3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.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
72 <td align="left" valign="top">
75 <!-- JAL-3493 -->Escape does not clear highlights on the
76 alignment (Since Jalview 2.10.3)
79 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
80 doesn't slide selected sequences
83 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
84 multiple EMBL gene products shown forĀ a single contig
90 <td width="60" align="center" nowrap><strong><a
91 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
92 <em>22/04/2020</em></strong></td>
93 <td align="left" valign="top">
96 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
97 'virtual' codon features shown on protein (or vice versa)
98 for display in alignments, on structure views (including
99 transfer to UCSF chimera), in feature reports and for
103 <!-- JAL-3121 -->Feature attributes from VCF files can be
104 exported and re-imported as GFF3 files
107 <!-- JAL-3376 -->Capture VCF "fixed column" values
108 POS, ID, QUAL, FILTER as Feature Attributes
111 <!-- JAL-3375 -->More robust VCF numeric data field
112 validation while parsing
115 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
119 <!-- JAL-3535 -->Feature Settings dialog title includes name
123 <!-- JAL-3538 -->Font anti-aliasing in alignment views
127 <!-- JAL-3468 -->Very long feature descriptions truncated in
131 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
132 with no feature types visible
135 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
137 </ul><em>Jalview Installer</em>
140 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
141 in console (may be null when Jalview launched as executable jar or via conda)
144 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
147 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
150 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
152 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
153 </ul> <em>Release processes</em>
156 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
159 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
161 </ul> <em>Build System</em>
164 <!-- JAL-3510 -->Clover updated to 4.4.1
167 <!-- JAL-3513 -->Test code included in Clover coverage
171 <em>Groovy Scripts</em>
174 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
175 to stdout containing the consensus sequence for each
176 alignment in a Jalview session
179 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
180 genomic sequence_variant annotation from CDS as
181 missense_variant or synonymous_variant on protein products.
185 <td align="left" valign="top">
188 <!-- JAL-3581 -->Hidden sequence markers still visible when
189 'Show hidden markers' option is not ticked
192 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
193 PNG output when 'Automatically set ID width' is set in
194 jalview preferences or properties file
197 <!-- JAL-3571 -->Feature Editor dialog can be opened when
198 'Show Sequence Features' option is not ticked
201 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
202 buttons in Feature Settings dialog are clicked when no
206 <!-- JAL-3412 -->ID margins for CDS and Protein views not
207 equal when split frame is first opened
210 <!-- JAL-3296 -->Sequence position numbers in status bar not
211 correct after editing a sequence's start position
214 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
215 with annotation and exceptions thrown when only a few
216 columns shown in wrapped mode
219 <!-- JAL-3386 -->Sequence IDs missing in headless export of
220 wrapped alignment figure with annotations
223 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
224 ID fails with ClassCastException
227 <!-- JAL-3389 -->Chimera session not restored from Jalview
231 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
232 feature settings dialog also selects columns
235 <!-- JAL-3473 -->SpinnerNumberModel causes
236 IllegalArgumentException in some circumstances
239 <!-- JAL-3534 -->Multiple feature settings dialogs can be
243 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
244 alignment window is closed
247 <!-- JAL-3406 -->Credits missing some authors in Jalview
248 help documentation for 2.11.0 release
251 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
252 includes Pfam ID as sequence's accession rather than its
255 </ul> <em>Java 11 Compatibility issues</em>
258 <!-- JAL-2987 -->OSX - Can't view some search results in
259 PDB/Uniprot search panel
261 </ul> <em>Installer</em>
264 <!-- JAL-3447 -->Jalview should not create file associations
265 for 3D structure files (.pdb, .mmcif. .cif)
267 </ul> <em>Repository and Source Release</em>
270 <!-- JAL-3474 -->removed obsolete .cvsignore files from
274 <!-- JAL-3541 -->Clover report generation running out of
277 </ul> <em>New Known Issues</em>
280 <!-- JAL-3523 -->OSX - Current working directory not
281 preserved when Jalview.app launched with parameters from
285 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
286 clipped in headless figure export when Right Align option
290 <!-- JAL-3542 -->Jalview Installation type always reports
291 'Source' in console output
294 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
295 bamboo server but run fine locally.
301 <td width="60" align="center" nowrap>
302 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
303 <em>04/07/2019</em></strong>
305 <td align="left" valign="top">
308 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
309 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
310 source project) rather than InstallAnywhere
313 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
314 settings, receive over the air updates and launch specific
315 versions via (<a href="https://github.com/threerings/getdown">Three
319 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
320 formats supported by Jalview (including .jvp project files)
323 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
324 arguments and switch between different getdown channels
327 <!-- JAL-3141 -->Backup files created when saving Jalview project
332 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
333 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
335 <!-- JAL-2620 -->Alternative genetic code tables for
336 'Translate as cDNA'</li>
338 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
339 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
342 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
343 implementation that allows updates) used for Sequence Feature collections</li>
345 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
346 features can be filtered and shaded according to any
347 associated attributes (e.g. variant attributes from VCF
348 file, or key-value pairs imported from column 9 of GFF
352 <!-- JAL-2879 -->Feature Attributes and shading schemes
353 stored and restored from Jalview Projects
356 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
357 recognise variant features
360 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
361 sequences (also coloured red by default)
364 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
368 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
369 algorithm (Z-sort/transparency and filter aware)
372 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
378 <!-- JAL-3205 -->Symmetric score matrices for faster
379 tree and PCA calculations
381 <li><strong>Principal Components Analysis Viewer</strong>
384 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
385 and Viewer state saved in Jalview Project
387 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
390 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
394 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
399 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
401 <li><strong>Speed and Efficiency</strong>
404 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
405 multiple groups when working with large alignments
408 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
412 <li><strong>User Interface</strong>
415 <!-- JAL-2933 -->Finder panel remembers last position in each
419 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
420 what is shown)<br />Only visible regions of alignment are shown by
421 default (can be changed in user preferences)
424 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
425 to the Overwrite Dialog
428 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
432 <!-- JAL-1244 -->Status bar shows bounds when dragging a
433 selection region, and gap count when inserting or deleting gaps
436 <!-- JAL-3132 -->Status bar updates over sequence and annotation
440 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
444 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
448 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
451 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
455 <!-- JAL-3181 -->Consistent ordering of links in sequence id
459 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
461 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
465 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
466 <li><strong>Java 11 Support (not yet on general release)</strong>
469 <!-- -->OSX GUI integrations for App menu's 'About' entry and
474 <em>Deprecations</em>
476 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
477 capabilities removed from the Jalview Desktop
479 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
480 unmarshalling has been replaced by JAXB for Jalview projects
481 and XML based data retrieval clients</li>
482 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
483 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
484 </ul> <em>Documentation</em>
486 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
487 not supported in EPS figure export
489 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
490 </ul> <em>Development and Release Processes</em>
493 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
496 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
498 <!-- JAL-3225 -->Eclipse project configuration managed with
502 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
503 Bamboo continuous integration for unattended Test Suite
507 <!-- JAL-2864 -->Memory test suite to detect leaks in common
511 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
515 <!-- JAL-3248 -->Developer documentation migrated to
516 markdown (with HTML rendering)
519 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
522 <!-- JAL-3289 -->New URLs for publishing development
527 <td align="left" valign="top">
530 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
533 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
534 superposition in Jmol fail on Windows
537 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
538 structures for sequences with lots of PDB structures
541 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
545 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
546 project involving multiple views
549 <!-- JAL-3164 -->Overview for complementary view in a linked
550 CDS/Protein alignment is not updated when Hide Columns by
551 Annotation dialog hides columns
554 <!-- JAL-3158 -->Selection highlighting in the complement of a
555 CDS/Protein alignment stops working after making a selection in
556 one view, then making another selection in the other view
559 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
563 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
564 Settings and Jalview Preferences panels
567 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
568 overview with large alignments
571 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
572 region if columns were selected by dragging right-to-left and the
573 mouse moved to the left of the first column
576 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
577 hidden column marker via scale popup menu
580 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
581 doesn't tell users the invalid URL
584 <!-- JAL-2816 -->Tooltips displayed for features filtered by
588 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
589 show cross references or Fetch Database References are shown in
593 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
594 peptide sequence (computed variant shown as p.Res.null)
597 <!-- JAL-2060 -->'Graduated colour' option not offered for
598 manually created features (where feature score is Float.NaN)
601 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
602 when columns are hidden
605 <!-- JAL-3082 -->Regular expression error for '(' in Select
606 Columns by Annotation description
609 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
610 out of Scale or Annotation Panel
613 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
617 <!-- JAL-3074 -->Left/right drag in annotation can scroll
621 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
625 <!-- JAL-3002 -->Column display is out by one after Page Down,
626 Page Up in wrapped mode
629 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
632 <!-- JAL-2932 -->Finder searches in minimised alignments
635 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
636 on opening an alignment
639 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
643 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
644 different groups in the alignment are selected
647 <!-- JAL-2717 -->Internationalised colour scheme names not shown
651 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
655 <!-- JAL-3125 -->Value input for graduated feature colour
656 threshold gets 'unrounded'
659 <!-- JAL-2982 -->PCA image export doesn't respect background
663 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
666 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
669 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
673 <!-- JAL-2964 -->Associate Tree with All Views not restored from
677 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
678 shown in complementary view
681 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
682 without normalisation
685 <!-- JAL-3021 -->Sequence Details report should open positioned at top
689 <!-- JAL-914 -->Help page can be opened twice
692 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
694 </ul> <em>Editing</em>
697 <!-- JAL-2822 -->Start and End should be updated when sequence
698 data at beginning or end of alignment added/removed via 'Edit'
702 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
703 relocate sequence features correctly when start of sequence is
704 removed (Known defect since 2.10)
707 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
708 dialog corrupts dataset sequence
711 <!-- JAL-868 -->Structure colours not updated when associated tree
712 repartitions the alignment view (Regression in 2.10.5)
714 </ul> <em>Datamodel</em>
717 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
718 sequence's End is greater than its length
720 </ul> <em>Bugs fixed for Java 11 Support (not yet on
721 general release)</em>
724 <!-- JAL-3288 -->Menus work properly in split-screen
726 </ul> <em>New Known Defects</em>
729 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
732 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
733 regions of protein alignment.
736 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
737 is restored from a Jalview 2.11 project
740 <!-- JAL-3213 -->Alignment panel height can be too small after
744 <!-- JAL-3240 -->Display is incorrect after removing gapped
745 columns within hidden columns
748 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
749 window after dragging left to select columns to left of visible
753 <!-- JAL-2876 -->Features coloured according to their description
754 string and thresholded by score in earlier versions of Jalview are
755 not shown as thresholded features in 2.11. To workaround please
756 create a Score filter instead.
759 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
761 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
764 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
765 alignments with multiple views can close views unexpectedly
768 <em>Java 11 Specific defects</em>
771 <!-- JAL-3235 -->Jalview Properties file is not sorted
772 alphabetically when saved
778 <td width="60" nowrap>
780 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
783 <td><div align="left">
787 <!-- JAL-3101 -->Default memory for Jalview webstart and
788 InstallAnywhere increased to 1G.
791 <!-- JAL-247 -->Hidden sequence markers and representative
792 sequence bolding included when exporting alignment as EPS,
793 SVG, PNG or HTML. <em>Display is configured via the
794 Format menu, or for command-line use via a Jalview
795 properties file.</em>
798 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
799 API and sequence data now imported as JSON.
802 <!-- JAL-3065 -->Change in recommended way of starting
803 Jalview via a Java command line: add jars in lib directory
804 to CLASSPATH, rather than via the deprecated java.ext.dirs
811 <!-- JAL-3047 -->Support added to execute test suite
812 instrumented with <a href="http://openclover.org/">Open
817 <td><div align="left">
821 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
822 row shown in Feredoxin Structure alignment view of example
826 <!-- JAL-2854 -->Annotation obscures sequences if lots of
827 annotation displayed.
830 <!-- JAL-3107 -->Group conservation/consensus not shown
831 for newly created group when 'Apply to all groups'
835 <!-- JAL-3087 -->Corrupted display when switching to
836 wrapped mode when sequence panel's vertical scrollbar is
840 <!-- JAL-3003 -->Alignment is black in exported EPS file
841 when sequences are selected in exported view.</em>
844 <!-- JAL-3059 -->Groups with different coloured borders
845 aren't rendered with correct colour.
848 <!-- JAL-3092 -->Jalview could hang when importing certain
849 types of knotted RNA secondary structure.
852 <!-- JAL-3095 -->Sequence highlight and selection in
853 trimmed VARNA 2D structure is incorrect for sequences that
857 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
858 annotation when columns are inserted into an alignment,
859 and when exporting as Stockholm flatfile.
862 <!-- JAL-3053 -->Jalview annotation rows containing upper
863 and lower-case 'E' and 'H' do not automatically get
864 treated as RNA secondary structure.
867 <!-- JAL-3106 -->.jvp should be used as default extension
868 (not .jar) when saving a Jalview project file.
871 <!-- JAL-3105 -->Mac Users: closing a window correctly
872 transfers focus to previous window on OSX
875 <em>Java 10 Issues Resolved</em>
878 <!-- JAL-2988 -->OSX - Can't save new files via the File
879 or export menus by typing in a name into the Save dialog
883 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
884 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
885 'look and feel' which has improved compatibility with the
886 latest version of OSX.
893 <td width="60" nowrap>
895 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
896 <em>7/06/2018</em></strong>
899 <td><div align="left">
903 <!-- JAL-2920 -->Use HGVS nomenclature for variant
904 annotation retrieved from Uniprot
907 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
908 onto the Jalview Desktop
912 <td><div align="left">
916 <!-- JAL-3017 -->Cannot import features with multiple
917 variant elements (blocks import of some Uniprot records)
920 <!-- JAL-2997 -->Clustal files with sequence positions in
921 right-hand column parsed correctly
924 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
925 not alignment area in exported graphic
928 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
929 window has input focus
932 <!-- JAL-2992 -->Annotation panel set too high when
933 annotation added to view (Windows)
936 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
937 network connectivity is poor
940 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
941 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
942 the currently open URL and links from a page viewed in
943 Firefox or Chrome on Windows is now fully supported. If
944 you are using Edge, only links in the page can be
945 dragged, and with Internet Explorer, only the currently
946 open URL in the browser can be dropped onto Jalview.</em>
949 <em>New Known Defects</em>
951 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
956 <td width="60" nowrap>
958 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
961 <td><div align="left">
965 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
966 for disabling automatic superposition of multiple
967 structures and open structures in existing views
970 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
971 ID and annotation area margins can be click-dragged to
975 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
979 <!-- JAL-2759 -->Improved performance for large alignments
980 and lots of hidden columns
983 <!-- JAL-2593 -->Improved performance when rendering lots
984 of features (particularly when transparency is disabled)
987 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
988 exchange of Jalview features and Chimera attributes made
994 <td><div align="left">
997 <!-- JAL-2899 -->Structure and Overview aren't updated
998 when Colour By Annotation threshold slider is adjusted
1001 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1002 overlapping alignment panel
1005 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1009 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1010 improved: CDS not handled correctly if transcript has no
1014 <!-- JAL-2321 -->Secondary structure and temperature
1015 factor annotation not added to sequence when local PDB
1016 file associated with it by drag'n'drop or structure
1020 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1021 dialog doesn't import PDB files dropped on an alignment
1024 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1025 scroll bar doesn't work for some CDS/Protein views
1028 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1029 Java 1.8u153 onwards and Java 1.9u4+.
1032 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1033 columns in annotation row
1036 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1037 honored in batch mode
1040 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1041 for structures added to existing Jmol view
1044 <!-- JAL-2223 -->'View Mappings' includes duplicate
1045 entries after importing project with multiple views
1048 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1049 protein sequences via SIFTS from associated PDB entries
1050 with negative residue numbers or missing residues fails
1053 <!-- JAL-2952 -->Exception when shading sequence with negative
1054 Temperature Factor values from annotated PDB files (e.g.
1055 as generated by CONSURF)
1058 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1059 tooltip doesn't include a text description of mutation
1062 <!-- JAL-2922 -->Invert displayed features very slow when
1063 structure and/or overview windows are also shown
1066 <!-- JAL-2954 -->Selecting columns from highlighted regions
1067 very slow for alignments with large numbers of sequences
1070 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1071 with 'StringIndexOutOfBounds'
1074 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1075 platforms running Java 10
1078 <!-- JAL-2960 -->Adding a structure to existing structure
1079 view appears to do nothing because the view is hidden behind the alignment view
1085 <!-- JAL-2926 -->Copy consensus sequence option in applet
1086 should copy the group consensus when popup is opened on it
1092 <!-- JAL-2913 -->Fixed ID width preference is not respected
1095 <em>New Known Defects</em>
1098 <!-- JAL-2973 --> Exceptions occasionally raised when
1099 editing a large alignment and overview is displayed
1102 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1103 repeatedly after a series of edits even when the overview
1104 is no longer reflecting updates
1107 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1108 structures for protein subsequence (if 'Trim Retrieved
1109 Sequences' enabled) or Ensembl isoforms (Workaround in
1110 2.10.4 is to fail back to N&W mapping)
1113 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1114 option gives blank output
1121 <td width="60" nowrap>
1122 <div align="center">
1123 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1126 <td><div align="left">
1127 <ul><li>Updated Certum Codesigning Certificate
1128 (Valid till 30th November 2018)</li></ul></div></td>
1129 <td><div align="left">
1130 <em>Desktop</em><ul>
1132 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1133 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1134 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1135 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1136 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1137 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1138 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1144 <td width="60" nowrap>
1145 <div align="center">
1146 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1149 <td><div align="left">
1153 <!-- JAL-2446 -->Faster and more efficient management and
1154 rendering of sequence features
1157 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1158 429 rate limit request hander
1161 <!-- JAL-2773 -->Structure views don't get updated unless
1162 their colours have changed
1165 <!-- JAL-2495 -->All linked sequences are highlighted for
1166 a structure mousover (Jmol) or selection (Chimera)
1169 <!-- JAL-2790 -->'Cancel' button in progress bar for
1170 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1173 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1174 view from Ensembl locus cross-references
1177 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1181 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1182 feature can be disabled
1185 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1186 PDB easier retrieval of sequences for lists of IDs
1189 <!-- JAL-2758 -->Short names for sequences retrieved from
1195 <li>Groovy interpreter updated to 2.4.12</li>
1196 <li>Example groovy script for generating a matrix of
1197 percent identity scores for current alignment.</li>
1199 <em>Testing and Deployment</em>
1202 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1206 <td><div align="left">
1210 <!-- JAL-2643 -->Pressing tab after updating the colour
1211 threshold text field doesn't trigger an update to the
1215 <!-- JAL-2682 -->Race condition when parsing sequence ID
1219 <!-- JAL-2608 -->Overview windows are also closed when
1220 alignment window is closed
1223 <!-- JAL-2548 -->Export of features doesn't always respect
1227 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1228 takes a long time in Cursor mode
1234 <!-- JAL-2777 -->Structures with whitespace chainCode
1235 cannot be viewed in Chimera
1238 <!-- JAL-2728 -->Protein annotation panel too high in
1242 <!-- JAL-2757 -->Can't edit the query after the server
1243 error warning icon is shown in Uniprot and PDB Free Text
1247 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1250 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1253 <!-- JAL-2739 -->Hidden column marker in last column not
1254 rendered when switching back from Wrapped to normal view
1257 <!-- JAL-2768 -->Annotation display corrupted when
1258 scrolling right in unwapped alignment view
1261 <!-- JAL-2542 -->Existing features on subsequence
1262 incorrectly relocated when full sequence retrieved from
1266 <!-- JAL-2733 -->Last reported memory still shown when
1267 Desktop->Show Memory is unticked (OSX only)
1270 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1271 features of same type and group to be selected for
1275 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1276 alignments when hidden columns are present
1279 <!-- JAL-2392 -->Jalview freezes when loading and
1280 displaying several structures
1283 <!-- JAL-2732 -->Black outlines left after resizing or
1287 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1288 within the Jalview desktop on OSX
1291 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1292 when in wrapped alignment mode
1295 <!-- JAL-2636 -->Scale mark not shown when close to right
1296 hand end of alignment
1299 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1300 each selected sequence do not have correct start/end
1304 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1305 after canceling the Alignment Window's Font dialog
1308 <!-- JAL-2036 -->Show cross-references not enabled after
1309 restoring project until a new view is created
1312 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1313 URL links appears when only default EMBL-EBI link is
1314 configured (since 2.10.2b2)
1317 <!-- JAL-2775 -->Overview redraws whole window when box
1318 position is adjusted
1321 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1322 in a multi-chain structure when viewing alignment
1323 involving more than one chain (since 2.10)
1326 <!-- JAL-2811 -->Double residue highlights in cursor mode
1327 if new selection moves alignment window
1330 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1331 arrow key in cursor mode to pass hidden column marker
1334 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1335 that produces correctly annotated transcripts and products
1338 <!-- JAL-2776 -->Toggling a feature group after first time
1339 doesn't update associated structure view
1342 <em>Applet</em><br />
1345 <!-- JAL-2687 -->Concurrent modification exception when
1346 closing alignment panel
1349 <em>BioJSON</em><br />
1352 <!-- JAL-2546 -->BioJSON export does not preserve
1353 non-positional features
1356 <em>New Known Issues</em>
1359 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1360 sequence features correctly (for many previous versions of
1364 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1365 using cursor in wrapped panel other than top
1368 <!-- JAL-2791 -->Select columns containing feature ignores
1369 graduated colour threshold
1372 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1373 always preserve numbering and sequence features
1376 <em>Known Java 9 Issues</em>
1379 <!-- JAL-2902 -->Groovy Console very slow to open and is
1380 not responsive when entering characters (Webstart, Java
1387 <td width="60" nowrap>
1388 <div align="center">
1389 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1390 <em>2/10/2017</em></strong>
1393 <td><div align="left">
1394 <em>New features in Jalview Desktop</em>
1397 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1399 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1403 <td><div align="left">
1407 <td width="60" nowrap>
1408 <div align="center">
1409 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1410 <em>7/9/2017</em></strong>
1413 <td><div align="left">
1417 <!-- JAL-2588 -->Show gaps in overview window by colouring
1418 in grey (sequences used to be coloured grey, and gaps were
1422 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1426 <!-- JAL-2587 -->Overview updates immediately on increase
1427 in size and progress bar shown as higher resolution
1428 overview is recalculated
1433 <td><div align="left">
1437 <!-- JAL-2664 -->Overview window redraws every hidden
1438 column region row by row
1441 <!-- JAL-2681 -->duplicate protein sequences shown after
1442 retrieving Ensembl crossrefs for sequences from Uniprot
1445 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1446 format setting is unticked
1449 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1450 if group has show boxes format setting unticked
1453 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1454 autoscrolling whilst dragging current selection group to
1455 include sequences and columns not currently displayed
1458 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1459 assemblies are imported via CIF file
1462 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1463 displayed when threshold or conservation colouring is also
1467 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1471 <!-- JAL-2673 -->Jalview continues to scroll after
1472 dragging a selected region off the visible region of the
1476 <!-- JAL-2724 -->Cannot apply annotation based
1477 colourscheme to all groups in a view
1480 <!-- JAL-2511 -->IDs don't line up with sequences
1481 initially after font size change using the Font chooser or
1488 <td width="60" nowrap>
1489 <div align="center">
1490 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1493 <td><div align="left">
1494 <em>Calculations</em>
1498 <!-- JAL-1933 -->Occupancy annotation row shows number of
1499 ungapped positions in each column of the alignment.
1502 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1503 a calculation dialog box
1506 <!-- JAL-2379 -->Revised implementation of PCA for speed
1507 and memory efficiency (~30x faster)
1510 <!-- JAL-2403 -->Revised implementation of sequence
1511 similarity scores as used by Tree, PCA, Shading Consensus
1512 and other calculations
1515 <!-- JAL-2416 -->Score matrices are stored as resource
1516 files within the Jalview codebase
1519 <!-- JAL-2500 -->Trees computed on Sequence Feature
1520 Similarity may have different topology due to increased
1527 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1528 model for alignments and groups
1531 <!-- JAL-384 -->Custom shading schemes created via groovy
1538 <!-- JAL-2526 -->Efficiency improvements for interacting
1539 with alignment and overview windows
1542 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1546 <!-- JAL-2388 -->Hidden columns and sequences can be
1550 <!-- JAL-2611 -->Click-drag in visible area allows fine
1551 adjustment of visible position
1555 <em>Data import/export</em>
1558 <!-- JAL-2535 -->Posterior probability annotation from
1559 Stockholm files imported as sequence associated annotation
1562 <!-- JAL-2507 -->More robust per-sequence positional
1563 annotation input/output via stockholm flatfile
1566 <!-- JAL-2533 -->Sequence names don't include file
1567 extension when importing structure files without embedded
1568 names or PDB accessions
1571 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1572 format sequence substitution matrices
1575 <em>User Interface</em>
1578 <!-- JAL-2447 --> Experimental Features Checkbox in
1579 Desktop's Tools menu to hide or show untested features in
1583 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1584 via Overview or sequence motif search operations
1587 <!-- JAL-2547 -->Amend sequence features dialog box can be
1588 opened by double clicking gaps within sequence feature
1592 <!-- JAL-1476 -->Status bar message shown when not enough
1593 aligned positions were available to create a 3D structure
1597 <em>3D Structure</em>
1600 <!-- JAL-2430 -->Hidden regions in alignment views are not
1601 coloured in linked structure views
1604 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1605 file-based command exchange
1608 <!-- JAL-2375 -->Structure chooser automatically shows
1609 Cached Structures rather than querying the PDBe if
1610 structures are already available for sequences
1613 <!-- JAL-2520 -->Structures imported via URL are cached in
1614 the Jalview project rather than downloaded again when the
1615 project is reopened.
1618 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1619 to transfer Chimera's structure attributes as Jalview
1620 features, and vice-versa (<strong>Experimental
1624 <em>Web Services</em>
1627 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1630 <!-- JAL-2335 -->Filter non-standard amino acids and
1631 nucleotides when submitting to AACon and other MSA
1635 <!-- JAL-2316, -->URLs for viewing database
1636 cross-references provided by identifiers.org and the
1637 EMBL-EBI's MIRIAM DB
1644 <!-- JAL-2344 -->FileFormatI interface for describing and
1645 identifying file formats (instead of String constants)
1648 <!-- JAL-2228 -->FeatureCounter script refactored for
1649 efficiency when counting all displayed features (not
1650 backwards compatible with 2.10.1)
1653 <em>Example files</em>
1656 <!-- JAL-2631 -->Graduated feature colour style example
1657 included in the example feature file
1660 <em>Documentation</em>
1663 <!-- JAL-2339 -->Release notes reformatted for readability
1664 with the built-in Java help viewer
1667 <!-- JAL-1644 -->Find documentation updated with 'search
1668 sequence description' option
1674 <!-- JAL-2485, -->External service integration tests for
1675 Uniprot REST Free Text Search Client
1678 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1681 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1686 <td><div align="left">
1687 <em>Calculations</em>
1690 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1691 matrix - C->R should be '-3'<br />Old matrix restored
1692 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1694 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1695 Jalview's treatment of gaps in PCA and substitution matrix
1696 based Tree calculations.<br /> <br />In earlier versions
1697 of Jalview, gaps matching gaps were penalised, and gaps
1698 matching non-gaps penalised even more. In the PCA
1699 calculation, gaps were actually treated as non-gaps - so
1700 different costs were applied, which meant Jalview's PCAs
1701 were different to those produced by SeqSpace.<br />Jalview
1702 now treats gaps in the same way as SeqSpace (ie it scores
1703 them as 0). <br /> <br />Enter the following in the
1704 Groovy console to restore pre-2.10.2 behaviour:<br />
1705 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1706 // for 2.10.1 mode <br />
1707 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1708 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1709 these settings will affect all subsequent tree and PCA
1710 calculations (not recommended)</em></li>
1712 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1713 scaling of branch lengths for trees computed using
1714 Sequence Feature Similarity.
1717 <!-- JAL-2377 -->PCA calculation could hang when
1718 generating output report when working with highly
1719 redundant alignments
1722 <!-- JAL-2544 --> Sort by features includes features to
1723 right of selected region when gaps present on right-hand
1727 <em>User Interface</em>
1730 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1731 doesn't reselect a specific sequence's associated
1732 annotation after it was used for colouring a view
1735 <!-- JAL-2419 -->Current selection lost if popup menu
1736 opened on a region of alignment without groups
1739 <!-- JAL-2374 -->Popup menu not always shown for regions
1740 of an alignment with overlapping groups
1743 <!-- JAL-2310 -->Finder double counts if both a sequence's
1744 name and description match
1747 <!-- JAL-2370 -->Hiding column selection containing two
1748 hidden regions results in incorrect hidden regions
1751 <!-- JAL-2386 -->'Apply to all groups' setting when
1752 changing colour does not apply Conservation slider value
1756 <!-- JAL-2373 -->Percentage identity and conservation menu
1757 items do not show a tick or allow shading to be disabled
1760 <!-- JAL-2385 -->Conservation shading or PID threshold
1761 lost when base colourscheme changed if slider not visible
1764 <!-- JAL-2547 -->Sequence features shown in tooltip for
1765 gaps before start of features
1768 <!-- JAL-2623 -->Graduated feature colour threshold not
1769 restored to UI when feature colour is edited
1772 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1773 a time when scrolling vertically in wrapped mode.
1776 <!-- JAL-2630 -->Structure and alignment overview update
1777 as graduate feature colour settings are modified via the
1781 <!-- JAL-2034 -->Overview window doesn't always update
1782 when a group defined on the alignment is resized
1785 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1786 wrapped view result in positional status updates
1790 <!-- JAL-2563 -->Status bar doesn't show position for
1791 ambiguous amino acid and nucleotide symbols
1794 <!-- JAL-2602 -->Copy consensus sequence failed if
1795 alignment included gapped columns
1798 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1799 widgets don't permanently disappear
1802 <!-- JAL-2503 -->Cannot select or filter quantitative
1803 annotation that are shown only as column labels (e.g.
1804 T-Coffee column reliability scores)
1807 <!-- JAL-2594 -->Exception thrown if trying to create a
1808 sequence feature on gaps only
1811 <!-- JAL-2504 -->Features created with 'New feature'
1812 button from a Find inherit previously defined feature type
1813 rather than the Find query string
1816 <!-- JAL-2423 -->incorrect title in output window when
1817 exporting tree calculated in Jalview
1820 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1821 and then revealing them reorders sequences on the
1825 <!-- JAL-964 -->Group panel in sequence feature settings
1826 doesn't update to reflect available set of groups after
1827 interactively adding or modifying features
1830 <!-- JAL-2225 -->Sequence Database chooser unusable on
1834 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1835 only excluded gaps in current sequence and ignored
1842 <!-- JAL-2421 -->Overview window visible region moves
1843 erratically when hidden rows or columns are present
1846 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1847 Structure Viewer's colour menu don't correspond to
1851 <!-- JAL-2405 -->Protein specific colours only offered in
1852 colour and group colour menu for protein alignments
1855 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1856 reflect currently selected view or group's shading
1860 <!-- JAL-2624 -->Feature colour thresholds not respected
1861 when rendered on overview and structures when opacity at
1865 <!-- JAL-2589 -->User defined gap colour not shown in
1866 overview when features overlaid on alignment
1869 <!-- JAL-2567 -->Feature settings for different views not
1870 recovered correctly from Jalview project file
1873 <!-- JAL-2256 -->Feature colours in overview when first opened
1874 (automatically via preferences) are different to the main
1878 <em>Data import/export</em>
1881 <!-- JAL-2576 -->Very large alignments take a long time to
1885 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1886 added after a sequence was imported are not written to
1890 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1891 when importing RNA secondary structure via Stockholm
1894 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1895 not shown in correct direction for simple pseudoknots
1898 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1899 with lightGray or darkGray via features file (but can
1903 <!-- JAL-2383 -->Above PID colour threshold not recovered
1904 when alignment view imported from project
1907 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1908 structure and sequences extracted from structure files
1909 imported via URL and viewed in Jmol
1912 <!-- JAL-2520 -->Structures loaded via URL are saved in
1913 Jalview Projects rather than fetched via URL again when
1914 the project is loaded and the structure viewed
1917 <em>Web Services</em>
1920 <!-- JAL-2519 -->EnsemblGenomes example failing after
1921 release of Ensembl v.88
1924 <!-- JAL-2366 -->Proxy server address and port always
1925 appear enabled in Preferences->Connections
1928 <!-- JAL-2461 -->DAS registry not found exceptions
1929 removed from console output
1932 <!-- JAL-2582 -->Cannot retrieve protein products from
1933 Ensembl by Peptide ID
1936 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1937 created from SIFTs, and spurious 'Couldn't open structure
1938 in Chimera' errors raised after April 2017 update (problem
1939 due to 'null' string rather than empty string used for
1940 residues with no corresponding PDB mapping).
1943 <em>Application UI</em>
1946 <!-- JAL-2361 -->User Defined Colours not added to Colour
1950 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1951 case' residues (button in colourscheme editor debugged and
1952 new documentation and tooltips added)
1955 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1956 doesn't restore group-specific text colour thresholds
1959 <!-- JAL-2243 -->Feature settings panel does not update as
1960 new features are added to alignment
1963 <!-- JAL-2532 -->Cancel in feature settings reverts
1964 changes to feature colours via the Amend features dialog
1967 <!-- JAL-2506 -->Null pointer exception when attempting to
1968 edit graduated feature colour via amend features dialog
1972 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1973 selection menu changes colours of alignment views
1976 <!-- JAL-2426 -->Spurious exceptions in console raised
1977 from alignment calculation workers after alignment has
1981 <!-- JAL-1608 -->Typo in selection popup menu - Create
1982 groups now 'Create Group'
1985 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1986 Create/Undefine group doesn't always work
1989 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1990 shown again after pressing 'Cancel'
1993 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1994 adjusts start position in wrap mode
1997 <!-- JAL-2563 -->Status bar doesn't show positions for
1998 ambiguous amino acids
2001 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2002 CDS/Protein view after CDS sequences added for aligned
2006 <!-- JAL-2592 -->User defined colourschemes called 'User
2007 Defined' don't appear in Colours menu
2013 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2014 score models doesn't always result in an updated PCA plot
2017 <!-- JAL-2442 -->Features not rendered as transparent on
2018 overview or linked structure view
2021 <!-- JAL-2372 -->Colour group by conservation doesn't
2025 <!-- JAL-2517 -->Hitting Cancel after applying
2026 user-defined colourscheme doesn't restore original
2033 <!-- JAL-2314 -->Unit test failure:
2034 jalview.ws.jabaws.RNAStructExportImport setup fails
2037 <!-- JAL-2307 -->Unit test failure:
2038 jalview.ws.sifts.SiftsClientTest due to compatibility
2039 problems with deep array comparison equality asserts in
2040 successive versions of TestNG
2043 <!-- JAL-2479 -->Relocated StructureChooserTest and
2044 ParameterUtilsTest Unit tests to Network suite
2047 <em>New Known Issues</em>
2050 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2051 phase after a sequence motif find operation
2054 <!-- JAL-2550 -->Importing annotation file with rows
2055 containing just upper and lower case letters are
2056 interpreted as WUSS RNA secondary structure symbols
2059 <!-- JAL-2590 -->Cannot load and display Newick trees
2060 reliably from eggnog Ortholog database
2063 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2064 containing features of type Highlight' when 'B' is pressed
2065 to mark columns containing highlighted regions.
2068 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2069 doesn't always add secondary structure annotation.
2074 <td width="60" nowrap>
2075 <div align="center">
2076 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2079 <td><div align="left">
2083 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2084 for all consensus calculations
2087 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2090 <li>Updated Jalview's Certum code signing certificate
2093 <em>Application</em>
2096 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2097 set of database cross-references, sorted alphabetically
2100 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2101 from database cross references. Users with custom links
2102 will receive a <a href="webServices/urllinks.html#warning">warning
2103 dialog</a> asking them to update their preferences.
2106 <!-- JAL-2287-->Cancel button and escape listener on
2107 dialog warning user about disconnecting Jalview from a
2111 <!-- JAL-2320-->Jalview's Chimera control window closes if
2112 the Chimera it is connected to is shut down
2115 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2116 columns menu item to mark columns containing highlighted
2117 regions (e.g. from structure selections or results of a
2121 <!-- JAL-2284-->Command line option for batch-generation
2122 of HTML pages rendering alignment data with the BioJS
2132 <!-- JAL-2286 -->Columns with more than one modal residue
2133 are not coloured or thresholded according to percent
2134 identity (first observed in Jalview 2.8.2)
2137 <!-- JAL-2301 -->Threonine incorrectly reported as not
2141 <!-- JAL-2318 -->Updates to documentation pages (above PID
2142 threshold, amino acid properties)
2145 <!-- JAL-2292 -->Lower case residues in sequences are not
2146 reported as mapped to residues in a structure file in the
2150 <!--JAL-2324 -->Identical features with non-numeric scores
2151 could be added multiple times to a sequence
2154 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2155 bond features shown as two highlighted residues rather
2156 than a range in linked structure views, and treated
2157 correctly when selecting and computing trees from features
2160 <!-- JAL-2281-->Custom URL links for database
2161 cross-references are matched to database name regardless
2166 <em>Application</em>
2169 <!-- JAL-2282-->Custom URL links for specific database
2170 names without regular expressions also offer links from
2174 <!-- JAL-2315-->Removing a single configured link in the
2175 URL links pane in Connections preferences doesn't actually
2176 update Jalview configuration
2179 <!-- JAL-2272-->CTRL-Click on a selected region to open
2180 the alignment area popup menu doesn't work on El-Capitan
2183 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2184 files with similarly named sequences if dropped onto the
2188 <!-- JAL-2312 -->Additional mappings are shown for PDB
2189 entries where more chains exist in the PDB accession than
2190 are reported in the SIFTS file
2193 <!-- JAL-2317-->Certain structures do not get mapped to
2194 the structure view when displayed with Chimera
2197 <!-- JAL-2317-->No chains shown in the Chimera view
2198 panel's View->Show Chains submenu
2201 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2202 work for wrapped alignment views
2205 <!--JAL-2197 -->Rename UI components for running JPred
2206 predictions from 'JNet' to 'JPred'
2209 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2210 corrupted when annotation panel vertical scroll is not at
2211 first annotation row
2214 <!--JAL-2332 -->Attempting to view structure for Hen
2215 lysozyme results in a PDB Client error dialog box
2218 <!-- JAL-2319 -->Structure View's mapping report switched
2219 ranges for PDB and sequence for SIFTS
2222 SIFTS 'Not_Observed' residues mapped to non-existant
2226 <!-- <em>New Known Issues</em>
2233 <td width="60" nowrap>
2234 <div align="center">
2235 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2236 <em>25/10/2016</em></strong>
2239 <td><em>Application</em>
2241 <li>3D Structure chooser opens with 'Cached structures'
2242 view if structures already loaded</li>
2243 <li>Progress bar reports models as they are loaded to
2244 structure views</li>
2250 <li>Colour by conservation always enabled and no tick
2251 shown in menu when BLOSUM or PID shading applied</li>
2252 <li>FER1_ARATH and FER2_ARATH labels were switched in
2253 example sequences/projects/trees</li>
2255 <em>Application</em>
2257 <li>Jalview projects with views of local PDB structure
2258 files saved on Windows cannot be opened on OSX</li>
2259 <li>Multiple structure views can be opened and superposed
2260 without timeout for structures with multiple models or
2261 multiple sequences in alignment</li>
2262 <li>Cannot import or associated local PDB files without a
2263 PDB ID HEADER line</li>
2264 <li>RMSD is not output in Jmol console when superposition
2266 <li>Drag and drop of URL from Browser fails for Linux and
2267 OSX versions earlier than El Capitan</li>
2268 <li>ENA client ignores invalid content from ENA server</li>
2269 <li>Exceptions are not raised in console when ENA client
2270 attempts to fetch non-existent IDs via Fetch DB Refs UI
2272 <li>Exceptions are not raised in console when a new view
2273 is created on the alignment</li>
2274 <li>OSX right-click fixed for group selections: CMD-click
2275 to insert/remove gaps in groups and CTRL-click to open group
2278 <em>Build and deployment</em>
2280 <li>URL link checker now copes with multi-line anchor
2283 <em>New Known Issues</em>
2285 <li>Drag and drop from URL links in browsers do not work
2292 <td width="60" nowrap>
2293 <div align="center">
2294 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2297 <td><em>General</em>
2300 <!-- JAL-2124 -->Updated Spanish translations.
2303 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2304 for importing structure data to Jalview. Enables mmCIF and
2308 <!-- JAL-192 --->Alignment ruler shows positions relative to
2312 <!-- JAL-2202 -->Position/residue shown in status bar when
2313 mousing over sequence associated annotation
2316 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2320 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2321 '()', canonical '[]' and invalid '{}' base pair populations
2325 <!-- JAL-2092 -->Feature settings popup menu options for
2326 showing or hiding columns containing a feature
2329 <!-- JAL-1557 -->Edit selected group by double clicking on
2330 group and sequence associated annotation labels
2333 <!-- JAL-2236 -->Sequence name added to annotation label in
2334 select/hide columns by annotation and colour by annotation
2338 </ul> <em>Application</em>
2341 <!-- JAL-2050-->Automatically hide introns when opening a
2342 gene/transcript view
2345 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2349 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2350 structure mappings with the EMBL-EBI PDBe SIFTS database
2353 <!-- JAL-2079 -->Updated download sites used for Rfam and
2354 Pfam sources to xfam.org
2357 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2360 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2361 over sequences in Jalview
2364 <!-- JAL-2027-->Support for reverse-complement coding
2365 regions in ENA and EMBL
2368 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2369 for record retrieval via ENA rest API
2372 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2376 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2377 groovy script execution
2380 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2381 alignment window's Calculate menu
2384 <!-- JAL-1812 -->Allow groovy scripts that call
2385 Jalview.getAlignFrames() to run in headless mode
2388 <!-- JAL-2068 -->Support for creating new alignment
2389 calculation workers from groovy scripts
2392 <!-- JAL-1369 --->Store/restore reference sequence in
2396 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2397 associations are now saved/restored from project
2400 <!-- JAL-1993 -->Database selection dialog always shown
2401 before sequence fetcher is opened
2404 <!-- JAL-2183 -->Double click on an entry in Jalview's
2405 database chooser opens a sequence fetcher
2408 <!-- JAL-1563 -->Free-text search client for UniProt using
2409 the UniProt REST API
2412 <!-- JAL-2168 -->-nonews command line parameter to prevent
2413 the news reader opening
2416 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2417 querying stored in preferences
2420 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2424 <!-- JAL-1977-->Tooltips shown on database chooser
2427 <!-- JAL-391 -->Reverse complement function in calculate
2428 menu for nucleotide sequences
2431 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2432 and feature counts preserves alignment ordering (and
2433 debugged for complex feature sets).
2436 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2437 viewing structures with Jalview 2.10
2440 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2441 genome, transcript CCDS and gene ids via the Ensembl and
2442 Ensembl Genomes REST API
2445 <!-- JAL-2049 -->Protein sequence variant annotation
2446 computed for 'sequence_variant' annotation on CDS regions
2450 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2454 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2455 Ref Fetcher fails to match, or otherwise updates sequence
2456 data from external database records.
2459 <!-- JAL-2154 -->Revised Jalview Project format for
2460 efficient recovery of sequence coding and alignment
2461 annotation relationships.
2463 </ul> <!-- <em>Applet</em>
2474 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2478 <!-- JAL-2018-->Export features in Jalview format (again)
2479 includes graduated colourschemes
2482 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2483 working with big alignments and lots of hidden columns
2486 <!-- JAL-2053-->Hidden column markers not always rendered
2487 at right of alignment window
2490 <!-- JAL-2067 -->Tidied up links in help file table of
2494 <!-- JAL-2072 -->Feature based tree calculation not shown
2498 <!-- JAL-2075 -->Hidden columns ignored during feature
2499 based tree calculation
2502 <!-- JAL-2065 -->Alignment view stops updating when show
2503 unconserved enabled for group on alignment
2506 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2510 <!-- JAL-2146 -->Alignment column in status incorrectly
2511 shown as "Sequence position" when mousing over
2515 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2516 hidden columns present
2519 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2520 user created annotation added to alignment
2523 <!-- JAL-1841 -->RNA Structure consensus only computed for
2524 '()' base pair annotation
2527 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2528 in zero scores for all base pairs in RNA Structure
2532 <!-- JAL-2174-->Extend selection with columns containing
2536 <!-- JAL-2275 -->Pfam format writer puts extra space at
2537 beginning of sequence
2540 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2544 <!-- JAL-2238 -->Cannot create groups on an alignment from
2545 from a tree when t-coffee scores are shown
2548 <!-- JAL-1836,1967 -->Cannot import and view PDB
2549 structures with chains containing negative resnums (4q4h)
2552 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2556 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2557 to Clustal, PIR and PileUp output
2560 <!-- JAL-2008 -->Reordering sequence features that are
2561 not visible causes alignment window to repaint
2564 <!-- JAL-2006 -->Threshold sliders don't work in
2565 graduated colour and colour by annotation row for e-value
2566 scores associated with features and annotation rows
2569 <!-- JAL-1797 -->amino acid physicochemical conservation
2570 calculation should be case independent
2573 <!-- JAL-2173 -->Remove annotation also updates hidden
2577 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2578 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2579 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2582 <!-- JAL-2065 -->Null pointer exceptions and redraw
2583 problems when reference sequence defined and 'show
2584 non-conserved' enabled
2587 <!-- JAL-1306 -->Quality and Conservation are now shown on
2588 load even when Consensus calculation is disabled
2591 <!-- JAL-1932 -->Remove right on penultimate column of
2592 alignment does nothing
2595 <em>Application</em>
2598 <!-- JAL-1552-->URLs and links can't be imported by
2599 drag'n'drop on OSX when launched via webstart (note - not
2600 yet fixed for El Capitan)
2603 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2604 output when running on non-gb/us i18n platforms
2607 <!-- JAL-1944 -->Error thrown when exporting a view with
2608 hidden sequences as flat-file alignment
2611 <!-- JAL-2030-->InstallAnywhere distribution fails when
2615 <!-- JAL-2080-->Jalview very slow to launch via webstart
2616 (also hotfix for 2.9.0b2)
2619 <!-- JAL-2085 -->Cannot save project when view has a
2620 reference sequence defined
2623 <!-- JAL-1011 -->Columns are suddenly selected in other
2624 alignments and views when revealing hidden columns
2627 <!-- JAL-1989 -->Hide columns not mirrored in complement
2628 view in a cDNA/Protein splitframe
2631 <!-- JAL-1369 -->Cannot save/restore representative
2632 sequence from project when only one sequence is
2636 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2637 in Structure Chooser
2640 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2641 structure consensus didn't refresh annotation panel
2644 <!-- JAL-1962 -->View mapping in structure view shows
2645 mappings between sequence and all chains in a PDB file
2648 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2649 dialogs format columns correctly, don't display array
2650 data, sort columns according to type
2653 <!-- JAL-1975 -->Export complete shown after destination
2654 file chooser is cancelled during an image export
2657 <!-- JAL-2025 -->Error when querying PDB Service with
2658 sequence name containing special characters
2661 <!-- JAL-2024 -->Manual PDB structure querying should be
2665 <!-- JAL-2104 -->Large tooltips with broken HTML
2666 formatting don't wrap
2669 <!-- JAL-1128 -->Figures exported from wrapped view are
2670 truncated so L looks like I in consensus annotation
2673 <!-- JAL-2003 -->Export features should only export the
2674 currently displayed features for the current selection or
2678 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2679 after fetching cross-references, and restoring from
2683 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2684 followed in the structure viewer
2687 <!-- JAL-2163 -->Titles for individual alignments in
2688 splitframe not restored from project
2691 <!-- JAL-2145 -->missing autocalculated annotation at
2692 trailing end of protein alignment in transcript/product
2693 splitview when pad-gaps not enabled by default
2696 <!-- JAL-1797 -->amino acid physicochemical conservation
2700 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2701 article has been read (reopened issue due to
2702 internationalisation problems)
2705 <!-- JAL-1960 -->Only offer PDB structures in structure
2706 viewer based on sequence name, PDB and UniProt
2711 <!-- JAL-1976 -->No progress bar shown during export of
2715 <!-- JAL-2213 -->Structures not always superimposed after
2716 multiple structures are shown for one or more sequences.
2719 <!-- JAL-1370 -->Reference sequence characters should not
2720 be replaced with '.' when 'Show unconserved' format option
2724 <!-- JAL-1823 -->Cannot specify chain code when entering
2725 specific PDB id for sequence
2728 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2729 'Export hidden sequences' is enabled, but 'export hidden
2730 columns' is disabled.
2733 <!--JAL-2026-->Best Quality option in structure chooser
2734 selects lowest rather than highest resolution structures
2738 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2739 to sequence mapping in 'View Mappings' report
2742 <!-- JAL-2284 -->Unable to read old Jalview projects that
2743 contain non-XML data added after Jalvew wrote project.
2746 <!-- JAL-2118 -->Newly created annotation row reorders
2747 after clicking on it to create new annotation for a
2751 <!-- JAL-1980 -->Null Pointer Exception raised when
2752 pressing Add on an orphaned cut'n'paste window.
2754 <!-- may exclude, this is an external service stability issue JAL-1941
2755 -- > RNA 3D structure not added via DSSR service</li> -->
2760 <!-- JAL-2151 -->Incorrect columns are selected when
2761 hidden columns present before start of sequence
2764 <!-- JAL-1986 -->Missing dependencies on applet pages
2768 <!-- JAL-1947 -->Overview pixel size changes when
2769 sequences are hidden in applet
2772 <!-- JAL-1996 -->Updated instructions for applet
2773 deployment on examples pages.
2780 <td width="60" nowrap>
2781 <div align="center">
2782 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2783 <em>16/10/2015</em></strong>
2786 <td><em>General</em>
2788 <li>Time stamps for signed Jalview application and applet
2793 <em>Application</em>
2795 <li>Duplicate group consensus and conservation rows
2796 shown when tree is partitioned</li>
2797 <li>Erratic behaviour when tree partitions made with
2798 multiple cDNA/Protein split views</li>
2804 <td width="60" nowrap>
2805 <div align="center">
2806 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2807 <em>8/10/2015</em></strong>
2810 <td><em>General</em>
2812 <li>Updated Spanish translations of localized text for
2814 </ul> <em>Application</em>
2816 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2817 <li>Signed OSX InstallAnywhere installer<br></li>
2818 <li>Support for per-sequence based annotations in BioJSON</li>
2819 </ul> <em>Applet</em>
2821 <li>Split frame example added to applet examples page</li>
2822 </ul> <em>Build and Deployment</em>
2825 <!-- JAL-1888 -->New ant target for running Jalview's test
2833 <li>Mapping of cDNA to protein in split frames
2834 incorrect when sequence start > 1</li>
2835 <li>Broken images in filter column by annotation dialog
2837 <li>Feature colours not parsed from features file</li>
2838 <li>Exceptions and incomplete link URLs recovered when
2839 loading a features file containing HTML tags in feature
2843 <em>Application</em>
2845 <li>Annotations corrupted after BioJS export and
2847 <li>Incorrect sequence limits after Fetch DB References
2848 with 'trim retrieved sequences'</li>
2849 <li>Incorrect warning about deleting all data when
2850 deleting selected columns</li>
2851 <li>Patch to build system for shipping properly signed
2852 JNLP templates for webstart launch</li>
2853 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2854 unreleased structures for download or viewing</li>
2855 <li>Tab/space/return keystroke operation of EMBL-PDBe
2856 fetcher/viewer dialogs works correctly</li>
2857 <li>Disabled 'minimise' button on Jalview windows
2858 running on OSX to workaround redraw hang bug</li>
2859 <li>Split cDNA/Protein view position and geometry not
2860 recovered from jalview project</li>
2861 <li>Initial enabled/disabled state of annotation menu
2862 sorter 'show autocalculated first/last' corresponds to
2864 <li>Restoring of Clustal, RNA Helices and T-Coffee
2865 color schemes from BioJSON</li>
2869 <li>Reorder sequences mirrored in cDNA/Protein split
2871 <li>Applet with Jmol examples not loading correctly</li>
2877 <td><div align="center">
2878 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2880 <td><em>General</em>
2882 <li>Linked visualisation and analysis of DNA and Protein
2885 <li>Translated cDNA alignments shown as split protein
2886 and DNA alignment views</li>
2887 <li>Codon consensus annotation for linked protein and
2888 cDNA alignment views</li>
2889 <li>Link cDNA or Protein product sequences by loading
2890 them onto Protein or cDNA alignments</li>
2891 <li>Reconstruct linked cDNA alignment from aligned
2892 protein sequences</li>
2895 <li>Jmol integration updated to Jmol v14.2.14</li>
2896 <li>Import and export of Jalview alignment views as <a
2897 href="features/bioJsonFormat.html">BioJSON</a></li>
2898 <li>New alignment annotation file statements for
2899 reference sequences and marking hidden columns</li>
2900 <li>Reference sequence based alignment shading to
2901 highlight variation</li>
2902 <li>Select or hide columns according to alignment
2904 <li>Find option for locating sequences by description</li>
2905 <li>Conserved physicochemical properties shown in amino
2906 acid conservation row</li>
2907 <li>Alignments can be sorted by number of RNA helices</li>
2908 </ul> <em>Application</em>
2910 <li>New cDNA/Protein analysis capabilities
2912 <li>Get Cross-References should open a Split Frame
2913 view with cDNA/Protein</li>
2914 <li>Detect when nucleotide sequences and protein
2915 sequences are placed in the same alignment</li>
2916 <li>Split cDNA/Protein views are saved in Jalview
2921 <li>Use REST API to talk to Chimera</li>
2922 <li>Selected regions in Chimera are highlighted in linked
2923 Jalview windows</li>
2925 <li>VARNA RNA viewer updated to v3.93</li>
2926 <li>VARNA views are saved in Jalview Projects</li>
2927 <li>Pseudoknots displayed as Jalview RNA annotation can
2928 be shown in VARNA</li>
2930 <li>Make groups for selection uses marked columns as well
2931 as the active selected region</li>
2933 <li>Calculate UPGMA and NJ trees using sequence feature
2935 <li>New Export options
2937 <li>New Export Settings dialog to control hidden
2938 region export in flat file generation</li>
2940 <li>Export alignment views for display with the <a
2941 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2943 <li>Export scrollable SVG in HTML page</li>
2944 <li>Optional embedding of BioJSON data when exporting
2945 alignment figures to HTML</li>
2947 <li>3D structure retrieval and display
2949 <li>Free text and structured queries with the PDBe
2951 <li>PDBe Search API based discovery and selection of
2952 PDB structures for a sequence set</li>
2956 <li>JPred4 employed for protein secondary structure
2958 <li>Hide Insertions menu option to hide unaligned columns
2959 for one or a group of sequences</li>
2960 <li>Automatically hide insertions in alignments imported
2961 from the JPred4 web server</li>
2962 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2963 system on OSX<br />LGPL libraries courtesy of <a
2964 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2966 <li>changed 'View nucleotide structure' submenu to 'View
2967 VARNA 2D Structure'</li>
2968 <li>change "View protein structure" menu option to "3D
2971 </ul> <em>Applet</em>
2973 <li>New layout for applet example pages</li>
2974 <li>New parameters to enable SplitFrame view
2975 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2976 <li>New example demonstrating linked viewing of cDNA and
2977 Protein alignments</li>
2978 </ul> <em>Development and deployment</em>
2980 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2981 <li>Include installation type and git revision in build
2982 properties and console log output</li>
2983 <li>Jalview Github organisation, and new github site for
2984 storing BioJsMSA Templates</li>
2985 <li>Jalview's unit tests now managed with TestNG</li>
2988 <!-- <em>General</em>
2990 </ul> --> <!-- issues resolved --> <em>Application</em>
2992 <li>Escape should close any open find dialogs</li>
2993 <li>Typo in select-by-features status report</li>
2994 <li>Consensus RNA secondary secondary structure
2995 predictions are not highlighted in amber</li>
2996 <li>Missing gap character in v2.7 example file means
2997 alignment appears unaligned when pad-gaps is not enabled</li>
2998 <li>First switch to RNA Helices colouring doesn't colour
2999 associated structure views</li>
3000 <li>ID width preference option is greyed out when auto
3001 width checkbox not enabled</li>
3002 <li>Stopped a warning dialog from being shown when
3003 creating user defined colours</li>
3004 <li>'View Mapping' in structure viewer shows sequence
3005 mappings for just that viewer's sequences</li>
3006 <li>Workaround for superposing PDB files containing
3007 multiple models in Chimera</li>
3008 <li>Report sequence position in status bar when hovering
3009 over Jmol structure</li>
3010 <li>Cannot output gaps as '.' symbols with Selection ->
3011 output to text box</li>
3012 <li>Flat file exports of alignments with hidden columns
3013 have incorrect sequence start/end</li>
3014 <li>'Aligning' a second chain to a Chimera structure from
3016 <li>Colour schemes applied to structure viewers don't
3017 work for nucleotide</li>
3018 <li>Loading/cut'n'pasting an empty or invalid file leads
3019 to a grey/invisible alignment window</li>
3020 <li>Exported Jpred annotation from a sequence region
3021 imports to different position</li>
3022 <li>Space at beginning of sequence feature tooltips shown
3023 on some platforms</li>
3024 <li>Chimera viewer 'View | Show Chain' menu is not
3026 <li>'New View' fails with a Null Pointer Exception in
3027 console if Chimera has been opened</li>
3028 <li>Mouseover to Chimera not working</li>
3029 <li>Miscellaneous ENA XML feature qualifiers not
3031 <li>NPE in annotation renderer after 'Extract Scores'</li>
3032 <li>If two structures in one Chimera window, mouseover of
3033 either sequence shows on first structure</li>
3034 <li>'Show annotations' options should not make
3035 non-positional annotations visible</li>
3036 <li>Subsequence secondary structure annotation not shown
3037 in right place after 'view flanking regions'</li>
3038 <li>File Save As type unset when current file format is
3040 <li>Save as '.jar' option removed for saving Jalview
3042 <li>Colour by Sequence colouring in Chimera more
3044 <li>Cannot 'add reference annotation' for a sequence in
3045 several views on same alignment</li>
3046 <li>Cannot show linked products for EMBL / ENA records</li>
3047 <li>Jalview's tooltip wraps long texts containing no
3049 </ul> <em>Applet</em>
3051 <li>Jmol to JalviewLite mouseover/link not working</li>
3052 <li>JalviewLite can't import sequences with ID
3053 descriptions containing angle brackets</li>
3054 </ul> <em>General</em>
3056 <li>Cannot export and reimport RNA secondary structure
3057 via jalview annotation file</li>
3058 <li>Random helix colour palette for colour by annotation
3059 with RNA secondary structure</li>
3060 <li>Mouseover to cDNA from STOP residue in protein
3061 translation doesn't work.</li>
3062 <li>hints when using the select by annotation dialog box</li>
3063 <li>Jmol alignment incorrect if PDB file has alternate CA
3065 <li>FontChooser message dialog appears to hang after
3066 choosing 1pt font</li>
3067 <li>Peptide secondary structure incorrectly imported from
3068 annotation file when annotation display text includes 'e' or
3070 <li>Cannot set colour of new feature type whilst creating
3072 <li>cDNA translation alignment should not be sequence
3073 order dependent</li>
3074 <li>'Show unconserved' doesn't work for lower case
3076 <li>Nucleotide ambiguity codes involving R not recognised</li>
3077 </ul> <em>Deployment and Documentation</em>
3079 <li>Applet example pages appear different to the rest of
3080 www.jalview.org</li>
3081 </ul> <em>Application Known issues</em>
3083 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3084 <li>Misleading message appears after trying to delete
3086 <li>Jalview icon not shown in dock after InstallAnywhere
3087 version launches</li>
3088 <li>Fetching EMBL reference for an RNA sequence results
3089 fails with a sequence mismatch</li>
3090 <li>Corrupted or unreadable alignment display when
3091 scrolling alignment to right</li>
3092 <li>ArrayIndexOutOfBoundsException thrown when remove
3093 empty columns called on alignment with ragged gapped ends</li>
3094 <li>auto calculated alignment annotation rows do not get
3095 placed above or below non-autocalculated rows</li>
3096 <li>Jalview dekstop becomes sluggish at full screen in
3097 ultra-high resolution</li>
3098 <li>Cannot disable consensus calculation independently of
3099 quality and conservation</li>
3100 <li>Mouseover highlighting between cDNA and protein can
3101 become sluggish with more than one splitframe shown</li>
3102 </ul> <em>Applet Known Issues</em>
3104 <li>Core PDB parsing code requires Jmol</li>
3105 <li>Sequence canvas panel goes white when alignment
3106 window is being resized</li>
3112 <td><div align="center">
3113 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3115 <td><em>General</em>
3117 <li>Updated Java code signing certificate donated by
3119 <li>Features and annotation preserved when performing
3120 pairwise alignment</li>
3121 <li>RNA pseudoknot annotation can be
3122 imported/exported/displayed</li>
3123 <li>'colour by annotation' can colour by RNA and
3124 protein secondary structure</li>
3125 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3126 post-hoc with 2.9 release</em>)
3129 </ul> <em>Application</em>
3131 <li>Extract and display secondary structure for sequences
3132 with 3D structures</li>
3133 <li>Support for parsing RNAML</li>
3134 <li>Annotations menu for layout
3136 <li>sort sequence annotation rows by alignment</li>
3137 <li>place sequence annotation above/below alignment
3140 <li>Output in Stockholm format</li>
3141 <li>Internationalisation: improved Spanish (es)
3143 <li>Structure viewer preferences tab</li>
3144 <li>Disorder and Secondary Structure annotation tracks
3145 shared between alignments</li>
3146 <li>UCSF Chimera launch and linked highlighting from
3148 <li>Show/hide all sequence associated annotation rows for
3149 all or current selection</li>
3150 <li>disorder and secondary structure predictions
3151 available as dataset annotation</li>
3152 <li>Per-sequence rna helices colouring</li>
3155 <li>Sequence database accessions imported when fetching
3156 alignments from Rfam</li>
3157 <li>update VARNA version to 3.91</li>
3159 <li>New groovy scripts for exporting aligned positions,
3160 conservation values, and calculating sum of pairs scores.</li>
3161 <li>Command line argument to set default JABAWS server</li>
3162 <li>include installation type in build properties and
3163 console log output</li>
3164 <li>Updated Jalview project format to preserve dataset
3168 <!-- issues resolved --> <em>Application</em>
3170 <li>Distinguish alignment and sequence associated RNA
3171 structure in structure->view->VARNA</li>
3172 <li>Raise dialog box if user deletes all sequences in an
3174 <li>Pressing F1 results in documentation opening twice</li>
3175 <li>Sequence feature tooltip is wrapped</li>
3176 <li>Double click on sequence associated annotation
3177 selects only first column</li>
3178 <li>Redundancy removal doesn't result in unlinked
3179 leaves shown in tree</li>
3180 <li>Undos after several redundancy removals don't undo
3182 <li>Hide sequence doesn't hide associated annotation</li>
3183 <li>User defined colours dialog box too big to fit on
3184 screen and buttons not visible</li>
3185 <li>author list isn't updated if already written to
3186 Jalview properties</li>
3187 <li>Popup menu won't open after retrieving sequence
3189 <li>File open window for associate PDB doesn't open</li>
3190 <li>Left-then-right click on a sequence id opens a
3191 browser search window</li>
3192 <li>Cannot open sequence feature shading/sort popup menu
3193 in feature settings dialog</li>
3194 <li>better tooltip placement for some areas of Jalview
3196 <li>Allow addition of JABAWS Server which doesn't
3197 pass validation</li>
3198 <li>Web services parameters dialog box is too large to
3200 <li>Muscle nucleotide alignment preset obscured by
3202 <li>JABAWS preset submenus don't contain newly
3203 defined user preset</li>
3204 <li>MSA web services warns user if they were launched
3205 with invalid input</li>
3206 <li>Jalview cannot contact DAS Registy when running on
3209 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3210 'Superpose with' submenu not shown when new view
3214 </ul> <!-- <em>Applet</em>
3216 </ul> <em>General</em>
3218 </ul>--> <em>Deployment and Documentation</em>
3220 <li>2G and 1G options in launchApp have no effect on
3221 memory allocation</li>
3222 <li>launchApp service doesn't automatically open
3223 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3225 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3226 InstallAnywhere reports cannot find valid JVM when Java
3227 1.7_055 is available
3229 </ul> <em>Application Known issues</em>
3232 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3233 corrupted or unreadable alignment display when scrolling
3237 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3238 retrieval fails but progress bar continues for DAS retrieval
3239 with large number of ID
3242 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3243 flatfile output of visible region has incorrect sequence
3247 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3248 rna structure consensus doesn't update when secondary
3249 structure tracks are rearranged
3252 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3253 invalid rna structure positional highlighting does not
3254 highlight position of invalid base pairs
3257 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3258 out of memory errors are not raised when saving Jalview
3259 project from alignment window file menu
3262 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3263 Switching to RNA Helices colouring doesn't propagate to
3267 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3268 colour by RNA Helices not enabled when user created
3269 annotation added to alignment
3272 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3273 Jalview icon not shown on dock in Mountain Lion/Webstart
3275 </ul> <em>Applet Known Issues</em>
3278 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3279 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3282 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3283 Jalview and Jmol example not compatible with IE9
3286 <li>Sort by annotation score doesn't reverse order
3292 <td><div align="center">
3293 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3296 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3299 <li>Internationalisation of user interface (usually
3300 called i18n support) and translation for Spanish locale</li>
3301 <li>Define/Undefine group on current selection with
3302 Ctrl-G/Shift Ctrl-G</li>
3303 <li>Improved group creation/removal options in
3304 alignment/sequence Popup menu</li>
3305 <li>Sensible precision for symbol distribution
3306 percentages shown in logo tooltip.</li>
3307 <li>Annotation panel height set according to amount of
3308 annotation when alignment first opened</li>
3309 </ul> <em>Application</em>
3311 <li>Interactive consensus RNA secondary structure
3312 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3313 <li>Select columns containing particular features from
3314 Feature Settings dialog</li>
3315 <li>View all 'representative' PDB structures for selected
3317 <li>Update Jalview project format:
3319 <li>New file extension for Jalview projects '.jvp'</li>
3320 <li>Preserve sequence and annotation dataset (to
3321 store secondary structure annotation,etc)</li>
3322 <li>Per group and alignment annotation and RNA helix
3326 <li>New similarity measures for PCA and Tree calculation
3328 <li>Experimental support for retrieval and viewing of
3329 flanking regions for an alignment</li>
3333 <!-- issues resolved --> <em>Application</em>
3335 <li>logo keeps spinning and status remains at queued or
3336 running after job is cancelled</li>
3337 <li>cannot export features from alignments imported from
3338 Jalview/VAMSAS projects</li>
3339 <li>Buggy slider for web service parameters that take
3341 <li>Newly created RNA secondary structure line doesn't
3342 have 'display all symbols' flag set</li>
3343 <li>T-COFFEE alignment score shading scheme and other
3344 annotation shading not saved in Jalview project</li>
3345 <li>Local file cannot be loaded in freshly downloaded
3347 <li>Jalview icon not shown on dock in Mountain
3349 <li>Load file from desktop file browser fails</li>
3350 <li>Occasional NPE thrown when calculating large trees</li>
3351 <li>Cannot reorder or slide sequences after dragging an
3352 alignment onto desktop</li>
3353 <li>Colour by annotation dialog throws NPE after using
3354 'extract scores' function</li>
3355 <li>Loading/cut'n'pasting an empty file leads to a grey
3356 alignment window</li>
3357 <li>Disorder thresholds rendered incorrectly after
3358 performing IUPred disorder prediction</li>
3359 <li>Multiple group annotated consensus rows shown when
3360 changing 'normalise logo' display setting</li>
3361 <li>Find shows blank dialog after 'finished searching' if
3362 nothing matches query</li>
3363 <li>Null Pointer Exceptions raised when sorting by
3364 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3366 <li>Errors in Jmol console when structures in alignment
3367 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3369 <li>Not all working JABAWS services are shown in
3371 <li>JAVAWS version of Jalview fails to launch with
3372 'invalid literal/length code'</li>
3373 <li>Annotation/RNA Helix colourschemes cannot be applied
3374 to alignment with groups (actually fixed in 2.8.0b1)</li>
3375 <li>RNA Helices and T-Coffee Scores available as default
3378 </ul> <em>Applet</em>
3380 <li>Remove group option is shown even when selection is
3382 <li>Apply to all groups ticked but colourscheme changes
3383 don't affect groups</li>
3384 <li>Documented RNA Helices and T-Coffee Scores as valid
3385 colourscheme name</li>
3386 <li>Annotation labels drawn on sequence IDs when
3387 Annotation panel is not displayed</li>
3388 <li>Increased font size for dropdown menus on OSX and
3389 embedded windows</li>
3390 </ul> <em>Other</em>
3392 <li>Consensus sequence for alignments/groups with a
3393 single sequence were not calculated</li>
3394 <li>annotation files that contain only groups imported as
3395 annotation and junk sequences</li>
3396 <li>Fasta files with sequences containing '*' incorrectly
3397 recognised as PFAM or BLC</li>
3398 <li>conservation/PID slider apply all groups option
3399 doesn't affect background (2.8.0b1)
3401 <li>redundancy highlighting is erratic at 0% and 100%</li>
3402 <li>Remove gapped columns fails for sequences with ragged
3404 <li>AMSA annotation row with leading spaces is not
3405 registered correctly on import</li>
3406 <li>Jalview crashes when selecting PCA analysis for
3407 certain alignments</li>
3408 <li>Opening the colour by annotation dialog for an
3409 existing annotation based 'use original colours'
3410 colourscheme loses original colours setting</li>
3415 <td><div align="center">
3416 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3417 <em>30/1/2014</em></strong>
3421 <li>Trusted certificates for JalviewLite applet and
3422 Jalview Desktop application<br />Certificate was donated by
3423 <a href="https://www.certum.eu">Certum</a> to the Jalview
3424 open source project).
3426 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3427 <li>Output in Stockholm format</li>
3428 <li>Allow import of data from gzipped files</li>
3429 <li>Export/import group and sequence associated line
3430 graph thresholds</li>
3431 <li>Nucleotide substitution matrix that supports RNA and
3432 ambiguity codes</li>
3433 <li>Allow disorder predictions to be made on the current
3434 selection (or visible selection) in the same way that JPred
3436 <li>Groovy scripting for headless Jalview operation</li>
3437 </ul> <em>Other improvements</em>
3439 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3440 <li>COMBINE statement uses current SEQUENCE_REF and
3441 GROUP_REF scope to group annotation rows</li>
3442 <li>Support '' style escaping of quotes in Newick
3444 <li>Group options for JABAWS service by command line name</li>
3445 <li>Empty tooltip shown for JABA service options with a
3446 link but no description</li>
3447 <li>Select primary source when selecting authority in
3448 database fetcher GUI</li>
3449 <li>Add .mfa to FASTA file extensions recognised by
3451 <li>Annotation label tooltip text wrap</li>
3456 <li>Slow scrolling when lots of annotation rows are
3458 <li>Lots of NPE (and slowness) after creating RNA
3459 secondary structure annotation line</li>
3460 <li>Sequence database accessions not imported when
3461 fetching alignments from Rfam</li>
3462 <li>Incorrect SHMR submission for sequences with
3464 <li>View all structures does not always superpose
3466 <li>Option widgets in service parameters not updated to
3467 reflect user or preset settings</li>
3468 <li>Null pointer exceptions for some services without
3469 presets or adjustable parameters</li>
3470 <li>Discover PDB IDs entry in structure menu doesn't
3471 discover PDB xRefs</li>
3472 <li>Exception encountered while trying to retrieve
3473 features with DAS</li>
3474 <li>Lowest value in annotation row isn't coloured
3475 when colour by annotation (per sequence) is coloured</li>
3476 <li>Keyboard mode P jumps to start of gapped region when
3477 residue follows a gap</li>
3478 <li>Jalview appears to hang importing an alignment with
3479 Wrap as default or after enabling Wrap</li>
3480 <li>'Right click to add annotations' message
3481 shown in wrap mode when no annotations present</li>
3482 <li>Disorder predictions fail with NPE if no automatic
3483 annotation already exists on alignment</li>
3484 <li>oninit javascript function should be called after
3485 initialisation completes</li>
3486 <li>Remove redundancy after disorder prediction corrupts
3487 alignment window display</li>
3488 <li>Example annotation file in documentation is invalid</li>
3489 <li>Grouped line graph annotation rows are not exported
3490 to annotation file</li>
3491 <li>Multi-harmony analysis cannot be run when only two
3493 <li>Cannot create multiple groups of line graphs with
3494 several 'combine' statements in annotation file</li>
3495 <li>Pressing return several times causes Number Format
3496 exceptions in keyboard mode</li>
3497 <li>Multi-harmony (SHMMR) method doesn't submit
3498 correct partitions for input data</li>
3499 <li>Translation from DNA to Amino Acids fails</li>
3500 <li>Jalview fail to load newick tree with quoted label</li>
3501 <li>--headless flag isn't understood</li>
3502 <li>ClassCastException when generating EPS in headless
3504 <li>Adjusting sequence-associated shading threshold only
3505 changes one row's threshold</li>
3506 <li>Preferences and Feature settings panel panel
3507 doesn't open</li>
3508 <li>hide consensus histogram also hides conservation and
3509 quality histograms</li>
3514 <td><div align="center">
3515 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3517 <td><em>Application</em>
3519 <li>Support for JABAWS 2.0 Services (AACon alignment
3520 conservation, protein disorder and Clustal Omega)</li>
3521 <li>JABAWS server status indicator in Web Services
3523 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3524 in Jalview alignment window</li>
3525 <li>Updated Jalview build and deploy framework for OSX
3526 mountain lion, windows 7, and 8</li>
3527 <li>Nucleotide substitution matrix for PCA that supports
3528 RNA and ambiguity codes</li>
3530 <li>Improved sequence database retrieval GUI</li>
3531 <li>Support fetching and database reference look up
3532 against multiple DAS sources (Fetch all from in 'fetch db
3534 <li>Jalview project improvements
3536 <li>Store and retrieve the 'belowAlignment'
3537 flag for annotation</li>
3538 <li>calcId attribute to group annotation rows on the
3540 <li>Store AACon calculation settings for a view in
3541 Jalview project</li>
3545 <li>horizontal scrolling gesture support</li>
3546 <li>Visual progress indicator when PCA calculation is
3548 <li>Simpler JABA web services menus</li>
3549 <li>visual indication that web service results are still
3550 being retrieved from server</li>
3551 <li>Serialise the dialogs that are shown when Jalview
3552 starts up for first time</li>
3553 <li>Jalview user agent string for interacting with HTTP
3555 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3557 <li>Examples directory and Groovy library included in
3558 InstallAnywhere distribution</li>
3559 </ul> <em>Applet</em>
3561 <li>RNA alignment and secondary structure annotation
3562 visualization applet example</li>
3563 </ul> <em>General</em>
3565 <li>Normalise option for consensus sequence logo</li>
3566 <li>Reset button in PCA window to return dimensions to
3568 <li>Allow seqspace or Jalview variant of alignment PCA
3570 <li>PCA with either nucleic acid and protein substitution
3572 <li>Allow windows containing HTML reports to be exported
3574 <li>Interactive display and editing of RNA secondary
3575 structure contacts</li>
3576 <li>RNA Helix Alignment Colouring</li>
3577 <li>RNA base pair logo consensus</li>
3578 <li>Parse sequence associated secondary structure
3579 information in Stockholm files</li>
3580 <li>HTML Export database accessions and annotation
3581 information presented in tooltip for sequences</li>
3582 <li>Import secondary structure from LOCARNA clustalw
3583 style RNA alignment files</li>
3584 <li>import and visualise T-COFFEE quality scores for an
3586 <li>'colour by annotation' per sequence option to
3587 shade each sequence according to its associated alignment
3589 <li>New Jalview Logo</li>
3590 </ul> <em>Documentation and Development</em>
3592 <li>documentation for score matrices used in Jalview</li>
3593 <li>New Website!</li>
3595 <td><em>Application</em>
3597 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3598 wsdbfetch REST service</li>
3599 <li>Stop windows being moved outside desktop on OSX</li>
3600 <li>Filetype associations not installed for webstart
3602 <li>Jalview does not always retrieve progress of a JABAWS
3603 job execution in full once it is complete</li>
3604 <li>revise SHMR RSBS definition to ensure alignment is
3605 uploaded via ali_file parameter</li>
3606 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3607 <li>View all structures superposed fails with exception</li>
3608 <li>Jnet job queues forever if a very short sequence is
3609 submitted for prediction</li>
3610 <li>Cut and paste menu not opened when mouse clicked on
3612 <li>Putting fractional value into integer text box in
3613 alignment parameter dialog causes Jalview to hang</li>
3614 <li>Structure view highlighting doesn't work on
3616 <li>View all structures fails with exception shown in
3618 <li>Characters in filename associated with PDBEntry not
3619 escaped in a platform independent way</li>
3620 <li>Jalview desktop fails to launch with exception when
3622 <li>Tree calculation reports 'you must have 2 or more
3623 sequences selected' when selection is empty</li>
3624 <li>Jalview desktop fails to launch with jar signature
3625 failure when java web start temporary file caching is
3627 <li>DAS Sequence retrieval with range qualification
3628 results in sequence xref which includes range qualification</li>
3629 <li>Errors during processing of command line arguments
3630 cause progress bar (JAL-898) to be removed</li>
3631 <li>Replace comma for semi-colon option not disabled for
3632 DAS sources in sequence fetcher</li>
3633 <li>Cannot close news reader when JABAWS server warning
3634 dialog is shown</li>
3635 <li>Option widgets not updated to reflect user settings</li>
3636 <li>Edited sequence not submitted to web service</li>
3637 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3638 <li>InstallAnywhere installer doesn't unpack and run
3639 on OSX Mountain Lion</li>
3640 <li>Annotation panel not given a scroll bar when
3641 sequences with alignment annotation are pasted into the
3643 <li>Sequence associated annotation rows not associated
3644 when loaded from Jalview project</li>
3645 <li>Browser launch fails with NPE on java 1.7</li>
3646 <li>JABAWS alignment marked as finished when job was
3647 cancelled or job failed due to invalid input</li>
3648 <li>NPE with v2.7 example when clicking on Tree
3649 associated with all views</li>
3650 <li>Exceptions when copy/paste sequences with grouped
3651 annotation rows to new window</li>
3652 </ul> <em>Applet</em>
3654 <li>Sequence features are momentarily displayed before
3655 they are hidden using hidefeaturegroups applet parameter</li>
3656 <li>loading features via javascript API automatically
3657 enables feature display</li>
3658 <li>scrollToColumnIn javascript API method doesn't
3660 </ul> <em>General</em>
3662 <li>Redundancy removal fails for rna alignment</li>
3663 <li>PCA calculation fails when sequence has been selected
3664 and then deselected</li>
3665 <li>PCA window shows grey box when first opened on OSX</li>
3666 <li>Letters coloured pink in sequence logo when alignment
3667 coloured with clustalx</li>
3668 <li>Choosing fonts without letter symbols defined causes
3669 exceptions and redraw errors</li>
3670 <li>Initial PCA plot view is not same as manually
3671 reconfigured view</li>
3672 <li>Grouped annotation graph label has incorrect line
3674 <li>Grouped annotation graph label display is corrupted
3675 for lots of labels</li>
3680 <div align="center">
3681 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3684 <td><em>Application</em>
3686 <li>Jalview Desktop News Reader</li>
3687 <li>Tweaked default layout of web services menu</li>
3688 <li>View/alignment association menu to enable user to
3689 easily specify which alignment a multi-structure view takes
3690 its colours/correspondences from</li>
3691 <li>Allow properties file location to be specified as URL</li>
3692 <li>Extend Jalview project to preserve associations
3693 between many alignment views and a single Jmol display</li>
3694 <li>Store annotation row height in Jalview project file</li>
3695 <li>Annotation row column label formatting attributes
3696 stored in project file</li>
3697 <li>Annotation row order for auto-calculated annotation
3698 rows preserved in Jalview project file</li>
3699 <li>Visual progress indication when Jalview state is
3700 saved using Desktop window menu</li>
3701 <li>Visual indication that command line arguments are
3702 still being processed</li>
3703 <li>Groovy script execution from URL</li>
3704 <li>Colour by annotation default min and max colours in
3706 <li>Automatically associate PDB files dragged onto an
3707 alignment with sequences that have high similarity and
3709 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3710 <li>'view structures' option to open many
3711 structures in same window</li>
3712 <li>Sort associated views menu option for tree panel</li>
3713 <li>Group all JABA and non-JABA services for a particular
3714 analysis function in its own submenu</li>
3715 </ul> <em>Applet</em>
3717 <li>Userdefined and autogenerated annotation rows for
3719 <li>Adjustment of alignment annotation pane height</li>
3720 <li>Annotation scrollbar for annotation panel</li>
3721 <li>Drag to reorder annotation rows in annotation panel</li>
3722 <li>'automaticScrolling' parameter</li>
3723 <li>Allow sequences with partial ID string matches to be
3724 annotated from GFF/Jalview features files</li>
3725 <li>Sequence logo annotation row in applet</li>
3726 <li>Absolute paths relative to host server in applet
3727 parameters are treated as such</li>
3728 <li>New in the JalviewLite javascript API:
3730 <li>JalviewLite.js javascript library</li>
3731 <li>Javascript callbacks for
3733 <li>Applet initialisation</li>
3734 <li>Sequence/alignment mouse-overs and selections</li>
3737 <li>scrollTo row and column alignment scrolling
3739 <li>Select sequence/alignment regions from javascript</li>
3740 <li>javascript structure viewer harness to pass
3741 messages between Jmol and Jalview when running as
3742 distinct applets</li>
3743 <li>sortBy method</li>
3744 <li>Set of applet and application examples shipped
3745 with documentation</li>
3746 <li>New example to demonstrate JalviewLite and Jmol
3747 javascript message exchange</li>
3749 </ul> <em>General</em>
3751 <li>Enable Jmol displays to be associated with multiple
3752 multiple alignments</li>
3753 <li>Option to automatically sort alignment with new tree</li>
3754 <li>User configurable link to enable redirects to a
3755 www.Jalview.org mirror</li>
3756 <li>Jmol colours option for Jmol displays</li>
3757 <li>Configurable newline string when writing alignment
3758 and other flat files</li>
3759 <li>Allow alignment annotation description lines to
3760 contain html tags</li>
3761 </ul> <em>Documentation and Development</em>
3763 <li>Add groovy test harness for bulk load testing to
3765 <li>Groovy script to load and align a set of sequences
3766 using a web service before displaying the result in the
3767 Jalview desktop</li>
3768 <li>Restructured javascript and applet api documentation</li>
3769 <li>Ant target to publish example html files with applet
3771 <li>Netbeans project for building Jalview from source</li>
3772 <li>ant task to create online javadoc for Jalview source</li>
3774 <td><em>Application</em>
3776 <li>User defined colourscheme throws exception when
3777 current built in colourscheme is saved as new scheme</li>
3778 <li>AlignFrame->Save in application pops up save
3779 dialog for valid filename/format</li>
3780 <li>Cannot view associated structure for UniProt sequence</li>
3781 <li>PDB file association breaks for UniProt sequence
3783 <li>Associate PDB from file dialog does not tell you
3784 which sequence is to be associated with the file</li>
3785 <li>Find All raises null pointer exception when query
3786 only matches sequence IDs</li>
3787 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3788 <li>Jalview project with Jmol views created with Jalview
3789 2.4 cannot be loaded</li>
3790 <li>Filetype associations not installed for webstart
3792 <li>Two or more chains in a single PDB file associated
3793 with sequences in different alignments do not get coloured
3794 by their associated sequence</li>
3795 <li>Visibility status of autocalculated annotation row
3796 not preserved when project is loaded</li>
3797 <li>Annotation row height and visibility attributes not
3798 stored in Jalview project</li>
3799 <li>Tree bootstraps are not preserved when saved as a
3800 Jalview project</li>
3801 <li>Envision2 workflow tooltips are corrupted</li>
3802 <li>Enabling show group conservation also enables colour
3803 by conservation</li>
3804 <li>Duplicate group associated conservation or consensus
3805 created on new view</li>
3806 <li>Annotation scrollbar not displayed after 'show
3807 all hidden annotation rows' option selected</li>
3808 <li>Alignment quality not updated after alignment
3809 annotation row is hidden then shown</li>
3810 <li>Preserve colouring of structures coloured by
3811 sequences in pre Jalview 2.7 projects</li>
3812 <li>Web service job parameter dialog is not laid out
3814 <li>Web services menu not refreshed after 'reset
3815 services' button is pressed in preferences</li>
3816 <li>Annotation off by one in Jalview v2_3 example project</li>
3817 <li>Structures imported from file and saved in project
3818 get name like jalview_pdb1234.txt when reloaded</li>
3819 <li>Jalview does not always retrieve progress of a JABAWS
3820 job execution in full once it is complete</li>
3821 </ul> <em>Applet</em>
3823 <li>Alignment height set incorrectly when lots of
3824 annotation rows are displayed</li>
3825 <li>Relative URLs in feature HTML text not resolved to
3827 <li>View follows highlighting does not work for positions
3829 <li><= shown as = in tooltip</li>
3830 <li>Export features raises exception when no features
3832 <li>Separator string used for serialising lists of IDs
3833 for javascript api is modified when separator string
3834 provided as parameter</li>
3835 <li>Null pointer exception when selecting tree leaves for
3836 alignment with no existing selection</li>
3837 <li>Relative URLs for datasources assumed to be relative
3838 to applet's codebase</li>
3839 <li>Status bar not updated after finished searching and
3840 search wraps around to first result</li>
3841 <li>StructureSelectionManager instance shared between
3842 several Jalview applets causes race conditions and memory
3844 <li>Hover tooltip and mouseover of position on structure
3845 not sent from Jmol in applet</li>
3846 <li>Certain sequences of javascript method calls to
3847 applet API fatally hang browser</li>
3848 </ul> <em>General</em>
3850 <li>View follows structure mouseover scrolls beyond
3851 position with wrapped view and hidden regions</li>
3852 <li>Find sequence position moves to wrong residue
3853 with/without hidden columns</li>
3854 <li>Sequence length given in alignment properties window
3856 <li>InvalidNumberFormat exceptions thrown when trying to
3857 import PDB like structure files</li>
3858 <li>Positional search results are only highlighted
3859 between user-supplied sequence start/end bounds</li>
3860 <li>End attribute of sequence is not validated</li>
3861 <li>Find dialog only finds first sequence containing a
3862 given sequence position</li>
3863 <li>Sequence numbering not preserved in MSF alignment
3865 <li>Jalview PDB file reader does not extract sequence
3866 from nucleotide chains correctly</li>
3867 <li>Structure colours not updated when tree partition
3868 changed in alignment</li>
3869 <li>Sequence associated secondary structure not correctly
3870 parsed in interleaved stockholm</li>
3871 <li>Colour by annotation dialog does not restore current
3873 <li>Hiding (nearly) all sequences doesn't work
3875 <li>Sequences containing lowercase letters are not
3876 properly associated with their pdb files</li>
3877 </ul> <em>Documentation and Development</em>
3879 <li>schemas/JalviewWsParamSet.xsd corrupted by
3880 ApplyCopyright tool</li>
3885 <div align="center">
3886 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3889 <td><em>Application</em>
3891 <li>New warning dialog when the Jalview Desktop cannot
3892 contact web services</li>
3893 <li>JABA service parameters for a preset are shown in
3894 service job window</li>
3895 <li>JABA Service menu entries reworded</li>
3899 <li>Modeller PIR IO broken - cannot correctly import a
3900 pir file emitted by Jalview</li>
3901 <li>Existing feature settings transferred to new
3902 alignment view created from cut'n'paste</li>
3903 <li>Improved test for mixed amino/nucleotide chains when
3904 parsing PDB files</li>
3905 <li>Consensus and conservation annotation rows
3906 occasionally become blank for all new windows</li>
3907 <li>Exception raised when right clicking above sequences
3908 in wrapped view mode</li>
3909 </ul> <em>Application</em>
3911 <li>multiple multiply aligned structure views cause cpu
3912 usage to hit 100% and computer to hang</li>
3913 <li>Web Service parameter layout breaks for long user
3914 parameter names</li>
3915 <li>Jaba service discovery hangs desktop if Jaba server
3922 <div align="center">
3923 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3926 <td><em>Application</em>
3928 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3929 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3932 <li>Web Services preference tab</li>
3933 <li>Analysis parameters dialog box and user defined
3935 <li>Improved speed and layout of Envision2 service menu</li>
3936 <li>Superpose structures using associated sequence
3938 <li>Export coordinates and projection as CSV from PCA
3940 </ul> <em>Applet</em>
3942 <li>enable javascript: execution by the applet via the
3943 link out mechanism</li>
3944 </ul> <em>Other</em>
3946 <li>Updated the Jmol Jalview interface to work with Jmol
3948 <li>The Jalview Desktop and JalviewLite applet now
3949 require Java 1.5</li>
3950 <li>Allow Jalview feature colour specification for GFF
3951 sequence annotation files</li>
3952 <li>New 'colour by label' keword in Jalview feature file
3953 type colour specification</li>
3954 <li>New Jalview Desktop Groovy API method that allows a
3955 script to check if it being run in an interactive session or
3956 in a batch operation from the Jalview command line</li>
3960 <li>clustalx colourscheme colours Ds preferentially when
3961 both D+E are present in over 50% of the column</li>
3962 </ul> <em>Application</em>
3964 <li>typo in AlignmentFrame->View->Hide->all but
3965 selected Regions menu item</li>
3966 <li>sequence fetcher replaces ',' for ';' when the ',' is
3967 part of a valid accession ID</li>
3968 <li>fatal OOM if object retrieved by sequence fetcher
3969 runs out of memory</li>
3970 <li>unhandled Out of Memory Error when viewing pca
3971 analysis results</li>
3972 <li>InstallAnywhere builds fail to launch on OS X java
3973 10.5 update 4 (due to apple Java 1.6 update)</li>
3974 <li>Installanywhere Jalview silently fails to launch</li>
3975 </ul> <em>Applet</em>
3977 <li>Jalview.getFeatureGroups() raises an
3978 ArrayIndexOutOfBoundsException if no feature groups are
3985 <div align="center">
3986 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3992 <li>Alignment prettyprinter doesn't cope with long
3994 <li>clustalx colourscheme colours Ds preferentially when
3995 both D+E are present in over 50% of the column</li>
3996 <li>nucleic acid structures retrieved from PDB do not
3997 import correctly</li>
3998 <li>More columns get selected than were clicked on when a
3999 number of columns are hidden</li>
4000 <li>annotation label popup menu not providing correct
4001 add/hide/show options when rows are hidden or none are
4003 <li>Stockholm format shown in list of readable formats,
4004 and parser copes better with alignments from RFAM.</li>
4005 <li>CSV output of consensus only includes the percentage
4006 of all symbols if sequence logo display is enabled</li>
4008 </ul> <em>Applet</em>
4010 <li>annotation panel disappears when annotation is
4012 </ul> <em>Application</em>
4014 <li>Alignment view not redrawn properly when new
4015 alignment opened where annotation panel is visible but no
4016 annotations are present on alignment</li>
4017 <li>pasted region containing hidden columns is
4018 incorrectly displayed in new alignment window</li>
4019 <li>Jalview slow to complete operations when stdout is
4020 flooded (fix is to close the Jalview console)</li>
4021 <li>typo in AlignmentFrame->View->Hide->all but
4022 selected Rregions menu item.</li>
4023 <li>inconsistent group submenu and Format submenu entry
4024 'Un' or 'Non'conserved</li>
4025 <li>Sequence feature settings are being shared by
4026 multiple distinct alignments</li>
4027 <li>group annotation not recreated when tree partition is
4029 <li>double click on group annotation to select sequences
4030 does not propagate to associated trees</li>
4031 <li>Mac OSX specific issues:
4033 <li>exception raised when mouse clicked on desktop
4034 window background</li>
4035 <li>Desktop menu placed on menu bar and application
4036 name set correctly</li>
4037 <li>sequence feature settings not wide enough for the
4038 save feature colourscheme button</li>
4047 <div align="center">
4048 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4051 <td><em>New Capabilities</em>
4053 <li>URL links generated from description line for
4054 regular-expression based URL links (applet and application)
4056 <li>Non-positional feature URL links are shown in link
4058 <li>Linked viewing of nucleic acid sequences and
4060 <li>Automatic Scrolling option in View menu to display
4061 the currently highlighted region of an alignment.</li>
4062 <li>Order an alignment by sequence length, or using the
4063 average score or total feature count for each sequence.</li>
4064 <li>Shading features by score or associated description</li>
4065 <li>Subdivide alignment and groups based on identity of
4066 selected subsequence (Make Groups from Selection).</li>
4067 <li>New hide/show options including Shift+Control+H to
4068 hide everything but the currently selected region.</li>
4069 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4070 </ul> <em>Application</em>
4072 <li>Fetch DB References capabilities and UI expanded to
4073 support retrieval from DAS sequence sources</li>
4074 <li>Local DAS Sequence sources can be added via the
4075 command line or via the Add local source dialog box.</li>
4076 <li>DAS Dbref and DbxRef feature types are parsed as
4077 database references and protein_name is parsed as
4078 description line (BioSapiens terms).</li>
4079 <li>Enable or disable non-positional feature and database
4080 references in sequence ID tooltip from View menu in
4082 <!-- <li>New hidden columns and rows and representatives capabilities
4083 in annotations file (in progress - not yet fully implemented)</li> -->
4084 <li>Group-associated consensus, sequence logos and
4085 conservation plots</li>
4086 <li>Symbol distributions for each column can be exported
4087 and visualized as sequence logos</li>
4088 <li>Optionally scale multi-character column labels to fit
4089 within each column of annotation row<!-- todo for applet -->
4091 <li>Optional automatic sort of associated alignment view
4092 when a new tree is opened.</li>
4093 <li>Jalview Java Console</li>
4094 <li>Better placement of desktop window when moving
4095 between different screens.</li>
4096 <li>New preference items for sequence ID tooltip and
4097 consensus annotation</li>
4098 <li>Client to submit sequences and IDs to Envision2
4100 <li><em>Vamsas Capabilities</em>
4102 <li>Improved VAMSAS synchronization (Jalview archive
4103 used to preserve views, structures, and tree display
4105 <li>Import of vamsas documents from disk or URL via
4107 <li>Sharing of selected regions between views and
4108 with other VAMSAS applications (Experimental feature!)</li>
4109 <li>Updated API to VAMSAS version 0.2</li>
4111 </ul> <em>Applet</em>
4113 <li>Middle button resizes annotation row height</li>
4116 <li>sortByTree (true/false) - automatically sort the
4117 associated alignment view by the tree when a new tree is
4119 <li>showTreeBootstraps (true/false) - show or hide
4120 branch bootstraps (default is to show them if available)</li>
4121 <li>showTreeDistances (true/false) - show or hide
4122 branch lengths (default is to show them if available)</li>
4123 <li>showUnlinkedTreeNodes (true/false) - indicate if
4124 unassociated nodes should be highlighted in the tree
4126 <li>heightScale and widthScale (1.0 or more) -
4127 increase the height or width of a cell in the alignment
4128 grid relative to the current font size.</li>
4131 <li>Non-positional features displayed in sequence ID
4133 </ul> <em>Other</em>
4135 <li>Features format: graduated colour definitions and
4136 specification of feature scores</li>
4137 <li>Alignment Annotations format: new keywords for group
4138 associated annotation (GROUP_REF) and annotation row display
4139 properties (ROW_PROPERTIES)</li>
4140 <li>XML formats extended to support graduated feature
4141 colourschemes, group associated annotation, and profile
4142 visualization settings.</li></td>
4145 <li>Source field in GFF files parsed as feature source
4146 rather than description</li>
4147 <li>Non-positional features are now included in sequence
4148 feature and gff files (controlled via non-positional feature
4149 visibility in tooltip).</li>
4150 <li>URL links generated for all feature links (bugfix)</li>
4151 <li>Added URL embedding instructions to features file
4153 <li>Codons containing ambiguous nucleotides translated as
4154 'X' in peptide product</li>
4155 <li>Match case switch in find dialog box works for both
4156 sequence ID and sequence string and query strings do not
4157 have to be in upper case to match case-insensitively.</li>
4158 <li>AMSA files only contain first column of
4159 multi-character column annotation labels</li>
4160 <li>Jalview Annotation File generation/parsing consistent
4161 with documentation (e.g. Stockholm annotation can be
4162 exported and re-imported)</li>
4163 <li>PDB files without embedded PDB IDs given a friendly
4165 <li>Find incrementally searches ID string matches as well
4166 as subsequence matches, and correctly reports total number
4170 <li>Better handling of exceptions during sequence
4172 <li>Dasobert generated non-positional feature URL
4173 link text excludes the start_end suffix</li>
4174 <li>DAS feature and source retrieval buttons disabled
4175 when fetch or registry operations in progress.</li>
4176 <li>PDB files retrieved from URLs are cached properly</li>
4177 <li>Sequence description lines properly shared via
4179 <li>Sequence fetcher fetches multiple records for all
4181 <li>Ensured that command line das feature retrieval
4182 completes before alignment figures are generated.</li>
4183 <li>Reduced time taken when opening file browser for
4185 <li>isAligned check prior to calculating tree, PCA or
4186 submitting an MSA to JNet now excludes hidden sequences.</li>
4187 <li>User defined group colours properly recovered
4188 from Jalview projects.</li>
4197 <div align="center">
4198 <strong>2.4.0.b2</strong><br> 28/10/2009
4203 <li>Experimental support for google analytics usage
4205 <li>Jalview privacy settings (user preferences and docs).</li>
4210 <li>Race condition in applet preventing startup in
4212 <li>Exception when feature created from selection beyond
4213 length of sequence.</li>
4214 <li>Allow synthetic PDB files to be imported gracefully</li>
4215 <li>Sequence associated annotation rows associate with
4216 all sequences with a given id</li>
4217 <li>Find function matches case-insensitively for sequence
4218 ID string searches</li>
4219 <li>Non-standard characters do not cause pairwise
4220 alignment to fail with exception</li>
4221 </ul> <em>Application Issues</em>
4223 <li>Sequences are now validated against EMBL database</li>
4224 <li>Sequence fetcher fetches multiple records for all
4226 </ul> <em>InstallAnywhere Issues</em>
4228 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4229 issue with installAnywhere mechanism)</li>
4230 <li>Command line launching of JARs from InstallAnywhere
4231 version (java class versioning error fixed)</li>
4238 <div align="center">
4239 <strong>2.4</strong><br> 27/8/2008
4242 <td><em>User Interface</em>
4244 <li>Linked highlighting of codon and amino acid from
4245 translation and protein products</li>
4246 <li>Linked highlighting of structure associated with
4247 residue mapping to codon position</li>
4248 <li>Sequence Fetcher provides example accession numbers
4249 and 'clear' button</li>
4250 <li>MemoryMonitor added as an option under Desktop's
4252 <li>Extract score function to parse whitespace separated
4253 numeric data in description line</li>
4254 <li>Column labels in alignment annotation can be centred.</li>
4255 <li>Tooltip for sequence associated annotation give name
4257 </ul> <em>Web Services and URL fetching</em>
4259 <li>JPred3 web service</li>
4260 <li>Prototype sequence search client (no public services
4262 <li>Fetch either seed alignment or full alignment from
4264 <li>URL Links created for matching database cross
4265 references as well as sequence ID</li>
4266 <li>URL Links can be created using regular-expressions</li>
4267 </ul> <em>Sequence Database Connectivity</em>
4269 <li>Retrieval of cross-referenced sequences from other
4271 <li>Generalised database reference retrieval and
4272 validation to all fetchable databases</li>
4273 <li>Fetch sequences from DAS sources supporting the
4274 sequence command</li>
4275 </ul> <em>Import and Export</em>
4276 <li>export annotation rows as CSV for spreadsheet import</li>
4277 <li>Jalview projects record alignment dataset associations,
4278 EMBL products, and cDNA sequence mappings</li>
4279 <li>Sequence Group colour can be specified in Annotation
4281 <li>Ad-hoc colouring of group in Annotation File using RGB
4282 triplet as name of colourscheme</li>
4283 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4285 <li>treenode binding for VAMSAS tree exchange</li>
4286 <li>local editing and update of sequences in VAMSAS
4287 alignments (experimental)</li>
4288 <li>Create new or select existing session to join</li>
4289 <li>load and save of vamsas documents</li>
4290 </ul> <em>Application command line</em>
4292 <li>-tree parameter to open trees (introduced for passing
4294 <li>-fetchfrom command line argument to specify nicknames
4295 of DAS servers to query for alignment features</li>
4296 <li>-dasserver command line argument to add new servers
4297 that are also automatically queried for features</li>
4298 <li>-groovy command line argument executes a given groovy
4299 script after all input data has been loaded and parsed</li>
4300 </ul> <em>Applet-Application data exchange</em>
4302 <li>Trees passed as applet parameters can be passed to
4303 application (when using "View in full
4304 application")</li>
4305 </ul> <em>Applet Parameters</em>
4307 <li>feature group display control parameter</li>
4308 <li>debug parameter</li>
4309 <li>showbutton parameter</li>
4310 </ul> <em>Applet API methods</em>
4312 <li>newView public method</li>
4313 <li>Window (current view) specific get/set public methods</li>
4314 <li>Feature display control methods</li>
4315 <li>get list of currently selected sequences</li>
4316 </ul> <em>New Jalview distribution features</em>
4318 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4319 <li>RELEASE file gives build properties for the latest
4320 Jalview release.</li>
4321 <li>Java 1.1 Applet build made easier and donotobfuscate
4322 property controls execution of obfuscator</li>
4323 <li>Build target for generating source distribution</li>
4324 <li>Debug flag for javacc</li>
4325 <li>.jalview_properties file is documented (slightly) in
4326 jalview.bin.Cache</li>
4327 <li>Continuous Build Integration for stable and
4328 development version of Application, Applet and source
4333 <li>selected region output includes visible annotations
4334 (for certain formats)</li>
4335 <li>edit label/displaychar contains existing label/char
4337 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4338 <li>shorter peptide product names from EMBL records</li>
4339 <li>Newick string generator makes compact representations</li>
4340 <li>bootstrap values parsed correctly for tree files with
4342 <li>pathological filechooser bug avoided by not allowing
4343 filenames containing a ':'</li>
4344 <li>Fixed exception when parsing GFF files containing
4345 global sequence features</li>
4346 <li>Alignment datasets are finalized only when number of
4347 references from alignment sequences goes to zero</li>
4348 <li>Close of tree branch colour box without colour
4349 selection causes cascading exceptions</li>
4350 <li>occasional negative imgwidth exceptions</li>
4351 <li>better reporting of non-fatal warnings to user when
4352 file parsing fails.</li>
4353 <li>Save works when Jalview project is default format</li>
4354 <li>Save as dialog opened if current alignment format is
4355 not a valid output format</li>
4356 <li>UniProt canonical names introduced for both das and
4358 <li>Histidine should be midblue (not pink!) in Zappo</li>
4359 <li>error messages passed up and output when data read
4361 <li>edit undo recovers previous dataset sequence when
4362 sequence is edited</li>
4363 <li>allow PDB files without pdb ID HEADER lines (like
4364 those generated by MODELLER) to be read in properly</li>
4365 <li>allow reading of JPred concise files as a normal
4367 <li>Stockholm annotation parsing and alignment properties
4368 import fixed for PFAM records</li>
4369 <li>Structure view windows have correct name in Desktop
4371 <li>annotation consisting of sequence associated scores
4372 can be read and written correctly to annotation file</li>
4373 <li>Aligned cDNA translation to aligned peptide works
4375 <li>Fixed display of hidden sequence markers and
4376 non-italic font for representatives in Applet</li>
4377 <li>Applet Menus are always embedded in applet window on
4379 <li>Newly shown features appear at top of stack (in
4381 <li>Annotations added via parameter not drawn properly
4382 due to null pointer exceptions</li>
4383 <li>Secondary structure lines are drawn starting from
4384 first column of alignment</li>
4385 <li>UniProt XML import updated for new schema release in
4387 <li>Sequence feature to sequence ID match for Features
4388 file is case-insensitive</li>
4389 <li>Sequence features read from Features file appended to
4390 all sequences with matching IDs</li>
4391 <li>PDB structure coloured correctly for associated views
4392 containing a sub-sequence</li>
4393 <li>PDB files can be retrieved by applet from Jar files</li>
4394 <li>feature and annotation file applet parameters
4395 referring to different directories are retrieved correctly</li>
4396 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4397 <li>Fixed application hang whilst waiting for
4398 splash-screen version check to complete</li>
4399 <li>Applet properly URLencodes input parameter values
4400 when passing them to the launchApp service</li>
4401 <li>display name and local features preserved in results
4402 retrieved from web service</li>
4403 <li>Visual delay indication for sequence retrieval and
4404 sequence fetcher initialisation</li>
4405 <li>updated Application to use DAS 1.53e version of
4406 dasobert DAS client</li>
4407 <li>Re-instated Full AMSA support and .amsa file
4409 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4417 <div align="center">
4418 <strong>2.3</strong><br> 9/5/07
4423 <li>Jmol 11.0.2 integration</li>
4424 <li>PDB views stored in Jalview XML files</li>
4425 <li>Slide sequences</li>
4426 <li>Edit sequence in place</li>
4427 <li>EMBL CDS features</li>
4428 <li>DAS Feature mapping</li>
4429 <li>Feature ordering</li>
4430 <li>Alignment Properties</li>
4431 <li>Annotation Scores</li>
4432 <li>Sort by scores</li>
4433 <li>Feature/annotation editing in applet</li>
4438 <li>Headless state operation in 2.2.1</li>
4439 <li>Incorrect and unstable DNA pairwise alignment</li>
4440 <li>Cut and paste of sequences with annotation</li>
4441 <li>Feature group display state in XML</li>
4442 <li>Feature ordering in XML</li>
4443 <li>blc file iteration selection using filename # suffix</li>
4444 <li>Stockholm alignment properties</li>
4445 <li>Stockhom alignment secondary structure annotation</li>
4446 <li>2.2.1 applet had no feature transparency</li>
4447 <li>Number pad keys can be used in cursor mode</li>
4448 <li>Structure Viewer mirror image resolved</li>
4455 <div align="center">
4456 <strong>2.2.1</strong><br> 12/2/07
4461 <li>Non standard characters can be read and displayed
4462 <li>Annotations/Features can be imported/exported to the
4464 <li>Applet allows editing of sequence/annotation/group
4465 name & description
4466 <li>Preference setting to display sequence name in
4468 <li>Annotation file format extended to allow
4469 Sequence_groups to be defined
4470 <li>Default opening of alignment overview panel can be
4471 specified in preferences
4472 <li>PDB residue numbering annotation added to associated
4478 <li>Applet crash under certain Linux OS with Java 1.6
4480 <li>Annotation file export / import bugs fixed
4481 <li>PNG / EPS image output bugs fixed
4487 <div align="center">
4488 <strong>2.2</strong><br> 27/11/06
4493 <li>Multiple views on alignment
4494 <li>Sequence feature editing
4495 <li>"Reload" alignment
4496 <li>"Save" to current filename
4497 <li>Background dependent text colour
4498 <li>Right align sequence ids
4499 <li>User-defined lower case residue colours
4502 <li>Menu item accelerator keys
4503 <li>Control-V pastes to current alignment
4504 <li>Cancel button for DAS Feature Fetching
4505 <li>PCA and PDB Viewers zoom via mouse roller
4506 <li>User-defined sub-tree colours and sub-tree selection
4508 <li>'New Window' button on the 'Output to Text box'
4513 <li>New memory efficient Undo/Redo System
4514 <li>Optimised symbol lookups and conservation/consensus
4516 <li>Region Conservation/Consensus recalculated after
4518 <li>Fixed Remove Empty Columns Bug (empty columns at end
4520 <li>Slowed DAS Feature Fetching for increased robustness.
4522 <li>Made angle brackets in ASCII feature descriptions
4524 <li>Re-instated Zoom function for PCA
4525 <li>Sequence descriptions conserved in web service
4527 <li>UniProt ID discoverer uses any word separated by
4529 <li>WsDbFetch query/result association resolved
4530 <li>Tree leaf to sequence mapping improved
4531 <li>Smooth fonts switch moved to FontChooser dialog box.
4538 <div align="center">
4539 <strong>2.1.1</strong><br> 12/9/06
4544 <li>Copy consensus sequence to clipboard</li>
4549 <li>Image output - rightmost residues are rendered if
4550 sequence id panel has been resized</li>
4551 <li>Image output - all offscreen group boundaries are
4553 <li>Annotation files with sequence references - all
4554 elements in file are relative to sequence position</li>
4555 <li>Mac Applet users can use Alt key for group editing</li>
4561 <div align="center">
4562 <strong>2.1</strong><br> 22/8/06
4567 <li>MAFFT Multiple Alignment in default Web Service list</li>
4568 <li>DAS Feature fetching</li>
4569 <li>Hide sequences and columns</li>
4570 <li>Export Annotations and Features</li>
4571 <li>GFF file reading / writing</li>
4572 <li>Associate structures with sequences from local PDB
4574 <li>Add sequences to exisiting alignment</li>
4575 <li>Recently opened files / URL lists</li>
4576 <li>Applet can launch the full application</li>
4577 <li>Applet has transparency for features (Java 1.2
4579 <li>Applet has user defined colours parameter</li>
4580 <li>Applet can load sequences from parameter
4581 "sequence<em>x</em>"
4587 <li>Redundancy Panel reinstalled in the Applet</li>
4588 <li>Monospaced font - EPS / rescaling bug fixed</li>
4589 <li>Annotation files with sequence references bug fixed</li>
4595 <div align="center">
4596 <strong>2.08.1</strong><br> 2/5/06
4601 <li>Change case of selected region from Popup menu</li>
4602 <li>Choose to match case when searching</li>
4603 <li>Middle mouse button and mouse movement can compress /
4604 expand the visible width and height of the alignment</li>
4609 <li>Annotation Panel displays complete JNet results</li>
4615 <div align="center">
4616 <strong>2.08b</strong><br> 18/4/06
4622 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4623 <li>Righthand label on wrapped alignments shows correct
4630 <div align="center">
4631 <strong>2.08</strong><br> 10/4/06
4636 <li>Editing can be locked to the selection area</li>
4637 <li>Keyboard editing</li>
4638 <li>Create sequence features from searches</li>
4639 <li>Precalculated annotations can be loaded onto
4641 <li>Features file allows grouping of features</li>
4642 <li>Annotation Colouring scheme added</li>
4643 <li>Smooth fonts off by default - Faster rendering</li>
4644 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4649 <li>Drag & Drop fixed on Linux</li>
4650 <li>Jalview Archive file faster to load/save, sequence
4651 descriptions saved.</li>
4657 <div align="center">
4658 <strong>2.07</strong><br> 12/12/05
4663 <li>PDB Structure Viewer enhanced</li>
4664 <li>Sequence Feature retrieval and display enhanced</li>
4665 <li>Choose to output sequence start-end after sequence
4666 name for file output</li>
4667 <li>Sequence Fetcher WSDBFetch@EBI</li>
4668 <li>Applet can read feature files, PDB files and can be
4669 used for HTML form input</li>
4674 <li>HTML output writes groups and features</li>
4675 <li>Group editing is Control and mouse click</li>
4676 <li>File IO bugs</li>
4682 <div align="center">
4683 <strong>2.06</strong><br> 28/9/05
4688 <li>View annotations in wrapped mode</li>
4689 <li>More options for PCA viewer</li>
4694 <li>GUI bugs resolved</li>
4695 <li>Runs with -nodisplay from command line</li>
4701 <div align="center">
4702 <strong>2.05b</strong><br> 15/9/05
4707 <li>Choose EPS export as lineart or text</li>
4708 <li>Jar files are executable</li>
4709 <li>Can read in Uracil - maps to unknown residue</li>
4714 <li>Known OutOfMemory errors give warning message</li>
4715 <li>Overview window calculated more efficiently</li>
4716 <li>Several GUI bugs resolved</li>
4722 <div align="center">
4723 <strong>2.05</strong><br> 30/8/05
4728 <li>Edit and annotate in "Wrapped" view</li>
4733 <li>Several GUI bugs resolved</li>
4739 <div align="center">
4740 <strong>2.04</strong><br> 24/8/05
4745 <li>Hold down mouse wheel & scroll to change font
4751 <li>Improved JPred client reliability</li>
4752 <li>Improved loading of Jalview files</li>
4758 <div align="center">
4759 <strong>2.03</strong><br> 18/8/05
4764 <li>Set Proxy server name and port in preferences</li>
4765 <li>Multiple URL links from sequence ids</li>
4766 <li>User Defined Colours can have a scheme name and added
4768 <li>Choose to ignore gaps in consensus calculation</li>
4769 <li>Unix users can set default web browser</li>
4770 <li>Runs without GUI for batch processing</li>
4771 <li>Dynamically generated Web Service Menus</li>
4776 <li>InstallAnywhere download for Sparc Solaris</li>
4782 <div align="center">
4783 <strong>2.02</strong><br> 18/7/05
4789 <li>Copy & Paste order of sequences maintains
4790 alignment order.</li>
4796 <div align="center">
4797 <strong>2.01</strong><br> 12/7/05
4802 <li>Use delete key for deleting selection.</li>
4803 <li>Use Mouse wheel to scroll sequences.</li>
4804 <li>Help file updated to describe how to add alignment
4806 <li>Version and build date written to build properties
4808 <li>InstallAnywhere installation will check for updates
4809 at launch of Jalview.</li>
4814 <li>Delete gaps bug fixed.</li>
4815 <li>FileChooser sorts columns.</li>
4816 <li>Can remove groups one by one.</li>
4817 <li>Filechooser icons installed.</li>
4818 <li>Finder ignores return character when searching.
4819 Return key will initiate a search.<br>
4826 <div align="center">
4827 <strong>2.0</strong><br> 20/6/05
4832 <li>New codebase</li>