4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
35 /* separate the items from eachother */
42 /* doesnt get processed in javahelp */
51 <strong>Release History</strong>
55 <th nowrap><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <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.2.11.1.4">.4</a><br />
61 <em>09/03/2021</em></strong></td>
62 <td align="left" valign="top"><em>Improved control of
63 Jalview's use of network services via jalview_properties</em>
66 <!-- JAL-3814 -->New .jalview_properties token controlling
67 launch of the news browser (like -nonews argument)
70 <!-- JAL-3813 -->New .jalview_properties token controlling
71 download of linkout URLs from
72 www.jalview.org/services/identifiers
75 <!-- JAL-3812 -->New .jalview_properties token controlling
76 download of BIOJSHTML templates
79 <!-- JAL-3811 -->New 'Discover Web Services' option to trigger
80 a one off JABAWS discovery if autodiscovery was disabled
83 <td align="left" valign="top">
86 <!-- JAL-3818 -->Intermittent deadlock opening structure in
89 </ul> <em>New Known defects</em>
92 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
93 always restored from project (since 2.10.3)
96 <!-- JAL-3806 -->Selections from tree built from CDS aren't
97 propagated to Protein alignment (since 2.11.1.3)
103 <td width="60" align="center" nowrap><strong><a
104 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
105 <em>29/10/2020</em></strong></td>
106 <td align="left" valign="top">
111 <td align="left" valign="top">
114 <!-- JAL-3765 -->Find doesn't always highlight all matching
115 positions in a sequence (bug introduced in 2.11.1.2)
118 <!-- JAL-3760 -->Alignments containing one or more protein
119 sequences can be classed as nucleotide
122 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
123 sequences after alignment of protein products (known defect
124 first reported for 2.11.1.0)
127 <!-- JAL-3725 -->No tooltip or popup menu for genomic
128 features outwith CDS shown overlaid on protein
131 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
132 correctly mapped by Jalview (e.g. affects viral CDS with
133 ribosomal slippage, since 2.9.0)
136 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
140 <!-- JAL-3700 -->Selections in CDS sequence panel don't
141 always select corresponding protein sequences
144 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
145 column selection doesn't always ignore hidden columns
147 </ul> <em>Installer</em>
150 <!-- JAL-3611 -->Space character in Jalview install path on
151 Windows prevents install4j launching getdown
153 </ul> <em>Development</em>
156 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
157 version numbers in doc/building.md
163 <td width="60" align="center" nowrap><strong><a
164 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
165 <em>25/09/2020</em></strong></td>
166 <td align="left" valign="top">
170 <td align="left" valign="top">
173 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
174 "Encountered problems opening
175 https://www.jalview.org/examples/exampleFile_2_7.jvp"
181 <td width="60" align="center" nowrap><strong><a
182 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
183 <em>17/09/2020</em></strong></td>
184 <td align="left" valign="top">
187 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
188 residue in cursor mode
191 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
192 HTSJDK from 2.12 to 2.23
195 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
196 optimisations and improvements suggested by Bob Hanson and
197 improved compatibility with JalviewJS
200 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
201 alignments from Pfam and Rfam
204 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
205 import (no longer based on .gz extension)
208 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
211 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
212 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
216 <!-- JAL-3667 -->Improved warning messages, debug logging
217 and fixed Retry action when Jalview encounters errors when
218 saving or making backup files.
221 <!-- JAL-3676 -->Enhanced Jalview Java Console:
223 <li>Jalview's logging level can be configured</li>
224 <li>Copy to Clipboard Buttion</li>
228 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
229 when running on Linux (Requires Java 11+)
231 </ul> <em>Launching Jalview</em>
234 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
235 through a system property
238 <!-- JAL-3477 -->Improved built-in documentation and command
239 line help for configuring Jalview's memory
243 <td align="left" valign="top">
246 <!-- JAL-3691 -->Conservation and Quality tracks are shown
247 but not calculated and no protein or DNA score models are
248 available for tree/PCA calculation when launched with
249 Turkish language locale
252 <!-- JAL-3493 -->Escape does not clear highlights on the
253 alignment (Since Jalview 2.10.3)
256 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
257 doesn't slide selected sequences, just sequence under cursor
260 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
261 sequence under the cursor
264 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
265 multiple EMBL gene products shown for a single contig
268 <!-- JAL-3696 -->Errors encountered when processing variants
269 from VCF files yield "Error processing VCF: Format specifier
273 <!-- JAL-3697 -->Count of features not shown can be wrong
274 when there are both local and complementary features mapped
275 to the position under the cursor
278 <!-- JAL-3673 -->Sequence ID for reference sequence is
279 clipped when Right align Sequence IDs enabled
282 <!-- JAL-2983 -->Slider with negative range values not
283 rendered correctly in VAqua4 (Since 2.10.4)
286 <!-- JAL-3685 -->Single quotes not displayed correctly in
287 internationalised text for some messages and log output
290 <!-- JAL-3490 -->Find doesn't report matches that span
291 hidden gapped columns
294 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
295 panels, Alignment viewport and annotation renderer.
298 <!-- JAL-3561 -->Jalview ignores file format parameter
299 specifying output format when exporting an alignment via the
303 <!-- JAL-3667 -->Windows 10: For a minority of users, if
304 backups are not enabled, Jalview sometimes fails to
305 overwrite an existing file and raises a warning dialog. (in
306 2.11.0, and 2.11.1.0, the workaround is to try to save the
307 file again, and if that fails, delete the original file and
311 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
315 <!-- JAL-3741 -->References to http://www.jalview.org in
316 program and documentation
318 </ul> <em>Launching Jalview</em>
321 <!-- JAL-3718 -->Jalview application fails when launched the
322 first time for a version that has different jars to the
323 previous launched version.
325 </ul> <em>Developing Jalview</em>
328 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
329 data, causing cloverReport gradle task to fail with an
333 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
334 monitor the release channel
336 </ul> <em>New Known defects</em>
339 <!-- JAL-3748 -->CDS shown in result of submitting proteins
340 in a CDS/Protein alignment to a web service is wrong when
341 proteins share a common transcript sequence (e.g.
342 genome of RNA viruses)
345 <!-- JAL-3576 -->Co-located features exported and re-imported
346 are ordered differently when shown on alignment and in
347 tooltips. (Also affects v2.11.1.0)
350 <!-- JAL-3702 -->Drag and drop of alignment file onto
351 alignment window when in a HiDPI scaled mode in Linux only
352 works for the top left quadrant of the alignment window
355 <!-- JAL-3701 -->Stale build data in jalview standalone jar
356 builds (only affects 2.11.1.1 branch)
359 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
360 when alignment view restored from project (since Jalview 2.11.0)
363 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
364 protein products for certain ENA records are repeatedly
365 shown via Calculate->Show Cross Refs
371 <td width="60" align="center" nowrap><strong><a
372 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
373 <em>22/04/2020</em></strong></td>
374 <td align="left" valign="top">
377 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
378 'virtual' codon features shown on protein (or vice versa)
379 for display in alignments, on structure views (including
380 transfer to UCSF chimera), in feature reports and for
384 <!-- JAL-3121 -->Feature attributes from VCF files can be
385 exported and re-imported as GFF3 files
388 <!-- JAL-3376 -->Capture VCF "fixed column" values
389 POS, ID, QUAL, FILTER as Feature Attributes
392 <!-- JAL-3375 -->More robust VCF numeric data field
393 validation while parsing
396 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
400 <!-- JAL-3535 -->Feature Settings dialog title includes name
404 <!-- JAL-3538 -->Font anti-aliasing in alignment views
408 <!-- JAL-3468 -->Very long feature descriptions truncated in
412 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
413 with no feature types visible
416 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
418 </ul><em>Jalview Installer</em>
421 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
422 in console (may be null when Jalview launched as executable jar or via conda)
425 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
428 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
431 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
433 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
434 </ul> <em>Release processes</em>
437 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
440 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
442 </ul> <em>Build System</em>
445 <!-- JAL-3510 -->Clover updated to 4.4.1
448 <!-- JAL-3513 -->Test code included in Clover coverage
452 <em>Groovy Scripts</em>
455 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
456 to stdout containing the consensus sequence for each
457 alignment in a Jalview session
460 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
461 genomic sequence_variant annotation from CDS as
462 missense_variant or synonymous_variant on protein products.
466 <td align="left" valign="top">
469 <!-- JAL-3581 -->Hidden sequence markers still visible when
470 'Show hidden markers' option is not ticked
473 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
474 PNG output when 'Automatically set ID width' is set in
475 jalview preferences or properties file
478 <!-- JAL-3571 -->Feature Editor dialog can be opened when
479 'Show Sequence Features' option is not ticked
482 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
483 buttons in Feature Settings dialog are clicked when no
487 <!-- JAL-3412 -->ID margins for CDS and Protein views not
488 equal when split frame is first opened
491 <!-- JAL-3296 -->Sequence position numbers in status bar not
492 correct after editing a sequence's start position
495 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
496 with annotation and exceptions thrown when only a few
497 columns shown in wrapped mode
500 <!-- JAL-3386 -->Sequence IDs missing in headless export of
501 wrapped alignment figure with annotations
504 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
505 ID fails with ClassCastException
508 <!-- JAL-3389 -->Chimera session not restored from Jalview
512 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
513 feature settings dialog also selects columns
516 <!-- JAL-3473 -->SpinnerNumberModel causes
517 IllegalArgumentException in some circumstances
520 <!-- JAL-3534 -->Multiple feature settings dialogs can be
524 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
525 alignment window is closed
528 <!-- JAL-3406 -->Credits missing some authors in Jalview
529 help documentation for 2.11.0 release
532 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
533 includes Pfam ID as sequence's accession rather than its
536 </ul> <em>Java 11 Compatibility issues</em>
539 <!-- JAL-2987 -->OSX - Can't view some search results in
540 PDB/Uniprot search panel
542 </ul> <em>Installer</em>
545 <!-- JAL-3447 -->Jalview should not create file associations
546 for 3D structure files (.pdb, .mmcif. .cif)
548 </ul> <em>Repository and Source Release</em>
551 <!-- JAL-3474 -->removed obsolete .cvsignore files from
555 <!-- JAL-3541 -->Clover report generation running out of
558 </ul> <em>New Known Issues</em>
561 <!-- JAL-3523 -->OSX - Current working directory not
562 preserved when Jalview.app launched with parameters from
566 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
567 clipped in headless figure export when Right Align option
571 <!-- JAL-3542 -->Jalview Installation type always reports
572 'Source' in console output
575 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
576 bamboo server but run fine locally.
582 <td width="60" align="center" nowrap>
583 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
584 <em>04/07/2019</em></strong>
586 <td align="left" valign="top">
589 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
590 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
591 source project) rather than InstallAnywhere
594 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
595 settings, receive over the air updates and launch specific
596 versions via (<a href="https://github.com/threerings/getdown">Three
600 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
601 formats supported by Jalview (including .jvp project files)
604 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
605 arguments and switch between different getdown channels
608 <!-- JAL-3141 -->Backup files created when saving Jalview project
613 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
614 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
616 <!-- JAL-2620 -->Alternative genetic code tables for
617 'Translate as cDNA'</li>
619 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
620 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
623 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
624 implementation that allows updates) used for Sequence Feature collections</li>
626 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
627 features can be filtered and shaded according to any
628 associated attributes (e.g. variant attributes from VCF
629 file, or key-value pairs imported from column 9 of GFF
633 <!-- JAL-2879 -->Feature Attributes and shading schemes
634 stored and restored from Jalview Projects
637 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
638 recognise variant features
641 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
642 sequences (also coloured red by default)
645 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
649 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
650 algorithm (Z-sort/transparency and filter aware)
653 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
659 <!-- JAL-3205 -->Symmetric score matrices for faster
660 tree and PCA calculations
662 <li><strong>Principal Components Analysis Viewer</strong>
665 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
666 and Viewer state saved in Jalview Project
668 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
671 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
675 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
680 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
682 <li><strong>Speed and Efficiency</strong>
685 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
686 multiple groups when working with large alignments
689 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
693 <li><strong>User Interface</strong>
696 <!-- JAL-2933 -->Finder panel remembers last position in each
700 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
701 what is shown)<br />Only visible regions of alignment are shown by
702 default (can be changed in user preferences)
705 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
706 to the Overwrite Dialog
709 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
713 <!-- JAL-1244 -->Status bar shows bounds when dragging a
714 selection region, and gap count when inserting or deleting gaps
717 <!-- JAL-3132 -->Status bar updates over sequence and annotation
721 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
725 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
729 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
732 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
736 <!-- JAL-3181 -->Consistent ordering of links in sequence id
740 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
742 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
746 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
747 <li><strong>Java 11 Support (not yet on general release)</strong>
750 <!-- -->OSX GUI integrations for App menu's 'About' entry and
755 <em>Deprecations</em>
757 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
758 capabilities removed from the Jalview Desktop
760 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
761 unmarshalling has been replaced by JAXB for Jalview projects
762 and XML based data retrieval clients</li>
763 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
764 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
765 </ul> <em>Documentation</em>
767 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
768 not supported in EPS figure export
770 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
771 </ul> <em>Development and Release Processes</em>
774 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
777 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
779 <!-- JAL-3225 -->Eclipse project configuration managed with
783 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
784 Bamboo continuous integration for unattended Test Suite
788 <!-- JAL-2864 -->Memory test suite to detect leaks in common
792 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
796 <!-- JAL-3248 -->Developer documentation migrated to
797 markdown (with HTML rendering)
800 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
803 <!-- JAL-3289 -->New URLs for publishing development
808 <td align="left" valign="top">
811 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
814 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
815 superposition in Jmol fail on Windows
818 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
819 structures for sequences with lots of PDB structures
822 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
826 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
827 project involving multiple views
830 <!-- JAL-3164 -->Overview for complementary view in a linked
831 CDS/Protein alignment is not updated when Hide Columns by
832 Annotation dialog hides columns
835 <!-- JAL-3158 -->Selection highlighting in the complement of a
836 CDS/Protein alignment stops working after making a selection in
837 one view, then making another selection in the other view
840 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
844 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
845 Settings and Jalview Preferences panels
848 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
849 overview with large alignments
852 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
853 region if columns were selected by dragging right-to-left and the
854 mouse moved to the left of the first column
857 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
858 hidden column marker via scale popup menu
861 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
862 doesn't tell users the invalid URL
865 <!-- JAL-2816 -->Tooltips displayed for features filtered by
869 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
870 show cross references or Fetch Database References are shown in
874 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
875 peptide sequence (computed variant shown as p.Res.null)
878 <!-- JAL-2060 -->'Graduated colour' option not offered for
879 manually created features (where feature score is Float.NaN)
882 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
883 when columns are hidden
886 <!-- JAL-3082 -->Regular expression error for '(' in Select
887 Columns by Annotation description
890 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
891 out of Scale or Annotation Panel
894 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
898 <!-- JAL-3074 -->Left/right drag in annotation can scroll
902 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
906 <!-- JAL-3002 -->Column display is out by one after Page Down,
907 Page Up in wrapped mode
910 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
913 <!-- JAL-2932 -->Finder searches in minimised alignments
916 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
917 on opening an alignment
920 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
924 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
925 different groups in the alignment are selected
928 <!-- JAL-2717 -->Internationalised colour scheme names not shown
932 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
936 <!-- JAL-3125 -->Value input for graduated feature colour
937 threshold gets 'unrounded'
940 <!-- JAL-2982 -->PCA image export doesn't respect background
944 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
947 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
950 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
954 <!-- JAL-2964 -->Associate Tree with All Views not restored from
958 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
959 shown in complementary view
962 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
963 without normalisation
966 <!-- JAL-3021 -->Sequence Details report should open positioned at top
970 <!-- JAL-914 -->Help page can be opened twice
973 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
975 </ul> <em>Editing</em>
978 <!-- JAL-2822 -->Start and End should be updated when sequence
979 data at beginning or end of alignment added/removed via 'Edit'
983 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
984 relocate sequence features correctly when start of sequence is
985 removed (Known defect since 2.10)
988 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
989 dialog corrupts dataset sequence
992 <!-- JAL-868 -->Structure colours not updated when associated tree
993 repartitions the alignment view (Regression in 2.10.5)
995 </ul> <em>Datamodel</em>
998 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
999 sequence's End is greater than its length
1001 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1002 general release)</em>
1005 <!-- JAL-3288 -->Menus work properly in split-screen
1007 </ul> <em>New Known Defects</em>
1010 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1013 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1014 regions of protein alignment.
1017 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1018 is restored from a Jalview 2.11 project
1021 <!-- JAL-3213 -->Alignment panel height can be too small after
1025 <!-- JAL-3240 -->Display is incorrect after removing gapped
1026 columns within hidden columns
1029 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1030 window after dragging left to select columns to left of visible
1034 <!-- JAL-2876 -->Features coloured according to their description
1035 string and thresholded by score in earlier versions of Jalview are
1036 not shown as thresholded features in 2.11. To workaround please
1037 create a Score filter instead.
1040 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1042 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1045 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1046 alignments with multiple views can close views unexpectedly
1049 <em>Java 11 Specific defects</em>
1052 <!-- JAL-3235 -->Jalview Properties file is not sorted
1053 alphabetically when saved
1059 <td width="60" nowrap>
1060 <div align="center">
1061 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1064 <td><div align="left">
1068 <!-- JAL-3101 -->Default memory for Jalview webstart and
1069 InstallAnywhere increased to 1G.
1072 <!-- JAL-247 -->Hidden sequence markers and representative
1073 sequence bolding included when exporting alignment as EPS,
1074 SVG, PNG or HTML. <em>Display is configured via the
1075 Format menu, or for command-line use via a Jalview
1076 properties file.</em>
1079 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1080 API and sequence data now imported as JSON.
1083 <!-- JAL-3065 -->Change in recommended way of starting
1084 Jalview via a Java command line: add jars in lib directory
1085 to CLASSPATH, rather than via the deprecated java.ext.dirs
1089 <em>Development</em>
1092 <!-- JAL-3047 -->Support added to execute test suite
1093 instrumented with <a href="http://openclover.org/">Open
1098 <td><div align="left">
1102 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1103 row shown in Feredoxin Structure alignment view of example
1107 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1108 annotation displayed.
1111 <!-- JAL-3107 -->Group conservation/consensus not shown
1112 for newly created group when 'Apply to all groups'
1116 <!-- JAL-3087 -->Corrupted display when switching to
1117 wrapped mode when sequence panel's vertical scrollbar is
1121 <!-- JAL-3003 -->Alignment is black in exported EPS file
1122 when sequences are selected in exported view.</em>
1125 <!-- JAL-3059 -->Groups with different coloured borders
1126 aren't rendered with correct colour.
1129 <!-- JAL-3092 -->Jalview could hang when importing certain
1130 types of knotted RNA secondary structure.
1133 <!-- JAL-3095 -->Sequence highlight and selection in
1134 trimmed VARNA 2D structure is incorrect for sequences that
1138 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1139 annotation when columns are inserted into an alignment,
1140 and when exporting as Stockholm flatfile.
1143 <!-- JAL-3053 -->Jalview annotation rows containing upper
1144 and lower-case 'E' and 'H' do not automatically get
1145 treated as RNA secondary structure.
1148 <!-- JAL-3106 -->.jvp should be used as default extension
1149 (not .jar) when saving a Jalview project file.
1152 <!-- JAL-3105 -->Mac Users: closing a window correctly
1153 transfers focus to previous window on OSX
1156 <em>Java 10 Issues Resolved</em>
1159 <!-- JAL-2988 -->OSX - Can't save new files via the File
1160 or export menus by typing in a name into the Save dialog
1164 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1165 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1166 'look and feel' which has improved compatibility with the
1167 latest version of OSX.
1174 <td width="60" nowrap>
1175 <div align="center">
1176 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1177 <em>7/06/2018</em></strong>
1180 <td><div align="left">
1184 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1185 annotation retrieved from Uniprot
1188 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1189 onto the Jalview Desktop
1193 <td><div align="left">
1197 <!-- JAL-3017 -->Cannot import features with multiple
1198 variant elements (blocks import of some Uniprot records)
1201 <!-- JAL-2997 -->Clustal files with sequence positions in
1202 right-hand column parsed correctly
1205 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1206 not alignment area in exported graphic
1209 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1210 window has input focus
1213 <!-- JAL-2992 -->Annotation panel set too high when
1214 annotation added to view (Windows)
1217 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1218 network connectivity is poor
1221 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1222 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1223 the currently open URL and links from a page viewed in
1224 Firefox or Chrome on Windows is now fully supported. If
1225 you are using Edge, only links in the page can be
1226 dragged, and with Internet Explorer, only the currently
1227 open URL in the browser can be dropped onto Jalview.</em>
1230 <em>New Known Defects</em>
1232 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1237 <td width="60" nowrap>
1238 <div align="center">
1239 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1242 <td><div align="left">
1246 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1247 for disabling automatic superposition of multiple
1248 structures and open structures in existing views
1251 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1252 ID and annotation area margins can be click-dragged to
1256 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1260 <!-- JAL-2759 -->Improved performance for large alignments
1261 and lots of hidden columns
1264 <!-- JAL-2593 -->Improved performance when rendering lots
1265 of features (particularly when transparency is disabled)
1268 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1269 exchange of Jalview features and Chimera attributes made
1275 <td><div align="left">
1278 <!-- JAL-2899 -->Structure and Overview aren't updated
1279 when Colour By Annotation threshold slider is adjusted
1282 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1283 overlapping alignment panel
1286 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1290 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1291 improved: CDS not handled correctly if transcript has no
1295 <!-- JAL-2321 -->Secondary structure and temperature
1296 factor annotation not added to sequence when local PDB
1297 file associated with it by drag'n'drop or structure
1301 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1302 dialog doesn't import PDB files dropped on an alignment
1305 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1306 scroll bar doesn't work for some CDS/Protein views
1309 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1310 Java 1.8u153 onwards and Java 1.9u4+.
1313 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1314 columns in annotation row
1317 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1318 honored in batch mode
1321 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1322 for structures added to existing Jmol view
1325 <!-- JAL-2223 -->'View Mappings' includes duplicate
1326 entries after importing project with multiple views
1329 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1330 protein sequences via SIFTS from associated PDB entries
1331 with negative residue numbers or missing residues fails
1334 <!-- JAL-2952 -->Exception when shading sequence with negative
1335 Temperature Factor values from annotated PDB files (e.g.
1336 as generated by CONSURF)
1339 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1340 tooltip doesn't include a text description of mutation
1343 <!-- JAL-2922 -->Invert displayed features very slow when
1344 structure and/or overview windows are also shown
1347 <!-- JAL-2954 -->Selecting columns from highlighted regions
1348 very slow for alignments with large numbers of sequences
1351 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1352 with 'StringIndexOutOfBounds'
1355 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1356 platforms running Java 10
1359 <!-- JAL-2960 -->Adding a structure to existing structure
1360 view appears to do nothing because the view is hidden behind the alignment view
1366 <!-- JAL-2926 -->Copy consensus sequence option in applet
1367 should copy the group consensus when popup is opened on it
1373 <!-- JAL-2913 -->Fixed ID width preference is not respected
1376 <em>New Known Defects</em>
1379 <!-- JAL-2973 --> Exceptions occasionally raised when
1380 editing a large alignment and overview is displayed
1383 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1384 repeatedly after a series of edits even when the overview
1385 is no longer reflecting updates
1388 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1389 structures for protein subsequence (if 'Trim Retrieved
1390 Sequences' enabled) or Ensembl isoforms (Workaround in
1391 2.10.4 is to fail back to N&W mapping)
1394 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1395 option gives blank output
1402 <td width="60" nowrap>
1403 <div align="center">
1404 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1407 <td><div align="left">
1408 <ul><li>Updated Certum Codesigning Certificate
1409 (Valid till 30th November 2018)</li></ul></div></td>
1410 <td><div align="left">
1411 <em>Desktop</em><ul>
1413 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1414 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1415 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1416 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1417 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1418 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1419 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1425 <td width="60" nowrap>
1426 <div align="center">
1427 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1430 <td><div align="left">
1434 <!-- JAL-2446 -->Faster and more efficient management and
1435 rendering of sequence features
1438 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1439 429 rate limit request hander
1442 <!-- JAL-2773 -->Structure views don't get updated unless
1443 their colours have changed
1446 <!-- JAL-2495 -->All linked sequences are highlighted for
1447 a structure mousover (Jmol) or selection (Chimera)
1450 <!-- JAL-2790 -->'Cancel' button in progress bar for
1451 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1454 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1455 view from Ensembl locus cross-references
1458 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1462 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1463 feature can be disabled
1466 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1467 PDB easier retrieval of sequences for lists of IDs
1470 <!-- JAL-2758 -->Short names for sequences retrieved from
1476 <li>Groovy interpreter updated to 2.4.12</li>
1477 <li>Example groovy script for generating a matrix of
1478 percent identity scores for current alignment.</li>
1480 <em>Testing and Deployment</em>
1483 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1487 <td><div align="left">
1491 <!-- JAL-2643 -->Pressing tab after updating the colour
1492 threshold text field doesn't trigger an update to the
1496 <!-- JAL-2682 -->Race condition when parsing sequence ID
1500 <!-- JAL-2608 -->Overview windows are also closed when
1501 alignment window is closed
1504 <!-- JAL-2548 -->Export of features doesn't always respect
1508 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1509 takes a long time in Cursor mode
1515 <!-- JAL-2777 -->Structures with whitespace chainCode
1516 cannot be viewed in Chimera
1519 <!-- JAL-2728 -->Protein annotation panel too high in
1523 <!-- JAL-2757 -->Can't edit the query after the server
1524 error warning icon is shown in Uniprot and PDB Free Text
1528 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1531 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1534 <!-- JAL-2739 -->Hidden column marker in last column not
1535 rendered when switching back from Wrapped to normal view
1538 <!-- JAL-2768 -->Annotation display corrupted when
1539 scrolling right in unwapped alignment view
1542 <!-- JAL-2542 -->Existing features on subsequence
1543 incorrectly relocated when full sequence retrieved from
1547 <!-- JAL-2733 -->Last reported memory still shown when
1548 Desktop->Show Memory is unticked (OSX only)
1551 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1552 features of same type and group to be selected for
1556 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1557 alignments when hidden columns are present
1560 <!-- JAL-2392 -->Jalview freezes when loading and
1561 displaying several structures
1564 <!-- JAL-2732 -->Black outlines left after resizing or
1568 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1569 within the Jalview desktop on OSX
1572 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1573 when in wrapped alignment mode
1576 <!-- JAL-2636 -->Scale mark not shown when close to right
1577 hand end of alignment
1580 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1581 each selected sequence do not have correct start/end
1585 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1586 after canceling the Alignment Window's Font dialog
1589 <!-- JAL-2036 -->Show cross-references not enabled after
1590 restoring project until a new view is created
1593 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1594 URL links appears when only default EMBL-EBI link is
1595 configured (since 2.10.2b2)
1598 <!-- JAL-2775 -->Overview redraws whole window when box
1599 position is adjusted
1602 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1603 in a multi-chain structure when viewing alignment
1604 involving more than one chain (since 2.10)
1607 <!-- JAL-2811 -->Double residue highlights in cursor mode
1608 if new selection moves alignment window
1611 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1612 arrow key in cursor mode to pass hidden column marker
1615 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1616 that produces correctly annotated transcripts and products
1619 <!-- JAL-2776 -->Toggling a feature group after first time
1620 doesn't update associated structure view
1623 <em>Applet</em><br />
1626 <!-- JAL-2687 -->Concurrent modification exception when
1627 closing alignment panel
1630 <em>BioJSON</em><br />
1633 <!-- JAL-2546 -->BioJSON export does not preserve
1634 non-positional features
1637 <em>New Known Issues</em>
1640 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1641 sequence features correctly (for many previous versions of
1645 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1646 using cursor in wrapped panel other than top
1649 <!-- JAL-2791 -->Select columns containing feature ignores
1650 graduated colour threshold
1653 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1654 always preserve numbering and sequence features
1657 <em>Known Java 9 Issues</em>
1660 <!-- JAL-2902 -->Groovy Console very slow to open and is
1661 not responsive when entering characters (Webstart, Java
1668 <td width="60" nowrap>
1669 <div align="center">
1670 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1671 <em>2/10/2017</em></strong>
1674 <td><div align="left">
1675 <em>New features in Jalview Desktop</em>
1678 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1680 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1684 <td><div align="left">
1688 <td width="60" nowrap>
1689 <div align="center">
1690 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1691 <em>7/9/2017</em></strong>
1694 <td><div align="left">
1698 <!-- JAL-2588 -->Show gaps in overview window by colouring
1699 in grey (sequences used to be coloured grey, and gaps were
1703 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1707 <!-- JAL-2587 -->Overview updates immediately on increase
1708 in size and progress bar shown as higher resolution
1709 overview is recalculated
1714 <td><div align="left">
1718 <!-- JAL-2664 -->Overview window redraws every hidden
1719 column region row by row
1722 <!-- JAL-2681 -->duplicate protein sequences shown after
1723 retrieving Ensembl crossrefs for sequences from Uniprot
1726 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1727 format setting is unticked
1730 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1731 if group has show boxes format setting unticked
1734 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1735 autoscrolling whilst dragging current selection group to
1736 include sequences and columns not currently displayed
1739 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1740 assemblies are imported via CIF file
1743 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1744 displayed when threshold or conservation colouring is also
1748 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1752 <!-- JAL-2673 -->Jalview continues to scroll after
1753 dragging a selected region off the visible region of the
1757 <!-- JAL-2724 -->Cannot apply annotation based
1758 colourscheme to all groups in a view
1761 <!-- JAL-2511 -->IDs don't line up with sequences
1762 initially after font size change using the Font chooser or
1769 <td width="60" nowrap>
1770 <div align="center">
1771 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1774 <td><div align="left">
1775 <em>Calculations</em>
1779 <!-- JAL-1933 -->Occupancy annotation row shows number of
1780 ungapped positions in each column of the alignment.
1783 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1784 a calculation dialog box
1787 <!-- JAL-2379 -->Revised implementation of PCA for speed
1788 and memory efficiency (~30x faster)
1791 <!-- JAL-2403 -->Revised implementation of sequence
1792 similarity scores as used by Tree, PCA, Shading Consensus
1793 and other calculations
1796 <!-- JAL-2416 -->Score matrices are stored as resource
1797 files within the Jalview codebase
1800 <!-- JAL-2500 -->Trees computed on Sequence Feature
1801 Similarity may have different topology due to increased
1808 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1809 model for alignments and groups
1812 <!-- JAL-384 -->Custom shading schemes created via groovy
1819 <!-- JAL-2526 -->Efficiency improvements for interacting
1820 with alignment and overview windows
1823 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1827 <!-- JAL-2388 -->Hidden columns and sequences can be
1831 <!-- JAL-2611 -->Click-drag in visible area allows fine
1832 adjustment of visible position
1836 <em>Data import/export</em>
1839 <!-- JAL-2535 -->Posterior probability annotation from
1840 Stockholm files imported as sequence associated annotation
1843 <!-- JAL-2507 -->More robust per-sequence positional
1844 annotation input/output via stockholm flatfile
1847 <!-- JAL-2533 -->Sequence names don't include file
1848 extension when importing structure files without embedded
1849 names or PDB accessions
1852 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1853 format sequence substitution matrices
1856 <em>User Interface</em>
1859 <!-- JAL-2447 --> Experimental Features Checkbox in
1860 Desktop's Tools menu to hide or show untested features in
1864 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1865 via Overview or sequence motif search operations
1868 <!-- JAL-2547 -->Amend sequence features dialog box can be
1869 opened by double clicking gaps within sequence feature
1873 <!-- JAL-1476 -->Status bar message shown when not enough
1874 aligned positions were available to create a 3D structure
1878 <em>3D Structure</em>
1881 <!-- JAL-2430 -->Hidden regions in alignment views are not
1882 coloured in linked structure views
1885 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1886 file-based command exchange
1889 <!-- JAL-2375 -->Structure chooser automatically shows
1890 Cached Structures rather than querying the PDBe if
1891 structures are already available for sequences
1894 <!-- JAL-2520 -->Structures imported via URL are cached in
1895 the Jalview project rather than downloaded again when the
1896 project is reopened.
1899 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1900 to transfer Chimera's structure attributes as Jalview
1901 features, and vice-versa (<strong>Experimental
1905 <em>Web Services</em>
1908 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1911 <!-- JAL-2335 -->Filter non-standard amino acids and
1912 nucleotides when submitting to AACon and other MSA
1916 <!-- JAL-2316, -->URLs for viewing database
1917 cross-references provided by identifiers.org and the
1918 EMBL-EBI's MIRIAM DB
1925 <!-- JAL-2344 -->FileFormatI interface for describing and
1926 identifying file formats (instead of String constants)
1929 <!-- JAL-2228 -->FeatureCounter script refactored for
1930 efficiency when counting all displayed features (not
1931 backwards compatible with 2.10.1)
1934 <em>Example files</em>
1937 <!-- JAL-2631 -->Graduated feature colour style example
1938 included in the example feature file
1941 <em>Documentation</em>
1944 <!-- JAL-2339 -->Release notes reformatted for readability
1945 with the built-in Java help viewer
1948 <!-- JAL-1644 -->Find documentation updated with 'search
1949 sequence description' option
1955 <!-- JAL-2485, -->External service integration tests for
1956 Uniprot REST Free Text Search Client
1959 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1962 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1967 <td><div align="left">
1968 <em>Calculations</em>
1971 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1972 matrix - C->R should be '-3'<br />Old matrix restored
1973 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1975 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1976 Jalview's treatment of gaps in PCA and substitution matrix
1977 based Tree calculations.<br /> <br />In earlier versions
1978 of Jalview, gaps matching gaps were penalised, and gaps
1979 matching non-gaps penalised even more. In the PCA
1980 calculation, gaps were actually treated as non-gaps - so
1981 different costs were applied, which meant Jalview's PCAs
1982 were different to those produced by SeqSpace.<br />Jalview
1983 now treats gaps in the same way as SeqSpace (ie it scores
1984 them as 0). <br /> <br />Enter the following in the
1985 Groovy console to restore pre-2.10.2 behaviour:<br />
1986 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1987 // for 2.10.1 mode <br />
1988 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1989 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1990 these settings will affect all subsequent tree and PCA
1991 calculations (not recommended)</em></li>
1993 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1994 scaling of branch lengths for trees computed using
1995 Sequence Feature Similarity.
1998 <!-- JAL-2377 -->PCA calculation could hang when
1999 generating output report when working with highly
2000 redundant alignments
2003 <!-- JAL-2544 --> Sort by features includes features to
2004 right of selected region when gaps present on right-hand
2008 <em>User Interface</em>
2011 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2012 doesn't reselect a specific sequence's associated
2013 annotation after it was used for colouring a view
2016 <!-- JAL-2419 -->Current selection lost if popup menu
2017 opened on a region of alignment without groups
2020 <!-- JAL-2374 -->Popup menu not always shown for regions
2021 of an alignment with overlapping groups
2024 <!-- JAL-2310 -->Finder double counts if both a sequence's
2025 name and description match
2028 <!-- JAL-2370 -->Hiding column selection containing two
2029 hidden regions results in incorrect hidden regions
2032 <!-- JAL-2386 -->'Apply to all groups' setting when
2033 changing colour does not apply Conservation slider value
2037 <!-- JAL-2373 -->Percentage identity and conservation menu
2038 items do not show a tick or allow shading to be disabled
2041 <!-- JAL-2385 -->Conservation shading or PID threshold
2042 lost when base colourscheme changed if slider not visible
2045 <!-- JAL-2547 -->Sequence features shown in tooltip for
2046 gaps before start of features
2049 <!-- JAL-2623 -->Graduated feature colour threshold not
2050 restored to UI when feature colour is edited
2053 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2054 a time when scrolling vertically in wrapped mode.
2057 <!-- JAL-2630 -->Structure and alignment overview update
2058 as graduate feature colour settings are modified via the
2062 <!-- JAL-2034 -->Overview window doesn't always update
2063 when a group defined on the alignment is resized
2066 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2067 wrapped view result in positional status updates
2071 <!-- JAL-2563 -->Status bar doesn't show position for
2072 ambiguous amino acid and nucleotide symbols
2075 <!-- JAL-2602 -->Copy consensus sequence failed if
2076 alignment included gapped columns
2079 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2080 widgets don't permanently disappear
2083 <!-- JAL-2503 -->Cannot select or filter quantitative
2084 annotation that are shown only as column labels (e.g.
2085 T-Coffee column reliability scores)
2088 <!-- JAL-2594 -->Exception thrown if trying to create a
2089 sequence feature on gaps only
2092 <!-- JAL-2504 -->Features created with 'New feature'
2093 button from a Find inherit previously defined feature type
2094 rather than the Find query string
2097 <!-- JAL-2423 -->incorrect title in output window when
2098 exporting tree calculated in Jalview
2101 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2102 and then revealing them reorders sequences on the
2106 <!-- JAL-964 -->Group panel in sequence feature settings
2107 doesn't update to reflect available set of groups after
2108 interactively adding or modifying features
2111 <!-- JAL-2225 -->Sequence Database chooser unusable on
2115 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2116 only excluded gaps in current sequence and ignored
2123 <!-- JAL-2421 -->Overview window visible region moves
2124 erratically when hidden rows or columns are present
2127 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2128 Structure Viewer's colour menu don't correspond to
2132 <!-- JAL-2405 -->Protein specific colours only offered in
2133 colour and group colour menu for protein alignments
2136 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2137 reflect currently selected view or group's shading
2141 <!-- JAL-2624 -->Feature colour thresholds not respected
2142 when rendered on overview and structures when opacity at
2146 <!-- JAL-2589 -->User defined gap colour not shown in
2147 overview when features overlaid on alignment
2150 <!-- JAL-2567 -->Feature settings for different views not
2151 recovered correctly from Jalview project file
2154 <!-- JAL-2256 -->Feature colours in overview when first opened
2155 (automatically via preferences) are different to the main
2159 <em>Data import/export</em>
2162 <!-- JAL-2576 -->Very large alignments take a long time to
2166 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2167 added after a sequence was imported are not written to
2171 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2172 when importing RNA secondary structure via Stockholm
2175 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2176 not shown in correct direction for simple pseudoknots
2179 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2180 with lightGray or darkGray via features file (but can
2184 <!-- JAL-2383 -->Above PID colour threshold not recovered
2185 when alignment view imported from project
2188 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2189 structure and sequences extracted from structure files
2190 imported via URL and viewed in Jmol
2193 <!-- JAL-2520 -->Structures loaded via URL are saved in
2194 Jalview Projects rather than fetched via URL again when
2195 the project is loaded and the structure viewed
2198 <em>Web Services</em>
2201 <!-- JAL-2519 -->EnsemblGenomes example failing after
2202 release of Ensembl v.88
2205 <!-- JAL-2366 -->Proxy server address and port always
2206 appear enabled in Preferences->Connections
2209 <!-- JAL-2461 -->DAS registry not found exceptions
2210 removed from console output
2213 <!-- JAL-2582 -->Cannot retrieve protein products from
2214 Ensembl by Peptide ID
2217 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2218 created from SIFTs, and spurious 'Couldn't open structure
2219 in Chimera' errors raised after April 2017 update (problem
2220 due to 'null' string rather than empty string used for
2221 residues with no corresponding PDB mapping).
2224 <em>Application UI</em>
2227 <!-- JAL-2361 -->User Defined Colours not added to Colour
2231 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2232 case' residues (button in colourscheme editor debugged and
2233 new documentation and tooltips added)
2236 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2237 doesn't restore group-specific text colour thresholds
2240 <!-- JAL-2243 -->Feature settings panel does not update as
2241 new features are added to alignment
2244 <!-- JAL-2532 -->Cancel in feature settings reverts
2245 changes to feature colours via the Amend features dialog
2248 <!-- JAL-2506 -->Null pointer exception when attempting to
2249 edit graduated feature colour via amend features dialog
2253 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2254 selection menu changes colours of alignment views
2257 <!-- JAL-2426 -->Spurious exceptions in console raised
2258 from alignment calculation workers after alignment has
2262 <!-- JAL-1608 -->Typo in selection popup menu - Create
2263 groups now 'Create Group'
2266 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2267 Create/Undefine group doesn't always work
2270 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2271 shown again after pressing 'Cancel'
2274 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2275 adjusts start position in wrap mode
2278 <!-- JAL-2563 -->Status bar doesn't show positions for
2279 ambiguous amino acids
2282 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2283 CDS/Protein view after CDS sequences added for aligned
2287 <!-- JAL-2592 -->User defined colourschemes called 'User
2288 Defined' don't appear in Colours menu
2294 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2295 score models doesn't always result in an updated PCA plot
2298 <!-- JAL-2442 -->Features not rendered as transparent on
2299 overview or linked structure view
2302 <!-- JAL-2372 -->Colour group by conservation doesn't
2306 <!-- JAL-2517 -->Hitting Cancel after applying
2307 user-defined colourscheme doesn't restore original
2314 <!-- JAL-2314 -->Unit test failure:
2315 jalview.ws.jabaws.RNAStructExportImport setup fails
2318 <!-- JAL-2307 -->Unit test failure:
2319 jalview.ws.sifts.SiftsClientTest due to compatibility
2320 problems with deep array comparison equality asserts in
2321 successive versions of TestNG
2324 <!-- JAL-2479 -->Relocated StructureChooserTest and
2325 ParameterUtilsTest Unit tests to Network suite
2328 <em>New Known Issues</em>
2331 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2332 phase after a sequence motif find operation
2335 <!-- JAL-2550 -->Importing annotation file with rows
2336 containing just upper and lower case letters are
2337 interpreted as WUSS RNA secondary structure symbols
2340 <!-- JAL-2590 -->Cannot load and display Newick trees
2341 reliably from eggnog Ortholog database
2344 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2345 containing features of type Highlight' when 'B' is pressed
2346 to mark columns containing highlighted regions.
2349 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2350 doesn't always add secondary structure annotation.
2355 <td width="60" nowrap>
2356 <div align="center">
2357 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2360 <td><div align="left">
2364 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2365 for all consensus calculations
2368 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2371 <li>Updated Jalview's Certum code signing certificate
2374 <em>Application</em>
2377 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2378 set of database cross-references, sorted alphabetically
2381 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2382 from database cross references. Users with custom links
2383 will receive a <a href="webServices/urllinks.html#warning">warning
2384 dialog</a> asking them to update their preferences.
2387 <!-- JAL-2287-->Cancel button and escape listener on
2388 dialog warning user about disconnecting Jalview from a
2392 <!-- JAL-2320-->Jalview's Chimera control window closes if
2393 the Chimera it is connected to is shut down
2396 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2397 columns menu item to mark columns containing highlighted
2398 regions (e.g. from structure selections or results of a
2402 <!-- JAL-2284-->Command line option for batch-generation
2403 of HTML pages rendering alignment data with the BioJS
2413 <!-- JAL-2286 -->Columns with more than one modal residue
2414 are not coloured or thresholded according to percent
2415 identity (first observed in Jalview 2.8.2)
2418 <!-- JAL-2301 -->Threonine incorrectly reported as not
2422 <!-- JAL-2318 -->Updates to documentation pages (above PID
2423 threshold, amino acid properties)
2426 <!-- JAL-2292 -->Lower case residues in sequences are not
2427 reported as mapped to residues in a structure file in the
2431 <!--JAL-2324 -->Identical features with non-numeric scores
2432 could be added multiple times to a sequence
2435 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2436 bond features shown as two highlighted residues rather
2437 than a range in linked structure views, and treated
2438 correctly when selecting and computing trees from features
2441 <!-- JAL-2281-->Custom URL links for database
2442 cross-references are matched to database name regardless
2447 <em>Application</em>
2450 <!-- JAL-2282-->Custom URL links for specific database
2451 names without regular expressions also offer links from
2455 <!-- JAL-2315-->Removing a single configured link in the
2456 URL links pane in Connections preferences doesn't actually
2457 update Jalview configuration
2460 <!-- JAL-2272-->CTRL-Click on a selected region to open
2461 the alignment area popup menu doesn't work on El-Capitan
2464 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2465 files with similarly named sequences if dropped onto the
2469 <!-- JAL-2312 -->Additional mappings are shown for PDB
2470 entries where more chains exist in the PDB accession than
2471 are reported in the SIFTS file
2474 <!-- JAL-2317-->Certain structures do not get mapped to
2475 the structure view when displayed with Chimera
2478 <!-- JAL-2317-->No chains shown in the Chimera view
2479 panel's View->Show Chains submenu
2482 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2483 work for wrapped alignment views
2486 <!--JAL-2197 -->Rename UI components for running JPred
2487 predictions from 'JNet' to 'JPred'
2490 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2491 corrupted when annotation panel vertical scroll is not at
2492 first annotation row
2495 <!--JAL-2332 -->Attempting to view structure for Hen
2496 lysozyme results in a PDB Client error dialog box
2499 <!-- JAL-2319 -->Structure View's mapping report switched
2500 ranges for PDB and sequence for SIFTS
2503 SIFTS 'Not_Observed' residues mapped to non-existant
2507 <!-- <em>New Known Issues</em>
2514 <td width="60" nowrap>
2515 <div align="center">
2516 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2517 <em>25/10/2016</em></strong>
2520 <td><em>Application</em>
2522 <li>3D Structure chooser opens with 'Cached structures'
2523 view if structures already loaded</li>
2524 <li>Progress bar reports models as they are loaded to
2525 structure views</li>
2531 <li>Colour by conservation always enabled and no tick
2532 shown in menu when BLOSUM or PID shading applied</li>
2533 <li>FER1_ARATH and FER2_ARATH labels were switched in
2534 example sequences/projects/trees</li>
2536 <em>Application</em>
2538 <li>Jalview projects with views of local PDB structure
2539 files saved on Windows cannot be opened on OSX</li>
2540 <li>Multiple structure views can be opened and superposed
2541 without timeout for structures with multiple models or
2542 multiple sequences in alignment</li>
2543 <li>Cannot import or associated local PDB files without a
2544 PDB ID HEADER line</li>
2545 <li>RMSD is not output in Jmol console when superposition
2547 <li>Drag and drop of URL from Browser fails for Linux and
2548 OSX versions earlier than El Capitan</li>
2549 <li>ENA client ignores invalid content from ENA server</li>
2550 <li>Exceptions are not raised in console when ENA client
2551 attempts to fetch non-existent IDs via Fetch DB Refs UI
2553 <li>Exceptions are not raised in console when a new view
2554 is created on the alignment</li>
2555 <li>OSX right-click fixed for group selections: CMD-click
2556 to insert/remove gaps in groups and CTRL-click to open group
2559 <em>Build and deployment</em>
2561 <li>URL link checker now copes with multi-line anchor
2564 <em>New Known Issues</em>
2566 <li>Drag and drop from URL links in browsers do not work
2573 <td width="60" nowrap>
2574 <div align="center">
2575 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2578 <td><em>General</em>
2581 <!-- JAL-2124 -->Updated Spanish translations.
2584 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2585 for importing structure data to Jalview. Enables mmCIF and
2589 <!-- JAL-192 --->Alignment ruler shows positions relative to
2593 <!-- JAL-2202 -->Position/residue shown in status bar when
2594 mousing over sequence associated annotation
2597 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2601 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2602 '()', canonical '[]' and invalid '{}' base pair populations
2606 <!-- JAL-2092 -->Feature settings popup menu options for
2607 showing or hiding columns containing a feature
2610 <!-- JAL-1557 -->Edit selected group by double clicking on
2611 group and sequence associated annotation labels
2614 <!-- JAL-2236 -->Sequence name added to annotation label in
2615 select/hide columns by annotation and colour by annotation
2619 </ul> <em>Application</em>
2622 <!-- JAL-2050-->Automatically hide introns when opening a
2623 gene/transcript view
2626 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2630 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2631 structure mappings with the EMBL-EBI PDBe SIFTS database
2634 <!-- JAL-2079 -->Updated download sites used for Rfam and
2635 Pfam sources to xfam.org
2638 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2641 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2642 over sequences in Jalview
2645 <!-- JAL-2027-->Support for reverse-complement coding
2646 regions in ENA and EMBL
2649 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2650 for record retrieval via ENA rest API
2653 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2657 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2658 groovy script execution
2661 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2662 alignment window's Calculate menu
2665 <!-- JAL-1812 -->Allow groovy scripts that call
2666 Jalview.getAlignFrames() to run in headless mode
2669 <!-- JAL-2068 -->Support for creating new alignment
2670 calculation workers from groovy scripts
2673 <!-- JAL-1369 --->Store/restore reference sequence in
2677 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2678 associations are now saved/restored from project
2681 <!-- JAL-1993 -->Database selection dialog always shown
2682 before sequence fetcher is opened
2685 <!-- JAL-2183 -->Double click on an entry in Jalview's
2686 database chooser opens a sequence fetcher
2689 <!-- JAL-1563 -->Free-text search client for UniProt using
2690 the UniProt REST API
2693 <!-- JAL-2168 -->-nonews command line parameter to prevent
2694 the news reader opening
2697 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2698 querying stored in preferences
2701 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2705 <!-- JAL-1977-->Tooltips shown on database chooser
2708 <!-- JAL-391 -->Reverse complement function in calculate
2709 menu for nucleotide sequences
2712 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2713 and feature counts preserves alignment ordering (and
2714 debugged for complex feature sets).
2717 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2718 viewing structures with Jalview 2.10
2721 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2722 genome, transcript CCDS and gene ids via the Ensembl and
2723 Ensembl Genomes REST API
2726 <!-- JAL-2049 -->Protein sequence variant annotation
2727 computed for 'sequence_variant' annotation on CDS regions
2731 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2735 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2736 Ref Fetcher fails to match, or otherwise updates sequence
2737 data from external database records.
2740 <!-- JAL-2154 -->Revised Jalview Project format for
2741 efficient recovery of sequence coding and alignment
2742 annotation relationships.
2744 </ul> <!-- <em>Applet</em>
2755 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2759 <!-- JAL-2018-->Export features in Jalview format (again)
2760 includes graduated colourschemes
2763 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2764 working with big alignments and lots of hidden columns
2767 <!-- JAL-2053-->Hidden column markers not always rendered
2768 at right of alignment window
2771 <!-- JAL-2067 -->Tidied up links in help file table of
2775 <!-- JAL-2072 -->Feature based tree calculation not shown
2779 <!-- JAL-2075 -->Hidden columns ignored during feature
2780 based tree calculation
2783 <!-- JAL-2065 -->Alignment view stops updating when show
2784 unconserved enabled for group on alignment
2787 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2791 <!-- JAL-2146 -->Alignment column in status incorrectly
2792 shown as "Sequence position" when mousing over
2796 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2797 hidden columns present
2800 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2801 user created annotation added to alignment
2804 <!-- JAL-1841 -->RNA Structure consensus only computed for
2805 '()' base pair annotation
2808 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2809 in zero scores for all base pairs in RNA Structure
2813 <!-- JAL-2174-->Extend selection with columns containing
2817 <!-- JAL-2275 -->Pfam format writer puts extra space at
2818 beginning of sequence
2821 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2825 <!-- JAL-2238 -->Cannot create groups on an alignment from
2826 from a tree when t-coffee scores are shown
2829 <!-- JAL-1836,1967 -->Cannot import and view PDB
2830 structures with chains containing negative resnums (4q4h)
2833 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2837 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2838 to Clustal, PIR and PileUp output
2841 <!-- JAL-2008 -->Reordering sequence features that are
2842 not visible causes alignment window to repaint
2845 <!-- JAL-2006 -->Threshold sliders don't work in
2846 graduated colour and colour by annotation row for e-value
2847 scores associated with features and annotation rows
2850 <!-- JAL-1797 -->amino acid physicochemical conservation
2851 calculation should be case independent
2854 <!-- JAL-2173 -->Remove annotation also updates hidden
2858 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2859 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2860 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2863 <!-- JAL-2065 -->Null pointer exceptions and redraw
2864 problems when reference sequence defined and 'show
2865 non-conserved' enabled
2868 <!-- JAL-1306 -->Quality and Conservation are now shown on
2869 load even when Consensus calculation is disabled
2872 <!-- JAL-1932 -->Remove right on penultimate column of
2873 alignment does nothing
2876 <em>Application</em>
2879 <!-- JAL-1552-->URLs and links can't be imported by
2880 drag'n'drop on OSX when launched via webstart (note - not
2881 yet fixed for El Capitan)
2884 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2885 output when running on non-gb/us i18n platforms
2888 <!-- JAL-1944 -->Error thrown when exporting a view with
2889 hidden sequences as flat-file alignment
2892 <!-- JAL-2030-->InstallAnywhere distribution fails when
2896 <!-- JAL-2080-->Jalview very slow to launch via webstart
2897 (also hotfix for 2.9.0b2)
2900 <!-- JAL-2085 -->Cannot save project when view has a
2901 reference sequence defined
2904 <!-- JAL-1011 -->Columns are suddenly selected in other
2905 alignments and views when revealing hidden columns
2908 <!-- JAL-1989 -->Hide columns not mirrored in complement
2909 view in a cDNA/Protein splitframe
2912 <!-- JAL-1369 -->Cannot save/restore representative
2913 sequence from project when only one sequence is
2917 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2918 in Structure Chooser
2921 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2922 structure consensus didn't refresh annotation panel
2925 <!-- JAL-1962 -->View mapping in structure view shows
2926 mappings between sequence and all chains in a PDB file
2929 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2930 dialogs format columns correctly, don't display array
2931 data, sort columns according to type
2934 <!-- JAL-1975 -->Export complete shown after destination
2935 file chooser is cancelled during an image export
2938 <!-- JAL-2025 -->Error when querying PDB Service with
2939 sequence name containing special characters
2942 <!-- JAL-2024 -->Manual PDB structure querying should be
2946 <!-- JAL-2104 -->Large tooltips with broken HTML
2947 formatting don't wrap
2950 <!-- JAL-1128 -->Figures exported from wrapped view are
2951 truncated so L looks like I in consensus annotation
2954 <!-- JAL-2003 -->Export features should only export the
2955 currently displayed features for the current selection or
2959 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2960 after fetching cross-references, and restoring from
2964 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2965 followed in the structure viewer
2968 <!-- JAL-2163 -->Titles for individual alignments in
2969 splitframe not restored from project
2972 <!-- JAL-2145 -->missing autocalculated annotation at
2973 trailing end of protein alignment in transcript/product
2974 splitview when pad-gaps not enabled by default
2977 <!-- JAL-1797 -->amino acid physicochemical conservation
2981 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2982 article has been read (reopened issue due to
2983 internationalisation problems)
2986 <!-- JAL-1960 -->Only offer PDB structures in structure
2987 viewer based on sequence name, PDB and UniProt
2992 <!-- JAL-1976 -->No progress bar shown during export of
2996 <!-- JAL-2213 -->Structures not always superimposed after
2997 multiple structures are shown for one or more sequences.
3000 <!-- JAL-1370 -->Reference sequence characters should not
3001 be replaced with '.' when 'Show unconserved' format option
3005 <!-- JAL-1823 -->Cannot specify chain code when entering
3006 specific PDB id for sequence
3009 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3010 'Export hidden sequences' is enabled, but 'export hidden
3011 columns' is disabled.
3014 <!--JAL-2026-->Best Quality option in structure chooser
3015 selects lowest rather than highest resolution structures
3019 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3020 to sequence mapping in 'View Mappings' report
3023 <!-- JAL-2284 -->Unable to read old Jalview projects that
3024 contain non-XML data added after Jalvew wrote project.
3027 <!-- JAL-2118 -->Newly created annotation row reorders
3028 after clicking on it to create new annotation for a
3032 <!-- JAL-1980 -->Null Pointer Exception raised when
3033 pressing Add on an orphaned cut'n'paste window.
3035 <!-- may exclude, this is an external service stability issue JAL-1941
3036 -- > RNA 3D structure not added via DSSR service</li> -->
3041 <!-- JAL-2151 -->Incorrect columns are selected when
3042 hidden columns present before start of sequence
3045 <!-- JAL-1986 -->Missing dependencies on applet pages
3049 <!-- JAL-1947 -->Overview pixel size changes when
3050 sequences are hidden in applet
3053 <!-- JAL-1996 -->Updated instructions for applet
3054 deployment on examples pages.
3061 <td width="60" nowrap>
3062 <div align="center">
3063 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3064 <em>16/10/2015</em></strong>
3067 <td><em>General</em>
3069 <li>Time stamps for signed Jalview application and applet
3074 <em>Application</em>
3076 <li>Duplicate group consensus and conservation rows
3077 shown when tree is partitioned</li>
3078 <li>Erratic behaviour when tree partitions made with
3079 multiple cDNA/Protein split views</li>
3085 <td width="60" nowrap>
3086 <div align="center">
3087 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3088 <em>8/10/2015</em></strong>
3091 <td><em>General</em>
3093 <li>Updated Spanish translations of localized text for
3095 </ul> <em>Application</em>
3097 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3098 <li>Signed OSX InstallAnywhere installer<br></li>
3099 <li>Support for per-sequence based annotations in BioJSON</li>
3100 </ul> <em>Applet</em>
3102 <li>Split frame example added to applet examples page</li>
3103 </ul> <em>Build and Deployment</em>
3106 <!-- JAL-1888 -->New ant target for running Jalview's test
3114 <li>Mapping of cDNA to protein in split frames
3115 incorrect when sequence start > 1</li>
3116 <li>Broken images in filter column by annotation dialog
3118 <li>Feature colours not parsed from features file</li>
3119 <li>Exceptions and incomplete link URLs recovered when
3120 loading a features file containing HTML tags in feature
3124 <em>Application</em>
3126 <li>Annotations corrupted after BioJS export and
3128 <li>Incorrect sequence limits after Fetch DB References
3129 with 'trim retrieved sequences'</li>
3130 <li>Incorrect warning about deleting all data when
3131 deleting selected columns</li>
3132 <li>Patch to build system for shipping properly signed
3133 JNLP templates for webstart launch</li>
3134 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3135 unreleased structures for download or viewing</li>
3136 <li>Tab/space/return keystroke operation of EMBL-PDBe
3137 fetcher/viewer dialogs works correctly</li>
3138 <li>Disabled 'minimise' button on Jalview windows
3139 running on OSX to workaround redraw hang bug</li>
3140 <li>Split cDNA/Protein view position and geometry not
3141 recovered from jalview project</li>
3142 <li>Initial enabled/disabled state of annotation menu
3143 sorter 'show autocalculated first/last' corresponds to
3145 <li>Restoring of Clustal, RNA Helices and T-Coffee
3146 color schemes from BioJSON</li>
3150 <li>Reorder sequences mirrored in cDNA/Protein split
3152 <li>Applet with Jmol examples not loading correctly</li>
3158 <td><div align="center">
3159 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3161 <td><em>General</em>
3163 <li>Linked visualisation and analysis of DNA and Protein
3166 <li>Translated cDNA alignments shown as split protein
3167 and DNA alignment views</li>
3168 <li>Codon consensus annotation for linked protein and
3169 cDNA alignment views</li>
3170 <li>Link cDNA or Protein product sequences by loading
3171 them onto Protein or cDNA alignments</li>
3172 <li>Reconstruct linked cDNA alignment from aligned
3173 protein sequences</li>
3176 <li>Jmol integration updated to Jmol v14.2.14</li>
3177 <li>Import and export of Jalview alignment views as <a
3178 href="features/bioJsonFormat.html">BioJSON</a></li>
3179 <li>New alignment annotation file statements for
3180 reference sequences and marking hidden columns</li>
3181 <li>Reference sequence based alignment shading to
3182 highlight variation</li>
3183 <li>Select or hide columns according to alignment
3185 <li>Find option for locating sequences by description</li>
3186 <li>Conserved physicochemical properties shown in amino
3187 acid conservation row</li>
3188 <li>Alignments can be sorted by number of RNA helices</li>
3189 </ul> <em>Application</em>
3191 <li>New cDNA/Protein analysis capabilities
3193 <li>Get Cross-References should open a Split Frame
3194 view with cDNA/Protein</li>
3195 <li>Detect when nucleotide sequences and protein
3196 sequences are placed in the same alignment</li>
3197 <li>Split cDNA/Protein views are saved in Jalview
3202 <li>Use REST API to talk to Chimera</li>
3203 <li>Selected regions in Chimera are highlighted in linked
3204 Jalview windows</li>
3206 <li>VARNA RNA viewer updated to v3.93</li>
3207 <li>VARNA views are saved in Jalview Projects</li>
3208 <li>Pseudoknots displayed as Jalview RNA annotation can
3209 be shown in VARNA</li>
3211 <li>Make groups for selection uses marked columns as well
3212 as the active selected region</li>
3214 <li>Calculate UPGMA and NJ trees using sequence feature
3216 <li>New Export options
3218 <li>New Export Settings dialog to control hidden
3219 region export in flat file generation</li>
3221 <li>Export alignment views for display with the <a
3222 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3224 <li>Export scrollable SVG in HTML page</li>
3225 <li>Optional embedding of BioJSON data when exporting
3226 alignment figures to HTML</li>
3228 <li>3D structure retrieval and display
3230 <li>Free text and structured queries with the PDBe
3232 <li>PDBe Search API based discovery and selection of
3233 PDB structures for a sequence set</li>
3237 <li>JPred4 employed for protein secondary structure
3239 <li>Hide Insertions menu option to hide unaligned columns
3240 for one or a group of sequences</li>
3241 <li>Automatically hide insertions in alignments imported
3242 from the JPred4 web server</li>
3243 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3244 system on OSX<br />LGPL libraries courtesy of <a
3245 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3247 <li>changed 'View nucleotide structure' submenu to 'View
3248 VARNA 2D Structure'</li>
3249 <li>change "View protein structure" menu option to "3D
3252 </ul> <em>Applet</em>
3254 <li>New layout for applet example pages</li>
3255 <li>New parameters to enable SplitFrame view
3256 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3257 <li>New example demonstrating linked viewing of cDNA and
3258 Protein alignments</li>
3259 </ul> <em>Development and deployment</em>
3261 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3262 <li>Include installation type and git revision in build
3263 properties and console log output</li>
3264 <li>Jalview Github organisation, and new github site for
3265 storing BioJsMSA Templates</li>
3266 <li>Jalview's unit tests now managed with TestNG</li>
3269 <!-- <em>General</em>
3271 </ul> --> <!-- issues resolved --> <em>Application</em>
3273 <li>Escape should close any open find dialogs</li>
3274 <li>Typo in select-by-features status report</li>
3275 <li>Consensus RNA secondary secondary structure
3276 predictions are not highlighted in amber</li>
3277 <li>Missing gap character in v2.7 example file means
3278 alignment appears unaligned when pad-gaps is not enabled</li>
3279 <li>First switch to RNA Helices colouring doesn't colour
3280 associated structure views</li>
3281 <li>ID width preference option is greyed out when auto
3282 width checkbox not enabled</li>
3283 <li>Stopped a warning dialog from being shown when
3284 creating user defined colours</li>
3285 <li>'View Mapping' in structure viewer shows sequence
3286 mappings for just that viewer's sequences</li>
3287 <li>Workaround for superposing PDB files containing
3288 multiple models in Chimera</li>
3289 <li>Report sequence position in status bar when hovering
3290 over Jmol structure</li>
3291 <li>Cannot output gaps as '.' symbols with Selection ->
3292 output to text box</li>
3293 <li>Flat file exports of alignments with hidden columns
3294 have incorrect sequence start/end</li>
3295 <li>'Aligning' a second chain to a Chimera structure from
3297 <li>Colour schemes applied to structure viewers don't
3298 work for nucleotide</li>
3299 <li>Loading/cut'n'pasting an empty or invalid file leads
3300 to a grey/invisible alignment window</li>
3301 <li>Exported Jpred annotation from a sequence region
3302 imports to different position</li>
3303 <li>Space at beginning of sequence feature tooltips shown
3304 on some platforms</li>
3305 <li>Chimera viewer 'View | Show Chain' menu is not
3307 <li>'New View' fails with a Null Pointer Exception in
3308 console if Chimera has been opened</li>
3309 <li>Mouseover to Chimera not working</li>
3310 <li>Miscellaneous ENA XML feature qualifiers not
3312 <li>NPE in annotation renderer after 'Extract Scores'</li>
3313 <li>If two structures in one Chimera window, mouseover of
3314 either sequence shows on first structure</li>
3315 <li>'Show annotations' options should not make
3316 non-positional annotations visible</li>
3317 <li>Subsequence secondary structure annotation not shown
3318 in right place after 'view flanking regions'</li>
3319 <li>File Save As type unset when current file format is
3321 <li>Save as '.jar' option removed for saving Jalview
3323 <li>Colour by Sequence colouring in Chimera more
3325 <li>Cannot 'add reference annotation' for a sequence in
3326 several views on same alignment</li>
3327 <li>Cannot show linked products for EMBL / ENA records</li>
3328 <li>Jalview's tooltip wraps long texts containing no
3330 </ul> <em>Applet</em>
3332 <li>Jmol to JalviewLite mouseover/link not working</li>
3333 <li>JalviewLite can't import sequences with ID
3334 descriptions containing angle brackets</li>
3335 </ul> <em>General</em>
3337 <li>Cannot export and reimport RNA secondary structure
3338 via jalview annotation file</li>
3339 <li>Random helix colour palette for colour by annotation
3340 with RNA secondary structure</li>
3341 <li>Mouseover to cDNA from STOP residue in protein
3342 translation doesn't work.</li>
3343 <li>hints when using the select by annotation dialog box</li>
3344 <li>Jmol alignment incorrect if PDB file has alternate CA
3346 <li>FontChooser message dialog appears to hang after
3347 choosing 1pt font</li>
3348 <li>Peptide secondary structure incorrectly imported from
3349 annotation file when annotation display text includes 'e' or
3351 <li>Cannot set colour of new feature type whilst creating
3353 <li>cDNA translation alignment should not be sequence
3354 order dependent</li>
3355 <li>'Show unconserved' doesn't work for lower case
3357 <li>Nucleotide ambiguity codes involving R not recognised</li>
3358 </ul> <em>Deployment and Documentation</em>
3360 <li>Applet example pages appear different to the rest of
3361 www.jalview.org</li>
3362 </ul> <em>Application Known issues</em>
3364 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3365 <li>Misleading message appears after trying to delete
3367 <li>Jalview icon not shown in dock after InstallAnywhere
3368 version launches</li>
3369 <li>Fetching EMBL reference for an RNA sequence results
3370 fails with a sequence mismatch</li>
3371 <li>Corrupted or unreadable alignment display when
3372 scrolling alignment to right</li>
3373 <li>ArrayIndexOutOfBoundsException thrown when remove
3374 empty columns called on alignment with ragged gapped ends</li>
3375 <li>auto calculated alignment annotation rows do not get
3376 placed above or below non-autocalculated rows</li>
3377 <li>Jalview dekstop becomes sluggish at full screen in
3378 ultra-high resolution</li>
3379 <li>Cannot disable consensus calculation independently of
3380 quality and conservation</li>
3381 <li>Mouseover highlighting between cDNA and protein can
3382 become sluggish with more than one splitframe shown</li>
3383 </ul> <em>Applet Known Issues</em>
3385 <li>Core PDB parsing code requires Jmol</li>
3386 <li>Sequence canvas panel goes white when alignment
3387 window is being resized</li>
3393 <td><div align="center">
3394 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3396 <td><em>General</em>
3398 <li>Updated Java code signing certificate donated by
3400 <li>Features and annotation preserved when performing
3401 pairwise alignment</li>
3402 <li>RNA pseudoknot annotation can be
3403 imported/exported/displayed</li>
3404 <li>'colour by annotation' can colour by RNA and
3405 protein secondary structure</li>
3406 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3407 post-hoc with 2.9 release</em>)
3410 </ul> <em>Application</em>
3412 <li>Extract and display secondary structure for sequences
3413 with 3D structures</li>
3414 <li>Support for parsing RNAML</li>
3415 <li>Annotations menu for layout
3417 <li>sort sequence annotation rows by alignment</li>
3418 <li>place sequence annotation above/below alignment
3421 <li>Output in Stockholm format</li>
3422 <li>Internationalisation: improved Spanish (es)
3424 <li>Structure viewer preferences tab</li>
3425 <li>Disorder and Secondary Structure annotation tracks
3426 shared between alignments</li>
3427 <li>UCSF Chimera launch and linked highlighting from
3429 <li>Show/hide all sequence associated annotation rows for
3430 all or current selection</li>
3431 <li>disorder and secondary structure predictions
3432 available as dataset annotation</li>
3433 <li>Per-sequence rna helices colouring</li>
3436 <li>Sequence database accessions imported when fetching
3437 alignments from Rfam</li>
3438 <li>update VARNA version to 3.91</li>
3440 <li>New groovy scripts for exporting aligned positions,
3441 conservation values, and calculating sum of pairs scores.</li>
3442 <li>Command line argument to set default JABAWS server</li>
3443 <li>include installation type in build properties and
3444 console log output</li>
3445 <li>Updated Jalview project format to preserve dataset
3449 <!-- issues resolved --> <em>Application</em>
3451 <li>Distinguish alignment and sequence associated RNA
3452 structure in structure->view->VARNA</li>
3453 <li>Raise dialog box if user deletes all sequences in an
3455 <li>Pressing F1 results in documentation opening twice</li>
3456 <li>Sequence feature tooltip is wrapped</li>
3457 <li>Double click on sequence associated annotation
3458 selects only first column</li>
3459 <li>Redundancy removal doesn't result in unlinked
3460 leaves shown in tree</li>
3461 <li>Undos after several redundancy removals don't undo
3463 <li>Hide sequence doesn't hide associated annotation</li>
3464 <li>User defined colours dialog box too big to fit on
3465 screen and buttons not visible</li>
3466 <li>author list isn't updated if already written to
3467 Jalview properties</li>
3468 <li>Popup menu won't open after retrieving sequence
3470 <li>File open window for associate PDB doesn't open</li>
3471 <li>Left-then-right click on a sequence id opens a
3472 browser search window</li>
3473 <li>Cannot open sequence feature shading/sort popup menu
3474 in feature settings dialog</li>
3475 <li>better tooltip placement for some areas of Jalview
3477 <li>Allow addition of JABAWS Server which doesn't
3478 pass validation</li>
3479 <li>Web services parameters dialog box is too large to
3481 <li>Muscle nucleotide alignment preset obscured by
3483 <li>JABAWS preset submenus don't contain newly
3484 defined user preset</li>
3485 <li>MSA web services warns user if they were launched
3486 with invalid input</li>
3487 <li>Jalview cannot contact DAS Registy when running on
3490 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3491 'Superpose with' submenu not shown when new view
3495 </ul> <!-- <em>Applet</em>
3497 </ul> <em>General</em>
3499 </ul>--> <em>Deployment and Documentation</em>
3501 <li>2G and 1G options in launchApp have no effect on
3502 memory allocation</li>
3503 <li>launchApp service doesn't automatically open
3504 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3506 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3507 InstallAnywhere reports cannot find valid JVM when Java
3508 1.7_055 is available
3510 </ul> <em>Application Known issues</em>
3513 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3514 corrupted or unreadable alignment display when scrolling
3518 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3519 retrieval fails but progress bar continues for DAS retrieval
3520 with large number of ID
3523 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3524 flatfile output of visible region has incorrect sequence
3528 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3529 rna structure consensus doesn't update when secondary
3530 structure tracks are rearranged
3533 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3534 invalid rna structure positional highlighting does not
3535 highlight position of invalid base pairs
3538 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3539 out of memory errors are not raised when saving Jalview
3540 project from alignment window file menu
3543 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3544 Switching to RNA Helices colouring doesn't propagate to
3548 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3549 colour by RNA Helices not enabled when user created
3550 annotation added to alignment
3553 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3554 Jalview icon not shown on dock in Mountain Lion/Webstart
3556 </ul> <em>Applet Known Issues</em>
3559 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3560 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3563 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3564 Jalview and Jmol example not compatible with IE9
3567 <li>Sort by annotation score doesn't reverse order
3573 <td><div align="center">
3574 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3577 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3580 <li>Internationalisation of user interface (usually
3581 called i18n support) and translation for Spanish locale</li>
3582 <li>Define/Undefine group on current selection with
3583 Ctrl-G/Shift Ctrl-G</li>
3584 <li>Improved group creation/removal options in
3585 alignment/sequence Popup menu</li>
3586 <li>Sensible precision for symbol distribution
3587 percentages shown in logo tooltip.</li>
3588 <li>Annotation panel height set according to amount of
3589 annotation when alignment first opened</li>
3590 </ul> <em>Application</em>
3592 <li>Interactive consensus RNA secondary structure
3593 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3594 <li>Select columns containing particular features from
3595 Feature Settings dialog</li>
3596 <li>View all 'representative' PDB structures for selected
3598 <li>Update Jalview project format:
3600 <li>New file extension for Jalview projects '.jvp'</li>
3601 <li>Preserve sequence and annotation dataset (to
3602 store secondary structure annotation,etc)</li>
3603 <li>Per group and alignment annotation and RNA helix
3607 <li>New similarity measures for PCA and Tree calculation
3609 <li>Experimental support for retrieval and viewing of
3610 flanking regions for an alignment</li>
3614 <!-- issues resolved --> <em>Application</em>
3616 <li>logo keeps spinning and status remains at queued or
3617 running after job is cancelled</li>
3618 <li>cannot export features from alignments imported from
3619 Jalview/VAMSAS projects</li>
3620 <li>Buggy slider for web service parameters that take
3622 <li>Newly created RNA secondary structure line doesn't
3623 have 'display all symbols' flag set</li>
3624 <li>T-COFFEE alignment score shading scheme and other
3625 annotation shading not saved in Jalview project</li>
3626 <li>Local file cannot be loaded in freshly downloaded
3628 <li>Jalview icon not shown on dock in Mountain
3630 <li>Load file from desktop file browser fails</li>
3631 <li>Occasional NPE thrown when calculating large trees</li>
3632 <li>Cannot reorder or slide sequences after dragging an
3633 alignment onto desktop</li>
3634 <li>Colour by annotation dialog throws NPE after using
3635 'extract scores' function</li>
3636 <li>Loading/cut'n'pasting an empty file leads to a grey
3637 alignment window</li>
3638 <li>Disorder thresholds rendered incorrectly after
3639 performing IUPred disorder prediction</li>
3640 <li>Multiple group annotated consensus rows shown when
3641 changing 'normalise logo' display setting</li>
3642 <li>Find shows blank dialog after 'finished searching' if
3643 nothing matches query</li>
3644 <li>Null Pointer Exceptions raised when sorting by
3645 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3647 <li>Errors in Jmol console when structures in alignment
3648 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3650 <li>Not all working JABAWS services are shown in
3652 <li>JAVAWS version of Jalview fails to launch with
3653 'invalid literal/length code'</li>
3654 <li>Annotation/RNA Helix colourschemes cannot be applied
3655 to alignment with groups (actually fixed in 2.8.0b1)</li>
3656 <li>RNA Helices and T-Coffee Scores available as default
3659 </ul> <em>Applet</em>
3661 <li>Remove group option is shown even when selection is
3663 <li>Apply to all groups ticked but colourscheme changes
3664 don't affect groups</li>
3665 <li>Documented RNA Helices and T-Coffee Scores as valid
3666 colourscheme name</li>
3667 <li>Annotation labels drawn on sequence IDs when
3668 Annotation panel is not displayed</li>
3669 <li>Increased font size for dropdown menus on OSX and
3670 embedded windows</li>
3671 </ul> <em>Other</em>
3673 <li>Consensus sequence for alignments/groups with a
3674 single sequence were not calculated</li>
3675 <li>annotation files that contain only groups imported as
3676 annotation and junk sequences</li>
3677 <li>Fasta files with sequences containing '*' incorrectly
3678 recognised as PFAM or BLC</li>
3679 <li>conservation/PID slider apply all groups option
3680 doesn't affect background (2.8.0b1)
3682 <li>redundancy highlighting is erratic at 0% and 100%</li>
3683 <li>Remove gapped columns fails for sequences with ragged
3685 <li>AMSA annotation row with leading spaces is not
3686 registered correctly on import</li>
3687 <li>Jalview crashes when selecting PCA analysis for
3688 certain alignments</li>
3689 <li>Opening the colour by annotation dialog for an
3690 existing annotation based 'use original colours'
3691 colourscheme loses original colours setting</li>
3696 <td><div align="center">
3697 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3698 <em>30/1/2014</em></strong>
3702 <li>Trusted certificates for JalviewLite applet and
3703 Jalview Desktop application<br />Certificate was donated by
3704 <a href="https://www.certum.eu">Certum</a> to the Jalview
3705 open source project).
3707 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3708 <li>Output in Stockholm format</li>
3709 <li>Allow import of data from gzipped files</li>
3710 <li>Export/import group and sequence associated line
3711 graph thresholds</li>
3712 <li>Nucleotide substitution matrix that supports RNA and
3713 ambiguity codes</li>
3714 <li>Allow disorder predictions to be made on the current
3715 selection (or visible selection) in the same way that JPred
3717 <li>Groovy scripting for headless Jalview operation</li>
3718 </ul> <em>Other improvements</em>
3720 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3721 <li>COMBINE statement uses current SEQUENCE_REF and
3722 GROUP_REF scope to group annotation rows</li>
3723 <li>Support '' style escaping of quotes in Newick
3725 <li>Group options for JABAWS service by command line name</li>
3726 <li>Empty tooltip shown for JABA service options with a
3727 link but no description</li>
3728 <li>Select primary source when selecting authority in
3729 database fetcher GUI</li>
3730 <li>Add .mfa to FASTA file extensions recognised by
3732 <li>Annotation label tooltip text wrap</li>
3737 <li>Slow scrolling when lots of annotation rows are
3739 <li>Lots of NPE (and slowness) after creating RNA
3740 secondary structure annotation line</li>
3741 <li>Sequence database accessions not imported when
3742 fetching alignments from Rfam</li>
3743 <li>Incorrect SHMR submission for sequences with
3745 <li>View all structures does not always superpose
3747 <li>Option widgets in service parameters not updated to
3748 reflect user or preset settings</li>
3749 <li>Null pointer exceptions for some services without
3750 presets or adjustable parameters</li>
3751 <li>Discover PDB IDs entry in structure menu doesn't
3752 discover PDB xRefs</li>
3753 <li>Exception encountered while trying to retrieve
3754 features with DAS</li>
3755 <li>Lowest value in annotation row isn't coloured
3756 when colour by annotation (per sequence) is coloured</li>
3757 <li>Keyboard mode P jumps to start of gapped region when
3758 residue follows a gap</li>
3759 <li>Jalview appears to hang importing an alignment with
3760 Wrap as default or after enabling Wrap</li>
3761 <li>'Right click to add annotations' message
3762 shown in wrap mode when no annotations present</li>
3763 <li>Disorder predictions fail with NPE if no automatic
3764 annotation already exists on alignment</li>
3765 <li>oninit javascript function should be called after
3766 initialisation completes</li>
3767 <li>Remove redundancy after disorder prediction corrupts
3768 alignment window display</li>
3769 <li>Example annotation file in documentation is invalid</li>
3770 <li>Grouped line graph annotation rows are not exported
3771 to annotation file</li>
3772 <li>Multi-harmony analysis cannot be run when only two
3774 <li>Cannot create multiple groups of line graphs with
3775 several 'combine' statements in annotation file</li>
3776 <li>Pressing return several times causes Number Format
3777 exceptions in keyboard mode</li>
3778 <li>Multi-harmony (SHMMR) method doesn't submit
3779 correct partitions for input data</li>
3780 <li>Translation from DNA to Amino Acids fails</li>
3781 <li>Jalview fail to load newick tree with quoted label</li>
3782 <li>--headless flag isn't understood</li>
3783 <li>ClassCastException when generating EPS in headless
3785 <li>Adjusting sequence-associated shading threshold only
3786 changes one row's threshold</li>
3787 <li>Preferences and Feature settings panel panel
3788 doesn't open</li>
3789 <li>hide consensus histogram also hides conservation and
3790 quality histograms</li>
3795 <td><div align="center">
3796 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3798 <td><em>Application</em>
3800 <li>Support for JABAWS 2.0 Services (AACon alignment
3801 conservation, protein disorder and Clustal Omega)</li>
3802 <li>JABAWS server status indicator in Web Services
3804 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3805 in Jalview alignment window</li>
3806 <li>Updated Jalview build and deploy framework for OSX
3807 mountain lion, windows 7, and 8</li>
3808 <li>Nucleotide substitution matrix for PCA that supports
3809 RNA and ambiguity codes</li>
3811 <li>Improved sequence database retrieval GUI</li>
3812 <li>Support fetching and database reference look up
3813 against multiple DAS sources (Fetch all from in 'fetch db
3815 <li>Jalview project improvements
3817 <li>Store and retrieve the 'belowAlignment'
3818 flag for annotation</li>
3819 <li>calcId attribute to group annotation rows on the
3821 <li>Store AACon calculation settings for a view in
3822 Jalview project</li>
3826 <li>horizontal scrolling gesture support</li>
3827 <li>Visual progress indicator when PCA calculation is
3829 <li>Simpler JABA web services menus</li>
3830 <li>visual indication that web service results are still
3831 being retrieved from server</li>
3832 <li>Serialise the dialogs that are shown when Jalview
3833 starts up for first time</li>
3834 <li>Jalview user agent string for interacting with HTTP
3836 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3838 <li>Examples directory and Groovy library included in
3839 InstallAnywhere distribution</li>
3840 </ul> <em>Applet</em>
3842 <li>RNA alignment and secondary structure annotation
3843 visualization applet example</li>
3844 </ul> <em>General</em>
3846 <li>Normalise option for consensus sequence logo</li>
3847 <li>Reset button in PCA window to return dimensions to
3849 <li>Allow seqspace or Jalview variant of alignment PCA
3851 <li>PCA with either nucleic acid and protein substitution
3853 <li>Allow windows containing HTML reports to be exported
3855 <li>Interactive display and editing of RNA secondary
3856 structure contacts</li>
3857 <li>RNA Helix Alignment Colouring</li>
3858 <li>RNA base pair logo consensus</li>
3859 <li>Parse sequence associated secondary structure
3860 information in Stockholm files</li>
3861 <li>HTML Export database accessions and annotation
3862 information presented in tooltip for sequences</li>
3863 <li>Import secondary structure from LOCARNA clustalw
3864 style RNA alignment files</li>
3865 <li>import and visualise T-COFFEE quality scores for an
3867 <li>'colour by annotation' per sequence option to
3868 shade each sequence according to its associated alignment
3870 <li>New Jalview Logo</li>
3871 </ul> <em>Documentation and Development</em>
3873 <li>documentation for score matrices used in Jalview</li>
3874 <li>New Website!</li>
3876 <td><em>Application</em>
3878 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3879 wsdbfetch REST service</li>
3880 <li>Stop windows being moved outside desktop on OSX</li>
3881 <li>Filetype associations not installed for webstart
3883 <li>Jalview does not always retrieve progress of a JABAWS
3884 job execution in full once it is complete</li>
3885 <li>revise SHMR RSBS definition to ensure alignment is
3886 uploaded via ali_file parameter</li>
3887 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3888 <li>View all structures superposed fails with exception</li>
3889 <li>Jnet job queues forever if a very short sequence is
3890 submitted for prediction</li>
3891 <li>Cut and paste menu not opened when mouse clicked on
3893 <li>Putting fractional value into integer text box in
3894 alignment parameter dialog causes Jalview to hang</li>
3895 <li>Structure view highlighting doesn't work on
3897 <li>View all structures fails with exception shown in
3899 <li>Characters in filename associated with PDBEntry not
3900 escaped in a platform independent way</li>
3901 <li>Jalview desktop fails to launch with exception when
3903 <li>Tree calculation reports 'you must have 2 or more
3904 sequences selected' when selection is empty</li>
3905 <li>Jalview desktop fails to launch with jar signature
3906 failure when java web start temporary file caching is
3908 <li>DAS Sequence retrieval with range qualification
3909 results in sequence xref which includes range qualification</li>
3910 <li>Errors during processing of command line arguments
3911 cause progress bar (JAL-898) to be removed</li>
3912 <li>Replace comma for semi-colon option not disabled for
3913 DAS sources in sequence fetcher</li>
3914 <li>Cannot close news reader when JABAWS server warning
3915 dialog is shown</li>
3916 <li>Option widgets not updated to reflect user settings</li>
3917 <li>Edited sequence not submitted to web service</li>
3918 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3919 <li>InstallAnywhere installer doesn't unpack and run
3920 on OSX Mountain Lion</li>
3921 <li>Annotation panel not given a scroll bar when
3922 sequences with alignment annotation are pasted into the
3924 <li>Sequence associated annotation rows not associated
3925 when loaded from Jalview project</li>
3926 <li>Browser launch fails with NPE on java 1.7</li>
3927 <li>JABAWS alignment marked as finished when job was
3928 cancelled or job failed due to invalid input</li>
3929 <li>NPE with v2.7 example when clicking on Tree
3930 associated with all views</li>
3931 <li>Exceptions when copy/paste sequences with grouped
3932 annotation rows to new window</li>
3933 </ul> <em>Applet</em>
3935 <li>Sequence features are momentarily displayed before
3936 they are hidden using hidefeaturegroups applet parameter</li>
3937 <li>loading features via javascript API automatically
3938 enables feature display</li>
3939 <li>scrollToColumnIn javascript API method doesn't
3941 </ul> <em>General</em>
3943 <li>Redundancy removal fails for rna alignment</li>
3944 <li>PCA calculation fails when sequence has been selected
3945 and then deselected</li>
3946 <li>PCA window shows grey box when first opened on OSX</li>
3947 <li>Letters coloured pink in sequence logo when alignment
3948 coloured with clustalx</li>
3949 <li>Choosing fonts without letter symbols defined causes
3950 exceptions and redraw errors</li>
3951 <li>Initial PCA plot view is not same as manually
3952 reconfigured view</li>
3953 <li>Grouped annotation graph label has incorrect line
3955 <li>Grouped annotation graph label display is corrupted
3956 for lots of labels</li>
3961 <div align="center">
3962 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3965 <td><em>Application</em>
3967 <li>Jalview Desktop News Reader</li>
3968 <li>Tweaked default layout of web services menu</li>
3969 <li>View/alignment association menu to enable user to
3970 easily specify which alignment a multi-structure view takes
3971 its colours/correspondences from</li>
3972 <li>Allow properties file location to be specified as URL</li>
3973 <li>Extend Jalview project to preserve associations
3974 between many alignment views and a single Jmol display</li>
3975 <li>Store annotation row height in Jalview project file</li>
3976 <li>Annotation row column label formatting attributes
3977 stored in project file</li>
3978 <li>Annotation row order for auto-calculated annotation
3979 rows preserved in Jalview project file</li>
3980 <li>Visual progress indication when Jalview state is
3981 saved using Desktop window menu</li>
3982 <li>Visual indication that command line arguments are
3983 still being processed</li>
3984 <li>Groovy script execution from URL</li>
3985 <li>Colour by annotation default min and max colours in
3987 <li>Automatically associate PDB files dragged onto an
3988 alignment with sequences that have high similarity and
3990 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3991 <li>'view structures' option to open many
3992 structures in same window</li>
3993 <li>Sort associated views menu option for tree panel</li>
3994 <li>Group all JABA and non-JABA services for a particular
3995 analysis function in its own submenu</li>
3996 </ul> <em>Applet</em>
3998 <li>Userdefined and autogenerated annotation rows for
4000 <li>Adjustment of alignment annotation pane height</li>
4001 <li>Annotation scrollbar for annotation panel</li>
4002 <li>Drag to reorder annotation rows in annotation panel</li>
4003 <li>'automaticScrolling' parameter</li>
4004 <li>Allow sequences with partial ID string matches to be
4005 annotated from GFF/Jalview features files</li>
4006 <li>Sequence logo annotation row in applet</li>
4007 <li>Absolute paths relative to host server in applet
4008 parameters are treated as such</li>
4009 <li>New in the JalviewLite javascript API:
4011 <li>JalviewLite.js javascript library</li>
4012 <li>Javascript callbacks for
4014 <li>Applet initialisation</li>
4015 <li>Sequence/alignment mouse-overs and selections</li>
4018 <li>scrollTo row and column alignment scrolling
4020 <li>Select sequence/alignment regions from javascript</li>
4021 <li>javascript structure viewer harness to pass
4022 messages between Jmol and Jalview when running as
4023 distinct applets</li>
4024 <li>sortBy method</li>
4025 <li>Set of applet and application examples shipped
4026 with documentation</li>
4027 <li>New example to demonstrate JalviewLite and Jmol
4028 javascript message exchange</li>
4030 </ul> <em>General</em>
4032 <li>Enable Jmol displays to be associated with multiple
4033 multiple alignments</li>
4034 <li>Option to automatically sort alignment with new tree</li>
4035 <li>User configurable link to enable redirects to a
4036 www.Jalview.org mirror</li>
4037 <li>Jmol colours option for Jmol displays</li>
4038 <li>Configurable newline string when writing alignment
4039 and other flat files</li>
4040 <li>Allow alignment annotation description lines to
4041 contain html tags</li>
4042 </ul> <em>Documentation and Development</em>
4044 <li>Add groovy test harness for bulk load testing to
4046 <li>Groovy script to load and align a set of sequences
4047 using a web service before displaying the result in the
4048 Jalview desktop</li>
4049 <li>Restructured javascript and applet api documentation</li>
4050 <li>Ant target to publish example html files with applet
4052 <li>Netbeans project for building Jalview from source</li>
4053 <li>ant task to create online javadoc for Jalview source</li>
4055 <td><em>Application</em>
4057 <li>User defined colourscheme throws exception when
4058 current built in colourscheme is saved as new scheme</li>
4059 <li>AlignFrame->Save in application pops up save
4060 dialog for valid filename/format</li>
4061 <li>Cannot view associated structure for UniProt sequence</li>
4062 <li>PDB file association breaks for UniProt sequence
4064 <li>Associate PDB from file dialog does not tell you
4065 which sequence is to be associated with the file</li>
4066 <li>Find All raises null pointer exception when query
4067 only matches sequence IDs</li>
4068 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4069 <li>Jalview project with Jmol views created with Jalview
4070 2.4 cannot be loaded</li>
4071 <li>Filetype associations not installed for webstart
4073 <li>Two or more chains in a single PDB file associated
4074 with sequences in different alignments do not get coloured
4075 by their associated sequence</li>
4076 <li>Visibility status of autocalculated annotation row
4077 not preserved when project is loaded</li>
4078 <li>Annotation row height and visibility attributes not
4079 stored in Jalview project</li>
4080 <li>Tree bootstraps are not preserved when saved as a
4081 Jalview project</li>
4082 <li>Envision2 workflow tooltips are corrupted</li>
4083 <li>Enabling show group conservation also enables colour
4084 by conservation</li>
4085 <li>Duplicate group associated conservation or consensus
4086 created on new view</li>
4087 <li>Annotation scrollbar not displayed after 'show
4088 all hidden annotation rows' option selected</li>
4089 <li>Alignment quality not updated after alignment
4090 annotation row is hidden then shown</li>
4091 <li>Preserve colouring of structures coloured by
4092 sequences in pre Jalview 2.7 projects</li>
4093 <li>Web service job parameter dialog is not laid out
4095 <li>Web services menu not refreshed after 'reset
4096 services' button is pressed in preferences</li>
4097 <li>Annotation off by one in Jalview v2_3 example project</li>
4098 <li>Structures imported from file and saved in project
4099 get name like jalview_pdb1234.txt when reloaded</li>
4100 <li>Jalview does not always retrieve progress of a JABAWS
4101 job execution in full once it is complete</li>
4102 </ul> <em>Applet</em>
4104 <li>Alignment height set incorrectly when lots of
4105 annotation rows are displayed</li>
4106 <li>Relative URLs in feature HTML text not resolved to
4108 <li>View follows highlighting does not work for positions
4110 <li><= shown as = in tooltip</li>
4111 <li>Export features raises exception when no features
4113 <li>Separator string used for serialising lists of IDs
4114 for javascript api is modified when separator string
4115 provided as parameter</li>
4116 <li>Null pointer exception when selecting tree leaves for
4117 alignment with no existing selection</li>
4118 <li>Relative URLs for datasources assumed to be relative
4119 to applet's codebase</li>
4120 <li>Status bar not updated after finished searching and
4121 search wraps around to first result</li>
4122 <li>StructureSelectionManager instance shared between
4123 several Jalview applets causes race conditions and memory
4125 <li>Hover tooltip and mouseover of position on structure
4126 not sent from Jmol in applet</li>
4127 <li>Certain sequences of javascript method calls to
4128 applet API fatally hang browser</li>
4129 </ul> <em>General</em>
4131 <li>View follows structure mouseover scrolls beyond
4132 position with wrapped view and hidden regions</li>
4133 <li>Find sequence position moves to wrong residue
4134 with/without hidden columns</li>
4135 <li>Sequence length given in alignment properties window
4137 <li>InvalidNumberFormat exceptions thrown when trying to
4138 import PDB like structure files</li>
4139 <li>Positional search results are only highlighted
4140 between user-supplied sequence start/end bounds</li>
4141 <li>End attribute of sequence is not validated</li>
4142 <li>Find dialog only finds first sequence containing a
4143 given sequence position</li>
4144 <li>Sequence numbering not preserved in MSF alignment
4146 <li>Jalview PDB file reader does not extract sequence
4147 from nucleotide chains correctly</li>
4148 <li>Structure colours not updated when tree partition
4149 changed in alignment</li>
4150 <li>Sequence associated secondary structure not correctly
4151 parsed in interleaved stockholm</li>
4152 <li>Colour by annotation dialog does not restore current
4154 <li>Hiding (nearly) all sequences doesn't work
4156 <li>Sequences containing lowercase letters are not
4157 properly associated with their pdb files</li>
4158 </ul> <em>Documentation and Development</em>
4160 <li>schemas/JalviewWsParamSet.xsd corrupted by
4161 ApplyCopyright tool</li>
4166 <div align="center">
4167 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4170 <td><em>Application</em>
4172 <li>New warning dialog when the Jalview Desktop cannot
4173 contact web services</li>
4174 <li>JABA service parameters for a preset are shown in
4175 service job window</li>
4176 <li>JABA Service menu entries reworded</li>
4180 <li>Modeller PIR IO broken - cannot correctly import a
4181 pir file emitted by Jalview</li>
4182 <li>Existing feature settings transferred to new
4183 alignment view created from cut'n'paste</li>
4184 <li>Improved test for mixed amino/nucleotide chains when
4185 parsing PDB files</li>
4186 <li>Consensus and conservation annotation rows
4187 occasionally become blank for all new windows</li>
4188 <li>Exception raised when right clicking above sequences
4189 in wrapped view mode</li>
4190 </ul> <em>Application</em>
4192 <li>multiple multiply aligned structure views cause cpu
4193 usage to hit 100% and computer to hang</li>
4194 <li>Web Service parameter layout breaks for long user
4195 parameter names</li>
4196 <li>Jaba service discovery hangs desktop if Jaba server
4203 <div align="center">
4204 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4207 <td><em>Application</em>
4209 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4210 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4213 <li>Web Services preference tab</li>
4214 <li>Analysis parameters dialog box and user defined
4216 <li>Improved speed and layout of Envision2 service menu</li>
4217 <li>Superpose structures using associated sequence
4219 <li>Export coordinates and projection as CSV from PCA
4221 </ul> <em>Applet</em>
4223 <li>enable javascript: execution by the applet via the
4224 link out mechanism</li>
4225 </ul> <em>Other</em>
4227 <li>Updated the Jmol Jalview interface to work with Jmol
4229 <li>The Jalview Desktop and JalviewLite applet now
4230 require Java 1.5</li>
4231 <li>Allow Jalview feature colour specification for GFF
4232 sequence annotation files</li>
4233 <li>New 'colour by label' keword in Jalview feature file
4234 type colour specification</li>
4235 <li>New Jalview Desktop Groovy API method that allows a
4236 script to check if it being run in an interactive session or
4237 in a batch operation from the Jalview command line</li>
4241 <li>clustalx colourscheme colours Ds preferentially when
4242 both D+E are present in over 50% of the column</li>
4243 </ul> <em>Application</em>
4245 <li>typo in AlignmentFrame->View->Hide->all but
4246 selected Regions menu item</li>
4247 <li>sequence fetcher replaces ',' for ';' when the ',' is
4248 part of a valid accession ID</li>
4249 <li>fatal OOM if object retrieved by sequence fetcher
4250 runs out of memory</li>
4251 <li>unhandled Out of Memory Error when viewing pca
4252 analysis results</li>
4253 <li>InstallAnywhere builds fail to launch on OS X java
4254 10.5 update 4 (due to apple Java 1.6 update)</li>
4255 <li>Installanywhere Jalview silently fails to launch</li>
4256 </ul> <em>Applet</em>
4258 <li>Jalview.getFeatureGroups() raises an
4259 ArrayIndexOutOfBoundsException if no feature groups are
4266 <div align="center">
4267 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4273 <li>Alignment prettyprinter doesn't cope with long
4275 <li>clustalx colourscheme colours Ds preferentially when
4276 both D+E are present in over 50% of the column</li>
4277 <li>nucleic acid structures retrieved from PDB do not
4278 import correctly</li>
4279 <li>More columns get selected than were clicked on when a
4280 number of columns are hidden</li>
4281 <li>annotation label popup menu not providing correct
4282 add/hide/show options when rows are hidden or none are
4284 <li>Stockholm format shown in list of readable formats,
4285 and parser copes better with alignments from RFAM.</li>
4286 <li>CSV output of consensus only includes the percentage
4287 of all symbols if sequence logo display is enabled</li>
4289 </ul> <em>Applet</em>
4291 <li>annotation panel disappears when annotation is
4293 </ul> <em>Application</em>
4295 <li>Alignment view not redrawn properly when new
4296 alignment opened where annotation panel is visible but no
4297 annotations are present on alignment</li>
4298 <li>pasted region containing hidden columns is
4299 incorrectly displayed in new alignment window</li>
4300 <li>Jalview slow to complete operations when stdout is
4301 flooded (fix is to close the Jalview console)</li>
4302 <li>typo in AlignmentFrame->View->Hide->all but
4303 selected Rregions menu item.</li>
4304 <li>inconsistent group submenu and Format submenu entry
4305 'Un' or 'Non'conserved</li>
4306 <li>Sequence feature settings are being shared by
4307 multiple distinct alignments</li>
4308 <li>group annotation not recreated when tree partition is
4310 <li>double click on group annotation to select sequences
4311 does not propagate to associated trees</li>
4312 <li>Mac OSX specific issues:
4314 <li>exception raised when mouse clicked on desktop
4315 window background</li>
4316 <li>Desktop menu placed on menu bar and application
4317 name set correctly</li>
4318 <li>sequence feature settings not wide enough for the
4319 save feature colourscheme button</li>
4328 <div align="center">
4329 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4332 <td><em>New Capabilities</em>
4334 <li>URL links generated from description line for
4335 regular-expression based URL links (applet and application)
4337 <li>Non-positional feature URL links are shown in link
4339 <li>Linked viewing of nucleic acid sequences and
4341 <li>Automatic Scrolling option in View menu to display
4342 the currently highlighted region of an alignment.</li>
4343 <li>Order an alignment by sequence length, or using the
4344 average score or total feature count for each sequence.</li>
4345 <li>Shading features by score or associated description</li>
4346 <li>Subdivide alignment and groups based on identity of
4347 selected subsequence (Make Groups from Selection).</li>
4348 <li>New hide/show options including Shift+Control+H to
4349 hide everything but the currently selected region.</li>
4350 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4351 </ul> <em>Application</em>
4353 <li>Fetch DB References capabilities and UI expanded to
4354 support retrieval from DAS sequence sources</li>
4355 <li>Local DAS Sequence sources can be added via the
4356 command line or via the Add local source dialog box.</li>
4357 <li>DAS Dbref and DbxRef feature types are parsed as
4358 database references and protein_name is parsed as
4359 description line (BioSapiens terms).</li>
4360 <li>Enable or disable non-positional feature and database
4361 references in sequence ID tooltip from View menu in
4363 <!-- <li>New hidden columns and rows and representatives capabilities
4364 in annotations file (in progress - not yet fully implemented)</li> -->
4365 <li>Group-associated consensus, sequence logos and
4366 conservation plots</li>
4367 <li>Symbol distributions for each column can be exported
4368 and visualized as sequence logos</li>
4369 <li>Optionally scale multi-character column labels to fit
4370 within each column of annotation row<!-- todo for applet -->
4372 <li>Optional automatic sort of associated alignment view
4373 when a new tree is opened.</li>
4374 <li>Jalview Java Console</li>
4375 <li>Better placement of desktop window when moving
4376 between different screens.</li>
4377 <li>New preference items for sequence ID tooltip and
4378 consensus annotation</li>
4379 <li>Client to submit sequences and IDs to Envision2
4381 <li><em>Vamsas Capabilities</em>
4383 <li>Improved VAMSAS synchronization (Jalview archive
4384 used to preserve views, structures, and tree display
4386 <li>Import of vamsas documents from disk or URL via
4388 <li>Sharing of selected regions between views and
4389 with other VAMSAS applications (Experimental feature!)</li>
4390 <li>Updated API to VAMSAS version 0.2</li>
4392 </ul> <em>Applet</em>
4394 <li>Middle button resizes annotation row height</li>
4397 <li>sortByTree (true/false) - automatically sort the
4398 associated alignment view by the tree when a new tree is
4400 <li>showTreeBootstraps (true/false) - show or hide
4401 branch bootstraps (default is to show them if available)</li>
4402 <li>showTreeDistances (true/false) - show or hide
4403 branch lengths (default is to show them if available)</li>
4404 <li>showUnlinkedTreeNodes (true/false) - indicate if
4405 unassociated nodes should be highlighted in the tree
4407 <li>heightScale and widthScale (1.0 or more) -
4408 increase the height or width of a cell in the alignment
4409 grid relative to the current font size.</li>
4412 <li>Non-positional features displayed in sequence ID
4414 </ul> <em>Other</em>
4416 <li>Features format: graduated colour definitions and
4417 specification of feature scores</li>
4418 <li>Alignment Annotations format: new keywords for group
4419 associated annotation (GROUP_REF) and annotation row display
4420 properties (ROW_PROPERTIES)</li>
4421 <li>XML formats extended to support graduated feature
4422 colourschemes, group associated annotation, and profile
4423 visualization settings.</li></td>
4426 <li>Source field in GFF files parsed as feature source
4427 rather than description</li>
4428 <li>Non-positional features are now included in sequence
4429 feature and gff files (controlled via non-positional feature
4430 visibility in tooltip).</li>
4431 <li>URL links generated for all feature links (bugfix)</li>
4432 <li>Added URL embedding instructions to features file
4434 <li>Codons containing ambiguous nucleotides translated as
4435 'X' in peptide product</li>
4436 <li>Match case switch in find dialog box works for both
4437 sequence ID and sequence string and query strings do not
4438 have to be in upper case to match case-insensitively.</li>
4439 <li>AMSA files only contain first column of
4440 multi-character column annotation labels</li>
4441 <li>Jalview Annotation File generation/parsing consistent
4442 with documentation (e.g. Stockholm annotation can be
4443 exported and re-imported)</li>
4444 <li>PDB files without embedded PDB IDs given a friendly
4446 <li>Find incrementally searches ID string matches as well
4447 as subsequence matches, and correctly reports total number
4451 <li>Better handling of exceptions during sequence
4453 <li>Dasobert generated non-positional feature URL
4454 link text excludes the start_end suffix</li>
4455 <li>DAS feature and source retrieval buttons disabled
4456 when fetch or registry operations in progress.</li>
4457 <li>PDB files retrieved from URLs are cached properly</li>
4458 <li>Sequence description lines properly shared via
4460 <li>Sequence fetcher fetches multiple records for all
4462 <li>Ensured that command line das feature retrieval
4463 completes before alignment figures are generated.</li>
4464 <li>Reduced time taken when opening file browser for
4466 <li>isAligned check prior to calculating tree, PCA or
4467 submitting an MSA to JNet now excludes hidden sequences.</li>
4468 <li>User defined group colours properly recovered
4469 from Jalview projects.</li>
4478 <div align="center">
4479 <strong>2.4.0.b2</strong><br> 28/10/2009
4484 <li>Experimental support for google analytics usage
4486 <li>Jalview privacy settings (user preferences and docs).</li>
4491 <li>Race condition in applet preventing startup in
4493 <li>Exception when feature created from selection beyond
4494 length of sequence.</li>
4495 <li>Allow synthetic PDB files to be imported gracefully</li>
4496 <li>Sequence associated annotation rows associate with
4497 all sequences with a given id</li>
4498 <li>Find function matches case-insensitively for sequence
4499 ID string searches</li>
4500 <li>Non-standard characters do not cause pairwise
4501 alignment to fail with exception</li>
4502 </ul> <em>Application Issues</em>
4504 <li>Sequences are now validated against EMBL database</li>
4505 <li>Sequence fetcher fetches multiple records for all
4507 </ul> <em>InstallAnywhere Issues</em>
4509 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4510 issue with installAnywhere mechanism)</li>
4511 <li>Command line launching of JARs from InstallAnywhere
4512 version (java class versioning error fixed)</li>
4519 <div align="center">
4520 <strong>2.4</strong><br> 27/8/2008
4523 <td><em>User Interface</em>
4525 <li>Linked highlighting of codon and amino acid from
4526 translation and protein products</li>
4527 <li>Linked highlighting of structure associated with
4528 residue mapping to codon position</li>
4529 <li>Sequence Fetcher provides example accession numbers
4530 and 'clear' button</li>
4531 <li>MemoryMonitor added as an option under Desktop's
4533 <li>Extract score function to parse whitespace separated
4534 numeric data in description line</li>
4535 <li>Column labels in alignment annotation can be centred.</li>
4536 <li>Tooltip for sequence associated annotation give name
4538 </ul> <em>Web Services and URL fetching</em>
4540 <li>JPred3 web service</li>
4541 <li>Prototype sequence search client (no public services
4543 <li>Fetch either seed alignment or full alignment from
4545 <li>URL Links created for matching database cross
4546 references as well as sequence ID</li>
4547 <li>URL Links can be created using regular-expressions</li>
4548 </ul> <em>Sequence Database Connectivity</em>
4550 <li>Retrieval of cross-referenced sequences from other
4552 <li>Generalised database reference retrieval and
4553 validation to all fetchable databases</li>
4554 <li>Fetch sequences from DAS sources supporting the
4555 sequence command</li>
4556 </ul> <em>Import and Export</em>
4557 <li>export annotation rows as CSV for spreadsheet import</li>
4558 <li>Jalview projects record alignment dataset associations,
4559 EMBL products, and cDNA sequence mappings</li>
4560 <li>Sequence Group colour can be specified in Annotation
4562 <li>Ad-hoc colouring of group in Annotation File using RGB
4563 triplet as name of colourscheme</li>
4564 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4566 <li>treenode binding for VAMSAS tree exchange</li>
4567 <li>local editing and update of sequences in VAMSAS
4568 alignments (experimental)</li>
4569 <li>Create new or select existing session to join</li>
4570 <li>load and save of vamsas documents</li>
4571 </ul> <em>Application command line</em>
4573 <li>-tree parameter to open trees (introduced for passing
4575 <li>-fetchfrom command line argument to specify nicknames
4576 of DAS servers to query for alignment features</li>
4577 <li>-dasserver command line argument to add new servers
4578 that are also automatically queried for features</li>
4579 <li>-groovy command line argument executes a given groovy
4580 script after all input data has been loaded and parsed</li>
4581 </ul> <em>Applet-Application data exchange</em>
4583 <li>Trees passed as applet parameters can be passed to
4584 application (when using "View in full
4585 application")</li>
4586 </ul> <em>Applet Parameters</em>
4588 <li>feature group display control parameter</li>
4589 <li>debug parameter</li>
4590 <li>showbutton parameter</li>
4591 </ul> <em>Applet API methods</em>
4593 <li>newView public method</li>
4594 <li>Window (current view) specific get/set public methods</li>
4595 <li>Feature display control methods</li>
4596 <li>get list of currently selected sequences</li>
4597 </ul> <em>New Jalview distribution features</em>
4599 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4600 <li>RELEASE file gives build properties for the latest
4601 Jalview release.</li>
4602 <li>Java 1.1 Applet build made easier and donotobfuscate
4603 property controls execution of obfuscator</li>
4604 <li>Build target for generating source distribution</li>
4605 <li>Debug flag for javacc</li>
4606 <li>.jalview_properties file is documented (slightly) in
4607 jalview.bin.Cache</li>
4608 <li>Continuous Build Integration for stable and
4609 development version of Application, Applet and source
4614 <li>selected region output includes visible annotations
4615 (for certain formats)</li>
4616 <li>edit label/displaychar contains existing label/char
4618 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4619 <li>shorter peptide product names from EMBL records</li>
4620 <li>Newick string generator makes compact representations</li>
4621 <li>bootstrap values parsed correctly for tree files with
4623 <li>pathological filechooser bug avoided by not allowing
4624 filenames containing a ':'</li>
4625 <li>Fixed exception when parsing GFF files containing
4626 global sequence features</li>
4627 <li>Alignment datasets are finalized only when number of
4628 references from alignment sequences goes to zero</li>
4629 <li>Close of tree branch colour box without colour
4630 selection causes cascading exceptions</li>
4631 <li>occasional negative imgwidth exceptions</li>
4632 <li>better reporting of non-fatal warnings to user when
4633 file parsing fails.</li>
4634 <li>Save works when Jalview project is default format</li>
4635 <li>Save as dialog opened if current alignment format is
4636 not a valid output format</li>
4637 <li>UniProt canonical names introduced for both das and
4639 <li>Histidine should be midblue (not pink!) in Zappo</li>
4640 <li>error messages passed up and output when data read
4642 <li>edit undo recovers previous dataset sequence when
4643 sequence is edited</li>
4644 <li>allow PDB files without pdb ID HEADER lines (like
4645 those generated by MODELLER) to be read in properly</li>
4646 <li>allow reading of JPred concise files as a normal
4648 <li>Stockholm annotation parsing and alignment properties
4649 import fixed for PFAM records</li>
4650 <li>Structure view windows have correct name in Desktop
4652 <li>annotation consisting of sequence associated scores
4653 can be read and written correctly to annotation file</li>
4654 <li>Aligned cDNA translation to aligned peptide works
4656 <li>Fixed display of hidden sequence markers and
4657 non-italic font for representatives in Applet</li>
4658 <li>Applet Menus are always embedded in applet window on
4660 <li>Newly shown features appear at top of stack (in
4662 <li>Annotations added via parameter not drawn properly
4663 due to null pointer exceptions</li>
4664 <li>Secondary structure lines are drawn starting from
4665 first column of alignment</li>
4666 <li>UniProt XML import updated for new schema release in
4668 <li>Sequence feature to sequence ID match for Features
4669 file is case-insensitive</li>
4670 <li>Sequence features read from Features file appended to
4671 all sequences with matching IDs</li>
4672 <li>PDB structure coloured correctly for associated views
4673 containing a sub-sequence</li>
4674 <li>PDB files can be retrieved by applet from Jar files</li>
4675 <li>feature and annotation file applet parameters
4676 referring to different directories are retrieved correctly</li>
4677 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4678 <li>Fixed application hang whilst waiting for
4679 splash-screen version check to complete</li>
4680 <li>Applet properly URLencodes input parameter values
4681 when passing them to the launchApp service</li>
4682 <li>display name and local features preserved in results
4683 retrieved from web service</li>
4684 <li>Visual delay indication for sequence retrieval and
4685 sequence fetcher initialisation</li>
4686 <li>updated Application to use DAS 1.53e version of
4687 dasobert DAS client</li>
4688 <li>Re-instated Full AMSA support and .amsa file
4690 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4698 <div align="center">
4699 <strong>2.3</strong><br> 9/5/07
4704 <li>Jmol 11.0.2 integration</li>
4705 <li>PDB views stored in Jalview XML files</li>
4706 <li>Slide sequences</li>
4707 <li>Edit sequence in place</li>
4708 <li>EMBL CDS features</li>
4709 <li>DAS Feature mapping</li>
4710 <li>Feature ordering</li>
4711 <li>Alignment Properties</li>
4712 <li>Annotation Scores</li>
4713 <li>Sort by scores</li>
4714 <li>Feature/annotation editing in applet</li>
4719 <li>Headless state operation in 2.2.1</li>
4720 <li>Incorrect and unstable DNA pairwise alignment</li>
4721 <li>Cut and paste of sequences with annotation</li>
4722 <li>Feature group display state in XML</li>
4723 <li>Feature ordering in XML</li>
4724 <li>blc file iteration selection using filename # suffix</li>
4725 <li>Stockholm alignment properties</li>
4726 <li>Stockhom alignment secondary structure annotation</li>
4727 <li>2.2.1 applet had no feature transparency</li>
4728 <li>Number pad keys can be used in cursor mode</li>
4729 <li>Structure Viewer mirror image resolved</li>
4736 <div align="center">
4737 <strong>2.2.1</strong><br> 12/2/07
4742 <li>Non standard characters can be read and displayed
4743 <li>Annotations/Features can be imported/exported to the
4745 <li>Applet allows editing of sequence/annotation/group
4746 name & description
4747 <li>Preference setting to display sequence name in
4749 <li>Annotation file format extended to allow
4750 Sequence_groups to be defined
4751 <li>Default opening of alignment overview panel can be
4752 specified in preferences
4753 <li>PDB residue numbering annotation added to associated
4759 <li>Applet crash under certain Linux OS with Java 1.6
4761 <li>Annotation file export / import bugs fixed
4762 <li>PNG / EPS image output bugs fixed
4768 <div align="center">
4769 <strong>2.2</strong><br> 27/11/06
4774 <li>Multiple views on alignment
4775 <li>Sequence feature editing
4776 <li>"Reload" alignment
4777 <li>"Save" to current filename
4778 <li>Background dependent text colour
4779 <li>Right align sequence ids
4780 <li>User-defined lower case residue colours
4783 <li>Menu item accelerator keys
4784 <li>Control-V pastes to current alignment
4785 <li>Cancel button for DAS Feature Fetching
4786 <li>PCA and PDB Viewers zoom via mouse roller
4787 <li>User-defined sub-tree colours and sub-tree selection
4789 <li>'New Window' button on the 'Output to Text box'
4794 <li>New memory efficient Undo/Redo System
4795 <li>Optimised symbol lookups and conservation/consensus
4797 <li>Region Conservation/Consensus recalculated after
4799 <li>Fixed Remove Empty Columns Bug (empty columns at end
4801 <li>Slowed DAS Feature Fetching for increased robustness.
4803 <li>Made angle brackets in ASCII feature descriptions
4805 <li>Re-instated Zoom function for PCA
4806 <li>Sequence descriptions conserved in web service
4808 <li>UniProt ID discoverer uses any word separated by
4810 <li>WsDbFetch query/result association resolved
4811 <li>Tree leaf to sequence mapping improved
4812 <li>Smooth fonts switch moved to FontChooser dialog box.
4819 <div align="center">
4820 <strong>2.1.1</strong><br> 12/9/06
4825 <li>Copy consensus sequence to clipboard</li>
4830 <li>Image output - rightmost residues are rendered if
4831 sequence id panel has been resized</li>
4832 <li>Image output - all offscreen group boundaries are
4834 <li>Annotation files with sequence references - all
4835 elements in file are relative to sequence position</li>
4836 <li>Mac Applet users can use Alt key for group editing</li>
4842 <div align="center">
4843 <strong>2.1</strong><br> 22/8/06
4848 <li>MAFFT Multiple Alignment in default Web Service list</li>
4849 <li>DAS Feature fetching</li>
4850 <li>Hide sequences and columns</li>
4851 <li>Export Annotations and Features</li>
4852 <li>GFF file reading / writing</li>
4853 <li>Associate structures with sequences from local PDB
4855 <li>Add sequences to exisiting alignment</li>
4856 <li>Recently opened files / URL lists</li>
4857 <li>Applet can launch the full application</li>
4858 <li>Applet has transparency for features (Java 1.2
4860 <li>Applet has user defined colours parameter</li>
4861 <li>Applet can load sequences from parameter
4862 "sequence<em>x</em>"
4868 <li>Redundancy Panel reinstalled in the Applet</li>
4869 <li>Monospaced font - EPS / rescaling bug fixed</li>
4870 <li>Annotation files with sequence references bug fixed</li>
4876 <div align="center">
4877 <strong>2.08.1</strong><br> 2/5/06
4882 <li>Change case of selected region from Popup menu</li>
4883 <li>Choose to match case when searching</li>
4884 <li>Middle mouse button and mouse movement can compress /
4885 expand the visible width and height of the alignment</li>
4890 <li>Annotation Panel displays complete JNet results</li>
4896 <div align="center">
4897 <strong>2.08b</strong><br> 18/4/06
4903 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4904 <li>Righthand label on wrapped alignments shows correct
4911 <div align="center">
4912 <strong>2.08</strong><br> 10/4/06
4917 <li>Editing can be locked to the selection area</li>
4918 <li>Keyboard editing</li>
4919 <li>Create sequence features from searches</li>
4920 <li>Precalculated annotations can be loaded onto
4922 <li>Features file allows grouping of features</li>
4923 <li>Annotation Colouring scheme added</li>
4924 <li>Smooth fonts off by default - Faster rendering</li>
4925 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4930 <li>Drag & Drop fixed on Linux</li>
4931 <li>Jalview Archive file faster to load/save, sequence
4932 descriptions saved.</li>
4938 <div align="center">
4939 <strong>2.07</strong><br> 12/12/05
4944 <li>PDB Structure Viewer enhanced</li>
4945 <li>Sequence Feature retrieval and display enhanced</li>
4946 <li>Choose to output sequence start-end after sequence
4947 name for file output</li>
4948 <li>Sequence Fetcher WSDBFetch@EBI</li>
4949 <li>Applet can read feature files, PDB files and can be
4950 used for HTML form input</li>
4955 <li>HTML output writes groups and features</li>
4956 <li>Group editing is Control and mouse click</li>
4957 <li>File IO bugs</li>
4963 <div align="center">
4964 <strong>2.06</strong><br> 28/9/05
4969 <li>View annotations in wrapped mode</li>
4970 <li>More options for PCA viewer</li>
4975 <li>GUI bugs resolved</li>
4976 <li>Runs with -nodisplay from command line</li>
4982 <div align="center">
4983 <strong>2.05b</strong><br> 15/9/05
4988 <li>Choose EPS export as lineart or text</li>
4989 <li>Jar files are executable</li>
4990 <li>Can read in Uracil - maps to unknown residue</li>
4995 <li>Known OutOfMemory errors give warning message</li>
4996 <li>Overview window calculated more efficiently</li>
4997 <li>Several GUI bugs resolved</li>
5003 <div align="center">
5004 <strong>2.05</strong><br> 30/8/05
5009 <li>Edit and annotate in "Wrapped" view</li>
5014 <li>Several GUI bugs resolved</li>
5020 <div align="center">
5021 <strong>2.04</strong><br> 24/8/05
5026 <li>Hold down mouse wheel & scroll to change font
5032 <li>Improved JPred client reliability</li>
5033 <li>Improved loading of Jalview files</li>
5039 <div align="center">
5040 <strong>2.03</strong><br> 18/8/05
5045 <li>Set Proxy server name and port in preferences</li>
5046 <li>Multiple URL links from sequence ids</li>
5047 <li>User Defined Colours can have a scheme name and added
5049 <li>Choose to ignore gaps in consensus calculation</li>
5050 <li>Unix users can set default web browser</li>
5051 <li>Runs without GUI for batch processing</li>
5052 <li>Dynamically generated Web Service Menus</li>
5057 <li>InstallAnywhere download for Sparc Solaris</li>
5063 <div align="center">
5064 <strong>2.02</strong><br> 18/7/05
5070 <li>Copy & Paste order of sequences maintains
5071 alignment order.</li>
5077 <div align="center">
5078 <strong>2.01</strong><br> 12/7/05
5083 <li>Use delete key for deleting selection.</li>
5084 <li>Use Mouse wheel to scroll sequences.</li>
5085 <li>Help file updated to describe how to add alignment
5087 <li>Version and build date written to build properties
5089 <li>InstallAnywhere installation will check for updates
5090 at launch of Jalview.</li>
5095 <li>Delete gaps bug fixed.</li>
5096 <li>FileChooser sorts columns.</li>
5097 <li>Can remove groups one by one.</li>
5098 <li>Filechooser icons installed.</li>
5099 <li>Finder ignores return character when searching.
5100 Return key will initiate a search.<br>
5107 <div align="center">
5108 <strong>2.0</strong><br> 20/6/05
5113 <li>New codebase</li>