histograms</li>
3452 <td><div align="center">
3453 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3455 <td><em>Application</em>
3457 <li>Support for JABAWS 2.0 Services (AACon alignment
3458 conservation, protein disorder and Clustal Omega)</li>
3459 <li>JABAWS server status indicator in Web Services
3461 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3462 in Jalview alignment window</li>
3463 <li>Updated Jalview build and deploy framework for OSX
3464 mountain lion, windows 7, and 8</li>
3465 <li>Nucleotide substitution matrix for PCA that supports
3466 RNA and ambiguity codes</li>
3468 <li>Improved sequence database retrieval GUI</li>
3469 <li>Support fetching and database reference look up
3470 against multiple DAS sources (Fetch all from in 'fetch db
3472 <li>Jalview project improvements
3474 <li>Store and retrieve the 'belowAlignment'
3475 flag for annotation</li>
3476 <li>calcId attribute to group annotation rows on the
3478 <li>Store AACon calculation settings for a view in
3479 Jalview project</li>
3483 <li>horizontal scrolling gesture support</li>
3484 <li>Visual progress indicator when PCA calculation is
3486 <li>Simpler JABA web services menus</li>
3487 <li>visual indication that web service results are still
3488 being retrieved from server</li>
3489 <li>Serialise the dialogs that are shown when Jalview
3490 starts up for first time</li>
3491 <li>Jalview user agent string for interacting with HTTP
3493 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3495 <li>Examples directory and Groovy library included in
3496 InstallAnywhere distribution</li>
3497 </ul> <em>Applet</em>
3499 <li>RNA alignment and secondary structure annotation
3500 visualization applet example</li>
3501 </ul> <em>General</em>
3503 <li>Normalise option for consensus sequence logo</li>
3504 <li>Reset button in PCA window to return dimensions to
3506 <li>Allow seqspace or Jalview variant of alignment PCA
3508 <li>PCA with either nucleic acid and protein substitution
3510 <li>Allow windows containing HTML reports to be exported
3512 <li>Interactive display and editing of RNA secondary
3513 structure contacts</li>
3514 <li>RNA Helix Alignment Colouring</li>
3515 <li>RNA base pair logo consensus</li>
3516 <li>Parse sequence associated secondary structure
3517 information in Stockholm files</li>
3518 <li>HTML Export database accessions and annotation
3519 information presented in tooltip for sequences</li>
3520 <li>Import secondary structure from LOCARNA clustalw
3521 style RNA alignment files</li>
3522 <li>import and visualise T-COFFEE quality scores for an
3524 <li>'colour by annotation' per sequence option to
3525 shade each sequence according to its associated alignment
3527 <li>New Jalview Logo</li>
3528 </ul> <em>Documentation and Development</em>
3530 <li>documentation for score matrices used in Jalview</li>
3531 <li>New Website!</li>
3533 <td><em>Application</em>
3535 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3536 wsdbfetch REST service</li>
3537 <li>Stop windows being moved outside desktop on OSX</li>
3538 <li>Filetype associations not installed for webstart
3540 <li>Jalview does not always retrieve progress of a JABAWS
3541 job execution in full once it is complete</li>
3542 <li>revise SHMR RSBS definition to ensure alignment is
3543 uploaded via ali_file parameter</li>
3544 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3545 <li>View all structures superposed fails with exception</li>
3546 <li>Jnet job queues forever if a very short sequence is
3547 submitted for prediction</li>
3548 <li>Cut and paste menu not opened when mouse clicked on
3550 <li>Putting fractional value into integer text box in
3551 alignment parameter dialog causes Jalview to hang</li>
3552 <li>Structure view highlighting doesn't work on
3554 <li>View all structures fails with exception shown in
3556 <li>Characters in filename associated with PDBEntry not
3557 escaped in a platform independent way</li>
3558 <li>Jalview desktop fails to launch with exception when
3560 <li>Tree calculation reports 'you must have 2 or more
3561 sequences selected' when selection is empty</li>
3562 <li>Jalview desktop fails to launch with jar signature
3563 failure when java web start temporary file caching is
3565 <li>DAS Sequence retrieval with range qualification
3566 results in sequence xref which includes range qualification</li>
3567 <li>Errors during processing of command line arguments
3568 cause progress bar (JAL-898) to be removed</li>
3569 <li>Replace comma for semi-colon option not disabled for
3570 DAS sources in sequence fetcher</li>
3571 <li>Cannot close news reader when JABAWS server warning
3572 dialog is shown</li>
3573 <li>Option widgets not updated to reflect user settings</li>
3574 <li>Edited sequence not submitted to web service</li>
3575 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3576 <li>InstallAnywhere installer doesn't unpack and run
3577 on OSX Mountain Lion</li>
3578 <li>Annotation panel not given a scroll bar when
3579 sequences with alignment annotation are pasted into the
3581 <li>Sequence associated annotation rows not associated
3582 when loaded from Jalview project</li>
3583 <li>Browser launch fails with NPE on java 1.7</li>
3584 <li>JABAWS alignment marked as finished when job was
3585 cancelled or job failed due to invalid input</li>
3586 <li>NPE with v2.7 example when clicking on Tree
3587 associated with all views</li>
3588 <li>Exceptions when copy/paste sequences with grouped
3589 annotation rows to new window</li>
3590 </ul> <em>Applet</em>
3592 <li>Sequence features are momentarily displayed before
3593 they are hidden using hidefeaturegroups applet parameter</li>
3594 <li>loading features via javascript API automatically
3595 enables feature display</li>
3596 <li>scrollToColumnIn javascript API method doesn't
3598 </ul> <em>General</em>
3600 <li>Redundancy removal fails for rna alignment</li>
3601 <li>PCA calculation fails when sequence has been selected
3602 and then deselected</li>
3603 <li>PCA window shows grey box when first opened on OSX</li>
3604 <li>Letters coloured pink in sequence logo when alignment
3605 coloured with clustalx</li>
3606 <li>Choosing fonts without letter symbols defined causes
3607 exceptions and redraw errors</li>
3608 <li>Initial PCA plot view is not same as manually
3609 reconfigured view</li>
3610 <li>Grouped annotation graph label has incorrect line
3612 <li>Grouped annotation graph label display is corrupted
3613 for lots of labels</li>
3618 <div align="center">
3619 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3622 <td><em>Application</em>
3624 <li>Jalview Desktop News Reader</li>
3625 <li>Tweaked default layout of web services menu</li>
3626 <li>View/alignment association menu to enable user to
3627 easily specify which alignment a multi-structure view takes
3628 its colours/correspondences from</li>
3629 <li>Allow properties file location to be specified as URL</li>
3630 <li>Extend Jalview project to preserve associations
3631 between many alignment views and a single Jmol display</li>
3632 <li>Store annotation row height in Jalview project file</li>
3633 <li>Annotation row column label formatting attributes
3634 stored in project file</li>
3635 <li>Annotation row order for auto-calculated annotation
3636 rows preserved in Jalview project file</li>
3637 <li>Visual progress indication when Jalview state is
3638 saved using Desktop window menu</li>
3639 <li>Visual indication that command line arguments are
3640 still being processed</li>
3641 <li>Groovy script execution from URL</li>
3642 <li>Colour by annotation default min and max colours in
3644 <li>Automatically associate PDB files dragged onto an
3645 alignment with sequences that have high similarity and
3647 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3648 <li>'view structures' option to open many
3649 structures in same window</li>
3650 <li>Sort associated views menu option for tree panel</li>
3651 <li>Group all JABA and non-JABA services for a particular
3652 analysis function in its own submenu</li>
3653 </ul> <em>Applet</em>
3655 <li>Userdefined and autogenerated annotation rows for
3657 <li>Adjustment of alignment annotation pane height</li>
3658 <li>Annotation scrollbar for annotation panel</li>
3659 <li>Drag to reorder annotation rows in annotation panel</li>
3660 <li>'automaticScrolling' parameter</li>
3661 <li>Allow sequences with partial ID string matches to be
3662 annotated from GFF/Jalview features files</li>
3663 <li>Sequence logo annotation row in applet</li>
3664 <li>Absolute paths relative to host server in applet
3665 parameters are treated as such</li>
3666 <li>New in the JalviewLite javascript API:
3668 <li>JalviewLite.js javascript library</li>
3669 <li>Javascript callbacks for
3671 <li>Applet initialisation</li>
3672 <li>Sequence/alignment mouse-overs and selections</li>
3675 <li>scrollTo row and column alignment scrolling
3677 <li>Select sequence/alignment regions from javascript</li>
3678 <li>javascript structure viewer harness to pass
3679 messages between Jmol and Jalview when running as
3680 distinct applets</li>
3681 <li>sortBy method</li>
3682 <li>Set of applet and application examples shipped
3683 with documentation</li>
3684 <li>New example to demonstrate JalviewLite and Jmol
3685 javascript message exchange</li>
3687 </ul> <em>General</em>
3689 <li>Enable Jmol displays to be associated with multiple
3690 multiple alignments</li>
3691 <li>Option to automatically sort alignment with new tree</li>
3692 <li>User configurable link to enable redirects to a
3693 www.Jalview.org mirror</li>
3694 <li>Jmol colours option for Jmol displays</li>
3695 <li>Configurable newline string when writing alignment
3696 and other flat files</li>
3697 <li>Allow alignment annotation description lines to
3698 contain html tags</li>
3699 </ul> <em>Documentation and Development</em>
3701 <li>Add groovy test harness for bulk load testing to
3703 <li>Groovy script to load and align a set of sequences
3704 using a web service before displaying the result in the
3705 Jalview desktop</li>
3706 <li>Restructured javascript and applet api documentation</li>
3707 <li>Ant target to publish example html files with applet
3709 <li>Netbeans project for building Jalview from source</li>
3710 <li>ant task to create online javadoc for Jalview source</li>
3712 <td><em>Application</em>
3714 <li>User defined colourscheme throws exception when
3715 current built in colourscheme is saved as new scheme</li>
3716 <li>AlignFrame->Save in application pops up save
3717 dialog for valid filename/format</li>
3718 <li>Cannot view associated structure for UniProt sequence</li>
3719 <li>PDB file association breaks for UniProt sequence
3721 <li>Associate PDB from file dialog does not tell you
3722 which sequence is to be associated with the file</li>
3723 <li>Find All raises null pointer exception when query
3724 only matches sequence IDs</li>
3725 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3726 <li>Jalview project with Jmol views created with Jalview
3727 2.4 cannot be loaded</li>
3728 <li>Filetype associations not installed for webstart
3730 <li>Two or more chains in a single PDB file associated
3731 with sequences in different alignments do not get coloured
3732 by their associated sequence</li>
3733 <li>Visibility status of autocalculated annotation row
3734 not preserved when project is loaded</li>
3735 <li>Annotation row height and visibility attributes not
3736 stored in Jalview project</li>
3737 <li>Tree bootstraps are not preserved when saved as a
3738 Jalview project</li>
3739 <li>Envision2 workflow tooltips are corrupted</li>
3740 <li>Enabling show group conservation also enables colour
3741 by conservation</li>
3742 <li>Duplicate group associated conservation or consensus
3743 created on new view</li>
3744 <li>Annotation scrollbar not displayed after 'show
3745 all hidden annotation rows' option selected</li>
3746 <li>Alignment quality not updated after alignment
3747 annotation row is hidden then shown</li>
3748 <li>Preserve colouring of structures coloured by
3749 sequences in pre Jalview 2.7 projects</li>
3750 <li>Web service job parameter dialog is not laid out
3752 <li>Web services menu not refreshed after 'reset
3753 services' button is pressed in preferences</li>
3754 <li>Annotation off by one in Jalview v2_3 example project</li>
3755 <li>Structures imported from file and saved in project
3756 get name like jalview_pdb1234.txt when reloaded</li>
3757 <li>Jalview does not always retrieve progress of a JABAWS
3758 job execution in full once it is complete</li>
3759 </ul> <em>Applet</em>
3761 <li>Alignment height set incorrectly when lots of
3762 annotation rows are displayed</li>
3763 <li>Relative URLs in feature HTML text not resolved to
3765 <li>View follows highlighting does not work for positions
3767 <li><= shown as = in tooltip</li>
3768 <li>Export features raises exception when no features
3770 <li>Separator string used for serialising lists of IDs
3771 for javascript api is modified when separator string
3772 provided as parameter</li>
3773 <li>Null pointer exception when selecting tree leaves for
3774 alignment with no existing selection</li>
3775 <li>Relative URLs for datasources assumed to be relative
3776 to applet's codebase</li>
3777 <li>Status bar not updated after finished searching and
3778 search wraps around to first result</li>
3779 <li>StructureSelectionManager instance shared between
3780 several Jalview applets causes race conditions and memory
3782 <li>Hover tooltip and mouseover of position on structure
3783 not sent from Jmol in applet</li>
3784 <li>Certain sequences of javascript method calls to
3785 applet API fatally hang browser</li>
3786 </ul> <em>General</em>
3788 <li>View follows structure mouseover scrolls beyond
3789 position with wrapped view and hidden regions</li>
3790 <li>Find sequence position moves to wrong residue
3791 with/without hidden columns</li>
3792 <li>Sequence length given in alignment properties window
3794 <li>InvalidNumberFormat exceptions thrown when trying to
3795 import PDB like structure files</li>
3796 <li>Positional search results are only highlighted
3797 between user-supplied sequence start/end bounds</li>
3798 <li>End attribute of sequence is not validated</li>
3799 <li>Find dialog only finds first sequence containing a
3800 given sequence position</li>
3801 <li>Sequence numbering not preserved in MSF alignment
3803 <li>Jalview PDB file reader does not extract sequence
3804 from nucleotide chains correctly</li>
3805 <li>Structure colours not updated when tree partition
3806 changed in alignment</li>
3807 <li>Sequence associated secondary structure not correctly
3808 parsed in interleaved stockholm</li>
3809 <li>Colour by annotation dialog does not restore current
3811 <li>Hiding (nearly) all sequences doesn't work
3813 <li>Sequences containing lowercase letters are not
3814 properly associated with their pdb files</li>
3815 </ul> <em>Documentation and Development</em>
3817 <li>schemas/JalviewWsParamSet.xsd corrupted by
3818 ApplyCopyright tool</li>
3823 <div align="center">
3824 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3827 <td><em>Application</em>
3829 <li>New warning dialog when the Jalview Desktop cannot
3830 contact web services</li>
3831 <li>JABA service parameters for a preset are shown in
3832 service job window</li>
3833 <li>JABA Service menu entries reworded</li>
3837 <li>Modeller PIR IO broken - cannot correctly import a
3838 pir file emitted by Jalview</li>
3839 <li>Existing feature settings transferred to new
3840 alignment view created from cut'n'paste</li>
3841 <li>Improved test for mixed amino/nucleotide chains when
3842 parsing PDB files</li>
3843 <li>Consensus and conservation annotation rows
3844 occasionally become blank for all new windows</li>
3845 <li>Exception raised when right clicking above sequences
3846 in wrapped view mode</li>
3847 </ul> <em>Application</em>
3849 <li>multiple multiply aligned structure views cause cpu
3850 usage to hit 100% and computer to hang</li>
3851 <li>Web Service parameter layout breaks for long user
3852 parameter names</li>
3853 <li>Jaba service discovery hangs desktop if Jaba server
3860 <div align="center">
3861 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3864 <td><em>Application</em>
3866 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3867 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3870 <li>Web Services preference tab</li>
3871 <li>Analysis parameters dialog box and user defined
3873 <li>Improved speed and layout of Envision2 service menu</li>
3874 <li>Superpose structures using associated sequence
3876 <li>Export coordinates and projection as CSV from PCA
3878 </ul> <em>Applet</em>
3880 <li>enable javascript: execution by the applet via the
3881 link out mechanism</li>
3882 </ul> <em>Other</em>
3884 <li>Updated the Jmol Jalview interface to work with Jmol
3886 <li>The Jalview Desktop and JalviewLite applet now
3887 require Java 1.5</li>
3888 <li>Allow Jalview feature colour specification for GFF
3889 sequence annotation files</li>
3890 <li>New 'colour by label' keword in Jalview feature file
3891 type colour specification</li>
3892 <li>New Jalview Desktop Groovy API method that allows a
3893 script to check if it being run in an interactive session or
3894 in a batch operation from the Jalview command line</li>
3898 <li>clustalx colourscheme colours Ds preferentially when
3899 both D+E are present in over 50% of the column</li>
3900 </ul> <em>Application</em>
3902 <li>typo in AlignmentFrame->View->Hide->all but
3903 selected Regions menu item</li>
3904 <li>sequence fetcher replaces ',' for ';' when the ',' is
3905 part of a valid accession ID</li>
3906 <li>fatal OOM if object retrieved by sequence fetcher
3907 runs out of memory</li>
3908 <li>unhandled Out of Memory Error when viewing pca
3909 analysis results</li>
3910 <li>InstallAnywhere builds fail to launch on OS X java
3911 10.5 update 4 (due to apple Java 1.6 update)</li>
3912 <li>Installanywhere Jalview silently fails to launch</li>
3913 </ul> <em>Applet</em>
3915 <li>Jalview.getFeatureGroups() raises an
3916 ArrayIndexOutOfBoundsException if no feature groups are
3923 <div align="center">
3924 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3930 <li>Alignment prettyprinter doesn't cope with long
3932 <li>clustalx colourscheme colours Ds preferentially when
3933 both D+E are present in over 50% of the column</li>
3934 <li>nucleic acid structures retrieved from PDB do not
3935 import correctly</li>
3936 <li>More columns get selected than were clicked on when a
3937 number of columns are hidden</li>
3938 <li>annotation label popup menu not providing correct
3939 add/hide/show options when rows are hidden or none are
3941 <li>Stockholm format shown in list of readable formats,
3942 and parser copes better with alignments from RFAM.</li>
3943 <li>CSV output of consensus only includes the percentage
3944 of all symbols if sequence logo display is enabled</li>
3946 </ul> <em>Applet</em>
3948 <li>annotation panel disappears when annotation is
3950 </ul> <em>Application</em>
3952 <li>Alignment view not redrawn properly when new
3953 alignment opened where annotation panel is visible but no
3954 annotations are present on alignment</li>
3955 <li>pasted region containing hidden columns is
3956 incorrectly displayed in new alignment window</li>
3957 <li>Jalview slow to complete operations when stdout is
3958 flooded (fix is to close the Jalview console)</li>
3959 <li>typo in AlignmentFrame->View->Hide->all but
3960 selected Rregions menu item.</li>
3961 <li>inconsistent group submenu and Format submenu entry
3962 'Un' or 'Non'conserved</li>
3963 <li>Sequence feature settings are being shared by
3964 multiple distinct alignments</li>
3965 <li>group annotation not recreated when tree partition is
3967 <li>double click on group annotation to select sequences
3968 does not propagate to associated trees</li>
3969 <li>Mac OSX specific issues:
3971 <li>exception raised when mouse clicked on desktop
3972 window background</li>
3973 <li>Desktop menu placed on menu bar and application
3974 name set correctly</li>
3975 <li>sequence feature settings not wide enough for the
3976 save feature colourscheme button</li>
3985 <div align="center">
3986 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3989 <td><em>New Capabilities</em>
3991 <li>URL links generated from description line for
3992 regular-expression based URL links (applet and application)
3994 <li>Non-positional feature URL links are shown in link
3996 <li>Linked viewing of nucleic acid sequences and
3998 <li>Automatic Scrolling option in View menu to display
3999 the currently highlighted region of an alignment.</li>
4000 <li>Order an alignment by sequence length, or using the
4001 average score or total feature count for each sequence.</li>
4002 <li>Shading features by score or associated description</li>
4003 <li>Subdivide alignment and groups based on identity of
4004 selected subsequence (Make Groups from Selection).</li>
4005 <li>New hide/show options including Shift+Control+H to
4006 hide everything but the currently selected region.</li>
4007 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4008 </ul> <em>Application</em>
4010 <li>Fetch DB References capabilities and UI expanded to
4011 support retrieval from DAS sequence sources</li>
4012 <li>Local DAS Sequence sources can be added via the
4013 command line or via the Add local source dialog box.</li>
4014 <li>DAS Dbref and DbxRef feature types are parsed as
4015 database references and protein_name is parsed as
4016 description line (BioSapiens terms).</li>
4017 <li>Enable or disable non-positional feature and database
4018 references in sequence ID tooltip from View menu in
4020 <!-- <li>New hidden columns and rows and representatives capabilities
4021 in annotations file (in progress - not yet fully implemented)</li> -->
4022 <li>Group-associated consensus, sequence logos and
4023 conservation plots</li>
4024 <li>Symbol distributions for each column can be exported
4025 and visualized as sequence logos</li>
4026 <li>Optionally scale multi-character column labels to fit
4027 within each column of annotation row<!-- todo for applet -->
4029 <li>Optional automatic sort of associated alignment view
4030 when a new tree is opened.</li>
4031 <li>Jalview Java Console</li>
4032 <li>Better placement of desktop window when moving
4033 between different screens.</li>
4034 <li>New preference items for sequence ID tooltip and
4035 consensus annotation</li>
4036 <li>Client to submit sequences and IDs to Envision2
4038 <li><em>Vamsas Capabilities</em>
4040 <li>Improved VAMSAS synchronization (Jalview archive
4041 used to preserve views, structures, and tree display
4043 <li>Import of vamsas documents from disk or URL via
4045 <li>Sharing of selected regions between views and
4046 with other VAMSAS applications (Experimental feature!)</li>
4047 <li>Updated API to VAMSAS version 0.2</li>
4049 </ul> <em>Applet</em>
4051 <li>Middle button resizes annotation row height</li>
4054 <li>sortByTree (true/false) - automatically sort the
4055 associated alignment view by the tree when a new tree is
4057 <li>showTreeBootstraps (true/false) - show or hide
4058 branch bootstraps (default is to show them if available)</li>
4059 <li>showTreeDistances (true/false) - show or hide
4060 branch lengths (default is to show them if available)</li>
4061 <li>showUnlinkedTreeNodes (true/false) - indicate if
4062 unassociated nodes should be highlighted in the tree
4064 <li>heightScale and widthScale (1.0 or more) -
4065 increase the height or width of a cell in the alignment
4066 grid relative to the current font size.</li>
4069 <li>Non-positional features displayed in sequence ID
4071 </ul> <em>Other</em>
4073 <li>Features format: graduated colour definitions and
4074 specification of feature scores</li>
4075 <li>Alignment Annotations format: new keywords for group
4076 associated annotation (GROUP_REF) and annotation row display
4077 properties (ROW_PROPERTIES)</li>
4078 <li>XML formats extended to support graduated feature
4079 colourschemes, group associated annotation, and profile
4080 visualization settings.</li></td>
4083 <li>Source field in GFF files parsed as feature source
4084 rather than description</li>
4085 <li>Non-positional features are now included in sequence
4086 feature and gff files (controlled via non-positional feature
4087 visibility in tooltip).</li>
4088 <li>URL links generated for all feature links (bugfix)</li>
4089 <li>Added URL embedding instructions to features file
4091 <li>Codons containing ambiguous nucleotides translated as
4092 'X' in peptide product</li>
4093 <li>Match case switch in find dialog box works for both
4094 sequence ID and sequence string and query strings do not
4095 have to be in upper case to match case-insensitively.</li>
4096 <li>AMSA files only contain first column of
4097 multi-character column annotation labels</li>
4098 <li>Jalview Annotation File generation/parsing consistent
4099 with documentation (e.g. Stockholm annotation can be
4100 exported and re-imported)</li>
4101 <li>PDB files without embedded PDB IDs given a friendly
4103 <li>Find incrementally searches ID string matches as well
4104 as subsequence matches, and correctly reports total number
4108 <li>Better handling of exceptions during sequence
4110 <li>Dasobert generated non-positional feature URL
4111 link text excludes the start_end suffix</li>
4112 <li>DAS feature and source retrieval buttons disabled
4113 when fetch or registry operations in progress.</li>
4114 <li>PDB files retrieved from URLs are cached properly</li>
4115 <li>Sequence description lines properly shared via
4117 <li>Sequence fetcher fetches multiple records for all
4119 <li>Ensured that command line das feature retrieval
4120 completes before alignment figures are generated.</li>
4121 <li>Reduced time taken when opening file browser for
4123 <li>isAligned check prior to calculating tree, PCA or
4124 submitting an MSA to JNet now excludes hidden sequences.</li>
4125 <li>User defined group colours properly recovered
4126 from Jalview projects.</li>
4135 <div align="center">
4136 <strong>2.4.0.b2</strong><br> 28/10/2009
4141 <li>Experimental support for google analytics usage
4143 <li>Jalview privacy settings (user preferences and docs).</li>
4148 <li>Race condition in applet preventing startup in
4150 <li>Exception when feature created from selection beyond
4151 length of sequence.</li>
4152 <li>Allow synthetic PDB files to be imported gracefully</li>
4153 <li>Sequence associated annotation rows associate with
4154 all sequences with a given id</li>
4155 <li>Find function matches case-insensitively for sequence
4156 ID string searches</li>
4157 <li>Non-standard characters do not cause pairwise
4158 alignment to fail with exception</li>
4159 </ul> <em>Application Issues</em>
4161 <li>Sequences are now validated against EMBL database</li>
4162 <li>Sequence fetcher fetches multiple records for all
4164 </ul> <em>InstallAnywhere Issues</em>
4166 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4167 issue with installAnywhere mechanism)</li>
4168 <li>Command line launching of JARs from InstallAnywhere
4169 version (java class versioning error fixed)</li>
4176 <div align="center">
4177 <strong>2.4</strong><br> 27/8/2008
4180 <td><em>User Interface</em>
4182 <li>Linked highlighting of codon and amino acid from
4183 translation and protein products</li>
4184 <li>Linked highlighting of structure associated with
4185 residue mapping to codon position</li>
4186 <li>Sequence Fetcher provides example accession numbers
4187 and 'clear' button</li>
4188 <li>MemoryMonitor added as an option under Desktop's
4190 <li>Extract score function to parse whitespace separated
4191 numeric data in description line</li>
4192 <li>Column labels in alignment annotation can be centred.</li>
4193 <li>Tooltip for sequence associated annotation give name
4195 </ul> <em>Web Services and URL fetching</em>
4197 <li>JPred3 web service</li>
4198 <li>Prototype sequence search client (no public services
4200 <li>Fetch either seed alignment or full alignment from
4202 <li>URL Links created for matching database cross
4203 references as well as sequence ID</li>
4204 <li>URL Links can be created using regular-expressions</li>
4205 </ul> <em>Sequence Database Connectivity</em>
4207 <li>Retrieval of cross-referenced sequences from other
4209 <li>Generalised database reference retrieval and
4210 validation to all fetchable databases</li>
4211 <li>Fetch sequences from DAS sources supporting the
4212 sequence command</li>
4213 </ul> <em>Import and Export</em>
4214 <li>export annotation rows as CSV for spreadsheet import</li>
4215 <li>Jalview projects record alignment dataset associations,
4216 EMBL products, and cDNA sequence mappings</li>
4217 <li>Sequence Group colour can be specified in Annotation
4219 <li>Ad-hoc colouring of group in Annotation File using RGB
4220 triplet as name of colourscheme</li>
4221 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4223 <li>treenode binding for VAMSAS tree exchange</li>
4224 <li>local editing and update of sequences in VAMSAS
4225 alignments (experimental)</li>
4226 <li>Create new or select existing session to join</li>
4227 <li>load and save of vamsas documents</li>
4228 </ul> <em>Application command line</em>
4230 <li>-tree parameter to open trees (introduced for passing
4232 <li>-fetchfrom command line argument to specify nicknames
4233 of DAS servers to query for alignment features</li>
4234 <li>-dasserver command line argument to add new servers
4235 that are also automatically queried for features</li>
4236 <li>-groovy command line argument executes a given groovy
4237 script after all input data has been loaded and parsed</li>
4238 </ul> <em>Applet-Application data exchange</em>
4240 <li>Trees passed as applet parameters can be passed to
4241 application (when using "View in full
4242 application")</li>
4243 </ul> <em>Applet Parameters</em>
4245 <li>feature group display control parameter</li>
4246 <li>debug parameter</li>
4247 <li>showbutton parameter</li>
4248 </ul> <em>Applet API methods</em>
4250 <li>newView public method</li>
4251 <li>Window (current view) specific get/set public methods</li>
4252 <li>Feature display control methods</li>
4253 <li>get list of currently selected sequences</li>
4254 </ul> <em>New Jalview distribution features</em>
4256 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4257 <li>RELEASE file gives build properties for the latest
4258 Jalview release.</li>
4259 <li>Java 1.1 Applet build made easier and donotobfuscate
4260 property controls execution of obfuscator</li>
4261 <li>Build target for generating source distribution</li>
4262 <li>Debug flag for javacc</li>
4263 <li>.jalview_properties file is documented (slightly) in
4264 jalview.bin.Cache</li>
4265 <li>Continuous Build Integration for stable and
4266 development version of Application, Applet and source
4271 <li>selected region output includes visible annotations
4272 (for certain formats)</li>
4273 <li>edit label/displaychar contains existing label/char
4275 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4276 <li>shorter peptide product names from EMBL records</li>
4277 <li>Newick string generator makes compact representations</li>
4278 <li>bootstrap values parsed correctly for tree files with
4280 <li>pathological filechooser bug avoided by not allowing
4281 filenames containing a ':'</li>
4282 <li>Fixed exception when parsing GFF files containing
4283 global sequence features</li>
4284 <li>Alignment datasets are finalized only when number of
4285 references from alignment sequences goes to zero</li>
4286 <li>Close of tree branch colour box without colour
4287 selection causes cascading exceptions</li>
4288 <li>occasional negative imgwidth exceptions</li>
4289 <li>better reporting of non-fatal warnings to user when
4290 file parsing fails.</li>
4291 <li>Save works when Jalview project is default format</li>
4292 <li>Save as dialog opened if current alignment format is
4293 not a valid output format</li>
4294 <li>UniProt canonical names introduced for both das and
4296 <li>Histidine should be midblue (not pink!) in Zappo</li>
4297 <li>error messages passed up and output when data read
4299 <li>edit undo recovers previous dataset sequence when
4300 sequence is edited</li>
4301 <li>allow PDB files without pdb ID HEADER lines (like
4302 those generated by MODELLER) to be read in properly</li>
4303 <li>allow reading of JPred concise files as a normal
4305 <li>Stockholm annotation parsing and alignment properties
4306 import fixed for PFAM records</li>
4307 <li>Structure view windows have correct name in Desktop
4309 <li>annotation consisting of sequence associated scores
4310 can be read and written correctly to annotation file</li>
4311 <li>Aligned cDNA translation to aligned peptide works
4313 <li>Fixed display of hidden sequence markers and
4314 non-italic font for representatives in Applet</li>
4315 <li>Applet Menus are always embedded in applet window on
4317 <li>Newly shown features appear at top of stack (in
4319 <li>Annotations added via parameter not drawn properly
4320 due to null pointer exceptions</li>
4321 <li>Secondary structure lines are drawn starting from
4322 first column of alignment</li>
4323 <li>UniProt XML import updated for new schema release in
4325 <li>Sequence feature to sequence ID match for Features
4326 file is case-insensitive</li>
4327 <li>Sequence features read from Features file appended to
4328 all sequences with matching IDs</li>
4329 <li>PDB structure coloured correctly for associated views
4330 containing a sub-sequence</li>
4331 <li>PDB files can be retrieved by applet from Jar files</li>
4332 <li>feature and annotation file applet parameters
4333 referring to different directories are retrieved correctly</li>
4334 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4335 <li>Fixed application hang whilst waiting for
4336 splash-screen version check to complete</li>
4337 <li>Applet properly URLencodes input parameter values
4338 when passing them to the launchApp service</li>
4339 <li>display name and local features preserved in results
4340 retrieved from web service</li>
4341 <li>Visual delay indication for sequence retrieval and
4342 sequence fetcher initialisation</li>
4343 <li>updated Application to use DAS 1.53e version of
4344 dasobert DAS client</li>
4345 <li>Re-instated Full AMSA support and .amsa file
4347 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4355 <div align="center">
4356 <strong>2.3</strong><br> 9/5/07
4361 <li>Jmol 11.0.2 integration</li>
4362 <li>PDB views stored in Jalview XML files</li>
4363 <li>Slide sequences</li>
4364 <li>Edit sequence in place</li>
4365 <li>EMBL CDS features</li>
4366 <li>DAS Feature mapping</li>
4367 <li>Feature ordering</li>
4368 <li>Alignment Properties</li>
4369 <li>Annotation Scores</li>
4370 <li>Sort by scores</li>
4371 <li>Feature/annotation editing in applet</li>
4376 <li>Headless state operation in 2.2.1</li>
4377 <li>Incorrect and unstable DNA pairwise alignment</li>
4378 <li>Cut and paste of sequences with annotation</li>
4379 <li>Feature group display state in XML</li>
4380 <li>Feature ordering in XML</li>
4381 <li>blc file iteration selection using filename # suffix</li>
4382 <li>Stockholm alignment properties</li>
4383 <li>Stockhom alignment secondary structure annotation</li>
4384 <li>2.2.1 applet had no feature transparency</li>
4385 <li>Number pad keys can be used in cursor mode</li>
4386 <li>Structure Viewer mirror image resolved</li>
4393 <div align="center">
4394 <strong>2.2.1</strong><br> 12/2/07
4399 <li>Non standard characters can be read and displayed
4400 <li>Annotations/Features can be imported/exported to the
4402 <li>Applet allows editing of sequence/annotation/group
4403 name & description
4404 <li>Preference setting to display sequence name in
4406 <li>Annotation file format extended to allow
4407 Sequence_groups to be defined
4408 <li>Default opening of alignment overview panel can be
4409 specified in preferences
4410 <li>PDB residue numbering annotation added to associated
4416 <li>Applet crash under certain Linux OS with Java 1.6
4418 <li>Annotation file export / import bugs fixed
4419 <li>PNG / EPS image output bugs fixed
4425 <div align="center">
4426 <strong>2.2</strong><br> 27/11/06
4431 <li>Multiple views on alignment
4432 <li>Sequence feature editing
4433 <li>"Reload" alignment
4434 <li>"Save" to current filename
4435 <li>Background dependent text colour
4436 <li>Right align sequence ids
4437 <li>User-defined lower case residue colours
4440 <li>Menu item accelerator keys
4441 <li>Control-V pastes to current alignment
4442 <li>Cancel button for DAS Feature Fetching
4443 <li>PCA and PDB Viewers zoom via mouse roller
4444 <li>User-defined sub-tree colours and sub-tree selection
4446 <li>'New Window' button on the 'Output to Text box'
4451 <li>New memory efficient Undo/Redo System
4452 <li>Optimised symbol lookups and conservation/consensus
4454 <li>Region Conservation/Consensus recalculated after
4456 <li>Fixed Remove Empty Columns Bug (empty columns at end
4458 <li>Slowed DAS Feature Fetching for increased robustness.
4460 <li>Made angle brackets in ASCII feature descriptions
4462 <li>Re-instated Zoom function for PCA
4463 <li>Sequence descriptions conserved in web service
4465 <li>UniProt ID discoverer uses any word separated by
4467 <li>WsDbFetch query/result association resolved
4468 <li>Tree leaf to sequence mapping improved
4469 <li>Smooth fonts switch moved to FontChooser dialog box.
4476 <div align="center">
4477 <strong>2.1.1</strong><br> 12/9/06
4482 <li>Copy consensus sequence to clipboard</li>
4487 <li>Image output - rightmost residues are rendered if
4488 sequence id panel has been resized</li>
4489 <li>Image output - all offscreen group boundaries are
4491 <li>Annotation files with sequence references - all
4492 elements in file are relative to sequence position</li>
4493 <li>Mac Applet users can use Alt key for group editing</li>
4499 <div align="center">
4500 <strong>2.1</strong><br> 22/8/06
4505 <li>MAFFT Multiple Alignment in default Web Service list</li>
4506 <li>DAS Feature fetching</li>
4507 <li>Hide sequences and columns</li>
4508 <li>Export Annotations and Features</li>
4509 <li>GFF file reading / writing</li>
4510 <li>Associate structures with sequences from local PDB
4512 <li>Add sequences to exisiting alignment</li>
4513 <li>Recently opened files / URL lists</li>
4514 <li>Applet can launch the full application</li>
4515 <li>Applet has transparency for features (Java 1.2
4517 <li>Applet has user defined colours parameter</li>
4518 <li>Applet can load sequences from parameter
4519 "sequence<em>x</em>"
4525 <li>Redundancy Panel reinstalled in the Applet</li>
4526 <li>Monospaced font - EPS / rescaling bug fixed</li>
4527 <li>Annotation files with sequence references bug fixed</li>
4533 <div align="center">
4534 <strong>2.08.1</strong><br> 2/5/06
4539 <li>Change case of selected region from Popup menu</li>
4540 <li>Choose to match case when searching</li>
4541 <li>Middle mouse button and mouse movement can compress /
4542 expand the visible width and height of the alignment</li>
4547 <li>Annotation Panel displays complete JNet results</li>
4553 <div align="center">
4554 <strong>2.08b</strong><br> 18/4/06
4560 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4561 <li>Righthand label on wrapped alignments shows correct
4568 <div align="center">
4569 <strong>2.08</strong><br> 10/4/06
4574 <li>Editing can be locked to the selection area</li>
4575 <li>Keyboard editing</li>
4576 <li>Create sequence features from searches</li>
4577 <li>Precalculated annotations can be loaded onto
4579 <li>Features file allows grouping of features</li>
4580 <li>Annotation Colouring scheme added</li>
4581 <li>Smooth fonts off by default - Faster rendering</li>
4582 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4587 <li>Drag & Drop fixed on Linux</li>
4588 <li>Jalview Archive file faster to load/save, sequence
4589 descriptions saved.</li>
4595 <div align="center">
4596 <strong>2.07</strong><br> 12/12/05
4601 <li>PDB Structure Viewer enhanced</li>
4602 <li>Sequence Feature retrieval and display enhanced</li>
4603 <li>Choose to output sequence start-end after sequence
4604 name for file output</li>
4605 <li>Sequence Fetcher WSDBFetch@EBI</li>
4606 <li>Applet can read feature files, PDB files and can be
4607 used for HTML form input</li>
4612 <li>HTML output writes groups and features</li>
4613 <li>Group editing is Control and mouse click</li>
4614 <li>File IO bugs</li>
4620 <div align="center">
4621 <strong>2.06</strong><br> 28/9/05
4626 <li>View annotations in wrapped mode</li>
4627 <li>More options for PCA viewer</li>
4632 <li>GUI bugs resolved</li>
4633 <li>Runs with -nodisplay from command line</li>
4639 <div align="center">
4640 <strong>2.05b</strong><br> 15/9/05
4645 <li>Choose EPS export as lineart or text</li>
4646 <li>Jar files are executable</li>
4647 <li>Can read in Uracil - maps to unknown residue</li>
4652 <li>Known OutOfMemory errors give warning message</li>
4653 <li>Overview window calculated more efficiently</li>
4654 <li>Several GUI bugs resolved</li>
4660 <div align="center">
4661 <strong>2.05</strong><br> 30/8/05
4666 <li>Edit and annotate in "Wrapped" view</li>
4671 <li>Several GUI bugs resolved</li>
4677 <div align="center">
4678 <strong>2.04</strong><br> 24/8/05
4683 <li>Hold down mouse wheel & scroll to change font
4689 <li>Improved JPred client reliability</li>
4690 <li>Improved loading of Jalview files</li>
4696 <div align="center">
4697 <strong>2.03</strong><br> 18/8/05
4702 <li>Set Proxy server name and port in preferences</li>
4703 <li>Multiple URL links from sequence ids</li>
4704 <li>User Defined Colours can have a scheme name and added
4706 <li>Choose to ignore gaps in consensus calculation</li>
4707 <li>Unix users can set default web browser</li>
4708 <li>Runs without GUI for batch processing</li>
4709 <li>Dynamically generated Web Service Menus</li>
4714 <li>InstallAnywhere download for Sparc Solaris</li>
4720 <div align="center">
4721 <strong>2.02</strong><br> 18/7/05
4727 <li>Copy & Paste order of sequences maintains
4728 alignment order.</li>
4734 <div align="center">
4735 <strong>2.01</strong><br> 12/7/05
4740 <li>Use delete key for deleting selection.</li>
4741 <li>Use Mouse wheel to scroll sequences.</li>
4742 <li>Help file updated to describe how to add alignment
4744 <li>Version and build date written to build properties
4746 <li>InstallAnywhere installation will check for updates
4747 at launch of Jalview.</li>
4752 <li>Delete gaps bug fixed.</li>
4753 <li>FileChooser sorts columns.</li>
4754 <li>Can remove groups one by one.</li>
4755 <li>Filechooser icons installed.</li>
4756 <li>Finder ignores return character when searching.
4757 Return key will initiate a search.<br>
4764 <div align="center">
4765 <strong>2.0</strong><br> 20/6/05
4770 <li>New codebase</li>