3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>13/07/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
71 HTSJDK from 2.12 to 2.23
74 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
75 optimisations and improvements suggested by Bob Hanson and
76 improved compatibility with JalviewJS
79 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
80 alignments from Pfam and Rfam
83 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
84 import (no longer based on .gz extension)
87 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
90 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
91 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
94 </ul> <em>Launching Jalview</em>
97 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
98 through a system property
102 <td align="left" valign="top">
105 <!-- JAL-3493 -->Escape does not clear highlights on the
106 alignment (Since Jalview 2.10.3)
109 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
110 doesn't slide selected sequences
113 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
114 multiple EMBL gene products shown forĀ a single contig
117 <!-- JAL-3696 -->Errors encountered when processing variants
118 from VCF files yield "Error processing VCF: Format specifier
122 <!-- JAL-3697 -->Count of features not shown can be wrong
123 when there are both local and complementary features mapped
124 to the position under the cursor
127 <!-- JAL-2983 -->Slider with negative range values not
128 rendered correctly in VAqua4 (Since 2.10.4)
131 <em>New Known defects</em>
133 <li><!-- JAL-3701 -->Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
139 <td width="60" align="center" nowrap><strong><a
140 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
141 <em>22/04/2020</em></strong></td>
142 <td align="left" valign="top">
145 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
146 'virtual' codon features shown on protein (or vice versa)
147 for display in alignments, on structure views (including
148 transfer to UCSF chimera), in feature reports and for
152 <!-- JAL-3121 -->Feature attributes from VCF files can be
153 exported and re-imported as GFF3 files
156 <!-- JAL-3376 -->Capture VCF "fixed column" values
157 POS, ID, QUAL, FILTER as Feature Attributes
160 <!-- JAL-3375 -->More robust VCF numeric data field
161 validation while parsing
164 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
168 <!-- JAL-3535 -->Feature Settings dialog title includes name
172 <!-- JAL-3538 -->Font anti-aliasing in alignment views
176 <!-- JAL-3468 -->Very long feature descriptions truncated in
180 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
181 with no feature types visible
184 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
186 </ul><em>Jalview Installer</em>
189 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
190 in console (may be null when Jalview launched as executable jar or via conda)
193 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
196 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
199 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
201 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
202 </ul> <em>Release processes</em>
205 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
208 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
210 </ul> <em>Build System</em>
213 <!-- JAL-3510 -->Clover updated to 4.4.1
216 <!-- JAL-3513 -->Test code included in Clover coverage
220 <em>Groovy Scripts</em>
223 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
224 to stdout containing the consensus sequence for each
225 alignment in a Jalview session
228 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
229 genomic sequence_variant annotation from CDS as
230 missense_variant or synonymous_variant on protein products.
234 <td align="left" valign="top">
237 <!-- JAL-3581 -->Hidden sequence markers still visible when
238 'Show hidden markers' option is not ticked
241 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
242 PNG output when 'Automatically set ID width' is set in
243 jalview preferences or properties file
246 <!-- JAL-3571 -->Feature Editor dialog can be opened when
247 'Show Sequence Features' option is not ticked
250 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
251 buttons in Feature Settings dialog are clicked when no
255 <!-- JAL-3412 -->ID margins for CDS and Protein views not
256 equal when split frame is first opened
259 <!-- JAL-3296 -->Sequence position numbers in status bar not
260 correct after editing a sequence's start position
263 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
264 with annotation and exceptions thrown when only a few
265 columns shown in wrapped mode
268 <!-- JAL-3386 -->Sequence IDs missing in headless export of
269 wrapped alignment figure with annotations
272 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
273 ID fails with ClassCastException
276 <!-- JAL-3389 -->Chimera session not restored from Jalview
280 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
281 feature settings dialog also selects columns
284 <!-- JAL-3473 -->SpinnerNumberModel causes
285 IllegalArgumentException in some circumstances
288 <!-- JAL-3534 -->Multiple feature settings dialogs can be
292 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
293 alignment window is closed
296 <!-- JAL-3406 -->Credits missing some authors in Jalview
297 help documentation for 2.11.0 release
300 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
301 includes Pfam ID as sequence's accession rather than its
304 </ul> <em>Java 11 Compatibility issues</em>
307 <!-- JAL-2987 -->OSX - Can't view some search results in
308 PDB/Uniprot search panel
310 </ul> <em>Installer</em>
313 <!-- JAL-3447 -->Jalview should not create file associations
314 for 3D structure files (.pdb, .mmcif. .cif)
316 </ul> <em>Repository and Source Release</em>
319 <!-- JAL-3474 -->removed obsolete .cvsignore files from
323 <!-- JAL-3541 -->Clover report generation running out of
326 </ul> <em>New Known Issues</em>
329 <!-- JAL-3523 -->OSX - Current working directory not
330 preserved when Jalview.app launched with parameters from
334 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
335 clipped in headless figure export when Right Align option
339 <!-- JAL-3542 -->Jalview Installation type always reports
340 'Source' in console output
343 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
344 bamboo server but run fine locally.
350 <td width="60" align="center" nowrap>
351 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
352 <em>04/07/2019</em></strong>
354 <td align="left" valign="top">
357 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
358 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
359 source project) rather than InstallAnywhere
362 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
363 settings, receive over the air updates and launch specific
364 versions via (<a href="https://github.com/threerings/getdown">Three
368 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
369 formats supported by Jalview (including .jvp project files)
372 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
373 arguments and switch between different getdown channels
376 <!-- JAL-3141 -->Backup files created when saving Jalview project
381 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
382 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
384 <!-- JAL-2620 -->Alternative genetic code tables for
385 'Translate as cDNA'</li>
387 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
388 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
391 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
392 implementation that allows updates) used for Sequence Feature collections</li>
394 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
395 features can be filtered and shaded according to any
396 associated attributes (e.g. variant attributes from VCF
397 file, or key-value pairs imported from column 9 of GFF
401 <!-- JAL-2879 -->Feature Attributes and shading schemes
402 stored and restored from Jalview Projects
405 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
406 recognise variant features
409 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
410 sequences (also coloured red by default)
413 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
417 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
418 algorithm (Z-sort/transparency and filter aware)
421 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
427 <!-- JAL-3205 -->Symmetric score matrices for faster
428 tree and PCA calculations
430 <li><strong>Principal Components Analysis Viewer</strong>
433 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
434 and Viewer state saved in Jalview Project
436 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
439 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
443 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
448 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
450 <li><strong>Speed and Efficiency</strong>
453 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
454 multiple groups when working with large alignments
457 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
461 <li><strong>User Interface</strong>
464 <!-- JAL-2933 -->Finder panel remembers last position in each
468 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
469 what is shown)<br />Only visible regions of alignment are shown by
470 default (can be changed in user preferences)
473 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
474 to the Overwrite Dialog
477 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
481 <!-- JAL-1244 -->Status bar shows bounds when dragging a
482 selection region, and gap count when inserting or deleting gaps
485 <!-- JAL-3132 -->Status bar updates over sequence and annotation
489 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
493 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
497 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
500 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
504 <!-- JAL-3181 -->Consistent ordering of links in sequence id
508 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
510 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
514 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
515 <li><strong>Java 11 Support (not yet on general release)</strong>
518 <!-- -->OSX GUI integrations for App menu's 'About' entry and
523 <em>Deprecations</em>
525 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
526 capabilities removed from the Jalview Desktop
528 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
529 unmarshalling has been replaced by JAXB for Jalview projects
530 and XML based data retrieval clients</li>
531 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
532 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
533 </ul> <em>Documentation</em>
535 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
536 not supported in EPS figure export
538 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
539 </ul> <em>Development and Release Processes</em>
542 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
545 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
547 <!-- JAL-3225 -->Eclipse project configuration managed with
551 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
552 Bamboo continuous integration for unattended Test Suite
556 <!-- JAL-2864 -->Memory test suite to detect leaks in common
560 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
564 <!-- JAL-3248 -->Developer documentation migrated to
565 markdown (with HTML rendering)
568 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
571 <!-- JAL-3289 -->New URLs for publishing development
576 <td align="left" valign="top">
579 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
582 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
583 superposition in Jmol fail on Windows
586 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
587 structures for sequences with lots of PDB structures
590 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
594 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
595 project involving multiple views
598 <!-- JAL-3164 -->Overview for complementary view in a linked
599 CDS/Protein alignment is not updated when Hide Columns by
600 Annotation dialog hides columns
603 <!-- JAL-3158 -->Selection highlighting in the complement of a
604 CDS/Protein alignment stops working after making a selection in
605 one view, then making another selection in the other view
608 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
612 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
613 Settings and Jalview Preferences panels
616 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
617 overview with large alignments
620 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
621 region if columns were selected by dragging right-to-left and the
622 mouse moved to the left of the first column
625 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
626 hidden column marker via scale popup menu
629 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
630 doesn't tell users the invalid URL
633 <!-- JAL-2816 -->Tooltips displayed for features filtered by
637 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
638 show cross references or Fetch Database References are shown in
642 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
643 peptide sequence (computed variant shown as p.Res.null)
646 <!-- JAL-2060 -->'Graduated colour' option not offered for
647 manually created features (where feature score is Float.NaN)
650 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
651 when columns are hidden
654 <!-- JAL-3082 -->Regular expression error for '(' in Select
655 Columns by Annotation description
658 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
659 out of Scale or Annotation Panel
662 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
666 <!-- JAL-3074 -->Left/right drag in annotation can scroll
670 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
674 <!-- JAL-3002 -->Column display is out by one after Page Down,
675 Page Up in wrapped mode
678 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
681 <!-- JAL-2932 -->Finder searches in minimised alignments
684 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
685 on opening an alignment
688 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
692 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
693 different groups in the alignment are selected
696 <!-- JAL-2717 -->Internationalised colour scheme names not shown
700 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
704 <!-- JAL-3125 -->Value input for graduated feature colour
705 threshold gets 'unrounded'
708 <!-- JAL-2982 -->PCA image export doesn't respect background
712 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
715 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
718 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
722 <!-- JAL-2964 -->Associate Tree with All Views not restored from
726 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
727 shown in complementary view
730 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
731 without normalisation
734 <!-- JAL-3021 -->Sequence Details report should open positioned at top
738 <!-- JAL-914 -->Help page can be opened twice
741 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
743 </ul> <em>Editing</em>
746 <!-- JAL-2822 -->Start and End should be updated when sequence
747 data at beginning or end of alignment added/removed via 'Edit'
751 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
752 relocate sequence features correctly when start of sequence is
753 removed (Known defect since 2.10)
756 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
757 dialog corrupts dataset sequence
760 <!-- JAL-868 -->Structure colours not updated when associated tree
761 repartitions the alignment view (Regression in 2.10.5)
763 </ul> <em>Datamodel</em>
766 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
767 sequence's End is greater than its length
769 </ul> <em>Bugs fixed for Java 11 Support (not yet on
770 general release)</em>
773 <!-- JAL-3288 -->Menus work properly in split-screen
775 </ul> <em>New Known Defects</em>
778 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
781 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
782 regions of protein alignment.
785 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
786 is restored from a Jalview 2.11 project
789 <!-- JAL-3213 -->Alignment panel height can be too small after
793 <!-- JAL-3240 -->Display is incorrect after removing gapped
794 columns within hidden columns
797 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
798 window after dragging left to select columns to left of visible
802 <!-- JAL-2876 -->Features coloured according to their description
803 string and thresholded by score in earlier versions of Jalview are
804 not shown as thresholded features in 2.11. To workaround please
805 create a Score filter instead.
808 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
810 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
813 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
814 alignments with multiple views can close views unexpectedly
817 <em>Java 11 Specific defects</em>
820 <!-- JAL-3235 -->Jalview Properties file is not sorted
821 alphabetically when saved
827 <td width="60" nowrap>
829 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
832 <td><div align="left">
836 <!-- JAL-3101 -->Default memory for Jalview webstart and
837 InstallAnywhere increased to 1G.
840 <!-- JAL-247 -->Hidden sequence markers and representative
841 sequence bolding included when exporting alignment as EPS,
842 SVG, PNG or HTML. <em>Display is configured via the
843 Format menu, or for command-line use via a Jalview
844 properties file.</em>
847 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
848 API and sequence data now imported as JSON.
851 <!-- JAL-3065 -->Change in recommended way of starting
852 Jalview via a Java command line: add jars in lib directory
853 to CLASSPATH, rather than via the deprecated java.ext.dirs
860 <!-- JAL-3047 -->Support added to execute test suite
861 instrumented with <a href="http://openclover.org/">Open
866 <td><div align="left">
870 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
871 row shown in Feredoxin Structure alignment view of example
875 <!-- JAL-2854 -->Annotation obscures sequences if lots of
876 annotation displayed.
879 <!-- JAL-3107 -->Group conservation/consensus not shown
880 for newly created group when 'Apply to all groups'
884 <!-- JAL-3087 -->Corrupted display when switching to
885 wrapped mode when sequence panel's vertical scrollbar is
889 <!-- JAL-3003 -->Alignment is black in exported EPS file
890 when sequences are selected in exported view.</em>
893 <!-- JAL-3059 -->Groups with different coloured borders
894 aren't rendered with correct colour.
897 <!-- JAL-3092 -->Jalview could hang when importing certain
898 types of knotted RNA secondary structure.
901 <!-- JAL-3095 -->Sequence highlight and selection in
902 trimmed VARNA 2D structure is incorrect for sequences that
906 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
907 annotation when columns are inserted into an alignment,
908 and when exporting as Stockholm flatfile.
911 <!-- JAL-3053 -->Jalview annotation rows containing upper
912 and lower-case 'E' and 'H' do not automatically get
913 treated as RNA secondary structure.
916 <!-- JAL-3106 -->.jvp should be used as default extension
917 (not .jar) when saving a Jalview project file.
920 <!-- JAL-3105 -->Mac Users: closing a window correctly
921 transfers focus to previous window on OSX
924 <em>Java 10 Issues Resolved</em>
927 <!-- JAL-2988 -->OSX - Can't save new files via the File
928 or export menus by typing in a name into the Save dialog
932 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
933 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
934 'look and feel' which has improved compatibility with the
935 latest version of OSX.
942 <td width="60" nowrap>
944 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
945 <em>7/06/2018</em></strong>
948 <td><div align="left">
952 <!-- JAL-2920 -->Use HGVS nomenclature for variant
953 annotation retrieved from Uniprot
956 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
957 onto the Jalview Desktop
961 <td><div align="left">
965 <!-- JAL-3017 -->Cannot import features with multiple
966 variant elements (blocks import of some Uniprot records)
969 <!-- JAL-2997 -->Clustal files with sequence positions in
970 right-hand column parsed correctly
973 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
974 not alignment area in exported graphic
977 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
978 window has input focus
981 <!-- JAL-2992 -->Annotation panel set too high when
982 annotation added to view (Windows)
985 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
986 network connectivity is poor
989 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
990 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
991 the currently open URL and links from a page viewed in
992 Firefox or Chrome on Windows is now fully supported. If
993 you are using Edge, only links in the page can be
994 dragged, and with Internet Explorer, only the currently
995 open URL in the browser can be dropped onto Jalview.</em>
998 <em>New Known Defects</em>
1000 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1005 <td width="60" nowrap>
1006 <div align="center">
1007 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1010 <td><div align="left">
1014 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1015 for disabling automatic superposition of multiple
1016 structures and open structures in existing views
1019 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1020 ID and annotation area margins can be click-dragged to
1024 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1028 <!-- JAL-2759 -->Improved performance for large alignments
1029 and lots of hidden columns
1032 <!-- JAL-2593 -->Improved performance when rendering lots
1033 of features (particularly when transparency is disabled)
1036 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1037 exchange of Jalview features and Chimera attributes made
1043 <td><div align="left">
1046 <!-- JAL-2899 -->Structure and Overview aren't updated
1047 when Colour By Annotation threshold slider is adjusted
1050 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1051 overlapping alignment panel
1054 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1058 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1059 improved: CDS not handled correctly if transcript has no
1063 <!-- JAL-2321 -->Secondary structure and temperature
1064 factor annotation not added to sequence when local PDB
1065 file associated with it by drag'n'drop or structure
1069 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1070 dialog doesn't import PDB files dropped on an alignment
1073 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1074 scroll bar doesn't work for some CDS/Protein views
1077 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1078 Java 1.8u153 onwards and Java 1.9u4+.
1081 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1082 columns in annotation row
1085 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1086 honored in batch mode
1089 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1090 for structures added to existing Jmol view
1093 <!-- JAL-2223 -->'View Mappings' includes duplicate
1094 entries after importing project with multiple views
1097 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1098 protein sequences via SIFTS from associated PDB entries
1099 with negative residue numbers or missing residues fails
1102 <!-- JAL-2952 -->Exception when shading sequence with negative
1103 Temperature Factor values from annotated PDB files (e.g.
1104 as generated by CONSURF)
1107 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1108 tooltip doesn't include a text description of mutation
1111 <!-- JAL-2922 -->Invert displayed features very slow when
1112 structure and/or overview windows are also shown
1115 <!-- JAL-2954 -->Selecting columns from highlighted regions
1116 very slow for alignments with large numbers of sequences
1119 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1120 with 'StringIndexOutOfBounds'
1123 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1124 platforms running Java 10
1127 <!-- JAL-2960 -->Adding a structure to existing structure
1128 view appears to do nothing because the view is hidden behind the alignment view
1134 <!-- JAL-2926 -->Copy consensus sequence option in applet
1135 should copy the group consensus when popup is opened on it
1141 <!-- JAL-2913 -->Fixed ID width preference is not respected
1144 <em>New Known Defects</em>
1147 <!-- JAL-2973 --> Exceptions occasionally raised when
1148 editing a large alignment and overview is displayed
1151 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1152 repeatedly after a series of edits even when the overview
1153 is no longer reflecting updates
1156 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1157 structures for protein subsequence (if 'Trim Retrieved
1158 Sequences' enabled) or Ensembl isoforms (Workaround in
1159 2.10.4 is to fail back to N&W mapping)
1162 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1163 option gives blank output
1170 <td width="60" nowrap>
1171 <div align="center">
1172 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1175 <td><div align="left">
1176 <ul><li>Updated Certum Codesigning Certificate
1177 (Valid till 30th November 2018)</li></ul></div></td>
1178 <td><div align="left">
1179 <em>Desktop</em><ul>
1181 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1182 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1183 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1184 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1185 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1186 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1187 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1193 <td width="60" nowrap>
1194 <div align="center">
1195 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1198 <td><div align="left">
1202 <!-- JAL-2446 -->Faster and more efficient management and
1203 rendering of sequence features
1206 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1207 429 rate limit request hander
1210 <!-- JAL-2773 -->Structure views don't get updated unless
1211 their colours have changed
1214 <!-- JAL-2495 -->All linked sequences are highlighted for
1215 a structure mousover (Jmol) or selection (Chimera)
1218 <!-- JAL-2790 -->'Cancel' button in progress bar for
1219 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1222 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1223 view from Ensembl locus cross-references
1226 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1230 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1231 feature can be disabled
1234 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1235 PDB easier retrieval of sequences for lists of IDs
1238 <!-- JAL-2758 -->Short names for sequences retrieved from
1244 <li>Groovy interpreter updated to 2.4.12</li>
1245 <li>Example groovy script for generating a matrix of
1246 percent identity scores for current alignment.</li>
1248 <em>Testing and Deployment</em>
1251 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1255 <td><div align="left">
1259 <!-- JAL-2643 -->Pressing tab after updating the colour
1260 threshold text field doesn't trigger an update to the
1264 <!-- JAL-2682 -->Race condition when parsing sequence ID
1268 <!-- JAL-2608 -->Overview windows are also closed when
1269 alignment window is closed
1272 <!-- JAL-2548 -->Export of features doesn't always respect
1276 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1277 takes a long time in Cursor mode
1283 <!-- JAL-2777 -->Structures with whitespace chainCode
1284 cannot be viewed in Chimera
1287 <!-- JAL-2728 -->Protein annotation panel too high in
1291 <!-- JAL-2757 -->Can't edit the query after the server
1292 error warning icon is shown in Uniprot and PDB Free Text
1296 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1299 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1302 <!-- JAL-2739 -->Hidden column marker in last column not
1303 rendered when switching back from Wrapped to normal view
1306 <!-- JAL-2768 -->Annotation display corrupted when
1307 scrolling right in unwapped alignment view
1310 <!-- JAL-2542 -->Existing features on subsequence
1311 incorrectly relocated when full sequence retrieved from
1315 <!-- JAL-2733 -->Last reported memory still shown when
1316 Desktop->Show Memory is unticked (OSX only)
1319 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1320 features of same type and group to be selected for
1324 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1325 alignments when hidden columns are present
1328 <!-- JAL-2392 -->Jalview freezes when loading and
1329 displaying several structures
1332 <!-- JAL-2732 -->Black outlines left after resizing or
1336 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1337 within the Jalview desktop on OSX
1340 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1341 when in wrapped alignment mode
1344 <!-- JAL-2636 -->Scale mark not shown when close to right
1345 hand end of alignment
1348 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1349 each selected sequence do not have correct start/end
1353 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1354 after canceling the Alignment Window's Font dialog
1357 <!-- JAL-2036 -->Show cross-references not enabled after
1358 restoring project until a new view is created
1361 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1362 URL links appears when only default EMBL-EBI link is
1363 configured (since 2.10.2b2)
1366 <!-- JAL-2775 -->Overview redraws whole window when box
1367 position is adjusted
1370 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1371 in a multi-chain structure when viewing alignment
1372 involving more than one chain (since 2.10)
1375 <!-- JAL-2811 -->Double residue highlights in cursor mode
1376 if new selection moves alignment window
1379 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1380 arrow key in cursor mode to pass hidden column marker
1383 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1384 that produces correctly annotated transcripts and products
1387 <!-- JAL-2776 -->Toggling a feature group after first time
1388 doesn't update associated structure view
1391 <em>Applet</em><br />
1394 <!-- JAL-2687 -->Concurrent modification exception when
1395 closing alignment panel
1398 <em>BioJSON</em><br />
1401 <!-- JAL-2546 -->BioJSON export does not preserve
1402 non-positional features
1405 <em>New Known Issues</em>
1408 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1409 sequence features correctly (for many previous versions of
1413 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1414 using cursor in wrapped panel other than top
1417 <!-- JAL-2791 -->Select columns containing feature ignores
1418 graduated colour threshold
1421 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1422 always preserve numbering and sequence features
1425 <em>Known Java 9 Issues</em>
1428 <!-- JAL-2902 -->Groovy Console very slow to open and is
1429 not responsive when entering characters (Webstart, Java
1436 <td width="60" nowrap>
1437 <div align="center">
1438 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1439 <em>2/10/2017</em></strong>
1442 <td><div align="left">
1443 <em>New features in Jalview Desktop</em>
1446 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1448 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1452 <td><div align="left">
1456 <td width="60" nowrap>
1457 <div align="center">
1458 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1459 <em>7/9/2017</em></strong>
1462 <td><div align="left">
1466 <!-- JAL-2588 -->Show gaps in overview window by colouring
1467 in grey (sequences used to be coloured grey, and gaps were
1471 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1475 <!-- JAL-2587 -->Overview updates immediately on increase
1476 in size and progress bar shown as higher resolution
1477 overview is recalculated
1482 <td><div align="left">
1486 <!-- JAL-2664 -->Overview window redraws every hidden
1487 column region row by row
1490 <!-- JAL-2681 -->duplicate protein sequences shown after
1491 retrieving Ensembl crossrefs for sequences from Uniprot
1494 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1495 format setting is unticked
1498 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1499 if group has show boxes format setting unticked
1502 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1503 autoscrolling whilst dragging current selection group to
1504 include sequences and columns not currently displayed
1507 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1508 assemblies are imported via CIF file
1511 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1512 displayed when threshold or conservation colouring is also
1516 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1520 <!-- JAL-2673 -->Jalview continues to scroll after
1521 dragging a selected region off the visible region of the
1525 <!-- JAL-2724 -->Cannot apply annotation based
1526 colourscheme to all groups in a view
1529 <!-- JAL-2511 -->IDs don't line up with sequences
1530 initially after font size change using the Font chooser or
1537 <td width="60" nowrap>
1538 <div align="center">
1539 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1542 <td><div align="left">
1543 <em>Calculations</em>
1547 <!-- JAL-1933 -->Occupancy annotation row shows number of
1548 ungapped positions in each column of the alignment.
1551 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1552 a calculation dialog box
1555 <!-- JAL-2379 -->Revised implementation of PCA for speed
1556 and memory efficiency (~30x faster)
1559 <!-- JAL-2403 -->Revised implementation of sequence
1560 similarity scores as used by Tree, PCA, Shading Consensus
1561 and other calculations
1564 <!-- JAL-2416 -->Score matrices are stored as resource
1565 files within the Jalview codebase
1568 <!-- JAL-2500 -->Trees computed on Sequence Feature
1569 Similarity may have different topology due to increased
1576 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1577 model for alignments and groups
1580 <!-- JAL-384 -->Custom shading schemes created via groovy
1587 <!-- JAL-2526 -->Efficiency improvements for interacting
1588 with alignment and overview windows
1591 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1595 <!-- JAL-2388 -->Hidden columns and sequences can be
1599 <!-- JAL-2611 -->Click-drag in visible area allows fine
1600 adjustment of visible position
1604 <em>Data import/export</em>
1607 <!-- JAL-2535 -->Posterior probability annotation from
1608 Stockholm files imported as sequence associated annotation
1611 <!-- JAL-2507 -->More robust per-sequence positional
1612 annotation input/output via stockholm flatfile
1615 <!-- JAL-2533 -->Sequence names don't include file
1616 extension when importing structure files without embedded
1617 names or PDB accessions
1620 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1621 format sequence substitution matrices
1624 <em>User Interface</em>
1627 <!-- JAL-2447 --> Experimental Features Checkbox in
1628 Desktop's Tools menu to hide or show untested features in
1632 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1633 via Overview or sequence motif search operations
1636 <!-- JAL-2547 -->Amend sequence features dialog box can be
1637 opened by double clicking gaps within sequence feature
1641 <!-- JAL-1476 -->Status bar message shown when not enough
1642 aligned positions were available to create a 3D structure
1646 <em>3D Structure</em>
1649 <!-- JAL-2430 -->Hidden regions in alignment views are not
1650 coloured in linked structure views
1653 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1654 file-based command exchange
1657 <!-- JAL-2375 -->Structure chooser automatically shows
1658 Cached Structures rather than querying the PDBe if
1659 structures are already available for sequences
1662 <!-- JAL-2520 -->Structures imported via URL are cached in
1663 the Jalview project rather than downloaded again when the
1664 project is reopened.
1667 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1668 to transfer Chimera's structure attributes as Jalview
1669 features, and vice-versa (<strong>Experimental
1673 <em>Web Services</em>
1676 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1679 <!-- JAL-2335 -->Filter non-standard amino acids and
1680 nucleotides when submitting to AACon and other MSA
1684 <!-- JAL-2316, -->URLs for viewing database
1685 cross-references provided by identifiers.org and the
1686 EMBL-EBI's MIRIAM DB
1693 <!-- JAL-2344 -->FileFormatI interface for describing and
1694 identifying file formats (instead of String constants)
1697 <!-- JAL-2228 -->FeatureCounter script refactored for
1698 efficiency when counting all displayed features (not
1699 backwards compatible with 2.10.1)
1702 <em>Example files</em>
1705 <!-- JAL-2631 -->Graduated feature colour style example
1706 included in the example feature file
1709 <em>Documentation</em>
1712 <!-- JAL-2339 -->Release notes reformatted for readability
1713 with the built-in Java help viewer
1716 <!-- JAL-1644 -->Find documentation updated with 'search
1717 sequence description' option
1723 <!-- JAL-2485, -->External service integration tests for
1724 Uniprot REST Free Text Search Client
1727 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1730 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1735 <td><div align="left">
1736 <em>Calculations</em>
1739 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1740 matrix - C->R should be '-3'<br />Old matrix restored
1741 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1743 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1744 Jalview's treatment of gaps in PCA and substitution matrix
1745 based Tree calculations.<br /> <br />In earlier versions
1746 of Jalview, gaps matching gaps were penalised, and gaps
1747 matching non-gaps penalised even more. In the PCA
1748 calculation, gaps were actually treated as non-gaps - so
1749 different costs were applied, which meant Jalview's PCAs
1750 were different to those produced by SeqSpace.<br />Jalview
1751 now treats gaps in the same way as SeqSpace (ie it scores
1752 them as 0). <br /> <br />Enter the following in the
1753 Groovy console to restore pre-2.10.2 behaviour:<br />
1754 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1755 // for 2.10.1 mode <br />
1756 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1757 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1758 these settings will affect all subsequent tree and PCA
1759 calculations (not recommended)</em></li>
1761 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1762 scaling of branch lengths for trees computed using
1763 Sequence Feature Similarity.
1766 <!-- JAL-2377 -->PCA calculation could hang when
1767 generating output report when working with highly
1768 redundant alignments
1771 <!-- JAL-2544 --> Sort by features includes features to
1772 right of selected region when gaps present on right-hand
1776 <em>User Interface</em>
1779 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1780 doesn't reselect a specific sequence's associated
1781 annotation after it was used for colouring a view
1784 <!-- JAL-2419 -->Current selection lost if popup menu
1785 opened on a region of alignment without groups
1788 <!-- JAL-2374 -->Popup menu not always shown for regions
1789 of an alignment with overlapping groups
1792 <!-- JAL-2310 -->Finder double counts if both a sequence's
1793 name and description match
1796 <!-- JAL-2370 -->Hiding column selection containing two
1797 hidden regions results in incorrect hidden regions
1800 <!-- JAL-2386 -->'Apply to all groups' setting when
1801 changing colour does not apply Conservation slider value
1805 <!-- JAL-2373 -->Percentage identity and conservation menu
1806 items do not show a tick or allow shading to be disabled
1809 <!-- JAL-2385 -->Conservation shading or PID threshold
1810 lost when base colourscheme changed if slider not visible
1813 <!-- JAL-2547 -->Sequence features shown in tooltip for
1814 gaps before start of features
1817 <!-- JAL-2623 -->Graduated feature colour threshold not
1818 restored to UI when feature colour is edited
1821 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1822 a time when scrolling vertically in wrapped mode.
1825 <!-- JAL-2630 -->Structure and alignment overview update
1826 as graduate feature colour settings are modified via the
1830 <!-- JAL-2034 -->Overview window doesn't always update
1831 when a group defined on the alignment is resized
1834 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1835 wrapped view result in positional status updates
1839 <!-- JAL-2563 -->Status bar doesn't show position for
1840 ambiguous amino acid and nucleotide symbols
1843 <!-- JAL-2602 -->Copy consensus sequence failed if
1844 alignment included gapped columns
1847 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1848 widgets don't permanently disappear
1851 <!-- JAL-2503 -->Cannot select or filter quantitative
1852 annotation that are shown only as column labels (e.g.
1853 T-Coffee column reliability scores)
1856 <!-- JAL-2594 -->Exception thrown if trying to create a
1857 sequence feature on gaps only
1860 <!-- JAL-2504 -->Features created with 'New feature'
1861 button from a Find inherit previously defined feature type
1862 rather than the Find query string
1865 <!-- JAL-2423 -->incorrect title in output window when
1866 exporting tree calculated in Jalview
1869 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1870 and then revealing them reorders sequences on the
1874 <!-- JAL-964 -->Group panel in sequence feature settings
1875 doesn't update to reflect available set of groups after
1876 interactively adding or modifying features
1879 <!-- JAL-2225 -->Sequence Database chooser unusable on
1883 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1884 only excluded gaps in current sequence and ignored
1891 <!-- JAL-2421 -->Overview window visible region moves
1892 erratically when hidden rows or columns are present
1895 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1896 Structure Viewer's colour menu don't correspond to
1900 <!-- JAL-2405 -->Protein specific colours only offered in
1901 colour and group colour menu for protein alignments
1904 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1905 reflect currently selected view or group's shading
1909 <!-- JAL-2624 -->Feature colour thresholds not respected
1910 when rendered on overview and structures when opacity at
1914 <!-- JAL-2589 -->User defined gap colour not shown in
1915 overview when features overlaid on alignment
1918 <!-- JAL-2567 -->Feature settings for different views not
1919 recovered correctly from Jalview project file
1922 <!-- JAL-2256 -->Feature colours in overview when first opened
1923 (automatically via preferences) are different to the main
1927 <em>Data import/export</em>
1930 <!-- JAL-2576 -->Very large alignments take a long time to
1934 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1935 added after a sequence was imported are not written to
1939 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1940 when importing RNA secondary structure via Stockholm
1943 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1944 not shown in correct direction for simple pseudoknots
1947 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1948 with lightGray or darkGray via features file (but can
1952 <!-- JAL-2383 -->Above PID colour threshold not recovered
1953 when alignment view imported from project
1956 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1957 structure and sequences extracted from structure files
1958 imported via URL and viewed in Jmol
1961 <!-- JAL-2520 -->Structures loaded via URL are saved in
1962 Jalview Projects rather than fetched via URL again when
1963 the project is loaded and the structure viewed
1966 <em>Web Services</em>
1969 <!-- JAL-2519 -->EnsemblGenomes example failing after
1970 release of Ensembl v.88
1973 <!-- JAL-2366 -->Proxy server address and port always
1974 appear enabled in Preferences->Connections
1977 <!-- JAL-2461 -->DAS registry not found exceptions
1978 removed from console output
1981 <!-- JAL-2582 -->Cannot retrieve protein products from
1982 Ensembl by Peptide ID
1985 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1986 created from SIFTs, and spurious 'Couldn't open structure
1987 in Chimera' errors raised after April 2017 update (problem
1988 due to 'null' string rather than empty string used for
1989 residues with no corresponding PDB mapping).
1992 <em>Application UI</em>
1995 <!-- JAL-2361 -->User Defined Colours not added to Colour
1999 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2000 case' residues (button in colourscheme editor debugged and
2001 new documentation and tooltips added)
2004 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2005 doesn't restore group-specific text colour thresholds
2008 <!-- JAL-2243 -->Feature settings panel does not update as
2009 new features are added to alignment
2012 <!-- JAL-2532 -->Cancel in feature settings reverts
2013 changes to feature colours via the Amend features dialog
2016 <!-- JAL-2506 -->Null pointer exception when attempting to
2017 edit graduated feature colour via amend features dialog
2021 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2022 selection menu changes colours of alignment views
2025 <!-- JAL-2426 -->Spurious exceptions in console raised
2026 from alignment calculation workers after alignment has
2030 <!-- JAL-1608 -->Typo in selection popup menu - Create
2031 groups now 'Create Group'
2034 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2035 Create/Undefine group doesn't always work
2038 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2039 shown again after pressing 'Cancel'
2042 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2043 adjusts start position in wrap mode
2046 <!-- JAL-2563 -->Status bar doesn't show positions for
2047 ambiguous amino acids
2050 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2051 CDS/Protein view after CDS sequences added for aligned
2055 <!-- JAL-2592 -->User defined colourschemes called 'User
2056 Defined' don't appear in Colours menu
2062 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2063 score models doesn't always result in an updated PCA plot
2066 <!-- JAL-2442 -->Features not rendered as transparent on
2067 overview or linked structure view
2070 <!-- JAL-2372 -->Colour group by conservation doesn't
2074 <!-- JAL-2517 -->Hitting Cancel after applying
2075 user-defined colourscheme doesn't restore original
2082 <!-- JAL-2314 -->Unit test failure:
2083 jalview.ws.jabaws.RNAStructExportImport setup fails
2086 <!-- JAL-2307 -->Unit test failure:
2087 jalview.ws.sifts.SiftsClientTest due to compatibility
2088 problems with deep array comparison equality asserts in
2089 successive versions of TestNG
2092 <!-- JAL-2479 -->Relocated StructureChooserTest and
2093 ParameterUtilsTest Unit tests to Network suite
2096 <em>New Known Issues</em>
2099 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2100 phase after a sequence motif find operation
2103 <!-- JAL-2550 -->Importing annotation file with rows
2104 containing just upper and lower case letters are
2105 interpreted as WUSS RNA secondary structure symbols
2108 <!-- JAL-2590 -->Cannot load and display Newick trees
2109 reliably from eggnog Ortholog database
2112 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2113 containing features of type Highlight' when 'B' is pressed
2114 to mark columns containing highlighted regions.
2117 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2118 doesn't always add secondary structure annotation.
2123 <td width="60" nowrap>
2124 <div align="center">
2125 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2128 <td><div align="left">
2132 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2133 for all consensus calculations
2136 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2139 <li>Updated Jalview's Certum code signing certificate
2142 <em>Application</em>
2145 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2146 set of database cross-references, sorted alphabetically
2149 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2150 from database cross references. Users with custom links
2151 will receive a <a href="webServices/urllinks.html#warning">warning
2152 dialog</a> asking them to update their preferences.
2155 <!-- JAL-2287-->Cancel button and escape listener on
2156 dialog warning user about disconnecting Jalview from a
2160 <!-- JAL-2320-->Jalview's Chimera control window closes if
2161 the Chimera it is connected to is shut down
2164 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2165 columns menu item to mark columns containing highlighted
2166 regions (e.g. from structure selections or results of a
2170 <!-- JAL-2284-->Command line option for batch-generation
2171 of HTML pages rendering alignment data with the BioJS
2181 <!-- JAL-2286 -->Columns with more than one modal residue
2182 are not coloured or thresholded according to percent
2183 identity (first observed in Jalview 2.8.2)
2186 <!-- JAL-2301 -->Threonine incorrectly reported as not
2190 <!-- JAL-2318 -->Updates to documentation pages (above PID
2191 threshold, amino acid properties)
2194 <!-- JAL-2292 -->Lower case residues in sequences are not
2195 reported as mapped to residues in a structure file in the
2199 <!--JAL-2324 -->Identical features with non-numeric scores
2200 could be added multiple times to a sequence
2203 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2204 bond features shown as two highlighted residues rather
2205 than a range in linked structure views, and treated
2206 correctly when selecting and computing trees from features
2209 <!-- JAL-2281-->Custom URL links for database
2210 cross-references are matched to database name regardless
2215 <em>Application</em>
2218 <!-- JAL-2282-->Custom URL links for specific database
2219 names without regular expressions also offer links from
2223 <!-- JAL-2315-->Removing a single configured link in the
2224 URL links pane in Connections preferences doesn't actually
2225 update Jalview configuration
2228 <!-- JAL-2272-->CTRL-Click on a selected region to open
2229 the alignment area popup menu doesn't work on El-Capitan
2232 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2233 files with similarly named sequences if dropped onto the
2237 <!-- JAL-2312 -->Additional mappings are shown for PDB
2238 entries where more chains exist in the PDB accession than
2239 are reported in the SIFTS file
2242 <!-- JAL-2317-->Certain structures do not get mapped to
2243 the structure view when displayed with Chimera
2246 <!-- JAL-2317-->No chains shown in the Chimera view
2247 panel's View->Show Chains submenu
2250 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2251 work for wrapped alignment views
2254 <!--JAL-2197 -->Rename UI components for running JPred
2255 predictions from 'JNet' to 'JPred'
2258 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2259 corrupted when annotation panel vertical scroll is not at
2260 first annotation row
2263 <!--JAL-2332 -->Attempting to view structure for Hen
2264 lysozyme results in a PDB Client error dialog box
2267 <!-- JAL-2319 -->Structure View's mapping report switched
2268 ranges for PDB and sequence for SIFTS
2271 SIFTS 'Not_Observed' residues mapped to non-existant
2275 <!-- <em>New Known Issues</em>
2282 <td width="60" nowrap>
2283 <div align="center">
2284 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2285 <em>25/10/2016</em></strong>
2288 <td><em>Application</em>
2290 <li>3D Structure chooser opens with 'Cached structures'
2291 view if structures already loaded</li>
2292 <li>Progress bar reports models as they are loaded to
2293 structure views</li>
2299 <li>Colour by conservation always enabled and no tick
2300 shown in menu when BLOSUM or PID shading applied</li>
2301 <li>FER1_ARATH and FER2_ARATH labels were switched in
2302 example sequences/projects/trees</li>
2304 <em>Application</em>
2306 <li>Jalview projects with views of local PDB structure
2307 files saved on Windows cannot be opened on OSX</li>
2308 <li>Multiple structure views can be opened and superposed
2309 without timeout for structures with multiple models or
2310 multiple sequences in alignment</li>
2311 <li>Cannot import or associated local PDB files without a
2312 PDB ID HEADER line</li>
2313 <li>RMSD is not output in Jmol console when superposition
2315 <li>Drag and drop of URL from Browser fails for Linux and
2316 OSX versions earlier than El Capitan</li>
2317 <li>ENA client ignores invalid content from ENA server</li>
2318 <li>Exceptions are not raised in console when ENA client
2319 attempts to fetch non-existent IDs via Fetch DB Refs UI
2321 <li>Exceptions are not raised in console when a new view
2322 is created on the alignment</li>
2323 <li>OSX right-click fixed for group selections: CMD-click
2324 to insert/remove gaps in groups and CTRL-click to open group
2327 <em>Build and deployment</em>
2329 <li>URL link checker now copes with multi-line anchor
2332 <em>New Known Issues</em>
2334 <li>Drag and drop from URL links in browsers do not work
2341 <td width="60" nowrap>
2342 <div align="center">
2343 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2346 <td><em>General</em>
2349 <!-- JAL-2124 -->Updated Spanish translations.
2352 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2353 for importing structure data to Jalview. Enables mmCIF and
2357 <!-- JAL-192 --->Alignment ruler shows positions relative to
2361 <!-- JAL-2202 -->Position/residue shown in status bar when
2362 mousing over sequence associated annotation
2365 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2369 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2370 '()', canonical '[]' and invalid '{}' base pair populations
2374 <!-- JAL-2092 -->Feature settings popup menu options for
2375 showing or hiding columns containing a feature
2378 <!-- JAL-1557 -->Edit selected group by double clicking on
2379 group and sequence associated annotation labels
2382 <!-- JAL-2236 -->Sequence name added to annotation label in
2383 select/hide columns by annotation and colour by annotation
2387 </ul> <em>Application</em>
2390 <!-- JAL-2050-->Automatically hide introns when opening a
2391 gene/transcript view
2394 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2398 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2399 structure mappings with the EMBL-EBI PDBe SIFTS database
2402 <!-- JAL-2079 -->Updated download sites used for Rfam and
2403 Pfam sources to xfam.org
2406 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2409 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2410 over sequences in Jalview
2413 <!-- JAL-2027-->Support for reverse-complement coding
2414 regions in ENA and EMBL
2417 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2418 for record retrieval via ENA rest API
2421 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2425 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2426 groovy script execution
2429 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2430 alignment window's Calculate menu
2433 <!-- JAL-1812 -->Allow groovy scripts that call
2434 Jalview.getAlignFrames() to run in headless mode
2437 <!-- JAL-2068 -->Support for creating new alignment
2438 calculation workers from groovy scripts
2441 <!-- JAL-1369 --->Store/restore reference sequence in
2445 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2446 associations are now saved/restored from project
2449 <!-- JAL-1993 -->Database selection dialog always shown
2450 before sequence fetcher is opened
2453 <!-- JAL-2183 -->Double click on an entry in Jalview's
2454 database chooser opens a sequence fetcher
2457 <!-- JAL-1563 -->Free-text search client for UniProt using
2458 the UniProt REST API
2461 <!-- JAL-2168 -->-nonews command line parameter to prevent
2462 the news reader opening
2465 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2466 querying stored in preferences
2469 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2473 <!-- JAL-1977-->Tooltips shown on database chooser
2476 <!-- JAL-391 -->Reverse complement function in calculate
2477 menu for nucleotide sequences
2480 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2481 and feature counts preserves alignment ordering (and
2482 debugged for complex feature sets).
2485 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2486 viewing structures with Jalview 2.10
2489 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2490 genome, transcript CCDS and gene ids via the Ensembl and
2491 Ensembl Genomes REST API
2494 <!-- JAL-2049 -->Protein sequence variant annotation
2495 computed for 'sequence_variant' annotation on CDS regions
2499 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2503 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2504 Ref Fetcher fails to match, or otherwise updates sequence
2505 data from external database records.
2508 <!-- JAL-2154 -->Revised Jalview Project format for
2509 efficient recovery of sequence coding and alignment
2510 annotation relationships.
2512 </ul> <!-- <em>Applet</em>
2523 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2527 <!-- JAL-2018-->Export features in Jalview format (again)
2528 includes graduated colourschemes
2531 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2532 working with big alignments and lots of hidden columns
2535 <!-- JAL-2053-->Hidden column markers not always rendered
2536 at right of alignment window
2539 <!-- JAL-2067 -->Tidied up links in help file table of
2543 <!-- JAL-2072 -->Feature based tree calculation not shown
2547 <!-- JAL-2075 -->Hidden columns ignored during feature
2548 based tree calculation
2551 <!-- JAL-2065 -->Alignment view stops updating when show
2552 unconserved enabled for group on alignment
2555 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2559 <!-- JAL-2146 -->Alignment column in status incorrectly
2560 shown as "Sequence position" when mousing over
2564 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2565 hidden columns present
2568 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2569 user created annotation added to alignment
2572 <!-- JAL-1841 -->RNA Structure consensus only computed for
2573 '()' base pair annotation
2576 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2577 in zero scores for all base pairs in RNA Structure
2581 <!-- JAL-2174-->Extend selection with columns containing
2585 <!-- JAL-2275 -->Pfam format writer puts extra space at
2586 beginning of sequence
2589 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2593 <!-- JAL-2238 -->Cannot create groups on an alignment from
2594 from a tree when t-coffee scores are shown
2597 <!-- JAL-1836,1967 -->Cannot import and view PDB
2598 structures with chains containing negative resnums (4q4h)
2601 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2605 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2606 to Clustal, PIR and PileUp output
2609 <!-- JAL-2008 -->Reordering sequence features that are
2610 not visible causes alignment window to repaint
2613 <!-- JAL-2006 -->Threshold sliders don't work in
2614 graduated colour and colour by annotation row for e-value
2615 scores associated with features and annotation rows
2618 <!-- JAL-1797 -->amino acid physicochemical conservation
2619 calculation should be case independent
2622 <!-- JAL-2173 -->Remove annotation also updates hidden
2626 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2627 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2628 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2631 <!-- JAL-2065 -->Null pointer exceptions and redraw
2632 problems when reference sequence defined and 'show
2633 non-conserved' enabled
2636 <!-- JAL-1306 -->Quality and Conservation are now shown on
2637 load even when Consensus calculation is disabled
2640 <!-- JAL-1932 -->Remove right on penultimate column of
2641 alignment does nothing
2644 <em>Application</em>
2647 <!-- JAL-1552-->URLs and links can't be imported by
2648 drag'n'drop on OSX when launched via webstart (note - not
2649 yet fixed for El Capitan)
2652 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2653 output when running on non-gb/us i18n platforms
2656 <!-- JAL-1944 -->Error thrown when exporting a view with
2657 hidden sequences as flat-file alignment
2660 <!-- JAL-2030-->InstallAnywhere distribution fails when
2664 <!-- JAL-2080-->Jalview very slow to launch via webstart
2665 (also hotfix for 2.9.0b2)
2668 <!-- JAL-2085 -->Cannot save project when view has a
2669 reference sequence defined
2672 <!-- JAL-1011 -->Columns are suddenly selected in other
2673 alignments and views when revealing hidden columns
2676 <!-- JAL-1989 -->Hide columns not mirrored in complement
2677 view in a cDNA/Protein splitframe
2680 <!-- JAL-1369 -->Cannot save/restore representative
2681 sequence from project when only one sequence is
2685 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2686 in Structure Chooser
2689 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2690 structure consensus didn't refresh annotation panel
2693 <!-- JAL-1962 -->View mapping in structure view shows
2694 mappings between sequence and all chains in a PDB file
2697 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2698 dialogs format columns correctly, don't display array
2699 data, sort columns according to type
2702 <!-- JAL-1975 -->Export complete shown after destination
2703 file chooser is cancelled during an image export
2706 <!-- JAL-2025 -->Error when querying PDB Service with
2707 sequence name containing special characters
2710 <!-- JAL-2024 -->Manual PDB structure querying should be
2714 <!-- JAL-2104 -->Large tooltips with broken HTML
2715 formatting don't wrap
2718 <!-- JAL-1128 -->Figures exported from wrapped view are
2719 truncated so L looks like I in consensus annotation
2722 <!-- JAL-2003 -->Export features should only export the
2723 currently displayed features for the current selection or
2727 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2728 after fetching cross-references, and restoring from
2732 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2733 followed in the structure viewer
2736 <!-- JAL-2163 -->Titles for individual alignments in
2737 splitframe not restored from project
2740 <!-- JAL-2145 -->missing autocalculated annotation at
2741 trailing end of protein alignment in transcript/product
2742 splitview when pad-gaps not enabled by default
2745 <!-- JAL-1797 -->amino acid physicochemical conservation
2749 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2750 article has been read (reopened issue due to
2751 internationalisation problems)
2754 <!-- JAL-1960 -->Only offer PDB structures in structure
2755 viewer based on sequence name, PDB and UniProt
2760 <!-- JAL-1976 -->No progress bar shown during export of
2764 <!-- JAL-2213 -->Structures not always superimposed after
2765 multiple structures are shown for one or more sequences.
2768 <!-- JAL-1370 -->Reference sequence characters should not
2769 be replaced with '.' when 'Show unconserved' format option
2773 <!-- JAL-1823 -->Cannot specify chain code when entering
2774 specific PDB id for sequence
2777 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2778 'Export hidden sequences' is enabled, but 'export hidden
2779 columns' is disabled.
2782 <!--JAL-2026-->Best Quality option in structure chooser
2783 selects lowest rather than highest resolution structures
2787 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2788 to sequence mapping in 'View Mappings' report
2791 <!-- JAL-2284 -->Unable to read old Jalview projects that
2792 contain non-XML data added after Jalvew wrote project.
2795 <!-- JAL-2118 -->Newly created annotation row reorders
2796 after clicking on it to create new annotation for a
2800 <!-- JAL-1980 -->Null Pointer Exception raised when
2801 pressing Add on an orphaned cut'n'paste window.
2803 <!-- may exclude, this is an external service stability issue JAL-1941
2804 -- > RNA 3D structure not added via DSSR service</li> -->
2809 <!-- JAL-2151 -->Incorrect columns are selected when
2810 hidden columns present before start of sequence
2813 <!-- JAL-1986 -->Missing dependencies on applet pages
2817 <!-- JAL-1947 -->Overview pixel size changes when
2818 sequences are hidden in applet
2821 <!-- JAL-1996 -->Updated instructions for applet
2822 deployment on examples pages.
2829 <td width="60" nowrap>
2830 <div align="center">
2831 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2832 <em>16/10/2015</em></strong>
2835 <td><em>General</em>
2837 <li>Time stamps for signed Jalview application and applet
2842 <em>Application</em>
2844 <li>Duplicate group consensus and conservation rows
2845 shown when tree is partitioned</li>
2846 <li>Erratic behaviour when tree partitions made with
2847 multiple cDNA/Protein split views</li>
2853 <td width="60" nowrap>
2854 <div align="center">
2855 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2856 <em>8/10/2015</em></strong>
2859 <td><em>General</em>
2861 <li>Updated Spanish translations of localized text for
2863 </ul> <em>Application</em>
2865 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2866 <li>Signed OSX InstallAnywhere installer<br></li>
2867 <li>Support for per-sequence based annotations in BioJSON</li>
2868 </ul> <em>Applet</em>
2870 <li>Split frame example added to applet examples page</li>
2871 </ul> <em>Build and Deployment</em>
2874 <!-- JAL-1888 -->New ant target for running Jalview's test
2882 <li>Mapping of cDNA to protein in split frames
2883 incorrect when sequence start > 1</li>
2884 <li>Broken images in filter column by annotation dialog
2886 <li>Feature colours not parsed from features file</li>
2887 <li>Exceptions and incomplete link URLs recovered when
2888 loading a features file containing HTML tags in feature
2892 <em>Application</em>
2894 <li>Annotations corrupted after BioJS export and
2896 <li>Incorrect sequence limits after Fetch DB References
2897 with 'trim retrieved sequences'</li>
2898 <li>Incorrect warning about deleting all data when
2899 deleting selected columns</li>
2900 <li>Patch to build system for shipping properly signed
2901 JNLP templates for webstart launch</li>
2902 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2903 unreleased structures for download or viewing</li>
2904 <li>Tab/space/return keystroke operation of EMBL-PDBe
2905 fetcher/viewer dialogs works correctly</li>
2906 <li>Disabled 'minimise' button on Jalview windows
2907 running on OSX to workaround redraw hang bug</li>
2908 <li>Split cDNA/Protein view position and geometry not
2909 recovered from jalview project</li>
2910 <li>Initial enabled/disabled state of annotation menu
2911 sorter 'show autocalculated first/last' corresponds to
2913 <li>Restoring of Clustal, RNA Helices and T-Coffee
2914 color schemes from BioJSON</li>
2918 <li>Reorder sequences mirrored in cDNA/Protein split
2920 <li>Applet with Jmol examples not loading correctly</li>
2926 <td><div align="center">
2927 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2929 <td><em>General</em>
2931 <li>Linked visualisation and analysis of DNA and Protein
2934 <li>Translated cDNA alignments shown as split protein
2935 and DNA alignment views</li>
2936 <li>Codon consensus annotation for linked protein and
2937 cDNA alignment views</li>
2938 <li>Link cDNA or Protein product sequences by loading
2939 them onto Protein or cDNA alignments</li>
2940 <li>Reconstruct linked cDNA alignment from aligned
2941 protein sequences</li>
2944 <li>Jmol integration updated to Jmol v14.2.14</li>
2945 <li>Import and export of Jalview alignment views as <a
2946 href="features/bioJsonFormat.html">BioJSON</a></li>
2947 <li>New alignment annotation file statements for
2948 reference sequences and marking hidden columns</li>
2949 <li>Reference sequence based alignment shading to
2950 highlight variation</li>
2951 <li>Select or hide columns according to alignment
2953 <li>Find option for locating sequences by description</li>
2954 <li>Conserved physicochemical properties shown in amino
2955 acid conservation row</li>
2956 <li>Alignments can be sorted by number of RNA helices</li>
2957 </ul> <em>Application</em>
2959 <li>New cDNA/Protein analysis capabilities
2961 <li>Get Cross-References should open a Split Frame
2962 view with cDNA/Protein</li>
2963 <li>Detect when nucleotide sequences and protein
2964 sequences are placed in the same alignment</li>
2965 <li>Split cDNA/Protein views are saved in Jalview
2970 <li>Use REST API to talk to Chimera</li>
2971 <li>Selected regions in Chimera are highlighted in linked
2972 Jalview windows</li>
2974 <li>VARNA RNA viewer updated to v3.93</li>
2975 <li>VARNA views are saved in Jalview Projects</li>
2976 <li>Pseudoknots displayed as Jalview RNA annotation can
2977 be shown in VARNA</li>
2979 <li>Make groups for selection uses marked columns as well
2980 as the active selected region</li>
2982 <li>Calculate UPGMA and NJ trees using sequence feature
2984 <li>New Export options
2986 <li>New Export Settings dialog to control hidden
2987 region export in flat file generation</li>
2989 <li>Export alignment views for display with the <a
2990 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2992 <li>Export scrollable SVG in HTML page</li>
2993 <li>Optional embedding of BioJSON data when exporting
2994 alignment figures to HTML</li>
2996 <li>3D structure retrieval and display
2998 <li>Free text and structured queries with the PDBe
3000 <li>PDBe Search API based discovery and selection of
3001 PDB structures for a sequence set</li>
3005 <li>JPred4 employed for protein secondary structure
3007 <li>Hide Insertions menu option to hide unaligned columns
3008 for one or a group of sequences</li>
3009 <li>Automatically hide insertions in alignments imported
3010 from the JPred4 web server</li>
3011 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3012 system on OSX<br />LGPL libraries courtesy of <a
3013 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3015 <li>changed 'View nucleotide structure' submenu to 'View
3016 VARNA 2D Structure'</li>
3017 <li>change "View protein structure" menu option to "3D
3020 </ul> <em>Applet</em>
3022 <li>New layout for applet example pages</li>
3023 <li>New parameters to enable SplitFrame view
3024 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3025 <li>New example demonstrating linked viewing of cDNA and
3026 Protein alignments</li>
3027 </ul> <em>Development and deployment</em>
3029 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3030 <li>Include installation type and git revision in build
3031 properties and console log output</li>
3032 <li>Jalview Github organisation, and new github site for
3033 storing BioJsMSA Templates</li>
3034 <li>Jalview's unit tests now managed with TestNG</li>
3037 <!-- <em>General</em>
3039 </ul> --> <!-- issues resolved --> <em>Application</em>
3041 <li>Escape should close any open find dialogs</li>
3042 <li>Typo in select-by-features status report</li>
3043 <li>Consensus RNA secondary secondary structure
3044 predictions are not highlighted in amber</li>
3045 <li>Missing gap character in v2.7 example file means
3046 alignment appears unaligned when pad-gaps is not enabled</li>
3047 <li>First switch to RNA Helices colouring doesn't colour
3048 associated structure views</li>
3049 <li>ID width preference option is greyed out when auto
3050 width checkbox not enabled</li>
3051 <li>Stopped a warning dialog from being shown when
3052 creating user defined colours</li>
3053 <li>'View Mapping' in structure viewer shows sequence
3054 mappings for just that viewer's sequences</li>
3055 <li>Workaround for superposing PDB files containing
3056 multiple models in Chimera</li>
3057 <li>Report sequence position in status bar when hovering
3058 over Jmol structure</li>
3059 <li>Cannot output gaps as '.' symbols with Selection ->
3060 output to text box</li>
3061 <li>Flat file exports of alignments with hidden columns
3062 have incorrect sequence start/end</li>
3063 <li>'Aligning' a second chain to a Chimera structure from
3065 <li>Colour schemes applied to structure viewers don't
3066 work for nucleotide</li>
3067 <li>Loading/cut'n'pasting an empty or invalid file leads
3068 to a grey/invisible alignment window</li>
3069 <li>Exported Jpred annotation from a sequence region
3070 imports to different position</li>
3071 <li>Space at beginning of sequence feature tooltips shown
3072 on some platforms</li>
3073 <li>Chimera viewer 'View | Show Chain' menu is not
3075 <li>'New View' fails with a Null Pointer Exception in
3076 console if Chimera has been opened</li>
3077 <li>Mouseover to Chimera not working</li>
3078 <li>Miscellaneous ENA XML feature qualifiers not
3080 <li>NPE in annotation renderer after 'Extract Scores'</li>
3081 <li>If two structures in one Chimera window, mouseover of
3082 either sequence shows on first structure</li>
3083 <li>'Show annotations' options should not make
3084 non-positional annotations visible</li>
3085 <li>Subsequence secondary structure annotation not shown
3086 in right place after 'view flanking regions'</li>
3087 <li>File Save As type unset when current file format is
3089 <li>Save as '.jar' option removed for saving Jalview
3091 <li>Colour by Sequence colouring in Chimera more
3093 <li>Cannot 'add reference annotation' for a sequence in
3094 several views on same alignment</li>
3095 <li>Cannot show linked products for EMBL / ENA records</li>
3096 <li>Jalview's tooltip wraps long texts containing no
3098 </ul> <em>Applet</em>
3100 <li>Jmol to JalviewLite mouseover/link not working</li>
3101 <li>JalviewLite can't import sequences with ID
3102 descriptions containing angle brackets</li>
3103 </ul> <em>General</em>
3105 <li>Cannot export and reimport RNA secondary structure
3106 via jalview annotation file</li>
3107 <li>Random helix colour palette for colour by annotation
3108 with RNA secondary structure</li>
3109 <li>Mouseover to cDNA from STOP residue in protein
3110 translation doesn't work.</li>
3111 <li>hints when using the select by annotation dialog box</li>
3112 <li>Jmol alignment incorrect if PDB file has alternate CA
3114 <li>FontChooser message dialog appears to hang after
3115 choosing 1pt font</li>
3116 <li>Peptide secondary structure incorrectly imported from
3117 annotation file when annotation display text includes 'e' or
3119 <li>Cannot set colour of new feature type whilst creating
3121 <li>cDNA translation alignment should not be sequence
3122 order dependent</li>
3123 <li>'Show unconserved' doesn't work for lower case
3125 <li>Nucleotide ambiguity codes involving R not recognised</li>
3126 </ul> <em>Deployment and Documentation</em>
3128 <li>Applet example pages appear different to the rest of
3129 www.jalview.org</li>
3130 </ul> <em>Application Known issues</em>
3132 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3133 <li>Misleading message appears after trying to delete
3135 <li>Jalview icon not shown in dock after InstallAnywhere
3136 version launches</li>
3137 <li>Fetching EMBL reference for an RNA sequence results
3138 fails with a sequence mismatch</li>
3139 <li>Corrupted or unreadable alignment display when
3140 scrolling alignment to right</li>
3141 <li>ArrayIndexOutOfBoundsException thrown when remove
3142 empty columns called on alignment with ragged gapped ends</li>
3143 <li>auto calculated alignment annotation rows do not get
3144 placed above or below non-autocalculated rows</li>
3145 <li>Jalview dekstop becomes sluggish at full screen in
3146 ultra-high resolution</li>
3147 <li>Cannot disable consensus calculation independently of
3148 quality and conservation</li>
3149 <li>Mouseover highlighting between cDNA and protein can
3150 become sluggish with more than one splitframe shown</li>
3151 </ul> <em>Applet Known Issues</em>
3153 <li>Core PDB parsing code requires Jmol</li>
3154 <li>Sequence canvas panel goes white when alignment
3155 window is being resized</li>
3161 <td><div align="center">
3162 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3164 <td><em>General</em>
3166 <li>Updated Java code signing certificate donated by
3168 <li>Features and annotation preserved when performing
3169 pairwise alignment</li>
3170 <li>RNA pseudoknot annotation can be
3171 imported/exported/displayed</li>
3172 <li>'colour by annotation' can colour by RNA and
3173 protein secondary structure</li>
3174 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3175 post-hoc with 2.9 release</em>)
3178 </ul> <em>Application</em>
3180 <li>Extract and display secondary structure for sequences
3181 with 3D structures</li>
3182 <li>Support for parsing RNAML</li>
3183 <li>Annotations menu for layout
3185 <li>sort sequence annotation rows by alignment</li>
3186 <li>place sequence annotation above/below alignment
3189 <li>Output in Stockholm format</li>
3190 <li>Internationalisation: improved Spanish (es)
3192 <li>Structure viewer preferences tab</li>
3193 <li>Disorder and Secondary Structure annotation tracks
3194 shared between alignments</li>
3195 <li>UCSF Chimera launch and linked highlighting from
3197 <li>Show/hide all sequence associated annotation rows for
3198 all or current selection</li>
3199 <li>disorder and secondary structure predictions
3200 available as dataset annotation</li>
3201 <li>Per-sequence rna helices colouring</li>
3204 <li>Sequence database accessions imported when fetching
3205 alignments from Rfam</li>
3206 <li>update VARNA version to 3.91</li>
3208 <li>New groovy scripts for exporting aligned positions,
3209 conservation values, and calculating sum of pairs scores.</li>
3210 <li>Command line argument to set default JABAWS server</li>
3211 <li>include installation type in build properties and
3212 console log output</li>
3213 <li>Updated Jalview project format to preserve dataset
3217 <!-- issues resolved --> <em>Application</em>
3219 <li>Distinguish alignment and sequence associated RNA
3220 structure in structure->view->VARNA</li>
3221 <li>Raise dialog box if user deletes all sequences in an
3223 <li>Pressing F1 results in documentation opening twice</li>
3224 <li>Sequence feature tooltip is wrapped</li>
3225 <li>Double click on sequence associated annotation
3226 selects only first column</li>
3227 <li>Redundancy removal doesn't result in unlinked
3228 leaves shown in tree</li>
3229 <li>Undos after several redundancy removals don't undo
3231 <li>Hide sequence doesn't hide associated annotation</li>
3232 <li>User defined colours dialog box too big to fit on
3233 screen and buttons not visible</li>
3234 <li>author list isn't updated if already written to
3235 Jalview properties</li>
3236 <li>Popup menu won't open after retrieving sequence
3238 <li>File open window for associate PDB doesn't open</li>
3239 <li>Left-then-right click on a sequence id opens a
3240 browser search window</li>
3241 <li>Cannot open sequence feature shading/sort popup menu
3242 in feature settings dialog</li>
3243 <li>better tooltip placement for some areas of Jalview
3245 <li>Allow addition of JABAWS Server which doesn't
3246 pass validation</li>
3247 <li>Web services parameters dialog box is too large to
3249 <li>Muscle nucleotide alignment preset obscured by
3251 <li>JABAWS preset submenus don't contain newly
3252 defined user preset</li>
3253 <li>MSA web services warns user if they were launched
3254 with invalid input</li>
3255 <li>Jalview cannot contact DAS Registy when running on
3258 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3259 'Superpose with' submenu not shown when new view
3263 </ul> <!-- <em>Applet</em>
3265 </ul> <em>General</em>
3267 </ul>--> <em>Deployment and Documentation</em>
3269 <li>2G and 1G options in launchApp have no effect on
3270 memory allocation</li>
3271 <li>launchApp service doesn't automatically open
3272 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3274 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3275 InstallAnywhere reports cannot find valid JVM when Java
3276 1.7_055 is available
3278 </ul> <em>Application Known issues</em>
3281 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3282 corrupted or unreadable alignment display when scrolling
3286 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3287 retrieval fails but progress bar continues for DAS retrieval
3288 with large number of ID
3291 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3292 flatfile output of visible region has incorrect sequence
3296 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3297 rna structure consensus doesn't update when secondary
3298 structure tracks are rearranged
3301 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3302 invalid rna structure positional highlighting does not
3303 highlight position of invalid base pairs
3306 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3307 out of memory errors are not raised when saving Jalview
3308 project from alignment window file menu
3311 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3312 Switching to RNA Helices colouring doesn't propagate to
3316 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3317 colour by RNA Helices not enabled when user created
3318 annotation added to alignment
3321 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3322 Jalview icon not shown on dock in Mountain Lion/Webstart
3324 </ul> <em>Applet Known Issues</em>
3327 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3328 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3331 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3332 Jalview and Jmol example not compatible with IE9
3335 <li>Sort by annotation score doesn't reverse order
3341 <td><div align="center">
3342 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3345 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3348 <li>Internationalisation of user interface (usually
3349 called i18n support) and translation for Spanish locale</li>
3350 <li>Define/Undefine group on current selection with
3351 Ctrl-G/Shift Ctrl-G</li>
3352 <li>Improved group creation/removal options in
3353 alignment/sequence Popup menu</li>
3354 <li>Sensible precision for symbol distribution
3355 percentages shown in logo tooltip.</li>
3356 <li>Annotation panel height set according to amount of
3357 annotation when alignment first opened</li>
3358 </ul> <em>Application</em>
3360 <li>Interactive consensus RNA secondary structure
3361 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3362 <li>Select columns containing particular features from
3363 Feature Settings dialog</li>
3364 <li>View all 'representative' PDB structures for selected
3366 <li>Update Jalview project format:
3368 <li>New file extension for Jalview projects '.jvp'</li>
3369 <li>Preserve sequence and annotation dataset (to
3370 store secondary structure annotation,etc)</li>
3371 <li>Per group and alignment annotation and RNA helix
3375 <li>New similarity measures for PCA and Tree calculation
3377 <li>Experimental support for retrieval and viewing of
3378 flanking regions for an alignment</li>
3382 <!-- issues resolved --> <em>Application</em>
3384 <li>logo keeps spinning and status remains at queued or
3385 running after job is cancelled</li>
3386 <li>cannot export features from alignments imported from
3387 Jalview/VAMSAS projects</li>
3388 <li>Buggy slider for web service parameters that take
3390 <li>Newly created RNA secondary structure line doesn't
3391 have 'display all symbols' flag set</li>
3392 <li>T-COFFEE alignment score shading scheme and other
3393 annotation shading not saved in Jalview project</li>
3394 <li>Local file cannot be loaded in freshly downloaded
3396 <li>Jalview icon not shown on dock in Mountain
3398 <li>Load file from desktop file browser fails</li>
3399 <li>Occasional NPE thrown when calculating large trees</li>
3400 <li>Cannot reorder or slide sequences after dragging an
3401 alignment onto desktop</li>
3402 <li>Colour by annotation dialog throws NPE after using
3403 'extract scores' function</li>
3404 <li>Loading/cut'n'pasting an empty file leads to a grey
3405 alignment window</li>
3406 <li>Disorder thresholds rendered incorrectly after
3407 performing IUPred disorder prediction</li>
3408 <li>Multiple group annotated consensus rows shown when
3409 changing 'normalise logo' display setting</li>
3410 <li>Find shows blank dialog after 'finished searching' if
3411 nothing matches query</li>
3412 <li>Null Pointer Exceptions raised when sorting by
3413 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3415 <li>Errors in Jmol console when structures in alignment
3416 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3418 <li>Not all working JABAWS services are shown in
3420 <li>JAVAWS version of Jalview fails to launch with
3421 'invalid literal/length code'</li>
3422 <li>Annotation/RNA Helix colourschemes cannot be applied
3423 to alignment with groups (actually fixed in 2.8.0b1)</li>
3424 <li>RNA Helices and T-Coffee Scores available as default
3427 </ul> <em>Applet</em>
3429 <li>Remove group option is shown even when selection is
3431 <li>Apply to all groups ticked but colourscheme changes
3432 don't affect groups</li>
3433 <li>Documented RNA Helices and T-Coffee Scores as valid
3434 colourscheme name</li>
3435 <li>Annotation labels drawn on sequence IDs when
3436 Annotation panel is not displayed</li>
3437 <li>Increased font size for dropdown menus on OSX and
3438 embedded windows</li>
3439 </ul> <em>Other</em>
3441 <li>Consensus sequence for alignments/groups with a
3442 single sequence were not calculated</li>
3443 <li>annotation files that contain only groups imported as
3444 annotation and junk sequences</li>
3445 <li>Fasta files with sequences containing '*' incorrectly
3446 recognised as PFAM or BLC</li>
3447 <li>conservation/PID slider apply all groups option
3448 doesn't affect background (2.8.0b1)
3450 <li>redundancy highlighting is erratic at 0% and 100%</li>
3451 <li>Remove gapped columns fails for sequences with ragged
3453 <li>AMSA annotation row with leading spaces is not
3454 registered correctly on import</li>
3455 <li>Jalview crashes when selecting PCA analysis for
3456 certain alignments</li>
3457 <li>Opening the colour by annotation dialog for an
3458 existing annotation based 'use original colours'
3459 colourscheme loses original colours setting</li>
3464 <td><div align="center">
3465 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3466 <em>30/1/2014</em></strong>
3470 <li>Trusted certificates for JalviewLite applet and
3471 Jalview Desktop application<br />Certificate was donated by
3472 <a href="https://www.certum.eu">Certum</a> to the Jalview
3473 open source project).
3475 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3476 <li>Output in Stockholm format</li>
3477 <li>Allow import of data from gzipped files</li>
3478 <li>Export/import group and sequence associated line
3479 graph thresholds</li>
3480 <li>Nucleotide substitution matrix that supports RNA and
3481 ambiguity codes</li>
3482 <li>Allow disorder predictions to be made on the current
3483 selection (or visible selection) in the same way that JPred
3485 <li>Groovy scripting for headless Jalview operation</li>
3486 </ul> <em>Other improvements</em>
3488 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3489 <li>COMBINE statement uses current SEQUENCE_REF and
3490 GROUP_REF scope to group annotation rows</li>
3491 <li>Support '' style escaping of quotes in Newick
3493 <li>Group options for JABAWS service by command line name</li>
3494 <li>Empty tooltip shown for JABA service options with a
3495 link but no description</li>
3496 <li>Select primary source when selecting authority in
3497 database fetcher GUI</li>
3498 <li>Add .mfa to FASTA file extensions recognised by
3500 <li>Annotation label tooltip text wrap</li>
3505 <li>Slow scrolling when lots of annotation rows are
3507 <li>Lots of NPE (and slowness) after creating RNA
3508 secondary structure annotation line</li>
3509 <li>Sequence database accessions not imported when
3510 fetching alignments from Rfam</li>
3511 <li>Incorrect SHMR submission for sequences with
3513 <li>View all structures does not always superpose
3515 <li>Option widgets in service parameters not updated to
3516 reflect user or preset settings</li>
3517 <li>Null pointer exceptions for some services without
3518 presets or adjustable parameters</li>
3519 <li>Discover PDB IDs entry in structure menu doesn't
3520 discover PDB xRefs</li>
3521 <li>Exception encountered while trying to retrieve
3522 features with DAS</li>
3523 <li>Lowest value in annotation row isn't coloured
3524 when colour by annotation (per sequence) is coloured</li>
3525 <li>Keyboard mode P jumps to start of gapped region when
3526 residue follows a gap</li>
3527 <li>Jalview appears to hang importing an alignment with
3528 Wrap as default or after enabling Wrap</li>
3529 <li>'Right click to add annotations' message
3530 shown in wrap mode when no annotations present</li>
3531 <li>Disorder predictions fail with NPE if no automatic
3532 annotation already exists on alignment</li>
3533 <li>oninit javascript function should be called after
3534 initialisation completes</li>
3535 <li>Remove redundancy after disorder prediction corrupts
3536 alignment window display</li>
3537 <li>Example annotation file in documentation is invalid</li>
3538 <li>Grouped line graph annotation rows are not exported
3539 to annotation file</li>
3540 <li>Multi-harmony analysis cannot be run when only two
3542 <li>Cannot create multiple groups of line graphs with
3543 several 'combine' statements in annotation file</li>
3544 <li>Pressing return several times causes Number Format
3545 exceptions in keyboard mode</li>
3546 <li>Multi-harmony (SHMMR) method doesn't submit
3547 correct partitions for input data</li>
3548 <li>Translation from DNA to Amino Acids fails</li>
3549 <li>Jalview fail to load newick tree with quoted label</li>
3550 <li>--headless flag isn't understood</li>
3551 <li>ClassCastException when generating EPS in headless
3553 <li>Adjusting sequence-associated shading threshold only
3554 changes one row's threshold</li>
3555 <li>Preferences and Feature settings panel panel
3556 doesn't open</li>
3557 <li>hide consensus histogram also hides conservation and
3558 quality histograms</li>
3563 <td><div align="center">
3564 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3566 <td><em>Application</em>
3568 <li>Support for JABAWS 2.0 Services (AACon alignment
3569 conservation, protein disorder and Clustal Omega)</li>
3570 <li>JABAWS server status indicator in Web Services
3572 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3573 in Jalview alignment window</li>
3574 <li>Updated Jalview build and deploy framework for OSX
3575 mountain lion, windows 7, and 8</li>
3576 <li>Nucleotide substitution matrix for PCA that supports
3577 RNA and ambiguity codes</li>
3579 <li>Improved sequence database retrieval GUI</li>
3580 <li>Support fetching and database reference look up
3581 against multiple DAS sources (Fetch all from in 'fetch db
3583 <li>Jalview project improvements
3585 <li>Store and retrieve the 'belowAlignment'
3586 flag for annotation</li>
3587 <li>calcId attribute to group annotation rows on the
3589 <li>Store AACon calculation settings for a view in
3590 Jalview project</li>
3594 <li>horizontal scrolling gesture support</li>
3595 <li>Visual progress indicator when PCA calculation is
3597 <li>Simpler JABA web services menus</li>
3598 <li>visual indication that web service results are still
3599 being retrieved from server</li>
3600 <li>Serialise the dialogs that are shown when Jalview
3601 starts up for first time</li>
3602 <li>Jalview user agent string for interacting with HTTP
3604 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3606 <li>Examples directory and Groovy library included in
3607 InstallAnywhere distribution</li>
3608 </ul> <em>Applet</em>
3610 <li>RNA alignment and secondary structure annotation
3611 visualization applet example</li>
3612 </ul> <em>General</em>
3614 <li>Normalise option for consensus sequence logo</li>
3615 <li>Reset button in PCA window to return dimensions to
3617 <li>Allow seqspace or Jalview variant of alignment PCA
3619 <li>PCA with either nucleic acid and protein substitution
3621 <li>Allow windows containing HTML reports to be exported
3623 <li>Interactive display and editing of RNA secondary
3624 structure contacts</li>
3625 <li>RNA Helix Alignment Colouring</li>
3626 <li>RNA base pair logo consensus</li>
3627 <li>Parse sequence associated secondary structure
3628 information in Stockholm files</li>
3629 <li>HTML Export database accessions and annotation
3630 information presented in tooltip for sequences</li>
3631 <li>Import secondary structure from LOCARNA clustalw
3632 style RNA alignment files</li>
3633 <li>import and visualise T-COFFEE quality scores for an
3635 <li>'colour by annotation' per sequence option to
3636 shade each sequence according to its associated alignment
3638 <li>New Jalview Logo</li>
3639 </ul> <em>Documentation and Development</em>
3641 <li>documentation for score matrices used in Jalview</li>
3642 <li>New Website!</li>
3644 <td><em>Application</em>
3646 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3647 wsdbfetch REST service</li>
3648 <li>Stop windows being moved outside desktop on OSX</li>
3649 <li>Filetype associations not installed for webstart
3651 <li>Jalview does not always retrieve progress of a JABAWS
3652 job execution in full once it is complete</li>
3653 <li>revise SHMR RSBS definition to ensure alignment is
3654 uploaded via ali_file parameter</li>
3655 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3656 <li>View all structures superposed fails with exception</li>
3657 <li>Jnet job queues forever if a very short sequence is
3658 submitted for prediction</li>
3659 <li>Cut and paste menu not opened when mouse clicked on
3661 <li>Putting fractional value into integer text box in
3662 alignment parameter dialog causes Jalview to hang</li>
3663 <li>Structure view highlighting doesn't work on
3665 <li>View all structures fails with exception shown in
3667 <li>Characters in filename associated with PDBEntry not
3668 escaped in a platform independent way</li>
3669 <li>Jalview desktop fails to launch with exception when
3671 <li>Tree calculation reports 'you must have 2 or more
3672 sequences selected' when selection is empty</li>
3673 <li>Jalview desktop fails to launch with jar signature
3674 failure when java web start temporary file caching is
3676 <li>DAS Sequence retrieval with range qualification
3677 results in sequence xref which includes range qualification</li>
3678 <li>Errors during processing of command line arguments
3679 cause progress bar (JAL-898) to be removed</li>
3680 <li>Replace comma for semi-colon option not disabled for
3681 DAS sources in sequence fetcher</li>
3682 <li>Cannot close news reader when JABAWS server warning
3683 dialog is shown</li>
3684 <li>Option widgets not updated to reflect user settings</li>
3685 <li>Edited sequence not submitted to web service</li>
3686 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3687 <li>InstallAnywhere installer doesn't unpack and run
3688 on OSX Mountain Lion</li>
3689 <li>Annotation panel not given a scroll bar when
3690 sequences with alignment annotation are pasted into the
3692 <li>Sequence associated annotation rows not associated
3693 when loaded from Jalview project</li>
3694 <li>Browser launch fails with NPE on java 1.7</li>
3695 <li>JABAWS alignment marked as finished when job was
3696 cancelled or job failed due to invalid input</li>
3697 <li>NPE with v2.7 example when clicking on Tree
3698 associated with all views</li>
3699 <li>Exceptions when copy/paste sequences with grouped
3700 annotation rows to new window</li>
3701 </ul> <em>Applet</em>
3703 <li>Sequence features are momentarily displayed before
3704 they are hidden using hidefeaturegroups applet parameter</li>
3705 <li>loading features via javascript API automatically
3706 enables feature display</li>
3707 <li>scrollToColumnIn javascript API method doesn't
3709 </ul> <em>General</em>
3711 <li>Redundancy removal fails for rna alignment</li>
3712 <li>PCA calculation fails when sequence has been selected
3713 and then deselected</li>
3714 <li>PCA window shows grey box when first opened on OSX</li>
3715 <li>Letters coloured pink in sequence logo when alignment
3716 coloured with clustalx</li>
3717 <li>Choosing fonts without letter symbols defined causes
3718 exceptions and redraw errors</li>
3719 <li>Initial PCA plot view is not same as manually
3720 reconfigured view</li>
3721 <li>Grouped annotation graph label has incorrect line
3723 <li>Grouped annotation graph label display is corrupted
3724 for lots of labels</li>
3729 <div align="center">
3730 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3733 <td><em>Application</em>
3735 <li>Jalview Desktop News Reader</li>
3736 <li>Tweaked default layout of web services menu</li>
3737 <li>View/alignment association menu to enable user to
3738 easily specify which alignment a multi-structure view takes
3739 its colours/correspondences from</li>
3740 <li>Allow properties file location to be specified as URL</li>
3741 <li>Extend Jalview project to preserve associations
3742 between many alignment views and a single Jmol display</li>
3743 <li>Store annotation row height in Jalview project file</li>
3744 <li>Annotation row column label formatting attributes
3745 stored in project file</li>
3746 <li>Annotation row order for auto-calculated annotation
3747 rows preserved in Jalview project file</li>
3748 <li>Visual progress indication when Jalview state is
3749 saved using Desktop window menu</li>
3750 <li>Visual indication that command line arguments are
3751 still being processed</li>
3752 <li>Groovy script execution from URL</li>
3753 <li>Colour by annotation default min and max colours in
3755 <li>Automatically associate PDB files dragged onto an
3756 alignment with sequences that have high similarity and
3758 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3759 <li>'view structures' option to open many
3760 structures in same window</li>
3761 <li>Sort associated views menu option for tree panel</li>
3762 <li>Group all JABA and non-JABA services for a particular
3763 analysis function in its own submenu</li>
3764 </ul> <em>Applet</em>
3766 <li>Userdefined and autogenerated annotation rows for
3768 <li>Adjustment of alignment annotation pane height</li>
3769 <li>Annotation scrollbar for annotation panel</li>
3770 <li>Drag to reorder annotation rows in annotation panel</li>
3771 <li>'automaticScrolling' parameter</li>
3772 <li>Allow sequences with partial ID string matches to be
3773 annotated from GFF/Jalview features files</li>
3774 <li>Sequence logo annotation row in applet</li>
3775 <li>Absolute paths relative to host server in applet
3776 parameters are treated as such</li>
3777 <li>New in the JalviewLite javascript API:
3779 <li>JalviewLite.js javascript library</li>
3780 <li>Javascript callbacks for
3782 <li>Applet initialisation</li>
3783 <li>Sequence/alignment mouse-overs and selections</li>
3786 <li>scrollTo row and column alignment scrolling
3788 <li>Select sequence/alignment regions from javascript</li>
3789 <li>javascript structure viewer harness to pass
3790 messages between Jmol and Jalview when running as
3791 distinct applets</li>
3792 <li>sortBy method</li>
3793 <li>Set of applet and application examples shipped
3794 with documentation</li>
3795 <li>New example to demonstrate JalviewLite and Jmol
3796 javascript message exchange</li>
3798 </ul> <em>General</em>
3800 <li>Enable Jmol displays to be associated with multiple
3801 multiple alignments</li>
3802 <li>Option to automatically sort alignment with new tree</li>
3803 <li>User configurable link to enable redirects to a
3804 www.Jalview.org mirror</li>
3805 <li>Jmol colours option for Jmol displays</li>
3806 <li>Configurable newline string when writing alignment
3807 and other flat files</li>
3808 <li>Allow alignment annotation description lines to
3809 contain html tags</li>
3810 </ul> <em>Documentation and Development</em>
3812 <li>Add groovy test harness for bulk load testing to
3814 <li>Groovy script to load and align a set of sequences
3815 using a web service before displaying the result in the
3816 Jalview desktop</li>
3817 <li>Restructured javascript and applet api documentation</li>
3818 <li>Ant target to publish example html files with applet
3820 <li>Netbeans project for building Jalview from source</li>
3821 <li>ant task to create online javadoc for Jalview source</li>
3823 <td><em>Application</em>
3825 <li>User defined colourscheme throws exception when
3826 current built in colourscheme is saved as new scheme</li>
3827 <li>AlignFrame->Save in application pops up save
3828 dialog for valid filename/format</li>
3829 <li>Cannot view associated structure for UniProt sequence</li>
3830 <li>PDB file association breaks for UniProt sequence
3832 <li>Associate PDB from file dialog does not tell you
3833 which sequence is to be associated with the file</li>
3834 <li>Find All raises null pointer exception when query
3835 only matches sequence IDs</li>
3836 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3837 <li>Jalview project with Jmol views created with Jalview
3838 2.4 cannot be loaded</li>
3839 <li>Filetype associations not installed for webstart
3841 <li>Two or more chains in a single PDB file associated
3842 with sequences in different alignments do not get coloured
3843 by their associated sequence</li>
3844 <li>Visibility status of autocalculated annotation row
3845 not preserved when project is loaded</li>
3846 <li>Annotation row height and visibility attributes not
3847 stored in Jalview project</li>
3848 <li>Tree bootstraps are not preserved when saved as a
3849 Jalview project</li>
3850 <li>Envision2 workflow tooltips are corrupted</li>
3851 <li>Enabling show group conservation also enables colour
3852 by conservation</li>
3853 <li>Duplicate group associated conservation or consensus
3854 created on new view</li>
3855 <li>Annotation scrollbar not displayed after 'show
3856 all hidden annotation rows' option selected</li>
3857 <li>Alignment quality not updated after alignment
3858 annotation row is hidden then shown</li>
3859 <li>Preserve colouring of structures coloured by
3860 sequences in pre Jalview 2.7 projects</li>
3861 <li>Web service job parameter dialog is not laid out
3863 <li>Web services menu not refreshed after 'reset
3864 services' button is pressed in preferences</li>
3865 <li>Annotation off by one in Jalview v2_3 example project</li>
3866 <li>Structures imported from file and saved in project
3867 get name like jalview_pdb1234.txt when reloaded</li>
3868 <li>Jalview does not always retrieve progress of a JABAWS
3869 job execution in full once it is complete</li>
3870 </ul> <em>Applet</em>
3872 <li>Alignment height set incorrectly when lots of
3873 annotation rows are displayed</li>
3874 <li>Relative URLs in feature HTML text not resolved to
3876 <li>View follows highlighting does not work for positions
3878 <li><= shown as = in tooltip</li>
3879 <li>Export features raises exception when no features
3881 <li>Separator string used for serialising lists of IDs
3882 for javascript api is modified when separator string
3883 provided as parameter</li>
3884 <li>Null pointer exception when selecting tree leaves for
3885 alignment with no existing selection</li>
3886 <li>Relative URLs for datasources assumed to be relative
3887 to applet's codebase</li>
3888 <li>Status bar not updated after finished searching and
3889 search wraps around to first result</li>
3890 <li>StructureSelectionManager instance shared between
3891 several Jalview applets causes race conditions and memory
3893 <li>Hover tooltip and mouseover of position on structure
3894 not sent from Jmol in applet</li>
3895 <li>Certain sequences of javascript method calls to
3896 applet API fatally hang browser</li>
3897 </ul> <em>General</em>
3899 <li>View follows structure mouseover scrolls beyond
3900 position with wrapped view and hidden regions</li>
3901 <li>Find sequence position moves to wrong residue
3902 with/without hidden columns</li>
3903 <li>Sequence length given in alignment properties window
3905 <li>InvalidNumberFormat exceptions thrown when trying to
3906 import PDB like structure files</li>
3907 <li>Positional search results are only highlighted
3908 between user-supplied sequence start/end bounds</li>
3909 <li>End attribute of sequence is not validated</li>
3910 <li>Find dialog only finds first sequence containing a
3911 given sequence position</li>
3912 <li>Sequence numbering not preserved in MSF alignment
3914 <li>Jalview PDB file reader does not extract sequence
3915 from nucleotide chains correctly</li>
3916 <li>Structure colours not updated when tree partition
3917 changed in alignment</li>
3918 <li>Sequence associated secondary structure not correctly
3919 parsed in interleaved stockholm</li>
3920 <li>Colour by annotation dialog does not restore current
3922 <li>Hiding (nearly) all sequences doesn't work
3924 <li>Sequences containing lowercase letters are not
3925 properly associated with their pdb files</li>
3926 </ul> <em>Documentation and Development</em>
3928 <li>schemas/JalviewWsParamSet.xsd corrupted by
3929 ApplyCopyright tool</li>
3934 <div align="center">
3935 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3938 <td><em>Application</em>
3940 <li>New warning dialog when the Jalview Desktop cannot
3941 contact web services</li>
3942 <li>JABA service parameters for a preset are shown in
3943 service job window</li>
3944 <li>JABA Service menu entries reworded</li>
3948 <li>Modeller PIR IO broken - cannot correctly import a
3949 pir file emitted by Jalview</li>
3950 <li>Existing feature settings transferred to new
3951 alignment view created from cut'n'paste</li>
3952 <li>Improved test for mixed amino/nucleotide chains when
3953 parsing PDB files</li>
3954 <li>Consensus and conservation annotation rows
3955 occasionally become blank for all new windows</li>
3956 <li>Exception raised when right clicking above sequences
3957 in wrapped view mode</li>
3958 </ul> <em>Application</em>
3960 <li>multiple multiply aligned structure views cause cpu
3961 usage to hit 100% and computer to hang</li>
3962 <li>Web Service parameter layout breaks for long user
3963 parameter names</li>
3964 <li>Jaba service discovery hangs desktop if Jaba server
3971 <div align="center">
3972 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3975 <td><em>Application</em>
3977 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3978 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3981 <li>Web Services preference tab</li>
3982 <li>Analysis parameters dialog box and user defined
3984 <li>Improved speed and layout of Envision2 service menu</li>
3985 <li>Superpose structures using associated sequence
3987 <li>Export coordinates and projection as CSV from PCA
3989 </ul> <em>Applet</em>
3991 <li>enable javascript: execution by the applet via the
3992 link out mechanism</li>
3993 </ul> <em>Other</em>
3995 <li>Updated the Jmol Jalview interface to work with Jmol
3997 <li>The Jalview Desktop and JalviewLite applet now
3998 require Java 1.5</li>
3999 <li>Allow Jalview feature colour specification for GFF
4000 sequence annotation files</li>
4001 <li>New 'colour by label' keword in Jalview feature file
4002 type colour specification</li>
4003 <li>New Jalview Desktop Groovy API method that allows a
4004 script to check if it being run in an interactive session or
4005 in a batch operation from the Jalview command line</li>
4009 <li>clustalx colourscheme colours Ds preferentially when
4010 both D+E are present in over 50% of the column</li>
4011 </ul> <em>Application</em>
4013 <li>typo in AlignmentFrame->View->Hide->all but
4014 selected Regions menu item</li>
4015 <li>sequence fetcher replaces ',' for ';' when the ',' is
4016 part of a valid accession ID</li>
4017 <li>fatal OOM if object retrieved by sequence fetcher
4018 runs out of memory</li>
4019 <li>unhandled Out of Memory Error when viewing pca
4020 analysis results</li>
4021 <li>InstallAnywhere builds fail to launch on OS X java
4022 10.5 update 4 (due to apple Java 1.6 update)</li>
4023 <li>Installanywhere Jalview silently fails to launch</li>
4024 </ul> <em>Applet</em>
4026 <li>Jalview.getFeatureGroups() raises an
4027 ArrayIndexOutOfBoundsException if no feature groups are
4034 <div align="center">
4035 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4041 <li>Alignment prettyprinter doesn't cope with long
4043 <li>clustalx colourscheme colours Ds preferentially when
4044 both D+E are present in over 50% of the column</li>
4045 <li>nucleic acid structures retrieved from PDB do not
4046 import correctly</li>
4047 <li>More columns get selected than were clicked on when a
4048 number of columns are hidden</li>
4049 <li>annotation label popup menu not providing correct
4050 add/hide/show options when rows are hidden or none are
4052 <li>Stockholm format shown in list of readable formats,
4053 and parser copes better with alignments from RFAM.</li>
4054 <li>CSV output of consensus only includes the percentage
4055 of all symbols if sequence logo display is enabled</li>
4057 </ul> <em>Applet</em>
4059 <li>annotation panel disappears when annotation is
4061 </ul> <em>Application</em>
4063 <li>Alignment view not redrawn properly when new
4064 alignment opened where annotation panel is visible but no
4065 annotations are present on alignment</li>
4066 <li>pasted region containing hidden columns is
4067 incorrectly displayed in new alignment window</li>
4068 <li>Jalview slow to complete operations when stdout is
4069 flooded (fix is to close the Jalview console)</li>
4070 <li>typo in AlignmentFrame->View->Hide->all but
4071 selected Rregions menu item.</li>
4072 <li>inconsistent group submenu and Format submenu entry
4073 'Un' or 'Non'conserved</li>
4074 <li>Sequence feature settings are being shared by
4075 multiple distinct alignments</li>
4076 <li>group annotation not recreated when tree partition is
4078 <li>double click on group annotation to select sequences
4079 does not propagate to associated trees</li>
4080 <li>Mac OSX specific issues:
4082 <li>exception raised when mouse clicked on desktop
4083 window background</li>
4084 <li>Desktop menu placed on menu bar and application
4085 name set correctly</li>
4086 <li>sequence feature settings not wide enough for the
4087 save feature colourscheme button</li>
4096 <div align="center">
4097 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4100 <td><em>New Capabilities</em>
4102 <li>URL links generated from description line for
4103 regular-expression based URL links (applet and application)
4105 <li>Non-positional feature URL links are shown in link
4107 <li>Linked viewing of nucleic acid sequences and
4109 <li>Automatic Scrolling option in View menu to display
4110 the currently highlighted region of an alignment.</li>
4111 <li>Order an alignment by sequence length, or using the
4112 average score or total feature count for each sequence.</li>
4113 <li>Shading features by score or associated description</li>
4114 <li>Subdivide alignment and groups based on identity of
4115 selected subsequence (Make Groups from Selection).</li>
4116 <li>New hide/show options including Shift+Control+H to
4117 hide everything but the currently selected region.</li>
4118 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4119 </ul> <em>Application</em>
4121 <li>Fetch DB References capabilities and UI expanded to
4122 support retrieval from DAS sequence sources</li>
4123 <li>Local DAS Sequence sources can be added via the
4124 command line or via the Add local source dialog box.</li>
4125 <li>DAS Dbref and DbxRef feature types are parsed as
4126 database references and protein_name is parsed as
4127 description line (BioSapiens terms).</li>
4128 <li>Enable or disable non-positional feature and database
4129 references in sequence ID tooltip from View menu in
4131 <!-- <li>New hidden columns and rows and representatives capabilities
4132 in annotations file (in progress - not yet fully implemented)</li> -->
4133 <li>Group-associated consensus, sequence logos and
4134 conservation plots</li>
4135 <li>Symbol distributions for each column can be exported
4136 and visualized as sequence logos</li>
4137 <li>Optionally scale multi-character column labels to fit
4138 within each column of annotation row<!-- todo for applet -->
4140 <li>Optional automatic sort of associated alignment view
4141 when a new tree is opened.</li>
4142 <li>Jalview Java Console</li>
4143 <li>Better placement of desktop window when moving
4144 between different screens.</li>
4145 <li>New preference items for sequence ID tooltip and
4146 consensus annotation</li>
4147 <li>Client to submit sequences and IDs to Envision2
4149 <li><em>Vamsas Capabilities</em>
4151 <li>Improved VAMSAS synchronization (Jalview archive
4152 used to preserve views, structures, and tree display
4154 <li>Import of vamsas documents from disk or URL via
4156 <li>Sharing of selected regions between views and
4157 with other VAMSAS applications (Experimental feature!)</li>
4158 <li>Updated API to VAMSAS version 0.2</li>
4160 </ul> <em>Applet</em>
4162 <li>Middle button resizes annotation row height</li>
4165 <li>sortByTree (true/false) - automatically sort the
4166 associated alignment view by the tree when a new tree is
4168 <li>showTreeBootstraps (true/false) - show or hide
4169 branch bootstraps (default is to show them if available)</li>
4170 <li>showTreeDistances (true/false) - show or hide
4171 branch lengths (default is to show them if available)</li>
4172 <li>showUnlinkedTreeNodes (true/false) - indicate if
4173 unassociated nodes should be highlighted in the tree
4175 <li>heightScale and widthScale (1.0 or more) -
4176 increase the height or width of a cell in the alignment
4177 grid relative to the current font size.</li>
4180 <li>Non-positional features displayed in sequence ID
4182 </ul> <em>Other</em>
4184 <li>Features format: graduated colour definitions and
4185 specification of feature scores</li>
4186 <li>Alignment Annotations format: new keywords for group
4187 associated annotation (GROUP_REF) and annotation row display
4188 properties (ROW_PROPERTIES)</li>
4189 <li>XML formats extended to support graduated feature
4190 colourschemes, group associated annotation, and profile
4191 visualization settings.</li></td>
4194 <li>Source field in GFF files parsed as feature source
4195 rather than description</li>
4196 <li>Non-positional features are now included in sequence
4197 feature and gff files (controlled via non-positional feature
4198 visibility in tooltip).</li>
4199 <li>URL links generated for all feature links (bugfix)</li>
4200 <li>Added URL embedding instructions to features file
4202 <li>Codons containing ambiguous nucleotides translated as
4203 'X' in peptide product</li>
4204 <li>Match case switch in find dialog box works for both
4205 sequence ID and sequence string and query strings do not
4206 have to be in upper case to match case-insensitively.</li>
4207 <li>AMSA files only contain first column of
4208 multi-character column annotation labels</li>
4209 <li>Jalview Annotation File generation/parsing consistent
4210 with documentation (e.g. Stockholm annotation can be
4211 exported and re-imported)</li>
4212 <li>PDB files without embedded PDB IDs given a friendly
4214 <li>Find incrementally searches ID string matches as well
4215 as subsequence matches, and correctly reports total number
4219 <li>Better handling of exceptions during sequence
4221 <li>Dasobert generated non-positional feature URL
4222 link text excludes the start_end suffix</li>
4223 <li>DAS feature and source retrieval buttons disabled
4224 when fetch or registry operations in progress.</li>
4225 <li>PDB files retrieved from URLs are cached properly</li>
4226 <li>Sequence description lines properly shared via
4228 <li>Sequence fetcher fetches multiple records for all
4230 <li>Ensured that command line das feature retrieval
4231 completes before alignment figures are generated.</li>
4232 <li>Reduced time taken when opening file browser for
4234 <li>isAligned check prior to calculating tree, PCA or
4235 submitting an MSA to JNet now excludes hidden sequences.</li>
4236 <li>User defined group colours properly recovered
4237 from Jalview projects.</li>
4246 <div align="center">
4247 <strong>2.4.0.b2</strong><br> 28/10/2009
4252 <li>Experimental support for google analytics usage
4254 <li>Jalview privacy settings (user preferences and docs).</li>
4259 <li>Race condition in applet preventing startup in
4261 <li>Exception when feature created from selection beyond
4262 length of sequence.</li>
4263 <li>Allow synthetic PDB files to be imported gracefully</li>
4264 <li>Sequence associated annotation rows associate with
4265 all sequences with a given id</li>
4266 <li>Find function matches case-insensitively for sequence
4267 ID string searches</li>
4268 <li>Non-standard characters do not cause pairwise
4269 alignment to fail with exception</li>
4270 </ul> <em>Application Issues</em>
4272 <li>Sequences are now validated against EMBL database</li>
4273 <li>Sequence fetcher fetches multiple records for all
4275 </ul> <em>InstallAnywhere Issues</em>
4277 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4278 issue with installAnywhere mechanism)</li>
4279 <li>Command line launching of JARs from InstallAnywhere
4280 version (java class versioning error fixed)</li>
4287 <div align="center">
4288 <strong>2.4</strong><br> 27/8/2008
4291 <td><em>User Interface</em>
4293 <li>Linked highlighting of codon and amino acid from
4294 translation and protein products</li>
4295 <li>Linked highlighting of structure associated with
4296 residue mapping to codon position</li>
4297 <li>Sequence Fetcher provides example accession numbers
4298 and 'clear' button</li>
4299 <li>MemoryMonitor added as an option under Desktop's
4301 <li>Extract score function to parse whitespace separated
4302 numeric data in description line</li>
4303 <li>Column labels in alignment annotation can be centred.</li>
4304 <li>Tooltip for sequence associated annotation give name
4306 </ul> <em>Web Services and URL fetching</em>
4308 <li>JPred3 web service</li>
4309 <li>Prototype sequence search client (no public services
4311 <li>Fetch either seed alignment or full alignment from
4313 <li>URL Links created for matching database cross
4314 references as well as sequence ID</li>
4315 <li>URL Links can be created using regular-expressions</li>
4316 </ul> <em>Sequence Database Connectivity</em>
4318 <li>Retrieval of cross-referenced sequences from other
4320 <li>Generalised database reference retrieval and
4321 validation to all fetchable databases</li>
4322 <li>Fetch sequences from DAS sources supporting the
4323 sequence command</li>
4324 </ul> <em>Import and Export</em>
4325 <li>export annotation rows as CSV for spreadsheet import</li>
4326 <li>Jalview projects record alignment dataset associations,
4327 EMBL products, and cDNA sequence mappings</li>
4328 <li>Sequence Group colour can be specified in Annotation
4330 <li>Ad-hoc colouring of group in Annotation File using RGB
4331 triplet as name of colourscheme</li>
4332 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4334 <li>treenode binding for VAMSAS tree exchange</li>
4335 <li>local editing and update of sequences in VAMSAS
4336 alignments (experimental)</li>
4337 <li>Create new or select existing session to join</li>
4338 <li>load and save of vamsas documents</li>
4339 </ul> <em>Application command line</em>
4341 <li>-tree parameter to open trees (introduced for passing
4343 <li>-fetchfrom command line argument to specify nicknames
4344 of DAS servers to query for alignment features</li>
4345 <li>-dasserver command line argument to add new servers
4346 that are also automatically queried for features</li>
4347 <li>-groovy command line argument executes a given groovy
4348 script after all input data has been loaded and parsed</li>
4349 </ul> <em>Applet-Application data exchange</em>
4351 <li>Trees passed as applet parameters can be passed to
4352 application (when using "View in full
4353 application")</li>
4354 </ul> <em>Applet Parameters</em>
4356 <li>feature group display control parameter</li>
4357 <li>debug parameter</li>
4358 <li>showbutton parameter</li>
4359 </ul> <em>Applet API methods</em>
4361 <li>newView public method</li>
4362 <li>Window (current view) specific get/set public methods</li>
4363 <li>Feature display control methods</li>
4364 <li>get list of currently selected sequences</li>
4365 </ul> <em>New Jalview distribution features</em>
4367 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4368 <li>RELEASE file gives build properties for the latest
4369 Jalview release.</li>
4370 <li>Java 1.1 Applet build made easier and donotobfuscate
4371 property controls execution of obfuscator</li>
4372 <li>Build target for generating source distribution</li>
4373 <li>Debug flag for javacc</li>
4374 <li>.jalview_properties file is documented (slightly) in
4375 jalview.bin.Cache</li>
4376 <li>Continuous Build Integration for stable and
4377 development version of Application, Applet and source
4382 <li>selected region output includes visible annotations
4383 (for certain formats)</li>
4384 <li>edit label/displaychar contains existing label/char
4386 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4387 <li>shorter peptide product names from EMBL records</li>
4388 <li>Newick string generator makes compact representations</li>
4389 <li>bootstrap values parsed correctly for tree files with
4391 <li>pathological filechooser bug avoided by not allowing
4392 filenames containing a ':'</li>
4393 <li>Fixed exception when parsing GFF files containing
4394 global sequence features</li>
4395 <li>Alignment datasets are finalized only when number of
4396 references from alignment sequences goes to zero</li>
4397 <li>Close of tree branch colour box without colour
4398 selection causes cascading exceptions</li>
4399 <li>occasional negative imgwidth exceptions</li>
4400 <li>better reporting of non-fatal warnings to user when
4401 file parsing fails.</li>
4402 <li>Save works when Jalview project is default format</li>
4403 <li>Save as dialog opened if current alignment format is
4404 not a valid output format</li>
4405 <li>UniProt canonical names introduced for both das and
4407 <li>Histidine should be midblue (not pink!) in Zappo</li>
4408 <li>error messages passed up and output when data read
4410 <li>edit undo recovers previous dataset sequence when
4411 sequence is edited</li>
4412 <li>allow PDB files without pdb ID HEADER lines (like
4413 those generated by MODELLER) to be read in properly</li>
4414 <li>allow reading of JPred concise files as a normal
4416 <li>Stockholm annotation parsing and alignment properties
4417 import fixed for PFAM records</li>
4418 <li>Structure view windows have correct name in Desktop
4420 <li>annotation consisting of sequence associated scores
4421 can be read and written correctly to annotation file</li>
4422 <li>Aligned cDNA translation to aligned peptide works
4424 <li>Fixed display of hidden sequence markers and
4425 non-italic font for representatives in Applet</li>
4426 <li>Applet Menus are always embedded in applet window on
4428 <li>Newly shown features appear at top of stack (in
4430 <li>Annotations added via parameter not drawn properly
4431 due to null pointer exceptions</li>
4432 <li>Secondary structure lines are drawn starting from
4433 first column of alignment</li>
4434 <li>UniProt XML import updated for new schema release in
4436 <li>Sequence feature to sequence ID match for Features
4437 file is case-insensitive</li>
4438 <li>Sequence features read from Features file appended to
4439 all sequences with matching IDs</li>
4440 <li>PDB structure coloured correctly for associated views
4441 containing a sub-sequence</li>
4442 <li>PDB files can be retrieved by applet from Jar files</li>
4443 <li>feature and annotation file applet parameters
4444 referring to different directories are retrieved correctly</li>
4445 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4446 <li>Fixed application hang whilst waiting for
4447 splash-screen version check to complete</li>
4448 <li>Applet properly URLencodes input parameter values
4449 when passing them to the launchApp service</li>
4450 <li>display name and local features preserved in results
4451 retrieved from web service</li>
4452 <li>Visual delay indication for sequence retrieval and
4453 sequence fetcher initialisation</li>
4454 <li>updated Application to use DAS 1.53e version of
4455 dasobert DAS client</li>
4456 <li>Re-instated Full AMSA support and .amsa file
4458 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4466 <div align="center">
4467 <strong>2.3</strong><br> 9/5/07
4472 <li>Jmol 11.0.2 integration</li>
4473 <li>PDB views stored in Jalview XML files</li>
4474 <li>Slide sequences</li>
4475 <li>Edit sequence in place</li>
4476 <li>EMBL CDS features</li>
4477 <li>DAS Feature mapping</li>
4478 <li>Feature ordering</li>
4479 <li>Alignment Properties</li>
4480 <li>Annotation Scores</li>
4481 <li>Sort by scores</li>
4482 <li>Feature/annotation editing in applet</li>
4487 <li>Headless state operation in 2.2.1</li>
4488 <li>Incorrect and unstable DNA pairwise alignment</li>
4489 <li>Cut and paste of sequences with annotation</li>
4490 <li>Feature group display state in XML</li>
4491 <li>Feature ordering in XML</li>
4492 <li>blc file iteration selection using filename # suffix</li>
4493 <li>Stockholm alignment properties</li>
4494 <li>Stockhom alignment secondary structure annotation</li>
4495 <li>2.2.1 applet had no feature transparency</li>
4496 <li>Number pad keys can be used in cursor mode</li>
4497 <li>Structure Viewer mirror image resolved</li>
4504 <div align="center">
4505 <strong>2.2.1</strong><br> 12/2/07
4510 <li>Non standard characters can be read and displayed
4511 <li>Annotations/Features can be imported/exported to the
4513 <li>Applet allows editing of sequence/annotation/group
4514 name & description
4515 <li>Preference setting to display sequence name in
4517 <li>Annotation file format extended to allow
4518 Sequence_groups to be defined
4519 <li>Default opening of alignment overview panel can be
4520 specified in preferences
4521 <li>PDB residue numbering annotation added to associated
4527 <li>Applet crash under certain Linux OS with Java 1.6
4529 <li>Annotation file export / import bugs fixed
4530 <li>PNG / EPS image output bugs fixed
4536 <div align="center">
4537 <strong>2.2</strong><br> 27/11/06
4542 <li>Multiple views on alignment
4543 <li>Sequence feature editing
4544 <li>"Reload" alignment
4545 <li>"Save" to current filename
4546 <li>Background dependent text colour
4547 <li>Right align sequence ids
4548 <li>User-defined lower case residue colours
4551 <li>Menu item accelerator keys
4552 <li>Control-V pastes to current alignment
4553 <li>Cancel button for DAS Feature Fetching
4554 <li>PCA and PDB Viewers zoom via mouse roller
4555 <li>User-defined sub-tree colours and sub-tree selection
4557 <li>'New Window' button on the 'Output to Text box'
4562 <li>New memory efficient Undo/Redo System
4563 <li>Optimised symbol lookups and conservation/consensus
4565 <li>Region Conservation/Consensus recalculated after
4567 <li>Fixed Remove Empty Columns Bug (empty columns at end
4569 <li>Slowed DAS Feature Fetching for increased robustness.
4571 <li>Made angle brackets in ASCII feature descriptions
4573 <li>Re-instated Zoom function for PCA
4574 <li>Sequence descriptions conserved in web service
4576 <li>UniProt ID discoverer uses any word separated by
4578 <li>WsDbFetch query/result association resolved
4579 <li>Tree leaf to sequence mapping improved
4580 <li>Smooth fonts switch moved to FontChooser dialog box.
4587 <div align="center">
4588 <strong>2.1.1</strong><br> 12/9/06
4593 <li>Copy consensus sequence to clipboard</li>
4598 <li>Image output - rightmost residues are rendered if
4599 sequence id panel has been resized</li>
4600 <li>Image output - all offscreen group boundaries are
4602 <li>Annotation files with sequence references - all
4603 elements in file are relative to sequence position</li>
4604 <li>Mac Applet users can use Alt key for group editing</li>
4610 <div align="center">
4611 <strong>2.1</strong><br> 22/8/06
4616 <li>MAFFT Multiple Alignment in default Web Service list</li>
4617 <li>DAS Feature fetching</li>
4618 <li>Hide sequences and columns</li>
4619 <li>Export Annotations and Features</li>
4620 <li>GFF file reading / writing</li>
4621 <li>Associate structures with sequences from local PDB
4623 <li>Add sequences to exisiting alignment</li>
4624 <li>Recently opened files / URL lists</li>
4625 <li>Applet can launch the full application</li>
4626 <li>Applet has transparency for features (Java 1.2
4628 <li>Applet has user defined colours parameter</li>
4629 <li>Applet can load sequences from parameter
4630 "sequence<em>x</em>"
4636 <li>Redundancy Panel reinstalled in the Applet</li>
4637 <li>Monospaced font - EPS / rescaling bug fixed</li>
4638 <li>Annotation files with sequence references bug fixed</li>
4644 <div align="center">
4645 <strong>2.08.1</strong><br> 2/5/06
4650 <li>Change case of selected region from Popup menu</li>
4651 <li>Choose to match case when searching</li>
4652 <li>Middle mouse button and mouse movement can compress /
4653 expand the visible width and height of the alignment</li>
4658 <li>Annotation Panel displays complete JNet results</li>
4664 <div align="center">
4665 <strong>2.08b</strong><br> 18/4/06
4671 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4672 <li>Righthand label on wrapped alignments shows correct
4679 <div align="center">
4680 <strong>2.08</strong><br> 10/4/06
4685 <li>Editing can be locked to the selection area</li>
4686 <li>Keyboard editing</li>
4687 <li>Create sequence features from searches</li>
4688 <li>Precalculated annotations can be loaded onto
4690 <li>Features file allows grouping of features</li>
4691 <li>Annotation Colouring scheme added</li>
4692 <li>Smooth fonts off by default - Faster rendering</li>
4693 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4698 <li>Drag & Drop fixed on Linux</li>
4699 <li>Jalview Archive file faster to load/save, sequence
4700 descriptions saved.</li>
4706 <div align="center">
4707 <strong>2.07</strong><br> 12/12/05
4712 <li>PDB Structure Viewer enhanced</li>
4713 <li>Sequence Feature retrieval and display enhanced</li>
4714 <li>Choose to output sequence start-end after sequence
4715 name for file output</li>
4716 <li>Sequence Fetcher WSDBFetch@EBI</li>
4717 <li>Applet can read feature files, PDB files and can be
4718 used for HTML form input</li>
4723 <li>HTML output writes groups and features</li>
4724 <li>Group editing is Control and mouse click</li>
4725 <li>File IO bugs</li>
4731 <div align="center">
4732 <strong>2.06</strong><br> 28/9/05
4737 <li>View annotations in wrapped mode</li>
4738 <li>More options for PCA viewer</li>
4743 <li>GUI bugs resolved</li>
4744 <li>Runs with -nodisplay from command line</li>
4750 <div align="center">
4751 <strong>2.05b</strong><br> 15/9/05
4756 <li>Choose EPS export as lineart or text</li>
4757 <li>Jar files are executable</li>
4758 <li>Can read in Uracil - maps to unknown residue</li>
4763 <li>Known OutOfMemory errors give warning message</li>
4764 <li>Overview window calculated more efficiently</li>
4765 <li>Several GUI bugs resolved</li>
4771 <div align="center">
4772 <strong>2.05</strong><br> 30/8/05
4777 <li>Edit and annotate in "Wrapped" view</li>
4782 <li>Several GUI bugs resolved</li>
4788 <div align="center">
4789 <strong>2.04</strong><br> 24/8/05
4794 <li>Hold down mouse wheel & scroll to change font
4800 <li>Improved JPred client reliability</li>
4801 <li>Improved loading of Jalview files</li>
4807 <div align="center">
4808 <strong>2.03</strong><br> 18/8/05
4813 <li>Set Proxy server name and port in preferences</li>
4814 <li>Multiple URL links from sequence ids</li>
4815 <li>User Defined Colours can have a scheme name and added
4817 <li>Choose to ignore gaps in consensus calculation</li>
4818 <li>Unix users can set default web browser</li>
4819 <li>Runs without GUI for batch processing</li>
4820 <li>Dynamically generated Web Service Menus</li>
4825 <li>InstallAnywhere download for Sparc Solaris</li>
4831 <div align="center">
4832 <strong>2.02</strong><br> 18/7/05
4838 <li>Copy & Paste order of sequences maintains
4839 alignment order.</li>
4845 <div align="center">
4846 <strong>2.01</strong><br> 12/7/05
4851 <li>Use delete key for deleting selection.</li>
4852 <li>Use Mouse wheel to scroll sequences.</li>
4853 <li>Help file updated to describe how to add alignment
4855 <li>Version and build date written to build properties
4857 <li>InstallAnywhere installation will check for updates
4858 at launch of Jalview.</li>
4863 <li>Delete gaps bug fixed.</li>
4864 <li>FileChooser sorts columns.</li>
4865 <li>Can remove groups one by one.</li>
4866 <li>Filechooser icons installed.</li>
4867 <li>Finder ignores return character when searching.
4868 Return key will initiate a search.<br>
4875 <div align="center">
4876 <strong>2.0</strong><br> 20/6/05
4881 <li>New codebase</li>