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
76 <td align="left" valign="top">
79 <!-- JAL-3493 -->Escape does not clear highlights on the
80 alignment (Since Jalview 2.10.3)
83 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
84 doesn't slide selected sequences
87 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
88 multiple EMBL gene products shown forĀ a single contig
91 <!-- JAL-3696 -->Errors encountered when processing variants
92 from VCF files yield "Error processing VCF: Format specifier
96 <!-- JAL-3697 -->Count of features not shown can be wrong
97 when there are both local and complementary features mapped
98 to the position under the cursor
104 <td width="60" align="center" nowrap><strong><a
105 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
106 <em>22/04/2020</em></strong></td>
107 <td align="left" valign="top">
110 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
111 'virtual' codon features shown on protein (or vice versa)
112 for display in alignments, on structure views (including
113 transfer to UCSF chimera), in feature reports and for
117 <!-- JAL-3121 -->Feature attributes from VCF files can be
118 exported and re-imported as GFF3 files
121 <!-- JAL-3376 -->Capture VCF "fixed column" values
122 POS, ID, QUAL, FILTER as Feature Attributes
125 <!-- JAL-3375 -->More robust VCF numeric data field
126 validation while parsing
129 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
133 <!-- JAL-3535 -->Feature Settings dialog title includes name
137 <!-- JAL-3538 -->Font anti-aliasing in alignment views
141 <!-- JAL-3468 -->Very long feature descriptions truncated in
145 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
146 with no feature types visible
149 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
151 </ul><em>Jalview Installer</em>
154 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
155 in console (may be null when Jalview launched as executable jar or via conda)
158 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
161 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
164 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
166 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
167 </ul> <em>Release processes</em>
170 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
173 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
175 </ul> <em>Build System</em>
178 <!-- JAL-3510 -->Clover updated to 4.4.1
181 <!-- JAL-3513 -->Test code included in Clover coverage
185 <em>Groovy Scripts</em>
188 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
189 to stdout containing the consensus sequence for each
190 alignment in a Jalview session
193 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
194 genomic sequence_variant annotation from CDS as
195 missense_variant or synonymous_variant on protein products.
199 <td align="left" valign="top">
202 <!-- JAL-3581 -->Hidden sequence markers still visible when
203 'Show hidden markers' option is not ticked
206 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
207 PNG output when 'Automatically set ID width' is set in
208 jalview preferences or properties file
211 <!-- JAL-3571 -->Feature Editor dialog can be opened when
212 'Show Sequence Features' option is not ticked
215 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
216 buttons in Feature Settings dialog are clicked when no
220 <!-- JAL-3412 -->ID margins for CDS and Protein views not
221 equal when split frame is first opened
224 <!-- JAL-3296 -->Sequence position numbers in status bar not
225 correct after editing a sequence's start position
228 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
229 with annotation and exceptions thrown when only a few
230 columns shown in wrapped mode
233 <!-- JAL-3386 -->Sequence IDs missing in headless export of
234 wrapped alignment figure with annotations
237 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
238 ID fails with ClassCastException
241 <!-- JAL-3389 -->Chimera session not restored from Jalview
245 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
246 feature settings dialog also selects columns
249 <!-- JAL-3473 -->SpinnerNumberModel causes
250 IllegalArgumentException in some circumstances
253 <!-- JAL-3534 -->Multiple feature settings dialogs can be
257 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
258 alignment window is closed
261 <!-- JAL-3406 -->Credits missing some authors in Jalview
262 help documentation for 2.11.0 release
265 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
266 includes Pfam ID as sequence's accession rather than its
269 </ul> <em>Java 11 Compatibility issues</em>
272 <!-- JAL-2987 -->OSX - Can't view some search results in
273 PDB/Uniprot search panel
275 </ul> <em>Installer</em>
278 <!-- JAL-3447 -->Jalview should not create file associations
279 for 3D structure files (.pdb, .mmcif. .cif)
281 </ul> <em>Repository and Source Release</em>
284 <!-- JAL-3474 -->removed obsolete .cvsignore files from
288 <!-- JAL-3541 -->Clover report generation running out of
291 </ul> <em>New Known Issues</em>
294 <!-- JAL-3523 -->OSX - Current working directory not
295 preserved when Jalview.app launched with parameters from
299 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
300 clipped in headless figure export when Right Align option
304 <!-- JAL-3542 -->Jalview Installation type always reports
305 'Source' in console output
308 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
309 bamboo server but run fine locally.
315 <td width="60" align="center" nowrap>
316 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
317 <em>04/07/2019</em></strong>
319 <td align="left" valign="top">
322 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
323 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
324 source project) rather than InstallAnywhere
327 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
328 settings, receive over the air updates and launch specific
329 versions via (<a href="https://github.com/threerings/getdown">Three
333 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
334 formats supported by Jalview (including .jvp project files)
337 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
338 arguments and switch between different getdown channels
341 <!-- JAL-3141 -->Backup files created when saving Jalview project
346 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
347 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
349 <!-- JAL-2620 -->Alternative genetic code tables for
350 'Translate as cDNA'</li>
352 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
353 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
356 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
357 implementation that allows updates) used for Sequence Feature collections</li>
359 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
360 features can be filtered and shaded according to any
361 associated attributes (e.g. variant attributes from VCF
362 file, or key-value pairs imported from column 9 of GFF
366 <!-- JAL-2879 -->Feature Attributes and shading schemes
367 stored and restored from Jalview Projects
370 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
371 recognise variant features
374 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
375 sequences (also coloured red by default)
378 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
382 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
383 algorithm (Z-sort/transparency and filter aware)
386 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
392 <!-- JAL-3205 -->Symmetric score matrices for faster
393 tree and PCA calculations
395 <li><strong>Principal Components Analysis Viewer</strong>
398 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
399 and Viewer state saved in Jalview Project
401 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
404 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
408 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
413 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
415 <li><strong>Speed and Efficiency</strong>
418 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
419 multiple groups when working with large alignments
422 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
426 <li><strong>User Interface</strong>
429 <!-- JAL-2933 -->Finder panel remembers last position in each
433 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
434 what is shown)<br />Only visible regions of alignment are shown by
435 default (can be changed in user preferences)
438 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
439 to the Overwrite Dialog
442 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
446 <!-- JAL-1244 -->Status bar shows bounds when dragging a
447 selection region, and gap count when inserting or deleting gaps
450 <!-- JAL-3132 -->Status bar updates over sequence and annotation
454 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
458 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
462 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
465 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
469 <!-- JAL-3181 -->Consistent ordering of links in sequence id
473 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
475 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
479 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
480 <li><strong>Java 11 Support (not yet on general release)</strong>
483 <!-- -->OSX GUI integrations for App menu's 'About' entry and
488 <em>Deprecations</em>
490 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
491 capabilities removed from the Jalview Desktop
493 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
494 unmarshalling has been replaced by JAXB for Jalview projects
495 and XML based data retrieval clients</li>
496 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
497 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
498 </ul> <em>Documentation</em>
500 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
501 not supported in EPS figure export
503 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
504 </ul> <em>Development and Release Processes</em>
507 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
510 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
512 <!-- JAL-3225 -->Eclipse project configuration managed with
516 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
517 Bamboo continuous integration for unattended Test Suite
521 <!-- JAL-2864 -->Memory test suite to detect leaks in common
525 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
529 <!-- JAL-3248 -->Developer documentation migrated to
530 markdown (with HTML rendering)
533 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
536 <!-- JAL-3289 -->New URLs for publishing development
541 <td align="left" valign="top">
544 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
547 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
548 superposition in Jmol fail on Windows
551 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
552 structures for sequences with lots of PDB structures
555 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
559 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
560 project involving multiple views
563 <!-- JAL-3164 -->Overview for complementary view in a linked
564 CDS/Protein alignment is not updated when Hide Columns by
565 Annotation dialog hides columns
568 <!-- JAL-3158 -->Selection highlighting in the complement of a
569 CDS/Protein alignment stops working after making a selection in
570 one view, then making another selection in the other view
573 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
577 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
578 Settings and Jalview Preferences panels
581 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
582 overview with large alignments
585 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
586 region if columns were selected by dragging right-to-left and the
587 mouse moved to the left of the first column
590 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
591 hidden column marker via scale popup menu
594 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
595 doesn't tell users the invalid URL
598 <!-- JAL-2816 -->Tooltips displayed for features filtered by
602 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
603 show cross references or Fetch Database References are shown in
607 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
608 peptide sequence (computed variant shown as p.Res.null)
611 <!-- JAL-2060 -->'Graduated colour' option not offered for
612 manually created features (where feature score is Float.NaN)
615 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
616 when columns are hidden
619 <!-- JAL-3082 -->Regular expression error for '(' in Select
620 Columns by Annotation description
623 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
624 out of Scale or Annotation Panel
627 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
631 <!-- JAL-3074 -->Left/right drag in annotation can scroll
635 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
639 <!-- JAL-3002 -->Column display is out by one after Page Down,
640 Page Up in wrapped mode
643 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
646 <!-- JAL-2932 -->Finder searches in minimised alignments
649 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
650 on opening an alignment
653 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
657 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
658 different groups in the alignment are selected
661 <!-- JAL-2717 -->Internationalised colour scheme names not shown
665 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
669 <!-- JAL-3125 -->Value input for graduated feature colour
670 threshold gets 'unrounded'
673 <!-- JAL-2982 -->PCA image export doesn't respect background
677 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
680 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
683 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
687 <!-- JAL-2964 -->Associate Tree with All Views not restored from
691 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
692 shown in complementary view
695 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
696 without normalisation
699 <!-- JAL-3021 -->Sequence Details report should open positioned at top
703 <!-- JAL-914 -->Help page can be opened twice
706 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
708 </ul> <em>Editing</em>
711 <!-- JAL-2822 -->Start and End should be updated when sequence
712 data at beginning or end of alignment added/removed via 'Edit'
716 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
717 relocate sequence features correctly when start of sequence is
718 removed (Known defect since 2.10)
721 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
722 dialog corrupts dataset sequence
725 <!-- JAL-868 -->Structure colours not updated when associated tree
726 repartitions the alignment view (Regression in 2.10.5)
728 </ul> <em>Datamodel</em>
731 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
732 sequence's End is greater than its length
734 </ul> <em>Bugs fixed for Java 11 Support (not yet on
735 general release)</em>
738 <!-- JAL-3288 -->Menus work properly in split-screen
740 </ul> <em>New Known Defects</em>
743 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
746 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
747 regions of protein alignment.
750 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
751 is restored from a Jalview 2.11 project
754 <!-- JAL-3213 -->Alignment panel height can be too small after
758 <!-- JAL-3240 -->Display is incorrect after removing gapped
759 columns within hidden columns
762 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
763 window after dragging left to select columns to left of visible
767 <!-- JAL-2876 -->Features coloured according to their description
768 string and thresholded by score in earlier versions of Jalview are
769 not shown as thresholded features in 2.11. To workaround please
770 create a Score filter instead.
773 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
775 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
778 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
779 alignments with multiple views can close views unexpectedly
782 <em>Java 11 Specific defects</em>
785 <!-- JAL-3235 -->Jalview Properties file is not sorted
786 alphabetically when saved
792 <td width="60" nowrap>
794 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
797 <td><div align="left">
801 <!-- JAL-3101 -->Default memory for Jalview webstart and
802 InstallAnywhere increased to 1G.
805 <!-- JAL-247 -->Hidden sequence markers and representative
806 sequence bolding included when exporting alignment as EPS,
807 SVG, PNG or HTML. <em>Display is configured via the
808 Format menu, or for command-line use via a Jalview
809 properties file.</em>
812 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
813 API and sequence data now imported as JSON.
816 <!-- JAL-3065 -->Change in recommended way of starting
817 Jalview via a Java command line: add jars in lib directory
818 to CLASSPATH, rather than via the deprecated java.ext.dirs
825 <!-- JAL-3047 -->Support added to execute test suite
826 instrumented with <a href="http://openclover.org/">Open
831 <td><div align="left">
835 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
836 row shown in Feredoxin Structure alignment view of example
840 <!-- JAL-2854 -->Annotation obscures sequences if lots of
841 annotation displayed.
844 <!-- JAL-3107 -->Group conservation/consensus not shown
845 for newly created group when 'Apply to all groups'
849 <!-- JAL-3087 -->Corrupted display when switching to
850 wrapped mode when sequence panel's vertical scrollbar is
854 <!-- JAL-3003 -->Alignment is black in exported EPS file
855 when sequences are selected in exported view.</em>
858 <!-- JAL-3059 -->Groups with different coloured borders
859 aren't rendered with correct colour.
862 <!-- JAL-3092 -->Jalview could hang when importing certain
863 types of knotted RNA secondary structure.
866 <!-- JAL-3095 -->Sequence highlight and selection in
867 trimmed VARNA 2D structure is incorrect for sequences that
871 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
872 annotation when columns are inserted into an alignment,
873 and when exporting as Stockholm flatfile.
876 <!-- JAL-3053 -->Jalview annotation rows containing upper
877 and lower-case 'E' and 'H' do not automatically get
878 treated as RNA secondary structure.
881 <!-- JAL-3106 -->.jvp should be used as default extension
882 (not .jar) when saving a Jalview project file.
885 <!-- JAL-3105 -->Mac Users: closing a window correctly
886 transfers focus to previous window on OSX
889 <em>Java 10 Issues Resolved</em>
892 <!-- JAL-2988 -->OSX - Can't save new files via the File
893 or export menus by typing in a name into the Save dialog
897 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
898 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
899 'look and feel' which has improved compatibility with the
900 latest version of OSX.
907 <td width="60" nowrap>
909 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
910 <em>7/06/2018</em></strong>
913 <td><div align="left">
917 <!-- JAL-2920 -->Use HGVS nomenclature for variant
918 annotation retrieved from Uniprot
921 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
922 onto the Jalview Desktop
926 <td><div align="left">
930 <!-- JAL-3017 -->Cannot import features with multiple
931 variant elements (blocks import of some Uniprot records)
934 <!-- JAL-2997 -->Clustal files with sequence positions in
935 right-hand column parsed correctly
938 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
939 not alignment area in exported graphic
942 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
943 window has input focus
946 <!-- JAL-2992 -->Annotation panel set too high when
947 annotation added to view (Windows)
950 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
951 network connectivity is poor
954 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
955 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
956 the currently open URL and links from a page viewed in
957 Firefox or Chrome on Windows is now fully supported. If
958 you are using Edge, only links in the page can be
959 dragged, and with Internet Explorer, only the currently
960 open URL in the browser can be dropped onto Jalview.</em>
963 <em>New Known Defects</em>
965 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
970 <td width="60" nowrap>
972 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
975 <td><div align="left">
979 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
980 for disabling automatic superposition of multiple
981 structures and open structures in existing views
984 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
985 ID and annotation area margins can be click-dragged to
989 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
993 <!-- JAL-2759 -->Improved performance for large alignments
994 and lots of hidden columns
997 <!-- JAL-2593 -->Improved performance when rendering lots
998 of features (particularly when transparency is disabled)
1001 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1002 exchange of Jalview features and Chimera attributes made
1008 <td><div align="left">
1011 <!-- JAL-2899 -->Structure and Overview aren't updated
1012 when Colour By Annotation threshold slider is adjusted
1015 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1016 overlapping alignment panel
1019 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1023 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1024 improved: CDS not handled correctly if transcript has no
1028 <!-- JAL-2321 -->Secondary structure and temperature
1029 factor annotation not added to sequence when local PDB
1030 file associated with it by drag'n'drop or structure
1034 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1035 dialog doesn't import PDB files dropped on an alignment
1038 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1039 scroll bar doesn't work for some CDS/Protein views
1042 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1043 Java 1.8u153 onwards and Java 1.9u4+.
1046 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1047 columns in annotation row
1050 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1051 honored in batch mode
1054 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1055 for structures added to existing Jmol view
1058 <!-- JAL-2223 -->'View Mappings' includes duplicate
1059 entries after importing project with multiple views
1062 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1063 protein sequences via SIFTS from associated PDB entries
1064 with negative residue numbers or missing residues fails
1067 <!-- JAL-2952 -->Exception when shading sequence with negative
1068 Temperature Factor values from annotated PDB files (e.g.
1069 as generated by CONSURF)
1072 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1073 tooltip doesn't include a text description of mutation
1076 <!-- JAL-2922 -->Invert displayed features very slow when
1077 structure and/or overview windows are also shown
1080 <!-- JAL-2954 -->Selecting columns from highlighted regions
1081 very slow for alignments with large numbers of sequences
1084 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1085 with 'StringIndexOutOfBounds'
1088 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1089 platforms running Java 10
1092 <!-- JAL-2960 -->Adding a structure to existing structure
1093 view appears to do nothing because the view is hidden behind the alignment view
1099 <!-- JAL-2926 -->Copy consensus sequence option in applet
1100 should copy the group consensus when popup is opened on it
1106 <!-- JAL-2913 -->Fixed ID width preference is not respected
1109 <em>New Known Defects</em>
1112 <!-- JAL-2973 --> Exceptions occasionally raised when
1113 editing a large alignment and overview is displayed
1116 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1117 repeatedly after a series of edits even when the overview
1118 is no longer reflecting updates
1121 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1122 structures for protein subsequence (if 'Trim Retrieved
1123 Sequences' enabled) or Ensembl isoforms (Workaround in
1124 2.10.4 is to fail back to N&W mapping)
1127 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1128 option gives blank output
1135 <td width="60" nowrap>
1136 <div align="center">
1137 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1140 <td><div align="left">
1141 <ul><li>Updated Certum Codesigning Certificate
1142 (Valid till 30th November 2018)</li></ul></div></td>
1143 <td><div align="left">
1144 <em>Desktop</em><ul>
1146 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1147 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1148 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1149 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1150 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1151 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1152 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1158 <td width="60" nowrap>
1159 <div align="center">
1160 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1163 <td><div align="left">
1167 <!-- JAL-2446 -->Faster and more efficient management and
1168 rendering of sequence features
1171 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1172 429 rate limit request hander
1175 <!-- JAL-2773 -->Structure views don't get updated unless
1176 their colours have changed
1179 <!-- JAL-2495 -->All linked sequences are highlighted for
1180 a structure mousover (Jmol) or selection (Chimera)
1183 <!-- JAL-2790 -->'Cancel' button in progress bar for
1184 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1187 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1188 view from Ensembl locus cross-references
1191 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1195 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1196 feature can be disabled
1199 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1200 PDB easier retrieval of sequences for lists of IDs
1203 <!-- JAL-2758 -->Short names for sequences retrieved from
1209 <li>Groovy interpreter updated to 2.4.12</li>
1210 <li>Example groovy script for generating a matrix of
1211 percent identity scores for current alignment.</li>
1213 <em>Testing and Deployment</em>
1216 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1220 <td><div align="left">
1224 <!-- JAL-2643 -->Pressing tab after updating the colour
1225 threshold text field doesn't trigger an update to the
1229 <!-- JAL-2682 -->Race condition when parsing sequence ID
1233 <!-- JAL-2608 -->Overview windows are also closed when
1234 alignment window is closed
1237 <!-- JAL-2548 -->Export of features doesn't always respect
1241 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1242 takes a long time in Cursor mode
1248 <!-- JAL-2777 -->Structures with whitespace chainCode
1249 cannot be viewed in Chimera
1252 <!-- JAL-2728 -->Protein annotation panel too high in
1256 <!-- JAL-2757 -->Can't edit the query after the server
1257 error warning icon is shown in Uniprot and PDB Free Text
1261 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1264 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1267 <!-- JAL-2739 -->Hidden column marker in last column not
1268 rendered when switching back from Wrapped to normal view
1271 <!-- JAL-2768 -->Annotation display corrupted when
1272 scrolling right in unwapped alignment view
1275 <!-- JAL-2542 -->Existing features on subsequence
1276 incorrectly relocated when full sequence retrieved from
1280 <!-- JAL-2733 -->Last reported memory still shown when
1281 Desktop->Show Memory is unticked (OSX only)
1284 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1285 features of same type and group to be selected for
1289 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1290 alignments when hidden columns are present
1293 <!-- JAL-2392 -->Jalview freezes when loading and
1294 displaying several structures
1297 <!-- JAL-2732 -->Black outlines left after resizing or
1301 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1302 within the Jalview desktop on OSX
1305 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1306 when in wrapped alignment mode
1309 <!-- JAL-2636 -->Scale mark not shown when close to right
1310 hand end of alignment
1313 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1314 each selected sequence do not have correct start/end
1318 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1319 after canceling the Alignment Window's Font dialog
1322 <!-- JAL-2036 -->Show cross-references not enabled after
1323 restoring project until a new view is created
1326 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1327 URL links appears when only default EMBL-EBI link is
1328 configured (since 2.10.2b2)
1331 <!-- JAL-2775 -->Overview redraws whole window when box
1332 position is adjusted
1335 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1336 in a multi-chain structure when viewing alignment
1337 involving more than one chain (since 2.10)
1340 <!-- JAL-2811 -->Double residue highlights in cursor mode
1341 if new selection moves alignment window
1344 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1345 arrow key in cursor mode to pass hidden column marker
1348 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1349 that produces correctly annotated transcripts and products
1352 <!-- JAL-2776 -->Toggling a feature group after first time
1353 doesn't update associated structure view
1356 <em>Applet</em><br />
1359 <!-- JAL-2687 -->Concurrent modification exception when
1360 closing alignment panel
1363 <em>BioJSON</em><br />
1366 <!-- JAL-2546 -->BioJSON export does not preserve
1367 non-positional features
1370 <em>New Known Issues</em>
1373 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1374 sequence features correctly (for many previous versions of
1378 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1379 using cursor in wrapped panel other than top
1382 <!-- JAL-2791 -->Select columns containing feature ignores
1383 graduated colour threshold
1386 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1387 always preserve numbering and sequence features
1390 <em>Known Java 9 Issues</em>
1393 <!-- JAL-2902 -->Groovy Console very slow to open and is
1394 not responsive when entering characters (Webstart, Java
1401 <td width="60" nowrap>
1402 <div align="center">
1403 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1404 <em>2/10/2017</em></strong>
1407 <td><div align="left">
1408 <em>New features in Jalview Desktop</em>
1411 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1413 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1417 <td><div align="left">
1421 <td width="60" nowrap>
1422 <div align="center">
1423 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1424 <em>7/9/2017</em></strong>
1427 <td><div align="left">
1431 <!-- JAL-2588 -->Show gaps in overview window by colouring
1432 in grey (sequences used to be coloured grey, and gaps were
1436 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1440 <!-- JAL-2587 -->Overview updates immediately on increase
1441 in size and progress bar shown as higher resolution
1442 overview is recalculated
1447 <td><div align="left">
1451 <!-- JAL-2664 -->Overview window redraws every hidden
1452 column region row by row
1455 <!-- JAL-2681 -->duplicate protein sequences shown after
1456 retrieving Ensembl crossrefs for sequences from Uniprot
1459 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1460 format setting is unticked
1463 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1464 if group has show boxes format setting unticked
1467 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1468 autoscrolling whilst dragging current selection group to
1469 include sequences and columns not currently displayed
1472 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1473 assemblies are imported via CIF file
1476 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1477 displayed when threshold or conservation colouring is also
1481 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1485 <!-- JAL-2673 -->Jalview continues to scroll after
1486 dragging a selected region off the visible region of the
1490 <!-- JAL-2724 -->Cannot apply annotation based
1491 colourscheme to all groups in a view
1494 <!-- JAL-2511 -->IDs don't line up with sequences
1495 initially after font size change using the Font chooser or
1502 <td width="60" nowrap>
1503 <div align="center">
1504 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1507 <td><div align="left">
1508 <em>Calculations</em>
1512 <!-- JAL-1933 -->Occupancy annotation row shows number of
1513 ungapped positions in each column of the alignment.
1516 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1517 a calculation dialog box
1520 <!-- JAL-2379 -->Revised implementation of PCA for speed
1521 and memory efficiency (~30x faster)
1524 <!-- JAL-2403 -->Revised implementation of sequence
1525 similarity scores as used by Tree, PCA, Shading Consensus
1526 and other calculations
1529 <!-- JAL-2416 -->Score matrices are stored as resource
1530 files within the Jalview codebase
1533 <!-- JAL-2500 -->Trees computed on Sequence Feature
1534 Similarity may have different topology due to increased
1541 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1542 model for alignments and groups
1545 <!-- JAL-384 -->Custom shading schemes created via groovy
1552 <!-- JAL-2526 -->Efficiency improvements for interacting
1553 with alignment and overview windows
1556 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1560 <!-- JAL-2388 -->Hidden columns and sequences can be
1564 <!-- JAL-2611 -->Click-drag in visible area allows fine
1565 adjustment of visible position
1569 <em>Data import/export</em>
1572 <!-- JAL-2535 -->Posterior probability annotation from
1573 Stockholm files imported as sequence associated annotation
1576 <!-- JAL-2507 -->More robust per-sequence positional
1577 annotation input/output via stockholm flatfile
1580 <!-- JAL-2533 -->Sequence names don't include file
1581 extension when importing structure files without embedded
1582 names or PDB accessions
1585 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1586 format sequence substitution matrices
1589 <em>User Interface</em>
1592 <!-- JAL-2447 --> Experimental Features Checkbox in
1593 Desktop's Tools menu to hide or show untested features in
1597 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1598 via Overview or sequence motif search operations
1601 <!-- JAL-2547 -->Amend sequence features dialog box can be
1602 opened by double clicking gaps within sequence feature
1606 <!-- JAL-1476 -->Status bar message shown when not enough
1607 aligned positions were available to create a 3D structure
1611 <em>3D Structure</em>
1614 <!-- JAL-2430 -->Hidden regions in alignment views are not
1615 coloured in linked structure views
1618 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1619 file-based command exchange
1622 <!-- JAL-2375 -->Structure chooser automatically shows
1623 Cached Structures rather than querying the PDBe if
1624 structures are already available for sequences
1627 <!-- JAL-2520 -->Structures imported via URL are cached in
1628 the Jalview project rather than downloaded again when the
1629 project is reopened.
1632 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1633 to transfer Chimera's structure attributes as Jalview
1634 features, and vice-versa (<strong>Experimental
1638 <em>Web Services</em>
1641 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1644 <!-- JAL-2335 -->Filter non-standard amino acids and
1645 nucleotides when submitting to AACon and other MSA
1649 <!-- JAL-2316, -->URLs for viewing database
1650 cross-references provided by identifiers.org and the
1651 EMBL-EBI's MIRIAM DB
1658 <!-- JAL-2344 -->FileFormatI interface for describing and
1659 identifying file formats (instead of String constants)
1662 <!-- JAL-2228 -->FeatureCounter script refactored for
1663 efficiency when counting all displayed features (not
1664 backwards compatible with 2.10.1)
1667 <em>Example files</em>
1670 <!-- JAL-2631 -->Graduated feature colour style example
1671 included in the example feature file
1674 <em>Documentation</em>
1677 <!-- JAL-2339 -->Release notes reformatted for readability
1678 with the built-in Java help viewer
1681 <!-- JAL-1644 -->Find documentation updated with 'search
1682 sequence description' option
1688 <!-- JAL-2485, -->External service integration tests for
1689 Uniprot REST Free Text Search Client
1692 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1695 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1700 <td><div align="left">
1701 <em>Calculations</em>
1704 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1705 matrix - C->R should be '-3'<br />Old matrix restored
1706 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1708 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1709 Jalview's treatment of gaps in PCA and substitution matrix
1710 based Tree calculations.<br /> <br />In earlier versions
1711 of Jalview, gaps matching gaps were penalised, and gaps
1712 matching non-gaps penalised even more. In the PCA
1713 calculation, gaps were actually treated as non-gaps - so
1714 different costs were applied, which meant Jalview's PCAs
1715 were different to those produced by SeqSpace.<br />Jalview
1716 now treats gaps in the same way as SeqSpace (ie it scores
1717 them as 0). <br /> <br />Enter the following in the
1718 Groovy console to restore pre-2.10.2 behaviour:<br />
1719 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1720 // for 2.10.1 mode <br />
1721 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1722 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1723 these settings will affect all subsequent tree and PCA
1724 calculations (not recommended)</em></li>
1726 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1727 scaling of branch lengths for trees computed using
1728 Sequence Feature Similarity.
1731 <!-- JAL-2377 -->PCA calculation could hang when
1732 generating output report when working with highly
1733 redundant alignments
1736 <!-- JAL-2544 --> Sort by features includes features to
1737 right of selected region when gaps present on right-hand
1741 <em>User Interface</em>
1744 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1745 doesn't reselect a specific sequence's associated
1746 annotation after it was used for colouring a view
1749 <!-- JAL-2419 -->Current selection lost if popup menu
1750 opened on a region of alignment without groups
1753 <!-- JAL-2374 -->Popup menu not always shown for regions
1754 of an alignment with overlapping groups
1757 <!-- JAL-2310 -->Finder double counts if both a sequence's
1758 name and description match
1761 <!-- JAL-2370 -->Hiding column selection containing two
1762 hidden regions results in incorrect hidden regions
1765 <!-- JAL-2386 -->'Apply to all groups' setting when
1766 changing colour does not apply Conservation slider value
1770 <!-- JAL-2373 -->Percentage identity and conservation menu
1771 items do not show a tick or allow shading to be disabled
1774 <!-- JAL-2385 -->Conservation shading or PID threshold
1775 lost when base colourscheme changed if slider not visible
1778 <!-- JAL-2547 -->Sequence features shown in tooltip for
1779 gaps before start of features
1782 <!-- JAL-2623 -->Graduated feature colour threshold not
1783 restored to UI when feature colour is edited
1786 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1787 a time when scrolling vertically in wrapped mode.
1790 <!-- JAL-2630 -->Structure and alignment overview update
1791 as graduate feature colour settings are modified via the
1795 <!-- JAL-2034 -->Overview window doesn't always update
1796 when a group defined on the alignment is resized
1799 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1800 wrapped view result in positional status updates
1804 <!-- JAL-2563 -->Status bar doesn't show position for
1805 ambiguous amino acid and nucleotide symbols
1808 <!-- JAL-2602 -->Copy consensus sequence failed if
1809 alignment included gapped columns
1812 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1813 widgets don't permanently disappear
1816 <!-- JAL-2503 -->Cannot select or filter quantitative
1817 annotation that are shown only as column labels (e.g.
1818 T-Coffee column reliability scores)
1821 <!-- JAL-2594 -->Exception thrown if trying to create a
1822 sequence feature on gaps only
1825 <!-- JAL-2504 -->Features created with 'New feature'
1826 button from a Find inherit previously defined feature type
1827 rather than the Find query string
1830 <!-- JAL-2423 -->incorrect title in output window when
1831 exporting tree calculated in Jalview
1834 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1835 and then revealing them reorders sequences on the
1839 <!-- JAL-964 -->Group panel in sequence feature settings
1840 doesn't update to reflect available set of groups after
1841 interactively adding or modifying features
1844 <!-- JAL-2225 -->Sequence Database chooser unusable on
1848 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1849 only excluded gaps in current sequence and ignored
1856 <!-- JAL-2421 -->Overview window visible region moves
1857 erratically when hidden rows or columns are present
1860 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1861 Structure Viewer's colour menu don't correspond to
1865 <!-- JAL-2405 -->Protein specific colours only offered in
1866 colour and group colour menu for protein alignments
1869 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1870 reflect currently selected view or group's shading
1874 <!-- JAL-2624 -->Feature colour thresholds not respected
1875 when rendered on overview and structures when opacity at
1879 <!-- JAL-2589 -->User defined gap colour not shown in
1880 overview when features overlaid on alignment
1883 <!-- JAL-2567 -->Feature settings for different views not
1884 recovered correctly from Jalview project file
1887 <!-- JAL-2256 -->Feature colours in overview when first opened
1888 (automatically via preferences) are different to the main
1892 <em>Data import/export</em>
1895 <!-- JAL-2576 -->Very large alignments take a long time to
1899 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1900 added after a sequence was imported are not written to
1904 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1905 when importing RNA secondary structure via Stockholm
1908 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1909 not shown in correct direction for simple pseudoknots
1912 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1913 with lightGray or darkGray via features file (but can
1917 <!-- JAL-2383 -->Above PID colour threshold not recovered
1918 when alignment view imported from project
1921 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1922 structure and sequences extracted from structure files
1923 imported via URL and viewed in Jmol
1926 <!-- JAL-2520 -->Structures loaded via URL are saved in
1927 Jalview Projects rather than fetched via URL again when
1928 the project is loaded and the structure viewed
1931 <em>Web Services</em>
1934 <!-- JAL-2519 -->EnsemblGenomes example failing after
1935 release of Ensembl v.88
1938 <!-- JAL-2366 -->Proxy server address and port always
1939 appear enabled in Preferences->Connections
1942 <!-- JAL-2461 -->DAS registry not found exceptions
1943 removed from console output
1946 <!-- JAL-2582 -->Cannot retrieve protein products from
1947 Ensembl by Peptide ID
1950 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1951 created from SIFTs, and spurious 'Couldn't open structure
1952 in Chimera' errors raised after April 2017 update (problem
1953 due to 'null' string rather than empty string used for
1954 residues with no corresponding PDB mapping).
1957 <em>Application UI</em>
1960 <!-- JAL-2361 -->User Defined Colours not added to Colour
1964 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1965 case' residues (button in colourscheme editor debugged and
1966 new documentation and tooltips added)
1969 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1970 doesn't restore group-specific text colour thresholds
1973 <!-- JAL-2243 -->Feature settings panel does not update as
1974 new features are added to alignment
1977 <!-- JAL-2532 -->Cancel in feature settings reverts
1978 changes to feature colours via the Amend features dialog
1981 <!-- JAL-2506 -->Null pointer exception when attempting to
1982 edit graduated feature colour via amend features dialog
1986 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1987 selection menu changes colours of alignment views
1990 <!-- JAL-2426 -->Spurious exceptions in console raised
1991 from alignment calculation workers after alignment has
1995 <!-- JAL-1608 -->Typo in selection popup menu - Create
1996 groups now 'Create Group'
1999 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2000 Create/Undefine group doesn't always work
2003 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2004 shown again after pressing 'Cancel'
2007 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2008 adjusts start position in wrap mode
2011 <!-- JAL-2563 -->Status bar doesn't show positions for
2012 ambiguous amino acids
2015 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2016 CDS/Protein view after CDS sequences added for aligned
2020 <!-- JAL-2592 -->User defined colourschemes called 'User
2021 Defined' don't appear in Colours menu
2027 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2028 score models doesn't always result in an updated PCA plot
2031 <!-- JAL-2442 -->Features not rendered as transparent on
2032 overview or linked structure view
2035 <!-- JAL-2372 -->Colour group by conservation doesn't
2039 <!-- JAL-2517 -->Hitting Cancel after applying
2040 user-defined colourscheme doesn't restore original
2047 <!-- JAL-2314 -->Unit test failure:
2048 jalview.ws.jabaws.RNAStructExportImport setup fails
2051 <!-- JAL-2307 -->Unit test failure:
2052 jalview.ws.sifts.SiftsClientTest due to compatibility
2053 problems with deep array comparison equality asserts in
2054 successive versions of TestNG
2057 <!-- JAL-2479 -->Relocated StructureChooserTest and
2058 ParameterUtilsTest Unit tests to Network suite
2061 <em>New Known Issues</em>
2064 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2065 phase after a sequence motif find operation
2068 <!-- JAL-2550 -->Importing annotation file with rows
2069 containing just upper and lower case letters are
2070 interpreted as WUSS RNA secondary structure symbols
2073 <!-- JAL-2590 -->Cannot load and display Newick trees
2074 reliably from eggnog Ortholog database
2077 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2078 containing features of type Highlight' when 'B' is pressed
2079 to mark columns containing highlighted regions.
2082 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2083 doesn't always add secondary structure annotation.
2088 <td width="60" nowrap>
2089 <div align="center">
2090 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2093 <td><div align="left">
2097 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2098 for all consensus calculations
2101 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2104 <li>Updated Jalview's Certum code signing certificate
2107 <em>Application</em>
2110 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2111 set of database cross-references, sorted alphabetically
2114 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2115 from database cross references. Users with custom links
2116 will receive a <a href="webServices/urllinks.html#warning">warning
2117 dialog</a> asking them to update their preferences.
2120 <!-- JAL-2287-->Cancel button and escape listener on
2121 dialog warning user about disconnecting Jalview from a
2125 <!-- JAL-2320-->Jalview's Chimera control window closes if
2126 the Chimera it is connected to is shut down
2129 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2130 columns menu item to mark columns containing highlighted
2131 regions (e.g. from structure selections or results of a
2135 <!-- JAL-2284-->Command line option for batch-generation
2136 of HTML pages rendering alignment data with the BioJS
2146 <!-- JAL-2286 -->Columns with more than one modal residue
2147 are not coloured or thresholded according to percent
2148 identity (first observed in Jalview 2.8.2)
2151 <!-- JAL-2301 -->Threonine incorrectly reported as not
2155 <!-- JAL-2318 -->Updates to documentation pages (above PID
2156 threshold, amino acid properties)
2159 <!-- JAL-2292 -->Lower case residues in sequences are not
2160 reported as mapped to residues in a structure file in the
2164 <!--JAL-2324 -->Identical features with non-numeric scores
2165 could be added multiple times to a sequence
2168 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2169 bond features shown as two highlighted residues rather
2170 than a range in linked structure views, and treated
2171 correctly when selecting and computing trees from features
2174 <!-- JAL-2281-->Custom URL links for database
2175 cross-references are matched to database name regardless
2180 <em>Application</em>
2183 <!-- JAL-2282-->Custom URL links for specific database
2184 names without regular expressions also offer links from
2188 <!-- JAL-2315-->Removing a single configured link in the
2189 URL links pane in Connections preferences doesn't actually
2190 update Jalview configuration
2193 <!-- JAL-2272-->CTRL-Click on a selected region to open
2194 the alignment area popup menu doesn't work on El-Capitan
2197 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2198 files with similarly named sequences if dropped onto the
2202 <!-- JAL-2312 -->Additional mappings are shown for PDB
2203 entries where more chains exist in the PDB accession than
2204 are reported in the SIFTS file
2207 <!-- JAL-2317-->Certain structures do not get mapped to
2208 the structure view when displayed with Chimera
2211 <!-- JAL-2317-->No chains shown in the Chimera view
2212 panel's View->Show Chains submenu
2215 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2216 work for wrapped alignment views
2219 <!--JAL-2197 -->Rename UI components for running JPred
2220 predictions from 'JNet' to 'JPred'
2223 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2224 corrupted when annotation panel vertical scroll is not at
2225 first annotation row
2228 <!--JAL-2332 -->Attempting to view structure for Hen
2229 lysozyme results in a PDB Client error dialog box
2232 <!-- JAL-2319 -->Structure View's mapping report switched
2233 ranges for PDB and sequence for SIFTS
2236 SIFTS 'Not_Observed' residues mapped to non-existant
2240 <!-- <em>New Known Issues</em>
2247 <td width="60" nowrap>
2248 <div align="center">
2249 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2250 <em>25/10/2016</em></strong>
2253 <td><em>Application</em>
2255 <li>3D Structure chooser opens with 'Cached structures'
2256 view if structures already loaded</li>
2257 <li>Progress bar reports models as they are loaded to
2258 structure views</li>
2264 <li>Colour by conservation always enabled and no tick
2265 shown in menu when BLOSUM or PID shading applied</li>
2266 <li>FER1_ARATH and FER2_ARATH labels were switched in
2267 example sequences/projects/trees</li>
2269 <em>Application</em>
2271 <li>Jalview projects with views of local PDB structure
2272 files saved on Windows cannot be opened on OSX</li>
2273 <li>Multiple structure views can be opened and superposed
2274 without timeout for structures with multiple models or
2275 multiple sequences in alignment</li>
2276 <li>Cannot import or associated local PDB files without a
2277 PDB ID HEADER line</li>
2278 <li>RMSD is not output in Jmol console when superposition
2280 <li>Drag and drop of URL from Browser fails for Linux and
2281 OSX versions earlier than El Capitan</li>
2282 <li>ENA client ignores invalid content from ENA server</li>
2283 <li>Exceptions are not raised in console when ENA client
2284 attempts to fetch non-existent IDs via Fetch DB Refs UI
2286 <li>Exceptions are not raised in console when a new view
2287 is created on the alignment</li>
2288 <li>OSX right-click fixed for group selections: CMD-click
2289 to insert/remove gaps in groups and CTRL-click to open group
2292 <em>Build and deployment</em>
2294 <li>URL link checker now copes with multi-line anchor
2297 <em>New Known Issues</em>
2299 <li>Drag and drop from URL links in browsers do not work
2306 <td width="60" nowrap>
2307 <div align="center">
2308 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2311 <td><em>General</em>
2314 <!-- JAL-2124 -->Updated Spanish translations.
2317 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2318 for importing structure data to Jalview. Enables mmCIF and
2322 <!-- JAL-192 --->Alignment ruler shows positions relative to
2326 <!-- JAL-2202 -->Position/residue shown in status bar when
2327 mousing over sequence associated annotation
2330 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2334 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2335 '()', canonical '[]' and invalid '{}' base pair populations
2339 <!-- JAL-2092 -->Feature settings popup menu options for
2340 showing or hiding columns containing a feature
2343 <!-- JAL-1557 -->Edit selected group by double clicking on
2344 group and sequence associated annotation labels
2347 <!-- JAL-2236 -->Sequence name added to annotation label in
2348 select/hide columns by annotation and colour by annotation
2352 </ul> <em>Application</em>
2355 <!-- JAL-2050-->Automatically hide introns when opening a
2356 gene/transcript view
2359 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2363 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2364 structure mappings with the EMBL-EBI PDBe SIFTS database
2367 <!-- JAL-2079 -->Updated download sites used for Rfam and
2368 Pfam sources to xfam.org
2371 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2374 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2375 over sequences in Jalview
2378 <!-- JAL-2027-->Support for reverse-complement coding
2379 regions in ENA and EMBL
2382 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2383 for record retrieval via ENA rest API
2386 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2390 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2391 groovy script execution
2394 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2395 alignment window's Calculate menu
2398 <!-- JAL-1812 -->Allow groovy scripts that call
2399 Jalview.getAlignFrames() to run in headless mode
2402 <!-- JAL-2068 -->Support for creating new alignment
2403 calculation workers from groovy scripts
2406 <!-- JAL-1369 --->Store/restore reference sequence in
2410 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2411 associations are now saved/restored from project
2414 <!-- JAL-1993 -->Database selection dialog always shown
2415 before sequence fetcher is opened
2418 <!-- JAL-2183 -->Double click on an entry in Jalview's
2419 database chooser opens a sequence fetcher
2422 <!-- JAL-1563 -->Free-text search client for UniProt using
2423 the UniProt REST API
2426 <!-- JAL-2168 -->-nonews command line parameter to prevent
2427 the news reader opening
2430 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2431 querying stored in preferences
2434 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2438 <!-- JAL-1977-->Tooltips shown on database chooser
2441 <!-- JAL-391 -->Reverse complement function in calculate
2442 menu for nucleotide sequences
2445 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2446 and feature counts preserves alignment ordering (and
2447 debugged for complex feature sets).
2450 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2451 viewing structures with Jalview 2.10
2454 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2455 genome, transcript CCDS and gene ids via the Ensembl and
2456 Ensembl Genomes REST API
2459 <!-- JAL-2049 -->Protein sequence variant annotation
2460 computed for 'sequence_variant' annotation on CDS regions
2464 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2468 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2469 Ref Fetcher fails to match, or otherwise updates sequence
2470 data from external database records.
2473 <!-- JAL-2154 -->Revised Jalview Project format for
2474 efficient recovery of sequence coding and alignment
2475 annotation relationships.
2477 </ul> <!-- <em>Applet</em>
2488 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2492 <!-- JAL-2018-->Export features in Jalview format (again)
2493 includes graduated colourschemes
2496 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2497 working with big alignments and lots of hidden columns
2500 <!-- JAL-2053-->Hidden column markers not always rendered
2501 at right of alignment window
2504 <!-- JAL-2067 -->Tidied up links in help file table of
2508 <!-- JAL-2072 -->Feature based tree calculation not shown
2512 <!-- JAL-2075 -->Hidden columns ignored during feature
2513 based tree calculation
2516 <!-- JAL-2065 -->Alignment view stops updating when show
2517 unconserved enabled for group on alignment
2520 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2524 <!-- JAL-2146 -->Alignment column in status incorrectly
2525 shown as "Sequence position" when mousing over
2529 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2530 hidden columns present
2533 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2534 user created annotation added to alignment
2537 <!-- JAL-1841 -->RNA Structure consensus only computed for
2538 '()' base pair annotation
2541 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2542 in zero scores for all base pairs in RNA Structure
2546 <!-- JAL-2174-->Extend selection with columns containing
2550 <!-- JAL-2275 -->Pfam format writer puts extra space at
2551 beginning of sequence
2554 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2558 <!-- JAL-2238 -->Cannot create groups on an alignment from
2559 from a tree when t-coffee scores are shown
2562 <!-- JAL-1836,1967 -->Cannot import and view PDB
2563 structures with chains containing negative resnums (4q4h)
2566 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2570 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2571 to Clustal, PIR and PileUp output
2574 <!-- JAL-2008 -->Reordering sequence features that are
2575 not visible causes alignment window to repaint
2578 <!-- JAL-2006 -->Threshold sliders don't work in
2579 graduated colour and colour by annotation row for e-value
2580 scores associated with features and annotation rows
2583 <!-- JAL-1797 -->amino acid physicochemical conservation
2584 calculation should be case independent
2587 <!-- JAL-2173 -->Remove annotation also updates hidden
2591 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2592 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2593 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2596 <!-- JAL-2065 -->Null pointer exceptions and redraw
2597 problems when reference sequence defined and 'show
2598 non-conserved' enabled
2601 <!-- JAL-1306 -->Quality and Conservation are now shown on
2602 load even when Consensus calculation is disabled
2605 <!-- JAL-1932 -->Remove right on penultimate column of
2606 alignment does nothing
2609 <em>Application</em>
2612 <!-- JAL-1552-->URLs and links can't be imported by
2613 drag'n'drop on OSX when launched via webstart (note - not
2614 yet fixed for El Capitan)
2617 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2618 output when running on non-gb/us i18n platforms
2621 <!-- JAL-1944 -->Error thrown when exporting a view with
2622 hidden sequences as flat-file alignment
2625 <!-- JAL-2030-->InstallAnywhere distribution fails when
2629 <!-- JAL-2080-->Jalview very slow to launch via webstart
2630 (also hotfix for 2.9.0b2)
2633 <!-- JAL-2085 -->Cannot save project when view has a
2634 reference sequence defined
2637 <!-- JAL-1011 -->Columns are suddenly selected in other
2638 alignments and views when revealing hidden columns
2641 <!-- JAL-1989 -->Hide columns not mirrored in complement
2642 view in a cDNA/Protein splitframe
2645 <!-- JAL-1369 -->Cannot save/restore representative
2646 sequence from project when only one sequence is
2650 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2651 in Structure Chooser
2654 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2655 structure consensus didn't refresh annotation panel
2658 <!-- JAL-1962 -->View mapping in structure view shows
2659 mappings between sequence and all chains in a PDB file
2662 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2663 dialogs format columns correctly, don't display array
2664 data, sort columns according to type
2667 <!-- JAL-1975 -->Export complete shown after destination
2668 file chooser is cancelled during an image export
2671 <!-- JAL-2025 -->Error when querying PDB Service with
2672 sequence name containing special characters
2675 <!-- JAL-2024 -->Manual PDB structure querying should be
2679 <!-- JAL-2104 -->Large tooltips with broken HTML
2680 formatting don't wrap
2683 <!-- JAL-1128 -->Figures exported from wrapped view are
2684 truncated so L looks like I in consensus annotation
2687 <!-- JAL-2003 -->Export features should only export the
2688 currently displayed features for the current selection or
2692 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2693 after fetching cross-references, and restoring from
2697 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2698 followed in the structure viewer
2701 <!-- JAL-2163 -->Titles for individual alignments in
2702 splitframe not restored from project
2705 <!-- JAL-2145 -->missing autocalculated annotation at
2706 trailing end of protein alignment in transcript/product
2707 splitview when pad-gaps not enabled by default
2710 <!-- JAL-1797 -->amino acid physicochemical conservation
2714 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2715 article has been read (reopened issue due to
2716 internationalisation problems)
2719 <!-- JAL-1960 -->Only offer PDB structures in structure
2720 viewer based on sequence name, PDB and UniProt
2725 <!-- JAL-1976 -->No progress bar shown during export of
2729 <!-- JAL-2213 -->Structures not always superimposed after
2730 multiple structures are shown for one or more sequences.
2733 <!-- JAL-1370 -->Reference sequence characters should not
2734 be replaced with '.' when 'Show unconserved' format option
2738 <!-- JAL-1823 -->Cannot specify chain code when entering
2739 specific PDB id for sequence
2742 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2743 'Export hidden sequences' is enabled, but 'export hidden
2744 columns' is disabled.
2747 <!--JAL-2026-->Best Quality option in structure chooser
2748 selects lowest rather than highest resolution structures
2752 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2753 to sequence mapping in 'View Mappings' report
2756 <!-- JAL-2284 -->Unable to read old Jalview projects that
2757 contain non-XML data added after Jalvew wrote project.
2760 <!-- JAL-2118 -->Newly created annotation row reorders
2761 after clicking on it to create new annotation for a
2765 <!-- JAL-1980 -->Null Pointer Exception raised when
2766 pressing Add on an orphaned cut'n'paste window.
2768 <!-- may exclude, this is an external service stability issue JAL-1941
2769 -- > RNA 3D structure not added via DSSR service</li> -->
2774 <!-- JAL-2151 -->Incorrect columns are selected when
2775 hidden columns present before start of sequence
2778 <!-- JAL-1986 -->Missing dependencies on applet pages
2782 <!-- JAL-1947 -->Overview pixel size changes when
2783 sequences are hidden in applet
2786 <!-- JAL-1996 -->Updated instructions for applet
2787 deployment on examples pages.
2794 <td width="60" nowrap>
2795 <div align="center">
2796 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2797 <em>16/10/2015</em></strong>
2800 <td><em>General</em>
2802 <li>Time stamps for signed Jalview application and applet
2807 <em>Application</em>
2809 <li>Duplicate group consensus and conservation rows
2810 shown when tree is partitioned</li>
2811 <li>Erratic behaviour when tree partitions made with
2812 multiple cDNA/Protein split views</li>
2818 <td width="60" nowrap>
2819 <div align="center">
2820 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2821 <em>8/10/2015</em></strong>
2824 <td><em>General</em>
2826 <li>Updated Spanish translations of localized text for
2828 </ul> <em>Application</em>
2830 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2831 <li>Signed OSX InstallAnywhere installer<br></li>
2832 <li>Support for per-sequence based annotations in BioJSON</li>
2833 </ul> <em>Applet</em>
2835 <li>Split frame example added to applet examples page</li>
2836 </ul> <em>Build and Deployment</em>
2839 <!-- JAL-1888 -->New ant target for running Jalview's test
2847 <li>Mapping of cDNA to protein in split frames
2848 incorrect when sequence start > 1</li>
2849 <li>Broken images in filter column by annotation dialog
2851 <li>Feature colours not parsed from features file</li>
2852 <li>Exceptions and incomplete link URLs recovered when
2853 loading a features file containing HTML tags in feature
2857 <em>Application</em>
2859 <li>Annotations corrupted after BioJS export and
2861 <li>Incorrect sequence limits after Fetch DB References
2862 with 'trim retrieved sequences'</li>
2863 <li>Incorrect warning about deleting all data when
2864 deleting selected columns</li>
2865 <li>Patch to build system for shipping properly signed
2866 JNLP templates for webstart launch</li>
2867 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2868 unreleased structures for download or viewing</li>
2869 <li>Tab/space/return keystroke operation of EMBL-PDBe
2870 fetcher/viewer dialogs works correctly</li>
2871 <li>Disabled 'minimise' button on Jalview windows
2872 running on OSX to workaround redraw hang bug</li>
2873 <li>Split cDNA/Protein view position and geometry not
2874 recovered from jalview project</li>
2875 <li>Initial enabled/disabled state of annotation menu
2876 sorter 'show autocalculated first/last' corresponds to
2878 <li>Restoring of Clustal, RNA Helices and T-Coffee
2879 color schemes from BioJSON</li>
2883 <li>Reorder sequences mirrored in cDNA/Protein split
2885 <li>Applet with Jmol examples not loading correctly</li>
2891 <td><div align="center">
2892 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2894 <td><em>General</em>
2896 <li>Linked visualisation and analysis of DNA and Protein
2899 <li>Translated cDNA alignments shown as split protein
2900 and DNA alignment views</li>
2901 <li>Codon consensus annotation for linked protein and
2902 cDNA alignment views</li>
2903 <li>Link cDNA or Protein product sequences by loading
2904 them onto Protein or cDNA alignments</li>
2905 <li>Reconstruct linked cDNA alignment from aligned
2906 protein sequences</li>
2909 <li>Jmol integration updated to Jmol v14.2.14</li>
2910 <li>Import and export of Jalview alignment views as <a
2911 href="features/bioJsonFormat.html">BioJSON</a></li>
2912 <li>New alignment annotation file statements for
2913 reference sequences and marking hidden columns</li>
2914 <li>Reference sequence based alignment shading to
2915 highlight variation</li>
2916 <li>Select or hide columns according to alignment
2918 <li>Find option for locating sequences by description</li>
2919 <li>Conserved physicochemical properties shown in amino
2920 acid conservation row</li>
2921 <li>Alignments can be sorted by number of RNA helices</li>
2922 </ul> <em>Application</em>
2924 <li>New cDNA/Protein analysis capabilities
2926 <li>Get Cross-References should open a Split Frame
2927 view with cDNA/Protein</li>
2928 <li>Detect when nucleotide sequences and protein
2929 sequences are placed in the same alignment</li>
2930 <li>Split cDNA/Protein views are saved in Jalview
2935 <li>Use REST API to talk to Chimera</li>
2936 <li>Selected regions in Chimera are highlighted in linked
2937 Jalview windows</li>
2939 <li>VARNA RNA viewer updated to v3.93</li>
2940 <li>VARNA views are saved in Jalview Projects</li>
2941 <li>Pseudoknots displayed as Jalview RNA annotation can
2942 be shown in VARNA</li>
2944 <li>Make groups for selection uses marked columns as well
2945 as the active selected region</li>
2947 <li>Calculate UPGMA and NJ trees using sequence feature
2949 <li>New Export options
2951 <li>New Export Settings dialog to control hidden
2952 region export in flat file generation</li>
2954 <li>Export alignment views for display with the <a
2955 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2957 <li>Export scrollable SVG in HTML page</li>
2958 <li>Optional embedding of BioJSON data when exporting
2959 alignment figures to HTML</li>
2961 <li>3D structure retrieval and display
2963 <li>Free text and structured queries with the PDBe
2965 <li>PDBe Search API based discovery and selection of
2966 PDB structures for a sequence set</li>
2970 <li>JPred4 employed for protein secondary structure
2972 <li>Hide Insertions menu option to hide unaligned columns
2973 for one or a group of sequences</li>
2974 <li>Automatically hide insertions in alignments imported
2975 from the JPred4 web server</li>
2976 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2977 system on OSX<br />LGPL libraries courtesy of <a
2978 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2980 <li>changed 'View nucleotide structure' submenu to 'View
2981 VARNA 2D Structure'</li>
2982 <li>change "View protein structure" menu option to "3D
2985 </ul> <em>Applet</em>
2987 <li>New layout for applet example pages</li>
2988 <li>New parameters to enable SplitFrame view
2989 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2990 <li>New example demonstrating linked viewing of cDNA and
2991 Protein alignments</li>
2992 </ul> <em>Development and deployment</em>
2994 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2995 <li>Include installation type and git revision in build
2996 properties and console log output</li>
2997 <li>Jalview Github organisation, and new github site for
2998 storing BioJsMSA Templates</li>
2999 <li>Jalview's unit tests now managed with TestNG</li>
3002 <!-- <em>General</em>
3004 </ul> --> <!-- issues resolved --> <em>Application</em>
3006 <li>Escape should close any open find dialogs</li>
3007 <li>Typo in select-by-features status report</li>
3008 <li>Consensus RNA secondary secondary structure
3009 predictions are not highlighted in amber</li>
3010 <li>Missing gap character in v2.7 example file means
3011 alignment appears unaligned when pad-gaps is not enabled</li>
3012 <li>First switch to RNA Helices colouring doesn't colour
3013 associated structure views</li>
3014 <li>ID width preference option is greyed out when auto
3015 width checkbox not enabled</li>
3016 <li>Stopped a warning dialog from being shown when
3017 creating user defined colours</li>
3018 <li>'View Mapping' in structure viewer shows sequence
3019 mappings for just that viewer's sequences</li>
3020 <li>Workaround for superposing PDB files containing
3021 multiple models in Chimera</li>
3022 <li>Report sequence position in status bar when hovering
3023 over Jmol structure</li>
3024 <li>Cannot output gaps as '.' symbols with Selection ->
3025 output to text box</li>
3026 <li>Flat file exports of alignments with hidden columns
3027 have incorrect sequence start/end</li>
3028 <li>'Aligning' a second chain to a Chimera structure from
3030 <li>Colour schemes applied to structure viewers don't
3031 work for nucleotide</li>
3032 <li>Loading/cut'n'pasting an empty or invalid file leads
3033 to a grey/invisible alignment window</li>
3034 <li>Exported Jpred annotation from a sequence region
3035 imports to different position</li>
3036 <li>Space at beginning of sequence feature tooltips shown
3037 on some platforms</li>
3038 <li>Chimera viewer 'View | Show Chain' menu is not
3040 <li>'New View' fails with a Null Pointer Exception in
3041 console if Chimera has been opened</li>
3042 <li>Mouseover to Chimera not working</li>
3043 <li>Miscellaneous ENA XML feature qualifiers not
3045 <li>NPE in annotation renderer after 'Extract Scores'</li>
3046 <li>If two structures in one Chimera window, mouseover of
3047 either sequence shows on first structure</li>
3048 <li>'Show annotations' options should not make
3049 non-positional annotations visible</li>
3050 <li>Subsequence secondary structure annotation not shown
3051 in right place after 'view flanking regions'</li>
3052 <li>File Save As type unset when current file format is
3054 <li>Save as '.jar' option removed for saving Jalview
3056 <li>Colour by Sequence colouring in Chimera more
3058 <li>Cannot 'add reference annotation' for a sequence in
3059 several views on same alignment</li>
3060 <li>Cannot show linked products for EMBL / ENA records</li>
3061 <li>Jalview's tooltip wraps long texts containing no
3063 </ul> <em>Applet</em>
3065 <li>Jmol to JalviewLite mouseover/link not working</li>
3066 <li>JalviewLite can't import sequences with ID
3067 descriptions containing angle brackets</li>
3068 </ul> <em>General</em>
3070 <li>Cannot export and reimport RNA secondary structure
3071 via jalview annotation file</li>
3072 <li>Random helix colour palette for colour by annotation
3073 with RNA secondary structure</li>
3074 <li>Mouseover to cDNA from STOP residue in protein
3075 translation doesn't work.</li>
3076 <li>hints when using the select by annotation dialog box</li>
3077 <li>Jmol alignment incorrect if PDB file has alternate CA
3079 <li>FontChooser message dialog appears to hang after
3080 choosing 1pt font</li>
3081 <li>Peptide secondary structure incorrectly imported from
3082 annotation file when annotation display text includes 'e' or
3084 <li>Cannot set colour of new feature type whilst creating
3086 <li>cDNA translation alignment should not be sequence
3087 order dependent</li>
3088 <li>'Show unconserved' doesn't work for lower case
3090 <li>Nucleotide ambiguity codes involving R not recognised</li>
3091 </ul> <em>Deployment and Documentation</em>
3093 <li>Applet example pages appear different to the rest of
3094 www.jalview.org</li>
3095 </ul> <em>Application Known issues</em>
3097 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3098 <li>Misleading message appears after trying to delete
3100 <li>Jalview icon not shown in dock after InstallAnywhere
3101 version launches</li>
3102 <li>Fetching EMBL reference for an RNA sequence results
3103 fails with a sequence mismatch</li>
3104 <li>Corrupted or unreadable alignment display when
3105 scrolling alignment to right</li>
3106 <li>ArrayIndexOutOfBoundsException thrown when remove
3107 empty columns called on alignment with ragged gapped ends</li>
3108 <li>auto calculated alignment annotation rows do not get
3109 placed above or below non-autocalculated rows</li>
3110 <li>Jalview dekstop becomes sluggish at full screen in
3111 ultra-high resolution</li>
3112 <li>Cannot disable consensus calculation independently of
3113 quality and conservation</li>
3114 <li>Mouseover highlighting between cDNA and protein can
3115 become sluggish with more than one splitframe shown</li>
3116 </ul> <em>Applet Known Issues</em>
3118 <li>Core PDB parsing code requires Jmol</li>
3119 <li>Sequence canvas panel goes white when alignment
3120 window is being resized</li>
3126 <td><div align="center">
3127 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3129 <td><em>General</em>
3131 <li>Updated Java code signing certificate donated by
3133 <li>Features and annotation preserved when performing
3134 pairwise alignment</li>
3135 <li>RNA pseudoknot annotation can be
3136 imported/exported/displayed</li>
3137 <li>'colour by annotation' can colour by RNA and
3138 protein secondary structure</li>
3139 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3140 post-hoc with 2.9 release</em>)
3143 </ul> <em>Application</em>
3145 <li>Extract and display secondary structure for sequences
3146 with 3D structures</li>
3147 <li>Support for parsing RNAML</li>
3148 <li>Annotations menu for layout
3150 <li>sort sequence annotation rows by alignment</li>
3151 <li>place sequence annotation above/below alignment
3154 <li>Output in Stockholm format</li>
3155 <li>Internationalisation: improved Spanish (es)
3157 <li>Structure viewer preferences tab</li>
3158 <li>Disorder and Secondary Structure annotation tracks
3159 shared between alignments</li>
3160 <li>UCSF Chimera launch and linked highlighting from
3162 <li>Show/hide all sequence associated annotation rows for
3163 all or current selection</li>
3164 <li>disorder and secondary structure predictions
3165 available as dataset annotation</li>
3166 <li>Per-sequence rna helices colouring</li>
3169 <li>Sequence database accessions imported when fetching
3170 alignments from Rfam</li>
3171 <li>update VARNA version to 3.91</li>
3173 <li>New groovy scripts for exporting aligned positions,
3174 conservation values, and calculating sum of pairs scores.</li>
3175 <li>Command line argument to set default JABAWS server</li>
3176 <li>include installation type in build properties and
3177 console log output</li>
3178 <li>Updated Jalview project format to preserve dataset
3182 <!-- issues resolved --> <em>Application</em>
3184 <li>Distinguish alignment and sequence associated RNA
3185 structure in structure->view->VARNA</li>
3186 <li>Raise dialog box if user deletes all sequences in an
3188 <li>Pressing F1 results in documentation opening twice</li>
3189 <li>Sequence feature tooltip is wrapped</li>
3190 <li>Double click on sequence associated annotation
3191 selects only first column</li>
3192 <li>Redundancy removal doesn't result in unlinked
3193 leaves shown in tree</li>
3194 <li>Undos after several redundancy removals don't undo
3196 <li>Hide sequence doesn't hide associated annotation</li>
3197 <li>User defined colours dialog box too big to fit on
3198 screen and buttons not visible</li>
3199 <li>author list isn't updated if already written to
3200 Jalview properties</li>
3201 <li>Popup menu won't open after retrieving sequence
3203 <li>File open window for associate PDB doesn't open</li>
3204 <li>Left-then-right click on a sequence id opens a
3205 browser search window</li>
3206 <li>Cannot open sequence feature shading/sort popup menu
3207 in feature settings dialog</li>
3208 <li>better tooltip placement for some areas of Jalview
3210 <li>Allow addition of JABAWS Server which doesn't
3211 pass validation</li>
3212 <li>Web services parameters dialog box is too large to
3214 <li>Muscle nucleotide alignment preset obscured by
3216 <li>JABAWS preset submenus don't contain newly
3217 defined user preset</li>
3218 <li>MSA web services warns user if they were launched
3219 with invalid input</li>
3220 <li>Jalview cannot contact DAS Registy when running on
3223 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3224 'Superpose with' submenu not shown when new view
3228 </ul> <!-- <em>Applet</em>
3230 </ul> <em>General</em>
3232 </ul>--> <em>Deployment and Documentation</em>
3234 <li>2G and 1G options in launchApp have no effect on
3235 memory allocation</li>
3236 <li>launchApp service doesn't automatically open
3237 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3239 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3240 InstallAnywhere reports cannot find valid JVM when Java
3241 1.7_055 is available
3243 </ul> <em>Application Known issues</em>
3246 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3247 corrupted or unreadable alignment display when scrolling
3251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3252 retrieval fails but progress bar continues for DAS retrieval
3253 with large number of ID
3256 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3257 flatfile output of visible region has incorrect sequence
3261 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3262 rna structure consensus doesn't update when secondary
3263 structure tracks are rearranged
3266 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3267 invalid rna structure positional highlighting does not
3268 highlight position of invalid base pairs
3271 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3272 out of memory errors are not raised when saving Jalview
3273 project from alignment window file menu
3276 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3277 Switching to RNA Helices colouring doesn't propagate to
3281 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3282 colour by RNA Helices not enabled when user created
3283 annotation added to alignment
3286 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3287 Jalview icon not shown on dock in Mountain Lion/Webstart
3289 </ul> <em>Applet Known Issues</em>
3292 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3293 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3296 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3297 Jalview and Jmol example not compatible with IE9
3300 <li>Sort by annotation score doesn't reverse order
3306 <td><div align="center">
3307 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3310 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3313 <li>Internationalisation of user interface (usually
3314 called i18n support) and translation for Spanish locale</li>
3315 <li>Define/Undefine group on current selection with
3316 Ctrl-G/Shift Ctrl-G</li>
3317 <li>Improved group creation/removal options in
3318 alignment/sequence Popup menu</li>
3319 <li>Sensible precision for symbol distribution
3320 percentages shown in logo tooltip.</li>
3321 <li>Annotation panel height set according to amount of
3322 annotation when alignment first opened</li>
3323 </ul> <em>Application</em>
3325 <li>Interactive consensus RNA secondary structure
3326 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3327 <li>Select columns containing particular features from
3328 Feature Settings dialog</li>
3329 <li>View all 'representative' PDB structures for selected
3331 <li>Update Jalview project format:
3333 <li>New file extension for Jalview projects '.jvp'</li>
3334 <li>Preserve sequence and annotation dataset (to
3335 store secondary structure annotation,etc)</li>
3336 <li>Per group and alignment annotation and RNA helix
3340 <li>New similarity measures for PCA and Tree calculation
3342 <li>Experimental support for retrieval and viewing of
3343 flanking regions for an alignment</li>
3347 <!-- issues resolved --> <em>Application</em>
3349 <li>logo keeps spinning and status remains at queued or
3350 running after job is cancelled</li>
3351 <li>cannot export features from alignments imported from
3352 Jalview/VAMSAS projects</li>
3353 <li>Buggy slider for web service parameters that take
3355 <li>Newly created RNA secondary structure line doesn't
3356 have 'display all symbols' flag set</li>
3357 <li>T-COFFEE alignment score shading scheme and other
3358 annotation shading not saved in Jalview project</li>
3359 <li>Local file cannot be loaded in freshly downloaded
3361 <li>Jalview icon not shown on dock in Mountain
3363 <li>Load file from desktop file browser fails</li>
3364 <li>Occasional NPE thrown when calculating large trees</li>
3365 <li>Cannot reorder or slide sequences after dragging an
3366 alignment onto desktop</li>
3367 <li>Colour by annotation dialog throws NPE after using
3368 'extract scores' function</li>
3369 <li>Loading/cut'n'pasting an empty file leads to a grey
3370 alignment window</li>
3371 <li>Disorder thresholds rendered incorrectly after
3372 performing IUPred disorder prediction</li>
3373 <li>Multiple group annotated consensus rows shown when
3374 changing 'normalise logo' display setting</li>
3375 <li>Find shows blank dialog after 'finished searching' if
3376 nothing matches query</li>
3377 <li>Null Pointer Exceptions raised when sorting by
3378 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3380 <li>Errors in Jmol console when structures in alignment
3381 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3383 <li>Not all working JABAWS services are shown in
3385 <li>JAVAWS version of Jalview fails to launch with
3386 'invalid literal/length code'</li>
3387 <li>Annotation/RNA Helix colourschemes cannot be applied
3388 to alignment with groups (actually fixed in 2.8.0b1)</li>
3389 <li>RNA Helices and T-Coffee Scores available as default
3392 </ul> <em>Applet</em>
3394 <li>Remove group option is shown even when selection is
3396 <li>Apply to all groups ticked but colourscheme changes
3397 don't affect groups</li>
3398 <li>Documented RNA Helices and T-Coffee Scores as valid
3399 colourscheme name</li>
3400 <li>Annotation labels drawn on sequence IDs when
3401 Annotation panel is not displayed</li>
3402 <li>Increased font size for dropdown menus on OSX and
3403 embedded windows</li>
3404 </ul> <em>Other</em>
3406 <li>Consensus sequence for alignments/groups with a
3407 single sequence were not calculated</li>
3408 <li>annotation files that contain only groups imported as
3409 annotation and junk sequences</li>
3410 <li>Fasta files with sequences containing '*' incorrectly
3411 recognised as PFAM or BLC</li>
3412 <li>conservation/PID slider apply all groups option
3413 doesn't affect background (2.8.0b1)
3415 <li>redundancy highlighting is erratic at 0% and 100%</li>
3416 <li>Remove gapped columns fails for sequences with ragged
3418 <li>AMSA annotation row with leading spaces is not
3419 registered correctly on import</li>
3420 <li>Jalview crashes when selecting PCA analysis for
3421 certain alignments</li>
3422 <li>Opening the colour by annotation dialog for an
3423 existing annotation based 'use original colours'
3424 colourscheme loses original colours setting</li>
3429 <td><div align="center">
3430 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3431 <em>30/1/2014</em></strong>
3435 <li>Trusted certificates for JalviewLite applet and
3436 Jalview Desktop application<br />Certificate was donated by
3437 <a href="https://www.certum.eu">Certum</a> to the Jalview
3438 open source project).
3440 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3441 <li>Output in Stockholm format</li>
3442 <li>Allow import of data from gzipped files</li>
3443 <li>Export/import group and sequence associated line
3444 graph thresholds</li>
3445 <li>Nucleotide substitution matrix that supports RNA and
3446 ambiguity codes</li>
3447 <li>Allow disorder predictions to be made on the current
3448 selection (or visible selection) in the same way that JPred
3450 <li>Groovy scripting for headless Jalview operation</li>
3451 </ul> <em>Other improvements</em>
3453 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3454 <li>COMBINE statement uses current SEQUENCE_REF and
3455 GROUP_REF scope to group annotation rows</li>
3456 <li>Support '' style escaping of quotes in Newick
3458 <li>Group options for JABAWS service by command line name</li>
3459 <li>Empty tooltip shown for JABA service options with a
3460 link but no description</li>
3461 <li>Select primary source when selecting authority in
3462 database fetcher GUI</li>
3463 <li>Add .mfa to FASTA file extensions recognised by
3465 <li>Annotation label tooltip text wrap</li>
3470 <li>Slow scrolling when lots of annotation rows are
3472 <li>Lots of NPE (and slowness) after creating RNA
3473 secondary structure annotation line</li>
3474 <li>Sequence database accessions not imported when
3475 fetching alignments from Rfam</li>
3476 <li>Incorrect SHMR submission for sequences with
3478 <li>View all structures does not always superpose
3480 <li>Option widgets in service parameters not updated to
3481 reflect user or preset settings</li>
3482 <li>Null pointer exceptions for some services without
3483 presets or adjustable parameters</li>
3484 <li>Discover PDB IDs entry in structure menu doesn't
3485 discover PDB xRefs</li>
3486 <li>Exception encountered while trying to retrieve
3487 features with DAS</li>
3488 <li>Lowest value in annotation row isn't coloured
3489 when colour by annotation (per sequence) is coloured</li>
3490 <li>Keyboard mode P jumps to start of gapped region when
3491 residue follows a gap</li>
3492 <li>Jalview appears to hang importing an alignment with
3493 Wrap as default or after enabling Wrap</li>
3494 <li>'Right click to add annotations' message
3495 shown in wrap mode when no annotations present</li>
3496 <li>Disorder predictions fail with NPE if no automatic
3497 annotation already exists on alignment</li>
3498 <li>oninit javascript function should be called after
3499 initialisation completes</li>
3500 <li>Remove redundancy after disorder prediction corrupts
3501 alignment window display</li>
3502 <li>Example annotation file in documentation is invalid</li>
3503 <li>Grouped line graph annotation rows are not exported
3504 to annotation file</li>
3505 <li>Multi-harmony analysis cannot be run when only two
3507 <li>Cannot create multiple groups of line graphs with
3508 several 'combine' statements in annotation file</li>
3509 <li>Pressing return several times causes Number Format
3510 exceptions in keyboard mode</li>
3511 <li>Multi-harmony (SHMMR) method doesn't submit
3512 correct partitions for input data</li>
3513 <li>Translation from DNA to Amino Acids fails</li>
3514 <li>Jalview fail to load newick tree with quoted label</li>
3515 <li>--headless flag isn't understood</li>
3516 <li>ClassCastException when generating EPS in headless
3518 <li>Adjusting sequence-associated shading threshold only
3519 changes one row's threshold</li>
3520 <li>Preferences and Feature settings panel panel
3521 doesn't open</li>
3522 <li>hide consensus histogram also hides conservation and
3523 quality histograms</li>
3528 <td><div align="center">
3529 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3531 <td><em>Application</em>
3533 <li>Support for JABAWS 2.0 Services (AACon alignment
3534 conservation, protein disorder and Clustal Omega)</li>
3535 <li>JABAWS server status indicator in Web Services
3537 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3538 in Jalview alignment window</li>
3539 <li>Updated Jalview build and deploy framework for OSX
3540 mountain lion, windows 7, and 8</li>
3541 <li>Nucleotide substitution matrix for PCA that supports
3542 RNA and ambiguity codes</li>
3544 <li>Improved sequence database retrieval GUI</li>
3545 <li>Support fetching and database reference look up
3546 against multiple DAS sources (Fetch all from in 'fetch db
3548 <li>Jalview project improvements
3550 <li>Store and retrieve the 'belowAlignment'
3551 flag for annotation</li>
3552 <li>calcId attribute to group annotation rows on the
3554 <li>Store AACon calculation settings for a view in
3555 Jalview project</li>
3559 <li>horizontal scrolling gesture support</li>
3560 <li>Visual progress indicator when PCA calculation is
3562 <li>Simpler JABA web services menus</li>
3563 <li>visual indication that web service results are still
3564 being retrieved from server</li>
3565 <li>Serialise the dialogs that are shown when Jalview
3566 starts up for first time</li>
3567 <li>Jalview user agent string for interacting with HTTP
3569 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3571 <li>Examples directory and Groovy library included in
3572 InstallAnywhere distribution</li>
3573 </ul> <em>Applet</em>
3575 <li>RNA alignment and secondary structure annotation
3576 visualization applet example</li>
3577 </ul> <em>General</em>
3579 <li>Normalise option for consensus sequence logo</li>
3580 <li>Reset button in PCA window to return dimensions to
3582 <li>Allow seqspace or Jalview variant of alignment PCA
3584 <li>PCA with either nucleic acid and protein substitution
3586 <li>Allow windows containing HTML reports to be exported
3588 <li>Interactive display and editing of RNA secondary
3589 structure contacts</li>
3590 <li>RNA Helix Alignment Colouring</li>
3591 <li>RNA base pair logo consensus</li>
3592 <li>Parse sequence associated secondary structure
3593 information in Stockholm files</li>
3594 <li>HTML Export database accessions and annotation
3595 information presented in tooltip for sequences</li>
3596 <li>Import secondary structure from LOCARNA clustalw
3597 style RNA alignment files</li>
3598 <li>import and visualise T-COFFEE quality scores for an
3600 <li>'colour by annotation' per sequence option to
3601 shade each sequence according to its associated alignment
3603 <li>New Jalview Logo</li>
3604 </ul> <em>Documentation and Development</em>
3606 <li>documentation for score matrices used in Jalview</li>
3607 <li>New Website!</li>
3609 <td><em>Application</em>
3611 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3612 wsdbfetch REST service</li>
3613 <li>Stop windows being moved outside desktop on OSX</li>
3614 <li>Filetype associations not installed for webstart
3616 <li>Jalview does not always retrieve progress of a JABAWS
3617 job execution in full once it is complete</li>
3618 <li>revise SHMR RSBS definition to ensure alignment is
3619 uploaded via ali_file parameter</li>
3620 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3621 <li>View all structures superposed fails with exception</li>
3622 <li>Jnet job queues forever if a very short sequence is
3623 submitted for prediction</li>
3624 <li>Cut and paste menu not opened when mouse clicked on
3626 <li>Putting fractional value into integer text box in
3627 alignment parameter dialog causes Jalview to hang</li>
3628 <li>Structure view highlighting doesn't work on
3630 <li>View all structures fails with exception shown in
3632 <li>Characters in filename associated with PDBEntry not
3633 escaped in a platform independent way</li>
3634 <li>Jalview desktop fails to launch with exception when
3636 <li>Tree calculation reports 'you must have 2 or more
3637 sequences selected' when selection is empty</li>
3638 <li>Jalview desktop fails to launch with jar signature
3639 failure when java web start temporary file caching is
3641 <li>DAS Sequence retrieval with range qualification
3642 results in sequence xref which includes range qualification</li>
3643 <li>Errors during processing of command line arguments
3644 cause progress bar (JAL-898) to be removed</li>
3645 <li>Replace comma for semi-colon option not disabled for
3646 DAS sources in sequence fetcher</li>
3647 <li>Cannot close news reader when JABAWS server warning
3648 dialog is shown</li>
3649 <li>Option widgets not updated to reflect user settings</li>
3650 <li>Edited sequence not submitted to web service</li>
3651 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3652 <li>InstallAnywhere installer doesn't unpack and run
3653 on OSX Mountain Lion</li>
3654 <li>Annotation panel not given a scroll bar when
3655 sequences with alignment annotation are pasted into the
3657 <li>Sequence associated annotation rows not associated
3658 when loaded from Jalview project</li>
3659 <li>Browser launch fails with NPE on java 1.7</li>
3660 <li>JABAWS alignment marked as finished when job was
3661 cancelled or job failed due to invalid input</li>
3662 <li>NPE with v2.7 example when clicking on Tree
3663 associated with all views</li>
3664 <li>Exceptions when copy/paste sequences with grouped
3665 annotation rows to new window</li>
3666 </ul> <em>Applet</em>
3668 <li>Sequence features are momentarily displayed before
3669 they are hidden using hidefeaturegroups applet parameter</li>
3670 <li>loading features via javascript API automatically
3671 enables feature display</li>
3672 <li>scrollToColumnIn javascript API method doesn't
3674 </ul> <em>General</em>
3676 <li>Redundancy removal fails for rna alignment</li>
3677 <li>PCA calculation fails when sequence has been selected
3678 and then deselected</li>
3679 <li>PCA window shows grey box when first opened on OSX</li>
3680 <li>Letters coloured pink in sequence logo when alignment
3681 coloured with clustalx</li>
3682 <li>Choosing fonts without letter symbols defined causes
3683 exceptions and redraw errors</li>
3684 <li>Initial PCA plot view is not same as manually
3685 reconfigured view</li>
3686 <li>Grouped annotation graph label has incorrect line
3688 <li>Grouped annotation graph label display is corrupted
3689 for lots of labels</li>
3694 <div align="center">
3695 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3698 <td><em>Application</em>
3700 <li>Jalview Desktop News Reader</li>
3701 <li>Tweaked default layout of web services menu</li>
3702 <li>View/alignment association menu to enable user to
3703 easily specify which alignment a multi-structure view takes
3704 its colours/correspondences from</li>
3705 <li>Allow properties file location to be specified as URL</li>
3706 <li>Extend Jalview project to preserve associations
3707 between many alignment views and a single Jmol display</li>
3708 <li>Store annotation row height in Jalview project file</li>
3709 <li>Annotation row column label formatting attributes
3710 stored in project file</li>
3711 <li>Annotation row order for auto-calculated annotation
3712 rows preserved in Jalview project file</li>
3713 <li>Visual progress indication when Jalview state is
3714 saved using Desktop window menu</li>
3715 <li>Visual indication that command line arguments are
3716 still being processed</li>
3717 <li>Groovy script execution from URL</li>
3718 <li>Colour by annotation default min and max colours in
3720 <li>Automatically associate PDB files dragged onto an
3721 alignment with sequences that have high similarity and
3723 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3724 <li>'view structures' option to open many
3725 structures in same window</li>
3726 <li>Sort associated views menu option for tree panel</li>
3727 <li>Group all JABA and non-JABA services for a particular
3728 analysis function in its own submenu</li>
3729 </ul> <em>Applet</em>
3731 <li>Userdefined and autogenerated annotation rows for
3733 <li>Adjustment of alignment annotation pane height</li>
3734 <li>Annotation scrollbar for annotation panel</li>
3735 <li>Drag to reorder annotation rows in annotation panel</li>
3736 <li>'automaticScrolling' parameter</li>
3737 <li>Allow sequences with partial ID string matches to be
3738 annotated from GFF/Jalview features files</li>
3739 <li>Sequence logo annotation row in applet</li>
3740 <li>Absolute paths relative to host server in applet
3741 parameters are treated as such</li>
3742 <li>New in the JalviewLite javascript API:
3744 <li>JalviewLite.js javascript library</li>
3745 <li>Javascript callbacks for
3747 <li>Applet initialisation</li>
3748 <li>Sequence/alignment mouse-overs and selections</li>
3751 <li>scrollTo row and column alignment scrolling
3753 <li>Select sequence/alignment regions from javascript</li>
3754 <li>javascript structure viewer harness to pass
3755 messages between Jmol and Jalview when running as
3756 distinct applets</li>
3757 <li>sortBy method</li>
3758 <li>Set of applet and application examples shipped
3759 with documentation</li>
3760 <li>New example to demonstrate JalviewLite and Jmol
3761 javascript message exchange</li>
3763 </ul> <em>General</em>
3765 <li>Enable Jmol displays to be associated with multiple
3766 multiple alignments</li>
3767 <li>Option to automatically sort alignment with new tree</li>
3768 <li>User configurable link to enable redirects to a
3769 www.Jalview.org mirror</li>
3770 <li>Jmol colours option for Jmol displays</li>
3771 <li>Configurable newline string when writing alignment
3772 and other flat files</li>
3773 <li>Allow alignment annotation description lines to
3774 contain html tags</li>
3775 </ul> <em>Documentation and Development</em>
3777 <li>Add groovy test harness for bulk load testing to
3779 <li>Groovy script to load and align a set of sequences
3780 using a web service before displaying the result in the
3781 Jalview desktop</li>
3782 <li>Restructured javascript and applet api documentation</li>
3783 <li>Ant target to publish example html files with applet
3785 <li>Netbeans project for building Jalview from source</li>
3786 <li>ant task to create online javadoc for Jalview source</li>
3788 <td><em>Application</em>
3790 <li>User defined colourscheme throws exception when
3791 current built in colourscheme is saved as new scheme</li>
3792 <li>AlignFrame->Save in application pops up save
3793 dialog for valid filename/format</li>
3794 <li>Cannot view associated structure for UniProt sequence</li>
3795 <li>PDB file association breaks for UniProt sequence
3797 <li>Associate PDB from file dialog does not tell you
3798 which sequence is to be associated with the file</li>
3799 <li>Find All raises null pointer exception when query
3800 only matches sequence IDs</li>
3801 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3802 <li>Jalview project with Jmol views created with Jalview
3803 2.4 cannot be loaded</li>
3804 <li>Filetype associations not installed for webstart
3806 <li>Two or more chains in a single PDB file associated
3807 with sequences in different alignments do not get coloured
3808 by their associated sequence</li>
3809 <li>Visibility status of autocalculated annotation row
3810 not preserved when project is loaded</li>
3811 <li>Annotation row height and visibility attributes not
3812 stored in Jalview project</li>
3813 <li>Tree bootstraps are not preserved when saved as a
3814 Jalview project</li>
3815 <li>Envision2 workflow tooltips are corrupted</li>
3816 <li>Enabling show group conservation also enables colour
3817 by conservation</li>
3818 <li>Duplicate group associated conservation or consensus
3819 created on new view</li>
3820 <li>Annotation scrollbar not displayed after 'show
3821 all hidden annotation rows' option selected</li>
3822 <li>Alignment quality not updated after alignment
3823 annotation row is hidden then shown</li>
3824 <li>Preserve colouring of structures coloured by
3825 sequences in pre Jalview 2.7 projects</li>
3826 <li>Web service job parameter dialog is not laid out
3828 <li>Web services menu not refreshed after 'reset
3829 services' button is pressed in preferences</li>
3830 <li>Annotation off by one in Jalview v2_3 example project</li>
3831 <li>Structures imported from file and saved in project
3832 get name like jalview_pdb1234.txt when reloaded</li>
3833 <li>Jalview does not always retrieve progress of a JABAWS
3834 job execution in full once it is complete</li>
3835 </ul> <em>Applet</em>
3837 <li>Alignment height set incorrectly when lots of
3838 annotation rows are displayed</li>
3839 <li>Relative URLs in feature HTML text not resolved to
3841 <li>View follows highlighting does not work for positions
3843 <li><= shown as = in tooltip</li>
3844 <li>Export features raises exception when no features
3846 <li>Separator string used for serialising lists of IDs
3847 for javascript api is modified when separator string
3848 provided as parameter</li>
3849 <li>Null pointer exception when selecting tree leaves for
3850 alignment with no existing selection</li>
3851 <li>Relative URLs for datasources assumed to be relative
3852 to applet's codebase</li>
3853 <li>Status bar not updated after finished searching and
3854 search wraps around to first result</li>
3855 <li>StructureSelectionManager instance shared between
3856 several Jalview applets causes race conditions and memory
3858 <li>Hover tooltip and mouseover of position on structure
3859 not sent from Jmol in applet</li>
3860 <li>Certain sequences of javascript method calls to
3861 applet API fatally hang browser</li>
3862 </ul> <em>General</em>
3864 <li>View follows structure mouseover scrolls beyond
3865 position with wrapped view and hidden regions</li>
3866 <li>Find sequence position moves to wrong residue
3867 with/without hidden columns</li>
3868 <li>Sequence length given in alignment properties window
3870 <li>InvalidNumberFormat exceptions thrown when trying to
3871 import PDB like structure files</li>
3872 <li>Positional search results are only highlighted
3873 between user-supplied sequence start/end bounds</li>
3874 <li>End attribute of sequence is not validated</li>
3875 <li>Find dialog only finds first sequence containing a
3876 given sequence position</li>
3877 <li>Sequence numbering not preserved in MSF alignment
3879 <li>Jalview PDB file reader does not extract sequence
3880 from nucleotide chains correctly</li>
3881 <li>Structure colours not updated when tree partition
3882 changed in alignment</li>
3883 <li>Sequence associated secondary structure not correctly
3884 parsed in interleaved stockholm</li>
3885 <li>Colour by annotation dialog does not restore current
3887 <li>Hiding (nearly) all sequences doesn't work
3889 <li>Sequences containing lowercase letters are not
3890 properly associated with their pdb files</li>
3891 </ul> <em>Documentation and Development</em>
3893 <li>schemas/JalviewWsParamSet.xsd corrupted by
3894 ApplyCopyright tool</li>
3899 <div align="center">
3900 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3903 <td><em>Application</em>
3905 <li>New warning dialog when the Jalview Desktop cannot
3906 contact web services</li>
3907 <li>JABA service parameters for a preset are shown in
3908 service job window</li>
3909 <li>JABA Service menu entries reworded</li>
3913 <li>Modeller PIR IO broken - cannot correctly import a
3914 pir file emitted by Jalview</li>
3915 <li>Existing feature settings transferred to new
3916 alignment view created from cut'n'paste</li>
3917 <li>Improved test for mixed amino/nucleotide chains when
3918 parsing PDB files</li>
3919 <li>Consensus and conservation annotation rows
3920 occasionally become blank for all new windows</li>
3921 <li>Exception raised when right clicking above sequences
3922 in wrapped view mode</li>
3923 </ul> <em>Application</em>
3925 <li>multiple multiply aligned structure views cause cpu
3926 usage to hit 100% and computer to hang</li>
3927 <li>Web Service parameter layout breaks for long user
3928 parameter names</li>
3929 <li>Jaba service discovery hangs desktop if Jaba server
3936 <div align="center">
3937 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3940 <td><em>Application</em>
3942 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3943 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3946 <li>Web Services preference tab</li>
3947 <li>Analysis parameters dialog box and user defined
3949 <li>Improved speed and layout of Envision2 service menu</li>
3950 <li>Superpose structures using associated sequence
3952 <li>Export coordinates and projection as CSV from PCA
3954 </ul> <em>Applet</em>
3956 <li>enable javascript: execution by the applet via the
3957 link out mechanism</li>
3958 </ul> <em>Other</em>
3960 <li>Updated the Jmol Jalview interface to work with Jmol
3962 <li>The Jalview Desktop and JalviewLite applet now
3963 require Java 1.5</li>
3964 <li>Allow Jalview feature colour specification for GFF
3965 sequence annotation files</li>
3966 <li>New 'colour by label' keword in Jalview feature file
3967 type colour specification</li>
3968 <li>New Jalview Desktop Groovy API method that allows a
3969 script to check if it being run in an interactive session or
3970 in a batch operation from the Jalview command line</li>
3974 <li>clustalx colourscheme colours Ds preferentially when
3975 both D+E are present in over 50% of the column</li>
3976 </ul> <em>Application</em>
3978 <li>typo in AlignmentFrame->View->Hide->all but
3979 selected Regions menu item</li>
3980 <li>sequence fetcher replaces ',' for ';' when the ',' is
3981 part of a valid accession ID</li>
3982 <li>fatal OOM if object retrieved by sequence fetcher
3983 runs out of memory</li>
3984 <li>unhandled Out of Memory Error when viewing pca
3985 analysis results</li>
3986 <li>InstallAnywhere builds fail to launch on OS X java
3987 10.5 update 4 (due to apple Java 1.6 update)</li>
3988 <li>Installanywhere Jalview silently fails to launch</li>
3989 </ul> <em>Applet</em>
3991 <li>Jalview.getFeatureGroups() raises an
3992 ArrayIndexOutOfBoundsException if no feature groups are
3999 <div align="center">
4000 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4006 <li>Alignment prettyprinter doesn't cope with long
4008 <li>clustalx colourscheme colours Ds preferentially when
4009 both D+E are present in over 50% of the column</li>
4010 <li>nucleic acid structures retrieved from PDB do not
4011 import correctly</li>
4012 <li>More columns get selected than were clicked on when a
4013 number of columns are hidden</li>
4014 <li>annotation label popup menu not providing correct
4015 add/hide/show options when rows are hidden or none are
4017 <li>Stockholm format shown in list of readable formats,
4018 and parser copes better with alignments from RFAM.</li>
4019 <li>CSV output of consensus only includes the percentage
4020 of all symbols if sequence logo display is enabled</li>
4022 </ul> <em>Applet</em>
4024 <li>annotation panel disappears when annotation is
4026 </ul> <em>Application</em>
4028 <li>Alignment view not redrawn properly when new
4029 alignment opened where annotation panel is visible but no
4030 annotations are present on alignment</li>
4031 <li>pasted region containing hidden columns is
4032 incorrectly displayed in new alignment window</li>
4033 <li>Jalview slow to complete operations when stdout is
4034 flooded (fix is to close the Jalview console)</li>
4035 <li>typo in AlignmentFrame->View->Hide->all but
4036 selected Rregions menu item.</li>
4037 <li>inconsistent group submenu and Format submenu entry
4038 'Un' or 'Non'conserved</li>
4039 <li>Sequence feature settings are being shared by
4040 multiple distinct alignments</li>
4041 <li>group annotation not recreated when tree partition is
4043 <li>double click on group annotation to select sequences
4044 does not propagate to associated trees</li>
4045 <li>Mac OSX specific issues:
4047 <li>exception raised when mouse clicked on desktop
4048 window background</li>
4049 <li>Desktop menu placed on menu bar and application
4050 name set correctly</li>
4051 <li>sequence feature settings not wide enough for the
4052 save feature colourscheme button</li>
4061 <div align="center">
4062 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4065 <td><em>New Capabilities</em>
4067 <li>URL links generated from description line for
4068 regular-expression based URL links (applet and application)
4070 <li>Non-positional feature URL links are shown in link
4072 <li>Linked viewing of nucleic acid sequences and
4074 <li>Automatic Scrolling option in View menu to display
4075 the currently highlighted region of an alignment.</li>
4076 <li>Order an alignment by sequence length, or using the
4077 average score or total feature count for each sequence.</li>
4078 <li>Shading features by score or associated description</li>
4079 <li>Subdivide alignment and groups based on identity of
4080 selected subsequence (Make Groups from Selection).</li>
4081 <li>New hide/show options including Shift+Control+H to
4082 hide everything but the currently selected region.</li>
4083 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4084 </ul> <em>Application</em>
4086 <li>Fetch DB References capabilities and UI expanded to
4087 support retrieval from DAS sequence sources</li>
4088 <li>Local DAS Sequence sources can be added via the
4089 command line or via the Add local source dialog box.</li>
4090 <li>DAS Dbref and DbxRef feature types are parsed as
4091 database references and protein_name is parsed as
4092 description line (BioSapiens terms).</li>
4093 <li>Enable or disable non-positional feature and database
4094 references in sequence ID tooltip from View menu in
4096 <!-- <li>New hidden columns and rows and representatives capabilities
4097 in annotations file (in progress - not yet fully implemented)</li> -->
4098 <li>Group-associated consensus, sequence logos and
4099 conservation plots</li>
4100 <li>Symbol distributions for each column can be exported
4101 and visualized as sequence logos</li>
4102 <li>Optionally scale multi-character column labels to fit
4103 within each column of annotation row<!-- todo for applet -->
4105 <li>Optional automatic sort of associated alignment view
4106 when a new tree is opened.</li>
4107 <li>Jalview Java Console</li>
4108 <li>Better placement of desktop window when moving
4109 between different screens.</li>
4110 <li>New preference items for sequence ID tooltip and
4111 consensus annotation</li>
4112 <li>Client to submit sequences and IDs to Envision2
4114 <li><em>Vamsas Capabilities</em>
4116 <li>Improved VAMSAS synchronization (Jalview archive
4117 used to preserve views, structures, and tree display
4119 <li>Import of vamsas documents from disk or URL via
4121 <li>Sharing of selected regions between views and
4122 with other VAMSAS applications (Experimental feature!)</li>
4123 <li>Updated API to VAMSAS version 0.2</li>
4125 </ul> <em>Applet</em>
4127 <li>Middle button resizes annotation row height</li>
4130 <li>sortByTree (true/false) - automatically sort the
4131 associated alignment view by the tree when a new tree is
4133 <li>showTreeBootstraps (true/false) - show or hide
4134 branch bootstraps (default is to show them if available)</li>
4135 <li>showTreeDistances (true/false) - show or hide
4136 branch lengths (default is to show them if available)</li>
4137 <li>showUnlinkedTreeNodes (true/false) - indicate if
4138 unassociated nodes should be highlighted in the tree
4140 <li>heightScale and widthScale (1.0 or more) -
4141 increase the height or width of a cell in the alignment
4142 grid relative to the current font size.</li>
4145 <li>Non-positional features displayed in sequence ID
4147 </ul> <em>Other</em>
4149 <li>Features format: graduated colour definitions and
4150 specification of feature scores</li>
4151 <li>Alignment Annotations format: new keywords for group
4152 associated annotation (GROUP_REF) and annotation row display
4153 properties (ROW_PROPERTIES)</li>
4154 <li>XML formats extended to support graduated feature
4155 colourschemes, group associated annotation, and profile
4156 visualization settings.</li></td>
4159 <li>Source field in GFF files parsed as feature source
4160 rather than description</li>
4161 <li>Non-positional features are now included in sequence
4162 feature and gff files (controlled via non-positional feature
4163 visibility in tooltip).</li>
4164 <li>URL links generated for all feature links (bugfix)</li>
4165 <li>Added URL embedding instructions to features file
4167 <li>Codons containing ambiguous nucleotides translated as
4168 'X' in peptide product</li>
4169 <li>Match case switch in find dialog box works for both
4170 sequence ID and sequence string and query strings do not
4171 have to be in upper case to match case-insensitively.</li>
4172 <li>AMSA files only contain first column of
4173 multi-character column annotation labels</li>
4174 <li>Jalview Annotation File generation/parsing consistent
4175 with documentation (e.g. Stockholm annotation can be
4176 exported and re-imported)</li>
4177 <li>PDB files without embedded PDB IDs given a friendly
4179 <li>Find incrementally searches ID string matches as well
4180 as subsequence matches, and correctly reports total number
4184 <li>Better handling of exceptions during sequence
4186 <li>Dasobert generated non-positional feature URL
4187 link text excludes the start_end suffix</li>
4188 <li>DAS feature and source retrieval buttons disabled
4189 when fetch or registry operations in progress.</li>
4190 <li>PDB files retrieved from URLs are cached properly</li>
4191 <li>Sequence description lines properly shared via
4193 <li>Sequence fetcher fetches multiple records for all
4195 <li>Ensured that command line das feature retrieval
4196 completes before alignment figures are generated.</li>
4197 <li>Reduced time taken when opening file browser for
4199 <li>isAligned check prior to calculating tree, PCA or
4200 submitting an MSA to JNet now excludes hidden sequences.</li>
4201 <li>User defined group colours properly recovered
4202 from Jalview projects.</li>
4211 <div align="center">
4212 <strong>2.4.0.b2</strong><br> 28/10/2009
4217 <li>Experimental support for google analytics usage
4219 <li>Jalview privacy settings (user preferences and docs).</li>
4224 <li>Race condition in applet preventing startup in
4226 <li>Exception when feature created from selection beyond
4227 length of sequence.</li>
4228 <li>Allow synthetic PDB files to be imported gracefully</li>
4229 <li>Sequence associated annotation rows associate with
4230 all sequences with a given id</li>
4231 <li>Find function matches case-insensitively for sequence
4232 ID string searches</li>
4233 <li>Non-standard characters do not cause pairwise
4234 alignment to fail with exception</li>
4235 </ul> <em>Application Issues</em>
4237 <li>Sequences are now validated against EMBL database</li>
4238 <li>Sequence fetcher fetches multiple records for all
4240 </ul> <em>InstallAnywhere Issues</em>
4242 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4243 issue with installAnywhere mechanism)</li>
4244 <li>Command line launching of JARs from InstallAnywhere
4245 version (java class versioning error fixed)</li>
4252 <div align="center">
4253 <strong>2.4</strong><br> 27/8/2008
4256 <td><em>User Interface</em>
4258 <li>Linked highlighting of codon and amino acid from
4259 translation and protein products</li>
4260 <li>Linked highlighting of structure associated with
4261 residue mapping to codon position</li>
4262 <li>Sequence Fetcher provides example accession numbers
4263 and 'clear' button</li>
4264 <li>MemoryMonitor added as an option under Desktop's
4266 <li>Extract score function to parse whitespace separated
4267 numeric data in description line</li>
4268 <li>Column labels in alignment annotation can be centred.</li>
4269 <li>Tooltip for sequence associated annotation give name
4271 </ul> <em>Web Services and URL fetching</em>
4273 <li>JPred3 web service</li>
4274 <li>Prototype sequence search client (no public services
4276 <li>Fetch either seed alignment or full alignment from
4278 <li>URL Links created for matching database cross
4279 references as well as sequence ID</li>
4280 <li>URL Links can be created using regular-expressions</li>
4281 </ul> <em>Sequence Database Connectivity</em>
4283 <li>Retrieval of cross-referenced sequences from other
4285 <li>Generalised database reference retrieval and
4286 validation to all fetchable databases</li>
4287 <li>Fetch sequences from DAS sources supporting the
4288 sequence command</li>
4289 </ul> <em>Import and Export</em>
4290 <li>export annotation rows as CSV for spreadsheet import</li>
4291 <li>Jalview projects record alignment dataset associations,
4292 EMBL products, and cDNA sequence mappings</li>
4293 <li>Sequence Group colour can be specified in Annotation
4295 <li>Ad-hoc colouring of group in Annotation File using RGB
4296 triplet as name of colourscheme</li>
4297 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4299 <li>treenode binding for VAMSAS tree exchange</li>
4300 <li>local editing and update of sequences in VAMSAS
4301 alignments (experimental)</li>
4302 <li>Create new or select existing session to join</li>
4303 <li>load and save of vamsas documents</li>
4304 </ul> <em>Application command line</em>
4306 <li>-tree parameter to open trees (introduced for passing
4308 <li>-fetchfrom command line argument to specify nicknames
4309 of DAS servers to query for alignment features</li>
4310 <li>-dasserver command line argument to add new servers
4311 that are also automatically queried for features</li>
4312 <li>-groovy command line argument executes a given groovy
4313 script after all input data has been loaded and parsed</li>
4314 </ul> <em>Applet-Application data exchange</em>
4316 <li>Trees passed as applet parameters can be passed to
4317 application (when using "View in full
4318 application")</li>
4319 </ul> <em>Applet Parameters</em>
4321 <li>feature group display control parameter</li>
4322 <li>debug parameter</li>
4323 <li>showbutton parameter</li>
4324 </ul> <em>Applet API methods</em>
4326 <li>newView public method</li>
4327 <li>Window (current view) specific get/set public methods</li>
4328 <li>Feature display control methods</li>
4329 <li>get list of currently selected sequences</li>
4330 </ul> <em>New Jalview distribution features</em>
4332 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4333 <li>RELEASE file gives build properties for the latest
4334 Jalview release.</li>
4335 <li>Java 1.1 Applet build made easier and donotobfuscate
4336 property controls execution of obfuscator</li>
4337 <li>Build target for generating source distribution</li>
4338 <li>Debug flag for javacc</li>
4339 <li>.jalview_properties file is documented (slightly) in
4340 jalview.bin.Cache</li>
4341 <li>Continuous Build Integration for stable and
4342 development version of Application, Applet and source
4347 <li>selected region output includes visible annotations
4348 (for certain formats)</li>
4349 <li>edit label/displaychar contains existing label/char
4351 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4352 <li>shorter peptide product names from EMBL records</li>
4353 <li>Newick string generator makes compact representations</li>
4354 <li>bootstrap values parsed correctly for tree files with
4356 <li>pathological filechooser bug avoided by not allowing
4357 filenames containing a ':'</li>
4358 <li>Fixed exception when parsing GFF files containing
4359 global sequence features</li>
4360 <li>Alignment datasets are finalized only when number of
4361 references from alignment sequences goes to zero</li>
4362 <li>Close of tree branch colour box without colour
4363 selection causes cascading exceptions</li>
4364 <li>occasional negative imgwidth exceptions</li>
4365 <li>better reporting of non-fatal warnings to user when
4366 file parsing fails.</li>
4367 <li>Save works when Jalview project is default format</li>
4368 <li>Save as dialog opened if current alignment format is
4369 not a valid output format</li>
4370 <li>UniProt canonical names introduced for both das and
4372 <li>Histidine should be midblue (not pink!) in Zappo</li>
4373 <li>error messages passed up and output when data read
4375 <li>edit undo recovers previous dataset sequence when
4376 sequence is edited</li>
4377 <li>allow PDB files without pdb ID HEADER lines (like
4378 those generated by MODELLER) to be read in properly</li>
4379 <li>allow reading of JPred concise files as a normal
4381 <li>Stockholm annotation parsing and alignment properties
4382 import fixed for PFAM records</li>
4383 <li>Structure view windows have correct name in Desktop
4385 <li>annotation consisting of sequence associated scores
4386 can be read and written correctly to annotation file</li>
4387 <li>Aligned cDNA translation to aligned peptide works
4389 <li>Fixed display of hidden sequence markers and
4390 non-italic font for representatives in Applet</li>
4391 <li>Applet Menus are always embedded in applet window on
4393 <li>Newly shown features appear at top of stack (in
4395 <li>Annotations added via parameter not drawn properly
4396 due to null pointer exceptions</li>
4397 <li>Secondary structure lines are drawn starting from
4398 first column of alignment</li>
4399 <li>UniProt XML import updated for new schema release in
4401 <li>Sequence feature to sequence ID match for Features
4402 file is case-insensitive</li>
4403 <li>Sequence features read from Features file appended to
4404 all sequences with matching IDs</li>
4405 <li>PDB structure coloured correctly for associated views
4406 containing a sub-sequence</li>
4407 <li>PDB files can be retrieved by applet from Jar files</li>
4408 <li>feature and annotation file applet parameters
4409 referring to different directories are retrieved correctly</li>
4410 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4411 <li>Fixed application hang whilst waiting for
4412 splash-screen version check to complete</li>
4413 <li>Applet properly URLencodes input parameter values
4414 when passing them to the launchApp service</li>
4415 <li>display name and local features preserved in results
4416 retrieved from web service</li>
4417 <li>Visual delay indication for sequence retrieval and
4418 sequence fetcher initialisation</li>
4419 <li>updated Application to use DAS 1.53e version of
4420 dasobert DAS client</li>
4421 <li>Re-instated Full AMSA support and .amsa file
4423 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4431 <div align="center">
4432 <strong>2.3</strong><br> 9/5/07
4437 <li>Jmol 11.0.2 integration</li>
4438 <li>PDB views stored in Jalview XML files</li>
4439 <li>Slide sequences</li>
4440 <li>Edit sequence in place</li>
4441 <li>EMBL CDS features</li>
4442 <li>DAS Feature mapping</li>
4443 <li>Feature ordering</li>
4444 <li>Alignment Properties</li>
4445 <li>Annotation Scores</li>
4446 <li>Sort by scores</li>
4447 <li>Feature/annotation editing in applet</li>
4452 <li>Headless state operation in 2.2.1</li>
4453 <li>Incorrect and unstable DNA pairwise alignment</li>
4454 <li>Cut and paste of sequences with annotation</li>
4455 <li>Feature group display state in XML</li>
4456 <li>Feature ordering in XML</li>
4457 <li>blc file iteration selection using filename # suffix</li>
4458 <li>Stockholm alignment properties</li>
4459 <li>Stockhom alignment secondary structure annotation</li>
4460 <li>2.2.1 applet had no feature transparency</li>
4461 <li>Number pad keys can be used in cursor mode</li>
4462 <li>Structure Viewer mirror image resolved</li>
4469 <div align="center">
4470 <strong>2.2.1</strong><br> 12/2/07
4475 <li>Non standard characters can be read and displayed
4476 <li>Annotations/Features can be imported/exported to the
4478 <li>Applet allows editing of sequence/annotation/group
4479 name & description
4480 <li>Preference setting to display sequence name in
4482 <li>Annotation file format extended to allow
4483 Sequence_groups to be defined
4484 <li>Default opening of alignment overview panel can be
4485 specified in preferences
4486 <li>PDB residue numbering annotation added to associated
4492 <li>Applet crash under certain Linux OS with Java 1.6
4494 <li>Annotation file export / import bugs fixed
4495 <li>PNG / EPS image output bugs fixed
4501 <div align="center">
4502 <strong>2.2</strong><br> 27/11/06
4507 <li>Multiple views on alignment
4508 <li>Sequence feature editing
4509 <li>"Reload" alignment
4510 <li>"Save" to current filename
4511 <li>Background dependent text colour
4512 <li>Right align sequence ids
4513 <li>User-defined lower case residue colours
4516 <li>Menu item accelerator keys
4517 <li>Control-V pastes to current alignment
4518 <li>Cancel button for DAS Feature Fetching
4519 <li>PCA and PDB Viewers zoom via mouse roller
4520 <li>User-defined sub-tree colours and sub-tree selection
4522 <li>'New Window' button on the 'Output to Text box'
4527 <li>New memory efficient Undo/Redo System
4528 <li>Optimised symbol lookups and conservation/consensus
4530 <li>Region Conservation/Consensus recalculated after
4532 <li>Fixed Remove Empty Columns Bug (empty columns at end
4534 <li>Slowed DAS Feature Fetching for increased robustness.
4536 <li>Made angle brackets in ASCII feature descriptions
4538 <li>Re-instated Zoom function for PCA
4539 <li>Sequence descriptions conserved in web service
4541 <li>UniProt ID discoverer uses any word separated by
4543 <li>WsDbFetch query/result association resolved
4544 <li>Tree leaf to sequence mapping improved
4545 <li>Smooth fonts switch moved to FontChooser dialog box.
4552 <div align="center">
4553 <strong>2.1.1</strong><br> 12/9/06
4558 <li>Copy consensus sequence to clipboard</li>
4563 <li>Image output - rightmost residues are rendered if
4564 sequence id panel has been resized</li>
4565 <li>Image output - all offscreen group boundaries are
4567 <li>Annotation files with sequence references - all
4568 elements in file are relative to sequence position</li>
4569 <li>Mac Applet users can use Alt key for group editing</li>
4575 <div align="center">
4576 <strong>2.1</strong><br> 22/8/06
4581 <li>MAFFT Multiple Alignment in default Web Service list</li>
4582 <li>DAS Feature fetching</li>
4583 <li>Hide sequences and columns</li>
4584 <li>Export Annotations and Features</li>
4585 <li>GFF file reading / writing</li>
4586 <li>Associate structures with sequences from local PDB
4588 <li>Add sequences to exisiting alignment</li>
4589 <li>Recently opened files / URL lists</li>
4590 <li>Applet can launch the full application</li>
4591 <li>Applet has transparency for features (Java 1.2
4593 <li>Applet has user defined colours parameter</li>
4594 <li>Applet can load sequences from parameter
4595 "sequence<em>x</em>"
4601 <li>Redundancy Panel reinstalled in the Applet</li>
4602 <li>Monospaced font - EPS / rescaling bug fixed</li>
4603 <li>Annotation files with sequence references bug fixed</li>
4609 <div align="center">
4610 <strong>2.08.1</strong><br> 2/5/06
4615 <li>Change case of selected region from Popup menu</li>
4616 <li>Choose to match case when searching</li>
4617 <li>Middle mouse button and mouse movement can compress /
4618 expand the visible width and height of the alignment</li>
4623 <li>Annotation Panel displays complete JNet results</li>
4629 <div align="center">
4630 <strong>2.08b</strong><br> 18/4/06
4636 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4637 <li>Righthand label on wrapped alignments shows correct
4644 <div align="center">
4645 <strong>2.08</strong><br> 10/4/06
4650 <li>Editing can be locked to the selection area</li>
4651 <li>Keyboard editing</li>
4652 <li>Create sequence features from searches</li>
4653 <li>Precalculated annotations can be loaded onto
4655 <li>Features file allows grouping of features</li>
4656 <li>Annotation Colouring scheme added</li>
4657 <li>Smooth fonts off by default - Faster rendering</li>
4658 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4663 <li>Drag & Drop fixed on Linux</li>
4664 <li>Jalview Archive file faster to load/save, sequence
4665 descriptions saved.</li>
4671 <div align="center">
4672 <strong>2.07</strong><br> 12/12/05
4677 <li>PDB Structure Viewer enhanced</li>
4678 <li>Sequence Feature retrieval and display enhanced</li>
4679 <li>Choose to output sequence start-end after sequence
4680 name for file output</li>
4681 <li>Sequence Fetcher WSDBFetch@EBI</li>
4682 <li>Applet can read feature files, PDB files and can be
4683 used for HTML form input</li>
4688 <li>HTML output writes groups and features</li>
4689 <li>Group editing is Control and mouse click</li>
4690 <li>File IO bugs</li>
4696 <div align="center">
4697 <strong>2.06</strong><br> 28/9/05
4702 <li>View annotations in wrapped mode</li>
4703 <li>More options for PCA viewer</li>
4708 <li>GUI bugs resolved</li>
4709 <li>Runs with -nodisplay from command line</li>
4715 <div align="center">
4716 <strong>2.05b</strong><br> 15/9/05
4721 <li>Choose EPS export as lineart or text</li>
4722 <li>Jar files are executable</li>
4723 <li>Can read in Uracil - maps to unknown residue</li>
4728 <li>Known OutOfMemory errors give warning message</li>
4729 <li>Overview window calculated more efficiently</li>
4730 <li>Several GUI bugs resolved</li>
4736 <div align="center">
4737 <strong>2.05</strong><br> 30/8/05
4742 <li>Edit and annotate in "Wrapped" view</li>
4747 <li>Several GUI bugs resolved</li>
4753 <div align="center">
4754 <strong>2.04</strong><br> 24/8/05
4759 <li>Hold down mouse wheel & scroll to change font
4765 <li>Improved JPred client reliability</li>
4766 <li>Improved loading of Jalview files</li>
4772 <div align="center">
4773 <strong>2.03</strong><br> 18/8/05
4778 <li>Set Proxy server name and port in preferences</li>
4779 <li>Multiple URL links from sequence ids</li>
4780 <li>User Defined Colours can have a scheme name and added
4782 <li>Choose to ignore gaps in consensus calculation</li>
4783 <li>Unix users can set default web browser</li>
4784 <li>Runs without GUI for batch processing</li>
4785 <li>Dynamically generated Web Service Menus</li>
4790 <li>InstallAnywhere download for Sparc Solaris</li>
4796 <div align="center">
4797 <strong>2.02</strong><br> 18/7/05
4803 <li>Copy & Paste order of sequences maintains
4804 alignment order.</li>
4810 <div align="center">
4811 <strong>2.01</strong><br> 12/7/05
4816 <li>Use delete key for deleting selection.</li>
4817 <li>Use Mouse wheel to scroll sequences.</li>
4818 <li>Help file updated to describe how to add alignment
4820 <li>Version and build date written to build properties
4822 <li>InstallAnywhere installation will check for updates
4823 at launch of Jalview.</li>
4828 <li>Delete gaps bug fixed.</li>
4829 <li>FileChooser sorts columns.</li>
4830 <li>Can remove groups one by one.</li>
4831 <li>Filechooser icons installed.</li>
4832 <li>Finder ignores return character when searching.
4833 Return key will initiate a search.<br>
4840 <div align="center">
4841 <strong>2.0</strong><br> 20/6/05
4846 <li>New codebase</li>