4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
35 /* separate the items from eachother */
42 /* doesnt get processed in javahelp */
51 <strong>Release History</strong>
55 <th nowrap><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.2.11.1.7">.7</a><br />
62 <em>18/01/2022</em></strong>
66 <td align="left" valign="top"><em>Security</em>
69 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
73 <!-- JAL-3702, JAL-3935 -->Files open in Jalview cannot be
74 updated by Jalview or other applications (Windows, other non
80 <td width="60" align="center" nowrap><strong><a
81 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
82 <em>6/01/2022</em></strong></td>
84 <td align="left" valign="top"><em>Security</em>
87 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
94 <td width="60" align="center" nowrap><strong><a
95 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
96 <em>20/12/2021</em></strong></td>
98 <td align="left" valign="top"><em>Security</em>
101 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
103 </ul> <em>Development</em>
105 <li>Updated building instructions</li>
110 <!-- JAL-3840 -->Occupancy calculation is incorrect for
111 alignment columns with over -1+2^32 gaps (breaking filtering
115 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
116 scale factors being set with buggy window-managers (linux
119 </ul> <em>Development</em>
121 <li>Fixed non-fatal gradle errors during build</li>
126 <td width="60" align="center" nowrap><strong><a
127 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
128 <em>09/03/2021</em></strong></td>
129 <td align="left" valign="top"><em>Improved control of
130 Jalview's use of network services via jalview_properties</em>
133 <!-- JAL-3814 -->New .jalview_properties token controlling
134 launch of the news browser (like -nonews argument)
137 <!-- JAL-3813 -->New .jalview_properties token controlling
138 download of linkout URLs from
139 www.jalview.org/services/identifiers
142 <!-- JAL-3812 -->New .jalview_properties token controlling
143 download of BIOJSHTML templates
146 <!-- JAL-3811 -->New 'Discover Web Services' option to
147 trigger a one off JABAWS discovery if autodiscovery was
151 <td align="left" valign="top">
154 <!-- JAL-3818 -->Intermittent deadlock opening structure in
157 </ul> <em>New Known defects</em>
160 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
161 always restored from project (since 2.10.3)
164 <!-- JAL-3806 -->Selections from tree built from CDS aren't
165 propagated to Protein alignment (since 2.11.1.3)
171 <td width="60" align="center" nowrap><strong><a
172 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
173 <em>29/10/2020</em></strong></td>
174 <td align="left" valign="top">
179 <td align="left" valign="top">
182 <!-- JAL-3765 -->Find doesn't always highlight all matching
183 positions in a sequence (bug introduced in 2.11.1.2)
186 <!-- JAL-3760 -->Alignments containing one or more protein
187 sequences can be classed as nucleotide
190 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
191 sequences after alignment of protein products (known defect
192 first reported for 2.11.1.0)
195 <!-- JAL-3725 -->No tooltip or popup menu for genomic
196 features outwith CDS shown overlaid on protein
199 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
200 correctly mapped by Jalview (e.g. affects viral CDS with
201 ribosomal slippage, since 2.9.0)
204 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
208 <!-- JAL-3700 -->Selections in CDS sequence panel don't
209 always select corresponding protein sequences
212 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
213 column selection doesn't always ignore hidden columns
215 </ul> <em>Installer</em>
218 <!-- JAL-3611 -->Space character in Jalview install path on
219 Windows prevents install4j launching getdown
221 </ul> <em>Development</em>
224 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
225 version numbers in doc/building.md
231 <td width="60" align="center" nowrap><strong><a
232 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
233 <em>25/09/2020</em></strong></td>
234 <td align="left" valign="top">
238 <td align="left" valign="top">
241 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
242 "Encountered problems opening
243 https://www.jalview.org/examples/exampleFile_2_7.jvp"
249 <td width="60" align="center" nowrap><strong><a
250 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
251 <em>17/09/2020</em></strong></td>
252 <td align="left" valign="top">
255 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
256 residue in cursor mode
259 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
260 HTSJDK from 2.12 to 2.23
263 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
264 optimisations and improvements suggested by Bob Hanson and
265 improved compatibility with JalviewJS
268 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
269 alignments from Pfam and Rfam
272 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
273 import (no longer based on .gz extension)
276 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
279 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
280 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
284 <!-- JAL-3667 -->Improved warning messages, debug logging
285 and fixed Retry action when Jalview encounters errors when
286 saving or making backup files.
289 <!-- JAL-3676 -->Enhanced Jalview Java Console:
291 <li>Jalview's logging level can be configured</li>
292 <li>Copy to Clipboard Buttion</li>
296 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
297 when running on Linux (Requires Java 11+)
299 </ul> <em>Launching Jalview</em>
302 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
303 through a system property
306 <!-- JAL-3477 -->Improved built-in documentation and command
307 line help for configuring Jalview's memory
311 <td align="left" valign="top">
314 <!-- JAL-3691 -->Conservation and Quality tracks are shown
315 but not calculated and no protein or DNA score models are
316 available for tree/PCA calculation when launched with
317 Turkish language locale
320 <!-- JAL-3493 -->Escape does not clear highlights on the
321 alignment (Since Jalview 2.10.3)
324 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
325 doesn't slide selected sequences, just sequence under cursor
328 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
329 sequence under the cursor
332 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
333 multiple EMBL gene products shown for a single contig
336 <!-- JAL-3696 -->Errors encountered when processing variants
337 from VCF files yield "Error processing VCF: Format specifier
341 <!-- JAL-3697 -->Count of features not shown can be wrong
342 when there are both local and complementary features mapped
343 to the position under the cursor
346 <!-- JAL-3673 -->Sequence ID for reference sequence is
347 clipped when Right align Sequence IDs enabled
350 <!-- JAL-2983 -->Slider with negative range values not
351 rendered correctly in VAqua4 (Since 2.10.4)
354 <!-- JAL-3685 -->Single quotes not displayed correctly in
355 internationalised text for some messages and log output
358 <!-- JAL-3490 -->Find doesn't report matches that span
359 hidden gapped columns
362 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
363 panels, Alignment viewport and annotation renderer.
366 <!-- JAL-3561 -->Jalview ignores file format parameter
367 specifying output format when exporting an alignment via the
371 <!-- JAL-3667 -->Windows 10: For a minority of users, if
372 backups are not enabled, Jalview sometimes fails to
373 overwrite an existing file and raises a warning dialog. (in
374 2.11.0, and 2.11.1.0, the workaround is to try to save the
375 file again, and if that fails, delete the original file and
379 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
383 <!-- JAL-3741 -->References to http://www.jalview.org in
384 program and documentation
386 </ul> <em>Launching Jalview</em>
389 <!-- JAL-3718 -->Jalview application fails when launched the
390 first time for a version that has different jars to the
391 previous launched version.
393 </ul> <em>Developing Jalview</em>
396 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
397 data, causing cloverReport gradle task to fail with an
401 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
402 monitor the release channel
404 </ul> <em>New Known defects</em>
407 <!-- JAL-3748 -->CDS shown in result of submitting proteins
408 in a CDS/Protein alignment to a web service is wrong when
409 proteins share a common transcript sequence (e.g.
410 genome of RNA viruses)
413 <!-- JAL-3576 -->Co-located features exported and re-imported
414 are ordered differently when shown on alignment and in
415 tooltips. (Also affects v2.11.1.0)
418 <!-- JAL-3702 -->Drag and drop of alignment file onto
419 alignment window when in a HiDPI scaled mode in Linux only
420 works for the top left quadrant of the alignment window
423 <!-- JAL-3701 -->Stale build data in jalview standalone jar
424 builds (only affects 2.11.1.1 branch)
427 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
428 when alignment view restored from project (since Jalview 2.11.0)
431 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
432 protein products for certain ENA records are repeatedly
433 shown via Calculate->Show Cross Refs
439 <td width="60" align="center" nowrap><strong><a
440 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
441 <em>22/04/2020</em></strong></td>
442 <td align="left" valign="top">
445 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
446 'virtual' codon features shown on protein (or vice versa)
447 for display in alignments, on structure views (including
448 transfer to UCSF chimera), in feature reports and for
452 <!-- JAL-3121 -->Feature attributes from VCF files can be
453 exported and re-imported as GFF3 files
456 <!-- JAL-3376 -->Capture VCF "fixed column" values
457 POS, ID, QUAL, FILTER as Feature Attributes
460 <!-- JAL-3375 -->More robust VCF numeric data field
461 validation while parsing
464 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
468 <!-- JAL-3535 -->Feature Settings dialog title includes name
472 <!-- JAL-3538 -->Font anti-aliasing in alignment views
476 <!-- JAL-3468 -->Very long feature descriptions truncated in
480 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
481 with no feature types visible
484 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
486 </ul><em>Jalview Installer</em>
489 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
490 in console (may be null when Jalview launched as executable jar or via conda)
493 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
496 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
499 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
501 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
502 </ul> <em>Release processes</em>
505 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
508 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
510 </ul> <em>Build System</em>
513 <!-- JAL-3510 -->Clover updated to 4.4.1
516 <!-- JAL-3513 -->Test code included in Clover coverage
520 <em>Groovy Scripts</em>
523 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
524 to stdout containing the consensus sequence for each
525 alignment in a Jalview session
528 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
529 genomic sequence_variant annotation from CDS as
530 missense_variant or synonymous_variant on protein products.
534 <td align="left" valign="top">
537 <!-- JAL-3581 -->Hidden sequence markers still visible when
538 'Show hidden markers' option is not ticked
541 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
542 PNG output when 'Automatically set ID width' is set in
543 jalview preferences or properties file
546 <!-- JAL-3571 -->Feature Editor dialog can be opened when
547 'Show Sequence Features' option is not ticked
550 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
551 buttons in Feature Settings dialog are clicked when no
555 <!-- JAL-3412 -->ID margins for CDS and Protein views not
556 equal when split frame is first opened
559 <!-- JAL-3296 -->Sequence position numbers in status bar not
560 correct after editing a sequence's start position
563 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
564 with annotation and exceptions thrown when only a few
565 columns shown in wrapped mode
568 <!-- JAL-3386 -->Sequence IDs missing in headless export of
569 wrapped alignment figure with annotations
572 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
573 ID fails with ClassCastException
576 <!-- JAL-3389 -->Chimera session not restored from Jalview
580 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
581 feature settings dialog also selects columns
584 <!-- JAL-3473 -->SpinnerNumberModel causes
585 IllegalArgumentException in some circumstances
588 <!-- JAL-3534 -->Multiple feature settings dialogs can be
592 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
593 alignment window is closed
596 <!-- JAL-3406 -->Credits missing some authors in Jalview
597 help documentation for 2.11.0 release
600 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
601 includes Pfam ID as sequence's accession rather than its
604 </ul> <em>Java 11 Compatibility issues</em>
607 <!-- JAL-2987 -->OSX - Can't view some search results in
608 PDB/Uniprot search panel
610 </ul> <em>Installer</em>
613 <!-- JAL-3447 -->Jalview should not create file associations
614 for 3D structure files (.pdb, .mmcif. .cif)
616 </ul> <em>Repository and Source Release</em>
619 <!-- JAL-3474 -->removed obsolete .cvsignore files from
623 <!-- JAL-3541 -->Clover report generation running out of
626 </ul> <em>New Known Issues</em>
629 <!-- JAL-3523 -->OSX - Current working directory not
630 preserved when Jalview.app launched with parameters from
634 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
635 clipped in headless figure export when Right Align option
639 <!-- JAL-3542 -->Jalview Installation type always reports
640 'Source' in console output
643 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
644 bamboo server but run fine locally.
650 <td width="60" align="center" nowrap>
651 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
652 <em>04/07/2019</em></strong>
654 <td align="left" valign="top">
657 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
658 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
659 source project) rather than InstallAnywhere
662 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
663 settings, receive over the air updates and launch specific
664 versions via (<a href="https://github.com/threerings/getdown">Three
668 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
669 formats supported by Jalview (including .jvp project files)
672 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
673 arguments and switch between different getdown channels
676 <!-- JAL-3141 -->Backup files created when saving Jalview project
681 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
682 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
684 <!-- JAL-2620 -->Alternative genetic code tables for
685 'Translate as cDNA'</li>
687 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
688 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
691 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
692 implementation that allows updates) used for Sequence Feature collections</li>
694 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
695 features can be filtered and shaded according to any
696 associated attributes (e.g. variant attributes from VCF
697 file, or key-value pairs imported from column 9 of GFF
701 <!-- JAL-2879 -->Feature Attributes and shading schemes
702 stored and restored from Jalview Projects
705 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
706 recognise variant features
709 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
710 sequences (also coloured red by default)
713 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
717 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
718 algorithm (Z-sort/transparency and filter aware)
721 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
727 <!-- JAL-3205 -->Symmetric score matrices for faster
728 tree and PCA calculations
730 <li><strong>Principal Components Analysis Viewer</strong>
733 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
734 and Viewer state saved in Jalview Project
736 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
739 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
743 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
748 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
750 <li><strong>Speed and Efficiency</strong>
753 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
754 multiple groups when working with large alignments
757 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
761 <li><strong>User Interface</strong>
764 <!-- JAL-2933 -->Finder panel remembers last position in each
768 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
769 what is shown)<br />Only visible regions of alignment are shown by
770 default (can be changed in user preferences)
773 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
774 to the Overwrite Dialog
777 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
781 <!-- JAL-1244 -->Status bar shows bounds when dragging a
782 selection region, and gap count when inserting or deleting gaps
785 <!-- JAL-3132 -->Status bar updates over sequence and annotation
789 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
793 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
797 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
800 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
804 <!-- JAL-3181 -->Consistent ordering of links in sequence id
808 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
810 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
814 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
815 <li><strong>Java 11 Support (not yet on general release)</strong>
818 <!-- -->OSX GUI integrations for App menu's 'About' entry and
823 <em>Deprecations</em>
825 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
826 capabilities removed from the Jalview Desktop
828 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
829 unmarshalling has been replaced by JAXB for Jalview projects
830 and XML based data retrieval clients</li>
831 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
832 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
833 </ul> <em>Documentation</em>
835 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
836 not supported in EPS figure export
838 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
839 </ul> <em>Development and Release Processes</em>
842 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
845 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
847 <!-- JAL-3225 -->Eclipse project configuration managed with
851 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
852 Bamboo continuous integration for unattended Test Suite
856 <!-- JAL-2864 -->Memory test suite to detect leaks in common
860 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
864 <!-- JAL-3248 -->Developer documentation migrated to
865 markdown (with HTML rendering)
868 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
871 <!-- JAL-3289 -->New URLs for publishing development
876 <td align="left" valign="top">
879 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
882 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
883 superposition in Jmol fail on Windows
886 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
887 structures for sequences with lots of PDB structures
890 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
894 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
895 project involving multiple views
898 <!-- JAL-3164 -->Overview for complementary view in a linked
899 CDS/Protein alignment is not updated when Hide Columns by
900 Annotation dialog hides columns
903 <!-- JAL-3158 -->Selection highlighting in the complement of a
904 CDS/Protein alignment stops working after making a selection in
905 one view, then making another selection in the other view
908 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
912 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
913 Settings and Jalview Preferences panels
916 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
917 overview with large alignments
920 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
921 region if columns were selected by dragging right-to-left and the
922 mouse moved to the left of the first column
925 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
926 hidden column marker via scale popup menu
929 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
930 doesn't tell users the invalid URL
933 <!-- JAL-2816 -->Tooltips displayed for features filtered by
937 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
938 show cross references or Fetch Database References are shown in
942 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
943 peptide sequence (computed variant shown as p.Res.null)
946 <!-- JAL-2060 -->'Graduated colour' option not offered for
947 manually created features (where feature score is Float.NaN)
950 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
951 when columns are hidden
954 <!-- JAL-3082 -->Regular expression error for '(' in Select
955 Columns by Annotation description
958 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
959 out of Scale or Annotation Panel
962 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
966 <!-- JAL-3074 -->Left/right drag in annotation can scroll
970 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
974 <!-- JAL-3002 -->Column display is out by one after Page Down,
975 Page Up in wrapped mode
978 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
981 <!-- JAL-2932 -->Finder searches in minimised alignments
984 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
985 on opening an alignment
988 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
992 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
993 different groups in the alignment are selected
996 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1000 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1004 <!-- JAL-3125 -->Value input for graduated feature colour
1005 threshold gets 'unrounded'
1008 <!-- JAL-2982 -->PCA image export doesn't respect background
1012 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1015 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1018 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1022 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1026 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1027 shown in complementary view
1030 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1031 without normalisation
1034 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1038 <!-- JAL-914 -->Help page can be opened twice
1041 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1043 </ul> <em>Editing</em>
1046 <!-- JAL-2822 -->Start and End should be updated when sequence
1047 data at beginning or end of alignment added/removed via 'Edit'
1051 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1052 relocate sequence features correctly when start of sequence is
1053 removed (Known defect since 2.10)
1056 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1057 dialog corrupts dataset sequence
1060 <!-- JAL-868 -->Structure colours not updated when associated tree
1061 repartitions the alignment view (Regression in 2.10.5)
1063 </ul> <em>Datamodel</em>
1066 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1067 sequence's End is greater than its length
1069 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1070 general release)</em>
1073 <!-- JAL-3288 -->Menus work properly in split-screen
1075 </ul> <em>New Known Defects</em>
1078 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1081 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1082 regions of protein alignment.
1085 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1086 is restored from a Jalview 2.11 project
1089 <!-- JAL-3213 -->Alignment panel height can be too small after
1093 <!-- JAL-3240 -->Display is incorrect after removing gapped
1094 columns within hidden columns
1097 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1098 window after dragging left to select columns to left of visible
1102 <!-- JAL-2876 -->Features coloured according to their description
1103 string and thresholded by score in earlier versions of Jalview are
1104 not shown as thresholded features in 2.11. To workaround please
1105 create a Score filter instead.
1108 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1110 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1113 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1114 alignments with multiple views can close views unexpectedly
1117 <em>Java 11 Specific defects</em>
1120 <!-- JAL-3235 -->Jalview Properties file is not sorted
1121 alphabetically when saved
1127 <td width="60" nowrap>
1128 <div align="center">
1129 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1132 <td><div align="left">
1136 <!-- JAL-3101 -->Default memory for Jalview webstart and
1137 InstallAnywhere increased to 1G.
1140 <!-- JAL-247 -->Hidden sequence markers and representative
1141 sequence bolding included when exporting alignment as EPS,
1142 SVG, PNG or HTML. <em>Display is configured via the
1143 Format menu, or for command-line use via a Jalview
1144 properties file.</em>
1147 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1148 API and sequence data now imported as JSON.
1151 <!-- JAL-3065 -->Change in recommended way of starting
1152 Jalview via a Java command line: add jars in lib directory
1153 to CLASSPATH, rather than via the deprecated java.ext.dirs
1157 <em>Development</em>
1160 <!-- JAL-3047 -->Support added to execute test suite
1161 instrumented with <a href="http://openclover.org/">Open
1166 <td><div align="left">
1170 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1171 row shown in Feredoxin Structure alignment view of example
1175 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1176 annotation displayed.
1179 <!-- JAL-3107 -->Group conservation/consensus not shown
1180 for newly created group when 'Apply to all groups'
1184 <!-- JAL-3087 -->Corrupted display when switching to
1185 wrapped mode when sequence panel's vertical scrollbar is
1189 <!-- JAL-3003 -->Alignment is black in exported EPS file
1190 when sequences are selected in exported view.</em>
1193 <!-- JAL-3059 -->Groups with different coloured borders
1194 aren't rendered with correct colour.
1197 <!-- JAL-3092 -->Jalview could hang when importing certain
1198 types of knotted RNA secondary structure.
1201 <!-- JAL-3095 -->Sequence highlight and selection in
1202 trimmed VARNA 2D structure is incorrect for sequences that
1206 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1207 annotation when columns are inserted into an alignment,
1208 and when exporting as Stockholm flatfile.
1211 <!-- JAL-3053 -->Jalview annotation rows containing upper
1212 and lower-case 'E' and 'H' do not automatically get
1213 treated as RNA secondary structure.
1216 <!-- JAL-3106 -->.jvp should be used as default extension
1217 (not .jar) when saving a Jalview project file.
1220 <!-- JAL-3105 -->Mac Users: closing a window correctly
1221 transfers focus to previous window on OSX
1224 <em>Java 10 Issues Resolved</em>
1227 <!-- JAL-2988 -->OSX - Can't save new files via the File
1228 or export menus by typing in a name into the Save dialog
1232 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1233 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1234 'look and feel' which has improved compatibility with the
1235 latest version of OSX.
1242 <td width="60" nowrap>
1243 <div align="center">
1244 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1245 <em>7/06/2018</em></strong>
1248 <td><div align="left">
1252 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1253 annotation retrieved from Uniprot
1256 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1257 onto the Jalview Desktop
1261 <td><div align="left">
1265 <!-- JAL-3017 -->Cannot import features with multiple
1266 variant elements (blocks import of some Uniprot records)
1269 <!-- JAL-2997 -->Clustal files with sequence positions in
1270 right-hand column parsed correctly
1273 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1274 not alignment area in exported graphic
1277 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1278 window has input focus
1281 <!-- JAL-2992 -->Annotation panel set too high when
1282 annotation added to view (Windows)
1285 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1286 network connectivity is poor
1289 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1290 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1291 the currently open URL and links from a page viewed in
1292 Firefox or Chrome on Windows is now fully supported. If
1293 you are using Edge, only links in the page can be
1294 dragged, and with Internet Explorer, only the currently
1295 open URL in the browser can be dropped onto Jalview.</em>
1298 <em>New Known Defects</em>
1300 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1305 <td width="60" nowrap>
1306 <div align="center">
1307 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1310 <td><div align="left">
1314 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1315 for disabling automatic superposition of multiple
1316 structures and open structures in existing views
1319 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1320 ID and annotation area margins can be click-dragged to
1324 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1328 <!-- JAL-2759 -->Improved performance for large alignments
1329 and lots of hidden columns
1332 <!-- JAL-2593 -->Improved performance when rendering lots
1333 of features (particularly when transparency is disabled)
1336 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1337 exchange of Jalview features and Chimera attributes made
1343 <td><div align="left">
1346 <!-- JAL-2899 -->Structure and Overview aren't updated
1347 when Colour By Annotation threshold slider is adjusted
1350 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1351 overlapping alignment panel
1354 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1358 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1359 improved: CDS not handled correctly if transcript has no
1363 <!-- JAL-2321 -->Secondary structure and temperature
1364 factor annotation not added to sequence when local PDB
1365 file associated with it by drag'n'drop or structure
1369 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1370 dialog doesn't import PDB files dropped on an alignment
1373 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1374 scroll bar doesn't work for some CDS/Protein views
1377 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1378 Java 1.8u153 onwards and Java 1.9u4+.
1381 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1382 columns in annotation row
1385 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1386 honored in batch mode
1389 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1390 for structures added to existing Jmol view
1393 <!-- JAL-2223 -->'View Mappings' includes duplicate
1394 entries after importing project with multiple views
1397 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1398 protein sequences via SIFTS from associated PDB entries
1399 with negative residue numbers or missing residues fails
1402 <!-- JAL-2952 -->Exception when shading sequence with negative
1403 Temperature Factor values from annotated PDB files (e.g.
1404 as generated by CONSURF)
1407 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1408 tooltip doesn't include a text description of mutation
1411 <!-- JAL-2922 -->Invert displayed features very slow when
1412 structure and/or overview windows are also shown
1415 <!-- JAL-2954 -->Selecting columns from highlighted regions
1416 very slow for alignments with large numbers of sequences
1419 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1420 with 'StringIndexOutOfBounds'
1423 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1424 platforms running Java 10
1427 <!-- JAL-2960 -->Adding a structure to existing structure
1428 view appears to do nothing because the view is hidden behind the alignment view
1434 <!-- JAL-2926 -->Copy consensus sequence option in applet
1435 should copy the group consensus when popup is opened on it
1441 <!-- JAL-2913 -->Fixed ID width preference is not respected
1444 <em>New Known Defects</em>
1447 <!-- JAL-2973 --> Exceptions occasionally raised when
1448 editing a large alignment and overview is displayed
1451 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1452 repeatedly after a series of edits even when the overview
1453 is no longer reflecting updates
1456 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1457 structures for protein subsequence (if 'Trim Retrieved
1458 Sequences' enabled) or Ensembl isoforms (Workaround in
1459 2.10.4 is to fail back to N&W mapping)
1462 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1463 option gives blank output
1470 <td width="60" nowrap>
1471 <div align="center">
1472 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1475 <td><div align="left">
1476 <ul><li>Updated Certum Codesigning Certificate
1477 (Valid till 30th November 2018)</li></ul></div></td>
1478 <td><div align="left">
1479 <em>Desktop</em><ul>
1481 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1482 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1483 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1484 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1485 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1486 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1487 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1493 <td width="60" nowrap>
1494 <div align="center">
1495 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1498 <td><div align="left">
1502 <!-- JAL-2446 -->Faster and more efficient management and
1503 rendering of sequence features
1506 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1507 429 rate limit request hander
1510 <!-- JAL-2773 -->Structure views don't get updated unless
1511 their colours have changed
1514 <!-- JAL-2495 -->All linked sequences are highlighted for
1515 a structure mousover (Jmol) or selection (Chimera)
1518 <!-- JAL-2790 -->'Cancel' button in progress bar for
1519 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1522 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1523 view from Ensembl locus cross-references
1526 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1530 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1531 feature can be disabled
1534 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1535 PDB easier retrieval of sequences for lists of IDs
1538 <!-- JAL-2758 -->Short names for sequences retrieved from
1544 <li>Groovy interpreter updated to 2.4.12</li>
1545 <li>Example groovy script for generating a matrix of
1546 percent identity scores for current alignment.</li>
1548 <em>Testing and Deployment</em>
1551 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1555 <td><div align="left">
1559 <!-- JAL-2643 -->Pressing tab after updating the colour
1560 threshold text field doesn't trigger an update to the
1564 <!-- JAL-2682 -->Race condition when parsing sequence ID
1568 <!-- JAL-2608 -->Overview windows are also closed when
1569 alignment window is closed
1572 <!-- JAL-2548 -->Export of features doesn't always respect
1576 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1577 takes a long time in Cursor mode
1583 <!-- JAL-2777 -->Structures with whitespace chainCode
1584 cannot be viewed in Chimera
1587 <!-- JAL-2728 -->Protein annotation panel too high in
1591 <!-- JAL-2757 -->Can't edit the query after the server
1592 error warning icon is shown in Uniprot and PDB Free Text
1596 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1599 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1602 <!-- JAL-2739 -->Hidden column marker in last column not
1603 rendered when switching back from Wrapped to normal view
1606 <!-- JAL-2768 -->Annotation display corrupted when
1607 scrolling right in unwapped alignment view
1610 <!-- JAL-2542 -->Existing features on subsequence
1611 incorrectly relocated when full sequence retrieved from
1615 <!-- JAL-2733 -->Last reported memory still shown when
1616 Desktop->Show Memory is unticked (OSX only)
1619 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1620 features of same type and group to be selected for
1624 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1625 alignments when hidden columns are present
1628 <!-- JAL-2392 -->Jalview freezes when loading and
1629 displaying several structures
1632 <!-- JAL-2732 -->Black outlines left after resizing or
1636 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1637 within the Jalview desktop on OSX
1640 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1641 when in wrapped alignment mode
1644 <!-- JAL-2636 -->Scale mark not shown when close to right
1645 hand end of alignment
1648 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1649 each selected sequence do not have correct start/end
1653 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1654 after canceling the Alignment Window's Font dialog
1657 <!-- JAL-2036 -->Show cross-references not enabled after
1658 restoring project until a new view is created
1661 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1662 URL links appears when only default EMBL-EBI link is
1663 configured (since 2.10.2b2)
1666 <!-- JAL-2775 -->Overview redraws whole window when box
1667 position is adjusted
1670 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1671 in a multi-chain structure when viewing alignment
1672 involving more than one chain (since 2.10)
1675 <!-- JAL-2811 -->Double residue highlights in cursor mode
1676 if new selection moves alignment window
1679 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1680 arrow key in cursor mode to pass hidden column marker
1683 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1684 that produces correctly annotated transcripts and products
1687 <!-- JAL-2776 -->Toggling a feature group after first time
1688 doesn't update associated structure view
1691 <em>Applet</em><br />
1694 <!-- JAL-2687 -->Concurrent modification exception when
1695 closing alignment panel
1698 <em>BioJSON</em><br />
1701 <!-- JAL-2546 -->BioJSON export does not preserve
1702 non-positional features
1705 <em>New Known Issues</em>
1708 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1709 sequence features correctly (for many previous versions of
1713 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1714 using cursor in wrapped panel other than top
1717 <!-- JAL-2791 -->Select columns containing feature ignores
1718 graduated colour threshold
1721 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1722 always preserve numbering and sequence features
1725 <em>Known Java 9 Issues</em>
1728 <!-- JAL-2902 -->Groovy Console very slow to open and is
1729 not responsive when entering characters (Webstart, Java
1736 <td width="60" nowrap>
1737 <div align="center">
1738 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1739 <em>2/10/2017</em></strong>
1742 <td><div align="left">
1743 <em>New features in Jalview Desktop</em>
1746 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1748 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1752 <td><div align="left">
1756 <td width="60" nowrap>
1757 <div align="center">
1758 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1759 <em>7/9/2017</em></strong>
1762 <td><div align="left">
1766 <!-- JAL-2588 -->Show gaps in overview window by colouring
1767 in grey (sequences used to be coloured grey, and gaps were
1771 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1775 <!-- JAL-2587 -->Overview updates immediately on increase
1776 in size and progress bar shown as higher resolution
1777 overview is recalculated
1782 <td><div align="left">
1786 <!-- JAL-2664 -->Overview window redraws every hidden
1787 column region row by row
1790 <!-- JAL-2681 -->duplicate protein sequences shown after
1791 retrieving Ensembl crossrefs for sequences from Uniprot
1794 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1795 format setting is unticked
1798 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1799 if group has show boxes format setting unticked
1802 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1803 autoscrolling whilst dragging current selection group to
1804 include sequences and columns not currently displayed
1807 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1808 assemblies are imported via CIF file
1811 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1812 displayed when threshold or conservation colouring is also
1816 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1820 <!-- JAL-2673 -->Jalview continues to scroll after
1821 dragging a selected region off the visible region of the
1825 <!-- JAL-2724 -->Cannot apply annotation based
1826 colourscheme to all groups in a view
1829 <!-- JAL-2511 -->IDs don't line up with sequences
1830 initially after font size change using the Font chooser or
1837 <td width="60" nowrap>
1838 <div align="center">
1839 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1842 <td><div align="left">
1843 <em>Calculations</em>
1847 <!-- JAL-1933 -->Occupancy annotation row shows number of
1848 ungapped positions in each column of the alignment.
1851 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1852 a calculation dialog box
1855 <!-- JAL-2379 -->Revised implementation of PCA for speed
1856 and memory efficiency (~30x faster)
1859 <!-- JAL-2403 -->Revised implementation of sequence
1860 similarity scores as used by Tree, PCA, Shading Consensus
1861 and other calculations
1864 <!-- JAL-2416 -->Score matrices are stored as resource
1865 files within the Jalview codebase
1868 <!-- JAL-2500 -->Trees computed on Sequence Feature
1869 Similarity may have different topology due to increased
1876 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1877 model for alignments and groups
1880 <!-- JAL-384 -->Custom shading schemes created via groovy
1887 <!-- JAL-2526 -->Efficiency improvements for interacting
1888 with alignment and overview windows
1891 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1895 <!-- JAL-2388 -->Hidden columns and sequences can be
1899 <!-- JAL-2611 -->Click-drag in visible area allows fine
1900 adjustment of visible position
1904 <em>Data import/export</em>
1907 <!-- JAL-2535 -->Posterior probability annotation from
1908 Stockholm files imported as sequence associated annotation
1911 <!-- JAL-2507 -->More robust per-sequence positional
1912 annotation input/output via stockholm flatfile
1915 <!-- JAL-2533 -->Sequence names don't include file
1916 extension when importing structure files without embedded
1917 names or PDB accessions
1920 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1921 format sequence substitution matrices
1924 <em>User Interface</em>
1927 <!-- JAL-2447 --> Experimental Features Checkbox in
1928 Desktop's Tools menu to hide or show untested features in
1932 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1933 via Overview or sequence motif search operations
1936 <!-- JAL-2547 -->Amend sequence features dialog box can be
1937 opened by double clicking gaps within sequence feature
1941 <!-- JAL-1476 -->Status bar message shown when not enough
1942 aligned positions were available to create a 3D structure
1946 <em>3D Structure</em>
1949 <!-- JAL-2430 -->Hidden regions in alignment views are not
1950 coloured in linked structure views
1953 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1954 file-based command exchange
1957 <!-- JAL-2375 -->Structure chooser automatically shows
1958 Cached Structures rather than querying the PDBe if
1959 structures are already available for sequences
1962 <!-- JAL-2520 -->Structures imported via URL are cached in
1963 the Jalview project rather than downloaded again when the
1964 project is reopened.
1967 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1968 to transfer Chimera's structure attributes as Jalview
1969 features, and vice-versa (<strong>Experimental
1973 <em>Web Services</em>
1976 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1979 <!-- JAL-2335 -->Filter non-standard amino acids and
1980 nucleotides when submitting to AACon and other MSA
1984 <!-- JAL-2316, -->URLs for viewing database
1985 cross-references provided by identifiers.org and the
1986 EMBL-EBI's MIRIAM DB
1993 <!-- JAL-2344 -->FileFormatI interface for describing and
1994 identifying file formats (instead of String constants)
1997 <!-- JAL-2228 -->FeatureCounter script refactored for
1998 efficiency when counting all displayed features (not
1999 backwards compatible with 2.10.1)
2002 <em>Example files</em>
2005 <!-- JAL-2631 -->Graduated feature colour style example
2006 included in the example feature file
2009 <em>Documentation</em>
2012 <!-- JAL-2339 -->Release notes reformatted for readability
2013 with the built-in Java help viewer
2016 <!-- JAL-1644 -->Find documentation updated with 'search
2017 sequence description' option
2023 <!-- JAL-2485, -->External service integration tests for
2024 Uniprot REST Free Text Search Client
2027 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2030 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2035 <td><div align="left">
2036 <em>Calculations</em>
2039 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2040 matrix - C->R should be '-3'<br />Old matrix restored
2041 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2043 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2044 Jalview's treatment of gaps in PCA and substitution matrix
2045 based Tree calculations.<br /> <br />In earlier versions
2046 of Jalview, gaps matching gaps were penalised, and gaps
2047 matching non-gaps penalised even more. In the PCA
2048 calculation, gaps were actually treated as non-gaps - so
2049 different costs were applied, which meant Jalview's PCAs
2050 were different to those produced by SeqSpace.<br />Jalview
2051 now treats gaps in the same way as SeqSpace (ie it scores
2052 them as 0). <br /> <br />Enter the following in the
2053 Groovy console to restore pre-2.10.2 behaviour:<br />
2054 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2055 // for 2.10.1 mode <br />
2056 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2057 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2058 these settings will affect all subsequent tree and PCA
2059 calculations (not recommended)</em></li>
2061 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2062 scaling of branch lengths for trees computed using
2063 Sequence Feature Similarity.
2066 <!-- JAL-2377 -->PCA calculation could hang when
2067 generating output report when working with highly
2068 redundant alignments
2071 <!-- JAL-2544 --> Sort by features includes features to
2072 right of selected region when gaps present on right-hand
2076 <em>User Interface</em>
2079 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2080 doesn't reselect a specific sequence's associated
2081 annotation after it was used for colouring a view
2084 <!-- JAL-2419 -->Current selection lost if popup menu
2085 opened on a region of alignment without groups
2088 <!-- JAL-2374 -->Popup menu not always shown for regions
2089 of an alignment with overlapping groups
2092 <!-- JAL-2310 -->Finder double counts if both a sequence's
2093 name and description match
2096 <!-- JAL-2370 -->Hiding column selection containing two
2097 hidden regions results in incorrect hidden regions
2100 <!-- JAL-2386 -->'Apply to all groups' setting when
2101 changing colour does not apply Conservation slider value
2105 <!-- JAL-2373 -->Percentage identity and conservation menu
2106 items do not show a tick or allow shading to be disabled
2109 <!-- JAL-2385 -->Conservation shading or PID threshold
2110 lost when base colourscheme changed if slider not visible
2113 <!-- JAL-2547 -->Sequence features shown in tooltip for
2114 gaps before start of features
2117 <!-- JAL-2623 -->Graduated feature colour threshold not
2118 restored to UI when feature colour is edited
2121 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2122 a time when scrolling vertically in wrapped mode.
2125 <!-- JAL-2630 -->Structure and alignment overview update
2126 as graduate feature colour settings are modified via the
2130 <!-- JAL-2034 -->Overview window doesn't always update
2131 when a group defined on the alignment is resized
2134 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2135 wrapped view result in positional status updates
2139 <!-- JAL-2563 -->Status bar doesn't show position for
2140 ambiguous amino acid and nucleotide symbols
2143 <!-- JAL-2602 -->Copy consensus sequence failed if
2144 alignment included gapped columns
2147 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2148 widgets don't permanently disappear
2151 <!-- JAL-2503 -->Cannot select or filter quantitative
2152 annotation that are shown only as column labels (e.g.
2153 T-Coffee column reliability scores)
2156 <!-- JAL-2594 -->Exception thrown if trying to create a
2157 sequence feature on gaps only
2160 <!-- JAL-2504 -->Features created with 'New feature'
2161 button from a Find inherit previously defined feature type
2162 rather than the Find query string
2165 <!-- JAL-2423 -->incorrect title in output window when
2166 exporting tree calculated in Jalview
2169 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2170 and then revealing them reorders sequences on the
2174 <!-- JAL-964 -->Group panel in sequence feature settings
2175 doesn't update to reflect available set of groups after
2176 interactively adding or modifying features
2179 <!-- JAL-2225 -->Sequence Database chooser unusable on
2183 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2184 only excluded gaps in current sequence and ignored
2191 <!-- JAL-2421 -->Overview window visible region moves
2192 erratically when hidden rows or columns are present
2195 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2196 Structure Viewer's colour menu don't correspond to
2200 <!-- JAL-2405 -->Protein specific colours only offered in
2201 colour and group colour menu for protein alignments
2204 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2205 reflect currently selected view or group's shading
2209 <!-- JAL-2624 -->Feature colour thresholds not respected
2210 when rendered on overview and structures when opacity at
2214 <!-- JAL-2589 -->User defined gap colour not shown in
2215 overview when features overlaid on alignment
2218 <!-- JAL-2567 -->Feature settings for different views not
2219 recovered correctly from Jalview project file
2222 <!-- JAL-2256 -->Feature colours in overview when first opened
2223 (automatically via preferences) are different to the main
2227 <em>Data import/export</em>
2230 <!-- JAL-2576 -->Very large alignments take a long time to
2234 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2235 added after a sequence was imported are not written to
2239 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2240 when importing RNA secondary structure via Stockholm
2243 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2244 not shown in correct direction for simple pseudoknots
2247 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2248 with lightGray or darkGray via features file (but can
2252 <!-- JAL-2383 -->Above PID colour threshold not recovered
2253 when alignment view imported from project
2256 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2257 structure and sequences extracted from structure files
2258 imported via URL and viewed in Jmol
2261 <!-- JAL-2520 -->Structures loaded via URL are saved in
2262 Jalview Projects rather than fetched via URL again when
2263 the project is loaded and the structure viewed
2266 <em>Web Services</em>
2269 <!-- JAL-2519 -->EnsemblGenomes example failing after
2270 release of Ensembl v.88
2273 <!-- JAL-2366 -->Proxy server address and port always
2274 appear enabled in Preferences->Connections
2277 <!-- JAL-2461 -->DAS registry not found exceptions
2278 removed from console output
2281 <!-- JAL-2582 -->Cannot retrieve protein products from
2282 Ensembl by Peptide ID
2285 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2286 created from SIFTs, and spurious 'Couldn't open structure
2287 in Chimera' errors raised after April 2017 update (problem
2288 due to 'null' string rather than empty string used for
2289 residues with no corresponding PDB mapping).
2292 <em>Application UI</em>
2295 <!-- JAL-2361 -->User Defined Colours not added to Colour
2299 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2300 case' residues (button in colourscheme editor debugged and
2301 new documentation and tooltips added)
2304 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2305 doesn't restore group-specific text colour thresholds
2308 <!-- JAL-2243 -->Feature settings panel does not update as
2309 new features are added to alignment
2312 <!-- JAL-2532 -->Cancel in feature settings reverts
2313 changes to feature colours via the Amend features dialog
2316 <!-- JAL-2506 -->Null pointer exception when attempting to
2317 edit graduated feature colour via amend features dialog
2321 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2322 selection menu changes colours of alignment views
2325 <!-- JAL-2426 -->Spurious exceptions in console raised
2326 from alignment calculation workers after alignment has
2330 <!-- JAL-1608 -->Typo in selection popup menu - Create
2331 groups now 'Create Group'
2334 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2335 Create/Undefine group doesn't always work
2338 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2339 shown again after pressing 'Cancel'
2342 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2343 adjusts start position in wrap mode
2346 <!-- JAL-2563 -->Status bar doesn't show positions for
2347 ambiguous amino acids
2350 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2351 CDS/Protein view after CDS sequences added for aligned
2355 <!-- JAL-2592 -->User defined colourschemes called 'User
2356 Defined' don't appear in Colours menu
2362 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2363 score models doesn't always result in an updated PCA plot
2366 <!-- JAL-2442 -->Features not rendered as transparent on
2367 overview or linked structure view
2370 <!-- JAL-2372 -->Colour group by conservation doesn't
2374 <!-- JAL-2517 -->Hitting Cancel after applying
2375 user-defined colourscheme doesn't restore original
2382 <!-- JAL-2314 -->Unit test failure:
2383 jalview.ws.jabaws.RNAStructExportImport setup fails
2386 <!-- JAL-2307 -->Unit test failure:
2387 jalview.ws.sifts.SiftsClientTest due to compatibility
2388 problems with deep array comparison equality asserts in
2389 successive versions of TestNG
2392 <!-- JAL-2479 -->Relocated StructureChooserTest and
2393 ParameterUtilsTest Unit tests to Network suite
2396 <em>New Known Issues</em>
2399 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2400 phase after a sequence motif find operation
2403 <!-- JAL-2550 -->Importing annotation file with rows
2404 containing just upper and lower case letters are
2405 interpreted as WUSS RNA secondary structure symbols
2408 <!-- JAL-2590 -->Cannot load and display Newick trees
2409 reliably from eggnog Ortholog database
2412 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2413 containing features of type Highlight' when 'B' is pressed
2414 to mark columns containing highlighted regions.
2417 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2418 doesn't always add secondary structure annotation.
2423 <td width="60" nowrap>
2424 <div align="center">
2425 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2428 <td><div align="left">
2432 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2433 for all consensus calculations
2436 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2439 <li>Updated Jalview's Certum code signing certificate
2442 <em>Application</em>
2445 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2446 set of database cross-references, sorted alphabetically
2449 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2450 from database cross references. Users with custom links
2451 will receive a <a href="webServices/urllinks.html#warning">warning
2452 dialog</a> asking them to update their preferences.
2455 <!-- JAL-2287-->Cancel button and escape listener on
2456 dialog warning user about disconnecting Jalview from a
2460 <!-- JAL-2320-->Jalview's Chimera control window closes if
2461 the Chimera it is connected to is shut down
2464 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2465 columns menu item to mark columns containing highlighted
2466 regions (e.g. from structure selections or results of a
2470 <!-- JAL-2284-->Command line option for batch-generation
2471 of HTML pages rendering alignment data with the BioJS
2481 <!-- JAL-2286 -->Columns with more than one modal residue
2482 are not coloured or thresholded according to percent
2483 identity (first observed in Jalview 2.8.2)
2486 <!-- JAL-2301 -->Threonine incorrectly reported as not
2490 <!-- JAL-2318 -->Updates to documentation pages (above PID
2491 threshold, amino acid properties)
2494 <!-- JAL-2292 -->Lower case residues in sequences are not
2495 reported as mapped to residues in a structure file in the
2499 <!--JAL-2324 -->Identical features with non-numeric scores
2500 could be added multiple times to a sequence
2503 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2504 bond features shown as two highlighted residues rather
2505 than a range in linked structure views, and treated
2506 correctly when selecting and computing trees from features
2509 <!-- JAL-2281-->Custom URL links for database
2510 cross-references are matched to database name regardless
2515 <em>Application</em>
2518 <!-- JAL-2282-->Custom URL links for specific database
2519 names without regular expressions also offer links from
2523 <!-- JAL-2315-->Removing a single configured link in the
2524 URL links pane in Connections preferences doesn't actually
2525 update Jalview configuration
2528 <!-- JAL-2272-->CTRL-Click on a selected region to open
2529 the alignment area popup menu doesn't work on El-Capitan
2532 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2533 files with similarly named sequences if dropped onto the
2537 <!-- JAL-2312 -->Additional mappings are shown for PDB
2538 entries where more chains exist in the PDB accession than
2539 are reported in the SIFTS file
2542 <!-- JAL-2317-->Certain structures do not get mapped to
2543 the structure view when displayed with Chimera
2546 <!-- JAL-2317-->No chains shown in the Chimera view
2547 panel's View->Show Chains submenu
2550 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2551 work for wrapped alignment views
2554 <!--JAL-2197 -->Rename UI components for running JPred
2555 predictions from 'JNet' to 'JPred'
2558 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2559 corrupted when annotation panel vertical scroll is not at
2560 first annotation row
2563 <!--JAL-2332 -->Attempting to view structure for Hen
2564 lysozyme results in a PDB Client error dialog box
2567 <!-- JAL-2319 -->Structure View's mapping report switched
2568 ranges for PDB and sequence for SIFTS
2571 SIFTS 'Not_Observed' residues mapped to non-existant
2575 <!-- <em>New Known Issues</em>
2582 <td width="60" nowrap>
2583 <div align="center">
2584 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2585 <em>25/10/2016</em></strong>
2588 <td><em>Application</em>
2590 <li>3D Structure chooser opens with 'Cached structures'
2591 view if structures already loaded</li>
2592 <li>Progress bar reports models as they are loaded to
2593 structure views</li>
2599 <li>Colour by conservation always enabled and no tick
2600 shown in menu when BLOSUM or PID shading applied</li>
2601 <li>FER1_ARATH and FER2_ARATH labels were switched in
2602 example sequences/projects/trees</li>
2604 <em>Application</em>
2606 <li>Jalview projects with views of local PDB structure
2607 files saved on Windows cannot be opened on OSX</li>
2608 <li>Multiple structure views can be opened and superposed
2609 without timeout for structures with multiple models or
2610 multiple sequences in alignment</li>
2611 <li>Cannot import or associated local PDB files without a
2612 PDB ID HEADER line</li>
2613 <li>RMSD is not output in Jmol console when superposition
2615 <li>Drag and drop of URL from Browser fails for Linux and
2616 OSX versions earlier than El Capitan</li>
2617 <li>ENA client ignores invalid content from ENA server</li>
2618 <li>Exceptions are not raised in console when ENA client
2619 attempts to fetch non-existent IDs via Fetch DB Refs UI
2621 <li>Exceptions are not raised in console when a new view
2622 is created on the alignment</li>
2623 <li>OSX right-click fixed for group selections: CMD-click
2624 to insert/remove gaps in groups and CTRL-click to open group
2627 <em>Build and deployment</em>
2629 <li>URL link checker now copes with multi-line anchor
2632 <em>New Known Issues</em>
2634 <li>Drag and drop from URL links in browsers do not work
2641 <td width="60" nowrap>
2642 <div align="center">
2643 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2646 <td><em>General</em>
2649 <!-- JAL-2124 -->Updated Spanish translations.
2652 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2653 for importing structure data to Jalview. Enables mmCIF and
2657 <!-- JAL-192 --->Alignment ruler shows positions relative to
2661 <!-- JAL-2202 -->Position/residue shown in status bar when
2662 mousing over sequence associated annotation
2665 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2669 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2670 '()', canonical '[]' and invalid '{}' base pair populations
2674 <!-- JAL-2092 -->Feature settings popup menu options for
2675 showing or hiding columns containing a feature
2678 <!-- JAL-1557 -->Edit selected group by double clicking on
2679 group and sequence associated annotation labels
2682 <!-- JAL-2236 -->Sequence name added to annotation label in
2683 select/hide columns by annotation and colour by annotation
2687 </ul> <em>Application</em>
2690 <!-- JAL-2050-->Automatically hide introns when opening a
2691 gene/transcript view
2694 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2698 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2699 structure mappings with the EMBL-EBI PDBe SIFTS database
2702 <!-- JAL-2079 -->Updated download sites used for Rfam and
2703 Pfam sources to xfam.org
2706 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2709 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2710 over sequences in Jalview
2713 <!-- JAL-2027-->Support for reverse-complement coding
2714 regions in ENA and EMBL
2717 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2718 for record retrieval via ENA rest API
2721 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2725 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2726 groovy script execution
2729 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2730 alignment window's Calculate menu
2733 <!-- JAL-1812 -->Allow groovy scripts that call
2734 Jalview.getAlignFrames() to run in headless mode
2737 <!-- JAL-2068 -->Support for creating new alignment
2738 calculation workers from groovy scripts
2741 <!-- JAL-1369 --->Store/restore reference sequence in
2745 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2746 associations are now saved/restored from project
2749 <!-- JAL-1993 -->Database selection dialog always shown
2750 before sequence fetcher is opened
2753 <!-- JAL-2183 -->Double click on an entry in Jalview's
2754 database chooser opens a sequence fetcher
2757 <!-- JAL-1563 -->Free-text search client for UniProt using
2758 the UniProt REST API
2761 <!-- JAL-2168 -->-nonews command line parameter to prevent
2762 the news reader opening
2765 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2766 querying stored in preferences
2769 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2773 <!-- JAL-1977-->Tooltips shown on database chooser
2776 <!-- JAL-391 -->Reverse complement function in calculate
2777 menu for nucleotide sequences
2780 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2781 and feature counts preserves alignment ordering (and
2782 debugged for complex feature sets).
2785 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2786 viewing structures with Jalview 2.10
2789 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2790 genome, transcript CCDS and gene ids via the Ensembl and
2791 Ensembl Genomes REST API
2794 <!-- JAL-2049 -->Protein sequence variant annotation
2795 computed for 'sequence_variant' annotation on CDS regions
2799 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2803 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2804 Ref Fetcher fails to match, or otherwise updates sequence
2805 data from external database records.
2808 <!-- JAL-2154 -->Revised Jalview Project format for
2809 efficient recovery of sequence coding and alignment
2810 annotation relationships.
2812 </ul> <!-- <em>Applet</em>
2823 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2827 <!-- JAL-2018-->Export features in Jalview format (again)
2828 includes graduated colourschemes
2831 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2832 working with big alignments and lots of hidden columns
2835 <!-- JAL-2053-->Hidden column markers not always rendered
2836 at right of alignment window
2839 <!-- JAL-2067 -->Tidied up links in help file table of
2843 <!-- JAL-2072 -->Feature based tree calculation not shown
2847 <!-- JAL-2075 -->Hidden columns ignored during feature
2848 based tree calculation
2851 <!-- JAL-2065 -->Alignment view stops updating when show
2852 unconserved enabled for group on alignment
2855 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2859 <!-- JAL-2146 -->Alignment column in status incorrectly
2860 shown as "Sequence position" when mousing over
2864 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2865 hidden columns present
2868 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2869 user created annotation added to alignment
2872 <!-- JAL-1841 -->RNA Structure consensus only computed for
2873 '()' base pair annotation
2876 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2877 in zero scores for all base pairs in RNA Structure
2881 <!-- JAL-2174-->Extend selection with columns containing
2885 <!-- JAL-2275 -->Pfam format writer puts extra space at
2886 beginning of sequence
2889 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2893 <!-- JAL-2238 -->Cannot create groups on an alignment from
2894 from a tree when t-coffee scores are shown
2897 <!-- JAL-1836,1967 -->Cannot import and view PDB
2898 structures with chains containing negative resnums (4q4h)
2901 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2905 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2906 to Clustal, PIR and PileUp output
2909 <!-- JAL-2008 -->Reordering sequence features that are
2910 not visible causes alignment window to repaint
2913 <!-- JAL-2006 -->Threshold sliders don't work in
2914 graduated colour and colour by annotation row for e-value
2915 scores associated with features and annotation rows
2918 <!-- JAL-1797 -->amino acid physicochemical conservation
2919 calculation should be case independent
2922 <!-- JAL-2173 -->Remove annotation also updates hidden
2926 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2927 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2928 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2931 <!-- JAL-2065 -->Null pointer exceptions and redraw
2932 problems when reference sequence defined and 'show
2933 non-conserved' enabled
2936 <!-- JAL-1306 -->Quality and Conservation are now shown on
2937 load even when Consensus calculation is disabled
2940 <!-- JAL-1932 -->Remove right on penultimate column of
2941 alignment does nothing
2944 <em>Application</em>
2947 <!-- JAL-1552-->URLs and links can't be imported by
2948 drag'n'drop on OSX when launched via webstart (note - not
2949 yet fixed for El Capitan)
2952 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2953 output when running on non-gb/us i18n platforms
2956 <!-- JAL-1944 -->Error thrown when exporting a view with
2957 hidden sequences as flat-file alignment
2960 <!-- JAL-2030-->InstallAnywhere distribution fails when
2964 <!-- JAL-2080-->Jalview very slow to launch via webstart
2965 (also hotfix for 2.9.0b2)
2968 <!-- JAL-2085 -->Cannot save project when view has a
2969 reference sequence defined
2972 <!-- JAL-1011 -->Columns are suddenly selected in other
2973 alignments and views when revealing hidden columns
2976 <!-- JAL-1989 -->Hide columns not mirrored in complement
2977 view in a cDNA/Protein splitframe
2980 <!-- JAL-1369 -->Cannot save/restore representative
2981 sequence from project when only one sequence is
2985 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2986 in Structure Chooser
2989 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2990 structure consensus didn't refresh annotation panel
2993 <!-- JAL-1962 -->View mapping in structure view shows
2994 mappings between sequence and all chains in a PDB file
2997 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2998 dialogs format columns correctly, don't display array
2999 data, sort columns according to type
3002 <!-- JAL-1975 -->Export complete shown after destination
3003 file chooser is cancelled during an image export
3006 <!-- JAL-2025 -->Error when querying PDB Service with
3007 sequence name containing special characters
3010 <!-- JAL-2024 -->Manual PDB structure querying should be
3014 <!-- JAL-2104 -->Large tooltips with broken HTML
3015 formatting don't wrap
3018 <!-- JAL-1128 -->Figures exported from wrapped view are
3019 truncated so L looks like I in consensus annotation
3022 <!-- JAL-2003 -->Export features should only export the
3023 currently displayed features for the current selection or
3027 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3028 after fetching cross-references, and restoring from
3032 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3033 followed in the structure viewer
3036 <!-- JAL-2163 -->Titles for individual alignments in
3037 splitframe not restored from project
3040 <!-- JAL-2145 -->missing autocalculated annotation at
3041 trailing end of protein alignment in transcript/product
3042 splitview when pad-gaps not enabled by default
3045 <!-- JAL-1797 -->amino acid physicochemical conservation
3049 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3050 article has been read (reopened issue due to
3051 internationalisation problems)
3054 <!-- JAL-1960 -->Only offer PDB structures in structure
3055 viewer based on sequence name, PDB and UniProt
3060 <!-- JAL-1976 -->No progress bar shown during export of
3064 <!-- JAL-2213 -->Structures not always superimposed after
3065 multiple structures are shown for one or more sequences.
3068 <!-- JAL-1370 -->Reference sequence characters should not
3069 be replaced with '.' when 'Show unconserved' format option
3073 <!-- JAL-1823 -->Cannot specify chain code when entering
3074 specific PDB id for sequence
3077 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3078 'Export hidden sequences' is enabled, but 'export hidden
3079 columns' is disabled.
3082 <!--JAL-2026-->Best Quality option in structure chooser
3083 selects lowest rather than highest resolution structures
3087 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3088 to sequence mapping in 'View Mappings' report
3091 <!-- JAL-2284 -->Unable to read old Jalview projects that
3092 contain non-XML data added after Jalvew wrote project.
3095 <!-- JAL-2118 -->Newly created annotation row reorders
3096 after clicking on it to create new annotation for a
3100 <!-- JAL-1980 -->Null Pointer Exception raised when
3101 pressing Add on an orphaned cut'n'paste window.
3103 <!-- may exclude, this is an external service stability issue JAL-1941
3104 -- > RNA 3D structure not added via DSSR service</li> -->
3109 <!-- JAL-2151 -->Incorrect columns are selected when
3110 hidden columns present before start of sequence
3113 <!-- JAL-1986 -->Missing dependencies on applet pages
3117 <!-- JAL-1947 -->Overview pixel size changes when
3118 sequences are hidden in applet
3121 <!-- JAL-1996 -->Updated instructions for applet
3122 deployment on examples pages.
3129 <td width="60" nowrap>
3130 <div align="center">
3131 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3132 <em>16/10/2015</em></strong>
3135 <td><em>General</em>
3137 <li>Time stamps for signed Jalview application and applet
3142 <em>Application</em>
3144 <li>Duplicate group consensus and conservation rows
3145 shown when tree is partitioned</li>
3146 <li>Erratic behaviour when tree partitions made with
3147 multiple cDNA/Protein split views</li>
3153 <td width="60" nowrap>
3154 <div align="center">
3155 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3156 <em>8/10/2015</em></strong>
3159 <td><em>General</em>
3161 <li>Updated Spanish translations of localized text for
3163 </ul> <em>Application</em>
3165 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3166 <li>Signed OSX InstallAnywhere installer<br></li>
3167 <li>Support for per-sequence based annotations in BioJSON</li>
3168 </ul> <em>Applet</em>
3170 <li>Split frame example added to applet examples page</li>
3171 </ul> <em>Build and Deployment</em>
3174 <!-- JAL-1888 -->New ant target for running Jalview's test
3182 <li>Mapping of cDNA to protein in split frames
3183 incorrect when sequence start > 1</li>
3184 <li>Broken images in filter column by annotation dialog
3186 <li>Feature colours not parsed from features file</li>
3187 <li>Exceptions and incomplete link URLs recovered when
3188 loading a features file containing HTML tags in feature
3192 <em>Application</em>
3194 <li>Annotations corrupted after BioJS export and
3196 <li>Incorrect sequence limits after Fetch DB References
3197 with 'trim retrieved sequences'</li>
3198 <li>Incorrect warning about deleting all data when
3199 deleting selected columns</li>
3200 <li>Patch to build system for shipping properly signed
3201 JNLP templates for webstart launch</li>
3202 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3203 unreleased structures for download or viewing</li>
3204 <li>Tab/space/return keystroke operation of EMBL-PDBe
3205 fetcher/viewer dialogs works correctly</li>
3206 <li>Disabled 'minimise' button on Jalview windows
3207 running on OSX to workaround redraw hang bug</li>
3208 <li>Split cDNA/Protein view position and geometry not
3209 recovered from jalview project</li>
3210 <li>Initial enabled/disabled state of annotation menu
3211 sorter 'show autocalculated first/last' corresponds to
3213 <li>Restoring of Clustal, RNA Helices and T-Coffee
3214 color schemes from BioJSON</li>
3218 <li>Reorder sequences mirrored in cDNA/Protein split
3220 <li>Applet with Jmol examples not loading correctly</li>
3226 <td><div align="center">
3227 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3229 <td><em>General</em>
3231 <li>Linked visualisation and analysis of DNA and Protein
3234 <li>Translated cDNA alignments shown as split protein
3235 and DNA alignment views</li>
3236 <li>Codon consensus annotation for linked protein and
3237 cDNA alignment views</li>
3238 <li>Link cDNA or Protein product sequences by loading
3239 them onto Protein or cDNA alignments</li>
3240 <li>Reconstruct linked cDNA alignment from aligned
3241 protein sequences</li>
3244 <li>Jmol integration updated to Jmol v14.2.14</li>
3245 <li>Import and export of Jalview alignment views as <a
3246 href="features/bioJsonFormat.html">BioJSON</a></li>
3247 <li>New alignment annotation file statements for
3248 reference sequences and marking hidden columns</li>
3249 <li>Reference sequence based alignment shading to
3250 highlight variation</li>
3251 <li>Select or hide columns according to alignment
3253 <li>Find option for locating sequences by description</li>
3254 <li>Conserved physicochemical properties shown in amino
3255 acid conservation row</li>
3256 <li>Alignments can be sorted by number of RNA helices</li>
3257 </ul> <em>Application</em>
3259 <li>New cDNA/Protein analysis capabilities
3261 <li>Get Cross-References should open a Split Frame
3262 view with cDNA/Protein</li>
3263 <li>Detect when nucleotide sequences and protein
3264 sequences are placed in the same alignment</li>
3265 <li>Split cDNA/Protein views are saved in Jalview
3270 <li>Use REST API to talk to Chimera</li>
3271 <li>Selected regions in Chimera are highlighted in linked
3272 Jalview windows</li>
3274 <li>VARNA RNA viewer updated to v3.93</li>
3275 <li>VARNA views are saved in Jalview Projects</li>
3276 <li>Pseudoknots displayed as Jalview RNA annotation can
3277 be shown in VARNA</li>
3279 <li>Make groups for selection uses marked columns as well
3280 as the active selected region</li>
3282 <li>Calculate UPGMA and NJ trees using sequence feature
3284 <li>New Export options
3286 <li>New Export Settings dialog to control hidden
3287 region export in flat file generation</li>
3289 <li>Export alignment views for display with the <a
3290 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3292 <li>Export scrollable SVG in HTML page</li>
3293 <li>Optional embedding of BioJSON data when exporting
3294 alignment figures to HTML</li>
3296 <li>3D structure retrieval and display
3298 <li>Free text and structured queries with the PDBe
3300 <li>PDBe Search API based discovery and selection of
3301 PDB structures for a sequence set</li>
3305 <li>JPred4 employed for protein secondary structure
3307 <li>Hide Insertions menu option to hide unaligned columns
3308 for one or a group of sequences</li>
3309 <li>Automatically hide insertions in alignments imported
3310 from the JPred4 web server</li>
3311 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3312 system on OSX<br />LGPL libraries courtesy of <a
3313 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3315 <li>changed 'View nucleotide structure' submenu to 'View
3316 VARNA 2D Structure'</li>
3317 <li>change "View protein structure" menu option to "3D
3320 </ul> <em>Applet</em>
3322 <li>New layout for applet example pages</li>
3323 <li>New parameters to enable SplitFrame view
3324 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3325 <li>New example demonstrating linked viewing of cDNA and
3326 Protein alignments</li>
3327 </ul> <em>Development and deployment</em>
3329 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3330 <li>Include installation type and git revision in build
3331 properties and console log output</li>
3332 <li>Jalview Github organisation, and new github site for
3333 storing BioJsMSA Templates</li>
3334 <li>Jalview's unit tests now managed with TestNG</li>
3337 <!-- <em>General</em>
3339 </ul> --> <!-- issues resolved --> <em>Application</em>
3341 <li>Escape should close any open find dialogs</li>
3342 <li>Typo in select-by-features status report</li>
3343 <li>Consensus RNA secondary secondary structure
3344 predictions are not highlighted in amber</li>
3345 <li>Missing gap character in v2.7 example file means
3346 alignment appears unaligned when pad-gaps is not enabled</li>
3347 <li>First switch to RNA Helices colouring doesn't colour
3348 associated structure views</li>
3349 <li>ID width preference option is greyed out when auto
3350 width checkbox not enabled</li>
3351 <li>Stopped a warning dialog from being shown when
3352 creating user defined colours</li>
3353 <li>'View Mapping' in structure viewer shows sequence
3354 mappings for just that viewer's sequences</li>
3355 <li>Workaround for superposing PDB files containing
3356 multiple models in Chimera</li>
3357 <li>Report sequence position in status bar when hovering
3358 over Jmol structure</li>
3359 <li>Cannot output gaps as '.' symbols with Selection ->
3360 output to text box</li>
3361 <li>Flat file exports of alignments with hidden columns
3362 have incorrect sequence start/end</li>
3363 <li>'Aligning' a second chain to a Chimera structure from
3365 <li>Colour schemes applied to structure viewers don't
3366 work for nucleotide</li>
3367 <li>Loading/cut'n'pasting an empty or invalid file leads
3368 to a grey/invisible alignment window</li>
3369 <li>Exported Jpred annotation from a sequence region
3370 imports to different position</li>
3371 <li>Space at beginning of sequence feature tooltips shown
3372 on some platforms</li>
3373 <li>Chimera viewer 'View | Show Chain' menu is not
3375 <li>'New View' fails with a Null Pointer Exception in
3376 console if Chimera has been opened</li>
3377 <li>Mouseover to Chimera not working</li>
3378 <li>Miscellaneous ENA XML feature qualifiers not
3380 <li>NPE in annotation renderer after 'Extract Scores'</li>
3381 <li>If two structures in one Chimera window, mouseover of
3382 either sequence shows on first structure</li>
3383 <li>'Show annotations' options should not make
3384 non-positional annotations visible</li>
3385 <li>Subsequence secondary structure annotation not shown
3386 in right place after 'view flanking regions'</li>
3387 <li>File Save As type unset when current file format is
3389 <li>Save as '.jar' option removed for saving Jalview
3391 <li>Colour by Sequence colouring in Chimera more
3393 <li>Cannot 'add reference annotation' for a sequence in
3394 several views on same alignment</li>
3395 <li>Cannot show linked products for EMBL / ENA records</li>
3396 <li>Jalview's tooltip wraps long texts containing no
3398 </ul> <em>Applet</em>
3400 <li>Jmol to JalviewLite mouseover/link not working</li>
3401 <li>JalviewLite can't import sequences with ID
3402 descriptions containing angle brackets</li>
3403 </ul> <em>General</em>
3405 <li>Cannot export and reimport RNA secondary structure
3406 via jalview annotation file</li>
3407 <li>Random helix colour palette for colour by annotation
3408 with RNA secondary structure</li>
3409 <li>Mouseover to cDNA from STOP residue in protein
3410 translation doesn't work.</li>
3411 <li>hints when using the select by annotation dialog box</li>
3412 <li>Jmol alignment incorrect if PDB file has alternate CA
3414 <li>FontChooser message dialog appears to hang after
3415 choosing 1pt font</li>
3416 <li>Peptide secondary structure incorrectly imported from
3417 annotation file when annotation display text includes 'e' or
3419 <li>Cannot set colour of new feature type whilst creating
3421 <li>cDNA translation alignment should not be sequence
3422 order dependent</li>
3423 <li>'Show unconserved' doesn't work for lower case
3425 <li>Nucleotide ambiguity codes involving R not recognised</li>
3426 </ul> <em>Deployment and Documentation</em>
3428 <li>Applet example pages appear different to the rest of
3429 www.jalview.org</li>
3430 </ul> <em>Application Known issues</em>
3432 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3433 <li>Misleading message appears after trying to delete
3435 <li>Jalview icon not shown in dock after InstallAnywhere
3436 version launches</li>
3437 <li>Fetching EMBL reference for an RNA sequence results
3438 fails with a sequence mismatch</li>
3439 <li>Corrupted or unreadable alignment display when
3440 scrolling alignment to right</li>
3441 <li>ArrayIndexOutOfBoundsException thrown when remove
3442 empty columns called on alignment with ragged gapped ends</li>
3443 <li>auto calculated alignment annotation rows do not get
3444 placed above or below non-autocalculated rows</li>
3445 <li>Jalview dekstop becomes sluggish at full screen in
3446 ultra-high resolution</li>
3447 <li>Cannot disable consensus calculation independently of
3448 quality and conservation</li>
3449 <li>Mouseover highlighting between cDNA and protein can
3450 become sluggish with more than one splitframe shown</li>
3451 </ul> <em>Applet Known Issues</em>
3453 <li>Core PDB parsing code requires Jmol</li>
3454 <li>Sequence canvas panel goes white when alignment
3455 window is being resized</li>
3461 <td><div align="center">
3462 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3464 <td><em>General</em>
3466 <li>Updated Java code signing certificate donated by
3468 <li>Features and annotation preserved when performing
3469 pairwise alignment</li>
3470 <li>RNA pseudoknot annotation can be
3471 imported/exported/displayed</li>
3472 <li>'colour by annotation' can colour by RNA and
3473 protein secondary structure</li>
3474 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3475 post-hoc with 2.9 release</em>)
3478 </ul> <em>Application</em>
3480 <li>Extract and display secondary structure for sequences
3481 with 3D structures</li>
3482 <li>Support for parsing RNAML</li>
3483 <li>Annotations menu for layout
3485 <li>sort sequence annotation rows by alignment</li>
3486 <li>place sequence annotation above/below alignment
3489 <li>Output in Stockholm format</li>
3490 <li>Internationalisation: improved Spanish (es)
3492 <li>Structure viewer preferences tab</li>
3493 <li>Disorder and Secondary Structure annotation tracks
3494 shared between alignments</li>
3495 <li>UCSF Chimera launch and linked highlighting from
3497 <li>Show/hide all sequence associated annotation rows for
3498 all or current selection</li>
3499 <li>disorder and secondary structure predictions
3500 available as dataset annotation</li>
3501 <li>Per-sequence rna helices colouring</li>
3504 <li>Sequence database accessions imported when fetching
3505 alignments from Rfam</li>
3506 <li>update VARNA version to 3.91</li>
3508 <li>New groovy scripts for exporting aligned positions,
3509 conservation values, and calculating sum of pairs scores.</li>
3510 <li>Command line argument to set default JABAWS server</li>
3511 <li>include installation type in build properties and
3512 console log output</li>
3513 <li>Updated Jalview project format to preserve dataset
3517 <!-- issues resolved --> <em>Application</em>
3519 <li>Distinguish alignment and sequence associated RNA
3520 structure in structure->view->VARNA</li>
3521 <li>Raise dialog box if user deletes all sequences in an
3523 <li>Pressing F1 results in documentation opening twice</li>
3524 <li>Sequence feature tooltip is wrapped</li>
3525 <li>Double click on sequence associated annotation
3526 selects only first column</li>
3527 <li>Redundancy removal doesn't result in unlinked
3528 leaves shown in tree</li>
3529 <li>Undos after several redundancy removals don't undo
3531 <li>Hide sequence doesn't hide associated annotation</li>
3532 <li>User defined colours dialog box too big to fit on
3533 screen and buttons not visible</li>
3534 <li>author list isn't updated if already written to
3535 Jalview properties</li>
3536 <li>Popup menu won't open after retrieving sequence
3538 <li>File open window for associate PDB doesn't open</li>
3539 <li>Left-then-right click on a sequence id opens a
3540 browser search window</li>
3541 <li>Cannot open sequence feature shading/sort popup menu
3542 in feature settings dialog</li>
3543 <li>better tooltip placement for some areas of Jalview
3545 <li>Allow addition of JABAWS Server which doesn't
3546 pass validation</li>
3547 <li>Web services parameters dialog box is too large to
3549 <li>Muscle nucleotide alignment preset obscured by
3551 <li>JABAWS preset submenus don't contain newly
3552 defined user preset</li>
3553 <li>MSA web services warns user if they were launched
3554 with invalid input</li>
3555 <li>Jalview cannot contact DAS Registy when running on
3558 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3559 'Superpose with' submenu not shown when new view
3563 </ul> <!-- <em>Applet</em>
3565 </ul> <em>General</em>
3567 </ul>--> <em>Deployment and Documentation</em>
3569 <li>2G and 1G options in launchApp have no effect on
3570 memory allocation</li>
3571 <li>launchApp service doesn't automatically open
3572 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3574 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3575 InstallAnywhere reports cannot find valid JVM when Java
3576 1.7_055 is available
3578 </ul> <em>Application Known issues</em>
3581 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3582 corrupted or unreadable alignment display when scrolling
3586 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3587 retrieval fails but progress bar continues for DAS retrieval
3588 with large number of ID
3591 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3592 flatfile output of visible region has incorrect sequence
3596 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3597 rna structure consensus doesn't update when secondary
3598 structure tracks are rearranged
3601 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3602 invalid rna structure positional highlighting does not
3603 highlight position of invalid base pairs
3606 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3607 out of memory errors are not raised when saving Jalview
3608 project from alignment window file menu
3611 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3612 Switching to RNA Helices colouring doesn't propagate to
3616 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3617 colour by RNA Helices not enabled when user created
3618 annotation added to alignment
3621 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3622 Jalview icon not shown on dock in Mountain Lion/Webstart
3624 </ul> <em>Applet Known Issues</em>
3627 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3628 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3631 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3632 Jalview and Jmol example not compatible with IE9
3635 <li>Sort by annotation score doesn't reverse order
3641 <td><div align="center">
3642 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3645 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3648 <li>Internationalisation of user interface (usually
3649 called i18n support) and translation for Spanish locale</li>
3650 <li>Define/Undefine group on current selection with
3651 Ctrl-G/Shift Ctrl-G</li>
3652 <li>Improved group creation/removal options in
3653 alignment/sequence Popup menu</li>
3654 <li>Sensible precision for symbol distribution
3655 percentages shown in logo tooltip.</li>
3656 <li>Annotation panel height set according to amount of
3657 annotation when alignment first opened</li>
3658 </ul> <em>Application</em>
3660 <li>Interactive consensus RNA secondary structure
3661 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3662 <li>Select columns containing particular features from
3663 Feature Settings dialog</li>
3664 <li>View all 'representative' PDB structures for selected
3666 <li>Update Jalview project format:
3668 <li>New file extension for Jalview projects '.jvp'</li>
3669 <li>Preserve sequence and annotation dataset (to
3670 store secondary structure annotation,etc)</li>
3671 <li>Per group and alignment annotation and RNA helix
3675 <li>New similarity measures for PCA and Tree calculation
3677 <li>Experimental support for retrieval and viewing of
3678 flanking regions for an alignment</li>
3682 <!-- issues resolved --> <em>Application</em>
3684 <li>logo keeps spinning and status remains at queued or
3685 running after job is cancelled</li>
3686 <li>cannot export features from alignments imported from
3687 Jalview/VAMSAS projects</li>
3688 <li>Buggy slider for web service parameters that take
3690 <li>Newly created RNA secondary structure line doesn't
3691 have 'display all symbols' flag set</li>
3692 <li>T-COFFEE alignment score shading scheme and other
3693 annotation shading not saved in Jalview project</li>
3694 <li>Local file cannot be loaded in freshly downloaded
3696 <li>Jalview icon not shown on dock in Mountain
3698 <li>Load file from desktop file browser fails</li>
3699 <li>Occasional NPE thrown when calculating large trees</li>
3700 <li>Cannot reorder or slide sequences after dragging an
3701 alignment onto desktop</li>
3702 <li>Colour by annotation dialog throws NPE after using
3703 'extract scores' function</li>
3704 <li>Loading/cut'n'pasting an empty file leads to a grey
3705 alignment window</li>
3706 <li>Disorder thresholds rendered incorrectly after
3707 performing IUPred disorder prediction</li>
3708 <li>Multiple group annotated consensus rows shown when
3709 changing 'normalise logo' display setting</li>
3710 <li>Find shows blank dialog after 'finished searching' if
3711 nothing matches query</li>
3712 <li>Null Pointer Exceptions raised when sorting by
3713 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3715 <li>Errors in Jmol console when structures in alignment
3716 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3718 <li>Not all working JABAWS services are shown in
3720 <li>JAVAWS version of Jalview fails to launch with
3721 'invalid literal/length code'</li>
3722 <li>Annotation/RNA Helix colourschemes cannot be applied
3723 to alignment with groups (actually fixed in 2.8.0b1)</li>
3724 <li>RNA Helices and T-Coffee Scores available as default
3727 </ul> <em>Applet</em>
3729 <li>Remove group option is shown even when selection is
3731 <li>Apply to all groups ticked but colourscheme changes
3732 don't affect groups</li>
3733 <li>Documented RNA Helices and T-Coffee Scores as valid
3734 colourscheme name</li>
3735 <li>Annotation labels drawn on sequence IDs when
3736 Annotation panel is not displayed</li>
3737 <li>Increased font size for dropdown menus on OSX and
3738 embedded windows</li>
3739 </ul> <em>Other</em>
3741 <li>Consensus sequence for alignments/groups with a
3742 single sequence were not calculated</li>
3743 <li>annotation files that contain only groups imported as
3744 annotation and junk sequences</li>
3745 <li>Fasta files with sequences containing '*' incorrectly
3746 recognised as PFAM or BLC</li>
3747 <li>conservation/PID slider apply all groups option
3748 doesn't affect background (2.8.0b1)
3750 <li>redundancy highlighting is erratic at 0% and 100%</li>
3751 <li>Remove gapped columns fails for sequences with ragged
3753 <li>AMSA annotation row with leading spaces is not
3754 registered correctly on import</li>
3755 <li>Jalview crashes when selecting PCA analysis for
3756 certain alignments</li>
3757 <li>Opening the colour by annotation dialog for an
3758 existing annotation based 'use original colours'
3759 colourscheme loses original colours setting</li>
3764 <td><div align="center">
3765 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3766 <em>30/1/2014</em></strong>
3770 <li>Trusted certificates for JalviewLite applet and
3771 Jalview Desktop application<br />Certificate was donated by
3772 <a href="https://www.certum.eu">Certum</a> to the Jalview
3773 open source project).
3775 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3776 <li>Output in Stockholm format</li>
3777 <li>Allow import of data from gzipped files</li>
3778 <li>Export/import group and sequence associated line
3779 graph thresholds</li>
3780 <li>Nucleotide substitution matrix that supports RNA and
3781 ambiguity codes</li>
3782 <li>Allow disorder predictions to be made on the current
3783 selection (or visible selection) in the same way that JPred
3785 <li>Groovy scripting for headless Jalview operation</li>
3786 </ul> <em>Other improvements</em>
3788 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3789 <li>COMBINE statement uses current SEQUENCE_REF and
3790 GROUP_REF scope to group annotation rows</li>
3791 <li>Support '' style escaping of quotes in Newick
3793 <li>Group options for JABAWS service by command line name</li>
3794 <li>Empty tooltip shown for JABA service options with a
3795 link but no description</li>
3796 <li>Select primary source when selecting authority in
3797 database fetcher GUI</li>
3798 <li>Add .mfa to FASTA file extensions recognised by
3800 <li>Annotation label tooltip text wrap</li>
3805 <li>Slow scrolling when lots of annotation rows are
3807 <li>Lots of NPE (and slowness) after creating RNA
3808 secondary structure annotation line</li>
3809 <li>Sequence database accessions not imported when
3810 fetching alignments from Rfam</li>
3811 <li>Incorrect SHMR submission for sequences with
3813 <li>View all structures does not always superpose
3815 <li>Option widgets in service parameters not updated to
3816 reflect user or preset settings</li>
3817 <li>Null pointer exceptions for some services without
3818 presets or adjustable parameters</li>
3819 <li>Discover PDB IDs entry in structure menu doesn't
3820 discover PDB xRefs</li>
3821 <li>Exception encountered while trying to retrieve
3822 features with DAS</li>
3823 <li>Lowest value in annotation row isn't coloured
3824 when colour by annotation (per sequence) is coloured</li>
3825 <li>Keyboard mode P jumps to start of gapped region when
3826 residue follows a gap</li>
3827 <li>Jalview appears to hang importing an alignment with
3828 Wrap as default or after enabling Wrap</li>
3829 <li>'Right click to add annotations' message
3830 shown in wrap mode when no annotations present</li>
3831 <li>Disorder predictions fail with NPE if no automatic
3832 annotation already exists on alignment</li>
3833 <li>oninit javascript function should be called after
3834 initialisation completes</li>
3835 <li>Remove redundancy after disorder prediction corrupts
3836 alignment window display</li>
3837 <li>Example annotation file in documentation is invalid</li>
3838 <li>Grouped line graph annotation rows are not exported
3839 to annotation file</li>
3840 <li>Multi-harmony analysis cannot be run when only two
3842 <li>Cannot create multiple groups of line graphs with
3843 several 'combine' statements in annotation file</li>
3844 <li>Pressing return several times causes Number Format
3845 exceptions in keyboard mode</li>
3846 <li>Multi-harmony (SHMMR) method doesn't submit
3847 correct partitions for input data</li>
3848 <li>Translation from DNA to Amino Acids fails</li>
3849 <li>Jalview fail to load newick tree with quoted label</li>
3850 <li>--headless flag isn't understood</li>
3851 <li>ClassCastException when generating EPS in headless
3853 <li>Adjusting sequence-associated shading threshold only
3854 changes one row's threshold</li>
3855 <li>Preferences and Feature settings panel panel
3856 doesn't open</li>
3857 <li>hide consensus histogram also hides conservation and
3858 quality histograms</li>
3863 <td><div align="center">
3864 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3866 <td><em>Application</em>
3868 <li>Support for JABAWS 2.0 Services (AACon alignment
3869 conservation, protein disorder and Clustal Omega)</li>
3870 <li>JABAWS server status indicator in Web Services
3872 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3873 in Jalview alignment window</li>
3874 <li>Updated Jalview build and deploy framework for OSX
3875 mountain lion, windows 7, and 8</li>
3876 <li>Nucleotide substitution matrix for PCA that supports
3877 RNA and ambiguity codes</li>
3879 <li>Improved sequence database retrieval GUI</li>
3880 <li>Support fetching and database reference look up
3881 against multiple DAS sources (Fetch all from in 'fetch db
3883 <li>Jalview project improvements
3885 <li>Store and retrieve the 'belowAlignment'
3886 flag for annotation</li>
3887 <li>calcId attribute to group annotation rows on the
3889 <li>Store AACon calculation settings for a view in
3890 Jalview project</li>
3894 <li>horizontal scrolling gesture support</li>
3895 <li>Visual progress indicator when PCA calculation is
3897 <li>Simpler JABA web services menus</li>
3898 <li>visual indication that web service results are still
3899 being retrieved from server</li>
3900 <li>Serialise the dialogs that are shown when Jalview
3901 starts up for first time</li>
3902 <li>Jalview user agent string for interacting with HTTP
3904 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3906 <li>Examples directory and Groovy library included in
3907 InstallAnywhere distribution</li>
3908 </ul> <em>Applet</em>
3910 <li>RNA alignment and secondary structure annotation
3911 visualization applet example</li>
3912 </ul> <em>General</em>
3914 <li>Normalise option for consensus sequence logo</li>
3915 <li>Reset button in PCA window to return dimensions to
3917 <li>Allow seqspace or Jalview variant of alignment PCA
3919 <li>PCA with either nucleic acid and protein substitution
3921 <li>Allow windows containing HTML reports to be exported
3923 <li>Interactive display and editing of RNA secondary
3924 structure contacts</li>
3925 <li>RNA Helix Alignment Colouring</li>
3926 <li>RNA base pair logo consensus</li>
3927 <li>Parse sequence associated secondary structure
3928 information in Stockholm files</li>
3929 <li>HTML Export database accessions and annotation
3930 information presented in tooltip for sequences</li>
3931 <li>Import secondary structure from LOCARNA clustalw
3932 style RNA alignment files</li>
3933 <li>import and visualise T-COFFEE quality scores for an
3935 <li>'colour by annotation' per sequence option to
3936 shade each sequence according to its associated alignment
3938 <li>New Jalview Logo</li>
3939 </ul> <em>Documentation and Development</em>
3941 <li>documentation for score matrices used in Jalview</li>
3942 <li>New Website!</li>
3944 <td><em>Application</em>
3946 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3947 wsdbfetch REST service</li>
3948 <li>Stop windows being moved outside desktop on OSX</li>
3949 <li>Filetype associations not installed for webstart
3951 <li>Jalview does not always retrieve progress of a JABAWS
3952 job execution in full once it is complete</li>
3953 <li>revise SHMR RSBS definition to ensure alignment is
3954 uploaded via ali_file parameter</li>
3955 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3956 <li>View all structures superposed fails with exception</li>
3957 <li>Jnet job queues forever if a very short sequence is
3958 submitted for prediction</li>
3959 <li>Cut and paste menu not opened when mouse clicked on
3961 <li>Putting fractional value into integer text box in
3962 alignment parameter dialog causes Jalview to hang</li>
3963 <li>Structure view highlighting doesn't work on
3965 <li>View all structures fails with exception shown in
3967 <li>Characters in filename associated with PDBEntry not
3968 escaped in a platform independent way</li>
3969 <li>Jalview desktop fails to launch with exception when
3971 <li>Tree calculation reports 'you must have 2 or more
3972 sequences selected' when selection is empty</li>
3973 <li>Jalview desktop fails to launch with jar signature
3974 failure when java web start temporary file caching is
3976 <li>DAS Sequence retrieval with range qualification
3977 results in sequence xref which includes range qualification</li>
3978 <li>Errors during processing of command line arguments
3979 cause progress bar (JAL-898) to be removed</li>
3980 <li>Replace comma for semi-colon option not disabled for
3981 DAS sources in sequence fetcher</li>
3982 <li>Cannot close news reader when JABAWS server warning
3983 dialog is shown</li>
3984 <li>Option widgets not updated to reflect user settings</li>
3985 <li>Edited sequence not submitted to web service</li>
3986 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3987 <li>InstallAnywhere installer doesn't unpack and run
3988 on OSX Mountain Lion</li>
3989 <li>Annotation panel not given a scroll bar when
3990 sequences with alignment annotation are pasted into the
3992 <li>Sequence associated annotation rows not associated
3993 when loaded from Jalview project</li>
3994 <li>Browser launch fails with NPE on java 1.7</li>
3995 <li>JABAWS alignment marked as finished when job was
3996 cancelled or job failed due to invalid input</li>
3997 <li>NPE with v2.7 example when clicking on Tree
3998 associated with all views</li>
3999 <li>Exceptions when copy/paste sequences with grouped
4000 annotation rows to new window</li>
4001 </ul> <em>Applet</em>
4003 <li>Sequence features are momentarily displayed before
4004 they are hidden using hidefeaturegroups applet parameter</li>
4005 <li>loading features via javascript API automatically
4006 enables feature display</li>
4007 <li>scrollToColumnIn javascript API method doesn't
4009 </ul> <em>General</em>
4011 <li>Redundancy removal fails for rna alignment</li>
4012 <li>PCA calculation fails when sequence has been selected
4013 and then deselected</li>
4014 <li>PCA window shows grey box when first opened on OSX</li>
4015 <li>Letters coloured pink in sequence logo when alignment
4016 coloured with clustalx</li>
4017 <li>Choosing fonts without letter symbols defined causes
4018 exceptions and redraw errors</li>
4019 <li>Initial PCA plot view is not same as manually
4020 reconfigured view</li>
4021 <li>Grouped annotation graph label has incorrect line
4023 <li>Grouped annotation graph label display is corrupted
4024 for lots of labels</li>
4029 <div align="center">
4030 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4033 <td><em>Application</em>
4035 <li>Jalview Desktop News Reader</li>
4036 <li>Tweaked default layout of web services menu</li>
4037 <li>View/alignment association menu to enable user to
4038 easily specify which alignment a multi-structure view takes
4039 its colours/correspondences from</li>
4040 <li>Allow properties file location to be specified as URL</li>
4041 <li>Extend Jalview project to preserve associations
4042 between many alignment views and a single Jmol display</li>
4043 <li>Store annotation row height in Jalview project file</li>
4044 <li>Annotation row column label formatting attributes
4045 stored in project file</li>
4046 <li>Annotation row order for auto-calculated annotation
4047 rows preserved in Jalview project file</li>
4048 <li>Visual progress indication when Jalview state is
4049 saved using Desktop window menu</li>
4050 <li>Visual indication that command line arguments are
4051 still being processed</li>
4052 <li>Groovy script execution from URL</li>
4053 <li>Colour by annotation default min and max colours in
4055 <li>Automatically associate PDB files dragged onto an
4056 alignment with sequences that have high similarity and
4058 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4059 <li>'view structures' option to open many
4060 structures in same window</li>
4061 <li>Sort associated views menu option for tree panel</li>
4062 <li>Group all JABA and non-JABA services for a particular
4063 analysis function in its own submenu</li>
4064 </ul> <em>Applet</em>
4066 <li>Userdefined and autogenerated annotation rows for
4068 <li>Adjustment of alignment annotation pane height</li>
4069 <li>Annotation scrollbar for annotation panel</li>
4070 <li>Drag to reorder annotation rows in annotation panel</li>
4071 <li>'automaticScrolling' parameter</li>
4072 <li>Allow sequences with partial ID string matches to be
4073 annotated from GFF/Jalview features files</li>
4074 <li>Sequence logo annotation row in applet</li>
4075 <li>Absolute paths relative to host server in applet
4076 parameters are treated as such</li>
4077 <li>New in the JalviewLite javascript API:
4079 <li>JalviewLite.js javascript library</li>
4080 <li>Javascript callbacks for
4082 <li>Applet initialisation</li>
4083 <li>Sequence/alignment mouse-overs and selections</li>
4086 <li>scrollTo row and column alignment scrolling
4088 <li>Select sequence/alignment regions from javascript</li>
4089 <li>javascript structure viewer harness to pass
4090 messages between Jmol and Jalview when running as
4091 distinct applets</li>
4092 <li>sortBy method</li>
4093 <li>Set of applet and application examples shipped
4094 with documentation</li>
4095 <li>New example to demonstrate JalviewLite and Jmol
4096 javascript message exchange</li>
4098 </ul> <em>General</em>
4100 <li>Enable Jmol displays to be associated with multiple
4101 multiple alignments</li>
4102 <li>Option to automatically sort alignment with new tree</li>
4103 <li>User configurable link to enable redirects to a
4104 www.Jalview.org mirror</li>
4105 <li>Jmol colours option for Jmol displays</li>
4106 <li>Configurable newline string when writing alignment
4107 and other flat files</li>
4108 <li>Allow alignment annotation description lines to
4109 contain html tags</li>
4110 </ul> <em>Documentation and Development</em>
4112 <li>Add groovy test harness for bulk load testing to
4114 <li>Groovy script to load and align a set of sequences
4115 using a web service before displaying the result in the
4116 Jalview desktop</li>
4117 <li>Restructured javascript and applet api documentation</li>
4118 <li>Ant target to publish example html files with applet
4120 <li>Netbeans project for building Jalview from source</li>
4121 <li>ant task to create online javadoc for Jalview source</li>
4123 <td><em>Application</em>
4125 <li>User defined colourscheme throws exception when
4126 current built in colourscheme is saved as new scheme</li>
4127 <li>AlignFrame->Save in application pops up save
4128 dialog for valid filename/format</li>
4129 <li>Cannot view associated structure for UniProt sequence</li>
4130 <li>PDB file association breaks for UniProt sequence
4132 <li>Associate PDB from file dialog does not tell you
4133 which sequence is to be associated with the file</li>
4134 <li>Find All raises null pointer exception when query
4135 only matches sequence IDs</li>
4136 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4137 <li>Jalview project with Jmol views created with Jalview
4138 2.4 cannot be loaded</li>
4139 <li>Filetype associations not installed for webstart
4141 <li>Two or more chains in a single PDB file associated
4142 with sequences in different alignments do not get coloured
4143 by their associated sequence</li>
4144 <li>Visibility status of autocalculated annotation row
4145 not preserved when project is loaded</li>
4146 <li>Annotation row height and visibility attributes not
4147 stored in Jalview project</li>
4148 <li>Tree bootstraps are not preserved when saved as a
4149 Jalview project</li>
4150 <li>Envision2 workflow tooltips are corrupted</li>
4151 <li>Enabling show group conservation also enables colour
4152 by conservation</li>
4153 <li>Duplicate group associated conservation or consensus
4154 created on new view</li>
4155 <li>Annotation scrollbar not displayed after 'show
4156 all hidden annotation rows' option selected</li>
4157 <li>Alignment quality not updated after alignment
4158 annotation row is hidden then shown</li>
4159 <li>Preserve colouring of structures coloured by
4160 sequences in pre Jalview 2.7 projects</li>
4161 <li>Web service job parameter dialog is not laid out
4163 <li>Web services menu not refreshed after 'reset
4164 services' button is pressed in preferences</li>
4165 <li>Annotation off by one in Jalview v2_3 example project</li>
4166 <li>Structures imported from file and saved in project
4167 get name like jalview_pdb1234.txt when reloaded</li>
4168 <li>Jalview does not always retrieve progress of a JABAWS
4169 job execution in full once it is complete</li>
4170 </ul> <em>Applet</em>
4172 <li>Alignment height set incorrectly when lots of
4173 annotation rows are displayed</li>
4174 <li>Relative URLs in feature HTML text not resolved to
4176 <li>View follows highlighting does not work for positions
4178 <li><= shown as = in tooltip</li>
4179 <li>Export features raises exception when no features
4181 <li>Separator string used for serialising lists of IDs
4182 for javascript api is modified when separator string
4183 provided as parameter</li>
4184 <li>Null pointer exception when selecting tree leaves for
4185 alignment with no existing selection</li>
4186 <li>Relative URLs for datasources assumed to be relative
4187 to applet's codebase</li>
4188 <li>Status bar not updated after finished searching and
4189 search wraps around to first result</li>
4190 <li>StructureSelectionManager instance shared between
4191 several Jalview applets causes race conditions and memory
4193 <li>Hover tooltip and mouseover of position on structure
4194 not sent from Jmol in applet</li>
4195 <li>Certain sequences of javascript method calls to
4196 applet API fatally hang browser</li>
4197 </ul> <em>General</em>
4199 <li>View follows structure mouseover scrolls beyond
4200 position with wrapped view and hidden regions</li>
4201 <li>Find sequence position moves to wrong residue
4202 with/without hidden columns</li>
4203 <li>Sequence length given in alignment properties window
4205 <li>InvalidNumberFormat exceptions thrown when trying to
4206 import PDB like structure files</li>
4207 <li>Positional search results are only highlighted
4208 between user-supplied sequence start/end bounds</li>
4209 <li>End attribute of sequence is not validated</li>
4210 <li>Find dialog only finds first sequence containing a
4211 given sequence position</li>
4212 <li>Sequence numbering not preserved in MSF alignment
4214 <li>Jalview PDB file reader does not extract sequence
4215 from nucleotide chains correctly</li>
4216 <li>Structure colours not updated when tree partition
4217 changed in alignment</li>
4218 <li>Sequence associated secondary structure not correctly
4219 parsed in interleaved stockholm</li>
4220 <li>Colour by annotation dialog does not restore current
4222 <li>Hiding (nearly) all sequences doesn't work
4224 <li>Sequences containing lowercase letters are not
4225 properly associated with their pdb files</li>
4226 </ul> <em>Documentation and Development</em>
4228 <li>schemas/JalviewWsParamSet.xsd corrupted by
4229 ApplyCopyright tool</li>
4234 <div align="center">
4235 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4238 <td><em>Application</em>
4240 <li>New warning dialog when the Jalview Desktop cannot
4241 contact web services</li>
4242 <li>JABA service parameters for a preset are shown in
4243 service job window</li>
4244 <li>JABA Service menu entries reworded</li>
4248 <li>Modeller PIR IO broken - cannot correctly import a
4249 pir file emitted by Jalview</li>
4250 <li>Existing feature settings transferred to new
4251 alignment view created from cut'n'paste</li>
4252 <li>Improved test for mixed amino/nucleotide chains when
4253 parsing PDB files</li>
4254 <li>Consensus and conservation annotation rows
4255 occasionally become blank for all new windows</li>
4256 <li>Exception raised when right clicking above sequences
4257 in wrapped view mode</li>
4258 </ul> <em>Application</em>
4260 <li>multiple multiply aligned structure views cause cpu
4261 usage to hit 100% and computer to hang</li>
4262 <li>Web Service parameter layout breaks for long user
4263 parameter names</li>
4264 <li>Jaba service discovery hangs desktop if Jaba server
4271 <div align="center">
4272 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4275 <td><em>Application</em>
4277 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4278 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4281 <li>Web Services preference tab</li>
4282 <li>Analysis parameters dialog box and user defined
4284 <li>Improved speed and layout of Envision2 service menu</li>
4285 <li>Superpose structures using associated sequence
4287 <li>Export coordinates and projection as CSV from PCA
4289 </ul> <em>Applet</em>
4291 <li>enable javascript: execution by the applet via the
4292 link out mechanism</li>
4293 </ul> <em>Other</em>
4295 <li>Updated the Jmol Jalview interface to work with Jmol
4297 <li>The Jalview Desktop and JalviewLite applet now
4298 require Java 1.5</li>
4299 <li>Allow Jalview feature colour specification for GFF
4300 sequence annotation files</li>
4301 <li>New 'colour by label' keword in Jalview feature file
4302 type colour specification</li>
4303 <li>New Jalview Desktop Groovy API method that allows a
4304 script to check if it being run in an interactive session or
4305 in a batch operation from the Jalview command line</li>
4309 <li>clustalx colourscheme colours Ds preferentially when
4310 both D+E are present in over 50% of the column</li>
4311 </ul> <em>Application</em>
4313 <li>typo in AlignmentFrame->View->Hide->all but
4314 selected Regions menu item</li>
4315 <li>sequence fetcher replaces ',' for ';' when the ',' is
4316 part of a valid accession ID</li>
4317 <li>fatal OOM if object retrieved by sequence fetcher
4318 runs out of memory</li>
4319 <li>unhandled Out of Memory Error when viewing pca
4320 analysis results</li>
4321 <li>InstallAnywhere builds fail to launch on OS X java
4322 10.5 update 4 (due to apple Java 1.6 update)</li>
4323 <li>Installanywhere Jalview silently fails to launch</li>
4324 </ul> <em>Applet</em>
4326 <li>Jalview.getFeatureGroups() raises an
4327 ArrayIndexOutOfBoundsException if no feature groups are
4334 <div align="center">
4335 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4341 <li>Alignment prettyprinter doesn't cope with long
4343 <li>clustalx colourscheme colours Ds preferentially when
4344 both D+E are present in over 50% of the column</li>
4345 <li>nucleic acid structures retrieved from PDB do not
4346 import correctly</li>
4347 <li>More columns get selected than were clicked on when a
4348 number of columns are hidden</li>
4349 <li>annotation label popup menu not providing correct
4350 add/hide/show options when rows are hidden or none are
4352 <li>Stockholm format shown in list of readable formats,
4353 and parser copes better with alignments from RFAM.</li>
4354 <li>CSV output of consensus only includes the percentage
4355 of all symbols if sequence logo display is enabled</li>
4357 </ul> <em>Applet</em>
4359 <li>annotation panel disappears when annotation is
4361 </ul> <em>Application</em>
4363 <li>Alignment view not redrawn properly when new
4364 alignment opened where annotation panel is visible but no
4365 annotations are present on alignment</li>
4366 <li>pasted region containing hidden columns is
4367 incorrectly displayed in new alignment window</li>
4368 <li>Jalview slow to complete operations when stdout is
4369 flooded (fix is to close the Jalview console)</li>
4370 <li>typo in AlignmentFrame->View->Hide->all but
4371 selected Rregions menu item.</li>
4372 <li>inconsistent group submenu and Format submenu entry
4373 'Un' or 'Non'conserved</li>
4374 <li>Sequence feature settings are being shared by
4375 multiple distinct alignments</li>
4376 <li>group annotation not recreated when tree partition is
4378 <li>double click on group annotation to select sequences
4379 does not propagate to associated trees</li>
4380 <li>Mac OSX specific issues:
4382 <li>exception raised when mouse clicked on desktop
4383 window background</li>
4384 <li>Desktop menu placed on menu bar and application
4385 name set correctly</li>
4386 <li>sequence feature settings not wide enough for the
4387 save feature colourscheme button</li>
4396 <div align="center">
4397 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4400 <td><em>New Capabilities</em>
4402 <li>URL links generated from description line for
4403 regular-expression based URL links (applet and application)
4405 <li>Non-positional feature URL links are shown in link
4407 <li>Linked viewing of nucleic acid sequences and
4409 <li>Automatic Scrolling option in View menu to display
4410 the currently highlighted region of an alignment.</li>
4411 <li>Order an alignment by sequence length, or using the
4412 average score or total feature count for each sequence.</li>
4413 <li>Shading features by score or associated description</li>
4414 <li>Subdivide alignment and groups based on identity of
4415 selected subsequence (Make Groups from Selection).</li>
4416 <li>New hide/show options including Shift+Control+H to
4417 hide everything but the currently selected region.</li>
4418 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4419 </ul> <em>Application</em>
4421 <li>Fetch DB References capabilities and UI expanded to
4422 support retrieval from DAS sequence sources</li>
4423 <li>Local DAS Sequence sources can be added via the
4424 command line or via the Add local source dialog box.</li>
4425 <li>DAS Dbref and DbxRef feature types are parsed as
4426 database references and protein_name is parsed as
4427 description line (BioSapiens terms).</li>
4428 <li>Enable or disable non-positional feature and database
4429 references in sequence ID tooltip from View menu in
4431 <!-- <li>New hidden columns and rows and representatives capabilities
4432 in annotations file (in progress - not yet fully implemented)</li> -->
4433 <li>Group-associated consensus, sequence logos and
4434 conservation plots</li>
4435 <li>Symbol distributions for each column can be exported
4436 and visualized as sequence logos</li>
4437 <li>Optionally scale multi-character column labels to fit
4438 within each column of annotation row<!-- todo for applet -->
4440 <li>Optional automatic sort of associated alignment view
4441 when a new tree is opened.</li>
4442 <li>Jalview Java Console</li>
4443 <li>Better placement of desktop window when moving
4444 between different screens.</li>
4445 <li>New preference items for sequence ID tooltip and
4446 consensus annotation</li>
4447 <li>Client to submit sequences and IDs to Envision2
4449 <li><em>Vamsas Capabilities</em>
4451 <li>Improved VAMSAS synchronization (Jalview archive
4452 used to preserve views, structures, and tree display
4454 <li>Import of vamsas documents from disk or URL via
4456 <li>Sharing of selected regions between views and
4457 with other VAMSAS applications (Experimental feature!)</li>
4458 <li>Updated API to VAMSAS version 0.2</li>
4460 </ul> <em>Applet</em>
4462 <li>Middle button resizes annotation row height</li>
4465 <li>sortByTree (true/false) - automatically sort the
4466 associated alignment view by the tree when a new tree is
4468 <li>showTreeBootstraps (true/false) - show or hide
4469 branch bootstraps (default is to show them if available)</li>
4470 <li>showTreeDistances (true/false) - show or hide
4471 branch lengths (default is to show them if available)</li>
4472 <li>showUnlinkedTreeNodes (true/false) - indicate if
4473 unassociated nodes should be highlighted in the tree
4475 <li>heightScale and widthScale (1.0 or more) -
4476 increase the height or width of a cell in the alignment
4477 grid relative to the current font size.</li>
4480 <li>Non-positional features displayed in sequence ID
4482 </ul> <em>Other</em>
4484 <li>Features format: graduated colour definitions and
4485 specification of feature scores</li>
4486 <li>Alignment Annotations format: new keywords for group
4487 associated annotation (GROUP_REF) and annotation row display
4488 properties (ROW_PROPERTIES)</li>
4489 <li>XML formats extended to support graduated feature
4490 colourschemes, group associated annotation, and profile
4491 visualization settings.</li></td>
4494 <li>Source field in GFF files parsed as feature source
4495 rather than description</li>
4496 <li>Non-positional features are now included in sequence
4497 feature and gff files (controlled via non-positional feature
4498 visibility in tooltip).</li>
4499 <li>URL links generated for all feature links (bugfix)</li>
4500 <li>Added URL embedding instructions to features file
4502 <li>Codons containing ambiguous nucleotides translated as
4503 'X' in peptide product</li>
4504 <li>Match case switch in find dialog box works for both
4505 sequence ID and sequence string and query strings do not
4506 have to be in upper case to match case-insensitively.</li>
4507 <li>AMSA files only contain first column of
4508 multi-character column annotation labels</li>
4509 <li>Jalview Annotation File generation/parsing consistent
4510 with documentation (e.g. Stockholm annotation can be
4511 exported and re-imported)</li>
4512 <li>PDB files without embedded PDB IDs given a friendly
4514 <li>Find incrementally searches ID string matches as well
4515 as subsequence matches, and correctly reports total number
4519 <li>Better handling of exceptions during sequence
4521 <li>Dasobert generated non-positional feature URL
4522 link text excludes the start_end suffix</li>
4523 <li>DAS feature and source retrieval buttons disabled
4524 when fetch or registry operations in progress.</li>
4525 <li>PDB files retrieved from URLs are cached properly</li>
4526 <li>Sequence description lines properly shared via
4528 <li>Sequence fetcher fetches multiple records for all
4530 <li>Ensured that command line das feature retrieval
4531 completes before alignment figures are generated.</li>
4532 <li>Reduced time taken when opening file browser for
4534 <li>isAligned check prior to calculating tree, PCA or
4535 submitting an MSA to JNet now excludes hidden sequences.</li>
4536 <li>User defined group colours properly recovered
4537 from Jalview projects.</li>
4546 <div align="center">
4547 <strong>2.4.0.b2</strong><br> 28/10/2009
4552 <li>Experimental support for google analytics usage
4554 <li>Jalview privacy settings (user preferences and docs).</li>
4559 <li>Race condition in applet preventing startup in
4561 <li>Exception when feature created from selection beyond
4562 length of sequence.</li>
4563 <li>Allow synthetic PDB files to be imported gracefully</li>
4564 <li>Sequence associated annotation rows associate with
4565 all sequences with a given id</li>
4566 <li>Find function matches case-insensitively for sequence
4567 ID string searches</li>
4568 <li>Non-standard characters do not cause pairwise
4569 alignment to fail with exception</li>
4570 </ul> <em>Application Issues</em>
4572 <li>Sequences are now validated against EMBL database</li>
4573 <li>Sequence fetcher fetches multiple records for all
4575 </ul> <em>InstallAnywhere Issues</em>
4577 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4578 issue with installAnywhere mechanism)</li>
4579 <li>Command line launching of JARs from InstallAnywhere
4580 version (java class versioning error fixed)</li>
4587 <div align="center">
4588 <strong>2.4</strong><br> 27/8/2008
4591 <td><em>User Interface</em>
4593 <li>Linked highlighting of codon and amino acid from
4594 translation and protein products</li>
4595 <li>Linked highlighting of structure associated with
4596 residue mapping to codon position</li>
4597 <li>Sequence Fetcher provides example accession numbers
4598 and 'clear' button</li>
4599 <li>MemoryMonitor added as an option under Desktop's
4601 <li>Extract score function to parse whitespace separated
4602 numeric data in description line</li>
4603 <li>Column labels in alignment annotation can be centred.</li>
4604 <li>Tooltip for sequence associated annotation give name
4606 </ul> <em>Web Services and URL fetching</em>
4608 <li>JPred3 web service</li>
4609 <li>Prototype sequence search client (no public services
4611 <li>Fetch either seed alignment or full alignment from
4613 <li>URL Links created for matching database cross
4614 references as well as sequence ID</li>
4615 <li>URL Links can be created using regular-expressions</li>
4616 </ul> <em>Sequence Database Connectivity</em>
4618 <li>Retrieval of cross-referenced sequences from other
4620 <li>Generalised database reference retrieval and
4621 validation to all fetchable databases</li>
4622 <li>Fetch sequences from DAS sources supporting the
4623 sequence command</li>
4624 </ul> <em>Import and Export</em>
4625 <li>export annotation rows as CSV for spreadsheet import</li>
4626 <li>Jalview projects record alignment dataset associations,
4627 EMBL products, and cDNA sequence mappings</li>
4628 <li>Sequence Group colour can be specified in Annotation
4630 <li>Ad-hoc colouring of group in Annotation File using RGB
4631 triplet as name of colourscheme</li>
4632 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4634 <li>treenode binding for VAMSAS tree exchange</li>
4635 <li>local editing and update of sequences in VAMSAS
4636 alignments (experimental)</li>
4637 <li>Create new or select existing session to join</li>
4638 <li>load and save of vamsas documents</li>
4639 </ul> <em>Application command line</em>
4641 <li>-tree parameter to open trees (introduced for passing
4643 <li>-fetchfrom command line argument to specify nicknames
4644 of DAS servers to query for alignment features</li>
4645 <li>-dasserver command line argument to add new servers
4646 that are also automatically queried for features</li>
4647 <li>-groovy command line argument executes a given groovy
4648 script after all input data has been loaded and parsed</li>
4649 </ul> <em>Applet-Application data exchange</em>
4651 <li>Trees passed as applet parameters can be passed to
4652 application (when using "View in full
4653 application")</li>
4654 </ul> <em>Applet Parameters</em>
4656 <li>feature group display control parameter</li>
4657 <li>debug parameter</li>
4658 <li>showbutton parameter</li>
4659 </ul> <em>Applet API methods</em>
4661 <li>newView public method</li>
4662 <li>Window (current view) specific get/set public methods</li>
4663 <li>Feature display control methods</li>
4664 <li>get list of currently selected sequences</li>
4665 </ul> <em>New Jalview distribution features</em>
4667 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4668 <li>RELEASE file gives build properties for the latest
4669 Jalview release.</li>
4670 <li>Java 1.1 Applet build made easier and donotobfuscate
4671 property controls execution of obfuscator</li>
4672 <li>Build target for generating source distribution</li>
4673 <li>Debug flag for javacc</li>
4674 <li>.jalview_properties file is documented (slightly) in
4675 jalview.bin.Cache</li>
4676 <li>Continuous Build Integration for stable and
4677 development version of Application, Applet and source
4682 <li>selected region output includes visible annotations
4683 (for certain formats)</li>
4684 <li>edit label/displaychar contains existing label/char
4686 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4687 <li>shorter peptide product names from EMBL records</li>
4688 <li>Newick string generator makes compact representations</li>
4689 <li>bootstrap values parsed correctly for tree files with
4691 <li>pathological filechooser bug avoided by not allowing
4692 filenames containing a ':'</li>
4693 <li>Fixed exception when parsing GFF files containing
4694 global sequence features</li>
4695 <li>Alignment datasets are finalized only when number of
4696 references from alignment sequences goes to zero</li>
4697 <li>Close of tree branch colour box without colour
4698 selection causes cascading exceptions</li>
4699 <li>occasional negative imgwidth exceptions</li>
4700 <li>better reporting of non-fatal warnings to user when
4701 file parsing fails.</li>
4702 <li>Save works when Jalview project is default format</li>
4703 <li>Save as dialog opened if current alignment format is
4704 not a valid output format</li>
4705 <li>UniProt canonical names introduced for both das and
4707 <li>Histidine should be midblue (not pink!) in Zappo</li>
4708 <li>error messages passed up and output when data read
4710 <li>edit undo recovers previous dataset sequence when
4711 sequence is edited</li>
4712 <li>allow PDB files without pdb ID HEADER lines (like
4713 those generated by MODELLER) to be read in properly</li>
4714 <li>allow reading of JPred concise files as a normal
4716 <li>Stockholm annotation parsing and alignment properties
4717 import fixed for PFAM records</li>
4718 <li>Structure view windows have correct name in Desktop
4720 <li>annotation consisting of sequence associated scores
4721 can be read and written correctly to annotation file</li>
4722 <li>Aligned cDNA translation to aligned peptide works
4724 <li>Fixed display of hidden sequence markers and
4725 non-italic font for representatives in Applet</li>
4726 <li>Applet Menus are always embedded in applet window on
4728 <li>Newly shown features appear at top of stack (in
4730 <li>Annotations added via parameter not drawn properly
4731 due to null pointer exceptions</li>
4732 <li>Secondary structure lines are drawn starting from
4733 first column of alignment</li>
4734 <li>UniProt XML import updated for new schema release in
4736 <li>Sequence feature to sequence ID match for Features
4737 file is case-insensitive</li>
4738 <li>Sequence features read from Features file appended to
4739 all sequences with matching IDs</li>
4740 <li>PDB structure coloured correctly for associated views
4741 containing a sub-sequence</li>
4742 <li>PDB files can be retrieved by applet from Jar files</li>
4743 <li>feature and annotation file applet parameters
4744 referring to different directories are retrieved correctly</li>
4745 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4746 <li>Fixed application hang whilst waiting for
4747 splash-screen version check to complete</li>
4748 <li>Applet properly URLencodes input parameter values
4749 when passing them to the launchApp service</li>
4750 <li>display name and local features preserved in results
4751 retrieved from web service</li>
4752 <li>Visual delay indication for sequence retrieval and
4753 sequence fetcher initialisation</li>
4754 <li>updated Application to use DAS 1.53e version of
4755 dasobert DAS client</li>
4756 <li>Re-instated Full AMSA support and .amsa file
4758 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4766 <div align="center">
4767 <strong>2.3</strong><br> 9/5/07
4772 <li>Jmol 11.0.2 integration</li>
4773 <li>PDB views stored in Jalview XML files</li>
4774 <li>Slide sequences</li>
4775 <li>Edit sequence in place</li>
4776 <li>EMBL CDS features</li>
4777 <li>DAS Feature mapping</li>
4778 <li>Feature ordering</li>
4779 <li>Alignment Properties</li>
4780 <li>Annotation Scores</li>
4781 <li>Sort by scores</li>
4782 <li>Feature/annotation editing in applet</li>
4787 <li>Headless state operation in 2.2.1</li>
4788 <li>Incorrect and unstable DNA pairwise alignment</li>
4789 <li>Cut and paste of sequences with annotation</li>
4790 <li>Feature group display state in XML</li>
4791 <li>Feature ordering in XML</li>
4792 <li>blc file iteration selection using filename # suffix</li>
4793 <li>Stockholm alignment properties</li>
4794 <li>Stockhom alignment secondary structure annotation</li>
4795 <li>2.2.1 applet had no feature transparency</li>
4796 <li>Number pad keys can be used in cursor mode</li>
4797 <li>Structure Viewer mirror image resolved</li>
4804 <div align="center">
4805 <strong>2.2.1</strong><br> 12/2/07
4810 <li>Non standard characters can be read and displayed
4811 <li>Annotations/Features can be imported/exported to the
4813 <li>Applet allows editing of sequence/annotation/group
4814 name & description
4815 <li>Preference setting to display sequence name in
4817 <li>Annotation file format extended to allow
4818 Sequence_groups to be defined
4819 <li>Default opening of alignment overview panel can be
4820 specified in preferences
4821 <li>PDB residue numbering annotation added to associated
4827 <li>Applet crash under certain Linux OS with Java 1.6
4829 <li>Annotation file export / import bugs fixed
4830 <li>PNG / EPS image output bugs fixed
4836 <div align="center">
4837 <strong>2.2</strong><br> 27/11/06
4842 <li>Multiple views on alignment
4843 <li>Sequence feature editing
4844 <li>"Reload" alignment
4845 <li>"Save" to current filename
4846 <li>Background dependent text colour
4847 <li>Right align sequence ids
4848 <li>User-defined lower case residue colours
4851 <li>Menu item accelerator keys
4852 <li>Control-V pastes to current alignment
4853 <li>Cancel button for DAS Feature Fetching
4854 <li>PCA and PDB Viewers zoom via mouse roller
4855 <li>User-defined sub-tree colours and sub-tree selection
4857 <li>'New Window' button on the 'Output to Text box'
4862 <li>New memory efficient Undo/Redo System
4863 <li>Optimised symbol lookups and conservation/consensus
4865 <li>Region Conservation/Consensus recalculated after
4867 <li>Fixed Remove Empty Columns Bug (empty columns at end
4869 <li>Slowed DAS Feature Fetching for increased robustness.
4871 <li>Made angle brackets in ASCII feature descriptions
4873 <li>Re-instated Zoom function for PCA
4874 <li>Sequence descriptions conserved in web service
4876 <li>UniProt ID discoverer uses any word separated by
4878 <li>WsDbFetch query/result association resolved
4879 <li>Tree leaf to sequence mapping improved
4880 <li>Smooth fonts switch moved to FontChooser dialog box.
4887 <div align="center">
4888 <strong>2.1.1</strong><br> 12/9/06
4893 <li>Copy consensus sequence to clipboard</li>
4898 <li>Image output - rightmost residues are rendered if
4899 sequence id panel has been resized</li>
4900 <li>Image output - all offscreen group boundaries are
4902 <li>Annotation files with sequence references - all
4903 elements in file are relative to sequence position</li>
4904 <li>Mac Applet users can use Alt key for group editing</li>
4910 <div align="center">
4911 <strong>2.1</strong><br> 22/8/06
4916 <li>MAFFT Multiple Alignment in default Web Service list</li>
4917 <li>DAS Feature fetching</li>
4918 <li>Hide sequences and columns</li>
4919 <li>Export Annotations and Features</li>
4920 <li>GFF file reading / writing</li>
4921 <li>Associate structures with sequences from local PDB
4923 <li>Add sequences to exisiting alignment</li>
4924 <li>Recently opened files / URL lists</li>
4925 <li>Applet can launch the full application</li>
4926 <li>Applet has transparency for features (Java 1.2
4928 <li>Applet has user defined colours parameter</li>
4929 <li>Applet can load sequences from parameter
4930 "sequence<em>x</em>"
4936 <li>Redundancy Panel reinstalled in the Applet</li>
4937 <li>Monospaced font - EPS / rescaling bug fixed</li>
4938 <li>Annotation files with sequence references bug fixed</li>
4944 <div align="center">
4945 <strong>2.08.1</strong><br> 2/5/06
4950 <li>Change case of selected region from Popup menu</li>
4951 <li>Choose to match case when searching</li>
4952 <li>Middle mouse button and mouse movement can compress /
4953 expand the visible width and height of the alignment</li>
4958 <li>Annotation Panel displays complete JNet results</li>
4964 <div align="center">
4965 <strong>2.08b</strong><br> 18/4/06
4971 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4972 <li>Righthand label on wrapped alignments shows correct
4979 <div align="center">
4980 <strong>2.08</strong><br> 10/4/06
4985 <li>Editing can be locked to the selection area</li>
4986 <li>Keyboard editing</li>
4987 <li>Create sequence features from searches</li>
4988 <li>Precalculated annotations can be loaded onto
4990 <li>Features file allows grouping of features</li>
4991 <li>Annotation Colouring scheme added</li>
4992 <li>Smooth fonts off by default - Faster rendering</li>
4993 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4998 <li>Drag & Drop fixed on Linux</li>
4999 <li>Jalview Archive file faster to load/save, sequence
5000 descriptions saved.</li>
5006 <div align="center">
5007 <strong>2.07</strong><br> 12/12/05
5012 <li>PDB Structure Viewer enhanced</li>
5013 <li>Sequence Feature retrieval and display enhanced</li>
5014 <li>Choose to output sequence start-end after sequence
5015 name for file output</li>
5016 <li>Sequence Fetcher WSDBFetch@EBI</li>
5017 <li>Applet can read feature files, PDB files and can be
5018 used for HTML form input</li>
5023 <li>HTML output writes groups and features</li>
5024 <li>Group editing is Control and mouse click</li>
5025 <li>File IO bugs</li>
5031 <div align="center">
5032 <strong>2.06</strong><br> 28/9/05
5037 <li>View annotations in wrapped mode</li>
5038 <li>More options for PCA viewer</li>
5043 <li>GUI bugs resolved</li>
5044 <li>Runs with -nodisplay from command line</li>
5050 <div align="center">
5051 <strong>2.05b</strong><br> 15/9/05
5056 <li>Choose EPS export as lineart or text</li>
5057 <li>Jar files are executable</li>
5058 <li>Can read in Uracil - maps to unknown residue</li>
5063 <li>Known OutOfMemory errors give warning message</li>
5064 <li>Overview window calculated more efficiently</li>
5065 <li>Several GUI bugs resolved</li>
5071 <div align="center">
5072 <strong>2.05</strong><br> 30/8/05
5077 <li>Edit and annotate in "Wrapped" view</li>
5082 <li>Several GUI bugs resolved</li>
5088 <div align="center">
5089 <strong>2.04</strong><br> 24/8/05
5094 <li>Hold down mouse wheel & scroll to change font
5100 <li>Improved JPred client reliability</li>
5101 <li>Improved loading of Jalview files</li>
5107 <div align="center">
5108 <strong>2.03</strong><br> 18/8/05
5113 <li>Set Proxy server name and port in preferences</li>
5114 <li>Multiple URL links from sequence ids</li>
5115 <li>User Defined Colours can have a scheme name and added
5117 <li>Choose to ignore gaps in consensus calculation</li>
5118 <li>Unix users can set default web browser</li>
5119 <li>Runs without GUI for batch processing</li>
5120 <li>Dynamically generated Web Service Menus</li>
5125 <li>InstallAnywhere download for Sparc Solaris</li>
5131 <div align="center">
5132 <strong>2.02</strong><br> 18/7/05
5138 <li>Copy & Paste order of sequences maintains
5139 alignment order.</li>
5145 <div align="center">
5146 <strong>2.01</strong><br> 12/7/05
5151 <li>Use delete key for deleting selection.</li>
5152 <li>Use Mouse wheel to scroll sequences.</li>
5153 <li>Help file updated to describe how to add alignment
5155 <li>Version and build date written to build properties
5157 <li>InstallAnywhere installation will check for updates
5158 at launch of Jalview.</li>
5163 <li>Delete gaps bug fixed.</li>
5164 <li>FileChooser sorts columns.</li>
5165 <li>Can remove groups one by one.</li>
5166 <li>Filechooser icons installed.</li>
5167 <li>Finder ignores return character when searching.
5168 Return key will initiate a search.<br>
5175 <div align="center">
5176 <strong>2.0</strong><br> 20/6/05
5181 <li>New codebase</li>