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>9/04/2020</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
123 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
125 </ul> <em>Build System</em>
128 <!-- JAL-3510 -->Clover updated to 4.4.1
131 <!-- JAL-3513 -->Test code included in Clover coverage
135 <em>Groovy Scripts</em>
138 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
139 to stdout containing the consensus sequence for each
140 alignment in a Jalview session
144 <td align="left" valign="top">
147 <!-- JAL-3581 -->Hidden sequence markers still visible when
148 'Show hidden markers' option is not ticked
151 <!-- JAL-3571 -->Feature Editor dialog can be opened when
152 'Show Sequence Features' option is not ticked
155 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
156 buttons in Feature Settings dialog are clicked when no
160 <!-- JAL-3412 -->ID margins for CDS and Protein views not
161 equal when split frame is first opened
164 <!-- JAL-3296 -->Sequence position numbers in status bar not
165 correct after editing a sequence's start position
168 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
169 with annotation and exceptions thrown when only a few
170 columns shown in wrapped mode
173 <!-- JAL-3386 -->Sequence IDs missing in headless export of
174 wrapped alignment figure with annotations
177 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
178 ID fails with ClassCastException
181 <!-- JAL-3389 -->Chimera session not restored from Jalview
185 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
186 feature settings dialog also selects columns
189 <!-- JAL-3473 -->SpinnerNumberModel causes
190 IllegalArgumentException in some circumstances
193 <!-- JAL-3534 -->Multiple feature settings dialogs can be
197 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
198 alignment window is closed
201 <!-- JAL-3406 -->Credits missing some authors in Jalview
202 help documentation for 2.11.0 release
204 </ul> <em>Java 11 Compatibility issues</em>
207 <!-- JAL-2987 -->OSX - Can't view some search results in
208 PDB/Uniprot search panel
210 </ul> <em>Installer</em>
213 <!-- JAL-3447 -->Jalview should not create file associations
214 for 3D structure files (.pdb, .mmcif. .cif)
216 </ul> <em>Repository and Source Release</em>
219 <!-- JAL-3474 -->removed obsolete .cvsignore files from
223 <!-- JAL-3541 -->Clover report generation running out of
226 </ul> <em>New Known Issues</em>
229 <!-- JAL-3523 -->OSX - Current working directory not
230 preserved when Jalview.app launched with parameters from
234 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
235 clipped in headless figure export when Right Align option
239 <!-- JAL-3542 -->Jalview Installation type always reports
240 'Source' in console output
243 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
244 bamboo server but run fine locally.
250 <td width="60" align="center" nowrap>
251 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
252 <em>04/07/2019</em></strong>
254 <td align="left" valign="top">
257 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
258 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
259 source project) rather than InstallAnywhere
262 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
263 settings, receive over the air updates and launch specific
264 versions via (<a href="https://github.com/threerings/getdown">Three
268 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
269 formats supported by Jalview (including .jvp project files)
272 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
273 arguments and switch between different getdown channels
276 <!-- JAL-3141 -->Backup files created when saving Jalview project
281 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
282 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
284 <!-- JAL-2620 -->Alternative genetic code tables for
285 'Translate as cDNA'</li>
287 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
288 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
291 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
292 implementation that allows updates) used for Sequence Feature collections</li>
294 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
295 features can be filtered and shaded according to any
296 associated attributes (e.g. variant attributes from VCF
297 file, or key-value pairs imported from column 9 of GFF
301 <!-- JAL-2879 -->Feature Attributes and shading schemes
302 stored and restored from Jalview Projects
305 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
306 recognise variant features
309 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
310 sequences (also coloured red by default)
313 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
317 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
318 algorithm (Z-sort/transparency and filter aware)
321 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
327 <!-- JAL-3205 -->Symmetric score matrices for faster
328 tree and PCA calculations
330 <li><strong>Principal Components Analysis Viewer</strong>
333 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
334 and Viewer state saved in Jalview Project
336 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
339 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
343 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
348 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
350 <li><strong>Speed and Efficiency</strong>
353 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
354 multiple groups when working with large alignments
357 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
361 <li><strong>User Interface</strong>
364 <!-- JAL-2933 -->Finder panel remembers last position in each
368 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
369 what is shown)<br />Only visible regions of alignment are shown by
370 default (can be changed in user preferences)
373 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
374 to the Overwrite Dialog
377 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
381 <!-- JAL-1244 -->Status bar shows bounds when dragging a
382 selection region, and gap count when inserting or deleting gaps
385 <!-- JAL-3132 -->Status bar updates over sequence and annotation
389 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
393 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
397 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
400 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
404 <!-- JAL-3181 -->Consistent ordering of links in sequence id
408 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
410 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
414 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
415 <li><strong>Java 11 Support (not yet on general release)</strong>
418 <!-- -->OSX GUI integrations for App menu's 'About' entry and
423 <em>Deprecations</em>
425 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
426 capabilities removed from the Jalview Desktop
428 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
429 unmarshalling has been replaced by JAXB for Jalview projects
430 and XML based data retrieval clients</li>
431 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
432 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
433 </ul> <em>Documentation</em>
435 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
436 not supported in EPS figure export
438 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
439 </ul> <em>Development and Release Processes</em>
442 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
445 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
447 <!-- JAL-3225 -->Eclipse project configuration managed with
451 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
452 Bamboo continuous integration for unattended Test Suite
456 <!-- JAL-2864 -->Memory test suite to detect leaks in common
460 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
464 <!-- JAL-3248 -->Developer documentation migrated to
465 markdown (with HTML rendering)
468 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
471 <!-- JAL-3289 -->New URLs for publishing development
476 <td align="left" valign="top">
479 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
482 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
483 superposition in Jmol fail on Windows
486 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
487 structures for sequences with lots of PDB structures
490 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
494 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
495 project involving multiple views
498 <!-- JAL-3164 -->Overview for complementary view in a linked
499 CDS/Protein alignment is not updated when Hide Columns by
500 Annotation dialog hides columns
503 <!-- JAL-3158 -->Selection highlighting in the complement of a
504 CDS/Protein alignment stops working after making a selection in
505 one view, then making another selection in the other view
508 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
512 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
513 Settings and Jalview Preferences panels
516 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
517 overview with large alignments
520 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
521 region if columns were selected by dragging right-to-left and the
522 mouse moved to the left of the first column
525 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
526 hidden column marker via scale popup menu
529 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
530 doesn't tell users the invalid URL
533 <!-- JAL-2816 -->Tooltips displayed for features filtered by
537 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
538 show cross references or Fetch Database References are shown in
542 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
543 peptide sequence (computed variant shown as p.Res.null)
546 <!-- JAL-2060 -->'Graduated colour' option not offered for
547 manually created features (where feature score is Float.NaN)
550 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
551 when columns are hidden
554 <!-- JAL-3082 -->Regular expression error for '(' in Select
555 Columns by Annotation description
558 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
559 out of Scale or Annotation Panel
562 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
566 <!-- JAL-3074 -->Left/right drag in annotation can scroll
570 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
574 <!-- JAL-3002 -->Column display is out by one after Page Down,
575 Page Up in wrapped mode
578 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
581 <!-- JAL-2932 -->Finder searches in minimised alignments
584 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
585 on opening an alignment
588 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
592 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
593 different groups in the alignment are selected
596 <!-- JAL-2717 -->Internationalised colour scheme names not shown
600 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
604 <!-- JAL-3125 -->Value input for graduated feature colour
605 threshold gets 'unrounded'
608 <!-- JAL-2982 -->PCA image export doesn't respect background
612 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
615 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
618 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
622 <!-- JAL-2964 -->Associate Tree with All Views not restored from
626 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
627 shown in complementary view
630 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
631 without normalisation
634 <!-- JAL-3021 -->Sequence Details report should open positioned at top
638 <!-- JAL-914 -->Help page can be opened twice
641 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
643 </ul> <em>Editing</em>
646 <!-- JAL-2822 -->Start and End should be updated when sequence
647 data at beginning or end of alignment added/removed via 'Edit'
651 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
652 relocate sequence features correctly when start of sequence is
653 removed (Known defect since 2.10)
656 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
657 dialog corrupts dataset sequence
660 <!-- JAL-868 -->Structure colours not updated when associated tree
661 repartitions the alignment view (Regression in 2.10.5)
663 </ul> <em>Datamodel</em>
666 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
667 sequence's End is greater than its length
669 </ul> <em>Bugs fixed for Java 11 Support (not yet on
670 general release)</em>
673 <!-- JAL-3288 -->Menus work properly in split-screen
675 </ul> <em>New Known Defects</em>
678 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
681 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
682 regions of protein alignment.
685 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
686 is restored from a Jalview 2.11 project
689 <!-- JAL-3213 -->Alignment panel height can be too small after
693 <!-- JAL-3240 -->Display is incorrect after removing gapped
694 columns within hidden columns
697 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
698 window after dragging left to select columns to left of visible
702 <!-- JAL-2876 -->Features coloured according to their description
703 string and thresholded by score in earlier versions of Jalview are
704 not shown as thresholded features in 2.11. To workaround please
705 create a Score filter instead.
708 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
710 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
713 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
714 alignments with multiple views can close views unexpectedly
717 <em>Java 11 Specific defects</em>
720 <!-- JAL-3235 -->Jalview Properties file is not sorted
721 alphabetically when saved
727 <td width="60" nowrap>
729 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
732 <td><div align="left">
736 <!-- JAL-3101 -->Default memory for Jalview webstart and
737 InstallAnywhere increased to 1G.
740 <!-- JAL-247 -->Hidden sequence markers and representative
741 sequence bolding included when exporting alignment as EPS,
742 SVG, PNG or HTML. <em>Display is configured via the
743 Format menu, or for command-line use via a Jalview
744 properties file.</em>
747 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
748 API and sequence data now imported as JSON.
751 <!-- JAL-3065 -->Change in recommended way of starting
752 Jalview via a Java command line: add jars in lib directory
753 to CLASSPATH, rather than via the deprecated java.ext.dirs
760 <!-- JAL-3047 -->Support added to execute test suite
761 instrumented with <a href="http://openclover.org/">Open
766 <td><div align="left">
770 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
771 row shown in Feredoxin Structure alignment view of example
775 <!-- JAL-2854 -->Annotation obscures sequences if lots of
776 annotation displayed.
779 <!-- JAL-3107 -->Group conservation/consensus not shown
780 for newly created group when 'Apply to all groups'
784 <!-- JAL-3087 -->Corrupted display when switching to
785 wrapped mode when sequence panel's vertical scrollbar is
789 <!-- JAL-3003 -->Alignment is black in exported EPS file
790 when sequences are selected in exported view.</em>
793 <!-- JAL-3059 -->Groups with different coloured borders
794 aren't rendered with correct colour.
797 <!-- JAL-3092 -->Jalview could hang when importing certain
798 types of knotted RNA secondary structure.
801 <!-- JAL-3095 -->Sequence highlight and selection in
802 trimmed VARNA 2D structure is incorrect for sequences that
806 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
807 annotation when columns are inserted into an alignment,
808 and when exporting as Stockholm flatfile.
811 <!-- JAL-3053 -->Jalview annotation rows containing upper
812 and lower-case 'E' and 'H' do not automatically get
813 treated as RNA secondary structure.
816 <!-- JAL-3106 -->.jvp should be used as default extension
817 (not .jar) when saving a Jalview project file.
820 <!-- JAL-3105 -->Mac Users: closing a window correctly
821 transfers focus to previous window on OSX
824 <em>Java 10 Issues Resolved</em>
827 <!-- JAL-2988 -->OSX - Can't save new files via the File
828 or export menus by typing in a name into the Save dialog
832 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
833 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
834 'look and feel' which has improved compatibility with the
835 latest version of OSX.
842 <td width="60" nowrap>
844 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
845 <em>7/06/2018</em></strong>
848 <td><div align="left">
852 <!-- JAL-2920 -->Use HGVS nomenclature for variant
853 annotation retrieved from Uniprot
856 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
857 onto the Jalview Desktop
861 <td><div align="left">
865 <!-- JAL-3017 -->Cannot import features with multiple
866 variant elements (blocks import of some Uniprot records)
869 <!-- JAL-2997 -->Clustal files with sequence positions in
870 right-hand column parsed correctly
873 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
874 not alignment area in exported graphic
877 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
878 window has input focus
881 <!-- JAL-2992 -->Annotation panel set too high when
882 annotation added to view (Windows)
885 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
886 network connectivity is poor
889 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
890 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
891 the currently open URL and links from a page viewed in
892 Firefox or Chrome on Windows is now fully supported. If
893 you are using Edge, only links in the page can be
894 dragged, and with Internet Explorer, only the currently
895 open URL in the browser can be dropped onto Jalview.</em>
898 <em>New Known Defects</em>
900 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
905 <td width="60" nowrap>
907 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
910 <td><div align="left">
914 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
915 for disabling automatic superposition of multiple
916 structures and open structures in existing views
919 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
920 ID and annotation area margins can be click-dragged to
924 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
928 <!-- JAL-2759 -->Improved performance for large alignments
929 and lots of hidden columns
932 <!-- JAL-2593 -->Improved performance when rendering lots
933 of features (particularly when transparency is disabled)
936 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
937 exchange of Jalview features and Chimera attributes made
943 <td><div align="left">
946 <!-- JAL-2899 -->Structure and Overview aren't updated
947 when Colour By Annotation threshold slider is adjusted
950 <!-- JAL-2778 -->Slow redraw when Overview panel shown
951 overlapping alignment panel
954 <!-- JAL-2929 -->Overview doesn't show end of unpadded
958 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
959 improved: CDS not handled correctly if transcript has no
963 <!-- JAL-2321 -->Secondary structure and temperature
964 factor annotation not added to sequence when local PDB
965 file associated with it by drag'n'drop or structure
969 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
970 dialog doesn't import PDB files dropped on an alignment
973 <!-- JAL-2666 -->Linked scrolling via protein horizontal
974 scroll bar doesn't work for some CDS/Protein views
977 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
978 Java 1.8u153 onwards and Java 1.9u4+.
981 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
982 columns in annotation row
985 <!-- JAL-2913 -->Preferences panel's ID Width control is not
986 honored in batch mode
989 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
990 for structures added to existing Jmol view
993 <!-- JAL-2223 -->'View Mappings' includes duplicate
994 entries after importing project with multiple views
997 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
998 protein sequences via SIFTS from associated PDB entries
999 with negative residue numbers or missing residues fails
1002 <!-- JAL-2952 -->Exception when shading sequence with negative
1003 Temperature Factor values from annotated PDB files (e.g.
1004 as generated by CONSURF)
1007 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1008 tooltip doesn't include a text description of mutation
1011 <!-- JAL-2922 -->Invert displayed features very slow when
1012 structure and/or overview windows are also shown
1015 <!-- JAL-2954 -->Selecting columns from highlighted regions
1016 very slow for alignments with large numbers of sequences
1019 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1020 with 'StringIndexOutOfBounds'
1023 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1024 platforms running Java 10
1027 <!-- JAL-2960 -->Adding a structure to existing structure
1028 view appears to do nothing because the view is hidden behind the alignment view
1034 <!-- JAL-2926 -->Copy consensus sequence option in applet
1035 should copy the group consensus when popup is opened on it
1041 <!-- JAL-2913 -->Fixed ID width preference is not respected
1044 <em>New Known Defects</em>
1047 <!-- JAL-2973 --> Exceptions occasionally raised when
1048 editing a large alignment and overview is displayed
1051 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1052 repeatedly after a series of edits even when the overview
1053 is no longer reflecting updates
1056 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1057 structures for protein subsequence (if 'Trim Retrieved
1058 Sequences' enabled) or Ensembl isoforms (Workaround in
1059 2.10.4 is to fail back to N&W mapping)
1062 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1063 option gives blank output
1070 <td width="60" nowrap>
1071 <div align="center">
1072 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1075 <td><div align="left">
1076 <ul><li>Updated Certum Codesigning Certificate
1077 (Valid till 30th November 2018)</li></ul></div></td>
1078 <td><div align="left">
1079 <em>Desktop</em><ul>
1081 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1082 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1083 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1084 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1085 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1086 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1087 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1093 <td width="60" nowrap>
1094 <div align="center">
1095 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1098 <td><div align="left">
1102 <!-- JAL-2446 -->Faster and more efficient management and
1103 rendering of sequence features
1106 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1107 429 rate limit request hander
1110 <!-- JAL-2773 -->Structure views don't get updated unless
1111 their colours have changed
1114 <!-- JAL-2495 -->All linked sequences are highlighted for
1115 a structure mousover (Jmol) or selection (Chimera)
1118 <!-- JAL-2790 -->'Cancel' button in progress bar for
1119 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1122 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1123 view from Ensembl locus cross-references
1126 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1130 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1131 feature can be disabled
1134 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1135 PDB easier retrieval of sequences for lists of IDs
1138 <!-- JAL-2758 -->Short names for sequences retrieved from
1144 <li>Groovy interpreter updated to 2.4.12</li>
1145 <li>Example groovy script for generating a matrix of
1146 percent identity scores for current alignment.</li>
1148 <em>Testing and Deployment</em>
1151 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1155 <td><div align="left">
1159 <!-- JAL-2643 -->Pressing tab after updating the colour
1160 threshold text field doesn't trigger an update to the
1164 <!-- JAL-2682 -->Race condition when parsing sequence ID
1168 <!-- JAL-2608 -->Overview windows are also closed when
1169 alignment window is closed
1172 <!-- JAL-2548 -->Export of features doesn't always respect
1176 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1177 takes a long time in Cursor mode
1183 <!-- JAL-2777 -->Structures with whitespace chainCode
1184 cannot be viewed in Chimera
1187 <!-- JAL-2728 -->Protein annotation panel too high in
1191 <!-- JAL-2757 -->Can't edit the query after the server
1192 error warning icon is shown in Uniprot and PDB Free Text
1196 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1199 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1202 <!-- JAL-2739 -->Hidden column marker in last column not
1203 rendered when switching back from Wrapped to normal view
1206 <!-- JAL-2768 -->Annotation display corrupted when
1207 scrolling right in unwapped alignment view
1210 <!-- JAL-2542 -->Existing features on subsequence
1211 incorrectly relocated when full sequence retrieved from
1215 <!-- JAL-2733 -->Last reported memory still shown when
1216 Desktop->Show Memory is unticked (OSX only)
1219 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1220 features of same type and group to be selected for
1224 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1225 alignments when hidden columns are present
1228 <!-- JAL-2392 -->Jalview freezes when loading and
1229 displaying several structures
1232 <!-- JAL-2732 -->Black outlines left after resizing or
1236 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1237 within the Jalview desktop on OSX
1240 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1241 when in wrapped alignment mode
1244 <!-- JAL-2636 -->Scale mark not shown when close to right
1245 hand end of alignment
1248 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1249 each selected sequence do not have correct start/end
1253 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1254 after canceling the Alignment Window's Font dialog
1257 <!-- JAL-2036 -->Show cross-references not enabled after
1258 restoring project until a new view is created
1261 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1262 URL links appears when only default EMBL-EBI link is
1263 configured (since 2.10.2b2)
1266 <!-- JAL-2775 -->Overview redraws whole window when box
1267 position is adjusted
1270 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1271 in a multi-chain structure when viewing alignment
1272 involving more than one chain (since 2.10)
1275 <!-- JAL-2811 -->Double residue highlights in cursor mode
1276 if new selection moves alignment window
1279 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1280 arrow key in cursor mode to pass hidden column marker
1283 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1284 that produces correctly annotated transcripts and products
1287 <!-- JAL-2776 -->Toggling a feature group after first time
1288 doesn't update associated structure view
1291 <em>Applet</em><br />
1294 <!-- JAL-2687 -->Concurrent modification exception when
1295 closing alignment panel
1298 <em>BioJSON</em><br />
1301 <!-- JAL-2546 -->BioJSON export does not preserve
1302 non-positional features
1305 <em>New Known Issues</em>
1308 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1309 sequence features correctly (for many previous versions of
1313 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1314 using cursor in wrapped panel other than top
1317 <!-- JAL-2791 -->Select columns containing feature ignores
1318 graduated colour threshold
1321 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1322 always preserve numbering and sequence features
1325 <em>Known Java 9 Issues</em>
1328 <!-- JAL-2902 -->Groovy Console very slow to open and is
1329 not responsive when entering characters (Webstart, Java
1336 <td width="60" nowrap>
1337 <div align="center">
1338 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1339 <em>2/10/2017</em></strong>
1342 <td><div align="left">
1343 <em>New features in Jalview Desktop</em>
1346 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1348 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1352 <td><div align="left">
1356 <td width="60" nowrap>
1357 <div align="center">
1358 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1359 <em>7/9/2017</em></strong>
1362 <td><div align="left">
1366 <!-- JAL-2588 -->Show gaps in overview window by colouring
1367 in grey (sequences used to be coloured grey, and gaps were
1371 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1375 <!-- JAL-2587 -->Overview updates immediately on increase
1376 in size and progress bar shown as higher resolution
1377 overview is recalculated
1382 <td><div align="left">
1386 <!-- JAL-2664 -->Overview window redraws every hidden
1387 column region row by row
1390 <!-- JAL-2681 -->duplicate protein sequences shown after
1391 retrieving Ensembl crossrefs for sequences from Uniprot
1394 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1395 format setting is unticked
1398 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1399 if group has show boxes format setting unticked
1402 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1403 autoscrolling whilst dragging current selection group to
1404 include sequences and columns not currently displayed
1407 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1408 assemblies are imported via CIF file
1411 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1412 displayed when threshold or conservation colouring is also
1416 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1420 <!-- JAL-2673 -->Jalview continues to scroll after
1421 dragging a selected region off the visible region of the
1425 <!-- JAL-2724 -->Cannot apply annotation based
1426 colourscheme to all groups in a view
1429 <!-- JAL-2511 -->IDs don't line up with sequences
1430 initially after font size change using the Font chooser or
1437 <td width="60" nowrap>
1438 <div align="center">
1439 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1442 <td><div align="left">
1443 <em>Calculations</em>
1447 <!-- JAL-1933 -->Occupancy annotation row shows number of
1448 ungapped positions in each column of the alignment.
1451 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1452 a calculation dialog box
1455 <!-- JAL-2379 -->Revised implementation of PCA for speed
1456 and memory efficiency (~30x faster)
1459 <!-- JAL-2403 -->Revised implementation of sequence
1460 similarity scores as used by Tree, PCA, Shading Consensus
1461 and other calculations
1464 <!-- JAL-2416 -->Score matrices are stored as resource
1465 files within the Jalview codebase
1468 <!-- JAL-2500 -->Trees computed on Sequence Feature
1469 Similarity may have different topology due to increased
1476 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1477 model for alignments and groups
1480 <!-- JAL-384 -->Custom shading schemes created via groovy
1487 <!-- JAL-2526 -->Efficiency improvements for interacting
1488 with alignment and overview windows
1491 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1495 <!-- JAL-2388 -->Hidden columns and sequences can be
1499 <!-- JAL-2611 -->Click-drag in visible area allows fine
1500 adjustment of visible position
1504 <em>Data import/export</em>
1507 <!-- JAL-2535 -->Posterior probability annotation from
1508 Stockholm files imported as sequence associated annotation
1511 <!-- JAL-2507 -->More robust per-sequence positional
1512 annotation input/output via stockholm flatfile
1515 <!-- JAL-2533 -->Sequence names don't include file
1516 extension when importing structure files without embedded
1517 names or PDB accessions
1520 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1521 format sequence substitution matrices
1524 <em>User Interface</em>
1527 <!-- JAL-2447 --> Experimental Features Checkbox in
1528 Desktop's Tools menu to hide or show untested features in
1532 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1533 via Overview or sequence motif search operations
1536 <!-- JAL-2547 -->Amend sequence features dialog box can be
1537 opened by double clicking gaps within sequence feature
1541 <!-- JAL-1476 -->Status bar message shown when not enough
1542 aligned positions were available to create a 3D structure
1546 <em>3D Structure</em>
1549 <!-- JAL-2430 -->Hidden regions in alignment views are not
1550 coloured in linked structure views
1553 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1554 file-based command exchange
1557 <!-- JAL-2375 -->Structure chooser automatically shows
1558 Cached Structures rather than querying the PDBe if
1559 structures are already available for sequences
1562 <!-- JAL-2520 -->Structures imported via URL are cached in
1563 the Jalview project rather than downloaded again when the
1564 project is reopened.
1567 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1568 to transfer Chimera's structure attributes as Jalview
1569 features, and vice-versa (<strong>Experimental
1573 <em>Web Services</em>
1576 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1579 <!-- JAL-2335 -->Filter non-standard amino acids and
1580 nucleotides when submitting to AACon and other MSA
1584 <!-- JAL-2316, -->URLs for viewing database
1585 cross-references provided by identifiers.org and the
1586 EMBL-EBI's MIRIAM DB
1593 <!-- JAL-2344 -->FileFormatI interface for describing and
1594 identifying file formats (instead of String constants)
1597 <!-- JAL-2228 -->FeatureCounter script refactored for
1598 efficiency when counting all displayed features (not
1599 backwards compatible with 2.10.1)
1602 <em>Example files</em>
1605 <!-- JAL-2631 -->Graduated feature colour style example
1606 included in the example feature file
1609 <em>Documentation</em>
1612 <!-- JAL-2339 -->Release notes reformatted for readability
1613 with the built-in Java help viewer
1616 <!-- JAL-1644 -->Find documentation updated with 'search
1617 sequence description' option
1623 <!-- JAL-2485, -->External service integration tests for
1624 Uniprot REST Free Text Search Client
1627 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1630 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1635 <td><div align="left">
1636 <em>Calculations</em>
1639 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1640 matrix - C->R should be '-3'<br />Old matrix restored
1641 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1643 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1644 Jalview's treatment of gaps in PCA and substitution matrix
1645 based Tree calculations.<br /> <br />In earlier versions
1646 of Jalview, gaps matching gaps were penalised, and gaps
1647 matching non-gaps penalised even more. In the PCA
1648 calculation, gaps were actually treated as non-gaps - so
1649 different costs were applied, which meant Jalview's PCAs
1650 were different to those produced by SeqSpace.<br />Jalview
1651 now treats gaps in the same way as SeqSpace (ie it scores
1652 them as 0). <br /> <br />Enter the following in the
1653 Groovy console to restore pre-2.10.2 behaviour:<br />
1654 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1655 // for 2.10.1 mode <br />
1656 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1657 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1658 these settings will affect all subsequent tree and PCA
1659 calculations (not recommended)</em></li>
1661 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1662 scaling of branch lengths for trees computed using
1663 Sequence Feature Similarity.
1666 <!-- JAL-2377 -->PCA calculation could hang when
1667 generating output report when working with highly
1668 redundant alignments
1671 <!-- JAL-2544 --> Sort by features includes features to
1672 right of selected region when gaps present on right-hand
1676 <em>User Interface</em>
1679 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1680 doesn't reselect a specific sequence's associated
1681 annotation after it was used for colouring a view
1684 <!-- JAL-2419 -->Current selection lost if popup menu
1685 opened on a region of alignment without groups
1688 <!-- JAL-2374 -->Popup menu not always shown for regions
1689 of an alignment with overlapping groups
1692 <!-- JAL-2310 -->Finder double counts if both a sequence's
1693 name and description match
1696 <!-- JAL-2370 -->Hiding column selection containing two
1697 hidden regions results in incorrect hidden regions
1700 <!-- JAL-2386 -->'Apply to all groups' setting when
1701 changing colour does not apply Conservation slider value
1705 <!-- JAL-2373 -->Percentage identity and conservation menu
1706 items do not show a tick or allow shading to be disabled
1709 <!-- JAL-2385 -->Conservation shading or PID threshold
1710 lost when base colourscheme changed if slider not visible
1713 <!-- JAL-2547 -->Sequence features shown in tooltip for
1714 gaps before start of features
1717 <!-- JAL-2623 -->Graduated feature colour threshold not
1718 restored to UI when feature colour is edited
1721 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1722 a time when scrolling vertically in wrapped mode.
1725 <!-- JAL-2630 -->Structure and alignment overview update
1726 as graduate feature colour settings are modified via the
1730 <!-- JAL-2034 -->Overview window doesn't always update
1731 when a group defined on the alignment is resized
1734 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1735 wrapped view result in positional status updates
1739 <!-- JAL-2563 -->Status bar doesn't show position for
1740 ambiguous amino acid and nucleotide symbols
1743 <!-- JAL-2602 -->Copy consensus sequence failed if
1744 alignment included gapped columns
1747 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1748 widgets don't permanently disappear
1751 <!-- JAL-2503 -->Cannot select or filter quantitative
1752 annotation that are shown only as column labels (e.g.
1753 T-Coffee column reliability scores)
1756 <!-- JAL-2594 -->Exception thrown if trying to create a
1757 sequence feature on gaps only
1760 <!-- JAL-2504 -->Features created with 'New feature'
1761 button from a Find inherit previously defined feature type
1762 rather than the Find query string
1765 <!-- JAL-2423 -->incorrect title in output window when
1766 exporting tree calculated in Jalview
1769 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1770 and then revealing them reorders sequences on the
1774 <!-- JAL-964 -->Group panel in sequence feature settings
1775 doesn't update to reflect available set of groups after
1776 interactively adding or modifying features
1779 <!-- JAL-2225 -->Sequence Database chooser unusable on
1783 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1784 only excluded gaps in current sequence and ignored
1791 <!-- JAL-2421 -->Overview window visible region moves
1792 erratically when hidden rows or columns are present
1795 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1796 Structure Viewer's colour menu don't correspond to
1800 <!-- JAL-2405 -->Protein specific colours only offered in
1801 colour and group colour menu for protein alignments
1804 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1805 reflect currently selected view or group's shading
1809 <!-- JAL-2624 -->Feature colour thresholds not respected
1810 when rendered on overview and structures when opacity at
1814 <!-- JAL-2589 -->User defined gap colour not shown in
1815 overview when features overlaid on alignment
1818 <!-- JAL-2567 -->Feature settings for different views not
1819 recovered correctly from Jalview project file
1822 <!-- JAL-2256 -->Feature colours in overview when first opened
1823 (automatically via preferences) are different to the main
1827 <em>Data import/export</em>
1830 <!-- JAL-2576 -->Very large alignments take a long time to
1834 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1835 added after a sequence was imported are not written to
1839 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1840 when importing RNA secondary structure via Stockholm
1843 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1844 not shown in correct direction for simple pseudoknots
1847 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1848 with lightGray or darkGray via features file (but can
1852 <!-- JAL-2383 -->Above PID colour threshold not recovered
1853 when alignment view imported from project
1856 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1857 structure and sequences extracted from structure files
1858 imported via URL and viewed in Jmol
1861 <!-- JAL-2520 -->Structures loaded via URL are saved in
1862 Jalview Projects rather than fetched via URL again when
1863 the project is loaded and the structure viewed
1866 <em>Web Services</em>
1869 <!-- JAL-2519 -->EnsemblGenomes example failing after
1870 release of Ensembl v.88
1873 <!-- JAL-2366 -->Proxy server address and port always
1874 appear enabled in Preferences->Connections
1877 <!-- JAL-2461 -->DAS registry not found exceptions
1878 removed from console output
1881 <!-- JAL-2582 -->Cannot retrieve protein products from
1882 Ensembl by Peptide ID
1885 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1886 created from SIFTs, and spurious 'Couldn't open structure
1887 in Chimera' errors raised after April 2017 update (problem
1888 due to 'null' string rather than empty string used for
1889 residues with no corresponding PDB mapping).
1892 <em>Application UI</em>
1895 <!-- JAL-2361 -->User Defined Colours not added to Colour
1899 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1900 case' residues (button in colourscheme editor debugged and
1901 new documentation and tooltips added)
1904 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1905 doesn't restore group-specific text colour thresholds
1908 <!-- JAL-2243 -->Feature settings panel does not update as
1909 new features are added to alignment
1912 <!-- JAL-2532 -->Cancel in feature settings reverts
1913 changes to feature colours via the Amend features dialog
1916 <!-- JAL-2506 -->Null pointer exception when attempting to
1917 edit graduated feature colour via amend features dialog
1921 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1922 selection menu changes colours of alignment views
1925 <!-- JAL-2426 -->Spurious exceptions in console raised
1926 from alignment calculation workers after alignment has
1930 <!-- JAL-1608 -->Typo in selection popup menu - Create
1931 groups now 'Create Group'
1934 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1935 Create/Undefine group doesn't always work
1938 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1939 shown again after pressing 'Cancel'
1942 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1943 adjusts start position in wrap mode
1946 <!-- JAL-2563 -->Status bar doesn't show positions for
1947 ambiguous amino acids
1950 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1951 CDS/Protein view after CDS sequences added for aligned
1955 <!-- JAL-2592 -->User defined colourschemes called 'User
1956 Defined' don't appear in Colours menu
1962 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1963 score models doesn't always result in an updated PCA plot
1966 <!-- JAL-2442 -->Features not rendered as transparent on
1967 overview or linked structure view
1970 <!-- JAL-2372 -->Colour group by conservation doesn't
1974 <!-- JAL-2517 -->Hitting Cancel after applying
1975 user-defined colourscheme doesn't restore original
1982 <!-- JAL-2314 -->Unit test failure:
1983 jalview.ws.jabaws.RNAStructExportImport setup fails
1986 <!-- JAL-2307 -->Unit test failure:
1987 jalview.ws.sifts.SiftsClientTest due to compatibility
1988 problems with deep array comparison equality asserts in
1989 successive versions of TestNG
1992 <!-- JAL-2479 -->Relocated StructureChooserTest and
1993 ParameterUtilsTest Unit tests to Network suite
1996 <em>New Known Issues</em>
1999 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2000 phase after a sequence motif find operation
2003 <!-- JAL-2550 -->Importing annotation file with rows
2004 containing just upper and lower case letters are
2005 interpreted as WUSS RNA secondary structure symbols
2008 <!-- JAL-2590 -->Cannot load and display Newick trees
2009 reliably from eggnog Ortholog database
2012 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2013 containing features of type Highlight' when 'B' is pressed
2014 to mark columns containing highlighted regions.
2017 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2018 doesn't always add secondary structure annotation.
2023 <td width="60" nowrap>
2024 <div align="center">
2025 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2028 <td><div align="left">
2032 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2033 for all consensus calculations
2036 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2039 <li>Updated Jalview's Certum code signing certificate
2042 <em>Application</em>
2045 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2046 set of database cross-references, sorted alphabetically
2049 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2050 from database cross references. Users with custom links
2051 will receive a <a href="webServices/urllinks.html#warning">warning
2052 dialog</a> asking them to update their preferences.
2055 <!-- JAL-2287-->Cancel button and escape listener on
2056 dialog warning user about disconnecting Jalview from a
2060 <!-- JAL-2320-->Jalview's Chimera control window closes if
2061 the Chimera it is connected to is shut down
2064 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2065 columns menu item to mark columns containing highlighted
2066 regions (e.g. from structure selections or results of a
2070 <!-- JAL-2284-->Command line option for batch-generation
2071 of HTML pages rendering alignment data with the BioJS
2081 <!-- JAL-2286 -->Columns with more than one modal residue
2082 are not coloured or thresholded according to percent
2083 identity (first observed in Jalview 2.8.2)
2086 <!-- JAL-2301 -->Threonine incorrectly reported as not
2090 <!-- JAL-2318 -->Updates to documentation pages (above PID
2091 threshold, amino acid properties)
2094 <!-- JAL-2292 -->Lower case residues in sequences are not
2095 reported as mapped to residues in a structure file in the
2099 <!--JAL-2324 -->Identical features with non-numeric scores
2100 could be added multiple times to a sequence
2103 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2104 bond features shown as two highlighted residues rather
2105 than a range in linked structure views, and treated
2106 correctly when selecting and computing trees from features
2109 <!-- JAL-2281-->Custom URL links for database
2110 cross-references are matched to database name regardless
2115 <em>Application</em>
2118 <!-- JAL-2282-->Custom URL links for specific database
2119 names without regular expressions also offer links from
2123 <!-- JAL-2315-->Removing a single configured link in the
2124 URL links pane in Connections preferences doesn't actually
2125 update Jalview configuration
2128 <!-- JAL-2272-->CTRL-Click on a selected region to open
2129 the alignment area popup menu doesn't work on El-Capitan
2132 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2133 files with similarly named sequences if dropped onto the
2137 <!-- JAL-2312 -->Additional mappings are shown for PDB
2138 entries where more chains exist in the PDB accession than
2139 are reported in the SIFTS file
2142 <!-- JAL-2317-->Certain structures do not get mapped to
2143 the structure view when displayed with Chimera
2146 <!-- JAL-2317-->No chains shown in the Chimera view
2147 panel's View->Show Chains submenu
2150 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2151 work for wrapped alignment views
2154 <!--JAL-2197 -->Rename UI components for running JPred
2155 predictions from 'JNet' to 'JPred'
2158 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2159 corrupted when annotation panel vertical scroll is not at
2160 first annotation row
2163 <!--JAL-2332 -->Attempting to view structure for Hen
2164 lysozyme results in a PDB Client error dialog box
2167 <!-- JAL-2319 -->Structure View's mapping report switched
2168 ranges for PDB and sequence for SIFTS
2171 SIFTS 'Not_Observed' residues mapped to non-existant
2175 <!-- <em>New Known Issues</em>
2182 <td width="60" nowrap>
2183 <div align="center">
2184 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2185 <em>25/10/2016</em></strong>
2188 <td><em>Application</em>
2190 <li>3D Structure chooser opens with 'Cached structures'
2191 view if structures already loaded</li>
2192 <li>Progress bar reports models as they are loaded to
2193 structure views</li>
2199 <li>Colour by conservation always enabled and no tick
2200 shown in menu when BLOSUM or PID shading applied</li>
2201 <li>FER1_ARATH and FER2_ARATH labels were switched in
2202 example sequences/projects/trees</li>
2204 <em>Application</em>
2206 <li>Jalview projects with views of local PDB structure
2207 files saved on Windows cannot be opened on OSX</li>
2208 <li>Multiple structure views can be opened and superposed
2209 without timeout for structures with multiple models or
2210 multiple sequences in alignment</li>
2211 <li>Cannot import or associated local PDB files without a
2212 PDB ID HEADER line</li>
2213 <li>RMSD is not output in Jmol console when superposition
2215 <li>Drag and drop of URL from Browser fails for Linux and
2216 OSX versions earlier than El Capitan</li>
2217 <li>ENA client ignores invalid content from ENA server</li>
2218 <li>Exceptions are not raised in console when ENA client
2219 attempts to fetch non-existent IDs via Fetch DB Refs UI
2221 <li>Exceptions are not raised in console when a new view
2222 is created on the alignment</li>
2223 <li>OSX right-click fixed for group selections: CMD-click
2224 to insert/remove gaps in groups and CTRL-click to open group
2227 <em>Build and deployment</em>
2229 <li>URL link checker now copes with multi-line anchor
2232 <em>New Known Issues</em>
2234 <li>Drag and drop from URL links in browsers do not work
2241 <td width="60" nowrap>
2242 <div align="center">
2243 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2246 <td><em>General</em>
2249 <!-- JAL-2124 -->Updated Spanish translations.
2252 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2253 for importing structure data to Jalview. Enables mmCIF and
2257 <!-- JAL-192 --->Alignment ruler shows positions relative to
2261 <!-- JAL-2202 -->Position/residue shown in status bar when
2262 mousing over sequence associated annotation
2265 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2269 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2270 '()', canonical '[]' and invalid '{}' base pair populations
2274 <!-- JAL-2092 -->Feature settings popup menu options for
2275 showing or hiding columns containing a feature
2278 <!-- JAL-1557 -->Edit selected group by double clicking on
2279 group and sequence associated annotation labels
2282 <!-- JAL-2236 -->Sequence name added to annotation label in
2283 select/hide columns by annotation and colour by annotation
2287 </ul> <em>Application</em>
2290 <!-- JAL-2050-->Automatically hide introns when opening a
2291 gene/transcript view
2294 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2298 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2299 structure mappings with the EMBL-EBI PDBe SIFTS database
2302 <!-- JAL-2079 -->Updated download sites used for Rfam and
2303 Pfam sources to xfam.org
2306 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2309 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2310 over sequences in Jalview
2313 <!-- JAL-2027-->Support for reverse-complement coding
2314 regions in ENA and EMBL
2317 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2318 for record retrieval via ENA rest API
2321 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2325 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2326 groovy script execution
2329 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2330 alignment window's Calculate menu
2333 <!-- JAL-1812 -->Allow groovy scripts that call
2334 Jalview.getAlignFrames() to run in headless mode
2337 <!-- JAL-2068 -->Support for creating new alignment
2338 calculation workers from groovy scripts
2341 <!-- JAL-1369 --->Store/restore reference sequence in
2345 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2346 associations are now saved/restored from project
2349 <!-- JAL-1993 -->Database selection dialog always shown
2350 before sequence fetcher is opened
2353 <!-- JAL-2183 -->Double click on an entry in Jalview's
2354 database chooser opens a sequence fetcher
2357 <!-- JAL-1563 -->Free-text search client for UniProt using
2358 the UniProt REST API
2361 <!-- JAL-2168 -->-nonews command line parameter to prevent
2362 the news reader opening
2365 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2366 querying stored in preferences
2369 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2373 <!-- JAL-1977-->Tooltips shown on database chooser
2376 <!-- JAL-391 -->Reverse complement function in calculate
2377 menu for nucleotide sequences
2380 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2381 and feature counts preserves alignment ordering (and
2382 debugged for complex feature sets).
2385 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2386 viewing structures with Jalview 2.10
2389 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2390 genome, transcript CCDS and gene ids via the Ensembl and
2391 Ensembl Genomes REST API
2394 <!-- JAL-2049 -->Protein sequence variant annotation
2395 computed for 'sequence_variant' annotation on CDS regions
2399 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2403 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2404 Ref Fetcher fails to match, or otherwise updates sequence
2405 data from external database records.
2408 <!-- JAL-2154 -->Revised Jalview Project format for
2409 efficient recovery of sequence coding and alignment
2410 annotation relationships.
2412 </ul> <!-- <em>Applet</em>
2423 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2427 <!-- JAL-2018-->Export features in Jalview format (again)
2428 includes graduated colourschemes
2431 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2432 working with big alignments and lots of hidden columns
2435 <!-- JAL-2053-->Hidden column markers not always rendered
2436 at right of alignment window
2439 <!-- JAL-2067 -->Tidied up links in help file table of
2443 <!-- JAL-2072 -->Feature based tree calculation not shown
2447 <!-- JAL-2075 -->Hidden columns ignored during feature
2448 based tree calculation
2451 <!-- JAL-2065 -->Alignment view stops updating when show
2452 unconserved enabled for group on alignment
2455 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2459 <!-- JAL-2146 -->Alignment column in status incorrectly
2460 shown as "Sequence position" when mousing over
2464 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2465 hidden columns present
2468 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2469 user created annotation added to alignment
2472 <!-- JAL-1841 -->RNA Structure consensus only computed for
2473 '()' base pair annotation
2476 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2477 in zero scores for all base pairs in RNA Structure
2481 <!-- JAL-2174-->Extend selection with columns containing
2485 <!-- JAL-2275 -->Pfam format writer puts extra space at
2486 beginning of sequence
2489 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2493 <!-- JAL-2238 -->Cannot create groups on an alignment from
2494 from a tree when t-coffee scores are shown
2497 <!-- JAL-1836,1967 -->Cannot import and view PDB
2498 structures with chains containing negative resnums (4q4h)
2501 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2505 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2506 to Clustal, PIR and PileUp output
2509 <!-- JAL-2008 -->Reordering sequence features that are
2510 not visible causes alignment window to repaint
2513 <!-- JAL-2006 -->Threshold sliders don't work in
2514 graduated colour and colour by annotation row for e-value
2515 scores associated with features and annotation rows
2518 <!-- JAL-1797 -->amino acid physicochemical conservation
2519 calculation should be case independent
2522 <!-- JAL-2173 -->Remove annotation also updates hidden
2526 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2527 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2528 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2531 <!-- JAL-2065 -->Null pointer exceptions and redraw
2532 problems when reference sequence defined and 'show
2533 non-conserved' enabled
2536 <!-- JAL-1306 -->Quality and Conservation are now shown on
2537 load even when Consensus calculation is disabled
2540 <!-- JAL-1932 -->Remove right on penultimate column of
2541 alignment does nothing
2544 <em>Application</em>
2547 <!-- JAL-1552-->URLs and links can't be imported by
2548 drag'n'drop on OSX when launched via webstart (note - not
2549 yet fixed for El Capitan)
2552 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2553 output when running on non-gb/us i18n platforms
2556 <!-- JAL-1944 -->Error thrown when exporting a view with
2557 hidden sequences as flat-file alignment
2560 <!-- JAL-2030-->InstallAnywhere distribution fails when
2564 <!-- JAL-2080-->Jalview very slow to launch via webstart
2565 (also hotfix for 2.9.0b2)
2568 <!-- JAL-2085 -->Cannot save project when view has a
2569 reference sequence defined
2572 <!-- JAL-1011 -->Columns are suddenly selected in other
2573 alignments and views when revealing hidden columns
2576 <!-- JAL-1989 -->Hide columns not mirrored in complement
2577 view in a cDNA/Protein splitframe
2580 <!-- JAL-1369 -->Cannot save/restore representative
2581 sequence from project when only one sequence is
2585 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2586 in Structure Chooser
2589 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2590 structure consensus didn't refresh annotation panel
2593 <!-- JAL-1962 -->View mapping in structure view shows
2594 mappings between sequence and all chains in a PDB file
2597 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2598 dialogs format columns correctly, don't display array
2599 data, sort columns according to type
2602 <!-- JAL-1975 -->Export complete shown after destination
2603 file chooser is cancelled during an image export
2606 <!-- JAL-2025 -->Error when querying PDB Service with
2607 sequence name containing special characters
2610 <!-- JAL-2024 -->Manual PDB structure querying should be
2614 <!-- JAL-2104 -->Large tooltips with broken HTML
2615 formatting don't wrap
2618 <!-- JAL-1128 -->Figures exported from wrapped view are
2619 truncated so L looks like I in consensus annotation
2622 <!-- JAL-2003 -->Export features should only export the
2623 currently displayed features for the current selection or
2627 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2628 after fetching cross-references, and restoring from
2632 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2633 followed in the structure viewer
2636 <!-- JAL-2163 -->Titles for individual alignments in
2637 splitframe not restored from project
2640 <!-- JAL-2145 -->missing autocalculated annotation at
2641 trailing end of protein alignment in transcript/product
2642 splitview when pad-gaps not enabled by default
2645 <!-- JAL-1797 -->amino acid physicochemical conservation
2649 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2650 article has been read (reopened issue due to
2651 internationalisation problems)
2654 <!-- JAL-1960 -->Only offer PDB structures in structure
2655 viewer based on sequence name, PDB and UniProt
2660 <!-- JAL-1976 -->No progress bar shown during export of
2664 <!-- JAL-2213 -->Structures not always superimposed after
2665 multiple structures are shown for one or more sequences.
2668 <!-- JAL-1370 -->Reference sequence characters should not
2669 be replaced with '.' when 'Show unconserved' format option
2673 <!-- JAL-1823 -->Cannot specify chain code when entering
2674 specific PDB id for sequence
2677 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2678 'Export hidden sequences' is enabled, but 'export hidden
2679 columns' is disabled.
2682 <!--JAL-2026-->Best Quality option in structure chooser
2683 selects lowest rather than highest resolution structures
2687 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2688 to sequence mapping in 'View Mappings' report
2691 <!-- JAL-2284 -->Unable to read old Jalview projects that
2692 contain non-XML data added after Jalvew wrote project.
2695 <!-- JAL-2118 -->Newly created annotation row reorders
2696 after clicking on it to create new annotation for a
2700 <!-- JAL-1980 -->Null Pointer Exception raised when
2701 pressing Add on an orphaned cut'n'paste window.
2703 <!-- may exclude, this is an external service stability issue JAL-1941
2704 -- > RNA 3D structure not added via DSSR service</li> -->
2709 <!-- JAL-2151 -->Incorrect columns are selected when
2710 hidden columns present before start of sequence
2713 <!-- JAL-1986 -->Missing dependencies on applet pages
2717 <!-- JAL-1947 -->Overview pixel size changes when
2718 sequences are hidden in applet
2721 <!-- JAL-1996 -->Updated instructions for applet
2722 deployment on examples pages.
2729 <td width="60" nowrap>
2730 <div align="center">
2731 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2732 <em>16/10/2015</em></strong>
2735 <td><em>General</em>
2737 <li>Time stamps for signed Jalview application and applet
2742 <em>Application</em>
2744 <li>Duplicate group consensus and conservation rows
2745 shown when tree is partitioned</li>
2746 <li>Erratic behaviour when tree partitions made with
2747 multiple cDNA/Protein split views</li>
2753 <td width="60" nowrap>
2754 <div align="center">
2755 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2756 <em>8/10/2015</em></strong>
2759 <td><em>General</em>
2761 <li>Updated Spanish translations of localized text for
2763 </ul> <em>Application</em>
2765 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2766 <li>Signed OSX InstallAnywhere installer<br></li>
2767 <li>Support for per-sequence based annotations in BioJSON</li>
2768 </ul> <em>Applet</em>
2770 <li>Split frame example added to applet examples page</li>
2771 </ul> <em>Build and Deployment</em>
2774 <!-- JAL-1888 -->New ant target for running Jalview's test
2782 <li>Mapping of cDNA to protein in split frames
2783 incorrect when sequence start > 1</li>
2784 <li>Broken images in filter column by annotation dialog
2786 <li>Feature colours not parsed from features file</li>
2787 <li>Exceptions and incomplete link URLs recovered when
2788 loading a features file containing HTML tags in feature
2792 <em>Application</em>
2794 <li>Annotations corrupted after BioJS export and
2796 <li>Incorrect sequence limits after Fetch DB References
2797 with 'trim retrieved sequences'</li>
2798 <li>Incorrect warning about deleting all data when
2799 deleting selected columns</li>
2800 <li>Patch to build system for shipping properly signed
2801 JNLP templates for webstart launch</li>
2802 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2803 unreleased structures for download or viewing</li>
2804 <li>Tab/space/return keystroke operation of EMBL-PDBe
2805 fetcher/viewer dialogs works correctly</li>
2806 <li>Disabled 'minimise' button on Jalview windows
2807 running on OSX to workaround redraw hang bug</li>
2808 <li>Split cDNA/Protein view position and geometry not
2809 recovered from jalview project</li>
2810 <li>Initial enabled/disabled state of annotation menu
2811 sorter 'show autocalculated first/last' corresponds to
2813 <li>Restoring of Clustal, RNA Helices and T-Coffee
2814 color schemes from BioJSON</li>
2818 <li>Reorder sequences mirrored in cDNA/Protein split
2820 <li>Applet with Jmol examples not loading correctly</li>
2826 <td><div align="center">
2827 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2829 <td><em>General</em>
2831 <li>Linked visualisation and analysis of DNA and Protein
2834 <li>Translated cDNA alignments shown as split protein
2835 and DNA alignment views</li>
2836 <li>Codon consensus annotation for linked protein and
2837 cDNA alignment views</li>
2838 <li>Link cDNA or Protein product sequences by loading
2839 them onto Protein or cDNA alignments</li>
2840 <li>Reconstruct linked cDNA alignment from aligned
2841 protein sequences</li>
2844 <li>Jmol integration updated to Jmol v14.2.14</li>
2845 <li>Import and export of Jalview alignment views as <a
2846 href="features/bioJsonFormat.html">BioJSON</a></li>
2847 <li>New alignment annotation file statements for
2848 reference sequences and marking hidden columns</li>
2849 <li>Reference sequence based alignment shading to
2850 highlight variation</li>
2851 <li>Select or hide columns according to alignment
2853 <li>Find option for locating sequences by description</li>
2854 <li>Conserved physicochemical properties shown in amino
2855 acid conservation row</li>
2856 <li>Alignments can be sorted by number of RNA helices</li>
2857 </ul> <em>Application</em>
2859 <li>New cDNA/Protein analysis capabilities
2861 <li>Get Cross-References should open a Split Frame
2862 view with cDNA/Protein</li>
2863 <li>Detect when nucleotide sequences and protein
2864 sequences are placed in the same alignment</li>
2865 <li>Split cDNA/Protein views are saved in Jalview
2870 <li>Use REST API to talk to Chimera</li>
2871 <li>Selected regions in Chimera are highlighted in linked
2872 Jalview windows</li>
2874 <li>VARNA RNA viewer updated to v3.93</li>
2875 <li>VARNA views are saved in Jalview Projects</li>
2876 <li>Pseudoknots displayed as Jalview RNA annotation can
2877 be shown in VARNA</li>
2879 <li>Make groups for selection uses marked columns as well
2880 as the active selected region</li>
2882 <li>Calculate UPGMA and NJ trees using sequence feature
2884 <li>New Export options
2886 <li>New Export Settings dialog to control hidden
2887 region export in flat file generation</li>
2889 <li>Export alignment views for display with the <a
2890 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2892 <li>Export scrollable SVG in HTML page</li>
2893 <li>Optional embedding of BioJSON data when exporting
2894 alignment figures to HTML</li>
2896 <li>3D structure retrieval and display
2898 <li>Free text and structured queries with the PDBe
2900 <li>PDBe Search API based discovery and selection of
2901 PDB structures for a sequence set</li>
2905 <li>JPred4 employed for protein secondary structure
2907 <li>Hide Insertions menu option to hide unaligned columns
2908 for one or a group of sequences</li>
2909 <li>Automatically hide insertions in alignments imported
2910 from the JPred4 web server</li>
2911 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2912 system on OSX<br />LGPL libraries courtesy of <a
2913 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2915 <li>changed 'View nucleotide structure' submenu to 'View
2916 VARNA 2D Structure'</li>
2917 <li>change "View protein structure" menu option to "3D
2920 </ul> <em>Applet</em>
2922 <li>New layout for applet example pages</li>
2923 <li>New parameters to enable SplitFrame view
2924 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2925 <li>New example demonstrating linked viewing of cDNA and
2926 Protein alignments</li>
2927 </ul> <em>Development and deployment</em>
2929 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2930 <li>Include installation type and git revision in build
2931 properties and console log output</li>
2932 <li>Jalview Github organisation, and new github site for
2933 storing BioJsMSA Templates</li>
2934 <li>Jalview's unit tests now managed with TestNG</li>
2937 <!-- <em>General</em>
2939 </ul> --> <!-- issues resolved --> <em>Application</em>
2941 <li>Escape should close any open find dialogs</li>
2942 <li>Typo in select-by-features status report</li>
2943 <li>Consensus RNA secondary secondary structure
2944 predictions are not highlighted in amber</li>
2945 <li>Missing gap character in v2.7 example file means
2946 alignment appears unaligned when pad-gaps is not enabled</li>
2947 <li>First switch to RNA Helices colouring doesn't colour
2948 associated structure views</li>
2949 <li>ID width preference option is greyed out when auto
2950 width checkbox not enabled</li>
2951 <li>Stopped a warning dialog from being shown when
2952 creating user defined colours</li>
2953 <li>'View Mapping' in structure viewer shows sequence
2954 mappings for just that viewer's sequences</li>
2955 <li>Workaround for superposing PDB files containing
2956 multiple models in Chimera</li>
2957 <li>Report sequence position in status bar when hovering
2958 over Jmol structure</li>
2959 <li>Cannot output gaps as '.' symbols with Selection ->
2960 output to text box</li>
2961 <li>Flat file exports of alignments with hidden columns
2962 have incorrect sequence start/end</li>
2963 <li>'Aligning' a second chain to a Chimera structure from
2965 <li>Colour schemes applied to structure viewers don't
2966 work for nucleotide</li>
2967 <li>Loading/cut'n'pasting an empty or invalid file leads
2968 to a grey/invisible alignment window</li>
2969 <li>Exported Jpred annotation from a sequence region
2970 imports to different position</li>
2971 <li>Space at beginning of sequence feature tooltips shown
2972 on some platforms</li>
2973 <li>Chimera viewer 'View | Show Chain' menu is not
2975 <li>'New View' fails with a Null Pointer Exception in
2976 console if Chimera has been opened</li>
2977 <li>Mouseover to Chimera not working</li>
2978 <li>Miscellaneous ENA XML feature qualifiers not
2980 <li>NPE in annotation renderer after 'Extract Scores'</li>
2981 <li>If two structures in one Chimera window, mouseover of
2982 either sequence shows on first structure</li>
2983 <li>'Show annotations' options should not make
2984 non-positional annotations visible</li>
2985 <li>Subsequence secondary structure annotation not shown
2986 in right place after 'view flanking regions'</li>
2987 <li>File Save As type unset when current file format is
2989 <li>Save as '.jar' option removed for saving Jalview
2991 <li>Colour by Sequence colouring in Chimera more
2993 <li>Cannot 'add reference annotation' for a sequence in
2994 several views on same alignment</li>
2995 <li>Cannot show linked products for EMBL / ENA records</li>
2996 <li>Jalview's tooltip wraps long texts containing no
2998 </ul> <em>Applet</em>
3000 <li>Jmol to JalviewLite mouseover/link not working</li>
3001 <li>JalviewLite can't import sequences with ID
3002 descriptions containing angle brackets</li>
3003 </ul> <em>General</em>
3005 <li>Cannot export and reimport RNA secondary structure
3006 via jalview annotation file</li>
3007 <li>Random helix colour palette for colour by annotation
3008 with RNA secondary structure</li>
3009 <li>Mouseover to cDNA from STOP residue in protein
3010 translation doesn't work.</li>
3011 <li>hints when using the select by annotation dialog box</li>
3012 <li>Jmol alignment incorrect if PDB file has alternate CA
3014 <li>FontChooser message dialog appears to hang after
3015 choosing 1pt font</li>
3016 <li>Peptide secondary structure incorrectly imported from
3017 annotation file when annotation display text includes 'e' or
3019 <li>Cannot set colour of new feature type whilst creating
3021 <li>cDNA translation alignment should not be sequence
3022 order dependent</li>
3023 <li>'Show unconserved' doesn't work for lower case
3025 <li>Nucleotide ambiguity codes involving R not recognised</li>
3026 </ul> <em>Deployment and Documentation</em>
3028 <li>Applet example pages appear different to the rest of
3029 www.jalview.org</li>
3030 </ul> <em>Application Known issues</em>
3032 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3033 <li>Misleading message appears after trying to delete
3035 <li>Jalview icon not shown in dock after InstallAnywhere
3036 version launches</li>
3037 <li>Fetching EMBL reference for an RNA sequence results
3038 fails with a sequence mismatch</li>
3039 <li>Corrupted or unreadable alignment display when
3040 scrolling alignment to right</li>
3041 <li>ArrayIndexOutOfBoundsException thrown when remove
3042 empty columns called on alignment with ragged gapped ends</li>
3043 <li>auto calculated alignment annotation rows do not get
3044 placed above or below non-autocalculated rows</li>
3045 <li>Jalview dekstop becomes sluggish at full screen in
3046 ultra-high resolution</li>
3047 <li>Cannot disable consensus calculation independently of
3048 quality and conservation</li>
3049 <li>Mouseover highlighting between cDNA and protein can
3050 become sluggish with more than one splitframe shown</li>
3051 </ul> <em>Applet Known Issues</em>
3053 <li>Core PDB parsing code requires Jmol</li>
3054 <li>Sequence canvas panel goes white when alignment
3055 window is being resized</li>
3061 <td><div align="center">
3062 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3064 <td><em>General</em>
3066 <li>Updated Java code signing certificate donated by
3068 <li>Features and annotation preserved when performing
3069 pairwise alignment</li>
3070 <li>RNA pseudoknot annotation can be
3071 imported/exported/displayed</li>
3072 <li>'colour by annotation' can colour by RNA and
3073 protein secondary structure</li>
3074 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3075 post-hoc with 2.9 release</em>)
3078 </ul> <em>Application</em>
3080 <li>Extract and display secondary structure for sequences
3081 with 3D structures</li>
3082 <li>Support for parsing RNAML</li>
3083 <li>Annotations menu for layout
3085 <li>sort sequence annotation rows by alignment</li>
3086 <li>place sequence annotation above/below alignment
3089 <li>Output in Stockholm format</li>
3090 <li>Internationalisation: improved Spanish (es)
3092 <li>Structure viewer preferences tab</li>
3093 <li>Disorder and Secondary Structure annotation tracks
3094 shared between alignments</li>
3095 <li>UCSF Chimera launch and linked highlighting from
3097 <li>Show/hide all sequence associated annotation rows for
3098 all or current selection</li>
3099 <li>disorder and secondary structure predictions
3100 available as dataset annotation</li>
3101 <li>Per-sequence rna helices colouring</li>
3104 <li>Sequence database accessions imported when fetching
3105 alignments from Rfam</li>
3106 <li>update VARNA version to 3.91</li>
3108 <li>New groovy scripts for exporting aligned positions,
3109 conservation values, and calculating sum of pairs scores.</li>
3110 <li>Command line argument to set default JABAWS server</li>
3111 <li>include installation type in build properties and
3112 console log output</li>
3113 <li>Updated Jalview project format to preserve dataset
3117 <!-- issues resolved --> <em>Application</em>
3119 <li>Distinguish alignment and sequence associated RNA
3120 structure in structure->view->VARNA</li>
3121 <li>Raise dialog box if user deletes all sequences in an
3123 <li>Pressing F1 results in documentation opening twice</li>
3124 <li>Sequence feature tooltip is wrapped</li>
3125 <li>Double click on sequence associated annotation
3126 selects only first column</li>
3127 <li>Redundancy removal doesn't result in unlinked
3128 leaves shown in tree</li>
3129 <li>Undos after several redundancy removals don't undo
3131 <li>Hide sequence doesn't hide associated annotation</li>
3132 <li>User defined colours dialog box too big to fit on
3133 screen and buttons not visible</li>
3134 <li>author list isn't updated if already written to
3135 Jalview properties</li>
3136 <li>Popup menu won't open after retrieving sequence
3138 <li>File open window for associate PDB doesn't open</li>
3139 <li>Left-then-right click on a sequence id opens a
3140 browser search window</li>
3141 <li>Cannot open sequence feature shading/sort popup menu
3142 in feature settings dialog</li>
3143 <li>better tooltip placement for some areas of Jalview
3145 <li>Allow addition of JABAWS Server which doesn't
3146 pass validation</li>
3147 <li>Web services parameters dialog box is too large to
3149 <li>Muscle nucleotide alignment preset obscured by
3151 <li>JABAWS preset submenus don't contain newly
3152 defined user preset</li>
3153 <li>MSA web services warns user if they were launched
3154 with invalid input</li>
3155 <li>Jalview cannot contact DAS Registy when running on
3158 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3159 'Superpose with' submenu not shown when new view
3163 </ul> <!-- <em>Applet</em>
3165 </ul> <em>General</em>
3167 </ul>--> <em>Deployment and Documentation</em>
3169 <li>2G and 1G options in launchApp have no effect on
3170 memory allocation</li>
3171 <li>launchApp service doesn't automatically open
3172 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3174 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3175 InstallAnywhere reports cannot find valid JVM when Java
3176 1.7_055 is available
3178 </ul> <em>Application Known issues</em>
3181 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3182 corrupted or unreadable alignment display when scrolling
3186 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3187 retrieval fails but progress bar continues for DAS retrieval
3188 with large number of ID
3191 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3192 flatfile output of visible region has incorrect sequence
3196 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3197 rna structure consensus doesn't update when secondary
3198 structure tracks are rearranged
3201 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3202 invalid rna structure positional highlighting does not
3203 highlight position of invalid base pairs
3206 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3207 out of memory errors are not raised when saving Jalview
3208 project from alignment window file menu
3211 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3212 Switching to RNA Helices colouring doesn't propagate to
3216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3217 colour by RNA Helices not enabled when user created
3218 annotation added to alignment
3221 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3222 Jalview icon not shown on dock in Mountain Lion/Webstart
3224 </ul> <em>Applet Known Issues</em>
3227 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3228 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3231 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3232 Jalview and Jmol example not compatible with IE9
3235 <li>Sort by annotation score doesn't reverse order
3241 <td><div align="center">
3242 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3245 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3248 <li>Internationalisation of user interface (usually
3249 called i18n support) and translation for Spanish locale</li>
3250 <li>Define/Undefine group on current selection with
3251 Ctrl-G/Shift Ctrl-G</li>
3252 <li>Improved group creation/removal options in
3253 alignment/sequence Popup menu</li>
3254 <li>Sensible precision for symbol distribution
3255 percentages shown in logo tooltip.</li>
3256 <li>Annotation panel height set according to amount of
3257 annotation when alignment first opened</li>
3258 </ul> <em>Application</em>
3260 <li>Interactive consensus RNA secondary structure
3261 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3262 <li>Select columns containing particular features from
3263 Feature Settings dialog</li>
3264 <li>View all 'representative' PDB structures for selected
3266 <li>Update Jalview project format:
3268 <li>New file extension for Jalview projects '.jvp'</li>
3269 <li>Preserve sequence and annotation dataset (to
3270 store secondary structure annotation,etc)</li>
3271 <li>Per group and alignment annotation and RNA helix
3275 <li>New similarity measures for PCA and Tree calculation
3277 <li>Experimental support for retrieval and viewing of
3278 flanking regions for an alignment</li>
3282 <!-- issues resolved --> <em>Application</em>
3284 <li>logo keeps spinning and status remains at queued or
3285 running after job is cancelled</li>
3286 <li>cannot export features from alignments imported from
3287 Jalview/VAMSAS projects</li>
3288 <li>Buggy slider for web service parameters that take
3290 <li>Newly created RNA secondary structure line doesn't
3291 have 'display all symbols' flag set</li>
3292 <li>T-COFFEE alignment score shading scheme and other
3293 annotation shading not saved in Jalview project</li>
3294 <li>Local file cannot be loaded in freshly downloaded
3296 <li>Jalview icon not shown on dock in Mountain
3298 <li>Load file from desktop file browser fails</li>
3299 <li>Occasional NPE thrown when calculating large trees</li>
3300 <li>Cannot reorder or slide sequences after dragging an
3301 alignment onto desktop</li>
3302 <li>Colour by annotation dialog throws NPE after using
3303 'extract scores' function</li>
3304 <li>Loading/cut'n'pasting an empty file leads to a grey
3305 alignment window</li>
3306 <li>Disorder thresholds rendered incorrectly after
3307 performing IUPred disorder prediction</li>
3308 <li>Multiple group annotated consensus rows shown when
3309 changing 'normalise logo' display setting</li>
3310 <li>Find shows blank dialog after 'finished searching' if
3311 nothing matches query</li>
3312 <li>Null Pointer Exceptions raised when sorting by
3313 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3315 <li>Errors in Jmol console when structures in alignment
3316 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3318 <li>Not all working JABAWS services are shown in
3320 <li>JAVAWS version of Jalview fails to launch with
3321 'invalid literal/length code'</li>
3322 <li>Annotation/RNA Helix colourschemes cannot be applied
3323 to alignment with groups (actually fixed in 2.8.0b1)</li>
3324 <li>RNA Helices and T-Coffee Scores available as default
3327 </ul> <em>Applet</em>
3329 <li>Remove group option is shown even when selection is
3331 <li>Apply to all groups ticked but colourscheme changes
3332 don't affect groups</li>
3333 <li>Documented RNA Helices and T-Coffee Scores as valid
3334 colourscheme name</li>
3335 <li>Annotation labels drawn on sequence IDs when
3336 Annotation panel is not displayed</li>
3337 <li>Increased font size for dropdown menus on OSX and
3338 embedded windows</li>
3339 </ul> <em>Other</em>
3341 <li>Consensus sequence for alignments/groups with a
3342 single sequence were not calculated</li>
3343 <li>annotation files that contain only groups imported as
3344 annotation and junk sequences</li>
3345 <li>Fasta files with sequences containing '*' incorrectly
3346 recognised as PFAM or BLC</li>
3347 <li>conservation/PID slider apply all groups option
3348 doesn't affect background (2.8.0b1)
3350 <li>redundancy highlighting is erratic at 0% and 100%</li>
3351 <li>Remove gapped columns fails for sequences with ragged
3353 <li>AMSA annotation row with leading spaces is not
3354 registered correctly on import</li>
3355 <li>Jalview crashes when selecting PCA analysis for
3356 certain alignments</li>
3357 <li>Opening the colour by annotation dialog for an
3358 existing annotation based 'use original colours'
3359 colourscheme loses original colours setting</li>
3364 <td><div align="center">
3365 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3366 <em>30/1/2014</em></strong>
3370 <li>Trusted certificates for JalviewLite applet and
3371 Jalview Desktop application<br />Certificate was donated by
3372 <a href="https://www.certum.eu">Certum</a> to the Jalview
3373 open source project).
3375 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3376 <li>Output in Stockholm format</li>
3377 <li>Allow import of data from gzipped files</li>
3378 <li>Export/import group and sequence associated line
3379 graph thresholds</li>
3380 <li>Nucleotide substitution matrix that supports RNA and
3381 ambiguity codes</li>
3382 <li>Allow disorder predictions to be made on the current
3383 selection (or visible selection) in the same way that JPred
3385 <li>Groovy scripting for headless Jalview operation</li>
3386 </ul> <em>Other improvements</em>
3388 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3389 <li>COMBINE statement uses current SEQUENCE_REF and
3390 GROUP_REF scope to group annotation rows</li>
3391 <li>Support '' style escaping of quotes in Newick
3393 <li>Group options for JABAWS service by command line name</li>
3394 <li>Empty tooltip shown for JABA service options with a
3395 link but no description</li>
3396 <li>Select primary source when selecting authority in
3397 database fetcher GUI</li>
3398 <li>Add .mfa to FASTA file extensions recognised by
3400 <li>Annotation label tooltip text wrap</li>
3405 <li>Slow scrolling when lots of annotation rows are
3407 <li>Lots of NPE (and slowness) after creating RNA
3408 secondary structure annotation line</li>
3409 <li>Sequence database accessions not imported when
3410 fetching alignments from Rfam</li>
3411 <li>Incorrect SHMR submission for sequences with
3413 <li>View all structures does not always superpose
3415 <li>Option widgets in service parameters not updated to
3416 reflect user or preset settings</li>
3417 <li>Null pointer exceptions for some services without
3418 presets or adjustable parameters</li>
3419 <li>Discover PDB IDs entry in structure menu doesn't
3420 discover PDB xRefs</li>
3421 <li>Exception encountered while trying to retrieve
3422 features with DAS</li>
3423 <li>Lowest value in annotation row isn't coloured
3424 when colour by annotation (per sequence) is coloured</li>
3425 <li>Keyboard mode P jumps to start of gapped region when
3426 residue follows a gap</li>
3427 <li>Jalview appears to hang importing an alignment with
3428 Wrap as default or after enabling Wrap</li>
3429 <li>'Right click to add annotations' message
3430 shown in wrap mode when no annotations present</li>
3431 <li>Disorder predictions fail with NPE if no automatic
3432 annotation already exists on alignment</li>
3433 <li>oninit javascript function should be called after
3434 initialisation completes</li>
3435 <li>Remove redundancy after disorder prediction corrupts
3436 alignment window display</li>
3437 <li>Example annotation file in documentation is invalid</li>
3438 <li>Grouped line graph annotation rows are not exported
3439 to annotation file</li>
3440 <li>Multi-harmony analysis cannot be run when only two
3442 <li>Cannot create multiple groups of line graphs with
3443 several 'combine' statements in annotation file</li>
3444 <li>Pressing return several times causes Number Format
3445 exceptions in keyboard mode</li>
3446 <li>Multi-harmony (SHMMR) method doesn't submit
3447 correct partitions for input data</li>
3448 <li>Translation from DNA to Amino Acids fails</li>
3449 <li>Jalview fail to load newick tree with quoted label</li>
3450 <li>--headless flag isn't understood</li>
3451 <li>ClassCastException when generating EPS in headless
3453 <li>Adjusting sequence-associated shading threshold only
3454 changes one row's threshold</li>
3455 <li>Preferences and Feature settings panel panel
3456 doesn't open</li>
3457 <li>hide consensus histogram also hides conservation and
3458 quality histograms</li>
3463 <td><div align="center">
3464 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3466 <td><em>Application</em>
3468 <li>Support for JABAWS 2.0 Services (AACon alignment
3469 conservation, protein disorder and Clustal Omega)</li>
3470 <li>JABAWS server status indicator in Web Services
3472 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3473 in Jalview alignment window</li>
3474 <li>Updated Jalview build and deploy framework for OSX
3475 mountain lion, windows 7, and 8</li>
3476 <li>Nucleotide substitution matrix for PCA that supports
3477 RNA and ambiguity codes</li>
3479 <li>Improved sequence database retrieval GUI</li>
3480 <li>Support fetching and database reference look up
3481 against multiple DAS sources (Fetch all from in 'fetch db
3483 <li>Jalview project improvements
3485 <li>Store and retrieve the 'belowAlignment'
3486 flag for annotation</li>
3487 <li>calcId attribute to group annotation rows on the
3489 <li>Store AACon calculation settings for a view in
3490 Jalview project</li>
3494 <li>horizontal scrolling gesture support</li>
3495 <li>Visual progress indicator when PCA calculation is
3497 <li>Simpler JABA web services menus</li>
3498 <li>visual indication that web service results are still
3499 being retrieved from server</li>
3500 <li>Serialise the dialogs that are shown when Jalview
3501 starts up for first time</li>
3502 <li>Jalview user agent string for interacting with HTTP
3504 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3506 <li>Examples directory and Groovy library included in
3507 InstallAnywhere distribution</li>
3508 </ul> <em>Applet</em>
3510 <li>RNA alignment and secondary structure annotation
3511 visualization applet example</li>
3512 </ul> <em>General</em>
3514 <li>Normalise option for consensus sequence logo</li>
3515 <li>Reset button in PCA window to return dimensions to
3517 <li>Allow seqspace or Jalview variant of alignment PCA
3519 <li>PCA with either nucleic acid and protein substitution
3521 <li>Allow windows containing HTML reports to be exported
3523 <li>Interactive display and editing of RNA secondary
3524 structure contacts</li>
3525 <li>RNA Helix Alignment Colouring</li>
3526 <li>RNA base pair logo consensus</li>
3527 <li>Parse sequence associated secondary structure
3528 information in Stockholm files</li>
3529 <li>HTML Export database accessions and annotation
3530 information presented in tooltip for sequences</li>
3531 <li>Import secondary structure from LOCARNA clustalw
3532 style RNA alignment files</li>
3533 <li>import and visualise T-COFFEE quality scores for an
3535 <li>'colour by annotation' per sequence option to
3536 shade each sequence according to its associated alignment
3538 <li>New Jalview Logo</li>
3539 </ul> <em>Documentation and Development</em>
3541 <li>documentation for score matrices used in Jalview</li>
3542 <li>New Website!</li>
3544 <td><em>Application</em>
3546 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3547 wsdbfetch REST service</li>
3548 <li>Stop windows being moved outside desktop on OSX</li>
3549 <li>Filetype associations not installed for webstart
3551 <li>Jalview does not always retrieve progress of a JABAWS
3552 job execution in full once it is complete</li>
3553 <li>revise SHMR RSBS definition to ensure alignment is
3554 uploaded via ali_file parameter</li>
3555 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3556 <li>View all structures superposed fails with exception</li>
3557 <li>Jnet job queues forever if a very short sequence is
3558 submitted for prediction</li>
3559 <li>Cut and paste menu not opened when mouse clicked on
3561 <li>Putting fractional value into integer text box in
3562 alignment parameter dialog causes Jalview to hang</li>
3563 <li>Structure view highlighting doesn't work on
3565 <li>View all structures fails with exception shown in
3567 <li>Characters in filename associated with PDBEntry not
3568 escaped in a platform independent way</li>
3569 <li>Jalview desktop fails to launch with exception when
3571 <li>Tree calculation reports 'you must have 2 or more
3572 sequences selected' when selection is empty</li>
3573 <li>Jalview desktop fails to launch with jar signature
3574 failure when java web start temporary file caching is
3576 <li>DAS Sequence retrieval with range qualification
3577 results in sequence xref which includes range qualification</li>
3578 <li>Errors during processing of command line arguments
3579 cause progress bar (JAL-898) to be removed</li>
3580 <li>Replace comma for semi-colon option not disabled for
3581 DAS sources in sequence fetcher</li>
3582 <li>Cannot close news reader when JABAWS server warning
3583 dialog is shown</li>
3584 <li>Option widgets not updated to reflect user settings</li>
3585 <li>Edited sequence not submitted to web service</li>
3586 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3587 <li>InstallAnywhere installer doesn't unpack and run
3588 on OSX Mountain Lion</li>
3589 <li>Annotation panel not given a scroll bar when
3590 sequences with alignment annotation are pasted into the
3592 <li>Sequence associated annotation rows not associated
3593 when loaded from Jalview project</li>
3594 <li>Browser launch fails with NPE on java 1.7</li>
3595 <li>JABAWS alignment marked as finished when job was
3596 cancelled or job failed due to invalid input</li>
3597 <li>NPE with v2.7 example when clicking on Tree
3598 associated with all views</li>
3599 <li>Exceptions when copy/paste sequences with grouped
3600 annotation rows to new window</li>
3601 </ul> <em>Applet</em>
3603 <li>Sequence features are momentarily displayed before
3604 they are hidden using hidefeaturegroups applet parameter</li>
3605 <li>loading features via javascript API automatically
3606 enables feature display</li>
3607 <li>scrollToColumnIn javascript API method doesn't
3609 </ul> <em>General</em>
3611 <li>Redundancy removal fails for rna alignment</li>
3612 <li>PCA calculation fails when sequence has been selected
3613 and then deselected</li>
3614 <li>PCA window shows grey box when first opened on OSX</li>
3615 <li>Letters coloured pink in sequence logo when alignment
3616 coloured with clustalx</li>
3617 <li>Choosing fonts without letter symbols defined causes
3618 exceptions and redraw errors</li>
3619 <li>Initial PCA plot view is not same as manually
3620 reconfigured view</li>
3621 <li>Grouped annotation graph label has incorrect line
3623 <li>Grouped annotation graph label display is corrupted
3624 for lots of labels</li>
3629 <div align="center">
3630 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3633 <td><em>Application</em>
3635 <li>Jalview Desktop News Reader</li>
3636 <li>Tweaked default layout of web services menu</li>
3637 <li>View/alignment association menu to enable user to
3638 easily specify which alignment a multi-structure view takes
3639 its colours/correspondences from</li>
3640 <li>Allow properties file location to be specified as URL</li>
3641 <li>Extend Jalview project to preserve associations
3642 between many alignment views and a single Jmol display</li>
3643 <li>Store annotation row height in Jalview project file</li>
3644 <li>Annotation row column label formatting attributes
3645 stored in project file</li>
3646 <li>Annotation row order for auto-calculated annotation
3647 rows preserved in Jalview project file</li>
3648 <li>Visual progress indication when Jalview state is
3649 saved using Desktop window menu</li>
3650 <li>Visual indication that command line arguments are
3651 still being processed</li>
3652 <li>Groovy script execution from URL</li>
3653 <li>Colour by annotation default min and max colours in
3655 <li>Automatically associate PDB files dragged onto an
3656 alignment with sequences that have high similarity and
3658 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3659 <li>'view structures' option to open many
3660 structures in same window</li>
3661 <li>Sort associated views menu option for tree panel</li>
3662 <li>Group all JABA and non-JABA services for a particular
3663 analysis function in its own submenu</li>
3664 </ul> <em>Applet</em>
3666 <li>Userdefined and autogenerated annotation rows for
3668 <li>Adjustment of alignment annotation pane height</li>
3669 <li>Annotation scrollbar for annotation panel</li>
3670 <li>Drag to reorder annotation rows in annotation panel</li>
3671 <li>'automaticScrolling' parameter</li>
3672 <li>Allow sequences with partial ID string matches to be
3673 annotated from GFF/Jalview features files</li>
3674 <li>Sequence logo annotation row in applet</li>
3675 <li>Absolute paths relative to host server in applet
3676 parameters are treated as such</li>
3677 <li>New in the JalviewLite javascript API:
3679 <li>JalviewLite.js javascript library</li>
3680 <li>Javascript callbacks for
3682 <li>Applet initialisation</li>
3683 <li>Sequence/alignment mouse-overs and selections</li>
3686 <li>scrollTo row and column alignment scrolling
3688 <li>Select sequence/alignment regions from javascript</li>
3689 <li>javascript structure viewer harness to pass
3690 messages between Jmol and Jalview when running as
3691 distinct applets</li>
3692 <li>sortBy method</li>
3693 <li>Set of applet and application examples shipped
3694 with documentation</li>
3695 <li>New example to demonstrate JalviewLite and Jmol
3696 javascript message exchange</li>
3698 </ul> <em>General</em>
3700 <li>Enable Jmol displays to be associated with multiple
3701 multiple alignments</li>
3702 <li>Option to automatically sort alignment with new tree</li>
3703 <li>User configurable link to enable redirects to a
3704 www.Jalview.org mirror</li>
3705 <li>Jmol colours option for Jmol displays</li>
3706 <li>Configurable newline string when writing alignment
3707 and other flat files</li>
3708 <li>Allow alignment annotation description lines to
3709 contain html tags</li>
3710 </ul> <em>Documentation and Development</em>
3712 <li>Add groovy test harness for bulk load testing to
3714 <li>Groovy script to load and align a set of sequences
3715 using a web service before displaying the result in the
3716 Jalview desktop</li>
3717 <li>Restructured javascript and applet api documentation</li>
3718 <li>Ant target to publish example html files with applet
3720 <li>Netbeans project for building Jalview from source</li>
3721 <li>ant task to create online javadoc for Jalview source</li>
3723 <td><em>Application</em>
3725 <li>User defined colourscheme throws exception when
3726 current built in colourscheme is saved as new scheme</li>
3727 <li>AlignFrame->Save in application pops up save
3728 dialog for valid filename/format</li>
3729 <li>Cannot view associated structure for UniProt sequence</li>
3730 <li>PDB file association breaks for UniProt sequence
3732 <li>Associate PDB from file dialog does not tell you
3733 which sequence is to be associated with the file</li>
3734 <li>Find All raises null pointer exception when query
3735 only matches sequence IDs</li>
3736 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3737 <li>Jalview project with Jmol views created with Jalview
3738 2.4 cannot be loaded</li>
3739 <li>Filetype associations not installed for webstart
3741 <li>Two or more chains in a single PDB file associated
3742 with sequences in different alignments do not get coloured
3743 by their associated sequence</li>
3744 <li>Visibility status of autocalculated annotation row
3745 not preserved when project is loaded</li>
3746 <li>Annotation row height and visibility attributes not
3747 stored in Jalview project</li>
3748 <li>Tree bootstraps are not preserved when saved as a
3749 Jalview project</li>
3750 <li>Envision2 workflow tooltips are corrupted</li>
3751 <li>Enabling show group conservation also enables colour
3752 by conservation</li>
3753 <li>Duplicate group associated conservation or consensus
3754 created on new view</li>
3755 <li>Annotation scrollbar not displayed after 'show
3756 all hidden annotation rows' option selected</li>
3757 <li>Alignment quality not updated after alignment
3758 annotation row is hidden then shown</li>
3759 <li>Preserve colouring of structures coloured by
3760 sequences in pre Jalview 2.7 projects</li>
3761 <li>Web service job parameter dialog is not laid out
3763 <li>Web services menu not refreshed after 'reset
3764 services' button is pressed in preferences</li>
3765 <li>Annotation off by one in Jalview v2_3 example project</li>
3766 <li>Structures imported from file and saved in project
3767 get name like jalview_pdb1234.txt when reloaded</li>
3768 <li>Jalview does not always retrieve progress of a JABAWS
3769 job execution in full once it is complete</li>
3770 </ul> <em>Applet</em>
3772 <li>Alignment height set incorrectly when lots of
3773 annotation rows are displayed</li>
3774 <li>Relative URLs in feature HTML text not resolved to
3776 <li>View follows highlighting does not work for positions
3778 <li><= shown as = in tooltip</li>
3779 <li>Export features raises exception when no features
3781 <li>Separator string used for serialising lists of IDs
3782 for javascript api is modified when separator string
3783 provided as parameter</li>
3784 <li>Null pointer exception when selecting tree leaves for
3785 alignment with no existing selection</li>
3786 <li>Relative URLs for datasources assumed to be relative
3787 to applet's codebase</li>
3788 <li>Status bar not updated after finished searching and
3789 search wraps around to first result</li>
3790 <li>StructureSelectionManager instance shared between
3791 several Jalview applets causes race conditions and memory
3793 <li>Hover tooltip and mouseover of position on structure
3794 not sent from Jmol in applet</li>
3795 <li>Certain sequences of javascript method calls to
3796 applet API fatally hang browser</li>
3797 </ul> <em>General</em>
3799 <li>View follows structure mouseover scrolls beyond
3800 position with wrapped view and hidden regions</li>
3801 <li>Find sequence position moves to wrong residue
3802 with/without hidden columns</li>
3803 <li>Sequence length given in alignment properties window
3805 <li>InvalidNumberFormat exceptions thrown when trying to
3806 import PDB like structure files</li>
3807 <li>Positional search results are only highlighted
3808 between user-supplied sequence start/end bounds</li>
3809 <li>End attribute of sequence is not validated</li>
3810 <li>Find dialog only finds first sequence containing a
3811 given sequence position</li>
3812 <li>Sequence numbering not preserved in MSF alignment
3814 <li>Jalview PDB file reader does not extract sequence
3815 from nucleotide chains correctly</li>
3816 <li>Structure colours not updated when tree partition
3817 changed in alignment</li>
3818 <li>Sequence associated secondary structure not correctly
3819 parsed in interleaved stockholm</li>
3820 <li>Colour by annotation dialog does not restore current
3822 <li>Hiding (nearly) all sequences doesn't work
3824 <li>Sequences containing lowercase letters are not
3825 properly associated with their pdb files</li>
3826 </ul> <em>Documentation and Development</em>
3828 <li>schemas/JalviewWsParamSet.xsd corrupted by
3829 ApplyCopyright tool</li>
3834 <div align="center">
3835 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3838 <td><em>Application</em>
3840 <li>New warning dialog when the Jalview Desktop cannot
3841 contact web services</li>
3842 <li>JABA service parameters for a preset are shown in
3843 service job window</li>
3844 <li>JABA Service menu entries reworded</li>
3848 <li>Modeller PIR IO broken - cannot correctly import a
3849 pir file emitted by Jalview</li>
3850 <li>Existing feature settings transferred to new
3851 alignment view created from cut'n'paste</li>
3852 <li>Improved test for mixed amino/nucleotide chains when
3853 parsing PDB files</li>
3854 <li>Consensus and conservation annotation rows
3855 occasionally become blank for all new windows</li>
3856 <li>Exception raised when right clicking above sequences
3857 in wrapped view mode</li>
3858 </ul> <em>Application</em>
3860 <li>multiple multiply aligned structure views cause cpu
3861 usage to hit 100% and computer to hang</li>
3862 <li>Web Service parameter layout breaks for long user
3863 parameter names</li>
3864 <li>Jaba service discovery hangs desktop if Jaba server
3871 <div align="center">
3872 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3875 <td><em>Application</em>
3877 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3878 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3881 <li>Web Services preference tab</li>
3882 <li>Analysis parameters dialog box and user defined
3884 <li>Improved speed and layout of Envision2 service menu</li>
3885 <li>Superpose structures using associated sequence
3887 <li>Export coordinates and projection as CSV from PCA
3889 </ul> <em>Applet</em>
3891 <li>enable javascript: execution by the applet via the
3892 link out mechanism</li>
3893 </ul> <em>Other</em>
3895 <li>Updated the Jmol Jalview interface to work with Jmol
3897 <li>The Jalview Desktop and JalviewLite applet now
3898 require Java 1.5</li>
3899 <li>Allow Jalview feature colour specification for GFF
3900 sequence annotation files</li>
3901 <li>New 'colour by label' keword in Jalview feature file
3902 type colour specification</li>
3903 <li>New Jalview Desktop Groovy API method that allows a
3904 script to check if it being run in an interactive session or
3905 in a batch operation from the Jalview command line</li>
3909 <li>clustalx colourscheme colours Ds preferentially when
3910 both D+E are present in over 50% of the column</li>
3911 </ul> <em>Application</em>
3913 <li>typo in AlignmentFrame->View->Hide->all but
3914 selected Regions menu item</li>
3915 <li>sequence fetcher replaces ',' for ';' when the ',' is
3916 part of a valid accession ID</li>
3917 <li>fatal OOM if object retrieved by sequence fetcher
3918 runs out of memory</li>
3919 <li>unhandled Out of Memory Error when viewing pca
3920 analysis results</li>
3921 <li>InstallAnywhere builds fail to launch on OS X java
3922 10.5 update 4 (due to apple Java 1.6 update)</li>
3923 <li>Installanywhere Jalview silently fails to launch</li>
3924 </ul> <em>Applet</em>
3926 <li>Jalview.getFeatureGroups() raises an
3927 ArrayIndexOutOfBoundsException if no feature groups are
3934 <div align="center">
3935 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3941 <li>Alignment prettyprinter doesn't cope with long
3943 <li>clustalx colourscheme colours Ds preferentially when
3944 both D+E are present in over 50% of the column</li>
3945 <li>nucleic acid structures retrieved from PDB do not
3946 import correctly</li>
3947 <li>More columns get selected than were clicked on when a
3948 number of columns are hidden</li>
3949 <li>annotation label popup menu not providing correct
3950 add/hide/show options when rows are hidden or none are
3952 <li>Stockholm format shown in list of readable formats,
3953 and parser copes better with alignments from RFAM.</li>
3954 <li>CSV output of consensus only includes the percentage
3955 of all symbols if sequence logo display is enabled</li>
3957 </ul> <em>Applet</em>
3959 <li>annotation panel disappears when annotation is
3961 </ul> <em>Application</em>
3963 <li>Alignment view not redrawn properly when new
3964 alignment opened where annotation panel is visible but no
3965 annotations are present on alignment</li>
3966 <li>pasted region containing hidden columns is
3967 incorrectly displayed in new alignment window</li>
3968 <li>Jalview slow to complete operations when stdout is
3969 flooded (fix is to close the Jalview console)</li>
3970 <li>typo in AlignmentFrame->View->Hide->all but
3971 selected Rregions menu item.</li>
3972 <li>inconsistent group submenu and Format submenu entry
3973 'Un' or 'Non'conserved</li>
3974 <li>Sequence feature settings are being shared by
3975 multiple distinct alignments</li>
3976 <li>group annotation not recreated when tree partition is
3978 <li>double click on group annotation to select sequences
3979 does not propagate to associated trees</li>
3980 <li>Mac OSX specific issues:
3982 <li>exception raised when mouse clicked on desktop
3983 window background</li>
3984 <li>Desktop menu placed on menu bar and application
3985 name set correctly</li>
3986 <li>sequence feature settings not wide enough for the
3987 save feature colourscheme button</li>
3996 <div align="center">
3997 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4000 <td><em>New Capabilities</em>
4002 <li>URL links generated from description line for
4003 regular-expression based URL links (applet and application)
4005 <li>Non-positional feature URL links are shown in link
4007 <li>Linked viewing of nucleic acid sequences and
4009 <li>Automatic Scrolling option in View menu to display
4010 the currently highlighted region of an alignment.</li>
4011 <li>Order an alignment by sequence length, or using the
4012 average score or total feature count for each sequence.</li>
4013 <li>Shading features by score or associated description</li>
4014 <li>Subdivide alignment and groups based on identity of
4015 selected subsequence (Make Groups from Selection).</li>
4016 <li>New hide/show options including Shift+Control+H to
4017 hide everything but the currently selected region.</li>
4018 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4019 </ul> <em>Application</em>
4021 <li>Fetch DB References capabilities and UI expanded to
4022 support retrieval from DAS sequence sources</li>
4023 <li>Local DAS Sequence sources can be added via the
4024 command line or via the Add local source dialog box.</li>
4025 <li>DAS Dbref and DbxRef feature types are parsed as
4026 database references and protein_name is parsed as
4027 description line (BioSapiens terms).</li>
4028 <li>Enable or disable non-positional feature and database
4029 references in sequence ID tooltip from View menu in
4031 <!-- <li>New hidden columns and rows and representatives capabilities
4032 in annotations file (in progress - not yet fully implemented)</li> -->
4033 <li>Group-associated consensus, sequence logos and
4034 conservation plots</li>
4035 <li>Symbol distributions for each column can be exported
4036 and visualized as sequence logos</li>
4037 <li>Optionally scale multi-character column labels to fit
4038 within each column of annotation row<!-- todo for applet -->
4040 <li>Optional automatic sort of associated alignment view
4041 when a new tree is opened.</li>
4042 <li>Jalview Java Console</li>
4043 <li>Better placement of desktop window when moving
4044 between different screens.</li>
4045 <li>New preference items for sequence ID tooltip and
4046 consensus annotation</li>
4047 <li>Client to submit sequences and IDs to Envision2
4049 <li><em>Vamsas Capabilities</em>
4051 <li>Improved VAMSAS synchronization (Jalview archive
4052 used to preserve views, structures, and tree display
4054 <li>Import of vamsas documents from disk or URL via
4056 <li>Sharing of selected regions between views and
4057 with other VAMSAS applications (Experimental feature!)</li>
4058 <li>Updated API to VAMSAS version 0.2</li>
4060 </ul> <em>Applet</em>
4062 <li>Middle button resizes annotation row height</li>
4065 <li>sortByTree (true/false) - automatically sort the
4066 associated alignment view by the tree when a new tree is
4068 <li>showTreeBootstraps (true/false) - show or hide
4069 branch bootstraps (default is to show them if available)</li>
4070 <li>showTreeDistances (true/false) - show or hide
4071 branch lengths (default is to show them if available)</li>
4072 <li>showUnlinkedTreeNodes (true/false) - indicate if
4073 unassociated nodes should be highlighted in the tree
4075 <li>heightScale and widthScale (1.0 or more) -
4076 increase the height or width of a cell in the alignment
4077 grid relative to the current font size.</li>
4080 <li>Non-positional features displayed in sequence ID
4082 </ul> <em>Other</em>
4084 <li>Features format: graduated colour definitions and
4085 specification of feature scores</li>
4086 <li>Alignment Annotations format: new keywords for group
4087 associated annotation (GROUP_REF) and annotation row display
4088 properties (ROW_PROPERTIES)</li>
4089 <li>XML formats extended to support graduated feature
4090 colourschemes, group associated annotation, and profile
4091 visualization settings.</li></td>
4094 <li>Source field in GFF files parsed as feature source
4095 rather than description</li>
4096 <li>Non-positional features are now included in sequence
4097 feature and gff files (controlled via non-positional feature
4098 visibility in tooltip).</li>
4099 <li>URL links generated for all feature links (bugfix)</li>
4100 <li>Added URL embedding instructions to features file
4102 <li>Codons containing ambiguous nucleotides translated as
4103 'X' in peptide product</li>
4104 <li>Match case switch in find dialog box works for both
4105 sequence ID and sequence string and query strings do not
4106 have to be in upper case to match case-insensitively.</li>
4107 <li>AMSA files only contain first column of
4108 multi-character column annotation labels</li>
4109 <li>Jalview Annotation File generation/parsing consistent
4110 with documentation (e.g. Stockholm annotation can be
4111 exported and re-imported)</li>
4112 <li>PDB files without embedded PDB IDs given a friendly
4114 <li>Find incrementally searches ID string matches as well
4115 as subsequence matches, and correctly reports total number
4119 <li>Better handling of exceptions during sequence
4121 <li>Dasobert generated non-positional feature URL
4122 link text excludes the start_end suffix</li>
4123 <li>DAS feature and source retrieval buttons disabled
4124 when fetch or registry operations in progress.</li>
4125 <li>PDB files retrieved from URLs are cached properly</li>
4126 <li>Sequence description lines properly shared via
4128 <li>Sequence fetcher fetches multiple records for all
4130 <li>Ensured that command line das feature retrieval
4131 completes before alignment figures are generated.</li>
4132 <li>Reduced time taken when opening file browser for
4134 <li>isAligned check prior to calculating tree, PCA or
4135 submitting an MSA to JNet now excludes hidden sequences.</li>
4136 <li>User defined group colours properly recovered
4137 from Jalview projects.</li>
4146 <div align="center">
4147 <strong>2.4.0.b2</strong><br> 28/10/2009
4152 <li>Experimental support for google analytics usage
4154 <li>Jalview privacy settings (user preferences and docs).</li>
4159 <li>Race condition in applet preventing startup in
4161 <li>Exception when feature created from selection beyond
4162 length of sequence.</li>
4163 <li>Allow synthetic PDB files to be imported gracefully</li>
4164 <li>Sequence associated annotation rows associate with
4165 all sequences with a given id</li>
4166 <li>Find function matches case-insensitively for sequence
4167 ID string searches</li>
4168 <li>Non-standard characters do not cause pairwise
4169 alignment to fail with exception</li>
4170 </ul> <em>Application Issues</em>
4172 <li>Sequences are now validated against EMBL database</li>
4173 <li>Sequence fetcher fetches multiple records for all
4175 </ul> <em>InstallAnywhere Issues</em>
4177 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4178 issue with installAnywhere mechanism)</li>
4179 <li>Command line launching of JARs from InstallAnywhere
4180 version (java class versioning error fixed)</li>
4187 <div align="center">
4188 <strong>2.4</strong><br> 27/8/2008
4191 <td><em>User Interface</em>
4193 <li>Linked highlighting of codon and amino acid from
4194 translation and protein products</li>
4195 <li>Linked highlighting of structure associated with
4196 residue mapping to codon position</li>
4197 <li>Sequence Fetcher provides example accession numbers
4198 and 'clear' button</li>
4199 <li>MemoryMonitor added as an option under Desktop's
4201 <li>Extract score function to parse whitespace separated
4202 numeric data in description line</li>
4203 <li>Column labels in alignment annotation can be centred.</li>
4204 <li>Tooltip for sequence associated annotation give name
4206 </ul> <em>Web Services and URL fetching</em>
4208 <li>JPred3 web service</li>
4209 <li>Prototype sequence search client (no public services
4211 <li>Fetch either seed alignment or full alignment from
4213 <li>URL Links created for matching database cross
4214 references as well as sequence ID</li>
4215 <li>URL Links can be created using regular-expressions</li>
4216 </ul> <em>Sequence Database Connectivity</em>
4218 <li>Retrieval of cross-referenced sequences from other
4220 <li>Generalised database reference retrieval and
4221 validation to all fetchable databases</li>
4222 <li>Fetch sequences from DAS sources supporting the
4223 sequence command</li>
4224 </ul> <em>Import and Export</em>
4225 <li>export annotation rows as CSV for spreadsheet import</li>
4226 <li>Jalview projects record alignment dataset associations,
4227 EMBL products, and cDNA sequence mappings</li>
4228 <li>Sequence Group colour can be specified in Annotation
4230 <li>Ad-hoc colouring of group in Annotation File using RGB
4231 triplet as name of colourscheme</li>
4232 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4234 <li>treenode binding for VAMSAS tree exchange</li>
4235 <li>local editing and update of sequences in VAMSAS
4236 alignments (experimental)</li>
4237 <li>Create new or select existing session to join</li>
4238 <li>load and save of vamsas documents</li>
4239 </ul> <em>Application command line</em>
4241 <li>-tree parameter to open trees (introduced for passing
4243 <li>-fetchfrom command line argument to specify nicknames
4244 of DAS servers to query for alignment features</li>
4245 <li>-dasserver command line argument to add new servers
4246 that are also automatically queried for features</li>
4247 <li>-groovy command line argument executes a given groovy
4248 script after all input data has been loaded and parsed</li>
4249 </ul> <em>Applet-Application data exchange</em>
4251 <li>Trees passed as applet parameters can be passed to
4252 application (when using "View in full
4253 application")</li>
4254 </ul> <em>Applet Parameters</em>
4256 <li>feature group display control parameter</li>
4257 <li>debug parameter</li>
4258 <li>showbutton parameter</li>
4259 </ul> <em>Applet API methods</em>
4261 <li>newView public method</li>
4262 <li>Window (current view) specific get/set public methods</li>
4263 <li>Feature display control methods</li>
4264 <li>get list of currently selected sequences</li>
4265 </ul> <em>New Jalview distribution features</em>
4267 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4268 <li>RELEASE file gives build properties for the latest
4269 Jalview release.</li>
4270 <li>Java 1.1 Applet build made easier and donotobfuscate
4271 property controls execution of obfuscator</li>
4272 <li>Build target for generating source distribution</li>
4273 <li>Debug flag for javacc</li>
4274 <li>.jalview_properties file is documented (slightly) in
4275 jalview.bin.Cache</li>
4276 <li>Continuous Build Integration for stable and
4277 development version of Application, Applet and source
4282 <li>selected region output includes visible annotations
4283 (for certain formats)</li>
4284 <li>edit label/displaychar contains existing label/char
4286 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4287 <li>shorter peptide product names from EMBL records</li>
4288 <li>Newick string generator makes compact representations</li>
4289 <li>bootstrap values parsed correctly for tree files with
4291 <li>pathological filechooser bug avoided by not allowing
4292 filenames containing a ':'</li>
4293 <li>Fixed exception when parsing GFF files containing
4294 global sequence features</li>
4295 <li>Alignment datasets are finalized only when number of
4296 references from alignment sequences goes to zero</li>
4297 <li>Close of tree branch colour box without colour
4298 selection causes cascading exceptions</li>
4299 <li>occasional negative imgwidth exceptions</li>
4300 <li>better reporting of non-fatal warnings to user when
4301 file parsing fails.</li>
4302 <li>Save works when Jalview project is default format</li>
4303 <li>Save as dialog opened if current alignment format is
4304 not a valid output format</li>
4305 <li>UniProt canonical names introduced for both das and
4307 <li>Histidine should be midblue (not pink!) in Zappo</li>
4308 <li>error messages passed up and output when data read
4310 <li>edit undo recovers previous dataset sequence when
4311 sequence is edited</li>
4312 <li>allow PDB files without pdb ID HEADER lines (like
4313 those generated by MODELLER) to be read in properly</li>
4314 <li>allow reading of JPred concise files as a normal
4316 <li>Stockholm annotation parsing and alignment properties
4317 import fixed for PFAM records</li>
4318 <li>Structure view windows have correct name in Desktop
4320 <li>annotation consisting of sequence associated scores
4321 can be read and written correctly to annotation file</li>
4322 <li>Aligned cDNA translation to aligned peptide works
4324 <li>Fixed display of hidden sequence markers and
4325 non-italic font for representatives in Applet</li>
4326 <li>Applet Menus are always embedded in applet window on
4328 <li>Newly shown features appear at top of stack (in
4330 <li>Annotations added via parameter not drawn properly
4331 due to null pointer exceptions</li>
4332 <li>Secondary structure lines are drawn starting from
4333 first column of alignment</li>
4334 <li>UniProt XML import updated for new schema release in
4336 <li>Sequence feature to sequence ID match for Features
4337 file is case-insensitive</li>
4338 <li>Sequence features read from Features file appended to
4339 all sequences with matching IDs</li>
4340 <li>PDB structure coloured correctly for associated views
4341 containing a sub-sequence</li>
4342 <li>PDB files can be retrieved by applet from Jar files</li>
4343 <li>feature and annotation file applet parameters
4344 referring to different directories are retrieved correctly</li>
4345 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4346 <li>Fixed application hang whilst waiting for
4347 splash-screen version check to complete</li>
4348 <li>Applet properly URLencodes input parameter values
4349 when passing them to the launchApp service</li>
4350 <li>display name and local features preserved in results
4351 retrieved from web service</li>
4352 <li>Visual delay indication for sequence retrieval and
4353 sequence fetcher initialisation</li>
4354 <li>updated Application to use DAS 1.53e version of
4355 dasobert DAS client</li>
4356 <li>Re-instated Full AMSA support and .amsa file
4358 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4366 <div align="center">
4367 <strong>2.3</strong><br> 9/5/07
4372 <li>Jmol 11.0.2 integration</li>
4373 <li>PDB views stored in Jalview XML files</li>
4374 <li>Slide sequences</li>
4375 <li>Edit sequence in place</li>
4376 <li>EMBL CDS features</li>
4377 <li>DAS Feature mapping</li>
4378 <li>Feature ordering</li>
4379 <li>Alignment Properties</li>
4380 <li>Annotation Scores</li>
4381 <li>Sort by scores</li>
4382 <li>Feature/annotation editing in applet</li>
4387 <li>Headless state operation in 2.2.1</li>
4388 <li>Incorrect and unstable DNA pairwise alignment</li>
4389 <li>Cut and paste of sequences with annotation</li>
4390 <li>Feature group display state in XML</li>
4391 <li>Feature ordering in XML</li>
4392 <li>blc file iteration selection using filename # suffix</li>
4393 <li>Stockholm alignment properties</li>
4394 <li>Stockhom alignment secondary structure annotation</li>
4395 <li>2.2.1 applet had no feature transparency</li>
4396 <li>Number pad keys can be used in cursor mode</li>
4397 <li>Structure Viewer mirror image resolved</li>
4404 <div align="center">
4405 <strong>2.2.1</strong><br> 12/2/07
4410 <li>Non standard characters can be read and displayed
4411 <li>Annotations/Features can be imported/exported to the
4413 <li>Applet allows editing of sequence/annotation/group
4414 name & description
4415 <li>Preference setting to display sequence name in
4417 <li>Annotation file format extended to allow
4418 Sequence_groups to be defined
4419 <li>Default opening of alignment overview panel can be
4420 specified in preferences
4421 <li>PDB residue numbering annotation added to associated
4427 <li>Applet crash under certain Linux OS with Java 1.6
4429 <li>Annotation file export / import bugs fixed
4430 <li>PNG / EPS image output bugs fixed
4436 <div align="center">
4437 <strong>2.2</strong><br> 27/11/06
4442 <li>Multiple views on alignment
4443 <li>Sequence feature editing
4444 <li>"Reload" alignment
4445 <li>"Save" to current filename
4446 <li>Background dependent text colour
4447 <li>Right align sequence ids
4448 <li>User-defined lower case residue colours
4451 <li>Menu item accelerator keys
4452 <li>Control-V pastes to current alignment
4453 <li>Cancel button for DAS Feature Fetching
4454 <li>PCA and PDB Viewers zoom via mouse roller
4455 <li>User-defined sub-tree colours and sub-tree selection
4457 <li>'New Window' button on the 'Output to Text box'
4462 <li>New memory efficient Undo/Redo System
4463 <li>Optimised symbol lookups and conservation/consensus
4465 <li>Region Conservation/Consensus recalculated after
4467 <li>Fixed Remove Empty Columns Bug (empty columns at end
4469 <li>Slowed DAS Feature Fetching for increased robustness.
4471 <li>Made angle brackets in ASCII feature descriptions
4473 <li>Re-instated Zoom function for PCA
4474 <li>Sequence descriptions conserved in web service
4476 <li>UniProt ID discoverer uses any word separated by
4478 <li>WsDbFetch query/result association resolved
4479 <li>Tree leaf to sequence mapping improved
4480 <li>Smooth fonts switch moved to FontChooser dialog box.
4487 <div align="center">
4488 <strong>2.1.1</strong><br> 12/9/06
4493 <li>Copy consensus sequence to clipboard</li>
4498 <li>Image output - rightmost residues are rendered if
4499 sequence id panel has been resized</li>
4500 <li>Image output - all offscreen group boundaries are
4502 <li>Annotation files with sequence references - all
4503 elements in file are relative to sequence position</li>
4504 <li>Mac Applet users can use Alt key for group editing</li>
4510 <div align="center">
4511 <strong>2.1</strong><br> 22/8/06
4516 <li>MAFFT Multiple Alignment in default Web Service list</li>
4517 <li>DAS Feature fetching</li>
4518 <li>Hide sequences and columns</li>
4519 <li>Export Annotations and Features</li>
4520 <li>GFF file reading / writing</li>
4521 <li>Associate structures with sequences from local PDB
4523 <li>Add sequences to exisiting alignment</li>
4524 <li>Recently opened files / URL lists</li>
4525 <li>Applet can launch the full application</li>
4526 <li>Applet has transparency for features (Java 1.2
4528 <li>Applet has user defined colours parameter</li>
4529 <li>Applet can load sequences from parameter
4530 "sequence<em>x</em>"
4536 <li>Redundancy Panel reinstalled in the Applet</li>
4537 <li>Monospaced font - EPS / rescaling bug fixed</li>
4538 <li>Annotation files with sequence references bug fixed</li>
4544 <div align="center">
4545 <strong>2.08.1</strong><br> 2/5/06
4550 <li>Change case of selected region from Popup menu</li>
4551 <li>Choose to match case when searching</li>
4552 <li>Middle mouse button and mouse movement can compress /
4553 expand the visible width and height of the alignment</li>
4558 <li>Annotation Panel displays complete JNet results</li>
4564 <div align="center">
4565 <strong>2.08b</strong><br> 18/4/06
4571 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4572 <li>Righthand label on wrapped alignments shows correct
4579 <div align="center">
4580 <strong>2.08</strong><br> 10/4/06
4585 <li>Editing can be locked to the selection area</li>
4586 <li>Keyboard editing</li>
4587 <li>Create sequence features from searches</li>
4588 <li>Precalculated annotations can be loaded onto
4590 <li>Features file allows grouping of features</li>
4591 <li>Annotation Colouring scheme added</li>
4592 <li>Smooth fonts off by default - Faster rendering</li>
4593 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4598 <li>Drag & Drop fixed on Linux</li>
4599 <li>Jalview Archive file faster to load/save, sequence
4600 descriptions saved.</li>
4606 <div align="center">
4607 <strong>2.07</strong><br> 12/12/05
4612 <li>PDB Structure Viewer enhanced</li>
4613 <li>Sequence Feature retrieval and display enhanced</li>
4614 <li>Choose to output sequence start-end after sequence
4615 name for file output</li>
4616 <li>Sequence Fetcher WSDBFetch@EBI</li>
4617 <li>Applet can read feature files, PDB files and can be
4618 used for HTML form input</li>
4623 <li>HTML output writes groups and features</li>
4624 <li>Group editing is Control and mouse click</li>
4625 <li>File IO bugs</li>
4631 <div align="center">
4632 <strong>2.06</strong><br> 28/9/05
4637 <li>View annotations in wrapped mode</li>
4638 <li>More options for PCA viewer</li>
4643 <li>GUI bugs resolved</li>
4644 <li>Runs with -nodisplay from command line</li>
4650 <div align="center">
4651 <strong>2.05b</strong><br> 15/9/05
4656 <li>Choose EPS export as lineart or text</li>
4657 <li>Jar files are executable</li>
4658 <li>Can read in Uracil - maps to unknown residue</li>
4663 <li>Known OutOfMemory errors give warning message</li>
4664 <li>Overview window calculated more efficiently</li>
4665 <li>Several GUI bugs resolved</li>
4671 <div align="center">
4672 <strong>2.05</strong><br> 30/8/05
4677 <li>Edit and annotate in "Wrapped" view</li>
4682 <li>Several GUI bugs resolved</li>
4688 <div align="center">
4689 <strong>2.04</strong><br> 24/8/05
4694 <li>Hold down mouse wheel & scroll to change font
4700 <li>Improved JPred client reliability</li>
4701 <li>Improved loading of Jalview files</li>
4707 <div align="center">
4708 <strong>2.03</strong><br> 18/8/05
4713 <li>Set Proxy server name and port in preferences</li>
4714 <li>Multiple URL links from sequence ids</li>
4715 <li>User Defined Colours can have a scheme name and added
4717 <li>Choose to ignore gaps in consensus calculation</li>
4718 <li>Unix users can set default web browser</li>
4719 <li>Runs without GUI for batch processing</li>
4720 <li>Dynamically generated Web Service Menus</li>
4725 <li>InstallAnywhere download for Sparc Solaris</li>
4731 <div align="center">
4732 <strong>2.02</strong><br> 18/7/05
4738 <li>Copy & Paste order of sequences maintains
4739 alignment order.</li>
4745 <div align="center">
4746 <strong>2.01</strong><br> 12/7/05
4751 <li>Use delete key for deleting selection.</li>
4752 <li>Use Mouse wheel to scroll sequences.</li>
4753 <li>Help file updated to describe how to add alignment
4755 <li>Version and build date written to build properties
4757 <li>InstallAnywhere installation will check for updates
4758 at launch of Jalview.</li>
4763 <li>Delete gaps bug fixed.</li>
4764 <li>FileChooser sorts columns.</li>
4765 <li>Can remove groups one by one.</li>
4766 <li>Filechooser icons installed.</li>
4767 <li>Finder ignores return character when searching.
4768 Return key will initiate a search.<br>
4775 <div align="center">
4776 <strong>2.0</strong><br> 20/6/05
4781 <li>New codebase</li>