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.2.11.1.3">.3</a><br />
61 <em>27/10/2020</em></strong></td>
62 <td align="left" valign="top">
66 <td align="left" valign="top">
69 <!-- JAL-3765 -->Find doesn't always highlight all matching
70 positions in a sequence
76 <td width="60" align="center" nowrap><strong><a
77 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
78 <em>25/09/2020</em></strong></td>
79 <td align="left" valign="top">
83 <td align="left" valign="top">
86 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
87 "Encountered problems opening
88 https://www.jalview.org/examples/exampleFile_2_7.jvp"
94 <td width="60" align="center" nowrap><strong><a
95 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
96 <em>17/09/2020</em></strong></td>
97 <td align="left" valign="top">
100 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
101 residue in cursor mode
104 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
105 HTSJDK from 2.12 to 2.23
108 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
109 optimisations and improvements suggested by Bob Hanson and
110 improved compatibility with JalviewJS
113 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
114 alignments from Pfam and Rfam
117 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
118 import (no longer based on .gz extension)
121 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
124 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
125 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
129 <!-- JAL-3667 -->Improved warning messages, debug logging
130 and fixed Retry action when Jalview encounters errors when
131 saving or making backup files.
134 <!-- JAL-3676 -->Enhanced Jalview Java Console:
136 <li>Jalview's logging level can be configured</li>
137 <li>Copy to Clipboard Buttion</li>
141 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
142 when running on Linux (Requires Java 11+)
144 </ul> <em>Launching Jalview</em>
147 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
148 through a system property
151 <!-- JAL-3477 -->Improved built-in documentation and command
152 line help for configuring Jalview's memory
156 <td align="left" valign="top">
159 <!-- JAL-3691 -->Conservation and Quality tracks are shown
160 but not calculated and no protein or DNA score models are
161 available for tree/PCA calculation when launched with
162 Turkish language locale
165 <!-- JAL-3493 -->Escape does not clear highlights on the
166 alignment (Since Jalview 2.10.3)
169 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
170 doesn't slide selected sequences, just sequence under cursor
173 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
174 sequence under the cursor
177 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
178 multiple EMBL gene products shown forĀ a single contig
181 <!-- JAL-3696 -->Errors encountered when processing variants
182 from VCF files yield "Error processing VCF: Format specifier
186 <!-- JAL-3697 -->Count of features not shown can be wrong
187 when there are both local and complementary features mapped
188 to the position under the cursor
191 <!-- JAL-3673 -->Sequence ID for reference sequence is
192 clipped when Right align Sequence IDs enabled
195 <!-- JAL-2983 -->Slider with negative range values not
196 rendered correctly in VAqua4 (Since 2.10.4)
199 <!-- JAL-3685 -->Single quotes not displayed correctly in
200 internationalised text for some messages and log output
203 <!-- JAL-3490 -->Find doesn't report matches that span
204 hidden gapped columns
207 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
208 panels, Alignment viewport and annotation renderer.
211 <!-- JAL-3561 -->Jalview ignores file format parameter
212 specifying output format when exporting an alignment via the
216 <!-- JAL-3667 -->Windows 10: For a minority of users, if
217 backups are not enabled, Jalview sometimes fails to
218 overwrite an existing file and raises a warning dialog. (in
219 2.11.0, and 2.11.1.0, the workaround is to try to save the
220 file again, and if that fails, delete the original file and
224 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
228 <!-- JAL-3741 -->References to http://www.jalview.org in
229 program and documentation
231 </ul> <em>Launching Jalview</em>
234 <!-- JAL-3718 -->Jalview application fails when launched the
235 first time for a version that has different jars to the
236 previous launched version.
238 </ul> <em>Developing Jalview</em>
241 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
242 data, causing cloverReport gradle task to fail with an
246 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
247 monitor the release channel
249 </ul> <em>New Known defects</em>
252 <!-- JAL-3748 -->CDS shown in result of submitting proteins
253 in a CDS/Protein alignment to a web service is wrong when
254 proteins share a common transcript sequence (e.g.
255 genome of RNA viruses)
258 <!-- JAL-3576 -->Co-located features exported and re-imported
259 are ordered differently when shown on alignment and in
260 tooltips. (Also affects v2.11.1.0)
263 <!-- JAL-3702 -->Drag and drop of alignment file onto
264 alignment window when in a HiDPI scaled mode in Linux only
265 works for the top left quadrant of the alignment window
268 <!-- JAL-3701 -->Stale build data in jalview standalone jar
269 builds (only affects 2.11.1.1 branch)
272 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
273 when alignment view restored from project (since Jalview 2.11.0)
279 <td width="60" align="center" nowrap><strong><a
280 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
281 <em>22/04/2020</em></strong></td>
282 <td align="left" valign="top">
285 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
286 'virtual' codon features shown on protein (or vice versa)
287 for display in alignments, on structure views (including
288 transfer to UCSF chimera), in feature reports and for
292 <!-- JAL-3121 -->Feature attributes from VCF files can be
293 exported and re-imported as GFF3 files
296 <!-- JAL-3376 -->Capture VCF "fixed column" values
297 POS, ID, QUAL, FILTER as Feature Attributes
300 <!-- JAL-3375 -->More robust VCF numeric data field
301 validation while parsing
304 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
308 <!-- JAL-3535 -->Feature Settings dialog title includes name
312 <!-- JAL-3538 -->Font anti-aliasing in alignment views
316 <!-- JAL-3468 -->Very long feature descriptions truncated in
320 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
321 with no feature types visible
324 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
326 </ul><em>Jalview Installer</em>
329 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
330 in console (may be null when Jalview launched as executable jar or via conda)
333 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
336 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
339 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
341 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
342 </ul> <em>Release processes</em>
345 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
348 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
350 </ul> <em>Build System</em>
353 <!-- JAL-3510 -->Clover updated to 4.4.1
356 <!-- JAL-3513 -->Test code included in Clover coverage
360 <em>Groovy Scripts</em>
363 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
364 to stdout containing the consensus sequence for each
365 alignment in a Jalview session
368 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
369 genomic sequence_variant annotation from CDS as
370 missense_variant or synonymous_variant on protein products.
374 <td align="left" valign="top">
377 <!-- JAL-3581 -->Hidden sequence markers still visible when
378 'Show hidden markers' option is not ticked
381 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
382 PNG output when 'Automatically set ID width' is set in
383 jalview preferences or properties file
386 <!-- JAL-3571 -->Feature Editor dialog can be opened when
387 'Show Sequence Features' option is not ticked
390 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
391 buttons in Feature Settings dialog are clicked when no
395 <!-- JAL-3412 -->ID margins for CDS and Protein views not
396 equal when split frame is first opened
399 <!-- JAL-3296 -->Sequence position numbers in status bar not
400 correct after editing a sequence's start position
403 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
404 with annotation and exceptions thrown when only a few
405 columns shown in wrapped mode
408 <!-- JAL-3386 -->Sequence IDs missing in headless export of
409 wrapped alignment figure with annotations
412 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
413 ID fails with ClassCastException
416 <!-- JAL-3389 -->Chimera session not restored from Jalview
420 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
421 feature settings dialog also selects columns
424 <!-- JAL-3473 -->SpinnerNumberModel causes
425 IllegalArgumentException in some circumstances
428 <!-- JAL-3534 -->Multiple feature settings dialogs can be
432 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
433 alignment window is closed
436 <!-- JAL-3406 -->Credits missing some authors in Jalview
437 help documentation for 2.11.0 release
440 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
441 includes Pfam ID as sequence's accession rather than its
444 </ul> <em>Java 11 Compatibility issues</em>
447 <!-- JAL-2987 -->OSX - Can't view some search results in
448 PDB/Uniprot search panel
450 </ul> <em>Installer</em>
453 <!-- JAL-3447 -->Jalview should not create file associations
454 for 3D structure files (.pdb, .mmcif. .cif)
456 </ul> <em>Repository and Source Release</em>
459 <!-- JAL-3474 -->removed obsolete .cvsignore files from
463 <!-- JAL-3541 -->Clover report generation running out of
466 </ul> <em>New Known Issues</em>
469 <!-- JAL-3523 -->OSX - Current working directory not
470 preserved when Jalview.app launched with parameters from
474 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
475 clipped in headless figure export when Right Align option
479 <!-- JAL-3542 -->Jalview Installation type always reports
480 'Source' in console output
483 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
484 bamboo server but run fine locally.
490 <td width="60" align="center" nowrap>
491 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
492 <em>04/07/2019</em></strong>
494 <td align="left" valign="top">
497 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
498 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
499 source project) rather than InstallAnywhere
502 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
503 settings, receive over the air updates and launch specific
504 versions via (<a href="https://github.com/threerings/getdown">Three
508 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
509 formats supported by Jalview (including .jvp project files)
512 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
513 arguments and switch between different getdown channels
516 <!-- JAL-3141 -->Backup files created when saving Jalview project
521 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
522 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
524 <!-- JAL-2620 -->Alternative genetic code tables for
525 'Translate as cDNA'</li>
527 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
528 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
531 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
532 implementation that allows updates) used for Sequence Feature collections</li>
534 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
535 features can be filtered and shaded according to any
536 associated attributes (e.g. variant attributes from VCF
537 file, or key-value pairs imported from column 9 of GFF
541 <!-- JAL-2879 -->Feature Attributes and shading schemes
542 stored and restored from Jalview Projects
545 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
546 recognise variant features
549 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
550 sequences (also coloured red by default)
553 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
557 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
558 algorithm (Z-sort/transparency and filter aware)
561 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
567 <!-- JAL-3205 -->Symmetric score matrices for faster
568 tree and PCA calculations
570 <li><strong>Principal Components Analysis Viewer</strong>
573 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
574 and Viewer state saved in Jalview Project
576 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
579 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
583 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
588 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
590 <li><strong>Speed and Efficiency</strong>
593 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
594 multiple groups when working with large alignments
597 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
601 <li><strong>User Interface</strong>
604 <!-- JAL-2933 -->Finder panel remembers last position in each
608 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
609 what is shown)<br />Only visible regions of alignment are shown by
610 default (can be changed in user preferences)
613 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
614 to the Overwrite Dialog
617 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
621 <!-- JAL-1244 -->Status bar shows bounds when dragging a
622 selection region, and gap count when inserting or deleting gaps
625 <!-- JAL-3132 -->Status bar updates over sequence and annotation
629 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
633 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
637 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
640 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
644 <!-- JAL-3181 -->Consistent ordering of links in sequence id
648 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
650 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
654 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
655 <li><strong>Java 11 Support (not yet on general release)</strong>
658 <!-- -->OSX GUI integrations for App menu's 'About' entry and
663 <em>Deprecations</em>
665 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
666 capabilities removed from the Jalview Desktop
668 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
669 unmarshalling has been replaced by JAXB for Jalview projects
670 and XML based data retrieval clients</li>
671 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
672 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
673 </ul> <em>Documentation</em>
675 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
676 not supported in EPS figure export
678 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
679 </ul> <em>Development and Release Processes</em>
682 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
685 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
687 <!-- JAL-3225 -->Eclipse project configuration managed with
691 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
692 Bamboo continuous integration for unattended Test Suite
696 <!-- JAL-2864 -->Memory test suite to detect leaks in common
700 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
704 <!-- JAL-3248 -->Developer documentation migrated to
705 markdown (with HTML rendering)
708 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
711 <!-- JAL-3289 -->New URLs for publishing development
716 <td align="left" valign="top">
719 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
722 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
723 superposition in Jmol fail on Windows
726 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
727 structures for sequences with lots of PDB structures
730 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
734 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
735 project involving multiple views
738 <!-- JAL-3164 -->Overview for complementary view in a linked
739 CDS/Protein alignment is not updated when Hide Columns by
740 Annotation dialog hides columns
743 <!-- JAL-3158 -->Selection highlighting in the complement of a
744 CDS/Protein alignment stops working after making a selection in
745 one view, then making another selection in the other view
748 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
752 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
753 Settings and Jalview Preferences panels
756 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
757 overview with large alignments
760 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
761 region if columns were selected by dragging right-to-left and the
762 mouse moved to the left of the first column
765 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
766 hidden column marker via scale popup menu
769 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
770 doesn't tell users the invalid URL
773 <!-- JAL-2816 -->Tooltips displayed for features filtered by
777 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
778 show cross references or Fetch Database References are shown in
782 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
783 peptide sequence (computed variant shown as p.Res.null)
786 <!-- JAL-2060 -->'Graduated colour' option not offered for
787 manually created features (where feature score is Float.NaN)
790 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
791 when columns are hidden
794 <!-- JAL-3082 -->Regular expression error for '(' in Select
795 Columns by Annotation description
798 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
799 out of Scale or Annotation Panel
802 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
806 <!-- JAL-3074 -->Left/right drag in annotation can scroll
810 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
814 <!-- JAL-3002 -->Column display is out by one after Page Down,
815 Page Up in wrapped mode
818 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
821 <!-- JAL-2932 -->Finder searches in minimised alignments
824 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
825 on opening an alignment
828 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
832 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
833 different groups in the alignment are selected
836 <!-- JAL-2717 -->Internationalised colour scheme names not shown
840 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
844 <!-- JAL-3125 -->Value input for graduated feature colour
845 threshold gets 'unrounded'
848 <!-- JAL-2982 -->PCA image export doesn't respect background
852 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
855 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
858 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
862 <!-- JAL-2964 -->Associate Tree with All Views not restored from
866 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
867 shown in complementary view
870 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
871 without normalisation
874 <!-- JAL-3021 -->Sequence Details report should open positioned at top
878 <!-- JAL-914 -->Help page can be opened twice
881 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
883 </ul> <em>Editing</em>
886 <!-- JAL-2822 -->Start and End should be updated when sequence
887 data at beginning or end of alignment added/removed via 'Edit'
891 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
892 relocate sequence features correctly when start of sequence is
893 removed (Known defect since 2.10)
896 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
897 dialog corrupts dataset sequence
900 <!-- JAL-868 -->Structure colours not updated when associated tree
901 repartitions the alignment view (Regression in 2.10.5)
903 </ul> <em>Datamodel</em>
906 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
907 sequence's End is greater than its length
909 </ul> <em>Bugs fixed for Java 11 Support (not yet on
910 general release)</em>
913 <!-- JAL-3288 -->Menus work properly in split-screen
915 </ul> <em>New Known Defects</em>
918 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
921 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
922 regions of protein alignment.
925 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
926 is restored from a Jalview 2.11 project
929 <!-- JAL-3213 -->Alignment panel height can be too small after
933 <!-- JAL-3240 -->Display is incorrect after removing gapped
934 columns within hidden columns
937 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
938 window after dragging left to select columns to left of visible
942 <!-- JAL-2876 -->Features coloured according to their description
943 string and thresholded by score in earlier versions of Jalview are
944 not shown as thresholded features in 2.11. To workaround please
945 create a Score filter instead.
948 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
950 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
953 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
954 alignments with multiple views can close views unexpectedly
957 <em>Java 11 Specific defects</em>
960 <!-- JAL-3235 -->Jalview Properties file is not sorted
961 alphabetically when saved
967 <td width="60" nowrap>
969 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
972 <td><div align="left">
976 <!-- JAL-3101 -->Default memory for Jalview webstart and
977 InstallAnywhere increased to 1G.
980 <!-- JAL-247 -->Hidden sequence markers and representative
981 sequence bolding included when exporting alignment as EPS,
982 SVG, PNG or HTML. <em>Display is configured via the
983 Format menu, or for command-line use via a Jalview
984 properties file.</em>
987 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
988 API and sequence data now imported as JSON.
991 <!-- JAL-3065 -->Change in recommended way of starting
992 Jalview via a Java command line: add jars in lib directory
993 to CLASSPATH, rather than via the deprecated java.ext.dirs
1000 <!-- JAL-3047 -->Support added to execute test suite
1001 instrumented with <a href="http://openclover.org/">Open
1006 <td><div align="left">
1010 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1011 row shown in Feredoxin Structure alignment view of example
1015 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1016 annotation displayed.
1019 <!-- JAL-3107 -->Group conservation/consensus not shown
1020 for newly created group when 'Apply to all groups'
1024 <!-- JAL-3087 -->Corrupted display when switching to
1025 wrapped mode when sequence panel's vertical scrollbar is
1029 <!-- JAL-3003 -->Alignment is black in exported EPS file
1030 when sequences are selected in exported view.</em>
1033 <!-- JAL-3059 -->Groups with different coloured borders
1034 aren't rendered with correct colour.
1037 <!-- JAL-3092 -->Jalview could hang when importing certain
1038 types of knotted RNA secondary structure.
1041 <!-- JAL-3095 -->Sequence highlight and selection in
1042 trimmed VARNA 2D structure is incorrect for sequences that
1046 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1047 annotation when columns are inserted into an alignment,
1048 and when exporting as Stockholm flatfile.
1051 <!-- JAL-3053 -->Jalview annotation rows containing upper
1052 and lower-case 'E' and 'H' do not automatically get
1053 treated as RNA secondary structure.
1056 <!-- JAL-3106 -->.jvp should be used as default extension
1057 (not .jar) when saving a Jalview project file.
1060 <!-- JAL-3105 -->Mac Users: closing a window correctly
1061 transfers focus to previous window on OSX
1064 <em>Java 10 Issues Resolved</em>
1067 <!-- JAL-2988 -->OSX - Can't save new files via the File
1068 or export menus by typing in a name into the Save dialog
1072 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1073 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1074 'look and feel' which has improved compatibility with the
1075 latest version of OSX.
1082 <td width="60" nowrap>
1083 <div align="center">
1084 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1085 <em>7/06/2018</em></strong>
1088 <td><div align="left">
1092 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1093 annotation retrieved from Uniprot
1096 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1097 onto the Jalview Desktop
1101 <td><div align="left">
1105 <!-- JAL-3017 -->Cannot import features with multiple
1106 variant elements (blocks import of some Uniprot records)
1109 <!-- JAL-2997 -->Clustal files with sequence positions in
1110 right-hand column parsed correctly
1113 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1114 not alignment area in exported graphic
1117 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1118 window has input focus
1121 <!-- JAL-2992 -->Annotation panel set too high when
1122 annotation added to view (Windows)
1125 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1126 network connectivity is poor
1129 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1130 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1131 the currently open URL and links from a page viewed in
1132 Firefox or Chrome on Windows is now fully supported. If
1133 you are using Edge, only links in the page can be
1134 dragged, and with Internet Explorer, only the currently
1135 open URL in the browser can be dropped onto Jalview.</em>
1138 <em>New Known Defects</em>
1140 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1145 <td width="60" nowrap>
1146 <div align="center">
1147 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1150 <td><div align="left">
1154 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1155 for disabling automatic superposition of multiple
1156 structures and open structures in existing views
1159 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1160 ID and annotation area margins can be click-dragged to
1164 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1168 <!-- JAL-2759 -->Improved performance for large alignments
1169 and lots of hidden columns
1172 <!-- JAL-2593 -->Improved performance when rendering lots
1173 of features (particularly when transparency is disabled)
1176 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1177 exchange of Jalview features and Chimera attributes made
1183 <td><div align="left">
1186 <!-- JAL-2899 -->Structure and Overview aren't updated
1187 when Colour By Annotation threshold slider is adjusted
1190 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1191 overlapping alignment panel
1194 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1198 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1199 improved: CDS not handled correctly if transcript has no
1203 <!-- JAL-2321 -->Secondary structure and temperature
1204 factor annotation not added to sequence when local PDB
1205 file associated with it by drag'n'drop or structure
1209 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1210 dialog doesn't import PDB files dropped on an alignment
1213 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1214 scroll bar doesn't work for some CDS/Protein views
1217 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1218 Java 1.8u153 onwards and Java 1.9u4+.
1221 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1222 columns in annotation row
1225 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1226 honored in batch mode
1229 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1230 for structures added to existing Jmol view
1233 <!-- JAL-2223 -->'View Mappings' includes duplicate
1234 entries after importing project with multiple views
1237 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1238 protein sequences via SIFTS from associated PDB entries
1239 with negative residue numbers or missing residues fails
1242 <!-- JAL-2952 -->Exception when shading sequence with negative
1243 Temperature Factor values from annotated PDB files (e.g.
1244 as generated by CONSURF)
1247 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1248 tooltip doesn't include a text description of mutation
1251 <!-- JAL-2922 -->Invert displayed features very slow when
1252 structure and/or overview windows are also shown
1255 <!-- JAL-2954 -->Selecting columns from highlighted regions
1256 very slow for alignments with large numbers of sequences
1259 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1260 with 'StringIndexOutOfBounds'
1263 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1264 platforms running Java 10
1267 <!-- JAL-2960 -->Adding a structure to existing structure
1268 view appears to do nothing because the view is hidden behind the alignment view
1274 <!-- JAL-2926 -->Copy consensus sequence option in applet
1275 should copy the group consensus when popup is opened on it
1281 <!-- JAL-2913 -->Fixed ID width preference is not respected
1284 <em>New Known Defects</em>
1287 <!-- JAL-2973 --> Exceptions occasionally raised when
1288 editing a large alignment and overview is displayed
1291 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1292 repeatedly after a series of edits even when the overview
1293 is no longer reflecting updates
1296 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1297 structures for protein subsequence (if 'Trim Retrieved
1298 Sequences' enabled) or Ensembl isoforms (Workaround in
1299 2.10.4 is to fail back to N&W mapping)
1302 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1303 option gives blank output
1310 <td width="60" nowrap>
1311 <div align="center">
1312 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1315 <td><div align="left">
1316 <ul><li>Updated Certum Codesigning Certificate
1317 (Valid till 30th November 2018)</li></ul></div></td>
1318 <td><div align="left">
1319 <em>Desktop</em><ul>
1321 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1322 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1323 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1324 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1325 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1326 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1327 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1333 <td width="60" nowrap>
1334 <div align="center">
1335 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1338 <td><div align="left">
1342 <!-- JAL-2446 -->Faster and more efficient management and
1343 rendering of sequence features
1346 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1347 429 rate limit request hander
1350 <!-- JAL-2773 -->Structure views don't get updated unless
1351 their colours have changed
1354 <!-- JAL-2495 -->All linked sequences are highlighted for
1355 a structure mousover (Jmol) or selection (Chimera)
1358 <!-- JAL-2790 -->'Cancel' button in progress bar for
1359 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1362 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1363 view from Ensembl locus cross-references
1366 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1370 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1371 feature can be disabled
1374 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1375 PDB easier retrieval of sequences for lists of IDs
1378 <!-- JAL-2758 -->Short names for sequences retrieved from
1384 <li>Groovy interpreter updated to 2.4.12</li>
1385 <li>Example groovy script for generating a matrix of
1386 percent identity scores for current alignment.</li>
1388 <em>Testing and Deployment</em>
1391 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1395 <td><div align="left">
1399 <!-- JAL-2643 -->Pressing tab after updating the colour
1400 threshold text field doesn't trigger an update to the
1404 <!-- JAL-2682 -->Race condition when parsing sequence ID
1408 <!-- JAL-2608 -->Overview windows are also closed when
1409 alignment window is closed
1412 <!-- JAL-2548 -->Export of features doesn't always respect
1416 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1417 takes a long time in Cursor mode
1423 <!-- JAL-2777 -->Structures with whitespace chainCode
1424 cannot be viewed in Chimera
1427 <!-- JAL-2728 -->Protein annotation panel too high in
1431 <!-- JAL-2757 -->Can't edit the query after the server
1432 error warning icon is shown in Uniprot and PDB Free Text
1436 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1439 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1442 <!-- JAL-2739 -->Hidden column marker in last column not
1443 rendered when switching back from Wrapped to normal view
1446 <!-- JAL-2768 -->Annotation display corrupted when
1447 scrolling right in unwapped alignment view
1450 <!-- JAL-2542 -->Existing features on subsequence
1451 incorrectly relocated when full sequence retrieved from
1455 <!-- JAL-2733 -->Last reported memory still shown when
1456 Desktop->Show Memory is unticked (OSX only)
1459 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1460 features of same type and group to be selected for
1464 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1465 alignments when hidden columns are present
1468 <!-- JAL-2392 -->Jalview freezes when loading and
1469 displaying several structures
1472 <!-- JAL-2732 -->Black outlines left after resizing or
1476 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1477 within the Jalview desktop on OSX
1480 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1481 when in wrapped alignment mode
1484 <!-- JAL-2636 -->Scale mark not shown when close to right
1485 hand end of alignment
1488 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1489 each selected sequence do not have correct start/end
1493 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1494 after canceling the Alignment Window's Font dialog
1497 <!-- JAL-2036 -->Show cross-references not enabled after
1498 restoring project until a new view is created
1501 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1502 URL links appears when only default EMBL-EBI link is
1503 configured (since 2.10.2b2)
1506 <!-- JAL-2775 -->Overview redraws whole window when box
1507 position is adjusted
1510 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1511 in a multi-chain structure when viewing alignment
1512 involving more than one chain (since 2.10)
1515 <!-- JAL-2811 -->Double residue highlights in cursor mode
1516 if new selection moves alignment window
1519 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1520 arrow key in cursor mode to pass hidden column marker
1523 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1524 that produces correctly annotated transcripts and products
1527 <!-- JAL-2776 -->Toggling a feature group after first time
1528 doesn't update associated structure view
1531 <em>Applet</em><br />
1534 <!-- JAL-2687 -->Concurrent modification exception when
1535 closing alignment panel
1538 <em>BioJSON</em><br />
1541 <!-- JAL-2546 -->BioJSON export does not preserve
1542 non-positional features
1545 <em>New Known Issues</em>
1548 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1549 sequence features correctly (for many previous versions of
1553 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1554 using cursor in wrapped panel other than top
1557 <!-- JAL-2791 -->Select columns containing feature ignores
1558 graduated colour threshold
1561 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1562 always preserve numbering and sequence features
1565 <em>Known Java 9 Issues</em>
1568 <!-- JAL-2902 -->Groovy Console very slow to open and is
1569 not responsive when entering characters (Webstart, Java
1576 <td width="60" nowrap>
1577 <div align="center">
1578 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1579 <em>2/10/2017</em></strong>
1582 <td><div align="left">
1583 <em>New features in Jalview Desktop</em>
1586 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1588 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1592 <td><div align="left">
1596 <td width="60" nowrap>
1597 <div align="center">
1598 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1599 <em>7/9/2017</em></strong>
1602 <td><div align="left">
1606 <!-- JAL-2588 -->Show gaps in overview window by colouring
1607 in grey (sequences used to be coloured grey, and gaps were
1611 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1615 <!-- JAL-2587 -->Overview updates immediately on increase
1616 in size and progress bar shown as higher resolution
1617 overview is recalculated
1622 <td><div align="left">
1626 <!-- JAL-2664 -->Overview window redraws every hidden
1627 column region row by row
1630 <!-- JAL-2681 -->duplicate protein sequences shown after
1631 retrieving Ensembl crossrefs for sequences from Uniprot
1634 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1635 format setting is unticked
1638 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1639 if group has show boxes format setting unticked
1642 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1643 autoscrolling whilst dragging current selection group to
1644 include sequences and columns not currently displayed
1647 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1648 assemblies are imported via CIF file
1651 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1652 displayed when threshold or conservation colouring is also
1656 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1660 <!-- JAL-2673 -->Jalview continues to scroll after
1661 dragging a selected region off the visible region of the
1665 <!-- JAL-2724 -->Cannot apply annotation based
1666 colourscheme to all groups in a view
1669 <!-- JAL-2511 -->IDs don't line up with sequences
1670 initially after font size change using the Font chooser or
1677 <td width="60" nowrap>
1678 <div align="center">
1679 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1682 <td><div align="left">
1683 <em>Calculations</em>
1687 <!-- JAL-1933 -->Occupancy annotation row shows number of
1688 ungapped positions in each column of the alignment.
1691 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1692 a calculation dialog box
1695 <!-- JAL-2379 -->Revised implementation of PCA for speed
1696 and memory efficiency (~30x faster)
1699 <!-- JAL-2403 -->Revised implementation of sequence
1700 similarity scores as used by Tree, PCA, Shading Consensus
1701 and other calculations
1704 <!-- JAL-2416 -->Score matrices are stored as resource
1705 files within the Jalview codebase
1708 <!-- JAL-2500 -->Trees computed on Sequence Feature
1709 Similarity may have different topology due to increased
1716 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1717 model for alignments and groups
1720 <!-- JAL-384 -->Custom shading schemes created via groovy
1727 <!-- JAL-2526 -->Efficiency improvements for interacting
1728 with alignment and overview windows
1731 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1735 <!-- JAL-2388 -->Hidden columns and sequences can be
1739 <!-- JAL-2611 -->Click-drag in visible area allows fine
1740 adjustment of visible position
1744 <em>Data import/export</em>
1747 <!-- JAL-2535 -->Posterior probability annotation from
1748 Stockholm files imported as sequence associated annotation
1751 <!-- JAL-2507 -->More robust per-sequence positional
1752 annotation input/output via stockholm flatfile
1755 <!-- JAL-2533 -->Sequence names don't include file
1756 extension when importing structure files without embedded
1757 names or PDB accessions
1760 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1761 format sequence substitution matrices
1764 <em>User Interface</em>
1767 <!-- JAL-2447 --> Experimental Features Checkbox in
1768 Desktop's Tools menu to hide or show untested features in
1772 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1773 via Overview or sequence motif search operations
1776 <!-- JAL-2547 -->Amend sequence features dialog box can be
1777 opened by double clicking gaps within sequence feature
1781 <!-- JAL-1476 -->Status bar message shown when not enough
1782 aligned positions were available to create a 3D structure
1786 <em>3D Structure</em>
1789 <!-- JAL-2430 -->Hidden regions in alignment views are not
1790 coloured in linked structure views
1793 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1794 file-based command exchange
1797 <!-- JAL-2375 -->Structure chooser automatically shows
1798 Cached Structures rather than querying the PDBe if
1799 structures are already available for sequences
1802 <!-- JAL-2520 -->Structures imported via URL are cached in
1803 the Jalview project rather than downloaded again when the
1804 project is reopened.
1807 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1808 to transfer Chimera's structure attributes as Jalview
1809 features, and vice-versa (<strong>Experimental
1813 <em>Web Services</em>
1816 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1819 <!-- JAL-2335 -->Filter non-standard amino acids and
1820 nucleotides when submitting to AACon and other MSA
1824 <!-- JAL-2316, -->URLs for viewing database
1825 cross-references provided by identifiers.org and the
1826 EMBL-EBI's MIRIAM DB
1833 <!-- JAL-2344 -->FileFormatI interface for describing and
1834 identifying file formats (instead of String constants)
1837 <!-- JAL-2228 -->FeatureCounter script refactored for
1838 efficiency when counting all displayed features (not
1839 backwards compatible with 2.10.1)
1842 <em>Example files</em>
1845 <!-- JAL-2631 -->Graduated feature colour style example
1846 included in the example feature file
1849 <em>Documentation</em>
1852 <!-- JAL-2339 -->Release notes reformatted for readability
1853 with the built-in Java help viewer
1856 <!-- JAL-1644 -->Find documentation updated with 'search
1857 sequence description' option
1863 <!-- JAL-2485, -->External service integration tests for
1864 Uniprot REST Free Text Search Client
1867 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1870 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1875 <td><div align="left">
1876 <em>Calculations</em>
1879 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1880 matrix - C->R should be '-3'<br />Old matrix restored
1881 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1883 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1884 Jalview's treatment of gaps in PCA and substitution matrix
1885 based Tree calculations.<br /> <br />In earlier versions
1886 of Jalview, gaps matching gaps were penalised, and gaps
1887 matching non-gaps penalised even more. In the PCA
1888 calculation, gaps were actually treated as non-gaps - so
1889 different costs were applied, which meant Jalview's PCAs
1890 were different to those produced by SeqSpace.<br />Jalview
1891 now treats gaps in the same way as SeqSpace (ie it scores
1892 them as 0). <br /> <br />Enter the following in the
1893 Groovy console to restore pre-2.10.2 behaviour:<br />
1894 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1895 // for 2.10.1 mode <br />
1896 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1897 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1898 these settings will affect all subsequent tree and PCA
1899 calculations (not recommended)</em></li>
1901 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1902 scaling of branch lengths for trees computed using
1903 Sequence Feature Similarity.
1906 <!-- JAL-2377 -->PCA calculation could hang when
1907 generating output report when working with highly
1908 redundant alignments
1911 <!-- JAL-2544 --> Sort by features includes features to
1912 right of selected region when gaps present on right-hand
1916 <em>User Interface</em>
1919 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1920 doesn't reselect a specific sequence's associated
1921 annotation after it was used for colouring a view
1924 <!-- JAL-2419 -->Current selection lost if popup menu
1925 opened on a region of alignment without groups
1928 <!-- JAL-2374 -->Popup menu not always shown for regions
1929 of an alignment with overlapping groups
1932 <!-- JAL-2310 -->Finder double counts if both a sequence's
1933 name and description match
1936 <!-- JAL-2370 -->Hiding column selection containing two
1937 hidden regions results in incorrect hidden regions
1940 <!-- JAL-2386 -->'Apply to all groups' setting when
1941 changing colour does not apply Conservation slider value
1945 <!-- JAL-2373 -->Percentage identity and conservation menu
1946 items do not show a tick or allow shading to be disabled
1949 <!-- JAL-2385 -->Conservation shading or PID threshold
1950 lost when base colourscheme changed if slider not visible
1953 <!-- JAL-2547 -->Sequence features shown in tooltip for
1954 gaps before start of features
1957 <!-- JAL-2623 -->Graduated feature colour threshold not
1958 restored to UI when feature colour is edited
1961 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1962 a time when scrolling vertically in wrapped mode.
1965 <!-- JAL-2630 -->Structure and alignment overview update
1966 as graduate feature colour settings are modified via the
1970 <!-- JAL-2034 -->Overview window doesn't always update
1971 when a group defined on the alignment is resized
1974 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1975 wrapped view result in positional status updates
1979 <!-- JAL-2563 -->Status bar doesn't show position for
1980 ambiguous amino acid and nucleotide symbols
1983 <!-- JAL-2602 -->Copy consensus sequence failed if
1984 alignment included gapped columns
1987 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1988 widgets don't permanently disappear
1991 <!-- JAL-2503 -->Cannot select or filter quantitative
1992 annotation that are shown only as column labels (e.g.
1993 T-Coffee column reliability scores)
1996 <!-- JAL-2594 -->Exception thrown if trying to create a
1997 sequence feature on gaps only
2000 <!-- JAL-2504 -->Features created with 'New feature'
2001 button from a Find inherit previously defined feature type
2002 rather than the Find query string
2005 <!-- JAL-2423 -->incorrect title in output window when
2006 exporting tree calculated in Jalview
2009 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2010 and then revealing them reorders sequences on the
2014 <!-- JAL-964 -->Group panel in sequence feature settings
2015 doesn't update to reflect available set of groups after
2016 interactively adding or modifying features
2019 <!-- JAL-2225 -->Sequence Database chooser unusable on
2023 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2024 only excluded gaps in current sequence and ignored
2031 <!-- JAL-2421 -->Overview window visible region moves
2032 erratically when hidden rows or columns are present
2035 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2036 Structure Viewer's colour menu don't correspond to
2040 <!-- JAL-2405 -->Protein specific colours only offered in
2041 colour and group colour menu for protein alignments
2044 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2045 reflect currently selected view or group's shading
2049 <!-- JAL-2624 -->Feature colour thresholds not respected
2050 when rendered on overview and structures when opacity at
2054 <!-- JAL-2589 -->User defined gap colour not shown in
2055 overview when features overlaid on alignment
2058 <!-- JAL-2567 -->Feature settings for different views not
2059 recovered correctly from Jalview project file
2062 <!-- JAL-2256 -->Feature colours in overview when first opened
2063 (automatically via preferences) are different to the main
2067 <em>Data import/export</em>
2070 <!-- JAL-2576 -->Very large alignments take a long time to
2074 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2075 added after a sequence was imported are not written to
2079 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2080 when importing RNA secondary structure via Stockholm
2083 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2084 not shown in correct direction for simple pseudoknots
2087 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2088 with lightGray or darkGray via features file (but can
2092 <!-- JAL-2383 -->Above PID colour threshold not recovered
2093 when alignment view imported from project
2096 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2097 structure and sequences extracted from structure files
2098 imported via URL and viewed in Jmol
2101 <!-- JAL-2520 -->Structures loaded via URL are saved in
2102 Jalview Projects rather than fetched via URL again when
2103 the project is loaded and the structure viewed
2106 <em>Web Services</em>
2109 <!-- JAL-2519 -->EnsemblGenomes example failing after
2110 release of Ensembl v.88
2113 <!-- JAL-2366 -->Proxy server address and port always
2114 appear enabled in Preferences->Connections
2117 <!-- JAL-2461 -->DAS registry not found exceptions
2118 removed from console output
2121 <!-- JAL-2582 -->Cannot retrieve protein products from
2122 Ensembl by Peptide ID
2125 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2126 created from SIFTs, and spurious 'Couldn't open structure
2127 in Chimera' errors raised after April 2017 update (problem
2128 due to 'null' string rather than empty string used for
2129 residues with no corresponding PDB mapping).
2132 <em>Application UI</em>
2135 <!-- JAL-2361 -->User Defined Colours not added to Colour
2139 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2140 case' residues (button in colourscheme editor debugged and
2141 new documentation and tooltips added)
2144 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2145 doesn't restore group-specific text colour thresholds
2148 <!-- JAL-2243 -->Feature settings panel does not update as
2149 new features are added to alignment
2152 <!-- JAL-2532 -->Cancel in feature settings reverts
2153 changes to feature colours via the Amend features dialog
2156 <!-- JAL-2506 -->Null pointer exception when attempting to
2157 edit graduated feature colour via amend features dialog
2161 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2162 selection menu changes colours of alignment views
2165 <!-- JAL-2426 -->Spurious exceptions in console raised
2166 from alignment calculation workers after alignment has
2170 <!-- JAL-1608 -->Typo in selection popup menu - Create
2171 groups now 'Create Group'
2174 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2175 Create/Undefine group doesn't always work
2178 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2179 shown again after pressing 'Cancel'
2182 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2183 adjusts start position in wrap mode
2186 <!-- JAL-2563 -->Status bar doesn't show positions for
2187 ambiguous amino acids
2190 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2191 CDS/Protein view after CDS sequences added for aligned
2195 <!-- JAL-2592 -->User defined colourschemes called 'User
2196 Defined' don't appear in Colours menu
2202 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2203 score models doesn't always result in an updated PCA plot
2206 <!-- JAL-2442 -->Features not rendered as transparent on
2207 overview or linked structure view
2210 <!-- JAL-2372 -->Colour group by conservation doesn't
2214 <!-- JAL-2517 -->Hitting Cancel after applying
2215 user-defined colourscheme doesn't restore original
2222 <!-- JAL-2314 -->Unit test failure:
2223 jalview.ws.jabaws.RNAStructExportImport setup fails
2226 <!-- JAL-2307 -->Unit test failure:
2227 jalview.ws.sifts.SiftsClientTest due to compatibility
2228 problems with deep array comparison equality asserts in
2229 successive versions of TestNG
2232 <!-- JAL-2479 -->Relocated StructureChooserTest and
2233 ParameterUtilsTest Unit tests to Network suite
2236 <em>New Known Issues</em>
2239 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2240 phase after a sequence motif find operation
2243 <!-- JAL-2550 -->Importing annotation file with rows
2244 containing just upper and lower case letters are
2245 interpreted as WUSS RNA secondary structure symbols
2248 <!-- JAL-2590 -->Cannot load and display Newick trees
2249 reliably from eggnog Ortholog database
2252 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2253 containing features of type Highlight' when 'B' is pressed
2254 to mark columns containing highlighted regions.
2257 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2258 doesn't always add secondary structure annotation.
2263 <td width="60" nowrap>
2264 <div align="center">
2265 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2268 <td><div align="left">
2272 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2273 for all consensus calculations
2276 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2279 <li>Updated Jalview's Certum code signing certificate
2282 <em>Application</em>
2285 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2286 set of database cross-references, sorted alphabetically
2289 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2290 from database cross references. Users with custom links
2291 will receive a <a href="webServices/urllinks.html#warning">warning
2292 dialog</a> asking them to update their preferences.
2295 <!-- JAL-2287-->Cancel button and escape listener on
2296 dialog warning user about disconnecting Jalview from a
2300 <!-- JAL-2320-->Jalview's Chimera control window closes if
2301 the Chimera it is connected to is shut down
2304 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2305 columns menu item to mark columns containing highlighted
2306 regions (e.g. from structure selections or results of a
2310 <!-- JAL-2284-->Command line option for batch-generation
2311 of HTML pages rendering alignment data with the BioJS
2321 <!-- JAL-2286 -->Columns with more than one modal residue
2322 are not coloured or thresholded according to percent
2323 identity (first observed in Jalview 2.8.2)
2326 <!-- JAL-2301 -->Threonine incorrectly reported as not
2330 <!-- JAL-2318 -->Updates to documentation pages (above PID
2331 threshold, amino acid properties)
2334 <!-- JAL-2292 -->Lower case residues in sequences are not
2335 reported as mapped to residues in a structure file in the
2339 <!--JAL-2324 -->Identical features with non-numeric scores
2340 could be added multiple times to a sequence
2343 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2344 bond features shown as two highlighted residues rather
2345 than a range in linked structure views, and treated
2346 correctly when selecting and computing trees from features
2349 <!-- JAL-2281-->Custom URL links for database
2350 cross-references are matched to database name regardless
2355 <em>Application</em>
2358 <!-- JAL-2282-->Custom URL links for specific database
2359 names without regular expressions also offer links from
2363 <!-- JAL-2315-->Removing a single configured link in the
2364 URL links pane in Connections preferences doesn't actually
2365 update Jalview configuration
2368 <!-- JAL-2272-->CTRL-Click on a selected region to open
2369 the alignment area popup menu doesn't work on El-Capitan
2372 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2373 files with similarly named sequences if dropped onto the
2377 <!-- JAL-2312 -->Additional mappings are shown for PDB
2378 entries where more chains exist in the PDB accession than
2379 are reported in the SIFTS file
2382 <!-- JAL-2317-->Certain structures do not get mapped to
2383 the structure view when displayed with Chimera
2386 <!-- JAL-2317-->No chains shown in the Chimera view
2387 panel's View->Show Chains submenu
2390 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2391 work for wrapped alignment views
2394 <!--JAL-2197 -->Rename UI components for running JPred
2395 predictions from 'JNet' to 'JPred'
2398 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2399 corrupted when annotation panel vertical scroll is not at
2400 first annotation row
2403 <!--JAL-2332 -->Attempting to view structure for Hen
2404 lysozyme results in a PDB Client error dialog box
2407 <!-- JAL-2319 -->Structure View's mapping report switched
2408 ranges for PDB and sequence for SIFTS
2411 SIFTS 'Not_Observed' residues mapped to non-existant
2415 <!-- <em>New Known Issues</em>
2422 <td width="60" nowrap>
2423 <div align="center">
2424 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2425 <em>25/10/2016</em></strong>
2428 <td><em>Application</em>
2430 <li>3D Structure chooser opens with 'Cached structures'
2431 view if structures already loaded</li>
2432 <li>Progress bar reports models as they are loaded to
2433 structure views</li>
2439 <li>Colour by conservation always enabled and no tick
2440 shown in menu when BLOSUM or PID shading applied</li>
2441 <li>FER1_ARATH and FER2_ARATH labels were switched in
2442 example sequences/projects/trees</li>
2444 <em>Application</em>
2446 <li>Jalview projects with views of local PDB structure
2447 files saved on Windows cannot be opened on OSX</li>
2448 <li>Multiple structure views can be opened and superposed
2449 without timeout for structures with multiple models or
2450 multiple sequences in alignment</li>
2451 <li>Cannot import or associated local PDB files without a
2452 PDB ID HEADER line</li>
2453 <li>RMSD is not output in Jmol console when superposition
2455 <li>Drag and drop of URL from Browser fails for Linux and
2456 OSX versions earlier than El Capitan</li>
2457 <li>ENA client ignores invalid content from ENA server</li>
2458 <li>Exceptions are not raised in console when ENA client
2459 attempts to fetch non-existent IDs via Fetch DB Refs UI
2461 <li>Exceptions are not raised in console when a new view
2462 is created on the alignment</li>
2463 <li>OSX right-click fixed for group selections: CMD-click
2464 to insert/remove gaps in groups and CTRL-click to open group
2467 <em>Build and deployment</em>
2469 <li>URL link checker now copes with multi-line anchor
2472 <em>New Known Issues</em>
2474 <li>Drag and drop from URL links in browsers do not work
2481 <td width="60" nowrap>
2482 <div align="center">
2483 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2486 <td><em>General</em>
2489 <!-- JAL-2124 -->Updated Spanish translations.
2492 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2493 for importing structure data to Jalview. Enables mmCIF and
2497 <!-- JAL-192 --->Alignment ruler shows positions relative to
2501 <!-- JAL-2202 -->Position/residue shown in status bar when
2502 mousing over sequence associated annotation
2505 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2509 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2510 '()', canonical '[]' and invalid '{}' base pair populations
2514 <!-- JAL-2092 -->Feature settings popup menu options for
2515 showing or hiding columns containing a feature
2518 <!-- JAL-1557 -->Edit selected group by double clicking on
2519 group and sequence associated annotation labels
2522 <!-- JAL-2236 -->Sequence name added to annotation label in
2523 select/hide columns by annotation and colour by annotation
2527 </ul> <em>Application</em>
2530 <!-- JAL-2050-->Automatically hide introns when opening a
2531 gene/transcript view
2534 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2538 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2539 structure mappings with the EMBL-EBI PDBe SIFTS database
2542 <!-- JAL-2079 -->Updated download sites used for Rfam and
2543 Pfam sources to xfam.org
2546 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2549 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2550 over sequences in Jalview
2553 <!-- JAL-2027-->Support for reverse-complement coding
2554 regions in ENA and EMBL
2557 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2558 for record retrieval via ENA rest API
2561 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2565 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2566 groovy script execution
2569 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2570 alignment window's Calculate menu
2573 <!-- JAL-1812 -->Allow groovy scripts that call
2574 Jalview.getAlignFrames() to run in headless mode
2577 <!-- JAL-2068 -->Support for creating new alignment
2578 calculation workers from groovy scripts
2581 <!-- JAL-1369 --->Store/restore reference sequence in
2585 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2586 associations are now saved/restored from project
2589 <!-- JAL-1993 -->Database selection dialog always shown
2590 before sequence fetcher is opened
2593 <!-- JAL-2183 -->Double click on an entry in Jalview's
2594 database chooser opens a sequence fetcher
2597 <!-- JAL-1563 -->Free-text search client for UniProt using
2598 the UniProt REST API
2601 <!-- JAL-2168 -->-nonews command line parameter to prevent
2602 the news reader opening
2605 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2606 querying stored in preferences
2609 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2613 <!-- JAL-1977-->Tooltips shown on database chooser
2616 <!-- JAL-391 -->Reverse complement function in calculate
2617 menu for nucleotide sequences
2620 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2621 and feature counts preserves alignment ordering (and
2622 debugged for complex feature sets).
2625 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2626 viewing structures with Jalview 2.10
2629 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2630 genome, transcript CCDS and gene ids via the Ensembl and
2631 Ensembl Genomes REST API
2634 <!-- JAL-2049 -->Protein sequence variant annotation
2635 computed for 'sequence_variant' annotation on CDS regions
2639 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2643 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2644 Ref Fetcher fails to match, or otherwise updates sequence
2645 data from external database records.
2648 <!-- JAL-2154 -->Revised Jalview Project format for
2649 efficient recovery of sequence coding and alignment
2650 annotation relationships.
2652 </ul> <!-- <em>Applet</em>
2663 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2667 <!-- JAL-2018-->Export features in Jalview format (again)
2668 includes graduated colourschemes
2671 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2672 working with big alignments and lots of hidden columns
2675 <!-- JAL-2053-->Hidden column markers not always rendered
2676 at right of alignment window
2679 <!-- JAL-2067 -->Tidied up links in help file table of
2683 <!-- JAL-2072 -->Feature based tree calculation not shown
2687 <!-- JAL-2075 -->Hidden columns ignored during feature
2688 based tree calculation
2691 <!-- JAL-2065 -->Alignment view stops updating when show
2692 unconserved enabled for group on alignment
2695 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2699 <!-- JAL-2146 -->Alignment column in status incorrectly
2700 shown as "Sequence position" when mousing over
2704 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2705 hidden columns present
2708 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2709 user created annotation added to alignment
2712 <!-- JAL-1841 -->RNA Structure consensus only computed for
2713 '()' base pair annotation
2716 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2717 in zero scores for all base pairs in RNA Structure
2721 <!-- JAL-2174-->Extend selection with columns containing
2725 <!-- JAL-2275 -->Pfam format writer puts extra space at
2726 beginning of sequence
2729 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2733 <!-- JAL-2238 -->Cannot create groups on an alignment from
2734 from a tree when t-coffee scores are shown
2737 <!-- JAL-1836,1967 -->Cannot import and view PDB
2738 structures with chains containing negative resnums (4q4h)
2741 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2745 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2746 to Clustal, PIR and PileUp output
2749 <!-- JAL-2008 -->Reordering sequence features that are
2750 not visible causes alignment window to repaint
2753 <!-- JAL-2006 -->Threshold sliders don't work in
2754 graduated colour and colour by annotation row for e-value
2755 scores associated with features and annotation rows
2758 <!-- JAL-1797 -->amino acid physicochemical conservation
2759 calculation should be case independent
2762 <!-- JAL-2173 -->Remove annotation also updates hidden
2766 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2767 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2768 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2771 <!-- JAL-2065 -->Null pointer exceptions and redraw
2772 problems when reference sequence defined and 'show
2773 non-conserved' enabled
2776 <!-- JAL-1306 -->Quality and Conservation are now shown on
2777 load even when Consensus calculation is disabled
2780 <!-- JAL-1932 -->Remove right on penultimate column of
2781 alignment does nothing
2784 <em>Application</em>
2787 <!-- JAL-1552-->URLs and links can't be imported by
2788 drag'n'drop on OSX when launched via webstart (note - not
2789 yet fixed for El Capitan)
2792 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2793 output when running on non-gb/us i18n platforms
2796 <!-- JAL-1944 -->Error thrown when exporting a view with
2797 hidden sequences as flat-file alignment
2800 <!-- JAL-2030-->InstallAnywhere distribution fails when
2804 <!-- JAL-2080-->Jalview very slow to launch via webstart
2805 (also hotfix for 2.9.0b2)
2808 <!-- JAL-2085 -->Cannot save project when view has a
2809 reference sequence defined
2812 <!-- JAL-1011 -->Columns are suddenly selected in other
2813 alignments and views when revealing hidden columns
2816 <!-- JAL-1989 -->Hide columns not mirrored in complement
2817 view in a cDNA/Protein splitframe
2820 <!-- JAL-1369 -->Cannot save/restore representative
2821 sequence from project when only one sequence is
2825 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2826 in Structure Chooser
2829 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2830 structure consensus didn't refresh annotation panel
2833 <!-- JAL-1962 -->View mapping in structure view shows
2834 mappings between sequence and all chains in a PDB file
2837 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2838 dialogs format columns correctly, don't display array
2839 data, sort columns according to type
2842 <!-- JAL-1975 -->Export complete shown after destination
2843 file chooser is cancelled during an image export
2846 <!-- JAL-2025 -->Error when querying PDB Service with
2847 sequence name containing special characters
2850 <!-- JAL-2024 -->Manual PDB structure querying should be
2854 <!-- JAL-2104 -->Large tooltips with broken HTML
2855 formatting don't wrap
2858 <!-- JAL-1128 -->Figures exported from wrapped view are
2859 truncated so L looks like I in consensus annotation
2862 <!-- JAL-2003 -->Export features should only export the
2863 currently displayed features for the current selection or
2867 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2868 after fetching cross-references, and restoring from
2872 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2873 followed in the structure viewer
2876 <!-- JAL-2163 -->Titles for individual alignments in
2877 splitframe not restored from project
2880 <!-- JAL-2145 -->missing autocalculated annotation at
2881 trailing end of protein alignment in transcript/product
2882 splitview when pad-gaps not enabled by default
2885 <!-- JAL-1797 -->amino acid physicochemical conservation
2889 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2890 article has been read (reopened issue due to
2891 internationalisation problems)
2894 <!-- JAL-1960 -->Only offer PDB structures in structure
2895 viewer based on sequence name, PDB and UniProt
2900 <!-- JAL-1976 -->No progress bar shown during export of
2904 <!-- JAL-2213 -->Structures not always superimposed after
2905 multiple structures are shown for one or more sequences.
2908 <!-- JAL-1370 -->Reference sequence characters should not
2909 be replaced with '.' when 'Show unconserved' format option
2913 <!-- JAL-1823 -->Cannot specify chain code when entering
2914 specific PDB id for sequence
2917 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2918 'Export hidden sequences' is enabled, but 'export hidden
2919 columns' is disabled.
2922 <!--JAL-2026-->Best Quality option in structure chooser
2923 selects lowest rather than highest resolution structures
2927 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2928 to sequence mapping in 'View Mappings' report
2931 <!-- JAL-2284 -->Unable to read old Jalview projects that
2932 contain non-XML data added after Jalvew wrote project.
2935 <!-- JAL-2118 -->Newly created annotation row reorders
2936 after clicking on it to create new annotation for a
2940 <!-- JAL-1980 -->Null Pointer Exception raised when
2941 pressing Add on an orphaned cut'n'paste window.
2943 <!-- may exclude, this is an external service stability issue JAL-1941
2944 -- > RNA 3D structure not added via DSSR service</li> -->
2949 <!-- JAL-2151 -->Incorrect columns are selected when
2950 hidden columns present before start of sequence
2953 <!-- JAL-1986 -->Missing dependencies on applet pages
2957 <!-- JAL-1947 -->Overview pixel size changes when
2958 sequences are hidden in applet
2961 <!-- JAL-1996 -->Updated instructions for applet
2962 deployment on examples pages.
2969 <td width="60" nowrap>
2970 <div align="center">
2971 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2972 <em>16/10/2015</em></strong>
2975 <td><em>General</em>
2977 <li>Time stamps for signed Jalview application and applet
2982 <em>Application</em>
2984 <li>Duplicate group consensus and conservation rows
2985 shown when tree is partitioned</li>
2986 <li>Erratic behaviour when tree partitions made with
2987 multiple cDNA/Protein split views</li>
2993 <td width="60" nowrap>
2994 <div align="center">
2995 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2996 <em>8/10/2015</em></strong>
2999 <td><em>General</em>
3001 <li>Updated Spanish translations of localized text for
3003 </ul> <em>Application</em>
3005 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3006 <li>Signed OSX InstallAnywhere installer<br></li>
3007 <li>Support for per-sequence based annotations in BioJSON</li>
3008 </ul> <em>Applet</em>
3010 <li>Split frame example added to applet examples page</li>
3011 </ul> <em>Build and Deployment</em>
3014 <!-- JAL-1888 -->New ant target for running Jalview's test
3022 <li>Mapping of cDNA to protein in split frames
3023 incorrect when sequence start > 1</li>
3024 <li>Broken images in filter column by annotation dialog
3026 <li>Feature colours not parsed from features file</li>
3027 <li>Exceptions and incomplete link URLs recovered when
3028 loading a features file containing HTML tags in feature
3032 <em>Application</em>
3034 <li>Annotations corrupted after BioJS export and
3036 <li>Incorrect sequence limits after Fetch DB References
3037 with 'trim retrieved sequences'</li>
3038 <li>Incorrect warning about deleting all data when
3039 deleting selected columns</li>
3040 <li>Patch to build system for shipping properly signed
3041 JNLP templates for webstart launch</li>
3042 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3043 unreleased structures for download or viewing</li>
3044 <li>Tab/space/return keystroke operation of EMBL-PDBe
3045 fetcher/viewer dialogs works correctly</li>
3046 <li>Disabled 'minimise' button on Jalview windows
3047 running on OSX to workaround redraw hang bug</li>
3048 <li>Split cDNA/Protein view position and geometry not
3049 recovered from jalview project</li>
3050 <li>Initial enabled/disabled state of annotation menu
3051 sorter 'show autocalculated first/last' corresponds to
3053 <li>Restoring of Clustal, RNA Helices and T-Coffee
3054 color schemes from BioJSON</li>
3058 <li>Reorder sequences mirrored in cDNA/Protein split
3060 <li>Applet with Jmol examples not loading correctly</li>
3066 <td><div align="center">
3067 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3069 <td><em>General</em>
3071 <li>Linked visualisation and analysis of DNA and Protein
3074 <li>Translated cDNA alignments shown as split protein
3075 and DNA alignment views</li>
3076 <li>Codon consensus annotation for linked protein and
3077 cDNA alignment views</li>
3078 <li>Link cDNA or Protein product sequences by loading
3079 them onto Protein or cDNA alignments</li>
3080 <li>Reconstruct linked cDNA alignment from aligned
3081 protein sequences</li>
3084 <li>Jmol integration updated to Jmol v14.2.14</li>
3085 <li>Import and export of Jalview alignment views as <a
3086 href="features/bioJsonFormat.html">BioJSON</a></li>
3087 <li>New alignment annotation file statements for
3088 reference sequences and marking hidden columns</li>
3089 <li>Reference sequence based alignment shading to
3090 highlight variation</li>
3091 <li>Select or hide columns according to alignment
3093 <li>Find option for locating sequences by description</li>
3094 <li>Conserved physicochemical properties shown in amino
3095 acid conservation row</li>
3096 <li>Alignments can be sorted by number of RNA helices</li>
3097 </ul> <em>Application</em>
3099 <li>New cDNA/Protein analysis capabilities
3101 <li>Get Cross-References should open a Split Frame
3102 view with cDNA/Protein</li>
3103 <li>Detect when nucleotide sequences and protein
3104 sequences are placed in the same alignment</li>
3105 <li>Split cDNA/Protein views are saved in Jalview
3110 <li>Use REST API to talk to Chimera</li>
3111 <li>Selected regions in Chimera are highlighted in linked
3112 Jalview windows</li>
3114 <li>VARNA RNA viewer updated to v3.93</li>
3115 <li>VARNA views are saved in Jalview Projects</li>
3116 <li>Pseudoknots displayed as Jalview RNA annotation can
3117 be shown in VARNA</li>
3119 <li>Make groups for selection uses marked columns as well
3120 as the active selected region</li>
3122 <li>Calculate UPGMA and NJ trees using sequence feature
3124 <li>New Export options
3126 <li>New Export Settings dialog to control hidden
3127 region export in flat file generation</li>
3129 <li>Export alignment views for display with the <a
3130 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3132 <li>Export scrollable SVG in HTML page</li>
3133 <li>Optional embedding of BioJSON data when exporting
3134 alignment figures to HTML</li>
3136 <li>3D structure retrieval and display
3138 <li>Free text and structured queries with the PDBe
3140 <li>PDBe Search API based discovery and selection of
3141 PDB structures for a sequence set</li>
3145 <li>JPred4 employed for protein secondary structure
3147 <li>Hide Insertions menu option to hide unaligned columns
3148 for one or a group of sequences</li>
3149 <li>Automatically hide insertions in alignments imported
3150 from the JPred4 web server</li>
3151 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3152 system on OSX<br />LGPL libraries courtesy of <a
3153 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3155 <li>changed 'View nucleotide structure' submenu to 'View
3156 VARNA 2D Structure'</li>
3157 <li>change "View protein structure" menu option to "3D
3160 </ul> <em>Applet</em>
3162 <li>New layout for applet example pages</li>
3163 <li>New parameters to enable SplitFrame view
3164 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3165 <li>New example demonstrating linked viewing of cDNA and
3166 Protein alignments</li>
3167 </ul> <em>Development and deployment</em>
3169 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3170 <li>Include installation type and git revision in build
3171 properties and console log output</li>
3172 <li>Jalview Github organisation, and new github site for
3173 storing BioJsMSA Templates</li>
3174 <li>Jalview's unit tests now managed with TestNG</li>
3177 <!-- <em>General</em>
3179 </ul> --> <!-- issues resolved --> <em>Application</em>
3181 <li>Escape should close any open find dialogs</li>
3182 <li>Typo in select-by-features status report</li>
3183 <li>Consensus RNA secondary secondary structure
3184 predictions are not highlighted in amber</li>
3185 <li>Missing gap character in v2.7 example file means
3186 alignment appears unaligned when pad-gaps is not enabled</li>
3187 <li>First switch to RNA Helices colouring doesn't colour
3188 associated structure views</li>
3189 <li>ID width preference option is greyed out when auto
3190 width checkbox not enabled</li>
3191 <li>Stopped a warning dialog from being shown when
3192 creating user defined colours</li>
3193 <li>'View Mapping' in structure viewer shows sequence
3194 mappings for just that viewer's sequences</li>
3195 <li>Workaround for superposing PDB files containing
3196 multiple models in Chimera</li>
3197 <li>Report sequence position in status bar when hovering
3198 over Jmol structure</li>
3199 <li>Cannot output gaps as '.' symbols with Selection ->
3200 output to text box</li>
3201 <li>Flat file exports of alignments with hidden columns
3202 have incorrect sequence start/end</li>
3203 <li>'Aligning' a second chain to a Chimera structure from
3205 <li>Colour schemes applied to structure viewers don't
3206 work for nucleotide</li>
3207 <li>Loading/cut'n'pasting an empty or invalid file leads
3208 to a grey/invisible alignment window</li>
3209 <li>Exported Jpred annotation from a sequence region
3210 imports to different position</li>
3211 <li>Space at beginning of sequence feature tooltips shown
3212 on some platforms</li>
3213 <li>Chimera viewer 'View | Show Chain' menu is not
3215 <li>'New View' fails with a Null Pointer Exception in
3216 console if Chimera has been opened</li>
3217 <li>Mouseover to Chimera not working</li>
3218 <li>Miscellaneous ENA XML feature qualifiers not
3220 <li>NPE in annotation renderer after 'Extract Scores'</li>
3221 <li>If two structures in one Chimera window, mouseover of
3222 either sequence shows on first structure</li>
3223 <li>'Show annotations' options should not make
3224 non-positional annotations visible</li>
3225 <li>Subsequence secondary structure annotation not shown
3226 in right place after 'view flanking regions'</li>
3227 <li>File Save As type unset when current file format is
3229 <li>Save as '.jar' option removed for saving Jalview
3231 <li>Colour by Sequence colouring in Chimera more
3233 <li>Cannot 'add reference annotation' for a sequence in
3234 several views on same alignment</li>
3235 <li>Cannot show linked products for EMBL / ENA records</li>
3236 <li>Jalview's tooltip wraps long texts containing no
3238 </ul> <em>Applet</em>
3240 <li>Jmol to JalviewLite mouseover/link not working</li>
3241 <li>JalviewLite can't import sequences with ID
3242 descriptions containing angle brackets</li>
3243 </ul> <em>General</em>
3245 <li>Cannot export and reimport RNA secondary structure
3246 via jalview annotation file</li>
3247 <li>Random helix colour palette for colour by annotation
3248 with RNA secondary structure</li>
3249 <li>Mouseover to cDNA from STOP residue in protein
3250 translation doesn't work.</li>
3251 <li>hints when using the select by annotation dialog box</li>
3252 <li>Jmol alignment incorrect if PDB file has alternate CA
3254 <li>FontChooser message dialog appears to hang after
3255 choosing 1pt font</li>
3256 <li>Peptide secondary structure incorrectly imported from
3257 annotation file when annotation display text includes 'e' or
3259 <li>Cannot set colour of new feature type whilst creating
3261 <li>cDNA translation alignment should not be sequence
3262 order dependent</li>
3263 <li>'Show unconserved' doesn't work for lower case
3265 <li>Nucleotide ambiguity codes involving R not recognised</li>
3266 </ul> <em>Deployment and Documentation</em>
3268 <li>Applet example pages appear different to the rest of
3269 www.jalview.org</li>
3270 </ul> <em>Application Known issues</em>
3272 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3273 <li>Misleading message appears after trying to delete
3275 <li>Jalview icon not shown in dock after InstallAnywhere
3276 version launches</li>
3277 <li>Fetching EMBL reference for an RNA sequence results
3278 fails with a sequence mismatch</li>
3279 <li>Corrupted or unreadable alignment display when
3280 scrolling alignment to right</li>
3281 <li>ArrayIndexOutOfBoundsException thrown when remove
3282 empty columns called on alignment with ragged gapped ends</li>
3283 <li>auto calculated alignment annotation rows do not get
3284 placed above or below non-autocalculated rows</li>
3285 <li>Jalview dekstop becomes sluggish at full screen in
3286 ultra-high resolution</li>
3287 <li>Cannot disable consensus calculation independently of
3288 quality and conservation</li>
3289 <li>Mouseover highlighting between cDNA and protein can
3290 become sluggish with more than one splitframe shown</li>
3291 </ul> <em>Applet Known Issues</em>
3293 <li>Core PDB parsing code requires Jmol</li>
3294 <li>Sequence canvas panel goes white when alignment
3295 window is being resized</li>
3301 <td><div align="center">
3302 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3304 <td><em>General</em>
3306 <li>Updated Java code signing certificate donated by
3308 <li>Features and annotation preserved when performing
3309 pairwise alignment</li>
3310 <li>RNA pseudoknot annotation can be
3311 imported/exported/displayed</li>
3312 <li>'colour by annotation' can colour by RNA and
3313 protein secondary structure</li>
3314 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3315 post-hoc with 2.9 release</em>)
3318 </ul> <em>Application</em>
3320 <li>Extract and display secondary structure for sequences
3321 with 3D structures</li>
3322 <li>Support for parsing RNAML</li>
3323 <li>Annotations menu for layout
3325 <li>sort sequence annotation rows by alignment</li>
3326 <li>place sequence annotation above/below alignment
3329 <li>Output in Stockholm format</li>
3330 <li>Internationalisation: improved Spanish (es)
3332 <li>Structure viewer preferences tab</li>
3333 <li>Disorder and Secondary Structure annotation tracks
3334 shared between alignments</li>
3335 <li>UCSF Chimera launch and linked highlighting from
3337 <li>Show/hide all sequence associated annotation rows for
3338 all or current selection</li>
3339 <li>disorder and secondary structure predictions
3340 available as dataset annotation</li>
3341 <li>Per-sequence rna helices colouring</li>
3344 <li>Sequence database accessions imported when fetching
3345 alignments from Rfam</li>
3346 <li>update VARNA version to 3.91</li>
3348 <li>New groovy scripts for exporting aligned positions,
3349 conservation values, and calculating sum of pairs scores.</li>
3350 <li>Command line argument to set default JABAWS server</li>
3351 <li>include installation type in build properties and
3352 console log output</li>
3353 <li>Updated Jalview project format to preserve dataset
3357 <!-- issues resolved --> <em>Application</em>
3359 <li>Distinguish alignment and sequence associated RNA
3360 structure in structure->view->VARNA</li>
3361 <li>Raise dialog box if user deletes all sequences in an
3363 <li>Pressing F1 results in documentation opening twice</li>
3364 <li>Sequence feature tooltip is wrapped</li>
3365 <li>Double click on sequence associated annotation
3366 selects only first column</li>
3367 <li>Redundancy removal doesn't result in unlinked
3368 leaves shown in tree</li>
3369 <li>Undos after several redundancy removals don't undo
3371 <li>Hide sequence doesn't hide associated annotation</li>
3372 <li>User defined colours dialog box too big to fit on
3373 screen and buttons not visible</li>
3374 <li>author list isn't updated if already written to
3375 Jalview properties</li>
3376 <li>Popup menu won't open after retrieving sequence
3378 <li>File open window for associate PDB doesn't open</li>
3379 <li>Left-then-right click on a sequence id opens a
3380 browser search window</li>
3381 <li>Cannot open sequence feature shading/sort popup menu
3382 in feature settings dialog</li>
3383 <li>better tooltip placement for some areas of Jalview
3385 <li>Allow addition of JABAWS Server which doesn't
3386 pass validation</li>
3387 <li>Web services parameters dialog box is too large to
3389 <li>Muscle nucleotide alignment preset obscured by
3391 <li>JABAWS preset submenus don't contain newly
3392 defined user preset</li>
3393 <li>MSA web services warns user if they were launched
3394 with invalid input</li>
3395 <li>Jalview cannot contact DAS Registy when running on
3398 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3399 'Superpose with' submenu not shown when new view
3403 </ul> <!-- <em>Applet</em>
3405 </ul> <em>General</em>
3407 </ul>--> <em>Deployment and Documentation</em>
3409 <li>2G and 1G options in launchApp have no effect on
3410 memory allocation</li>
3411 <li>launchApp service doesn't automatically open
3412 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3414 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3415 InstallAnywhere reports cannot find valid JVM when Java
3416 1.7_055 is available
3418 </ul> <em>Application Known issues</em>
3421 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3422 corrupted or unreadable alignment display when scrolling
3426 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3427 retrieval fails but progress bar continues for DAS retrieval
3428 with large number of ID
3431 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3432 flatfile output of visible region has incorrect sequence
3436 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3437 rna structure consensus doesn't update when secondary
3438 structure tracks are rearranged
3441 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3442 invalid rna structure positional highlighting does not
3443 highlight position of invalid base pairs
3446 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3447 out of memory errors are not raised when saving Jalview
3448 project from alignment window file menu
3451 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3452 Switching to RNA Helices colouring doesn't propagate to
3456 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3457 colour by RNA Helices not enabled when user created
3458 annotation added to alignment
3461 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3462 Jalview icon not shown on dock in Mountain Lion/Webstart
3464 </ul> <em>Applet Known Issues</em>
3467 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3468 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3471 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3472 Jalview and Jmol example not compatible with IE9
3475 <li>Sort by annotation score doesn't reverse order
3481 <td><div align="center">
3482 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3485 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3488 <li>Internationalisation of user interface (usually
3489 called i18n support) and translation for Spanish locale</li>
3490 <li>Define/Undefine group on current selection with
3491 Ctrl-G/Shift Ctrl-G</li>
3492 <li>Improved group creation/removal options in
3493 alignment/sequence Popup menu</li>
3494 <li>Sensible precision for symbol distribution
3495 percentages shown in logo tooltip.</li>
3496 <li>Annotation panel height set according to amount of
3497 annotation when alignment first opened</li>
3498 </ul> <em>Application</em>
3500 <li>Interactive consensus RNA secondary structure
3501 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3502 <li>Select columns containing particular features from
3503 Feature Settings dialog</li>
3504 <li>View all 'representative' PDB structures for selected
3506 <li>Update Jalview project format:
3508 <li>New file extension for Jalview projects '.jvp'</li>
3509 <li>Preserve sequence and annotation dataset (to
3510 store secondary structure annotation,etc)</li>
3511 <li>Per group and alignment annotation and RNA helix
3515 <li>New similarity measures for PCA and Tree calculation
3517 <li>Experimental support for retrieval and viewing of
3518 flanking regions for an alignment</li>
3522 <!-- issues resolved --> <em>Application</em>
3524 <li>logo keeps spinning and status remains at queued or
3525 running after job is cancelled</li>
3526 <li>cannot export features from alignments imported from
3527 Jalview/VAMSAS projects</li>
3528 <li>Buggy slider for web service parameters that take
3530 <li>Newly created RNA secondary structure line doesn't
3531 have 'display all symbols' flag set</li>
3532 <li>T-COFFEE alignment score shading scheme and other
3533 annotation shading not saved in Jalview project</li>
3534 <li>Local file cannot be loaded in freshly downloaded
3536 <li>Jalview icon not shown on dock in Mountain
3538 <li>Load file from desktop file browser fails</li>
3539 <li>Occasional NPE thrown when calculating large trees</li>
3540 <li>Cannot reorder or slide sequences after dragging an
3541 alignment onto desktop</li>
3542 <li>Colour by annotation dialog throws NPE after using
3543 'extract scores' function</li>
3544 <li>Loading/cut'n'pasting an empty file leads to a grey
3545 alignment window</li>
3546 <li>Disorder thresholds rendered incorrectly after
3547 performing IUPred disorder prediction</li>
3548 <li>Multiple group annotated consensus rows shown when
3549 changing 'normalise logo' display setting</li>
3550 <li>Find shows blank dialog after 'finished searching' if
3551 nothing matches query</li>
3552 <li>Null Pointer Exceptions raised when sorting by
3553 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3555 <li>Errors in Jmol console when structures in alignment
3556 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3558 <li>Not all working JABAWS services are shown in
3560 <li>JAVAWS version of Jalview fails to launch with
3561 'invalid literal/length code'</li>
3562 <li>Annotation/RNA Helix colourschemes cannot be applied
3563 to alignment with groups (actually fixed in 2.8.0b1)</li>
3564 <li>RNA Helices and T-Coffee Scores available as default
3567 </ul> <em>Applet</em>
3569 <li>Remove group option is shown even when selection is
3571 <li>Apply to all groups ticked but colourscheme changes
3572 don't affect groups</li>
3573 <li>Documented RNA Helices and T-Coffee Scores as valid
3574 colourscheme name</li>
3575 <li>Annotation labels drawn on sequence IDs when
3576 Annotation panel is not displayed</li>
3577 <li>Increased font size for dropdown menus on OSX and
3578 embedded windows</li>
3579 </ul> <em>Other</em>
3581 <li>Consensus sequence for alignments/groups with a
3582 single sequence were not calculated</li>
3583 <li>annotation files that contain only groups imported as
3584 annotation and junk sequences</li>
3585 <li>Fasta files with sequences containing '*' incorrectly
3586 recognised as PFAM or BLC</li>
3587 <li>conservation/PID slider apply all groups option
3588 doesn't affect background (2.8.0b1)
3590 <li>redundancy highlighting is erratic at 0% and 100%</li>
3591 <li>Remove gapped columns fails for sequences with ragged
3593 <li>AMSA annotation row with leading spaces is not
3594 registered correctly on import</li>
3595 <li>Jalview crashes when selecting PCA analysis for
3596 certain alignments</li>
3597 <li>Opening the colour by annotation dialog for an
3598 existing annotation based 'use original colours'
3599 colourscheme loses original colours setting</li>
3604 <td><div align="center">
3605 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3606 <em>30/1/2014</em></strong>
3610 <li>Trusted certificates for JalviewLite applet and
3611 Jalview Desktop application<br />Certificate was donated by
3612 <a href="https://www.certum.eu">Certum</a> to the Jalview
3613 open source project).
3615 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3616 <li>Output in Stockholm format</li>
3617 <li>Allow import of data from gzipped files</li>
3618 <li>Export/import group and sequence associated line
3619 graph thresholds</li>
3620 <li>Nucleotide substitution matrix that supports RNA and
3621 ambiguity codes</li>
3622 <li>Allow disorder predictions to be made on the current
3623 selection (or visible selection) in the same way that JPred
3625 <li>Groovy scripting for headless Jalview operation</li>
3626 </ul> <em>Other improvements</em>
3628 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3629 <li>COMBINE statement uses current SEQUENCE_REF and
3630 GROUP_REF scope to group annotation rows</li>
3631 <li>Support '' style escaping of quotes in Newick
3633 <li>Group options for JABAWS service by command line name</li>
3634 <li>Empty tooltip shown for JABA service options with a
3635 link but no description</li>
3636 <li>Select primary source when selecting authority in
3637 database fetcher GUI</li>
3638 <li>Add .mfa to FASTA file extensions recognised by
3640 <li>Annotation label tooltip text wrap</li>
3645 <li>Slow scrolling when lots of annotation rows are
3647 <li>Lots of NPE (and slowness) after creating RNA
3648 secondary structure annotation line</li>
3649 <li>Sequence database accessions not imported when
3650 fetching alignments from Rfam</li>
3651 <li>Incorrect SHMR submission for sequences with
3653 <li>View all structures does not always superpose
3655 <li>Option widgets in service parameters not updated to
3656 reflect user or preset settings</li>
3657 <li>Null pointer exceptions for some services without
3658 presets or adjustable parameters</li>
3659 <li>Discover PDB IDs entry in structure menu doesn't
3660 discover PDB xRefs</li>
3661 <li>Exception encountered while trying to retrieve
3662 features with DAS</li>
3663 <li>Lowest value in annotation row isn't coloured
3664 when colour by annotation (per sequence) is coloured</li>
3665 <li>Keyboard mode P jumps to start of gapped region when
3666 residue follows a gap</li>
3667 <li>Jalview appears to hang importing an alignment with
3668 Wrap as default or after enabling Wrap</li>
3669 <li>'Right click to add annotations' message
3670 shown in wrap mode when no annotations present</li>
3671 <li>Disorder predictions fail with NPE if no automatic
3672 annotation already exists on alignment</li>
3673 <li>oninit javascript function should be called after
3674 initialisation completes</li>
3675 <li>Remove redundancy after disorder prediction corrupts
3676 alignment window display</li>
3677 <li>Example annotation file in documentation is invalid</li>
3678 <li>Grouped line graph annotation rows are not exported
3679 to annotation file</li>
3680 <li>Multi-harmony analysis cannot be run when only two
3682 <li>Cannot create multiple groups of line graphs with
3683 several 'combine' statements in annotation file</li>
3684 <li>Pressing return several times causes Number Format
3685 exceptions in keyboard mode</li>
3686 <li>Multi-harmony (SHMMR) method doesn't submit
3687 correct partitions for input data</li>
3688 <li>Translation from DNA to Amino Acids fails</li>
3689 <li>Jalview fail to load newick tree with quoted label</li>
3690 <li>--headless flag isn't understood</li>
3691 <li>ClassCastException when generating EPS in headless
3693 <li>Adjusting sequence-associated shading threshold only
3694 changes one row's threshold</li>
3695 <li>Preferences and Feature settings panel panel
3696 doesn't open</li>
3697 <li>hide consensus histogram also hides conservation and
3698 quality histograms</li>
3703 <td><div align="center">
3704 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3706 <td><em>Application</em>
3708 <li>Support for JABAWS 2.0 Services (AACon alignment
3709 conservation, protein disorder and Clustal Omega)</li>
3710 <li>JABAWS server status indicator in Web Services
3712 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3713 in Jalview alignment window</li>
3714 <li>Updated Jalview build and deploy framework for OSX
3715 mountain lion, windows 7, and 8</li>
3716 <li>Nucleotide substitution matrix for PCA that supports
3717 RNA and ambiguity codes</li>
3719 <li>Improved sequence database retrieval GUI</li>
3720 <li>Support fetching and database reference look up
3721 against multiple DAS sources (Fetch all from in 'fetch db
3723 <li>Jalview project improvements
3725 <li>Store and retrieve the 'belowAlignment'
3726 flag for annotation</li>
3727 <li>calcId attribute to group annotation rows on the
3729 <li>Store AACon calculation settings for a view in
3730 Jalview project</li>
3734 <li>horizontal scrolling gesture support</li>
3735 <li>Visual progress indicator when PCA calculation is
3737 <li>Simpler JABA web services menus</li>
3738 <li>visual indication that web service results are still
3739 being retrieved from server</li>
3740 <li>Serialise the dialogs that are shown when Jalview
3741 starts up for first time</li>
3742 <li>Jalview user agent string for interacting with HTTP
3744 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3746 <li>Examples directory and Groovy library included in
3747 InstallAnywhere distribution</li>
3748 </ul> <em>Applet</em>
3750 <li>RNA alignment and secondary structure annotation
3751 visualization applet example</li>
3752 </ul> <em>General</em>
3754 <li>Normalise option for consensus sequence logo</li>
3755 <li>Reset button in PCA window to return dimensions to
3757 <li>Allow seqspace or Jalview variant of alignment PCA
3759 <li>PCA with either nucleic acid and protein substitution
3761 <li>Allow windows containing HTML reports to be exported
3763 <li>Interactive display and editing of RNA secondary
3764 structure contacts</li>
3765 <li>RNA Helix Alignment Colouring</li>
3766 <li>RNA base pair logo consensus</li>
3767 <li>Parse sequence associated secondary structure
3768 information in Stockholm files</li>
3769 <li>HTML Export database accessions and annotation
3770 information presented in tooltip for sequences</li>
3771 <li>Import secondary structure from LOCARNA clustalw
3772 style RNA alignment files</li>
3773 <li>import and visualise T-COFFEE quality scores for an
3775 <li>'colour by annotation' per sequence option to
3776 shade each sequence according to its associated alignment
3778 <li>New Jalview Logo</li>
3779 </ul> <em>Documentation and Development</em>
3781 <li>documentation for score matrices used in Jalview</li>
3782 <li>New Website!</li>
3784 <td><em>Application</em>
3786 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3787 wsdbfetch REST service</li>
3788 <li>Stop windows being moved outside desktop on OSX</li>
3789 <li>Filetype associations not installed for webstart
3791 <li>Jalview does not always retrieve progress of a JABAWS
3792 job execution in full once it is complete</li>
3793 <li>revise SHMR RSBS definition to ensure alignment is
3794 uploaded via ali_file parameter</li>
3795 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3796 <li>View all structures superposed fails with exception</li>
3797 <li>Jnet job queues forever if a very short sequence is
3798 submitted for prediction</li>
3799 <li>Cut and paste menu not opened when mouse clicked on
3801 <li>Putting fractional value into integer text box in
3802 alignment parameter dialog causes Jalview to hang</li>
3803 <li>Structure view highlighting doesn't work on
3805 <li>View all structures fails with exception shown in
3807 <li>Characters in filename associated with PDBEntry not
3808 escaped in a platform independent way</li>
3809 <li>Jalview desktop fails to launch with exception when
3811 <li>Tree calculation reports 'you must have 2 or more
3812 sequences selected' when selection is empty</li>
3813 <li>Jalview desktop fails to launch with jar signature
3814 failure when java web start temporary file caching is
3816 <li>DAS Sequence retrieval with range qualification
3817 results in sequence xref which includes range qualification</li>
3818 <li>Errors during processing of command line arguments
3819 cause progress bar (JAL-898) to be removed</li>
3820 <li>Replace comma for semi-colon option not disabled for
3821 DAS sources in sequence fetcher</li>
3822 <li>Cannot close news reader when JABAWS server warning
3823 dialog is shown</li>
3824 <li>Option widgets not updated to reflect user settings</li>
3825 <li>Edited sequence not submitted to web service</li>
3826 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3827 <li>InstallAnywhere installer doesn't unpack and run
3828 on OSX Mountain Lion</li>
3829 <li>Annotation panel not given a scroll bar when
3830 sequences with alignment annotation are pasted into the
3832 <li>Sequence associated annotation rows not associated
3833 when loaded from Jalview project</li>
3834 <li>Browser launch fails with NPE on java 1.7</li>
3835 <li>JABAWS alignment marked as finished when job was
3836 cancelled or job failed due to invalid input</li>
3837 <li>NPE with v2.7 example when clicking on Tree
3838 associated with all views</li>
3839 <li>Exceptions when copy/paste sequences with grouped
3840 annotation rows to new window</li>
3841 </ul> <em>Applet</em>
3843 <li>Sequence features are momentarily displayed before
3844 they are hidden using hidefeaturegroups applet parameter</li>
3845 <li>loading features via javascript API automatically
3846 enables feature display</li>
3847 <li>scrollToColumnIn javascript API method doesn't
3849 </ul> <em>General</em>
3851 <li>Redundancy removal fails for rna alignment</li>
3852 <li>PCA calculation fails when sequence has been selected
3853 and then deselected</li>
3854 <li>PCA window shows grey box when first opened on OSX</li>
3855 <li>Letters coloured pink in sequence logo when alignment
3856 coloured with clustalx</li>
3857 <li>Choosing fonts without letter symbols defined causes
3858 exceptions and redraw errors</li>
3859 <li>Initial PCA plot view is not same as manually
3860 reconfigured view</li>
3861 <li>Grouped annotation graph label has incorrect line
3863 <li>Grouped annotation graph label display is corrupted
3864 for lots of labels</li>
3869 <div align="center">
3870 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3873 <td><em>Application</em>
3875 <li>Jalview Desktop News Reader</li>
3876 <li>Tweaked default layout of web services menu</li>
3877 <li>View/alignment association menu to enable user to
3878 easily specify which alignment a multi-structure view takes
3879 its colours/correspondences from</li>
3880 <li>Allow properties file location to be specified as URL</li>
3881 <li>Extend Jalview project to preserve associations
3882 between many alignment views and a single Jmol display</li>
3883 <li>Store annotation row height in Jalview project file</li>
3884 <li>Annotation row column label formatting attributes
3885 stored in project file</li>
3886 <li>Annotation row order for auto-calculated annotation
3887 rows preserved in Jalview project file</li>
3888 <li>Visual progress indication when Jalview state is
3889 saved using Desktop window menu</li>
3890 <li>Visual indication that command line arguments are
3891 still being processed</li>
3892 <li>Groovy script execution from URL</li>
3893 <li>Colour by annotation default min and max colours in
3895 <li>Automatically associate PDB files dragged onto an
3896 alignment with sequences that have high similarity and
3898 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3899 <li>'view structures' option to open many
3900 structures in same window</li>
3901 <li>Sort associated views menu option for tree panel</li>
3902 <li>Group all JABA and non-JABA services for a particular
3903 analysis function in its own submenu</li>
3904 </ul> <em>Applet</em>
3906 <li>Userdefined and autogenerated annotation rows for
3908 <li>Adjustment of alignment annotation pane height</li>
3909 <li>Annotation scrollbar for annotation panel</li>
3910 <li>Drag to reorder annotation rows in annotation panel</li>
3911 <li>'automaticScrolling' parameter</li>
3912 <li>Allow sequences with partial ID string matches to be
3913 annotated from GFF/Jalview features files</li>
3914 <li>Sequence logo annotation row in applet</li>
3915 <li>Absolute paths relative to host server in applet
3916 parameters are treated as such</li>
3917 <li>New in the JalviewLite javascript API:
3919 <li>JalviewLite.js javascript library</li>
3920 <li>Javascript callbacks for
3922 <li>Applet initialisation</li>
3923 <li>Sequence/alignment mouse-overs and selections</li>
3926 <li>scrollTo row and column alignment scrolling
3928 <li>Select sequence/alignment regions from javascript</li>
3929 <li>javascript structure viewer harness to pass
3930 messages between Jmol and Jalview when running as
3931 distinct applets</li>
3932 <li>sortBy method</li>
3933 <li>Set of applet and application examples shipped
3934 with documentation</li>
3935 <li>New example to demonstrate JalviewLite and Jmol
3936 javascript message exchange</li>
3938 </ul> <em>General</em>
3940 <li>Enable Jmol displays to be associated with multiple
3941 multiple alignments</li>
3942 <li>Option to automatically sort alignment with new tree</li>
3943 <li>User configurable link to enable redirects to a
3944 www.Jalview.org mirror</li>
3945 <li>Jmol colours option for Jmol displays</li>
3946 <li>Configurable newline string when writing alignment
3947 and other flat files</li>
3948 <li>Allow alignment annotation description lines to
3949 contain html tags</li>
3950 </ul> <em>Documentation and Development</em>
3952 <li>Add groovy test harness for bulk load testing to
3954 <li>Groovy script to load and align a set of sequences
3955 using a web service before displaying the result in the
3956 Jalview desktop</li>
3957 <li>Restructured javascript and applet api documentation</li>
3958 <li>Ant target to publish example html files with applet
3960 <li>Netbeans project for building Jalview from source</li>
3961 <li>ant task to create online javadoc for Jalview source</li>
3963 <td><em>Application</em>
3965 <li>User defined colourscheme throws exception when
3966 current built in colourscheme is saved as new scheme</li>
3967 <li>AlignFrame->Save in application pops up save
3968 dialog for valid filename/format</li>
3969 <li>Cannot view associated structure for UniProt sequence</li>
3970 <li>PDB file association breaks for UniProt sequence
3972 <li>Associate PDB from file dialog does not tell you
3973 which sequence is to be associated with the file</li>
3974 <li>Find All raises null pointer exception when query
3975 only matches sequence IDs</li>
3976 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3977 <li>Jalview project with Jmol views created with Jalview
3978 2.4 cannot be loaded</li>
3979 <li>Filetype associations not installed for webstart
3981 <li>Two or more chains in a single PDB file associated
3982 with sequences in different alignments do not get coloured
3983 by their associated sequence</li>
3984 <li>Visibility status of autocalculated annotation row
3985 not preserved when project is loaded</li>
3986 <li>Annotation row height and visibility attributes not
3987 stored in Jalview project</li>
3988 <li>Tree bootstraps are not preserved when saved as a
3989 Jalview project</li>
3990 <li>Envision2 workflow tooltips are corrupted</li>
3991 <li>Enabling show group conservation also enables colour
3992 by conservation</li>
3993 <li>Duplicate group associated conservation or consensus
3994 created on new view</li>
3995 <li>Annotation scrollbar not displayed after 'show
3996 all hidden annotation rows' option selected</li>
3997 <li>Alignment quality not updated after alignment
3998 annotation row is hidden then shown</li>
3999 <li>Preserve colouring of structures coloured by
4000 sequences in pre Jalview 2.7 projects</li>
4001 <li>Web service job parameter dialog is not laid out
4003 <li>Web services menu not refreshed after 'reset
4004 services' button is pressed in preferences</li>
4005 <li>Annotation off by one in Jalview v2_3 example project</li>
4006 <li>Structures imported from file and saved in project
4007 get name like jalview_pdb1234.txt when reloaded</li>
4008 <li>Jalview does not always retrieve progress of a JABAWS
4009 job execution in full once it is complete</li>
4010 </ul> <em>Applet</em>
4012 <li>Alignment height set incorrectly when lots of
4013 annotation rows are displayed</li>
4014 <li>Relative URLs in feature HTML text not resolved to
4016 <li>View follows highlighting does not work for positions
4018 <li><= shown as = in tooltip</li>
4019 <li>Export features raises exception when no features
4021 <li>Separator string used for serialising lists of IDs
4022 for javascript api is modified when separator string
4023 provided as parameter</li>
4024 <li>Null pointer exception when selecting tree leaves for
4025 alignment with no existing selection</li>
4026 <li>Relative URLs for datasources assumed to be relative
4027 to applet's codebase</li>
4028 <li>Status bar not updated after finished searching and
4029 search wraps around to first result</li>
4030 <li>StructureSelectionManager instance shared between
4031 several Jalview applets causes race conditions and memory
4033 <li>Hover tooltip and mouseover of position on structure
4034 not sent from Jmol in applet</li>
4035 <li>Certain sequences of javascript method calls to
4036 applet API fatally hang browser</li>
4037 </ul> <em>General</em>
4039 <li>View follows structure mouseover scrolls beyond
4040 position with wrapped view and hidden regions</li>
4041 <li>Find sequence position moves to wrong residue
4042 with/without hidden columns</li>
4043 <li>Sequence length given in alignment properties window
4045 <li>InvalidNumberFormat exceptions thrown when trying to
4046 import PDB like structure files</li>
4047 <li>Positional search results are only highlighted
4048 between user-supplied sequence start/end bounds</li>
4049 <li>End attribute of sequence is not validated</li>
4050 <li>Find dialog only finds first sequence containing a
4051 given sequence position</li>
4052 <li>Sequence numbering not preserved in MSF alignment
4054 <li>Jalview PDB file reader does not extract sequence
4055 from nucleotide chains correctly</li>
4056 <li>Structure colours not updated when tree partition
4057 changed in alignment</li>
4058 <li>Sequence associated secondary structure not correctly
4059 parsed in interleaved stockholm</li>
4060 <li>Colour by annotation dialog does not restore current
4062 <li>Hiding (nearly) all sequences doesn't work
4064 <li>Sequences containing lowercase letters are not
4065 properly associated with their pdb files</li>
4066 </ul> <em>Documentation and Development</em>
4068 <li>schemas/JalviewWsParamSet.xsd corrupted by
4069 ApplyCopyright tool</li>
4074 <div align="center">
4075 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4078 <td><em>Application</em>
4080 <li>New warning dialog when the Jalview Desktop cannot
4081 contact web services</li>
4082 <li>JABA service parameters for a preset are shown in
4083 service job window</li>
4084 <li>JABA Service menu entries reworded</li>
4088 <li>Modeller PIR IO broken - cannot correctly import a
4089 pir file emitted by Jalview</li>
4090 <li>Existing feature settings transferred to new
4091 alignment view created from cut'n'paste</li>
4092 <li>Improved test for mixed amino/nucleotide chains when
4093 parsing PDB files</li>
4094 <li>Consensus and conservation annotation rows
4095 occasionally become blank for all new windows</li>
4096 <li>Exception raised when right clicking above sequences
4097 in wrapped view mode</li>
4098 </ul> <em>Application</em>
4100 <li>multiple multiply aligned structure views cause cpu
4101 usage to hit 100% and computer to hang</li>
4102 <li>Web Service parameter layout breaks for long user
4103 parameter names</li>
4104 <li>Jaba service discovery hangs desktop if Jaba server
4111 <div align="center">
4112 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4115 <td><em>Application</em>
4117 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4118 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4121 <li>Web Services preference tab</li>
4122 <li>Analysis parameters dialog box and user defined
4124 <li>Improved speed and layout of Envision2 service menu</li>
4125 <li>Superpose structures using associated sequence
4127 <li>Export coordinates and projection as CSV from PCA
4129 </ul> <em>Applet</em>
4131 <li>enable javascript: execution by the applet via the
4132 link out mechanism</li>
4133 </ul> <em>Other</em>
4135 <li>Updated the Jmol Jalview interface to work with Jmol
4137 <li>The Jalview Desktop and JalviewLite applet now
4138 require Java 1.5</li>
4139 <li>Allow Jalview feature colour specification for GFF
4140 sequence annotation files</li>
4141 <li>New 'colour by label' keword in Jalview feature file
4142 type colour specification</li>
4143 <li>New Jalview Desktop Groovy API method that allows a
4144 script to check if it being run in an interactive session or
4145 in a batch operation from the Jalview command line</li>
4149 <li>clustalx colourscheme colours Ds preferentially when
4150 both D+E are present in over 50% of the column</li>
4151 </ul> <em>Application</em>
4153 <li>typo in AlignmentFrame->View->Hide->all but
4154 selected Regions menu item</li>
4155 <li>sequence fetcher replaces ',' for ';' when the ',' is
4156 part of a valid accession ID</li>
4157 <li>fatal OOM if object retrieved by sequence fetcher
4158 runs out of memory</li>
4159 <li>unhandled Out of Memory Error when viewing pca
4160 analysis results</li>
4161 <li>InstallAnywhere builds fail to launch on OS X java
4162 10.5 update 4 (due to apple Java 1.6 update)</li>
4163 <li>Installanywhere Jalview silently fails to launch</li>
4164 </ul> <em>Applet</em>
4166 <li>Jalview.getFeatureGroups() raises an
4167 ArrayIndexOutOfBoundsException if no feature groups are
4174 <div align="center">
4175 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4181 <li>Alignment prettyprinter doesn't cope with long
4183 <li>clustalx colourscheme colours Ds preferentially when
4184 both D+E are present in over 50% of the column</li>
4185 <li>nucleic acid structures retrieved from PDB do not
4186 import correctly</li>
4187 <li>More columns get selected than were clicked on when a
4188 number of columns are hidden</li>
4189 <li>annotation label popup menu not providing correct
4190 add/hide/show options when rows are hidden or none are
4192 <li>Stockholm format shown in list of readable formats,
4193 and parser copes better with alignments from RFAM.</li>
4194 <li>CSV output of consensus only includes the percentage
4195 of all symbols if sequence logo display is enabled</li>
4197 </ul> <em>Applet</em>
4199 <li>annotation panel disappears when annotation is
4201 </ul> <em>Application</em>
4203 <li>Alignment view not redrawn properly when new
4204 alignment opened where annotation panel is visible but no
4205 annotations are present on alignment</li>
4206 <li>pasted region containing hidden columns is
4207 incorrectly displayed in new alignment window</li>
4208 <li>Jalview slow to complete operations when stdout is
4209 flooded (fix is to close the Jalview console)</li>
4210 <li>typo in AlignmentFrame->View->Hide->all but
4211 selected Rregions menu item.</li>
4212 <li>inconsistent group submenu and Format submenu entry
4213 'Un' or 'Non'conserved</li>
4214 <li>Sequence feature settings are being shared by
4215 multiple distinct alignments</li>
4216 <li>group annotation not recreated when tree partition is
4218 <li>double click on group annotation to select sequences
4219 does not propagate to associated trees</li>
4220 <li>Mac OSX specific issues:
4222 <li>exception raised when mouse clicked on desktop
4223 window background</li>
4224 <li>Desktop menu placed on menu bar and application
4225 name set correctly</li>
4226 <li>sequence feature settings not wide enough for the
4227 save feature colourscheme button</li>
4236 <div align="center">
4237 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4240 <td><em>New Capabilities</em>
4242 <li>URL links generated from description line for
4243 regular-expression based URL links (applet and application)
4245 <li>Non-positional feature URL links are shown in link
4247 <li>Linked viewing of nucleic acid sequences and
4249 <li>Automatic Scrolling option in View menu to display
4250 the currently highlighted region of an alignment.</li>
4251 <li>Order an alignment by sequence length, or using the
4252 average score or total feature count for each sequence.</li>
4253 <li>Shading features by score or associated description</li>
4254 <li>Subdivide alignment and groups based on identity of
4255 selected subsequence (Make Groups from Selection).</li>
4256 <li>New hide/show options including Shift+Control+H to
4257 hide everything but the currently selected region.</li>
4258 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4259 </ul> <em>Application</em>
4261 <li>Fetch DB References capabilities and UI expanded to
4262 support retrieval from DAS sequence sources</li>
4263 <li>Local DAS Sequence sources can be added via the
4264 command line or via the Add local source dialog box.</li>
4265 <li>DAS Dbref and DbxRef feature types are parsed as
4266 database references and protein_name is parsed as
4267 description line (BioSapiens terms).</li>
4268 <li>Enable or disable non-positional feature and database
4269 references in sequence ID tooltip from View menu in
4271 <!-- <li>New hidden columns and rows and representatives capabilities
4272 in annotations file (in progress - not yet fully implemented)</li> -->
4273 <li>Group-associated consensus, sequence logos and
4274 conservation plots</li>
4275 <li>Symbol distributions for each column can be exported
4276 and visualized as sequence logos</li>
4277 <li>Optionally scale multi-character column labels to fit
4278 within each column of annotation row<!-- todo for applet -->
4280 <li>Optional automatic sort of associated alignment view
4281 when a new tree is opened.</li>
4282 <li>Jalview Java Console</li>
4283 <li>Better placement of desktop window when moving
4284 between different screens.</li>
4285 <li>New preference items for sequence ID tooltip and
4286 consensus annotation</li>
4287 <li>Client to submit sequences and IDs to Envision2
4289 <li><em>Vamsas Capabilities</em>
4291 <li>Improved VAMSAS synchronization (Jalview archive
4292 used to preserve views, structures, and tree display
4294 <li>Import of vamsas documents from disk or URL via
4296 <li>Sharing of selected regions between views and
4297 with other VAMSAS applications (Experimental feature!)</li>
4298 <li>Updated API to VAMSAS version 0.2</li>
4300 </ul> <em>Applet</em>
4302 <li>Middle button resizes annotation row height</li>
4305 <li>sortByTree (true/false) - automatically sort the
4306 associated alignment view by the tree when a new tree is
4308 <li>showTreeBootstraps (true/false) - show or hide
4309 branch bootstraps (default is to show them if available)</li>
4310 <li>showTreeDistances (true/false) - show or hide
4311 branch lengths (default is to show them if available)</li>
4312 <li>showUnlinkedTreeNodes (true/false) - indicate if
4313 unassociated nodes should be highlighted in the tree
4315 <li>heightScale and widthScale (1.0 or more) -
4316 increase the height or width of a cell in the alignment
4317 grid relative to the current font size.</li>
4320 <li>Non-positional features displayed in sequence ID
4322 </ul> <em>Other</em>
4324 <li>Features format: graduated colour definitions and
4325 specification of feature scores</li>
4326 <li>Alignment Annotations format: new keywords for group
4327 associated annotation (GROUP_REF) and annotation row display
4328 properties (ROW_PROPERTIES)</li>
4329 <li>XML formats extended to support graduated feature
4330 colourschemes, group associated annotation, and profile
4331 visualization settings.</li></td>
4334 <li>Source field in GFF files parsed as feature source
4335 rather than description</li>
4336 <li>Non-positional features are now included in sequence
4337 feature and gff files (controlled via non-positional feature
4338 visibility in tooltip).</li>
4339 <li>URL links generated for all feature links (bugfix)</li>
4340 <li>Added URL embedding instructions to features file
4342 <li>Codons containing ambiguous nucleotides translated as
4343 'X' in peptide product</li>
4344 <li>Match case switch in find dialog box works for both
4345 sequence ID and sequence string and query strings do not
4346 have to be in upper case to match case-insensitively.</li>
4347 <li>AMSA files only contain first column of
4348 multi-character column annotation labels</li>
4349 <li>Jalview Annotation File generation/parsing consistent
4350 with documentation (e.g. Stockholm annotation can be
4351 exported and re-imported)</li>
4352 <li>PDB files without embedded PDB IDs given a friendly
4354 <li>Find incrementally searches ID string matches as well
4355 as subsequence matches, and correctly reports total number
4359 <li>Better handling of exceptions during sequence
4361 <li>Dasobert generated non-positional feature URL
4362 link text excludes the start_end suffix</li>
4363 <li>DAS feature and source retrieval buttons disabled
4364 when fetch or registry operations in progress.</li>
4365 <li>PDB files retrieved from URLs are cached properly</li>
4366 <li>Sequence description lines properly shared via
4368 <li>Sequence fetcher fetches multiple records for all
4370 <li>Ensured that command line das feature retrieval
4371 completes before alignment figures are generated.</li>
4372 <li>Reduced time taken when opening file browser for
4374 <li>isAligned check prior to calculating tree, PCA or
4375 submitting an MSA to JNet now excludes hidden sequences.</li>
4376 <li>User defined group colours properly recovered
4377 from Jalview projects.</li>
4386 <div align="center">
4387 <strong>2.4.0.b2</strong><br> 28/10/2009
4392 <li>Experimental support for google analytics usage
4394 <li>Jalview privacy settings (user preferences and docs).</li>
4399 <li>Race condition in applet preventing startup in
4401 <li>Exception when feature created from selection beyond
4402 length of sequence.</li>
4403 <li>Allow synthetic PDB files to be imported gracefully</li>
4404 <li>Sequence associated annotation rows associate with
4405 all sequences with a given id</li>
4406 <li>Find function matches case-insensitively for sequence
4407 ID string searches</li>
4408 <li>Non-standard characters do not cause pairwise
4409 alignment to fail with exception</li>
4410 </ul> <em>Application Issues</em>
4412 <li>Sequences are now validated against EMBL database</li>
4413 <li>Sequence fetcher fetches multiple records for all
4415 </ul> <em>InstallAnywhere Issues</em>
4417 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4418 issue with installAnywhere mechanism)</li>
4419 <li>Command line launching of JARs from InstallAnywhere
4420 version (java class versioning error fixed)</li>
4427 <div align="center">
4428 <strong>2.4</strong><br> 27/8/2008
4431 <td><em>User Interface</em>
4433 <li>Linked highlighting of codon and amino acid from
4434 translation and protein products</li>
4435 <li>Linked highlighting of structure associated with
4436 residue mapping to codon position</li>
4437 <li>Sequence Fetcher provides example accession numbers
4438 and 'clear' button</li>
4439 <li>MemoryMonitor added as an option under Desktop's
4441 <li>Extract score function to parse whitespace separated
4442 numeric data in description line</li>
4443 <li>Column labels in alignment annotation can be centred.</li>
4444 <li>Tooltip for sequence associated annotation give name
4446 </ul> <em>Web Services and URL fetching</em>
4448 <li>JPred3 web service</li>
4449 <li>Prototype sequence search client (no public services
4451 <li>Fetch either seed alignment or full alignment from
4453 <li>URL Links created for matching database cross
4454 references as well as sequence ID</li>
4455 <li>URL Links can be created using regular-expressions</li>
4456 </ul> <em>Sequence Database Connectivity</em>
4458 <li>Retrieval of cross-referenced sequences from other
4460 <li>Generalised database reference retrieval and
4461 validation to all fetchable databases</li>
4462 <li>Fetch sequences from DAS sources supporting the
4463 sequence command</li>
4464 </ul> <em>Import and Export</em>
4465 <li>export annotation rows as CSV for spreadsheet import</li>
4466 <li>Jalview projects record alignment dataset associations,
4467 EMBL products, and cDNA sequence mappings</li>
4468 <li>Sequence Group colour can be specified in Annotation
4470 <li>Ad-hoc colouring of group in Annotation File using RGB
4471 triplet as name of colourscheme</li>
4472 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4474 <li>treenode binding for VAMSAS tree exchange</li>
4475 <li>local editing and update of sequences in VAMSAS
4476 alignments (experimental)</li>
4477 <li>Create new or select existing session to join</li>
4478 <li>load and save of vamsas documents</li>
4479 </ul> <em>Application command line</em>
4481 <li>-tree parameter to open trees (introduced for passing
4483 <li>-fetchfrom command line argument to specify nicknames
4484 of DAS servers to query for alignment features</li>
4485 <li>-dasserver command line argument to add new servers
4486 that are also automatically queried for features</li>
4487 <li>-groovy command line argument executes a given groovy
4488 script after all input data has been loaded and parsed</li>
4489 </ul> <em>Applet-Application data exchange</em>
4491 <li>Trees passed as applet parameters can be passed to
4492 application (when using "View in full
4493 application")</li>
4494 </ul> <em>Applet Parameters</em>
4496 <li>feature group display control parameter</li>
4497 <li>debug parameter</li>
4498 <li>showbutton parameter</li>
4499 </ul> <em>Applet API methods</em>
4501 <li>newView public method</li>
4502 <li>Window (current view) specific get/set public methods</li>
4503 <li>Feature display control methods</li>
4504 <li>get list of currently selected sequences</li>
4505 </ul> <em>New Jalview distribution features</em>
4507 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4508 <li>RELEASE file gives build properties for the latest
4509 Jalview release.</li>
4510 <li>Java 1.1 Applet build made easier and donotobfuscate
4511 property controls execution of obfuscator</li>
4512 <li>Build target for generating source distribution</li>
4513 <li>Debug flag for javacc</li>
4514 <li>.jalview_properties file is documented (slightly) in
4515 jalview.bin.Cache</li>
4516 <li>Continuous Build Integration for stable and
4517 development version of Application, Applet and source
4522 <li>selected region output includes visible annotations
4523 (for certain formats)</li>
4524 <li>edit label/displaychar contains existing label/char
4526 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4527 <li>shorter peptide product names from EMBL records</li>
4528 <li>Newick string generator makes compact representations</li>
4529 <li>bootstrap values parsed correctly for tree files with
4531 <li>pathological filechooser bug avoided by not allowing
4532 filenames containing a ':'</li>
4533 <li>Fixed exception when parsing GFF files containing
4534 global sequence features</li>
4535 <li>Alignment datasets are finalized only when number of
4536 references from alignment sequences goes to zero</li>
4537 <li>Close of tree branch colour box without colour
4538 selection causes cascading exceptions</li>
4539 <li>occasional negative imgwidth exceptions</li>
4540 <li>better reporting of non-fatal warnings to user when
4541 file parsing fails.</li>
4542 <li>Save works when Jalview project is default format</li>
4543 <li>Save as dialog opened if current alignment format is
4544 not a valid output format</li>
4545 <li>UniProt canonical names introduced for both das and
4547 <li>Histidine should be midblue (not pink!) in Zappo</li>
4548 <li>error messages passed up and output when data read
4550 <li>edit undo recovers previous dataset sequence when
4551 sequence is edited</li>
4552 <li>allow PDB files without pdb ID HEADER lines (like
4553 those generated by MODELLER) to be read in properly</li>
4554 <li>allow reading of JPred concise files as a normal
4556 <li>Stockholm annotation parsing and alignment properties
4557 import fixed for PFAM records</li>
4558 <li>Structure view windows have correct name in Desktop
4560 <li>annotation consisting of sequence associated scores
4561 can be read and written correctly to annotation file</li>
4562 <li>Aligned cDNA translation to aligned peptide works
4564 <li>Fixed display of hidden sequence markers and
4565 non-italic font for representatives in Applet</li>
4566 <li>Applet Menus are always embedded in applet window on
4568 <li>Newly shown features appear at top of stack (in
4570 <li>Annotations added via parameter not drawn properly
4571 due to null pointer exceptions</li>
4572 <li>Secondary structure lines are drawn starting from
4573 first column of alignment</li>
4574 <li>UniProt XML import updated for new schema release in
4576 <li>Sequence feature to sequence ID match for Features
4577 file is case-insensitive</li>
4578 <li>Sequence features read from Features file appended to
4579 all sequences with matching IDs</li>
4580 <li>PDB structure coloured correctly for associated views
4581 containing a sub-sequence</li>
4582 <li>PDB files can be retrieved by applet from Jar files</li>
4583 <li>feature and annotation file applet parameters
4584 referring to different directories are retrieved correctly</li>
4585 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4586 <li>Fixed application hang whilst waiting for
4587 splash-screen version check to complete</li>
4588 <li>Applet properly URLencodes input parameter values
4589 when passing them to the launchApp service</li>
4590 <li>display name and local features preserved in results
4591 retrieved from web service</li>
4592 <li>Visual delay indication for sequence retrieval and
4593 sequence fetcher initialisation</li>
4594 <li>updated Application to use DAS 1.53e version of
4595 dasobert DAS client</li>
4596 <li>Re-instated Full AMSA support and .amsa file
4598 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4606 <div align="center">
4607 <strong>2.3</strong><br> 9/5/07
4612 <li>Jmol 11.0.2 integration</li>
4613 <li>PDB views stored in Jalview XML files</li>
4614 <li>Slide sequences</li>
4615 <li>Edit sequence in place</li>
4616 <li>EMBL CDS features</li>
4617 <li>DAS Feature mapping</li>
4618 <li>Feature ordering</li>
4619 <li>Alignment Properties</li>
4620 <li>Annotation Scores</li>
4621 <li>Sort by scores</li>
4622 <li>Feature/annotation editing in applet</li>
4627 <li>Headless state operation in 2.2.1</li>
4628 <li>Incorrect and unstable DNA pairwise alignment</li>
4629 <li>Cut and paste of sequences with annotation</li>
4630 <li>Feature group display state in XML</li>
4631 <li>Feature ordering in XML</li>
4632 <li>blc file iteration selection using filename # suffix</li>
4633 <li>Stockholm alignment properties</li>
4634 <li>Stockhom alignment secondary structure annotation</li>
4635 <li>2.2.1 applet had no feature transparency</li>
4636 <li>Number pad keys can be used in cursor mode</li>
4637 <li>Structure Viewer mirror image resolved</li>
4644 <div align="center">
4645 <strong>2.2.1</strong><br> 12/2/07
4650 <li>Non standard characters can be read and displayed
4651 <li>Annotations/Features can be imported/exported to the
4653 <li>Applet allows editing of sequence/annotation/group
4654 name & description
4655 <li>Preference setting to display sequence name in
4657 <li>Annotation file format extended to allow
4658 Sequence_groups to be defined
4659 <li>Default opening of alignment overview panel can be
4660 specified in preferences
4661 <li>PDB residue numbering annotation added to associated
4667 <li>Applet crash under certain Linux OS with Java 1.6
4669 <li>Annotation file export / import bugs fixed
4670 <li>PNG / EPS image output bugs fixed
4676 <div align="center">
4677 <strong>2.2</strong><br> 27/11/06
4682 <li>Multiple views on alignment
4683 <li>Sequence feature editing
4684 <li>"Reload" alignment
4685 <li>"Save" to current filename
4686 <li>Background dependent text colour
4687 <li>Right align sequence ids
4688 <li>User-defined lower case residue colours
4691 <li>Menu item accelerator keys
4692 <li>Control-V pastes to current alignment
4693 <li>Cancel button for DAS Feature Fetching
4694 <li>PCA and PDB Viewers zoom via mouse roller
4695 <li>User-defined sub-tree colours and sub-tree selection
4697 <li>'New Window' button on the 'Output to Text box'
4702 <li>New memory efficient Undo/Redo System
4703 <li>Optimised symbol lookups and conservation/consensus
4705 <li>Region Conservation/Consensus recalculated after
4707 <li>Fixed Remove Empty Columns Bug (empty columns at end
4709 <li>Slowed DAS Feature Fetching for increased robustness.
4711 <li>Made angle brackets in ASCII feature descriptions
4713 <li>Re-instated Zoom function for PCA
4714 <li>Sequence descriptions conserved in web service
4716 <li>UniProt ID discoverer uses any word separated by
4718 <li>WsDbFetch query/result association resolved
4719 <li>Tree leaf to sequence mapping improved
4720 <li>Smooth fonts switch moved to FontChooser dialog box.
4727 <div align="center">
4728 <strong>2.1.1</strong><br> 12/9/06
4733 <li>Copy consensus sequence to clipboard</li>
4738 <li>Image output - rightmost residues are rendered if
4739 sequence id panel has been resized</li>
4740 <li>Image output - all offscreen group boundaries are
4742 <li>Annotation files with sequence references - all
4743 elements in file are relative to sequence position</li>
4744 <li>Mac Applet users can use Alt key for group editing</li>
4750 <div align="center">
4751 <strong>2.1</strong><br> 22/8/06
4756 <li>MAFFT Multiple Alignment in default Web Service list</li>
4757 <li>DAS Feature fetching</li>
4758 <li>Hide sequences and columns</li>
4759 <li>Export Annotations and Features</li>
4760 <li>GFF file reading / writing</li>
4761 <li>Associate structures with sequences from local PDB
4763 <li>Add sequences to exisiting alignment</li>
4764 <li>Recently opened files / URL lists</li>
4765 <li>Applet can launch the full application</li>
4766 <li>Applet has transparency for features (Java 1.2
4768 <li>Applet has user defined colours parameter</li>
4769 <li>Applet can load sequences from parameter
4770 "sequence<em>x</em>"
4776 <li>Redundancy Panel reinstalled in the Applet</li>
4777 <li>Monospaced font - EPS / rescaling bug fixed</li>
4778 <li>Annotation files with sequence references bug fixed</li>
4784 <div align="center">
4785 <strong>2.08.1</strong><br> 2/5/06
4790 <li>Change case of selected region from Popup menu</li>
4791 <li>Choose to match case when searching</li>
4792 <li>Middle mouse button and mouse movement can compress /
4793 expand the visible width and height of the alignment</li>
4798 <li>Annotation Panel displays complete JNet results</li>
4804 <div align="center">
4805 <strong>2.08b</strong><br> 18/4/06
4811 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4812 <li>Righthand label on wrapped alignments shows correct
4819 <div align="center">
4820 <strong>2.08</strong><br> 10/4/06
4825 <li>Editing can be locked to the selection area</li>
4826 <li>Keyboard editing</li>
4827 <li>Create sequence features from searches</li>
4828 <li>Precalculated annotations can be loaded onto
4830 <li>Features file allows grouping of features</li>
4831 <li>Annotation Colouring scheme added</li>
4832 <li>Smooth fonts off by default - Faster rendering</li>
4833 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4838 <li>Drag & Drop fixed on Linux</li>
4839 <li>Jalview Archive file faster to load/save, sequence
4840 descriptions saved.</li>
4846 <div align="center">
4847 <strong>2.07</strong><br> 12/12/05
4852 <li>PDB Structure Viewer enhanced</li>
4853 <li>Sequence Feature retrieval and display enhanced</li>
4854 <li>Choose to output sequence start-end after sequence
4855 name for file output</li>
4856 <li>Sequence Fetcher WSDBFetch@EBI</li>
4857 <li>Applet can read feature files, PDB files and can be
4858 used for HTML form input</li>
4863 <li>HTML output writes groups and features</li>
4864 <li>Group editing is Control and mouse click</li>
4865 <li>File IO bugs</li>
4871 <div align="center">
4872 <strong>2.06</strong><br> 28/9/05
4877 <li>View annotations in wrapped mode</li>
4878 <li>More options for PCA viewer</li>
4883 <li>GUI bugs resolved</li>
4884 <li>Runs with -nodisplay from command line</li>
4890 <div align="center">
4891 <strong>2.05b</strong><br> 15/9/05
4896 <li>Choose EPS export as lineart or text</li>
4897 <li>Jar files are executable</li>
4898 <li>Can read in Uracil - maps to unknown residue</li>
4903 <li>Known OutOfMemory errors give warning message</li>
4904 <li>Overview window calculated more efficiently</li>
4905 <li>Several GUI bugs resolved</li>
4911 <div align="center">
4912 <strong>2.05</strong><br> 30/8/05
4917 <li>Edit and annotate in "Wrapped" view</li>
4922 <li>Several GUI bugs resolved</li>
4928 <div align="center">
4929 <strong>2.04</strong><br> 24/8/05
4934 <li>Hold down mouse wheel & scroll to change font
4940 <li>Improved JPred client reliability</li>
4941 <li>Improved loading of Jalview files</li>
4947 <div align="center">
4948 <strong>2.03</strong><br> 18/8/05
4953 <li>Set Proxy server name and port in preferences</li>
4954 <li>Multiple URL links from sequence ids</li>
4955 <li>User Defined Colours can have a scheme name and added
4957 <li>Choose to ignore gaps in consensus calculation</li>
4958 <li>Unix users can set default web browser</li>
4959 <li>Runs without GUI for batch processing</li>
4960 <li>Dynamically generated Web Service Menus</li>
4965 <li>InstallAnywhere download for Sparc Solaris</li>
4971 <div align="center">
4972 <strong>2.02</strong><br> 18/7/05
4978 <li>Copy & Paste order of sequences maintains
4979 alignment order.</li>
4985 <div align="center">
4986 <strong>2.01</strong><br> 12/7/05
4991 <li>Use delete key for deleting selection.</li>
4992 <li>Use Mouse wheel to scroll sequences.</li>
4993 <li>Help file updated to describe how to add alignment
4995 <li>Version and build date written to build properties
4997 <li>InstallAnywhere installation will check for updates
4998 at launch of Jalview.</li>
5003 <li>Delete gaps bug fixed.</li>
5004 <li>FileChooser sorts columns.</li>
5005 <li>Can remove groups one by one.</li>
5006 <li>Filechooser icons installed.</li>
5007 <li>Finder ignores return character when searching.
5008 Return key will initiate a search.<br>
5015 <div align="center">
5016 <strong>2.0</strong><br> 20/6/05
5021 <li>New codebase</li>