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;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
62 <em>6/01/2022</em></strong></td>
64 <td align="left" valign="top"><em>Security</em>
67 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
74 <td width="60" align="center" nowrap><strong><a
75 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
76 <em>20/12/2021</em></strong></td>
78 <td align="left" valign="top"><em>Security</em>
81 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
83 </ul> <em>Development</em>
85 <li>Updated building instructions</li>
90 <!-- JAL-3840 -->Occupancy calculation is incorrect for
91 alignment columns with over -1+2^32 gaps (breaking filtering
95 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
96 scale factors being set with buggy window-managers (linux
99 </ul> <em>Development</em>
101 <li>Fixed non-fatal gradle errors during build</li>
106 <td width="60" align="center" nowrap><strong><a
107 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
108 <em>09/03/2021</em></strong></td>
109 <td align="left" valign="top"><em>Improved control of
110 Jalview's use of network services via jalview_properties</em>
113 <!-- JAL-3814 -->New .jalview_properties token controlling
114 launch of the news browser (like -nonews argument)
117 <!-- JAL-3813 -->New .jalview_properties token controlling
118 download of linkout URLs from
119 www.jalview.org/services/identifiers
122 <!-- JAL-3812 -->New .jalview_properties token controlling
123 download of BIOJSHTML templates
126 <!-- JAL-3811 -->New 'Discover Web Services' option to
127 trigger a one off JABAWS discovery if autodiscovery was
131 <td align="left" valign="top">
134 <!-- JAL-3818 -->Intermittent deadlock opening structure in
137 </ul> <em>New Known defects</em>
140 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
141 always restored from project (since 2.10.3)
144 <!-- JAL-3806 -->Selections from tree built from CDS aren't
145 propagated to Protein alignment (since 2.11.1.3)
151 <td width="60" align="center" nowrap><strong><a
152 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
153 <em>29/10/2020</em></strong></td>
154 <td align="left" valign="top">
159 <td align="left" valign="top">
162 <!-- JAL-3765 -->Find doesn't always highlight all matching
163 positions in a sequence (bug introduced in 2.11.1.2)
166 <!-- JAL-3760 -->Alignments containing one or more protein
167 sequences can be classed as nucleotide
170 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
171 sequences after alignment of protein products (known defect
172 first reported for 2.11.1.0)
175 <!-- JAL-3725 -->No tooltip or popup menu for genomic
176 features outwith CDS shown overlaid on protein
179 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
180 correctly mapped by Jalview (e.g. affects viral CDS with
181 ribosomal slippage, since 2.9.0)
184 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
188 <!-- JAL-3700 -->Selections in CDS sequence panel don't
189 always select corresponding protein sequences
192 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
193 column selection doesn't always ignore hidden columns
195 </ul> <em>Installer</em>
198 <!-- JAL-3611 -->Space character in Jalview install path on
199 Windows prevents install4j launching getdown
201 </ul> <em>Development</em>
204 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
205 version numbers in doc/building.md
211 <td width="60" align="center" nowrap><strong><a
212 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
213 <em>25/09/2020</em></strong></td>
214 <td align="left" valign="top">
218 <td align="left" valign="top">
221 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
222 "Encountered problems opening
223 https://www.jalview.org/examples/exampleFile_2_7.jvp"
229 <td width="60" align="center" nowrap><strong><a
230 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
231 <em>17/09/2020</em></strong></td>
232 <td align="left" valign="top">
235 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
236 residue in cursor mode
239 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
240 HTSJDK from 2.12 to 2.23
243 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
244 optimisations and improvements suggested by Bob Hanson and
245 improved compatibility with JalviewJS
248 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
249 alignments from Pfam and Rfam
252 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
253 import (no longer based on .gz extension)
256 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
259 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
260 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
264 <!-- JAL-3667 -->Improved warning messages, debug logging
265 and fixed Retry action when Jalview encounters errors when
266 saving or making backup files.
269 <!-- JAL-3676 -->Enhanced Jalview Java Console:
271 <li>Jalview's logging level can be configured</li>
272 <li>Copy to Clipboard Buttion</li>
276 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
277 when running on Linux (Requires Java 11+)
279 </ul> <em>Launching Jalview</em>
282 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
283 through a system property
286 <!-- JAL-3477 -->Improved built-in documentation and command
287 line help for configuring Jalview's memory
291 <td align="left" valign="top">
294 <!-- JAL-3691 -->Conservation and Quality tracks are shown
295 but not calculated and no protein or DNA score models are
296 available for tree/PCA calculation when launched with
297 Turkish language locale
300 <!-- JAL-3493 -->Escape does not clear highlights on the
301 alignment (Since Jalview 2.10.3)
304 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
305 doesn't slide selected sequences, just sequence under cursor
308 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
309 sequence under the cursor
312 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
313 multiple EMBL gene products shown for a single contig
316 <!-- JAL-3696 -->Errors encountered when processing variants
317 from VCF files yield "Error processing VCF: Format specifier
321 <!-- JAL-3697 -->Count of features not shown can be wrong
322 when there are both local and complementary features mapped
323 to the position under the cursor
326 <!-- JAL-3673 -->Sequence ID for reference sequence is
327 clipped when Right align Sequence IDs enabled
330 <!-- JAL-2983 -->Slider with negative range values not
331 rendered correctly in VAqua4 (Since 2.10.4)
334 <!-- JAL-3685 -->Single quotes not displayed correctly in
335 internationalised text for some messages and log output
338 <!-- JAL-3490 -->Find doesn't report matches that span
339 hidden gapped columns
342 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
343 panels, Alignment viewport and annotation renderer.
346 <!-- JAL-3561 -->Jalview ignores file format parameter
347 specifying output format when exporting an alignment via the
351 <!-- JAL-3667 -->Windows 10: For a minority of users, if
352 backups are not enabled, Jalview sometimes fails to
353 overwrite an existing file and raises a warning dialog. (in
354 2.11.0, and 2.11.1.0, the workaround is to try to save the
355 file again, and if that fails, delete the original file and
359 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
363 <!-- JAL-3741 -->References to http://www.jalview.org in
364 program and documentation
366 </ul> <em>Launching Jalview</em>
369 <!-- JAL-3718 -->Jalview application fails when launched the
370 first time for a version that has different jars to the
371 previous launched version.
373 </ul> <em>Developing Jalview</em>
376 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
377 data, causing cloverReport gradle task to fail with an
381 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
382 monitor the release channel
384 </ul> <em>New Known defects</em>
387 <!-- JAL-3748 -->CDS shown in result of submitting proteins
388 in a CDS/Protein alignment to a web service is wrong when
389 proteins share a common transcript sequence (e.g.
390 genome of RNA viruses)
393 <!-- JAL-3576 -->Co-located features exported and re-imported
394 are ordered differently when shown on alignment and in
395 tooltips. (Also affects v2.11.1.0)
398 <!-- JAL-3702 -->Drag and drop of alignment file onto
399 alignment window when in a HiDPI scaled mode in Linux only
400 works for the top left quadrant of the alignment window
403 <!-- JAL-3701 -->Stale build data in jalview standalone jar
404 builds (only affects 2.11.1.1 branch)
407 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
408 when alignment view restored from project (since Jalview 2.11.0)
411 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
412 protein products for certain ENA records are repeatedly
413 shown via Calculate->Show Cross Refs
419 <td width="60" align="center" nowrap><strong><a
420 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
421 <em>22/04/2020</em></strong></td>
422 <td align="left" valign="top">
425 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
426 'virtual' codon features shown on protein (or vice versa)
427 for display in alignments, on structure views (including
428 transfer to UCSF chimera), in feature reports and for
432 <!-- JAL-3121 -->Feature attributes from VCF files can be
433 exported and re-imported as GFF3 files
436 <!-- JAL-3376 -->Capture VCF "fixed column" values
437 POS, ID, QUAL, FILTER as Feature Attributes
440 <!-- JAL-3375 -->More robust VCF numeric data field
441 validation while parsing
444 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
448 <!-- JAL-3535 -->Feature Settings dialog title includes name
452 <!-- JAL-3538 -->Font anti-aliasing in alignment views
456 <!-- JAL-3468 -->Very long feature descriptions truncated in
460 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
461 with no feature types visible
464 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
466 </ul><em>Jalview Installer</em>
469 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
470 in console (may be null when Jalview launched as executable jar or via conda)
473 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
476 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
479 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
481 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
482 </ul> <em>Release processes</em>
485 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
488 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
490 </ul> <em>Build System</em>
493 <!-- JAL-3510 -->Clover updated to 4.4.1
496 <!-- JAL-3513 -->Test code included in Clover coverage
500 <em>Groovy Scripts</em>
503 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
504 to stdout containing the consensus sequence for each
505 alignment in a Jalview session
508 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
509 genomic sequence_variant annotation from CDS as
510 missense_variant or synonymous_variant on protein products.
514 <td align="left" valign="top">
517 <!-- JAL-3581 -->Hidden sequence markers still visible when
518 'Show hidden markers' option is not ticked
521 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
522 PNG output when 'Automatically set ID width' is set in
523 jalview preferences or properties file
526 <!-- JAL-3571 -->Feature Editor dialog can be opened when
527 'Show Sequence Features' option is not ticked
530 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
531 buttons in Feature Settings dialog are clicked when no
535 <!-- JAL-3412 -->ID margins for CDS and Protein views not
536 equal when split frame is first opened
539 <!-- JAL-3296 -->Sequence position numbers in status bar not
540 correct after editing a sequence's start position
543 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
544 with annotation and exceptions thrown when only a few
545 columns shown in wrapped mode
548 <!-- JAL-3386 -->Sequence IDs missing in headless export of
549 wrapped alignment figure with annotations
552 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
553 ID fails with ClassCastException
556 <!-- JAL-3389 -->Chimera session not restored from Jalview
560 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
561 feature settings dialog also selects columns
564 <!-- JAL-3473 -->SpinnerNumberModel causes
565 IllegalArgumentException in some circumstances
568 <!-- JAL-3534 -->Multiple feature settings dialogs can be
572 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
573 alignment window is closed
576 <!-- JAL-3406 -->Credits missing some authors in Jalview
577 help documentation for 2.11.0 release
580 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
581 includes Pfam ID as sequence's accession rather than its
584 </ul> <em>Java 11 Compatibility issues</em>
587 <!-- JAL-2987 -->OSX - Can't view some search results in
588 PDB/Uniprot search panel
590 </ul> <em>Installer</em>
593 <!-- JAL-3447 -->Jalview should not create file associations
594 for 3D structure files (.pdb, .mmcif. .cif)
596 </ul> <em>Repository and Source Release</em>
599 <!-- JAL-3474 -->removed obsolete .cvsignore files from
603 <!-- JAL-3541 -->Clover report generation running out of
606 </ul> <em>New Known Issues</em>
609 <!-- JAL-3523 -->OSX - Current working directory not
610 preserved when Jalview.app launched with parameters from
614 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
615 clipped in headless figure export when Right Align option
619 <!-- JAL-3542 -->Jalview Installation type always reports
620 'Source' in console output
623 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
624 bamboo server but run fine locally.
630 <td width="60" align="center" nowrap>
631 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
632 <em>04/07/2019</em></strong>
634 <td align="left" valign="top">
637 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
638 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
639 source project) rather than InstallAnywhere
642 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
643 settings, receive over the air updates and launch specific
644 versions via (<a href="https://github.com/threerings/getdown">Three
648 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
649 formats supported by Jalview (including .jvp project files)
652 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
653 arguments and switch between different getdown channels
656 <!-- JAL-3141 -->Backup files created when saving Jalview project
661 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
662 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
664 <!-- JAL-2620 -->Alternative genetic code tables for
665 'Translate as cDNA'</li>
667 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
668 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
671 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
672 implementation that allows updates) used for Sequence Feature collections</li>
674 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
675 features can be filtered and shaded according to any
676 associated attributes (e.g. variant attributes from VCF
677 file, or key-value pairs imported from column 9 of GFF
681 <!-- JAL-2879 -->Feature Attributes and shading schemes
682 stored and restored from Jalview Projects
685 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
686 recognise variant features
689 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
690 sequences (also coloured red by default)
693 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
697 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
698 algorithm (Z-sort/transparency and filter aware)
701 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
707 <!-- JAL-3205 -->Symmetric score matrices for faster
708 tree and PCA calculations
710 <li><strong>Principal Components Analysis Viewer</strong>
713 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
714 and Viewer state saved in Jalview Project
716 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
719 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
723 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
728 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
730 <li><strong>Speed and Efficiency</strong>
733 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
734 multiple groups when working with large alignments
737 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
741 <li><strong>User Interface</strong>
744 <!-- JAL-2933 -->Finder panel remembers last position in each
748 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
749 what is shown)<br />Only visible regions of alignment are shown by
750 default (can be changed in user preferences)
753 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
754 to the Overwrite Dialog
757 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
761 <!-- JAL-1244 -->Status bar shows bounds when dragging a
762 selection region, and gap count when inserting or deleting gaps
765 <!-- JAL-3132 -->Status bar updates over sequence and annotation
769 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
773 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
777 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
780 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
784 <!-- JAL-3181 -->Consistent ordering of links in sequence id
788 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
790 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
794 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
795 <li><strong>Java 11 Support (not yet on general release)</strong>
798 <!-- -->OSX GUI integrations for App menu's 'About' entry and
803 <em>Deprecations</em>
805 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
806 capabilities removed from the Jalview Desktop
808 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
809 unmarshalling has been replaced by JAXB for Jalview projects
810 and XML based data retrieval clients</li>
811 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
812 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
813 </ul> <em>Documentation</em>
815 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
816 not supported in EPS figure export
818 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
819 </ul> <em>Development and Release Processes</em>
822 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
825 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
827 <!-- JAL-3225 -->Eclipse project configuration managed with
831 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
832 Bamboo continuous integration for unattended Test Suite
836 <!-- JAL-2864 -->Memory test suite to detect leaks in common
840 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
844 <!-- JAL-3248 -->Developer documentation migrated to
845 markdown (with HTML rendering)
848 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
851 <!-- JAL-3289 -->New URLs for publishing development
856 <td align="left" valign="top">
859 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
862 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
863 superposition in Jmol fail on Windows
866 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
867 structures for sequences with lots of PDB structures
870 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
874 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
875 project involving multiple views
878 <!-- JAL-3164 -->Overview for complementary view in a linked
879 CDS/Protein alignment is not updated when Hide Columns by
880 Annotation dialog hides columns
883 <!-- JAL-3158 -->Selection highlighting in the complement of a
884 CDS/Protein alignment stops working after making a selection in
885 one view, then making another selection in the other view
888 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
892 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
893 Settings and Jalview Preferences panels
896 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
897 overview with large alignments
900 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
901 region if columns were selected by dragging right-to-left and the
902 mouse moved to the left of the first column
905 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
906 hidden column marker via scale popup menu
909 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
910 doesn't tell users the invalid URL
913 <!-- JAL-2816 -->Tooltips displayed for features filtered by
917 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
918 show cross references or Fetch Database References are shown in
922 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
923 peptide sequence (computed variant shown as p.Res.null)
926 <!-- JAL-2060 -->'Graduated colour' option not offered for
927 manually created features (where feature score is Float.NaN)
930 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
931 when columns are hidden
934 <!-- JAL-3082 -->Regular expression error for '(' in Select
935 Columns by Annotation description
938 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
939 out of Scale or Annotation Panel
942 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
946 <!-- JAL-3074 -->Left/right drag in annotation can scroll
950 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
954 <!-- JAL-3002 -->Column display is out by one after Page Down,
955 Page Up in wrapped mode
958 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
961 <!-- JAL-2932 -->Finder searches in minimised alignments
964 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
965 on opening an alignment
968 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
972 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
973 different groups in the alignment are selected
976 <!-- JAL-2717 -->Internationalised colour scheme names not shown
980 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
984 <!-- JAL-3125 -->Value input for graduated feature colour
985 threshold gets 'unrounded'
988 <!-- JAL-2982 -->PCA image export doesn't respect background
992 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
995 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
998 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1002 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1006 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1007 shown in complementary view
1010 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1011 without normalisation
1014 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1018 <!-- JAL-914 -->Help page can be opened twice
1021 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1023 </ul> <em>Editing</em>
1026 <!-- JAL-2822 -->Start and End should be updated when sequence
1027 data at beginning or end of alignment added/removed via 'Edit'
1031 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1032 relocate sequence features correctly when start of sequence is
1033 removed (Known defect since 2.10)
1036 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1037 dialog corrupts dataset sequence
1040 <!-- JAL-868 -->Structure colours not updated when associated tree
1041 repartitions the alignment view (Regression in 2.10.5)
1043 </ul> <em>Datamodel</em>
1046 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1047 sequence's End is greater than its length
1049 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1050 general release)</em>
1053 <!-- JAL-3288 -->Menus work properly in split-screen
1055 </ul> <em>New Known Defects</em>
1058 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1061 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1062 regions of protein alignment.
1065 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1066 is restored from a Jalview 2.11 project
1069 <!-- JAL-3213 -->Alignment panel height can be too small after
1073 <!-- JAL-3240 -->Display is incorrect after removing gapped
1074 columns within hidden columns
1077 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1078 window after dragging left to select columns to left of visible
1082 <!-- JAL-2876 -->Features coloured according to their description
1083 string and thresholded by score in earlier versions of Jalview are
1084 not shown as thresholded features in 2.11. To workaround please
1085 create a Score filter instead.
1088 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1090 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1093 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1094 alignments with multiple views can close views unexpectedly
1097 <em>Java 11 Specific defects</em>
1100 <!-- JAL-3235 -->Jalview Properties file is not sorted
1101 alphabetically when saved
1107 <td width="60" nowrap>
1108 <div align="center">
1109 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1112 <td><div align="left">
1116 <!-- JAL-3101 -->Default memory for Jalview webstart and
1117 InstallAnywhere increased to 1G.
1120 <!-- JAL-247 -->Hidden sequence markers and representative
1121 sequence bolding included when exporting alignment as EPS,
1122 SVG, PNG or HTML. <em>Display is configured via the
1123 Format menu, or for command-line use via a Jalview
1124 properties file.</em>
1127 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1128 API and sequence data now imported as JSON.
1131 <!-- JAL-3065 -->Change in recommended way of starting
1132 Jalview via a Java command line: add jars in lib directory
1133 to CLASSPATH, rather than via the deprecated java.ext.dirs
1137 <em>Development</em>
1140 <!-- JAL-3047 -->Support added to execute test suite
1141 instrumented with <a href="http://openclover.org/">Open
1146 <td><div align="left">
1150 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1151 row shown in Feredoxin Structure alignment view of example
1155 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1156 annotation displayed.
1159 <!-- JAL-3107 -->Group conservation/consensus not shown
1160 for newly created group when 'Apply to all groups'
1164 <!-- JAL-3087 -->Corrupted display when switching to
1165 wrapped mode when sequence panel's vertical scrollbar is
1169 <!-- JAL-3003 -->Alignment is black in exported EPS file
1170 when sequences are selected in exported view.</em>
1173 <!-- JAL-3059 -->Groups with different coloured borders
1174 aren't rendered with correct colour.
1177 <!-- JAL-3092 -->Jalview could hang when importing certain
1178 types of knotted RNA secondary structure.
1181 <!-- JAL-3095 -->Sequence highlight and selection in
1182 trimmed VARNA 2D structure is incorrect for sequences that
1186 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1187 annotation when columns are inserted into an alignment,
1188 and when exporting as Stockholm flatfile.
1191 <!-- JAL-3053 -->Jalview annotation rows containing upper
1192 and lower-case 'E' and 'H' do not automatically get
1193 treated as RNA secondary structure.
1196 <!-- JAL-3106 -->.jvp should be used as default extension
1197 (not .jar) when saving a Jalview project file.
1200 <!-- JAL-3105 -->Mac Users: closing a window correctly
1201 transfers focus to previous window on OSX
1204 <em>Java 10 Issues Resolved</em>
1207 <!-- JAL-2988 -->OSX - Can't save new files via the File
1208 or export menus by typing in a name into the Save dialog
1212 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1213 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1214 'look and feel' which has improved compatibility with the
1215 latest version of OSX.
1222 <td width="60" nowrap>
1223 <div align="center">
1224 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1225 <em>7/06/2018</em></strong>
1228 <td><div align="left">
1232 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1233 annotation retrieved from Uniprot
1236 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1237 onto the Jalview Desktop
1241 <td><div align="left">
1245 <!-- JAL-3017 -->Cannot import features with multiple
1246 variant elements (blocks import of some Uniprot records)
1249 <!-- JAL-2997 -->Clustal files with sequence positions in
1250 right-hand column parsed correctly
1253 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1254 not alignment area in exported graphic
1257 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1258 window has input focus
1261 <!-- JAL-2992 -->Annotation panel set too high when
1262 annotation added to view (Windows)
1265 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1266 network connectivity is poor
1269 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1270 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1271 the currently open URL and links from a page viewed in
1272 Firefox or Chrome on Windows is now fully supported. If
1273 you are using Edge, only links in the page can be
1274 dragged, and with Internet Explorer, only the currently
1275 open URL in the browser can be dropped onto Jalview.</em>
1278 <em>New Known Defects</em>
1280 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1285 <td width="60" nowrap>
1286 <div align="center">
1287 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1290 <td><div align="left">
1294 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1295 for disabling automatic superposition of multiple
1296 structures and open structures in existing views
1299 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1300 ID and annotation area margins can be click-dragged to
1304 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1308 <!-- JAL-2759 -->Improved performance for large alignments
1309 and lots of hidden columns
1312 <!-- JAL-2593 -->Improved performance when rendering lots
1313 of features (particularly when transparency is disabled)
1316 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1317 exchange of Jalview features and Chimera attributes made
1323 <td><div align="left">
1326 <!-- JAL-2899 -->Structure and Overview aren't updated
1327 when Colour By Annotation threshold slider is adjusted
1330 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1331 overlapping alignment panel
1334 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1338 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1339 improved: CDS not handled correctly if transcript has no
1343 <!-- JAL-2321 -->Secondary structure and temperature
1344 factor annotation not added to sequence when local PDB
1345 file associated with it by drag'n'drop or structure
1349 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1350 dialog doesn't import PDB files dropped on an alignment
1353 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1354 scroll bar doesn't work for some CDS/Protein views
1357 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1358 Java 1.8u153 onwards and Java 1.9u4+.
1361 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1362 columns in annotation row
1365 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1366 honored in batch mode
1369 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1370 for structures added to existing Jmol view
1373 <!-- JAL-2223 -->'View Mappings' includes duplicate
1374 entries after importing project with multiple views
1377 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1378 protein sequences via SIFTS from associated PDB entries
1379 with negative residue numbers or missing residues fails
1382 <!-- JAL-2952 -->Exception when shading sequence with negative
1383 Temperature Factor values from annotated PDB files (e.g.
1384 as generated by CONSURF)
1387 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1388 tooltip doesn't include a text description of mutation
1391 <!-- JAL-2922 -->Invert displayed features very slow when
1392 structure and/or overview windows are also shown
1395 <!-- JAL-2954 -->Selecting columns from highlighted regions
1396 very slow for alignments with large numbers of sequences
1399 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1400 with 'StringIndexOutOfBounds'
1403 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1404 platforms running Java 10
1407 <!-- JAL-2960 -->Adding a structure to existing structure
1408 view appears to do nothing because the view is hidden behind the alignment view
1414 <!-- JAL-2926 -->Copy consensus sequence option in applet
1415 should copy the group consensus when popup is opened on it
1421 <!-- JAL-2913 -->Fixed ID width preference is not respected
1424 <em>New Known Defects</em>
1427 <!-- JAL-2973 --> Exceptions occasionally raised when
1428 editing a large alignment and overview is displayed
1431 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1432 repeatedly after a series of edits even when the overview
1433 is no longer reflecting updates
1436 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1437 structures for protein subsequence (if 'Trim Retrieved
1438 Sequences' enabled) or Ensembl isoforms (Workaround in
1439 2.10.4 is to fail back to N&W mapping)
1442 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1443 option gives blank output
1450 <td width="60" nowrap>
1451 <div align="center">
1452 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1455 <td><div align="left">
1456 <ul><li>Updated Certum Codesigning Certificate
1457 (Valid till 30th November 2018)</li></ul></div></td>
1458 <td><div align="left">
1459 <em>Desktop</em><ul>
1461 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1462 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1463 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1464 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1465 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1466 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1467 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1473 <td width="60" nowrap>
1474 <div align="center">
1475 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1478 <td><div align="left">
1482 <!-- JAL-2446 -->Faster and more efficient management and
1483 rendering of sequence features
1486 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1487 429 rate limit request hander
1490 <!-- JAL-2773 -->Structure views don't get updated unless
1491 their colours have changed
1494 <!-- JAL-2495 -->All linked sequences are highlighted for
1495 a structure mousover (Jmol) or selection (Chimera)
1498 <!-- JAL-2790 -->'Cancel' button in progress bar for
1499 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1502 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1503 view from Ensembl locus cross-references
1506 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1510 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1511 feature can be disabled
1514 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1515 PDB easier retrieval of sequences for lists of IDs
1518 <!-- JAL-2758 -->Short names for sequences retrieved from
1524 <li>Groovy interpreter updated to 2.4.12</li>
1525 <li>Example groovy script for generating a matrix of
1526 percent identity scores for current alignment.</li>
1528 <em>Testing and Deployment</em>
1531 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1535 <td><div align="left">
1539 <!-- JAL-2643 -->Pressing tab after updating the colour
1540 threshold text field doesn't trigger an update to the
1544 <!-- JAL-2682 -->Race condition when parsing sequence ID
1548 <!-- JAL-2608 -->Overview windows are also closed when
1549 alignment window is closed
1552 <!-- JAL-2548 -->Export of features doesn't always respect
1556 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1557 takes a long time in Cursor mode
1563 <!-- JAL-2777 -->Structures with whitespace chainCode
1564 cannot be viewed in Chimera
1567 <!-- JAL-2728 -->Protein annotation panel too high in
1571 <!-- JAL-2757 -->Can't edit the query after the server
1572 error warning icon is shown in Uniprot and PDB Free Text
1576 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1579 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1582 <!-- JAL-2739 -->Hidden column marker in last column not
1583 rendered when switching back from Wrapped to normal view
1586 <!-- JAL-2768 -->Annotation display corrupted when
1587 scrolling right in unwapped alignment view
1590 <!-- JAL-2542 -->Existing features on subsequence
1591 incorrectly relocated when full sequence retrieved from
1595 <!-- JAL-2733 -->Last reported memory still shown when
1596 Desktop->Show Memory is unticked (OSX only)
1599 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1600 features of same type and group to be selected for
1604 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1605 alignments when hidden columns are present
1608 <!-- JAL-2392 -->Jalview freezes when loading and
1609 displaying several structures
1612 <!-- JAL-2732 -->Black outlines left after resizing or
1616 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1617 within the Jalview desktop on OSX
1620 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1621 when in wrapped alignment mode
1624 <!-- JAL-2636 -->Scale mark not shown when close to right
1625 hand end of alignment
1628 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1629 each selected sequence do not have correct start/end
1633 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1634 after canceling the Alignment Window's Font dialog
1637 <!-- JAL-2036 -->Show cross-references not enabled after
1638 restoring project until a new view is created
1641 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1642 URL links appears when only default EMBL-EBI link is
1643 configured (since 2.10.2b2)
1646 <!-- JAL-2775 -->Overview redraws whole window when box
1647 position is adjusted
1650 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1651 in a multi-chain structure when viewing alignment
1652 involving more than one chain (since 2.10)
1655 <!-- JAL-2811 -->Double residue highlights in cursor mode
1656 if new selection moves alignment window
1659 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1660 arrow key in cursor mode to pass hidden column marker
1663 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1664 that produces correctly annotated transcripts and products
1667 <!-- JAL-2776 -->Toggling a feature group after first time
1668 doesn't update associated structure view
1671 <em>Applet</em><br />
1674 <!-- JAL-2687 -->Concurrent modification exception when
1675 closing alignment panel
1678 <em>BioJSON</em><br />
1681 <!-- JAL-2546 -->BioJSON export does not preserve
1682 non-positional features
1685 <em>New Known Issues</em>
1688 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1689 sequence features correctly (for many previous versions of
1693 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1694 using cursor in wrapped panel other than top
1697 <!-- JAL-2791 -->Select columns containing feature ignores
1698 graduated colour threshold
1701 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1702 always preserve numbering and sequence features
1705 <em>Known Java 9 Issues</em>
1708 <!-- JAL-2902 -->Groovy Console very slow to open and is
1709 not responsive when entering characters (Webstart, Java
1716 <td width="60" nowrap>
1717 <div align="center">
1718 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1719 <em>2/10/2017</em></strong>
1722 <td><div align="left">
1723 <em>New features in Jalview Desktop</em>
1726 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1728 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1732 <td><div align="left">
1736 <td width="60" nowrap>
1737 <div align="center">
1738 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1739 <em>7/9/2017</em></strong>
1742 <td><div align="left">
1746 <!-- JAL-2588 -->Show gaps in overview window by colouring
1747 in grey (sequences used to be coloured grey, and gaps were
1751 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1755 <!-- JAL-2587 -->Overview updates immediately on increase
1756 in size and progress bar shown as higher resolution
1757 overview is recalculated
1762 <td><div align="left">
1766 <!-- JAL-2664 -->Overview window redraws every hidden
1767 column region row by row
1770 <!-- JAL-2681 -->duplicate protein sequences shown after
1771 retrieving Ensembl crossrefs for sequences from Uniprot
1774 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1775 format setting is unticked
1778 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1779 if group has show boxes format setting unticked
1782 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1783 autoscrolling whilst dragging current selection group to
1784 include sequences and columns not currently displayed
1787 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1788 assemblies are imported via CIF file
1791 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1792 displayed when threshold or conservation colouring is also
1796 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1800 <!-- JAL-2673 -->Jalview continues to scroll after
1801 dragging a selected region off the visible region of the
1805 <!-- JAL-2724 -->Cannot apply annotation based
1806 colourscheme to all groups in a view
1809 <!-- JAL-2511 -->IDs don't line up with sequences
1810 initially after font size change using the Font chooser or
1817 <td width="60" nowrap>
1818 <div align="center">
1819 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1822 <td><div align="left">
1823 <em>Calculations</em>
1827 <!-- JAL-1933 -->Occupancy annotation row shows number of
1828 ungapped positions in each column of the alignment.
1831 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1832 a calculation dialog box
1835 <!-- JAL-2379 -->Revised implementation of PCA for speed
1836 and memory efficiency (~30x faster)
1839 <!-- JAL-2403 -->Revised implementation of sequence
1840 similarity scores as used by Tree, PCA, Shading Consensus
1841 and other calculations
1844 <!-- JAL-2416 -->Score matrices are stored as resource
1845 files within the Jalview codebase
1848 <!-- JAL-2500 -->Trees computed on Sequence Feature
1849 Similarity may have different topology due to increased
1856 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1857 model for alignments and groups
1860 <!-- JAL-384 -->Custom shading schemes created via groovy
1867 <!-- JAL-2526 -->Efficiency improvements for interacting
1868 with alignment and overview windows
1871 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1875 <!-- JAL-2388 -->Hidden columns and sequences can be
1879 <!-- JAL-2611 -->Click-drag in visible area allows fine
1880 adjustment of visible position
1884 <em>Data import/export</em>
1887 <!-- JAL-2535 -->Posterior probability annotation from
1888 Stockholm files imported as sequence associated annotation
1891 <!-- JAL-2507 -->More robust per-sequence positional
1892 annotation input/output via stockholm flatfile
1895 <!-- JAL-2533 -->Sequence names don't include file
1896 extension when importing structure files without embedded
1897 names or PDB accessions
1900 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1901 format sequence substitution matrices
1904 <em>User Interface</em>
1907 <!-- JAL-2447 --> Experimental Features Checkbox in
1908 Desktop's Tools menu to hide or show untested features in
1912 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1913 via Overview or sequence motif search operations
1916 <!-- JAL-2547 -->Amend sequence features dialog box can be
1917 opened by double clicking gaps within sequence feature
1921 <!-- JAL-1476 -->Status bar message shown when not enough
1922 aligned positions were available to create a 3D structure
1926 <em>3D Structure</em>
1929 <!-- JAL-2430 -->Hidden regions in alignment views are not
1930 coloured in linked structure views
1933 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1934 file-based command exchange
1937 <!-- JAL-2375 -->Structure chooser automatically shows
1938 Cached Structures rather than querying the PDBe if
1939 structures are already available for sequences
1942 <!-- JAL-2520 -->Structures imported via URL are cached in
1943 the Jalview project rather than downloaded again when the
1944 project is reopened.
1947 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1948 to transfer Chimera's structure attributes as Jalview
1949 features, and vice-versa (<strong>Experimental
1953 <em>Web Services</em>
1956 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1959 <!-- JAL-2335 -->Filter non-standard amino acids and
1960 nucleotides when submitting to AACon and other MSA
1964 <!-- JAL-2316, -->URLs for viewing database
1965 cross-references provided by identifiers.org and the
1966 EMBL-EBI's MIRIAM DB
1973 <!-- JAL-2344 -->FileFormatI interface for describing and
1974 identifying file formats (instead of String constants)
1977 <!-- JAL-2228 -->FeatureCounter script refactored for
1978 efficiency when counting all displayed features (not
1979 backwards compatible with 2.10.1)
1982 <em>Example files</em>
1985 <!-- JAL-2631 -->Graduated feature colour style example
1986 included in the example feature file
1989 <em>Documentation</em>
1992 <!-- JAL-2339 -->Release notes reformatted for readability
1993 with the built-in Java help viewer
1996 <!-- JAL-1644 -->Find documentation updated with 'search
1997 sequence description' option
2003 <!-- JAL-2485, -->External service integration tests for
2004 Uniprot REST Free Text Search Client
2007 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2010 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2015 <td><div align="left">
2016 <em>Calculations</em>
2019 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2020 matrix - C->R should be '-3'<br />Old matrix restored
2021 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2023 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2024 Jalview's treatment of gaps in PCA and substitution matrix
2025 based Tree calculations.<br /> <br />In earlier versions
2026 of Jalview, gaps matching gaps were penalised, and gaps
2027 matching non-gaps penalised even more. In the PCA
2028 calculation, gaps were actually treated as non-gaps - so
2029 different costs were applied, which meant Jalview's PCAs
2030 were different to those produced by SeqSpace.<br />Jalview
2031 now treats gaps in the same way as SeqSpace (ie it scores
2032 them as 0). <br /> <br />Enter the following in the
2033 Groovy console to restore pre-2.10.2 behaviour:<br />
2034 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2035 // for 2.10.1 mode <br />
2036 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2037 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2038 these settings will affect all subsequent tree and PCA
2039 calculations (not recommended)</em></li>
2041 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2042 scaling of branch lengths for trees computed using
2043 Sequence Feature Similarity.
2046 <!-- JAL-2377 -->PCA calculation could hang when
2047 generating output report when working with highly
2048 redundant alignments
2051 <!-- JAL-2544 --> Sort by features includes features to
2052 right of selected region when gaps present on right-hand
2056 <em>User Interface</em>
2059 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2060 doesn't reselect a specific sequence's associated
2061 annotation after it was used for colouring a view
2064 <!-- JAL-2419 -->Current selection lost if popup menu
2065 opened on a region of alignment without groups
2068 <!-- JAL-2374 -->Popup menu not always shown for regions
2069 of an alignment with overlapping groups
2072 <!-- JAL-2310 -->Finder double counts if both a sequence's
2073 name and description match
2076 <!-- JAL-2370 -->Hiding column selection containing two
2077 hidden regions results in incorrect hidden regions
2080 <!-- JAL-2386 -->'Apply to all groups' setting when
2081 changing colour does not apply Conservation slider value
2085 <!-- JAL-2373 -->Percentage identity and conservation menu
2086 items do not show a tick or allow shading to be disabled
2089 <!-- JAL-2385 -->Conservation shading or PID threshold
2090 lost when base colourscheme changed if slider not visible
2093 <!-- JAL-2547 -->Sequence features shown in tooltip for
2094 gaps before start of features
2097 <!-- JAL-2623 -->Graduated feature colour threshold not
2098 restored to UI when feature colour is edited
2101 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2102 a time when scrolling vertically in wrapped mode.
2105 <!-- JAL-2630 -->Structure and alignment overview update
2106 as graduate feature colour settings are modified via the
2110 <!-- JAL-2034 -->Overview window doesn't always update
2111 when a group defined on the alignment is resized
2114 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2115 wrapped view result in positional status updates
2119 <!-- JAL-2563 -->Status bar doesn't show position for
2120 ambiguous amino acid and nucleotide symbols
2123 <!-- JAL-2602 -->Copy consensus sequence failed if
2124 alignment included gapped columns
2127 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2128 widgets don't permanently disappear
2131 <!-- JAL-2503 -->Cannot select or filter quantitative
2132 annotation that are shown only as column labels (e.g.
2133 T-Coffee column reliability scores)
2136 <!-- JAL-2594 -->Exception thrown if trying to create a
2137 sequence feature on gaps only
2140 <!-- JAL-2504 -->Features created with 'New feature'
2141 button from a Find inherit previously defined feature type
2142 rather than the Find query string
2145 <!-- JAL-2423 -->incorrect title in output window when
2146 exporting tree calculated in Jalview
2149 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2150 and then revealing them reorders sequences on the
2154 <!-- JAL-964 -->Group panel in sequence feature settings
2155 doesn't update to reflect available set of groups after
2156 interactively adding or modifying features
2159 <!-- JAL-2225 -->Sequence Database chooser unusable on
2163 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2164 only excluded gaps in current sequence and ignored
2171 <!-- JAL-2421 -->Overview window visible region moves
2172 erratically when hidden rows or columns are present
2175 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2176 Structure Viewer's colour menu don't correspond to
2180 <!-- JAL-2405 -->Protein specific colours only offered in
2181 colour and group colour menu for protein alignments
2184 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2185 reflect currently selected view or group's shading
2189 <!-- JAL-2624 -->Feature colour thresholds not respected
2190 when rendered on overview and structures when opacity at
2194 <!-- JAL-2589 -->User defined gap colour not shown in
2195 overview when features overlaid on alignment
2198 <!-- JAL-2567 -->Feature settings for different views not
2199 recovered correctly from Jalview project file
2202 <!-- JAL-2256 -->Feature colours in overview when first opened
2203 (automatically via preferences) are different to the main
2207 <em>Data import/export</em>
2210 <!-- JAL-2576 -->Very large alignments take a long time to
2214 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2215 added after a sequence was imported are not written to
2219 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2220 when importing RNA secondary structure via Stockholm
2223 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2224 not shown in correct direction for simple pseudoknots
2227 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2228 with lightGray or darkGray via features file (but can
2232 <!-- JAL-2383 -->Above PID colour threshold not recovered
2233 when alignment view imported from project
2236 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2237 structure and sequences extracted from structure files
2238 imported via URL and viewed in Jmol
2241 <!-- JAL-2520 -->Structures loaded via URL are saved in
2242 Jalview Projects rather than fetched via URL again when
2243 the project is loaded and the structure viewed
2246 <em>Web Services</em>
2249 <!-- JAL-2519 -->EnsemblGenomes example failing after
2250 release of Ensembl v.88
2253 <!-- JAL-2366 -->Proxy server address and port always
2254 appear enabled in Preferences->Connections
2257 <!-- JAL-2461 -->DAS registry not found exceptions
2258 removed from console output
2261 <!-- JAL-2582 -->Cannot retrieve protein products from
2262 Ensembl by Peptide ID
2265 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2266 created from SIFTs, and spurious 'Couldn't open structure
2267 in Chimera' errors raised after April 2017 update (problem
2268 due to 'null' string rather than empty string used for
2269 residues with no corresponding PDB mapping).
2272 <em>Application UI</em>
2275 <!-- JAL-2361 -->User Defined Colours not added to Colour
2279 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2280 case' residues (button in colourscheme editor debugged and
2281 new documentation and tooltips added)
2284 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2285 doesn't restore group-specific text colour thresholds
2288 <!-- JAL-2243 -->Feature settings panel does not update as
2289 new features are added to alignment
2292 <!-- JAL-2532 -->Cancel in feature settings reverts
2293 changes to feature colours via the Amend features dialog
2296 <!-- JAL-2506 -->Null pointer exception when attempting to
2297 edit graduated feature colour via amend features dialog
2301 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2302 selection menu changes colours of alignment views
2305 <!-- JAL-2426 -->Spurious exceptions in console raised
2306 from alignment calculation workers after alignment has
2310 <!-- JAL-1608 -->Typo in selection popup menu - Create
2311 groups now 'Create Group'
2314 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2315 Create/Undefine group doesn't always work
2318 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2319 shown again after pressing 'Cancel'
2322 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2323 adjusts start position in wrap mode
2326 <!-- JAL-2563 -->Status bar doesn't show positions for
2327 ambiguous amino acids
2330 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2331 CDS/Protein view after CDS sequences added for aligned
2335 <!-- JAL-2592 -->User defined colourschemes called 'User
2336 Defined' don't appear in Colours menu
2342 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2343 score models doesn't always result in an updated PCA plot
2346 <!-- JAL-2442 -->Features not rendered as transparent on
2347 overview or linked structure view
2350 <!-- JAL-2372 -->Colour group by conservation doesn't
2354 <!-- JAL-2517 -->Hitting Cancel after applying
2355 user-defined colourscheme doesn't restore original
2362 <!-- JAL-2314 -->Unit test failure:
2363 jalview.ws.jabaws.RNAStructExportImport setup fails
2366 <!-- JAL-2307 -->Unit test failure:
2367 jalview.ws.sifts.SiftsClientTest due to compatibility
2368 problems with deep array comparison equality asserts in
2369 successive versions of TestNG
2372 <!-- JAL-2479 -->Relocated StructureChooserTest and
2373 ParameterUtilsTest Unit tests to Network suite
2376 <em>New Known Issues</em>
2379 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2380 phase after a sequence motif find operation
2383 <!-- JAL-2550 -->Importing annotation file with rows
2384 containing just upper and lower case letters are
2385 interpreted as WUSS RNA secondary structure symbols
2388 <!-- JAL-2590 -->Cannot load and display Newick trees
2389 reliably from eggnog Ortholog database
2392 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2393 containing features of type Highlight' when 'B' is pressed
2394 to mark columns containing highlighted regions.
2397 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2398 doesn't always add secondary structure annotation.
2403 <td width="60" nowrap>
2404 <div align="center">
2405 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2408 <td><div align="left">
2412 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2413 for all consensus calculations
2416 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2419 <li>Updated Jalview's Certum code signing certificate
2422 <em>Application</em>
2425 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2426 set of database cross-references, sorted alphabetically
2429 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2430 from database cross references. Users with custom links
2431 will receive a <a href="webServices/urllinks.html#warning">warning
2432 dialog</a> asking them to update their preferences.
2435 <!-- JAL-2287-->Cancel button and escape listener on
2436 dialog warning user about disconnecting Jalview from a
2440 <!-- JAL-2320-->Jalview's Chimera control window closes if
2441 the Chimera it is connected to is shut down
2444 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2445 columns menu item to mark columns containing highlighted
2446 regions (e.g. from structure selections or results of a
2450 <!-- JAL-2284-->Command line option for batch-generation
2451 of HTML pages rendering alignment data with the BioJS
2461 <!-- JAL-2286 -->Columns with more than one modal residue
2462 are not coloured or thresholded according to percent
2463 identity (first observed in Jalview 2.8.2)
2466 <!-- JAL-2301 -->Threonine incorrectly reported as not
2470 <!-- JAL-2318 -->Updates to documentation pages (above PID
2471 threshold, amino acid properties)
2474 <!-- JAL-2292 -->Lower case residues in sequences are not
2475 reported as mapped to residues in a structure file in the
2479 <!--JAL-2324 -->Identical features with non-numeric scores
2480 could be added multiple times to a sequence
2483 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2484 bond features shown as two highlighted residues rather
2485 than a range in linked structure views, and treated
2486 correctly when selecting and computing trees from features
2489 <!-- JAL-2281-->Custom URL links for database
2490 cross-references are matched to database name regardless
2495 <em>Application</em>
2498 <!-- JAL-2282-->Custom URL links for specific database
2499 names without regular expressions also offer links from
2503 <!-- JAL-2315-->Removing a single configured link in the
2504 URL links pane in Connections preferences doesn't actually
2505 update Jalview configuration
2508 <!-- JAL-2272-->CTRL-Click on a selected region to open
2509 the alignment area popup menu doesn't work on El-Capitan
2512 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2513 files with similarly named sequences if dropped onto the
2517 <!-- JAL-2312 -->Additional mappings are shown for PDB
2518 entries where more chains exist in the PDB accession than
2519 are reported in the SIFTS file
2522 <!-- JAL-2317-->Certain structures do not get mapped to
2523 the structure view when displayed with Chimera
2526 <!-- JAL-2317-->No chains shown in the Chimera view
2527 panel's View->Show Chains submenu
2530 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2531 work for wrapped alignment views
2534 <!--JAL-2197 -->Rename UI components for running JPred
2535 predictions from 'JNet' to 'JPred'
2538 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2539 corrupted when annotation panel vertical scroll is not at
2540 first annotation row
2543 <!--JAL-2332 -->Attempting to view structure for Hen
2544 lysozyme results in a PDB Client error dialog box
2547 <!-- JAL-2319 -->Structure View's mapping report switched
2548 ranges for PDB and sequence for SIFTS
2551 SIFTS 'Not_Observed' residues mapped to non-existant
2555 <!-- <em>New Known Issues</em>
2562 <td width="60" nowrap>
2563 <div align="center">
2564 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2565 <em>25/10/2016</em></strong>
2568 <td><em>Application</em>
2570 <li>3D Structure chooser opens with 'Cached structures'
2571 view if structures already loaded</li>
2572 <li>Progress bar reports models as they are loaded to
2573 structure views</li>
2579 <li>Colour by conservation always enabled and no tick
2580 shown in menu when BLOSUM or PID shading applied</li>
2581 <li>FER1_ARATH and FER2_ARATH labels were switched in
2582 example sequences/projects/trees</li>
2584 <em>Application</em>
2586 <li>Jalview projects with views of local PDB structure
2587 files saved on Windows cannot be opened on OSX</li>
2588 <li>Multiple structure views can be opened and superposed
2589 without timeout for structures with multiple models or
2590 multiple sequences in alignment</li>
2591 <li>Cannot import or associated local PDB files without a
2592 PDB ID HEADER line</li>
2593 <li>RMSD is not output in Jmol console when superposition
2595 <li>Drag and drop of URL from Browser fails for Linux and
2596 OSX versions earlier than El Capitan</li>
2597 <li>ENA client ignores invalid content from ENA server</li>
2598 <li>Exceptions are not raised in console when ENA client
2599 attempts to fetch non-existent IDs via Fetch DB Refs UI
2601 <li>Exceptions are not raised in console when a new view
2602 is created on the alignment</li>
2603 <li>OSX right-click fixed for group selections: CMD-click
2604 to insert/remove gaps in groups and CTRL-click to open group
2607 <em>Build and deployment</em>
2609 <li>URL link checker now copes with multi-line anchor
2612 <em>New Known Issues</em>
2614 <li>Drag and drop from URL links in browsers do not work
2621 <td width="60" nowrap>
2622 <div align="center">
2623 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2626 <td><em>General</em>
2629 <!-- JAL-2124 -->Updated Spanish translations.
2632 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2633 for importing structure data to Jalview. Enables mmCIF and
2637 <!-- JAL-192 --->Alignment ruler shows positions relative to
2641 <!-- JAL-2202 -->Position/residue shown in status bar when
2642 mousing over sequence associated annotation
2645 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2649 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2650 '()', canonical '[]' and invalid '{}' base pair populations
2654 <!-- JAL-2092 -->Feature settings popup menu options for
2655 showing or hiding columns containing a feature
2658 <!-- JAL-1557 -->Edit selected group by double clicking on
2659 group and sequence associated annotation labels
2662 <!-- JAL-2236 -->Sequence name added to annotation label in
2663 select/hide columns by annotation and colour by annotation
2667 </ul> <em>Application</em>
2670 <!-- JAL-2050-->Automatically hide introns when opening a
2671 gene/transcript view
2674 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2678 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2679 structure mappings with the EMBL-EBI PDBe SIFTS database
2682 <!-- JAL-2079 -->Updated download sites used for Rfam and
2683 Pfam sources to xfam.org
2686 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2689 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2690 over sequences in Jalview
2693 <!-- JAL-2027-->Support for reverse-complement coding
2694 regions in ENA and EMBL
2697 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2698 for record retrieval via ENA rest API
2701 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2705 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2706 groovy script execution
2709 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2710 alignment window's Calculate menu
2713 <!-- JAL-1812 -->Allow groovy scripts that call
2714 Jalview.getAlignFrames() to run in headless mode
2717 <!-- JAL-2068 -->Support for creating new alignment
2718 calculation workers from groovy scripts
2721 <!-- JAL-1369 --->Store/restore reference sequence in
2725 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2726 associations are now saved/restored from project
2729 <!-- JAL-1993 -->Database selection dialog always shown
2730 before sequence fetcher is opened
2733 <!-- JAL-2183 -->Double click on an entry in Jalview's
2734 database chooser opens a sequence fetcher
2737 <!-- JAL-1563 -->Free-text search client for UniProt using
2738 the UniProt REST API
2741 <!-- JAL-2168 -->-nonews command line parameter to prevent
2742 the news reader opening
2745 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2746 querying stored in preferences
2749 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2753 <!-- JAL-1977-->Tooltips shown on database chooser
2756 <!-- JAL-391 -->Reverse complement function in calculate
2757 menu for nucleotide sequences
2760 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2761 and feature counts preserves alignment ordering (and
2762 debugged for complex feature sets).
2765 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2766 viewing structures with Jalview 2.10
2769 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2770 genome, transcript CCDS and gene ids via the Ensembl and
2771 Ensembl Genomes REST API
2774 <!-- JAL-2049 -->Protein sequence variant annotation
2775 computed for 'sequence_variant' annotation on CDS regions
2779 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2783 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2784 Ref Fetcher fails to match, or otherwise updates sequence
2785 data from external database records.
2788 <!-- JAL-2154 -->Revised Jalview Project format for
2789 efficient recovery of sequence coding and alignment
2790 annotation relationships.
2792 </ul> <!-- <em>Applet</em>
2803 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2807 <!-- JAL-2018-->Export features in Jalview format (again)
2808 includes graduated colourschemes
2811 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2812 working with big alignments and lots of hidden columns
2815 <!-- JAL-2053-->Hidden column markers not always rendered
2816 at right of alignment window
2819 <!-- JAL-2067 -->Tidied up links in help file table of
2823 <!-- JAL-2072 -->Feature based tree calculation not shown
2827 <!-- JAL-2075 -->Hidden columns ignored during feature
2828 based tree calculation
2831 <!-- JAL-2065 -->Alignment view stops updating when show
2832 unconserved enabled for group on alignment
2835 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2839 <!-- JAL-2146 -->Alignment column in status incorrectly
2840 shown as "Sequence position" when mousing over
2844 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2845 hidden columns present
2848 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2849 user created annotation added to alignment
2852 <!-- JAL-1841 -->RNA Structure consensus only computed for
2853 '()' base pair annotation
2856 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2857 in zero scores for all base pairs in RNA Structure
2861 <!-- JAL-2174-->Extend selection with columns containing
2865 <!-- JAL-2275 -->Pfam format writer puts extra space at
2866 beginning of sequence
2869 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2873 <!-- JAL-2238 -->Cannot create groups on an alignment from
2874 from a tree when t-coffee scores are shown
2877 <!-- JAL-1836,1967 -->Cannot import and view PDB
2878 structures with chains containing negative resnums (4q4h)
2881 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2885 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2886 to Clustal, PIR and PileUp output
2889 <!-- JAL-2008 -->Reordering sequence features that are
2890 not visible causes alignment window to repaint
2893 <!-- JAL-2006 -->Threshold sliders don't work in
2894 graduated colour and colour by annotation row for e-value
2895 scores associated with features and annotation rows
2898 <!-- JAL-1797 -->amino acid physicochemical conservation
2899 calculation should be case independent
2902 <!-- JAL-2173 -->Remove annotation also updates hidden
2906 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2907 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2908 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2911 <!-- JAL-2065 -->Null pointer exceptions and redraw
2912 problems when reference sequence defined and 'show
2913 non-conserved' enabled
2916 <!-- JAL-1306 -->Quality and Conservation are now shown on
2917 load even when Consensus calculation is disabled
2920 <!-- JAL-1932 -->Remove right on penultimate column of
2921 alignment does nothing
2924 <em>Application</em>
2927 <!-- JAL-1552-->URLs and links can't be imported by
2928 drag'n'drop on OSX when launched via webstart (note - not
2929 yet fixed for El Capitan)
2932 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2933 output when running on non-gb/us i18n platforms
2936 <!-- JAL-1944 -->Error thrown when exporting a view with
2937 hidden sequences as flat-file alignment
2940 <!-- JAL-2030-->InstallAnywhere distribution fails when
2944 <!-- JAL-2080-->Jalview very slow to launch via webstart
2945 (also hotfix for 2.9.0b2)
2948 <!-- JAL-2085 -->Cannot save project when view has a
2949 reference sequence defined
2952 <!-- JAL-1011 -->Columns are suddenly selected in other
2953 alignments and views when revealing hidden columns
2956 <!-- JAL-1989 -->Hide columns not mirrored in complement
2957 view in a cDNA/Protein splitframe
2960 <!-- JAL-1369 -->Cannot save/restore representative
2961 sequence from project when only one sequence is
2965 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2966 in Structure Chooser
2969 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2970 structure consensus didn't refresh annotation panel
2973 <!-- JAL-1962 -->View mapping in structure view shows
2974 mappings between sequence and all chains in a PDB file
2977 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2978 dialogs format columns correctly, don't display array
2979 data, sort columns according to type
2982 <!-- JAL-1975 -->Export complete shown after destination
2983 file chooser is cancelled during an image export
2986 <!-- JAL-2025 -->Error when querying PDB Service with
2987 sequence name containing special characters
2990 <!-- JAL-2024 -->Manual PDB structure querying should be
2994 <!-- JAL-2104 -->Large tooltips with broken HTML
2995 formatting don't wrap
2998 <!-- JAL-1128 -->Figures exported from wrapped view are
2999 truncated so L looks like I in consensus annotation
3002 <!-- JAL-2003 -->Export features should only export the
3003 currently displayed features for the current selection or
3007 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3008 after fetching cross-references, and restoring from
3012 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3013 followed in the structure viewer
3016 <!-- JAL-2163 -->Titles for individual alignments in
3017 splitframe not restored from project
3020 <!-- JAL-2145 -->missing autocalculated annotation at
3021 trailing end of protein alignment in transcript/product
3022 splitview when pad-gaps not enabled by default
3025 <!-- JAL-1797 -->amino acid physicochemical conservation
3029 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3030 article has been read (reopened issue due to
3031 internationalisation problems)
3034 <!-- JAL-1960 -->Only offer PDB structures in structure
3035 viewer based on sequence name, PDB and UniProt
3040 <!-- JAL-1976 -->No progress bar shown during export of
3044 <!-- JAL-2213 -->Structures not always superimposed after
3045 multiple structures are shown for one or more sequences.
3048 <!-- JAL-1370 -->Reference sequence characters should not
3049 be replaced with '.' when 'Show unconserved' format option
3053 <!-- JAL-1823 -->Cannot specify chain code when entering
3054 specific PDB id for sequence
3057 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3058 'Export hidden sequences' is enabled, but 'export hidden
3059 columns' is disabled.
3062 <!--JAL-2026-->Best Quality option in structure chooser
3063 selects lowest rather than highest resolution structures
3067 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3068 to sequence mapping in 'View Mappings' report
3071 <!-- JAL-2284 -->Unable to read old Jalview projects that
3072 contain non-XML data added after Jalvew wrote project.
3075 <!-- JAL-2118 -->Newly created annotation row reorders
3076 after clicking on it to create new annotation for a
3080 <!-- JAL-1980 -->Null Pointer Exception raised when
3081 pressing Add on an orphaned cut'n'paste window.
3083 <!-- may exclude, this is an external service stability issue JAL-1941
3084 -- > RNA 3D structure not added via DSSR service</li> -->
3089 <!-- JAL-2151 -->Incorrect columns are selected when
3090 hidden columns present before start of sequence
3093 <!-- JAL-1986 -->Missing dependencies on applet pages
3097 <!-- JAL-1947 -->Overview pixel size changes when
3098 sequences are hidden in applet
3101 <!-- JAL-1996 -->Updated instructions for applet
3102 deployment on examples pages.
3109 <td width="60" nowrap>
3110 <div align="center">
3111 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3112 <em>16/10/2015</em></strong>
3115 <td><em>General</em>
3117 <li>Time stamps for signed Jalview application and applet
3122 <em>Application</em>
3124 <li>Duplicate group consensus and conservation rows
3125 shown when tree is partitioned</li>
3126 <li>Erratic behaviour when tree partitions made with
3127 multiple cDNA/Protein split views</li>
3133 <td width="60" nowrap>
3134 <div align="center">
3135 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3136 <em>8/10/2015</em></strong>
3139 <td><em>General</em>
3141 <li>Updated Spanish translations of localized text for
3143 </ul> <em>Application</em>
3145 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3146 <li>Signed OSX InstallAnywhere installer<br></li>
3147 <li>Support for per-sequence based annotations in BioJSON</li>
3148 </ul> <em>Applet</em>
3150 <li>Split frame example added to applet examples page</li>
3151 </ul> <em>Build and Deployment</em>
3154 <!-- JAL-1888 -->New ant target for running Jalview's test
3162 <li>Mapping of cDNA to protein in split frames
3163 incorrect when sequence start > 1</li>
3164 <li>Broken images in filter column by annotation dialog
3166 <li>Feature colours not parsed from features file</li>
3167 <li>Exceptions and incomplete link URLs recovered when
3168 loading a features file containing HTML tags in feature
3172 <em>Application</em>
3174 <li>Annotations corrupted after BioJS export and
3176 <li>Incorrect sequence limits after Fetch DB References
3177 with 'trim retrieved sequences'</li>
3178 <li>Incorrect warning about deleting all data when
3179 deleting selected columns</li>
3180 <li>Patch to build system for shipping properly signed
3181 JNLP templates for webstart launch</li>
3182 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3183 unreleased structures for download or viewing</li>
3184 <li>Tab/space/return keystroke operation of EMBL-PDBe
3185 fetcher/viewer dialogs works correctly</li>
3186 <li>Disabled 'minimise' button on Jalview windows
3187 running on OSX to workaround redraw hang bug</li>
3188 <li>Split cDNA/Protein view position and geometry not
3189 recovered from jalview project</li>
3190 <li>Initial enabled/disabled state of annotation menu
3191 sorter 'show autocalculated first/last' corresponds to
3193 <li>Restoring of Clustal, RNA Helices and T-Coffee
3194 color schemes from BioJSON</li>
3198 <li>Reorder sequences mirrored in cDNA/Protein split
3200 <li>Applet with Jmol examples not loading correctly</li>
3206 <td><div align="center">
3207 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3209 <td><em>General</em>
3211 <li>Linked visualisation and analysis of DNA and Protein
3214 <li>Translated cDNA alignments shown as split protein
3215 and DNA alignment views</li>
3216 <li>Codon consensus annotation for linked protein and
3217 cDNA alignment views</li>
3218 <li>Link cDNA or Protein product sequences by loading
3219 them onto Protein or cDNA alignments</li>
3220 <li>Reconstruct linked cDNA alignment from aligned
3221 protein sequences</li>
3224 <li>Jmol integration updated to Jmol v14.2.14</li>
3225 <li>Import and export of Jalview alignment views as <a
3226 href="features/bioJsonFormat.html">BioJSON</a></li>
3227 <li>New alignment annotation file statements for
3228 reference sequences and marking hidden columns</li>
3229 <li>Reference sequence based alignment shading to
3230 highlight variation</li>
3231 <li>Select or hide columns according to alignment
3233 <li>Find option for locating sequences by description</li>
3234 <li>Conserved physicochemical properties shown in amino
3235 acid conservation row</li>
3236 <li>Alignments can be sorted by number of RNA helices</li>
3237 </ul> <em>Application</em>
3239 <li>New cDNA/Protein analysis capabilities
3241 <li>Get Cross-References should open a Split Frame
3242 view with cDNA/Protein</li>
3243 <li>Detect when nucleotide sequences and protein
3244 sequences are placed in the same alignment</li>
3245 <li>Split cDNA/Protein views are saved in Jalview
3250 <li>Use REST API to talk to Chimera</li>
3251 <li>Selected regions in Chimera are highlighted in linked
3252 Jalview windows</li>
3254 <li>VARNA RNA viewer updated to v3.93</li>
3255 <li>VARNA views are saved in Jalview Projects</li>
3256 <li>Pseudoknots displayed as Jalview RNA annotation can
3257 be shown in VARNA</li>
3259 <li>Make groups for selection uses marked columns as well
3260 as the active selected region</li>
3262 <li>Calculate UPGMA and NJ trees using sequence feature
3264 <li>New Export options
3266 <li>New Export Settings dialog to control hidden
3267 region export in flat file generation</li>
3269 <li>Export alignment views for display with the <a
3270 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3272 <li>Export scrollable SVG in HTML page</li>
3273 <li>Optional embedding of BioJSON data when exporting
3274 alignment figures to HTML</li>
3276 <li>3D structure retrieval and display
3278 <li>Free text and structured queries with the PDBe
3280 <li>PDBe Search API based discovery and selection of
3281 PDB structures for a sequence set</li>
3285 <li>JPred4 employed for protein secondary structure
3287 <li>Hide Insertions menu option to hide unaligned columns
3288 for one or a group of sequences</li>
3289 <li>Automatically hide insertions in alignments imported
3290 from the JPred4 web server</li>
3291 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3292 system on OSX<br />LGPL libraries courtesy of <a
3293 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3295 <li>changed 'View nucleotide structure' submenu to 'View
3296 VARNA 2D Structure'</li>
3297 <li>change "View protein structure" menu option to "3D
3300 </ul> <em>Applet</em>
3302 <li>New layout for applet example pages</li>
3303 <li>New parameters to enable SplitFrame view
3304 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3305 <li>New example demonstrating linked viewing of cDNA and
3306 Protein alignments</li>
3307 </ul> <em>Development and deployment</em>
3309 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3310 <li>Include installation type and git revision in build
3311 properties and console log output</li>
3312 <li>Jalview Github organisation, and new github site for
3313 storing BioJsMSA Templates</li>
3314 <li>Jalview's unit tests now managed with TestNG</li>
3317 <!-- <em>General</em>
3319 </ul> --> <!-- issues resolved --> <em>Application</em>
3321 <li>Escape should close any open find dialogs</li>
3322 <li>Typo in select-by-features status report</li>
3323 <li>Consensus RNA secondary secondary structure
3324 predictions are not highlighted in amber</li>
3325 <li>Missing gap character in v2.7 example file means
3326 alignment appears unaligned when pad-gaps is not enabled</li>
3327 <li>First switch to RNA Helices colouring doesn't colour
3328 associated structure views</li>
3329 <li>ID width preference option is greyed out when auto
3330 width checkbox not enabled</li>
3331 <li>Stopped a warning dialog from being shown when
3332 creating user defined colours</li>
3333 <li>'View Mapping' in structure viewer shows sequence
3334 mappings for just that viewer's sequences</li>
3335 <li>Workaround for superposing PDB files containing
3336 multiple models in Chimera</li>
3337 <li>Report sequence position in status bar when hovering
3338 over Jmol structure</li>
3339 <li>Cannot output gaps as '.' symbols with Selection ->
3340 output to text box</li>
3341 <li>Flat file exports of alignments with hidden columns
3342 have incorrect sequence start/end</li>
3343 <li>'Aligning' a second chain to a Chimera structure from
3345 <li>Colour schemes applied to structure viewers don't
3346 work for nucleotide</li>
3347 <li>Loading/cut'n'pasting an empty or invalid file leads
3348 to a grey/invisible alignment window</li>
3349 <li>Exported Jpred annotation from a sequence region
3350 imports to different position</li>
3351 <li>Space at beginning of sequence feature tooltips shown
3352 on some platforms</li>
3353 <li>Chimera viewer 'View | Show Chain' menu is not
3355 <li>'New View' fails with a Null Pointer Exception in
3356 console if Chimera has been opened</li>
3357 <li>Mouseover to Chimera not working</li>
3358 <li>Miscellaneous ENA XML feature qualifiers not
3360 <li>NPE in annotation renderer after 'Extract Scores'</li>
3361 <li>If two structures in one Chimera window, mouseover of
3362 either sequence shows on first structure</li>
3363 <li>'Show annotations' options should not make
3364 non-positional annotations visible</li>
3365 <li>Subsequence secondary structure annotation not shown
3366 in right place after 'view flanking regions'</li>
3367 <li>File Save As type unset when current file format is
3369 <li>Save as '.jar' option removed for saving Jalview
3371 <li>Colour by Sequence colouring in Chimera more
3373 <li>Cannot 'add reference annotation' for a sequence in
3374 several views on same alignment</li>
3375 <li>Cannot show linked products for EMBL / ENA records</li>
3376 <li>Jalview's tooltip wraps long texts containing no
3378 </ul> <em>Applet</em>
3380 <li>Jmol to JalviewLite mouseover/link not working</li>
3381 <li>JalviewLite can't import sequences with ID
3382 descriptions containing angle brackets</li>
3383 </ul> <em>General</em>
3385 <li>Cannot export and reimport RNA secondary structure
3386 via jalview annotation file</li>
3387 <li>Random helix colour palette for colour by annotation
3388 with RNA secondary structure</li>
3389 <li>Mouseover to cDNA from STOP residue in protein
3390 translation doesn't work.</li>
3391 <li>hints when using the select by annotation dialog box</li>
3392 <li>Jmol alignment incorrect if PDB file has alternate CA
3394 <li>FontChooser message dialog appears to hang after
3395 choosing 1pt font</li>
3396 <li>Peptide secondary structure incorrectly imported from
3397 annotation file when annotation display text includes 'e' or
3399 <li>Cannot set colour of new feature type whilst creating
3401 <li>cDNA translation alignment should not be sequence
3402 order dependent</li>
3403 <li>'Show unconserved' doesn't work for lower case
3405 <li>Nucleotide ambiguity codes involving R not recognised</li>
3406 </ul> <em>Deployment and Documentation</em>
3408 <li>Applet example pages appear different to the rest of
3409 www.jalview.org</li>
3410 </ul> <em>Application Known issues</em>
3412 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3413 <li>Misleading message appears after trying to delete
3415 <li>Jalview icon not shown in dock after InstallAnywhere
3416 version launches</li>
3417 <li>Fetching EMBL reference for an RNA sequence results
3418 fails with a sequence mismatch</li>
3419 <li>Corrupted or unreadable alignment display when
3420 scrolling alignment to right</li>
3421 <li>ArrayIndexOutOfBoundsException thrown when remove
3422 empty columns called on alignment with ragged gapped ends</li>
3423 <li>auto calculated alignment annotation rows do not get
3424 placed above or below non-autocalculated rows</li>
3425 <li>Jalview dekstop becomes sluggish at full screen in
3426 ultra-high resolution</li>
3427 <li>Cannot disable consensus calculation independently of
3428 quality and conservation</li>
3429 <li>Mouseover highlighting between cDNA and protein can
3430 become sluggish with more than one splitframe shown</li>
3431 </ul> <em>Applet Known Issues</em>
3433 <li>Core PDB parsing code requires Jmol</li>
3434 <li>Sequence canvas panel goes white when alignment
3435 window is being resized</li>
3441 <td><div align="center">
3442 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3444 <td><em>General</em>
3446 <li>Updated Java code signing certificate donated by
3448 <li>Features and annotation preserved when performing
3449 pairwise alignment</li>
3450 <li>RNA pseudoknot annotation can be
3451 imported/exported/displayed</li>
3452 <li>'colour by annotation' can colour by RNA and
3453 protein secondary structure</li>
3454 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3455 post-hoc with 2.9 release</em>)
3458 </ul> <em>Application</em>
3460 <li>Extract and display secondary structure for sequences
3461 with 3D structures</li>
3462 <li>Support for parsing RNAML</li>
3463 <li>Annotations menu for layout
3465 <li>sort sequence annotation rows by alignment</li>
3466 <li>place sequence annotation above/below alignment
3469 <li>Output in Stockholm format</li>
3470 <li>Internationalisation: improved Spanish (es)
3472 <li>Structure viewer preferences tab</li>
3473 <li>Disorder and Secondary Structure annotation tracks
3474 shared between alignments</li>
3475 <li>UCSF Chimera launch and linked highlighting from
3477 <li>Show/hide all sequence associated annotation rows for
3478 all or current selection</li>
3479 <li>disorder and secondary structure predictions
3480 available as dataset annotation</li>
3481 <li>Per-sequence rna helices colouring</li>
3484 <li>Sequence database accessions imported when fetching
3485 alignments from Rfam</li>
3486 <li>update VARNA version to 3.91</li>
3488 <li>New groovy scripts for exporting aligned positions,
3489 conservation values, and calculating sum of pairs scores.</li>
3490 <li>Command line argument to set default JABAWS server</li>
3491 <li>include installation type in build properties and
3492 console log output</li>
3493 <li>Updated Jalview project format to preserve dataset
3497 <!-- issues resolved --> <em>Application</em>
3499 <li>Distinguish alignment and sequence associated RNA
3500 structure in structure->view->VARNA</li>
3501 <li>Raise dialog box if user deletes all sequences in an
3503 <li>Pressing F1 results in documentation opening twice</li>
3504 <li>Sequence feature tooltip is wrapped</li>
3505 <li>Double click on sequence associated annotation
3506 selects only first column</li>
3507 <li>Redundancy removal doesn't result in unlinked
3508 leaves shown in tree</li>
3509 <li>Undos after several redundancy removals don't undo
3511 <li>Hide sequence doesn't hide associated annotation</li>
3512 <li>User defined colours dialog box too big to fit on
3513 screen and buttons not visible</li>
3514 <li>author list isn't updated if already written to
3515 Jalview properties</li>
3516 <li>Popup menu won't open after retrieving sequence
3518 <li>File open window for associate PDB doesn't open</li>
3519 <li>Left-then-right click on a sequence id opens a
3520 browser search window</li>
3521 <li>Cannot open sequence feature shading/sort popup menu
3522 in feature settings dialog</li>
3523 <li>better tooltip placement for some areas of Jalview
3525 <li>Allow addition of JABAWS Server which doesn't
3526 pass validation</li>
3527 <li>Web services parameters dialog box is too large to
3529 <li>Muscle nucleotide alignment preset obscured by
3531 <li>JABAWS preset submenus don't contain newly
3532 defined user preset</li>
3533 <li>MSA web services warns user if they were launched
3534 with invalid input</li>
3535 <li>Jalview cannot contact DAS Registy when running on
3538 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3539 'Superpose with' submenu not shown when new view
3543 </ul> <!-- <em>Applet</em>
3545 </ul> <em>General</em>
3547 </ul>--> <em>Deployment and Documentation</em>
3549 <li>2G and 1G options in launchApp have no effect on
3550 memory allocation</li>
3551 <li>launchApp service doesn't automatically open
3552 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3554 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3555 InstallAnywhere reports cannot find valid JVM when Java
3556 1.7_055 is available
3558 </ul> <em>Application Known issues</em>
3561 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3562 corrupted or unreadable alignment display when scrolling
3566 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3567 retrieval fails but progress bar continues for DAS retrieval
3568 with large number of ID
3571 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3572 flatfile output of visible region has incorrect sequence
3576 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3577 rna structure consensus doesn't update when secondary
3578 structure tracks are rearranged
3581 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3582 invalid rna structure positional highlighting does not
3583 highlight position of invalid base pairs
3586 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3587 out of memory errors are not raised when saving Jalview
3588 project from alignment window file menu
3591 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3592 Switching to RNA Helices colouring doesn't propagate to
3596 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3597 colour by RNA Helices not enabled when user created
3598 annotation added to alignment
3601 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3602 Jalview icon not shown on dock in Mountain Lion/Webstart
3604 </ul> <em>Applet Known Issues</em>
3607 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3608 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3611 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3612 Jalview and Jmol example not compatible with IE9
3615 <li>Sort by annotation score doesn't reverse order
3621 <td><div align="center">
3622 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3625 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3628 <li>Internationalisation of user interface (usually
3629 called i18n support) and translation for Spanish locale</li>
3630 <li>Define/Undefine group on current selection with
3631 Ctrl-G/Shift Ctrl-G</li>
3632 <li>Improved group creation/removal options in
3633 alignment/sequence Popup menu</li>
3634 <li>Sensible precision for symbol distribution
3635 percentages shown in logo tooltip.</li>
3636 <li>Annotation panel height set according to amount of
3637 annotation when alignment first opened</li>
3638 </ul> <em>Application</em>
3640 <li>Interactive consensus RNA secondary structure
3641 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3642 <li>Select columns containing particular features from
3643 Feature Settings dialog</li>
3644 <li>View all 'representative' PDB structures for selected
3646 <li>Update Jalview project format:
3648 <li>New file extension for Jalview projects '.jvp'</li>
3649 <li>Preserve sequence and annotation dataset (to
3650 store secondary structure annotation,etc)</li>
3651 <li>Per group and alignment annotation and RNA helix
3655 <li>New similarity measures for PCA and Tree calculation
3657 <li>Experimental support for retrieval and viewing of
3658 flanking regions for an alignment</li>
3662 <!-- issues resolved --> <em>Application</em>
3664 <li>logo keeps spinning and status remains at queued or
3665 running after job is cancelled</li>
3666 <li>cannot export features from alignments imported from
3667 Jalview/VAMSAS projects</li>
3668 <li>Buggy slider for web service parameters that take
3670 <li>Newly created RNA secondary structure line doesn't
3671 have 'display all symbols' flag set</li>
3672 <li>T-COFFEE alignment score shading scheme and other
3673 annotation shading not saved in Jalview project</li>
3674 <li>Local file cannot be loaded in freshly downloaded
3676 <li>Jalview icon not shown on dock in Mountain
3678 <li>Load file from desktop file browser fails</li>
3679 <li>Occasional NPE thrown when calculating large trees</li>
3680 <li>Cannot reorder or slide sequences after dragging an
3681 alignment onto desktop</li>
3682 <li>Colour by annotation dialog throws NPE after using
3683 'extract scores' function</li>
3684 <li>Loading/cut'n'pasting an empty file leads to a grey
3685 alignment window</li>
3686 <li>Disorder thresholds rendered incorrectly after
3687 performing IUPred disorder prediction</li>
3688 <li>Multiple group annotated consensus rows shown when
3689 changing 'normalise logo' display setting</li>
3690 <li>Find shows blank dialog after 'finished searching' if
3691 nothing matches query</li>
3692 <li>Null Pointer Exceptions raised when sorting by
3693 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3695 <li>Errors in Jmol console when structures in alignment
3696 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3698 <li>Not all working JABAWS services are shown in
3700 <li>JAVAWS version of Jalview fails to launch with
3701 'invalid literal/length code'</li>
3702 <li>Annotation/RNA Helix colourschemes cannot be applied
3703 to alignment with groups (actually fixed in 2.8.0b1)</li>
3704 <li>RNA Helices and T-Coffee Scores available as default
3707 </ul> <em>Applet</em>
3709 <li>Remove group option is shown even when selection is
3711 <li>Apply to all groups ticked but colourscheme changes
3712 don't affect groups</li>
3713 <li>Documented RNA Helices and T-Coffee Scores as valid
3714 colourscheme name</li>
3715 <li>Annotation labels drawn on sequence IDs when
3716 Annotation panel is not displayed</li>
3717 <li>Increased font size for dropdown menus on OSX and
3718 embedded windows</li>
3719 </ul> <em>Other</em>
3721 <li>Consensus sequence for alignments/groups with a
3722 single sequence were not calculated</li>
3723 <li>annotation files that contain only groups imported as
3724 annotation and junk sequences</li>
3725 <li>Fasta files with sequences containing '*' incorrectly
3726 recognised as PFAM or BLC</li>
3727 <li>conservation/PID slider apply all groups option
3728 doesn't affect background (2.8.0b1)
3730 <li>redundancy highlighting is erratic at 0% and 100%</li>
3731 <li>Remove gapped columns fails for sequences with ragged
3733 <li>AMSA annotation row with leading spaces is not
3734 registered correctly on import</li>
3735 <li>Jalview crashes when selecting PCA analysis for
3736 certain alignments</li>
3737 <li>Opening the colour by annotation dialog for an
3738 existing annotation based 'use original colours'
3739 colourscheme loses original colours setting</li>
3744 <td><div align="center">
3745 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3746 <em>30/1/2014</em></strong>
3750 <li>Trusted certificates for JalviewLite applet and
3751 Jalview Desktop application<br />Certificate was donated by
3752 <a href="https://www.certum.eu">Certum</a> to the Jalview
3753 open source project).
3755 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3756 <li>Output in Stockholm format</li>
3757 <li>Allow import of data from gzipped files</li>
3758 <li>Export/import group and sequence associated line
3759 graph thresholds</li>
3760 <li>Nucleotide substitution matrix that supports RNA and
3761 ambiguity codes</li>
3762 <li>Allow disorder predictions to be made on the current
3763 selection (or visible selection) in the same way that JPred
3765 <li>Groovy scripting for headless Jalview operation</li>
3766 </ul> <em>Other improvements</em>
3768 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3769 <li>COMBINE statement uses current SEQUENCE_REF and
3770 GROUP_REF scope to group annotation rows</li>
3771 <li>Support '' style escaping of quotes in Newick
3773 <li>Group options for JABAWS service by command line name</li>
3774 <li>Empty tooltip shown for JABA service options with a
3775 link but no description</li>
3776 <li>Select primary source when selecting authority in
3777 database fetcher GUI</li>
3778 <li>Add .mfa to FASTA file extensions recognised by
3780 <li>Annotation label tooltip text wrap</li>
3785 <li>Slow scrolling when lots of annotation rows are
3787 <li>Lots of NPE (and slowness) after creating RNA
3788 secondary structure annotation line</li>
3789 <li>Sequence database accessions not imported when
3790 fetching alignments from Rfam</li>
3791 <li>Incorrect SHMR submission for sequences with
3793 <li>View all structures does not always superpose
3795 <li>Option widgets in service parameters not updated to
3796 reflect user or preset settings</li>
3797 <li>Null pointer exceptions for some services without
3798 presets or adjustable parameters</li>
3799 <li>Discover PDB IDs entry in structure menu doesn't
3800 discover PDB xRefs</li>
3801 <li>Exception encountered while trying to retrieve
3802 features with DAS</li>
3803 <li>Lowest value in annotation row isn't coloured
3804 when colour by annotation (per sequence) is coloured</li>
3805 <li>Keyboard mode P jumps to start of gapped region when
3806 residue follows a gap</li>
3807 <li>Jalview appears to hang importing an alignment with
3808 Wrap as default or after enabling Wrap</li>
3809 <li>'Right click to add annotations' message
3810 shown in wrap mode when no annotations present</li>
3811 <li>Disorder predictions fail with NPE if no automatic
3812 annotation already exists on alignment</li>
3813 <li>oninit javascript function should be called after
3814 initialisation completes</li>
3815 <li>Remove redundancy after disorder prediction corrupts
3816 alignment window display</li>
3817 <li>Example annotation file in documentation is invalid</li>
3818 <li>Grouped line graph annotation rows are not exported
3819 to annotation file</li>
3820 <li>Multi-harmony analysis cannot be run when only two
3822 <li>Cannot create multiple groups of line graphs with
3823 several 'combine' statements in annotation file</li>
3824 <li>Pressing return several times causes Number Format
3825 exceptions in keyboard mode</li>
3826 <li>Multi-harmony (SHMMR) method doesn't submit
3827 correct partitions for input data</li>
3828 <li>Translation from DNA to Amino Acids fails</li>
3829 <li>Jalview fail to load newick tree with quoted label</li>
3830 <li>--headless flag isn't understood</li>
3831 <li>ClassCastException when generating EPS in headless
3833 <li>Adjusting sequence-associated shading threshold only
3834 changes one row's threshold</li>
3835 <li>Preferences and Feature settings panel panel
3836 doesn't open</li>
3837 <li>hide consensus histogram also hides conservation and
3838 quality histograms</li>
3843 <td><div align="center">
3844 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3846 <td><em>Application</em>
3848 <li>Support for JABAWS 2.0 Services (AACon alignment
3849 conservation, protein disorder and Clustal Omega)</li>
3850 <li>JABAWS server status indicator in Web Services
3852 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3853 in Jalview alignment window</li>
3854 <li>Updated Jalview build and deploy framework for OSX
3855 mountain lion, windows 7, and 8</li>
3856 <li>Nucleotide substitution matrix for PCA that supports
3857 RNA and ambiguity codes</li>
3859 <li>Improved sequence database retrieval GUI</li>
3860 <li>Support fetching and database reference look up
3861 against multiple DAS sources (Fetch all from in 'fetch db
3863 <li>Jalview project improvements
3865 <li>Store and retrieve the 'belowAlignment'
3866 flag for annotation</li>
3867 <li>calcId attribute to group annotation rows on the
3869 <li>Store AACon calculation settings for a view in
3870 Jalview project</li>
3874 <li>horizontal scrolling gesture support</li>
3875 <li>Visual progress indicator when PCA calculation is
3877 <li>Simpler JABA web services menus</li>
3878 <li>visual indication that web service results are still
3879 being retrieved from server</li>
3880 <li>Serialise the dialogs that are shown when Jalview
3881 starts up for first time</li>
3882 <li>Jalview user agent string for interacting with HTTP
3884 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3886 <li>Examples directory and Groovy library included in
3887 InstallAnywhere distribution</li>
3888 </ul> <em>Applet</em>
3890 <li>RNA alignment and secondary structure annotation
3891 visualization applet example</li>
3892 </ul> <em>General</em>
3894 <li>Normalise option for consensus sequence logo</li>
3895 <li>Reset button in PCA window to return dimensions to
3897 <li>Allow seqspace or Jalview variant of alignment PCA
3899 <li>PCA with either nucleic acid and protein substitution
3901 <li>Allow windows containing HTML reports to be exported
3903 <li>Interactive display and editing of RNA secondary
3904 structure contacts</li>
3905 <li>RNA Helix Alignment Colouring</li>
3906 <li>RNA base pair logo consensus</li>
3907 <li>Parse sequence associated secondary structure
3908 information in Stockholm files</li>
3909 <li>HTML Export database accessions and annotation
3910 information presented in tooltip for sequences</li>
3911 <li>Import secondary structure from LOCARNA clustalw
3912 style RNA alignment files</li>
3913 <li>import and visualise T-COFFEE quality scores for an
3915 <li>'colour by annotation' per sequence option to
3916 shade each sequence according to its associated alignment
3918 <li>New Jalview Logo</li>
3919 </ul> <em>Documentation and Development</em>
3921 <li>documentation for score matrices used in Jalview</li>
3922 <li>New Website!</li>
3924 <td><em>Application</em>
3926 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3927 wsdbfetch REST service</li>
3928 <li>Stop windows being moved outside desktop on OSX</li>
3929 <li>Filetype associations not installed for webstart
3931 <li>Jalview does not always retrieve progress of a JABAWS
3932 job execution in full once it is complete</li>
3933 <li>revise SHMR RSBS definition to ensure alignment is
3934 uploaded via ali_file parameter</li>
3935 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3936 <li>View all structures superposed fails with exception</li>
3937 <li>Jnet job queues forever if a very short sequence is
3938 submitted for prediction</li>
3939 <li>Cut and paste menu not opened when mouse clicked on
3941 <li>Putting fractional value into integer text box in
3942 alignment parameter dialog causes Jalview to hang</li>
3943 <li>Structure view highlighting doesn't work on
3945 <li>View all structures fails with exception shown in
3947 <li>Characters in filename associated with PDBEntry not
3948 escaped in a platform independent way</li>
3949 <li>Jalview desktop fails to launch with exception when
3951 <li>Tree calculation reports 'you must have 2 or more
3952 sequences selected' when selection is empty</li>
3953 <li>Jalview desktop fails to launch with jar signature
3954 failure when java web start temporary file caching is
3956 <li>DAS Sequence retrieval with range qualification
3957 results in sequence xref which includes range qualification</li>
3958 <li>Errors during processing of command line arguments
3959 cause progress bar (JAL-898) to be removed</li>
3960 <li>Replace comma for semi-colon option not disabled for
3961 DAS sources in sequence fetcher</li>
3962 <li>Cannot close news reader when JABAWS server warning
3963 dialog is shown</li>
3964 <li>Option widgets not updated to reflect user settings</li>
3965 <li>Edited sequence not submitted to web service</li>
3966 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3967 <li>InstallAnywhere installer doesn't unpack and run
3968 on OSX Mountain Lion</li>
3969 <li>Annotation panel not given a scroll bar when
3970 sequences with alignment annotation are pasted into the
3972 <li>Sequence associated annotation rows not associated
3973 when loaded from Jalview project</li>
3974 <li>Browser launch fails with NPE on java 1.7</li>
3975 <li>JABAWS alignment marked as finished when job was
3976 cancelled or job failed due to invalid input</li>
3977 <li>NPE with v2.7 example when clicking on Tree
3978 associated with all views</li>
3979 <li>Exceptions when copy/paste sequences with grouped
3980 annotation rows to new window</li>
3981 </ul> <em>Applet</em>
3983 <li>Sequence features are momentarily displayed before
3984 they are hidden using hidefeaturegroups applet parameter</li>
3985 <li>loading features via javascript API automatically
3986 enables feature display</li>
3987 <li>scrollToColumnIn javascript API method doesn't
3989 </ul> <em>General</em>
3991 <li>Redundancy removal fails for rna alignment</li>
3992 <li>PCA calculation fails when sequence has been selected
3993 and then deselected</li>
3994 <li>PCA window shows grey box when first opened on OSX</li>
3995 <li>Letters coloured pink in sequence logo when alignment
3996 coloured with clustalx</li>
3997 <li>Choosing fonts without letter symbols defined causes
3998 exceptions and redraw errors</li>
3999 <li>Initial PCA plot view is not same as manually
4000 reconfigured view</li>
4001 <li>Grouped annotation graph label has incorrect line
4003 <li>Grouped annotation graph label display is corrupted
4004 for lots of labels</li>
4009 <div align="center">
4010 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4013 <td><em>Application</em>
4015 <li>Jalview Desktop News Reader</li>
4016 <li>Tweaked default layout of web services menu</li>
4017 <li>View/alignment association menu to enable user to
4018 easily specify which alignment a multi-structure view takes
4019 its colours/correspondences from</li>
4020 <li>Allow properties file location to be specified as URL</li>
4021 <li>Extend Jalview project to preserve associations
4022 between many alignment views and a single Jmol display</li>
4023 <li>Store annotation row height in Jalview project file</li>
4024 <li>Annotation row column label formatting attributes
4025 stored in project file</li>
4026 <li>Annotation row order for auto-calculated annotation
4027 rows preserved in Jalview project file</li>
4028 <li>Visual progress indication when Jalview state is
4029 saved using Desktop window menu</li>
4030 <li>Visual indication that command line arguments are
4031 still being processed</li>
4032 <li>Groovy script execution from URL</li>
4033 <li>Colour by annotation default min and max colours in
4035 <li>Automatically associate PDB files dragged onto an
4036 alignment with sequences that have high similarity and
4038 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4039 <li>'view structures' option to open many
4040 structures in same window</li>
4041 <li>Sort associated views menu option for tree panel</li>
4042 <li>Group all JABA and non-JABA services for a particular
4043 analysis function in its own submenu</li>
4044 </ul> <em>Applet</em>
4046 <li>Userdefined and autogenerated annotation rows for
4048 <li>Adjustment of alignment annotation pane height</li>
4049 <li>Annotation scrollbar for annotation panel</li>
4050 <li>Drag to reorder annotation rows in annotation panel</li>
4051 <li>'automaticScrolling' parameter</li>
4052 <li>Allow sequences with partial ID string matches to be
4053 annotated from GFF/Jalview features files</li>
4054 <li>Sequence logo annotation row in applet</li>
4055 <li>Absolute paths relative to host server in applet
4056 parameters are treated as such</li>
4057 <li>New in the JalviewLite javascript API:
4059 <li>JalviewLite.js javascript library</li>
4060 <li>Javascript callbacks for
4062 <li>Applet initialisation</li>
4063 <li>Sequence/alignment mouse-overs and selections</li>
4066 <li>scrollTo row and column alignment scrolling
4068 <li>Select sequence/alignment regions from javascript</li>
4069 <li>javascript structure viewer harness to pass
4070 messages between Jmol and Jalview when running as
4071 distinct applets</li>
4072 <li>sortBy method</li>
4073 <li>Set of applet and application examples shipped
4074 with documentation</li>
4075 <li>New example to demonstrate JalviewLite and Jmol
4076 javascript message exchange</li>
4078 </ul> <em>General</em>
4080 <li>Enable Jmol displays to be associated with multiple
4081 multiple alignments</li>
4082 <li>Option to automatically sort alignment with new tree</li>
4083 <li>User configurable link to enable redirects to a
4084 www.Jalview.org mirror</li>
4085 <li>Jmol colours option for Jmol displays</li>
4086 <li>Configurable newline string when writing alignment
4087 and other flat files</li>
4088 <li>Allow alignment annotation description lines to
4089 contain html tags</li>
4090 </ul> <em>Documentation and Development</em>
4092 <li>Add groovy test harness for bulk load testing to
4094 <li>Groovy script to load and align a set of sequences
4095 using a web service before displaying the result in the
4096 Jalview desktop</li>
4097 <li>Restructured javascript and applet api documentation</li>
4098 <li>Ant target to publish example html files with applet
4100 <li>Netbeans project for building Jalview from source</li>
4101 <li>ant task to create online javadoc for Jalview source</li>
4103 <td><em>Application</em>
4105 <li>User defined colourscheme throws exception when
4106 current built in colourscheme is saved as new scheme</li>
4107 <li>AlignFrame->Save in application pops up save
4108 dialog for valid filename/format</li>
4109 <li>Cannot view associated structure for UniProt sequence</li>
4110 <li>PDB file association breaks for UniProt sequence
4112 <li>Associate PDB from file dialog does not tell you
4113 which sequence is to be associated with the file</li>
4114 <li>Find All raises null pointer exception when query
4115 only matches sequence IDs</li>
4116 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4117 <li>Jalview project with Jmol views created with Jalview
4118 2.4 cannot be loaded</li>
4119 <li>Filetype associations not installed for webstart
4121 <li>Two or more chains in a single PDB file associated
4122 with sequences in different alignments do not get coloured
4123 by their associated sequence</li>
4124 <li>Visibility status of autocalculated annotation row
4125 not preserved when project is loaded</li>
4126 <li>Annotation row height and visibility attributes not
4127 stored in Jalview project</li>
4128 <li>Tree bootstraps are not preserved when saved as a
4129 Jalview project</li>
4130 <li>Envision2 workflow tooltips are corrupted</li>
4131 <li>Enabling show group conservation also enables colour
4132 by conservation</li>
4133 <li>Duplicate group associated conservation or consensus
4134 created on new view</li>
4135 <li>Annotation scrollbar not displayed after 'show
4136 all hidden annotation rows' option selected</li>
4137 <li>Alignment quality not updated after alignment
4138 annotation row is hidden then shown</li>
4139 <li>Preserve colouring of structures coloured by
4140 sequences in pre Jalview 2.7 projects</li>
4141 <li>Web service job parameter dialog is not laid out
4143 <li>Web services menu not refreshed after 'reset
4144 services' button is pressed in preferences</li>
4145 <li>Annotation off by one in Jalview v2_3 example project</li>
4146 <li>Structures imported from file and saved in project
4147 get name like jalview_pdb1234.txt when reloaded</li>
4148 <li>Jalview does not always retrieve progress of a JABAWS
4149 job execution in full once it is complete</li>
4150 </ul> <em>Applet</em>
4152 <li>Alignment height set incorrectly when lots of
4153 annotation rows are displayed</li>
4154 <li>Relative URLs in feature HTML text not resolved to
4156 <li>View follows highlighting does not work for positions
4158 <li><= shown as = in tooltip</li>
4159 <li>Export features raises exception when no features
4161 <li>Separator string used for serialising lists of IDs
4162 for javascript api is modified when separator string
4163 provided as parameter</li>
4164 <li>Null pointer exception when selecting tree leaves for
4165 alignment with no existing selection</li>
4166 <li>Relative URLs for datasources assumed to be relative
4167 to applet's codebase</li>
4168 <li>Status bar not updated after finished searching and
4169 search wraps around to first result</li>
4170 <li>StructureSelectionManager instance shared between
4171 several Jalview applets causes race conditions and memory
4173 <li>Hover tooltip and mouseover of position on structure
4174 not sent from Jmol in applet</li>
4175 <li>Certain sequences of javascript method calls to
4176 applet API fatally hang browser</li>
4177 </ul> <em>General</em>
4179 <li>View follows structure mouseover scrolls beyond
4180 position with wrapped view and hidden regions</li>
4181 <li>Find sequence position moves to wrong residue
4182 with/without hidden columns</li>
4183 <li>Sequence length given in alignment properties window
4185 <li>InvalidNumberFormat exceptions thrown when trying to
4186 import PDB like structure files</li>
4187 <li>Positional search results are only highlighted
4188 between user-supplied sequence start/end bounds</li>
4189 <li>End attribute of sequence is not validated</li>
4190 <li>Find dialog only finds first sequence containing a
4191 given sequence position</li>
4192 <li>Sequence numbering not preserved in MSF alignment
4194 <li>Jalview PDB file reader does not extract sequence
4195 from nucleotide chains correctly</li>
4196 <li>Structure colours not updated when tree partition
4197 changed in alignment</li>
4198 <li>Sequence associated secondary structure not correctly
4199 parsed in interleaved stockholm</li>
4200 <li>Colour by annotation dialog does not restore current
4202 <li>Hiding (nearly) all sequences doesn't work
4204 <li>Sequences containing lowercase letters are not
4205 properly associated with their pdb files</li>
4206 </ul> <em>Documentation and Development</em>
4208 <li>schemas/JalviewWsParamSet.xsd corrupted by
4209 ApplyCopyright tool</li>
4214 <div align="center">
4215 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4218 <td><em>Application</em>
4220 <li>New warning dialog when the Jalview Desktop cannot
4221 contact web services</li>
4222 <li>JABA service parameters for a preset are shown in
4223 service job window</li>
4224 <li>JABA Service menu entries reworded</li>
4228 <li>Modeller PIR IO broken - cannot correctly import a
4229 pir file emitted by Jalview</li>
4230 <li>Existing feature settings transferred to new
4231 alignment view created from cut'n'paste</li>
4232 <li>Improved test for mixed amino/nucleotide chains when
4233 parsing PDB files</li>
4234 <li>Consensus and conservation annotation rows
4235 occasionally become blank for all new windows</li>
4236 <li>Exception raised when right clicking above sequences
4237 in wrapped view mode</li>
4238 </ul> <em>Application</em>
4240 <li>multiple multiply aligned structure views cause cpu
4241 usage to hit 100% and computer to hang</li>
4242 <li>Web Service parameter layout breaks for long user
4243 parameter names</li>
4244 <li>Jaba service discovery hangs desktop if Jaba server
4251 <div align="center">
4252 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4255 <td><em>Application</em>
4257 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4258 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4261 <li>Web Services preference tab</li>
4262 <li>Analysis parameters dialog box and user defined
4264 <li>Improved speed and layout of Envision2 service menu</li>
4265 <li>Superpose structures using associated sequence
4267 <li>Export coordinates and projection as CSV from PCA
4269 </ul> <em>Applet</em>
4271 <li>enable javascript: execution by the applet via the
4272 link out mechanism</li>
4273 </ul> <em>Other</em>
4275 <li>Updated the Jmol Jalview interface to work with Jmol
4277 <li>The Jalview Desktop and JalviewLite applet now
4278 require Java 1.5</li>
4279 <li>Allow Jalview feature colour specification for GFF
4280 sequence annotation files</li>
4281 <li>New 'colour by label' keword in Jalview feature file
4282 type colour specification</li>
4283 <li>New Jalview Desktop Groovy API method that allows a
4284 script to check if it being run in an interactive session or
4285 in a batch operation from the Jalview command line</li>
4289 <li>clustalx colourscheme colours Ds preferentially when
4290 both D+E are present in over 50% of the column</li>
4291 </ul> <em>Application</em>
4293 <li>typo in AlignmentFrame->View->Hide->all but
4294 selected Regions menu item</li>
4295 <li>sequence fetcher replaces ',' for ';' when the ',' is
4296 part of a valid accession ID</li>
4297 <li>fatal OOM if object retrieved by sequence fetcher
4298 runs out of memory</li>
4299 <li>unhandled Out of Memory Error when viewing pca
4300 analysis results</li>
4301 <li>InstallAnywhere builds fail to launch on OS X java
4302 10.5 update 4 (due to apple Java 1.6 update)</li>
4303 <li>Installanywhere Jalview silently fails to launch</li>
4304 </ul> <em>Applet</em>
4306 <li>Jalview.getFeatureGroups() raises an
4307 ArrayIndexOutOfBoundsException if no feature groups are
4314 <div align="center">
4315 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4321 <li>Alignment prettyprinter doesn't cope with long
4323 <li>clustalx colourscheme colours Ds preferentially when
4324 both D+E are present in over 50% of the column</li>
4325 <li>nucleic acid structures retrieved from PDB do not
4326 import correctly</li>
4327 <li>More columns get selected than were clicked on when a
4328 number of columns are hidden</li>
4329 <li>annotation label popup menu not providing correct
4330 add/hide/show options when rows are hidden or none are
4332 <li>Stockholm format shown in list of readable formats,
4333 and parser copes better with alignments from RFAM.</li>
4334 <li>CSV output of consensus only includes the percentage
4335 of all symbols if sequence logo display is enabled</li>
4337 </ul> <em>Applet</em>
4339 <li>annotation panel disappears when annotation is
4341 </ul> <em>Application</em>
4343 <li>Alignment view not redrawn properly when new
4344 alignment opened where annotation panel is visible but no
4345 annotations are present on alignment</li>
4346 <li>pasted region containing hidden columns is
4347 incorrectly displayed in new alignment window</li>
4348 <li>Jalview slow to complete operations when stdout is
4349 flooded (fix is to close the Jalview console)</li>
4350 <li>typo in AlignmentFrame->View->Hide->all but
4351 selected Rregions menu item.</li>
4352 <li>inconsistent group submenu and Format submenu entry
4353 'Un' or 'Non'conserved</li>
4354 <li>Sequence feature settings are being shared by
4355 multiple distinct alignments</li>
4356 <li>group annotation not recreated when tree partition is
4358 <li>double click on group annotation to select sequences
4359 does not propagate to associated trees</li>
4360 <li>Mac OSX specific issues:
4362 <li>exception raised when mouse clicked on desktop
4363 window background</li>
4364 <li>Desktop menu placed on menu bar and application
4365 name set correctly</li>
4366 <li>sequence feature settings not wide enough for the
4367 save feature colourscheme button</li>
4376 <div align="center">
4377 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4380 <td><em>New Capabilities</em>
4382 <li>URL links generated from description line for
4383 regular-expression based URL links (applet and application)
4385 <li>Non-positional feature URL links are shown in link
4387 <li>Linked viewing of nucleic acid sequences and
4389 <li>Automatic Scrolling option in View menu to display
4390 the currently highlighted region of an alignment.</li>
4391 <li>Order an alignment by sequence length, or using the
4392 average score or total feature count for each sequence.</li>
4393 <li>Shading features by score or associated description</li>
4394 <li>Subdivide alignment and groups based on identity of
4395 selected subsequence (Make Groups from Selection).</li>
4396 <li>New hide/show options including Shift+Control+H to
4397 hide everything but the currently selected region.</li>
4398 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4399 </ul> <em>Application</em>
4401 <li>Fetch DB References capabilities and UI expanded to
4402 support retrieval from DAS sequence sources</li>
4403 <li>Local DAS Sequence sources can be added via the
4404 command line or via the Add local source dialog box.</li>
4405 <li>DAS Dbref and DbxRef feature types are parsed as
4406 database references and protein_name is parsed as
4407 description line (BioSapiens terms).</li>
4408 <li>Enable or disable non-positional feature and database
4409 references in sequence ID tooltip from View menu in
4411 <!-- <li>New hidden columns and rows and representatives capabilities
4412 in annotations file (in progress - not yet fully implemented)</li> -->
4413 <li>Group-associated consensus, sequence logos and
4414 conservation plots</li>
4415 <li>Symbol distributions for each column can be exported
4416 and visualized as sequence logos</li>
4417 <li>Optionally scale multi-character column labels to fit
4418 within each column of annotation row<!-- todo for applet -->
4420 <li>Optional automatic sort of associated alignment view
4421 when a new tree is opened.</li>
4422 <li>Jalview Java Console</li>
4423 <li>Better placement of desktop window when moving
4424 between different screens.</li>
4425 <li>New preference items for sequence ID tooltip and
4426 consensus annotation</li>
4427 <li>Client to submit sequences and IDs to Envision2
4429 <li><em>Vamsas Capabilities</em>
4431 <li>Improved VAMSAS synchronization (Jalview archive
4432 used to preserve views, structures, and tree display
4434 <li>Import of vamsas documents from disk or URL via
4436 <li>Sharing of selected regions between views and
4437 with other VAMSAS applications (Experimental feature!)</li>
4438 <li>Updated API to VAMSAS version 0.2</li>
4440 </ul> <em>Applet</em>
4442 <li>Middle button resizes annotation row height</li>
4445 <li>sortByTree (true/false) - automatically sort the
4446 associated alignment view by the tree when a new tree is
4448 <li>showTreeBootstraps (true/false) - show or hide
4449 branch bootstraps (default is to show them if available)</li>
4450 <li>showTreeDistances (true/false) - show or hide
4451 branch lengths (default is to show them if available)</li>
4452 <li>showUnlinkedTreeNodes (true/false) - indicate if
4453 unassociated nodes should be highlighted in the tree
4455 <li>heightScale and widthScale (1.0 or more) -
4456 increase the height or width of a cell in the alignment
4457 grid relative to the current font size.</li>
4460 <li>Non-positional features displayed in sequence ID
4462 </ul> <em>Other</em>
4464 <li>Features format: graduated colour definitions and
4465 specification of feature scores</li>
4466 <li>Alignment Annotations format: new keywords for group
4467 associated annotation (GROUP_REF) and annotation row display
4468 properties (ROW_PROPERTIES)</li>
4469 <li>XML formats extended to support graduated feature
4470 colourschemes, group associated annotation, and profile
4471 visualization settings.</li></td>
4474 <li>Source field in GFF files parsed as feature source
4475 rather than description</li>
4476 <li>Non-positional features are now included in sequence
4477 feature and gff files (controlled via non-positional feature
4478 visibility in tooltip).</li>
4479 <li>URL links generated for all feature links (bugfix)</li>
4480 <li>Added URL embedding instructions to features file
4482 <li>Codons containing ambiguous nucleotides translated as
4483 'X' in peptide product</li>
4484 <li>Match case switch in find dialog box works for both
4485 sequence ID and sequence string and query strings do not
4486 have to be in upper case to match case-insensitively.</li>
4487 <li>AMSA files only contain first column of
4488 multi-character column annotation labels</li>
4489 <li>Jalview Annotation File generation/parsing consistent
4490 with documentation (e.g. Stockholm annotation can be
4491 exported and re-imported)</li>
4492 <li>PDB files without embedded PDB IDs given a friendly
4494 <li>Find incrementally searches ID string matches as well
4495 as subsequence matches, and correctly reports total number
4499 <li>Better handling of exceptions during sequence
4501 <li>Dasobert generated non-positional feature URL
4502 link text excludes the start_end suffix</li>
4503 <li>DAS feature and source retrieval buttons disabled
4504 when fetch or registry operations in progress.</li>
4505 <li>PDB files retrieved from URLs are cached properly</li>
4506 <li>Sequence description lines properly shared via
4508 <li>Sequence fetcher fetches multiple records for all
4510 <li>Ensured that command line das feature retrieval
4511 completes before alignment figures are generated.</li>
4512 <li>Reduced time taken when opening file browser for
4514 <li>isAligned check prior to calculating tree, PCA or
4515 submitting an MSA to JNet now excludes hidden sequences.</li>
4516 <li>User defined group colours properly recovered
4517 from Jalview projects.</li>
4526 <div align="center">
4527 <strong>2.4.0.b2</strong><br> 28/10/2009
4532 <li>Experimental support for google analytics usage
4534 <li>Jalview privacy settings (user preferences and docs).</li>
4539 <li>Race condition in applet preventing startup in
4541 <li>Exception when feature created from selection beyond
4542 length of sequence.</li>
4543 <li>Allow synthetic PDB files to be imported gracefully</li>
4544 <li>Sequence associated annotation rows associate with
4545 all sequences with a given id</li>
4546 <li>Find function matches case-insensitively for sequence
4547 ID string searches</li>
4548 <li>Non-standard characters do not cause pairwise
4549 alignment to fail with exception</li>
4550 </ul> <em>Application Issues</em>
4552 <li>Sequences are now validated against EMBL database</li>
4553 <li>Sequence fetcher fetches multiple records for all
4555 </ul> <em>InstallAnywhere Issues</em>
4557 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4558 issue with installAnywhere mechanism)</li>
4559 <li>Command line launching of JARs from InstallAnywhere
4560 version (java class versioning error fixed)</li>
4567 <div align="center">
4568 <strong>2.4</strong><br> 27/8/2008
4571 <td><em>User Interface</em>
4573 <li>Linked highlighting of codon and amino acid from
4574 translation and protein products</li>
4575 <li>Linked highlighting of structure associated with
4576 residue mapping to codon position</li>
4577 <li>Sequence Fetcher provides example accession numbers
4578 and 'clear' button</li>
4579 <li>MemoryMonitor added as an option under Desktop's
4581 <li>Extract score function to parse whitespace separated
4582 numeric data in description line</li>
4583 <li>Column labels in alignment annotation can be centred.</li>
4584 <li>Tooltip for sequence associated annotation give name
4586 </ul> <em>Web Services and URL fetching</em>
4588 <li>JPred3 web service</li>
4589 <li>Prototype sequence search client (no public services
4591 <li>Fetch either seed alignment or full alignment from
4593 <li>URL Links created for matching database cross
4594 references as well as sequence ID</li>
4595 <li>URL Links can be created using regular-expressions</li>
4596 </ul> <em>Sequence Database Connectivity</em>
4598 <li>Retrieval of cross-referenced sequences from other
4600 <li>Generalised database reference retrieval and
4601 validation to all fetchable databases</li>
4602 <li>Fetch sequences from DAS sources supporting the
4603 sequence command</li>
4604 </ul> <em>Import and Export</em>
4605 <li>export annotation rows as CSV for spreadsheet import</li>
4606 <li>Jalview projects record alignment dataset associations,
4607 EMBL products, and cDNA sequence mappings</li>
4608 <li>Sequence Group colour can be specified in Annotation
4610 <li>Ad-hoc colouring of group in Annotation File using RGB
4611 triplet as name of colourscheme</li>
4612 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4614 <li>treenode binding for VAMSAS tree exchange</li>
4615 <li>local editing and update of sequences in VAMSAS
4616 alignments (experimental)</li>
4617 <li>Create new or select existing session to join</li>
4618 <li>load and save of vamsas documents</li>
4619 </ul> <em>Application command line</em>
4621 <li>-tree parameter to open trees (introduced for passing
4623 <li>-fetchfrom command line argument to specify nicknames
4624 of DAS servers to query for alignment features</li>
4625 <li>-dasserver command line argument to add new servers
4626 that are also automatically queried for features</li>
4627 <li>-groovy command line argument executes a given groovy
4628 script after all input data has been loaded and parsed</li>
4629 </ul> <em>Applet-Application data exchange</em>
4631 <li>Trees passed as applet parameters can be passed to
4632 application (when using "View in full
4633 application")</li>
4634 </ul> <em>Applet Parameters</em>
4636 <li>feature group display control parameter</li>
4637 <li>debug parameter</li>
4638 <li>showbutton parameter</li>
4639 </ul> <em>Applet API methods</em>
4641 <li>newView public method</li>
4642 <li>Window (current view) specific get/set public methods</li>
4643 <li>Feature display control methods</li>
4644 <li>get list of currently selected sequences</li>
4645 </ul> <em>New Jalview distribution features</em>
4647 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4648 <li>RELEASE file gives build properties for the latest
4649 Jalview release.</li>
4650 <li>Java 1.1 Applet build made easier and donotobfuscate
4651 property controls execution of obfuscator</li>
4652 <li>Build target for generating source distribution</li>
4653 <li>Debug flag for javacc</li>
4654 <li>.jalview_properties file is documented (slightly) in
4655 jalview.bin.Cache</li>
4656 <li>Continuous Build Integration for stable and
4657 development version of Application, Applet and source
4662 <li>selected region output includes visible annotations
4663 (for certain formats)</li>
4664 <li>edit label/displaychar contains existing label/char
4666 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4667 <li>shorter peptide product names from EMBL records</li>
4668 <li>Newick string generator makes compact representations</li>
4669 <li>bootstrap values parsed correctly for tree files with
4671 <li>pathological filechooser bug avoided by not allowing
4672 filenames containing a ':'</li>
4673 <li>Fixed exception when parsing GFF files containing
4674 global sequence features</li>
4675 <li>Alignment datasets are finalized only when number of
4676 references from alignment sequences goes to zero</li>
4677 <li>Close of tree branch colour box without colour
4678 selection causes cascading exceptions</li>
4679 <li>occasional negative imgwidth exceptions</li>
4680 <li>better reporting of non-fatal warnings to user when
4681 file parsing fails.</li>
4682 <li>Save works when Jalview project is default format</li>
4683 <li>Save as dialog opened if current alignment format is
4684 not a valid output format</li>
4685 <li>UniProt canonical names introduced for both das and
4687 <li>Histidine should be midblue (not pink!) in Zappo</li>
4688 <li>error messages passed up and output when data read
4690 <li>edit undo recovers previous dataset sequence when
4691 sequence is edited</li>
4692 <li>allow PDB files without pdb ID HEADER lines (like
4693 those generated by MODELLER) to be read in properly</li>
4694 <li>allow reading of JPred concise files as a normal
4696 <li>Stockholm annotation parsing and alignment properties
4697 import fixed for PFAM records</li>
4698 <li>Structure view windows have correct name in Desktop
4700 <li>annotation consisting of sequence associated scores
4701 can be read and written correctly to annotation file</li>
4702 <li>Aligned cDNA translation to aligned peptide works
4704 <li>Fixed display of hidden sequence markers and
4705 non-italic font for representatives in Applet</li>
4706 <li>Applet Menus are always embedded in applet window on
4708 <li>Newly shown features appear at top of stack (in
4710 <li>Annotations added via parameter not drawn properly
4711 due to null pointer exceptions</li>
4712 <li>Secondary structure lines are drawn starting from
4713 first column of alignment</li>
4714 <li>UniProt XML import updated for new schema release in
4716 <li>Sequence feature to sequence ID match for Features
4717 file is case-insensitive</li>
4718 <li>Sequence features read from Features file appended to
4719 all sequences with matching IDs</li>
4720 <li>PDB structure coloured correctly for associated views
4721 containing a sub-sequence</li>
4722 <li>PDB files can be retrieved by applet from Jar files</li>
4723 <li>feature and annotation file applet parameters
4724 referring to different directories are retrieved correctly</li>
4725 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4726 <li>Fixed application hang whilst waiting for
4727 splash-screen version check to complete</li>
4728 <li>Applet properly URLencodes input parameter values
4729 when passing them to the launchApp service</li>
4730 <li>display name and local features preserved in results
4731 retrieved from web service</li>
4732 <li>Visual delay indication for sequence retrieval and
4733 sequence fetcher initialisation</li>
4734 <li>updated Application to use DAS 1.53e version of
4735 dasobert DAS client</li>
4736 <li>Re-instated Full AMSA support and .amsa file
4738 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4746 <div align="center">
4747 <strong>2.3</strong><br> 9/5/07
4752 <li>Jmol 11.0.2 integration</li>
4753 <li>PDB views stored in Jalview XML files</li>
4754 <li>Slide sequences</li>
4755 <li>Edit sequence in place</li>
4756 <li>EMBL CDS features</li>
4757 <li>DAS Feature mapping</li>
4758 <li>Feature ordering</li>
4759 <li>Alignment Properties</li>
4760 <li>Annotation Scores</li>
4761 <li>Sort by scores</li>
4762 <li>Feature/annotation editing in applet</li>
4767 <li>Headless state operation in 2.2.1</li>
4768 <li>Incorrect and unstable DNA pairwise alignment</li>
4769 <li>Cut and paste of sequences with annotation</li>
4770 <li>Feature group display state in XML</li>
4771 <li>Feature ordering in XML</li>
4772 <li>blc file iteration selection using filename # suffix</li>
4773 <li>Stockholm alignment properties</li>
4774 <li>Stockhom alignment secondary structure annotation</li>
4775 <li>2.2.1 applet had no feature transparency</li>
4776 <li>Number pad keys can be used in cursor mode</li>
4777 <li>Structure Viewer mirror image resolved</li>
4784 <div align="center">
4785 <strong>2.2.1</strong><br> 12/2/07
4790 <li>Non standard characters can be read and displayed
4791 <li>Annotations/Features can be imported/exported to the
4793 <li>Applet allows editing of sequence/annotation/group
4794 name & description
4795 <li>Preference setting to display sequence name in
4797 <li>Annotation file format extended to allow
4798 Sequence_groups to be defined
4799 <li>Default opening of alignment overview panel can be
4800 specified in preferences
4801 <li>PDB residue numbering annotation added to associated
4807 <li>Applet crash under certain Linux OS with Java 1.6
4809 <li>Annotation file export / import bugs fixed
4810 <li>PNG / EPS image output bugs fixed
4816 <div align="center">
4817 <strong>2.2</strong><br> 27/11/06
4822 <li>Multiple views on alignment
4823 <li>Sequence feature editing
4824 <li>"Reload" alignment
4825 <li>"Save" to current filename
4826 <li>Background dependent text colour
4827 <li>Right align sequence ids
4828 <li>User-defined lower case residue colours
4831 <li>Menu item accelerator keys
4832 <li>Control-V pastes to current alignment
4833 <li>Cancel button for DAS Feature Fetching
4834 <li>PCA and PDB Viewers zoom via mouse roller
4835 <li>User-defined sub-tree colours and sub-tree selection
4837 <li>'New Window' button on the 'Output to Text box'
4842 <li>New memory efficient Undo/Redo System
4843 <li>Optimised symbol lookups and conservation/consensus
4845 <li>Region Conservation/Consensus recalculated after
4847 <li>Fixed Remove Empty Columns Bug (empty columns at end
4849 <li>Slowed DAS Feature Fetching for increased robustness.
4851 <li>Made angle brackets in ASCII feature descriptions
4853 <li>Re-instated Zoom function for PCA
4854 <li>Sequence descriptions conserved in web service
4856 <li>UniProt ID discoverer uses any word separated by
4858 <li>WsDbFetch query/result association resolved
4859 <li>Tree leaf to sequence mapping improved
4860 <li>Smooth fonts switch moved to FontChooser dialog box.
4867 <div align="center">
4868 <strong>2.1.1</strong><br> 12/9/06
4873 <li>Copy consensus sequence to clipboard</li>
4878 <li>Image output - rightmost residues are rendered if
4879 sequence id panel has been resized</li>
4880 <li>Image output - all offscreen group boundaries are
4882 <li>Annotation files with sequence references - all
4883 elements in file are relative to sequence position</li>
4884 <li>Mac Applet users can use Alt key for group editing</li>
4890 <div align="center">
4891 <strong>2.1</strong><br> 22/8/06
4896 <li>MAFFT Multiple Alignment in default Web Service list</li>
4897 <li>DAS Feature fetching</li>
4898 <li>Hide sequences and columns</li>
4899 <li>Export Annotations and Features</li>
4900 <li>GFF file reading / writing</li>
4901 <li>Associate structures with sequences from local PDB
4903 <li>Add sequences to exisiting alignment</li>
4904 <li>Recently opened files / URL lists</li>
4905 <li>Applet can launch the full application</li>
4906 <li>Applet has transparency for features (Java 1.2
4908 <li>Applet has user defined colours parameter</li>
4909 <li>Applet can load sequences from parameter
4910 "sequence<em>x</em>"
4916 <li>Redundancy Panel reinstalled in the Applet</li>
4917 <li>Monospaced font - EPS / rescaling bug fixed</li>
4918 <li>Annotation files with sequence references bug fixed</li>
4924 <div align="center">
4925 <strong>2.08.1</strong><br> 2/5/06
4930 <li>Change case of selected region from Popup menu</li>
4931 <li>Choose to match case when searching</li>
4932 <li>Middle mouse button and mouse movement can compress /
4933 expand the visible width and height of the alignment</li>
4938 <li>Annotation Panel displays complete JNet results</li>
4944 <div align="center">
4945 <strong>2.08b</strong><br> 18/4/06
4951 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4952 <li>Righthand label on wrapped alignments shows correct
4959 <div align="center">
4960 <strong>2.08</strong><br> 10/4/06
4965 <li>Editing can be locked to the selection area</li>
4966 <li>Keyboard editing</li>
4967 <li>Create sequence features from searches</li>
4968 <li>Precalculated annotations can be loaded onto
4970 <li>Features file allows grouping of features</li>
4971 <li>Annotation Colouring scheme added</li>
4972 <li>Smooth fonts off by default - Faster rendering</li>
4973 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4978 <li>Drag & Drop fixed on Linux</li>
4979 <li>Jalview Archive file faster to load/save, sequence
4980 descriptions saved.</li>
4986 <div align="center">
4987 <strong>2.07</strong><br> 12/12/05
4992 <li>PDB Structure Viewer enhanced</li>
4993 <li>Sequence Feature retrieval and display enhanced</li>
4994 <li>Choose to output sequence start-end after sequence
4995 name for file output</li>
4996 <li>Sequence Fetcher WSDBFetch@EBI</li>
4997 <li>Applet can read feature files, PDB files and can be
4998 used for HTML form input</li>
5003 <li>HTML output writes groups and features</li>
5004 <li>Group editing is Control and mouse click</li>
5005 <li>File IO bugs</li>
5011 <div align="center">
5012 <strong>2.06</strong><br> 28/9/05
5017 <li>View annotations in wrapped mode</li>
5018 <li>More options for PCA viewer</li>
5023 <li>GUI bugs resolved</li>
5024 <li>Runs with -nodisplay from command line</li>
5030 <div align="center">
5031 <strong>2.05b</strong><br> 15/9/05
5036 <li>Choose EPS export as lineart or text</li>
5037 <li>Jar files are executable</li>
5038 <li>Can read in Uracil - maps to unknown residue</li>
5043 <li>Known OutOfMemory errors give warning message</li>
5044 <li>Overview window calculated more efficiently</li>
5045 <li>Several GUI bugs resolved</li>
5051 <div align="center">
5052 <strong>2.05</strong><br> 30/8/05
5057 <li>Edit and annotate in "Wrapped" view</li>
5062 <li>Several GUI bugs resolved</li>
5068 <div align="center">
5069 <strong>2.04</strong><br> 24/8/05
5074 <li>Hold down mouse wheel & scroll to change font
5080 <li>Improved JPred client reliability</li>
5081 <li>Improved loading of Jalview files</li>
5087 <div align="center">
5088 <strong>2.03</strong><br> 18/8/05
5093 <li>Set Proxy server name and port in preferences</li>
5094 <li>Multiple URL links from sequence ids</li>
5095 <li>User Defined Colours can have a scheme name and added
5097 <li>Choose to ignore gaps in consensus calculation</li>
5098 <li>Unix users can set default web browser</li>
5099 <li>Runs without GUI for batch processing</li>
5100 <li>Dynamically generated Web Service Menus</li>
5105 <li>InstallAnywhere download for Sparc Solaris</li>
5111 <div align="center">
5112 <strong>2.02</strong><br> 18/7/05
5118 <li>Copy & Paste order of sequences maintains
5119 alignment order.</li>
5125 <div align="center">
5126 <strong>2.01</strong><br> 12/7/05
5131 <li>Use delete key for deleting selection.</li>
5132 <li>Use Mouse wheel to scroll sequences.</li>
5133 <li>Help file updated to describe how to add alignment
5135 <li>Version and build date written to build properties
5137 <li>InstallAnywhere installation will check for updates
5138 at launch of Jalview.</li>
5143 <li>Delete gaps bug fixed.</li>
5144 <li>FileChooser sorts columns.</li>
5145 <li>Can remove groups one by one.</li>
5146 <li>Filechooser icons installed.</li>
5147 <li>Finder ignores return character when searching.
5148 Return key will initiate a search.<br>
5155 <div align="center">
5156 <strong>2.0</strong><br> 20/6/05
5161 <li>New codebase</li>