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>
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28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
62 <em>22/06/2021</em></strong></td>
63 <td align="left" valign="top"><em>Development</em>
65 <li>Updated building instructions</li>
70 <!-- JAL-3840 -->Occupancy calculation is incorrect for
71 alignment columns with over -1+2^32 gaps (breaking filtering
75 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
76 scale factors being set with buggy window-managers (linux
79 </ul> <em>Development</em>
81 <li>Fixed non-fatal gradle errors during build</li>
86 <td width="60" align="center" nowrap><strong><a
87 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
88 <em>09/03/2021</em></strong></td>
89 <td align="left" valign="top"><em>Improved control of
90 Jalview's use of network services via jalview_properties</em>
93 <!-- JAL-3814 -->New .jalview_properties token controlling
94 launch of the news browser (like -nonews argument)
97 <!-- JAL-3813 -->New .jalview_properties token controlling
98 download of linkout URLs from
99 www.jalview.org/services/identifiers
102 <!-- JAL-3812 -->New .jalview_properties token controlling
103 download of BIOJSHTML templates
106 <!-- JAL-3811 -->New 'Discover Web Services' option to
107 trigger a one off JABAWS discovery if autodiscovery was
111 <td align="left" valign="top">
114 <!-- JAL-3818 -->Intermittent deadlock opening structure in
117 </ul> <em>New Known defects</em>
120 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
121 always restored from project (since 2.10.3)
124 <!-- JAL-3806 -->Selections from tree built from CDS aren't
125 propagated to Protein alignment (since 2.11.1.3)
131 <td width="60" align="center" nowrap><strong><a
132 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
133 <em>29/10/2020</em></strong></td>
134 <td align="left" valign="top">
139 <td align="left" valign="top">
142 <!-- JAL-3765 -->Find doesn't always highlight all matching
143 positions in a sequence (bug introduced in 2.11.1.2)
146 <!-- JAL-3760 -->Alignments containing one or more protein
147 sequences can be classed as nucleotide
150 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
151 sequences after alignment of protein products (known defect
152 first reported for 2.11.1.0)
155 <!-- JAL-3725 -->No tooltip or popup menu for genomic
156 features outwith CDS shown overlaid on protein
159 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
160 correctly mapped by Jalview (e.g. affects viral CDS with
161 ribosomal slippage, since 2.9.0)
164 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
168 <!-- JAL-3700 -->Selections in CDS sequence panel don't
169 always select corresponding protein sequences
172 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
173 column selection doesn't always ignore hidden columns
175 </ul> <em>Installer</em>
178 <!-- JAL-3611 -->Space character in Jalview install path on
179 Windows prevents install4j launching getdown
181 </ul> <em>Development</em>
184 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
185 version numbers in doc/building.md
191 <td width="60" align="center" nowrap><strong><a
192 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
193 <em>25/09/2020</em></strong></td>
194 <td align="left" valign="top">
198 <td align="left" valign="top">
201 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
202 "Encountered problems opening
203 https://www.jalview.org/examples/exampleFile_2_7.jvp"
209 <td width="60" align="center" nowrap><strong><a
210 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
211 <em>17/09/2020</em></strong></td>
212 <td align="left" valign="top">
215 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
216 residue in cursor mode
219 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
220 HTSJDK from 2.12 to 2.23
223 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
224 optimisations and improvements suggested by Bob Hanson and
225 improved compatibility with JalviewJS
228 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
229 alignments from Pfam and Rfam
232 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
233 import (no longer based on .gz extension)
236 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
239 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
240 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
244 <!-- JAL-3667 -->Improved warning messages, debug logging
245 and fixed Retry action when Jalview encounters errors when
246 saving or making backup files.
249 <!-- JAL-3676 -->Enhanced Jalview Java Console:
251 <li>Jalview's logging level can be configured</li>
252 <li>Copy to Clipboard Buttion</li>
256 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
257 when running on Linux (Requires Java 11+)
259 </ul> <em>Launching Jalview</em>
262 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
263 through a system property
266 <!-- JAL-3477 -->Improved built-in documentation and command
267 line help for configuring Jalview's memory
271 <td align="left" valign="top">
274 <!-- JAL-3691 -->Conservation and Quality tracks are shown
275 but not calculated and no protein or DNA score models are
276 available for tree/PCA calculation when launched with
277 Turkish language locale
280 <!-- JAL-3493 -->Escape does not clear highlights on the
281 alignment (Since Jalview 2.10.3)
284 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
285 doesn't slide selected sequences, just sequence under cursor
288 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
289 sequence under the cursor
292 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
293 multiple EMBL gene products shown for a single contig
296 <!-- JAL-3696 -->Errors encountered when processing variants
297 from VCF files yield "Error processing VCF: Format specifier
301 <!-- JAL-3697 -->Count of features not shown can be wrong
302 when there are both local and complementary features mapped
303 to the position under the cursor
306 <!-- JAL-3673 -->Sequence ID for reference sequence is
307 clipped when Right align Sequence IDs enabled
310 <!-- JAL-2983 -->Slider with negative range values not
311 rendered correctly in VAqua4 (Since 2.10.4)
314 <!-- JAL-3685 -->Single quotes not displayed correctly in
315 internationalised text for some messages and log output
318 <!-- JAL-3490 -->Find doesn't report matches that span
319 hidden gapped columns
322 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
323 panels, Alignment viewport and annotation renderer.
326 <!-- JAL-3561 -->Jalview ignores file format parameter
327 specifying output format when exporting an alignment via the
331 <!-- JAL-3667 -->Windows 10: For a minority of users, if
332 backups are not enabled, Jalview sometimes fails to
333 overwrite an existing file and raises a warning dialog. (in
334 2.11.0, and 2.11.1.0, the workaround is to try to save the
335 file again, and if that fails, delete the original file and
339 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
343 <!-- JAL-3741 -->References to http://www.jalview.org in
344 program and documentation
346 </ul> <em>Launching Jalview</em>
349 <!-- JAL-3718 -->Jalview application fails when launched the
350 first time for a version that has different jars to the
351 previous launched version.
353 </ul> <em>Developing Jalview</em>
356 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
357 data, causing cloverReport gradle task to fail with an
361 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
362 monitor the release channel
364 </ul> <em>New Known defects</em>
367 <!-- JAL-3748 -->CDS shown in result of submitting proteins
368 in a CDS/Protein alignment to a web service is wrong when
369 proteins share a common transcript sequence (e.g.
370 genome of RNA viruses)
373 <!-- JAL-3576 -->Co-located features exported and re-imported
374 are ordered differently when shown on alignment and in
375 tooltips. (Also affects v2.11.1.0)
378 <!-- JAL-3702 -->Drag and drop of alignment file onto
379 alignment window when in a HiDPI scaled mode in Linux only
380 works for the top left quadrant of the alignment window
383 <!-- JAL-3701 -->Stale build data in jalview standalone jar
384 builds (only affects 2.11.1.1 branch)
387 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
388 when alignment view restored from project (since Jalview 2.11.0)
391 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
392 protein products for certain ENA records are repeatedly
393 shown via Calculate->Show Cross Refs
399 <td width="60" align="center" nowrap><strong><a
400 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
401 <em>22/04/2020</em></strong></td>
402 <td align="left" valign="top">
405 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
406 'virtual' codon features shown on protein (or vice versa)
407 for display in alignments, on structure views (including
408 transfer to UCSF chimera), in feature reports and for
412 <!-- JAL-3121 -->Feature attributes from VCF files can be
413 exported and re-imported as GFF3 files
416 <!-- JAL-3376 -->Capture VCF "fixed column" values
417 POS, ID, QUAL, FILTER as Feature Attributes
420 <!-- JAL-3375 -->More robust VCF numeric data field
421 validation while parsing
424 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
428 <!-- JAL-3535 -->Feature Settings dialog title includes name
432 <!-- JAL-3538 -->Font anti-aliasing in alignment views
436 <!-- JAL-3468 -->Very long feature descriptions truncated in
440 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
441 with no feature types visible
444 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
446 </ul><em>Jalview Installer</em>
449 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
450 in console (may be null when Jalview launched as executable jar or via conda)
453 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
456 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
459 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
461 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
462 </ul> <em>Release processes</em>
465 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
468 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
470 </ul> <em>Build System</em>
473 <!-- JAL-3510 -->Clover updated to 4.4.1
476 <!-- JAL-3513 -->Test code included in Clover coverage
480 <em>Groovy Scripts</em>
483 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
484 to stdout containing the consensus sequence for each
485 alignment in a Jalview session
488 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
489 genomic sequence_variant annotation from CDS as
490 missense_variant or synonymous_variant on protein products.
494 <td align="left" valign="top">
497 <!-- JAL-3581 -->Hidden sequence markers still visible when
498 'Show hidden markers' option is not ticked
501 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
502 PNG output when 'Automatically set ID width' is set in
503 jalview preferences or properties file
506 <!-- JAL-3571 -->Feature Editor dialog can be opened when
507 'Show Sequence Features' option is not ticked
510 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
511 buttons in Feature Settings dialog are clicked when no
515 <!-- JAL-3412 -->ID margins for CDS and Protein views not
516 equal when split frame is first opened
519 <!-- JAL-3296 -->Sequence position numbers in status bar not
520 correct after editing a sequence's start position
523 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
524 with annotation and exceptions thrown when only a few
525 columns shown in wrapped mode
528 <!-- JAL-3386 -->Sequence IDs missing in headless export of
529 wrapped alignment figure with annotations
532 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
533 ID fails with ClassCastException
536 <!-- JAL-3389 -->Chimera session not restored from Jalview
540 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
541 feature settings dialog also selects columns
544 <!-- JAL-3473 -->SpinnerNumberModel causes
545 IllegalArgumentException in some circumstances
548 <!-- JAL-3534 -->Multiple feature settings dialogs can be
552 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
553 alignment window is closed
556 <!-- JAL-3406 -->Credits missing some authors in Jalview
557 help documentation for 2.11.0 release
560 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
561 includes Pfam ID as sequence's accession rather than its
564 </ul> <em>Java 11 Compatibility issues</em>
567 <!-- JAL-2987 -->OSX - Can't view some search results in
568 PDB/Uniprot search panel
570 </ul> <em>Installer</em>
573 <!-- JAL-3447 -->Jalview should not create file associations
574 for 3D structure files (.pdb, .mmcif. .cif)
576 </ul> <em>Repository and Source Release</em>
579 <!-- JAL-3474 -->removed obsolete .cvsignore files from
583 <!-- JAL-3541 -->Clover report generation running out of
586 </ul> <em>New Known Issues</em>
589 <!-- JAL-3523 -->OSX - Current working directory not
590 preserved when Jalview.app launched with parameters from
594 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
595 clipped in headless figure export when Right Align option
599 <!-- JAL-3542 -->Jalview Installation type always reports
600 'Source' in console output
603 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
604 bamboo server but run fine locally.
610 <td width="60" align="center" nowrap>
611 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
612 <em>04/07/2019</em></strong>
614 <td align="left" valign="top">
617 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
618 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
619 source project) rather than InstallAnywhere
622 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
623 settings, receive over the air updates and launch specific
624 versions via (<a href="https://github.com/threerings/getdown">Three
628 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
629 formats supported by Jalview (including .jvp project files)
632 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
633 arguments and switch between different getdown channels
636 <!-- JAL-3141 -->Backup files created when saving Jalview project
641 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
642 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
644 <!-- JAL-2620 -->Alternative genetic code tables for
645 'Translate as cDNA'</li>
647 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
648 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
651 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
652 implementation that allows updates) used for Sequence Feature collections</li>
654 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
655 features can be filtered and shaded according to any
656 associated attributes (e.g. variant attributes from VCF
657 file, or key-value pairs imported from column 9 of GFF
661 <!-- JAL-2879 -->Feature Attributes and shading schemes
662 stored and restored from Jalview Projects
665 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
666 recognise variant features
669 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
670 sequences (also coloured red by default)
673 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
677 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
678 algorithm (Z-sort/transparency and filter aware)
681 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
687 <!-- JAL-3205 -->Symmetric score matrices for faster
688 tree and PCA calculations
690 <li><strong>Principal Components Analysis Viewer</strong>
693 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
694 and Viewer state saved in Jalview Project
696 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
699 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
703 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
708 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
710 <li><strong>Speed and Efficiency</strong>
713 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
714 multiple groups when working with large alignments
717 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
721 <li><strong>User Interface</strong>
724 <!-- JAL-2933 -->Finder panel remembers last position in each
728 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
729 what is shown)<br />Only visible regions of alignment are shown by
730 default (can be changed in user preferences)
733 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
734 to the Overwrite Dialog
737 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
741 <!-- JAL-1244 -->Status bar shows bounds when dragging a
742 selection region, and gap count when inserting or deleting gaps
745 <!-- JAL-3132 -->Status bar updates over sequence and annotation
749 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
753 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
757 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
760 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
764 <!-- JAL-3181 -->Consistent ordering of links in sequence id
768 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
770 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
774 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
775 <li><strong>Java 11 Support (not yet on general release)</strong>
778 <!-- -->OSX GUI integrations for App menu's 'About' entry and
783 <em>Deprecations</em>
785 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
786 capabilities removed from the Jalview Desktop
788 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
789 unmarshalling has been replaced by JAXB for Jalview projects
790 and XML based data retrieval clients</li>
791 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
792 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
793 </ul> <em>Documentation</em>
795 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
796 not supported in EPS figure export
798 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
799 </ul> <em>Development and Release Processes</em>
802 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
805 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
807 <!-- JAL-3225 -->Eclipse project configuration managed with
811 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
812 Bamboo continuous integration for unattended Test Suite
816 <!-- JAL-2864 -->Memory test suite to detect leaks in common
820 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
824 <!-- JAL-3248 -->Developer documentation migrated to
825 markdown (with HTML rendering)
828 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
831 <!-- JAL-3289 -->New URLs for publishing development
836 <td align="left" valign="top">
839 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
842 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
843 superposition in Jmol fail on Windows
846 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
847 structures for sequences with lots of PDB structures
850 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
854 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
855 project involving multiple views
858 <!-- JAL-3164 -->Overview for complementary view in a linked
859 CDS/Protein alignment is not updated when Hide Columns by
860 Annotation dialog hides columns
863 <!-- JAL-3158 -->Selection highlighting in the complement of a
864 CDS/Protein alignment stops working after making a selection in
865 one view, then making another selection in the other view
868 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
872 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
873 Settings and Jalview Preferences panels
876 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
877 overview with large alignments
880 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
881 region if columns were selected by dragging right-to-left and the
882 mouse moved to the left of the first column
885 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
886 hidden column marker via scale popup menu
889 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
890 doesn't tell users the invalid URL
893 <!-- JAL-2816 -->Tooltips displayed for features filtered by
897 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
898 show cross references or Fetch Database References are shown in
902 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
903 peptide sequence (computed variant shown as p.Res.null)
906 <!-- JAL-2060 -->'Graduated colour' option not offered for
907 manually created features (where feature score is Float.NaN)
910 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
911 when columns are hidden
914 <!-- JAL-3082 -->Regular expression error for '(' in Select
915 Columns by Annotation description
918 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
919 out of Scale or Annotation Panel
922 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
926 <!-- JAL-3074 -->Left/right drag in annotation can scroll
930 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
934 <!-- JAL-3002 -->Column display is out by one after Page Down,
935 Page Up in wrapped mode
938 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
941 <!-- JAL-2932 -->Finder searches in minimised alignments
944 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
945 on opening an alignment
948 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
952 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
953 different groups in the alignment are selected
956 <!-- JAL-2717 -->Internationalised colour scheme names not shown
960 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
964 <!-- JAL-3125 -->Value input for graduated feature colour
965 threshold gets 'unrounded'
968 <!-- JAL-2982 -->PCA image export doesn't respect background
972 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
975 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
978 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
982 <!-- JAL-2964 -->Associate Tree with All Views not restored from
986 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
987 shown in complementary view
990 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
991 without normalisation
994 <!-- JAL-3021 -->Sequence Details report should open positioned at top
998 <!-- JAL-914 -->Help page can be opened twice
1001 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1003 </ul> <em>Editing</em>
1006 <!-- JAL-2822 -->Start and End should be updated when sequence
1007 data at beginning or end of alignment added/removed via 'Edit'
1011 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1012 relocate sequence features correctly when start of sequence is
1013 removed (Known defect since 2.10)
1016 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1017 dialog corrupts dataset sequence
1020 <!-- JAL-868 -->Structure colours not updated when associated tree
1021 repartitions the alignment view (Regression in 2.10.5)
1023 </ul> <em>Datamodel</em>
1026 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1027 sequence's End is greater than its length
1029 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1030 general release)</em>
1033 <!-- JAL-3288 -->Menus work properly in split-screen
1035 </ul> <em>New Known Defects</em>
1038 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1041 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1042 regions of protein alignment.
1045 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1046 is restored from a Jalview 2.11 project
1049 <!-- JAL-3213 -->Alignment panel height can be too small after
1053 <!-- JAL-3240 -->Display is incorrect after removing gapped
1054 columns within hidden columns
1057 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1058 window after dragging left to select columns to left of visible
1062 <!-- JAL-2876 -->Features coloured according to their description
1063 string and thresholded by score in earlier versions of Jalview are
1064 not shown as thresholded features in 2.11. To workaround please
1065 create a Score filter instead.
1068 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1070 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1073 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1074 alignments with multiple views can close views unexpectedly
1077 <em>Java 11 Specific defects</em>
1080 <!-- JAL-3235 -->Jalview Properties file is not sorted
1081 alphabetically when saved
1087 <td width="60" nowrap>
1088 <div align="center">
1089 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1092 <td><div align="left">
1096 <!-- JAL-3101 -->Default memory for Jalview webstart and
1097 InstallAnywhere increased to 1G.
1100 <!-- JAL-247 -->Hidden sequence markers and representative
1101 sequence bolding included when exporting alignment as EPS,
1102 SVG, PNG or HTML. <em>Display is configured via the
1103 Format menu, or for command-line use via a Jalview
1104 properties file.</em>
1107 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1108 API and sequence data now imported as JSON.
1111 <!-- JAL-3065 -->Change in recommended way of starting
1112 Jalview via a Java command line: add jars in lib directory
1113 to CLASSPATH, rather than via the deprecated java.ext.dirs
1117 <em>Development</em>
1120 <!-- JAL-3047 -->Support added to execute test suite
1121 instrumented with <a href="http://openclover.org/">Open
1126 <td><div align="left">
1130 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1131 row shown in Feredoxin Structure alignment view of example
1135 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1136 annotation displayed.
1139 <!-- JAL-3107 -->Group conservation/consensus not shown
1140 for newly created group when 'Apply to all groups'
1144 <!-- JAL-3087 -->Corrupted display when switching to
1145 wrapped mode when sequence panel's vertical scrollbar is
1149 <!-- JAL-3003 -->Alignment is black in exported EPS file
1150 when sequences are selected in exported view.</em>
1153 <!-- JAL-3059 -->Groups with different coloured borders
1154 aren't rendered with correct colour.
1157 <!-- JAL-3092 -->Jalview could hang when importing certain
1158 types of knotted RNA secondary structure.
1161 <!-- JAL-3095 -->Sequence highlight and selection in
1162 trimmed VARNA 2D structure is incorrect for sequences that
1166 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1167 annotation when columns are inserted into an alignment,
1168 and when exporting as Stockholm flatfile.
1171 <!-- JAL-3053 -->Jalview annotation rows containing upper
1172 and lower-case 'E' and 'H' do not automatically get
1173 treated as RNA secondary structure.
1176 <!-- JAL-3106 -->.jvp should be used as default extension
1177 (not .jar) when saving a Jalview project file.
1180 <!-- JAL-3105 -->Mac Users: closing a window correctly
1181 transfers focus to previous window on OSX
1184 <em>Java 10 Issues Resolved</em>
1187 <!-- JAL-2988 -->OSX - Can't save new files via the File
1188 or export menus by typing in a name into the Save dialog
1192 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1193 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1194 'look and feel' which has improved compatibility with the
1195 latest version of OSX.
1202 <td width="60" nowrap>
1203 <div align="center">
1204 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1205 <em>7/06/2018</em></strong>
1208 <td><div align="left">
1212 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1213 annotation retrieved from Uniprot
1216 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1217 onto the Jalview Desktop
1221 <td><div align="left">
1225 <!-- JAL-3017 -->Cannot import features with multiple
1226 variant elements (blocks import of some Uniprot records)
1229 <!-- JAL-2997 -->Clustal files with sequence positions in
1230 right-hand column parsed correctly
1233 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1234 not alignment area in exported graphic
1237 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1238 window has input focus
1241 <!-- JAL-2992 -->Annotation panel set too high when
1242 annotation added to view (Windows)
1245 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1246 network connectivity is poor
1249 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1250 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1251 the currently open URL and links from a page viewed in
1252 Firefox or Chrome on Windows is now fully supported. If
1253 you are using Edge, only links in the page can be
1254 dragged, and with Internet Explorer, only the currently
1255 open URL in the browser can be dropped onto Jalview.</em>
1258 <em>New Known Defects</em>
1260 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1265 <td width="60" nowrap>
1266 <div align="center">
1267 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1270 <td><div align="left">
1274 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1275 for disabling automatic superposition of multiple
1276 structures and open structures in existing views
1279 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1280 ID and annotation area margins can be click-dragged to
1284 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1288 <!-- JAL-2759 -->Improved performance for large alignments
1289 and lots of hidden columns
1292 <!-- JAL-2593 -->Improved performance when rendering lots
1293 of features (particularly when transparency is disabled)
1296 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1297 exchange of Jalview features and Chimera attributes made
1303 <td><div align="left">
1306 <!-- JAL-2899 -->Structure and Overview aren't updated
1307 when Colour By Annotation threshold slider is adjusted
1310 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1311 overlapping alignment panel
1314 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1318 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1319 improved: CDS not handled correctly if transcript has no
1323 <!-- JAL-2321 -->Secondary structure and temperature
1324 factor annotation not added to sequence when local PDB
1325 file associated with it by drag'n'drop or structure
1329 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1330 dialog doesn't import PDB files dropped on an alignment
1333 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1334 scroll bar doesn't work for some CDS/Protein views
1337 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1338 Java 1.8u153 onwards and Java 1.9u4+.
1341 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1342 columns in annotation row
1345 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1346 honored in batch mode
1349 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1350 for structures added to existing Jmol view
1353 <!-- JAL-2223 -->'View Mappings' includes duplicate
1354 entries after importing project with multiple views
1357 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1358 protein sequences via SIFTS from associated PDB entries
1359 with negative residue numbers or missing residues fails
1362 <!-- JAL-2952 -->Exception when shading sequence with negative
1363 Temperature Factor values from annotated PDB files (e.g.
1364 as generated by CONSURF)
1367 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1368 tooltip doesn't include a text description of mutation
1371 <!-- JAL-2922 -->Invert displayed features very slow when
1372 structure and/or overview windows are also shown
1375 <!-- JAL-2954 -->Selecting columns from highlighted regions
1376 very slow for alignments with large numbers of sequences
1379 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1380 with 'StringIndexOutOfBounds'
1383 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1384 platforms running Java 10
1387 <!-- JAL-2960 -->Adding a structure to existing structure
1388 view appears to do nothing because the view is hidden behind the alignment view
1394 <!-- JAL-2926 -->Copy consensus sequence option in applet
1395 should copy the group consensus when popup is opened on it
1401 <!-- JAL-2913 -->Fixed ID width preference is not respected
1404 <em>New Known Defects</em>
1407 <!-- JAL-2973 --> Exceptions occasionally raised when
1408 editing a large alignment and overview is displayed
1411 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1412 repeatedly after a series of edits even when the overview
1413 is no longer reflecting updates
1416 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1417 structures for protein subsequence (if 'Trim Retrieved
1418 Sequences' enabled) or Ensembl isoforms (Workaround in
1419 2.10.4 is to fail back to N&W mapping)
1422 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1423 option gives blank output
1430 <td width="60" nowrap>
1431 <div align="center">
1432 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1435 <td><div align="left">
1436 <ul><li>Updated Certum Codesigning Certificate
1437 (Valid till 30th November 2018)</li></ul></div></td>
1438 <td><div align="left">
1439 <em>Desktop</em><ul>
1441 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1442 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1443 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1444 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1445 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1446 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1447 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1453 <td width="60" nowrap>
1454 <div align="center">
1455 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1458 <td><div align="left">
1462 <!-- JAL-2446 -->Faster and more efficient management and
1463 rendering of sequence features
1466 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1467 429 rate limit request hander
1470 <!-- JAL-2773 -->Structure views don't get updated unless
1471 their colours have changed
1474 <!-- JAL-2495 -->All linked sequences are highlighted for
1475 a structure mousover (Jmol) or selection (Chimera)
1478 <!-- JAL-2790 -->'Cancel' button in progress bar for
1479 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1482 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1483 view from Ensembl locus cross-references
1486 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1490 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1491 feature can be disabled
1494 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1495 PDB easier retrieval of sequences for lists of IDs
1498 <!-- JAL-2758 -->Short names for sequences retrieved from
1504 <li>Groovy interpreter updated to 2.4.12</li>
1505 <li>Example groovy script for generating a matrix of
1506 percent identity scores for current alignment.</li>
1508 <em>Testing and Deployment</em>
1511 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1515 <td><div align="left">
1519 <!-- JAL-2643 -->Pressing tab after updating the colour
1520 threshold text field doesn't trigger an update to the
1524 <!-- JAL-2682 -->Race condition when parsing sequence ID
1528 <!-- JAL-2608 -->Overview windows are also closed when
1529 alignment window is closed
1532 <!-- JAL-2548 -->Export of features doesn't always respect
1536 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1537 takes a long time in Cursor mode
1543 <!-- JAL-2777 -->Structures with whitespace chainCode
1544 cannot be viewed in Chimera
1547 <!-- JAL-2728 -->Protein annotation panel too high in
1551 <!-- JAL-2757 -->Can't edit the query after the server
1552 error warning icon is shown in Uniprot and PDB Free Text
1556 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1559 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1562 <!-- JAL-2739 -->Hidden column marker in last column not
1563 rendered when switching back from Wrapped to normal view
1566 <!-- JAL-2768 -->Annotation display corrupted when
1567 scrolling right in unwapped alignment view
1570 <!-- JAL-2542 -->Existing features on subsequence
1571 incorrectly relocated when full sequence retrieved from
1575 <!-- JAL-2733 -->Last reported memory still shown when
1576 Desktop->Show Memory is unticked (OSX only)
1579 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1580 features of same type and group to be selected for
1584 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1585 alignments when hidden columns are present
1588 <!-- JAL-2392 -->Jalview freezes when loading and
1589 displaying several structures
1592 <!-- JAL-2732 -->Black outlines left after resizing or
1596 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1597 within the Jalview desktop on OSX
1600 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1601 when in wrapped alignment mode
1604 <!-- JAL-2636 -->Scale mark not shown when close to right
1605 hand end of alignment
1608 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1609 each selected sequence do not have correct start/end
1613 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1614 after canceling the Alignment Window's Font dialog
1617 <!-- JAL-2036 -->Show cross-references not enabled after
1618 restoring project until a new view is created
1621 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1622 URL links appears when only default EMBL-EBI link is
1623 configured (since 2.10.2b2)
1626 <!-- JAL-2775 -->Overview redraws whole window when box
1627 position is adjusted
1630 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1631 in a multi-chain structure when viewing alignment
1632 involving more than one chain (since 2.10)
1635 <!-- JAL-2811 -->Double residue highlights in cursor mode
1636 if new selection moves alignment window
1639 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1640 arrow key in cursor mode to pass hidden column marker
1643 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1644 that produces correctly annotated transcripts and products
1647 <!-- JAL-2776 -->Toggling a feature group after first time
1648 doesn't update associated structure view
1651 <em>Applet</em><br />
1654 <!-- JAL-2687 -->Concurrent modification exception when
1655 closing alignment panel
1658 <em>BioJSON</em><br />
1661 <!-- JAL-2546 -->BioJSON export does not preserve
1662 non-positional features
1665 <em>New Known Issues</em>
1668 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1669 sequence features correctly (for many previous versions of
1673 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1674 using cursor in wrapped panel other than top
1677 <!-- JAL-2791 -->Select columns containing feature ignores
1678 graduated colour threshold
1681 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1682 always preserve numbering and sequence features
1685 <em>Known Java 9 Issues</em>
1688 <!-- JAL-2902 -->Groovy Console very slow to open and is
1689 not responsive when entering characters (Webstart, Java
1696 <td width="60" nowrap>
1697 <div align="center">
1698 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1699 <em>2/10/2017</em></strong>
1702 <td><div align="left">
1703 <em>New features in Jalview Desktop</em>
1706 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1708 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1712 <td><div align="left">
1716 <td width="60" nowrap>
1717 <div align="center">
1718 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1719 <em>7/9/2017</em></strong>
1722 <td><div align="left">
1726 <!-- JAL-2588 -->Show gaps in overview window by colouring
1727 in grey (sequences used to be coloured grey, and gaps were
1731 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1735 <!-- JAL-2587 -->Overview updates immediately on increase
1736 in size and progress bar shown as higher resolution
1737 overview is recalculated
1742 <td><div align="left">
1746 <!-- JAL-2664 -->Overview window redraws every hidden
1747 column region row by row
1750 <!-- JAL-2681 -->duplicate protein sequences shown after
1751 retrieving Ensembl crossrefs for sequences from Uniprot
1754 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1755 format setting is unticked
1758 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1759 if group has show boxes format setting unticked
1762 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1763 autoscrolling whilst dragging current selection group to
1764 include sequences and columns not currently displayed
1767 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1768 assemblies are imported via CIF file
1771 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1772 displayed when threshold or conservation colouring is also
1776 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1780 <!-- JAL-2673 -->Jalview continues to scroll after
1781 dragging a selected region off the visible region of the
1785 <!-- JAL-2724 -->Cannot apply annotation based
1786 colourscheme to all groups in a view
1789 <!-- JAL-2511 -->IDs don't line up with sequences
1790 initially after font size change using the Font chooser or
1797 <td width="60" nowrap>
1798 <div align="center">
1799 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1802 <td><div align="left">
1803 <em>Calculations</em>
1807 <!-- JAL-1933 -->Occupancy annotation row shows number of
1808 ungapped positions in each column of the alignment.
1811 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1812 a calculation dialog box
1815 <!-- JAL-2379 -->Revised implementation of PCA for speed
1816 and memory efficiency (~30x faster)
1819 <!-- JAL-2403 -->Revised implementation of sequence
1820 similarity scores as used by Tree, PCA, Shading Consensus
1821 and other calculations
1824 <!-- JAL-2416 -->Score matrices are stored as resource
1825 files within the Jalview codebase
1828 <!-- JAL-2500 -->Trees computed on Sequence Feature
1829 Similarity may have different topology due to increased
1836 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1837 model for alignments and groups
1840 <!-- JAL-384 -->Custom shading schemes created via groovy
1847 <!-- JAL-2526 -->Efficiency improvements for interacting
1848 with alignment and overview windows
1851 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1855 <!-- JAL-2388 -->Hidden columns and sequences can be
1859 <!-- JAL-2611 -->Click-drag in visible area allows fine
1860 adjustment of visible position
1864 <em>Data import/export</em>
1867 <!-- JAL-2535 -->Posterior probability annotation from
1868 Stockholm files imported as sequence associated annotation
1871 <!-- JAL-2507 -->More robust per-sequence positional
1872 annotation input/output via stockholm flatfile
1875 <!-- JAL-2533 -->Sequence names don't include file
1876 extension when importing structure files without embedded
1877 names or PDB accessions
1880 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1881 format sequence substitution matrices
1884 <em>User Interface</em>
1887 <!-- JAL-2447 --> Experimental Features Checkbox in
1888 Desktop's Tools menu to hide or show untested features in
1892 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1893 via Overview or sequence motif search operations
1896 <!-- JAL-2547 -->Amend sequence features dialog box can be
1897 opened by double clicking gaps within sequence feature
1901 <!-- JAL-1476 -->Status bar message shown when not enough
1902 aligned positions were available to create a 3D structure
1906 <em>3D Structure</em>
1909 <!-- JAL-2430 -->Hidden regions in alignment views are not
1910 coloured in linked structure views
1913 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1914 file-based command exchange
1917 <!-- JAL-2375 -->Structure chooser automatically shows
1918 Cached Structures rather than querying the PDBe if
1919 structures are already available for sequences
1922 <!-- JAL-2520 -->Structures imported via URL are cached in
1923 the Jalview project rather than downloaded again when the
1924 project is reopened.
1927 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1928 to transfer Chimera's structure attributes as Jalview
1929 features, and vice-versa (<strong>Experimental
1933 <em>Web Services</em>
1936 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1939 <!-- JAL-2335 -->Filter non-standard amino acids and
1940 nucleotides when submitting to AACon and other MSA
1944 <!-- JAL-2316, -->URLs for viewing database
1945 cross-references provided by identifiers.org and the
1946 EMBL-EBI's MIRIAM DB
1953 <!-- JAL-2344 -->FileFormatI interface for describing and
1954 identifying file formats (instead of String constants)
1957 <!-- JAL-2228 -->FeatureCounter script refactored for
1958 efficiency when counting all displayed features (not
1959 backwards compatible with 2.10.1)
1962 <em>Example files</em>
1965 <!-- JAL-2631 -->Graduated feature colour style example
1966 included in the example feature file
1969 <em>Documentation</em>
1972 <!-- JAL-2339 -->Release notes reformatted for readability
1973 with the built-in Java help viewer
1976 <!-- JAL-1644 -->Find documentation updated with 'search
1977 sequence description' option
1983 <!-- JAL-2485, -->External service integration tests for
1984 Uniprot REST Free Text Search Client
1987 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1990 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1995 <td><div align="left">
1996 <em>Calculations</em>
1999 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2000 matrix - C->R should be '-3'<br />Old matrix restored
2001 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2003 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2004 Jalview's treatment of gaps in PCA and substitution matrix
2005 based Tree calculations.<br /> <br />In earlier versions
2006 of Jalview, gaps matching gaps were penalised, and gaps
2007 matching non-gaps penalised even more. In the PCA
2008 calculation, gaps were actually treated as non-gaps - so
2009 different costs were applied, which meant Jalview's PCAs
2010 were different to those produced by SeqSpace.<br />Jalview
2011 now treats gaps in the same way as SeqSpace (ie it scores
2012 them as 0). <br /> <br />Enter the following in the
2013 Groovy console to restore pre-2.10.2 behaviour:<br />
2014 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2015 // for 2.10.1 mode <br />
2016 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2017 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2018 these settings will affect all subsequent tree and PCA
2019 calculations (not recommended)</em></li>
2021 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2022 scaling of branch lengths for trees computed using
2023 Sequence Feature Similarity.
2026 <!-- JAL-2377 -->PCA calculation could hang when
2027 generating output report when working with highly
2028 redundant alignments
2031 <!-- JAL-2544 --> Sort by features includes features to
2032 right of selected region when gaps present on right-hand
2036 <em>User Interface</em>
2039 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2040 doesn't reselect a specific sequence's associated
2041 annotation after it was used for colouring a view
2044 <!-- JAL-2419 -->Current selection lost if popup menu
2045 opened on a region of alignment without groups
2048 <!-- JAL-2374 -->Popup menu not always shown for regions
2049 of an alignment with overlapping groups
2052 <!-- JAL-2310 -->Finder double counts if both a sequence's
2053 name and description match
2056 <!-- JAL-2370 -->Hiding column selection containing two
2057 hidden regions results in incorrect hidden regions
2060 <!-- JAL-2386 -->'Apply to all groups' setting when
2061 changing colour does not apply Conservation slider value
2065 <!-- JAL-2373 -->Percentage identity and conservation menu
2066 items do not show a tick or allow shading to be disabled
2069 <!-- JAL-2385 -->Conservation shading or PID threshold
2070 lost when base colourscheme changed if slider not visible
2073 <!-- JAL-2547 -->Sequence features shown in tooltip for
2074 gaps before start of features
2077 <!-- JAL-2623 -->Graduated feature colour threshold not
2078 restored to UI when feature colour is edited
2081 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2082 a time when scrolling vertically in wrapped mode.
2085 <!-- JAL-2630 -->Structure and alignment overview update
2086 as graduate feature colour settings are modified via the
2090 <!-- JAL-2034 -->Overview window doesn't always update
2091 when a group defined on the alignment is resized
2094 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2095 wrapped view result in positional status updates
2099 <!-- JAL-2563 -->Status bar doesn't show position for
2100 ambiguous amino acid and nucleotide symbols
2103 <!-- JAL-2602 -->Copy consensus sequence failed if
2104 alignment included gapped columns
2107 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2108 widgets don't permanently disappear
2111 <!-- JAL-2503 -->Cannot select or filter quantitative
2112 annotation that are shown only as column labels (e.g.
2113 T-Coffee column reliability scores)
2116 <!-- JAL-2594 -->Exception thrown if trying to create a
2117 sequence feature on gaps only
2120 <!-- JAL-2504 -->Features created with 'New feature'
2121 button from a Find inherit previously defined feature type
2122 rather than the Find query string
2125 <!-- JAL-2423 -->incorrect title in output window when
2126 exporting tree calculated in Jalview
2129 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2130 and then revealing them reorders sequences on the
2134 <!-- JAL-964 -->Group panel in sequence feature settings
2135 doesn't update to reflect available set of groups after
2136 interactively adding or modifying features
2139 <!-- JAL-2225 -->Sequence Database chooser unusable on
2143 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2144 only excluded gaps in current sequence and ignored
2151 <!-- JAL-2421 -->Overview window visible region moves
2152 erratically when hidden rows or columns are present
2155 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2156 Structure Viewer's colour menu don't correspond to
2160 <!-- JAL-2405 -->Protein specific colours only offered in
2161 colour and group colour menu for protein alignments
2164 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2165 reflect currently selected view or group's shading
2169 <!-- JAL-2624 -->Feature colour thresholds not respected
2170 when rendered on overview and structures when opacity at
2174 <!-- JAL-2589 -->User defined gap colour not shown in
2175 overview when features overlaid on alignment
2178 <!-- JAL-2567 -->Feature settings for different views not
2179 recovered correctly from Jalview project file
2182 <!-- JAL-2256 -->Feature colours in overview when first opened
2183 (automatically via preferences) are different to the main
2187 <em>Data import/export</em>
2190 <!-- JAL-2576 -->Very large alignments take a long time to
2194 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2195 added after a sequence was imported are not written to
2199 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2200 when importing RNA secondary structure via Stockholm
2203 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2204 not shown in correct direction for simple pseudoknots
2207 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2208 with lightGray or darkGray via features file (but can
2212 <!-- JAL-2383 -->Above PID colour threshold not recovered
2213 when alignment view imported from project
2216 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2217 structure and sequences extracted from structure files
2218 imported via URL and viewed in Jmol
2221 <!-- JAL-2520 -->Structures loaded via URL are saved in
2222 Jalview Projects rather than fetched via URL again when
2223 the project is loaded and the structure viewed
2226 <em>Web Services</em>
2229 <!-- JAL-2519 -->EnsemblGenomes example failing after
2230 release of Ensembl v.88
2233 <!-- JAL-2366 -->Proxy server address and port always
2234 appear enabled in Preferences->Connections
2237 <!-- JAL-2461 -->DAS registry not found exceptions
2238 removed from console output
2241 <!-- JAL-2582 -->Cannot retrieve protein products from
2242 Ensembl by Peptide ID
2245 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2246 created from SIFTs, and spurious 'Couldn't open structure
2247 in Chimera' errors raised after April 2017 update (problem
2248 due to 'null' string rather than empty string used for
2249 residues with no corresponding PDB mapping).
2252 <em>Application UI</em>
2255 <!-- JAL-2361 -->User Defined Colours not added to Colour
2259 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2260 case' residues (button in colourscheme editor debugged and
2261 new documentation and tooltips added)
2264 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2265 doesn't restore group-specific text colour thresholds
2268 <!-- JAL-2243 -->Feature settings panel does not update as
2269 new features are added to alignment
2272 <!-- JAL-2532 -->Cancel in feature settings reverts
2273 changes to feature colours via the Amend features dialog
2276 <!-- JAL-2506 -->Null pointer exception when attempting to
2277 edit graduated feature colour via amend features dialog
2281 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2282 selection menu changes colours of alignment views
2285 <!-- JAL-2426 -->Spurious exceptions in console raised
2286 from alignment calculation workers after alignment has
2290 <!-- JAL-1608 -->Typo in selection popup menu - Create
2291 groups now 'Create Group'
2294 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2295 Create/Undefine group doesn't always work
2298 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2299 shown again after pressing 'Cancel'
2302 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2303 adjusts start position in wrap mode
2306 <!-- JAL-2563 -->Status bar doesn't show positions for
2307 ambiguous amino acids
2310 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2311 CDS/Protein view after CDS sequences added for aligned
2315 <!-- JAL-2592 -->User defined colourschemes called 'User
2316 Defined' don't appear in Colours menu
2322 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2323 score models doesn't always result in an updated PCA plot
2326 <!-- JAL-2442 -->Features not rendered as transparent on
2327 overview or linked structure view
2330 <!-- JAL-2372 -->Colour group by conservation doesn't
2334 <!-- JAL-2517 -->Hitting Cancel after applying
2335 user-defined colourscheme doesn't restore original
2342 <!-- JAL-2314 -->Unit test failure:
2343 jalview.ws.jabaws.RNAStructExportImport setup fails
2346 <!-- JAL-2307 -->Unit test failure:
2347 jalview.ws.sifts.SiftsClientTest due to compatibility
2348 problems with deep array comparison equality asserts in
2349 successive versions of TestNG
2352 <!-- JAL-2479 -->Relocated StructureChooserTest and
2353 ParameterUtilsTest Unit tests to Network suite
2356 <em>New Known Issues</em>
2359 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2360 phase after a sequence motif find operation
2363 <!-- JAL-2550 -->Importing annotation file with rows
2364 containing just upper and lower case letters are
2365 interpreted as WUSS RNA secondary structure symbols
2368 <!-- JAL-2590 -->Cannot load and display Newick trees
2369 reliably from eggnog Ortholog database
2372 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2373 containing features of type Highlight' when 'B' is pressed
2374 to mark columns containing highlighted regions.
2377 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2378 doesn't always add secondary structure annotation.
2383 <td width="60" nowrap>
2384 <div align="center">
2385 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2388 <td><div align="left">
2392 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2393 for all consensus calculations
2396 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2399 <li>Updated Jalview's Certum code signing certificate
2402 <em>Application</em>
2405 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2406 set of database cross-references, sorted alphabetically
2409 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2410 from database cross references. Users with custom links
2411 will receive a <a href="webServices/urllinks.html#warning">warning
2412 dialog</a> asking them to update their preferences.
2415 <!-- JAL-2287-->Cancel button and escape listener on
2416 dialog warning user about disconnecting Jalview from a
2420 <!-- JAL-2320-->Jalview's Chimera control window closes if
2421 the Chimera it is connected to is shut down
2424 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2425 columns menu item to mark columns containing highlighted
2426 regions (e.g. from structure selections or results of a
2430 <!-- JAL-2284-->Command line option for batch-generation
2431 of HTML pages rendering alignment data with the BioJS
2441 <!-- JAL-2286 -->Columns with more than one modal residue
2442 are not coloured or thresholded according to percent
2443 identity (first observed in Jalview 2.8.2)
2446 <!-- JAL-2301 -->Threonine incorrectly reported as not
2450 <!-- JAL-2318 -->Updates to documentation pages (above PID
2451 threshold, amino acid properties)
2454 <!-- JAL-2292 -->Lower case residues in sequences are not
2455 reported as mapped to residues in a structure file in the
2459 <!--JAL-2324 -->Identical features with non-numeric scores
2460 could be added multiple times to a sequence
2463 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2464 bond features shown as two highlighted residues rather
2465 than a range in linked structure views, and treated
2466 correctly when selecting and computing trees from features
2469 <!-- JAL-2281-->Custom URL links for database
2470 cross-references are matched to database name regardless
2475 <em>Application</em>
2478 <!-- JAL-2282-->Custom URL links for specific database
2479 names without regular expressions also offer links from
2483 <!-- JAL-2315-->Removing a single configured link in the
2484 URL links pane in Connections preferences doesn't actually
2485 update Jalview configuration
2488 <!-- JAL-2272-->CTRL-Click on a selected region to open
2489 the alignment area popup menu doesn't work on El-Capitan
2492 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2493 files with similarly named sequences if dropped onto the
2497 <!-- JAL-2312 -->Additional mappings are shown for PDB
2498 entries where more chains exist in the PDB accession than
2499 are reported in the SIFTS file
2502 <!-- JAL-2317-->Certain structures do not get mapped to
2503 the structure view when displayed with Chimera
2506 <!-- JAL-2317-->No chains shown in the Chimera view
2507 panel's View->Show Chains submenu
2510 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2511 work for wrapped alignment views
2514 <!--JAL-2197 -->Rename UI components for running JPred
2515 predictions from 'JNet' to 'JPred'
2518 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2519 corrupted when annotation panel vertical scroll is not at
2520 first annotation row
2523 <!--JAL-2332 -->Attempting to view structure for Hen
2524 lysozyme results in a PDB Client error dialog box
2527 <!-- JAL-2319 -->Structure View's mapping report switched
2528 ranges for PDB and sequence for SIFTS
2531 SIFTS 'Not_Observed' residues mapped to non-existant
2535 <!-- <em>New Known Issues</em>
2542 <td width="60" nowrap>
2543 <div align="center">
2544 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2545 <em>25/10/2016</em></strong>
2548 <td><em>Application</em>
2550 <li>3D Structure chooser opens with 'Cached structures'
2551 view if structures already loaded</li>
2552 <li>Progress bar reports models as they are loaded to
2553 structure views</li>
2559 <li>Colour by conservation always enabled and no tick
2560 shown in menu when BLOSUM or PID shading applied</li>
2561 <li>FER1_ARATH and FER2_ARATH labels were switched in
2562 example sequences/projects/trees</li>
2564 <em>Application</em>
2566 <li>Jalview projects with views of local PDB structure
2567 files saved on Windows cannot be opened on OSX</li>
2568 <li>Multiple structure views can be opened and superposed
2569 without timeout for structures with multiple models or
2570 multiple sequences in alignment</li>
2571 <li>Cannot import or associated local PDB files without a
2572 PDB ID HEADER line</li>
2573 <li>RMSD is not output in Jmol console when superposition
2575 <li>Drag and drop of URL from Browser fails for Linux and
2576 OSX versions earlier than El Capitan</li>
2577 <li>ENA client ignores invalid content from ENA server</li>
2578 <li>Exceptions are not raised in console when ENA client
2579 attempts to fetch non-existent IDs via Fetch DB Refs UI
2581 <li>Exceptions are not raised in console when a new view
2582 is created on the alignment</li>
2583 <li>OSX right-click fixed for group selections: CMD-click
2584 to insert/remove gaps in groups and CTRL-click to open group
2587 <em>Build and deployment</em>
2589 <li>URL link checker now copes with multi-line anchor
2592 <em>New Known Issues</em>
2594 <li>Drag and drop from URL links in browsers do not work
2601 <td width="60" nowrap>
2602 <div align="center">
2603 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2606 <td><em>General</em>
2609 <!-- JAL-2124 -->Updated Spanish translations.
2612 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2613 for importing structure data to Jalview. Enables mmCIF and
2617 <!-- JAL-192 --->Alignment ruler shows positions relative to
2621 <!-- JAL-2202 -->Position/residue shown in status bar when
2622 mousing over sequence associated annotation
2625 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2629 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2630 '()', canonical '[]' and invalid '{}' base pair populations
2634 <!-- JAL-2092 -->Feature settings popup menu options for
2635 showing or hiding columns containing a feature
2638 <!-- JAL-1557 -->Edit selected group by double clicking on
2639 group and sequence associated annotation labels
2642 <!-- JAL-2236 -->Sequence name added to annotation label in
2643 select/hide columns by annotation and colour by annotation
2647 </ul> <em>Application</em>
2650 <!-- JAL-2050-->Automatically hide introns when opening a
2651 gene/transcript view
2654 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2658 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2659 structure mappings with the EMBL-EBI PDBe SIFTS database
2662 <!-- JAL-2079 -->Updated download sites used for Rfam and
2663 Pfam sources to xfam.org
2666 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2669 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2670 over sequences in Jalview
2673 <!-- JAL-2027-->Support for reverse-complement coding
2674 regions in ENA and EMBL
2677 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2678 for record retrieval via ENA rest API
2681 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2685 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2686 groovy script execution
2689 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2690 alignment window's Calculate menu
2693 <!-- JAL-1812 -->Allow groovy scripts that call
2694 Jalview.getAlignFrames() to run in headless mode
2697 <!-- JAL-2068 -->Support for creating new alignment
2698 calculation workers from groovy scripts
2701 <!-- JAL-1369 --->Store/restore reference sequence in
2705 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2706 associations are now saved/restored from project
2709 <!-- JAL-1993 -->Database selection dialog always shown
2710 before sequence fetcher is opened
2713 <!-- JAL-2183 -->Double click on an entry in Jalview's
2714 database chooser opens a sequence fetcher
2717 <!-- JAL-1563 -->Free-text search client for UniProt using
2718 the UniProt REST API
2721 <!-- JAL-2168 -->-nonews command line parameter to prevent
2722 the news reader opening
2725 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2726 querying stored in preferences
2729 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2733 <!-- JAL-1977-->Tooltips shown on database chooser
2736 <!-- JAL-391 -->Reverse complement function in calculate
2737 menu for nucleotide sequences
2740 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2741 and feature counts preserves alignment ordering (and
2742 debugged for complex feature sets).
2745 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2746 viewing structures with Jalview 2.10
2749 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2750 genome, transcript CCDS and gene ids via the Ensembl and
2751 Ensembl Genomes REST API
2754 <!-- JAL-2049 -->Protein sequence variant annotation
2755 computed for 'sequence_variant' annotation on CDS regions
2759 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2763 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2764 Ref Fetcher fails to match, or otherwise updates sequence
2765 data from external database records.
2768 <!-- JAL-2154 -->Revised Jalview Project format for
2769 efficient recovery of sequence coding and alignment
2770 annotation relationships.
2772 </ul> <!-- <em>Applet</em>
2783 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2787 <!-- JAL-2018-->Export features in Jalview format (again)
2788 includes graduated colourschemes
2791 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2792 working with big alignments and lots of hidden columns
2795 <!-- JAL-2053-->Hidden column markers not always rendered
2796 at right of alignment window
2799 <!-- JAL-2067 -->Tidied up links in help file table of
2803 <!-- JAL-2072 -->Feature based tree calculation not shown
2807 <!-- JAL-2075 -->Hidden columns ignored during feature
2808 based tree calculation
2811 <!-- JAL-2065 -->Alignment view stops updating when show
2812 unconserved enabled for group on alignment
2815 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2819 <!-- JAL-2146 -->Alignment column in status incorrectly
2820 shown as "Sequence position" when mousing over
2824 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2825 hidden columns present
2828 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2829 user created annotation added to alignment
2832 <!-- JAL-1841 -->RNA Structure consensus only computed for
2833 '()' base pair annotation
2836 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2837 in zero scores for all base pairs in RNA Structure
2841 <!-- JAL-2174-->Extend selection with columns containing
2845 <!-- JAL-2275 -->Pfam format writer puts extra space at
2846 beginning of sequence
2849 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2853 <!-- JAL-2238 -->Cannot create groups on an alignment from
2854 from a tree when t-coffee scores are shown
2857 <!-- JAL-1836,1967 -->Cannot import and view PDB
2858 structures with chains containing negative resnums (4q4h)
2861 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2865 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2866 to Clustal, PIR and PileUp output
2869 <!-- JAL-2008 -->Reordering sequence features that are
2870 not visible causes alignment window to repaint
2873 <!-- JAL-2006 -->Threshold sliders don't work in
2874 graduated colour and colour by annotation row for e-value
2875 scores associated with features and annotation rows
2878 <!-- JAL-1797 -->amino acid physicochemical conservation
2879 calculation should be case independent
2882 <!-- JAL-2173 -->Remove annotation also updates hidden
2886 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2887 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2888 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2891 <!-- JAL-2065 -->Null pointer exceptions and redraw
2892 problems when reference sequence defined and 'show
2893 non-conserved' enabled
2896 <!-- JAL-1306 -->Quality and Conservation are now shown on
2897 load even when Consensus calculation is disabled
2900 <!-- JAL-1932 -->Remove right on penultimate column of
2901 alignment does nothing
2904 <em>Application</em>
2907 <!-- JAL-1552-->URLs and links can't be imported by
2908 drag'n'drop on OSX when launched via webstart (note - not
2909 yet fixed for El Capitan)
2912 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2913 output when running on non-gb/us i18n platforms
2916 <!-- JAL-1944 -->Error thrown when exporting a view with
2917 hidden sequences as flat-file alignment
2920 <!-- JAL-2030-->InstallAnywhere distribution fails when
2924 <!-- JAL-2080-->Jalview very slow to launch via webstart
2925 (also hotfix for 2.9.0b2)
2928 <!-- JAL-2085 -->Cannot save project when view has a
2929 reference sequence defined
2932 <!-- JAL-1011 -->Columns are suddenly selected in other
2933 alignments and views when revealing hidden columns
2936 <!-- JAL-1989 -->Hide columns not mirrored in complement
2937 view in a cDNA/Protein splitframe
2940 <!-- JAL-1369 -->Cannot save/restore representative
2941 sequence from project when only one sequence is
2945 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2946 in Structure Chooser
2949 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2950 structure consensus didn't refresh annotation panel
2953 <!-- JAL-1962 -->View mapping in structure view shows
2954 mappings between sequence and all chains in a PDB file
2957 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2958 dialogs format columns correctly, don't display array
2959 data, sort columns according to type
2962 <!-- JAL-1975 -->Export complete shown after destination
2963 file chooser is cancelled during an image export
2966 <!-- JAL-2025 -->Error when querying PDB Service with
2967 sequence name containing special characters
2970 <!-- JAL-2024 -->Manual PDB structure querying should be
2974 <!-- JAL-2104 -->Large tooltips with broken HTML
2975 formatting don't wrap
2978 <!-- JAL-1128 -->Figures exported from wrapped view are
2979 truncated so L looks like I in consensus annotation
2982 <!-- JAL-2003 -->Export features should only export the
2983 currently displayed features for the current selection or
2987 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2988 after fetching cross-references, and restoring from
2992 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2993 followed in the structure viewer
2996 <!-- JAL-2163 -->Titles for individual alignments in
2997 splitframe not restored from project
3000 <!-- JAL-2145 -->missing autocalculated annotation at
3001 trailing end of protein alignment in transcript/product
3002 splitview when pad-gaps not enabled by default
3005 <!-- JAL-1797 -->amino acid physicochemical conservation
3009 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3010 article has been read (reopened issue due to
3011 internationalisation problems)
3014 <!-- JAL-1960 -->Only offer PDB structures in structure
3015 viewer based on sequence name, PDB and UniProt
3020 <!-- JAL-1976 -->No progress bar shown during export of
3024 <!-- JAL-2213 -->Structures not always superimposed after
3025 multiple structures are shown for one or more sequences.
3028 <!-- JAL-1370 -->Reference sequence characters should not
3029 be replaced with '.' when 'Show unconserved' format option
3033 <!-- JAL-1823 -->Cannot specify chain code when entering
3034 specific PDB id for sequence
3037 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3038 'Export hidden sequences' is enabled, but 'export hidden
3039 columns' is disabled.
3042 <!--JAL-2026-->Best Quality option in structure chooser
3043 selects lowest rather than highest resolution structures
3047 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3048 to sequence mapping in 'View Mappings' report
3051 <!-- JAL-2284 -->Unable to read old Jalview projects that
3052 contain non-XML data added after Jalvew wrote project.
3055 <!-- JAL-2118 -->Newly created annotation row reorders
3056 after clicking on it to create new annotation for a
3060 <!-- JAL-1980 -->Null Pointer Exception raised when
3061 pressing Add on an orphaned cut'n'paste window.
3063 <!-- may exclude, this is an external service stability issue JAL-1941
3064 -- > RNA 3D structure not added via DSSR service</li> -->
3069 <!-- JAL-2151 -->Incorrect columns are selected when
3070 hidden columns present before start of sequence
3073 <!-- JAL-1986 -->Missing dependencies on applet pages
3077 <!-- JAL-1947 -->Overview pixel size changes when
3078 sequences are hidden in applet
3081 <!-- JAL-1996 -->Updated instructions for applet
3082 deployment on examples pages.
3089 <td width="60" nowrap>
3090 <div align="center">
3091 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3092 <em>16/10/2015</em></strong>
3095 <td><em>General</em>
3097 <li>Time stamps for signed Jalview application and applet
3102 <em>Application</em>
3104 <li>Duplicate group consensus and conservation rows
3105 shown when tree is partitioned</li>
3106 <li>Erratic behaviour when tree partitions made with
3107 multiple cDNA/Protein split views</li>
3113 <td width="60" nowrap>
3114 <div align="center">
3115 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3116 <em>8/10/2015</em></strong>
3119 <td><em>General</em>
3121 <li>Updated Spanish translations of localized text for
3123 </ul> <em>Application</em>
3125 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3126 <li>Signed OSX InstallAnywhere installer<br></li>
3127 <li>Support for per-sequence based annotations in BioJSON</li>
3128 </ul> <em>Applet</em>
3130 <li>Split frame example added to applet examples page</li>
3131 </ul> <em>Build and Deployment</em>
3134 <!-- JAL-1888 -->New ant target for running Jalview's test
3142 <li>Mapping of cDNA to protein in split frames
3143 incorrect when sequence start > 1</li>
3144 <li>Broken images in filter column by annotation dialog
3146 <li>Feature colours not parsed from features file</li>
3147 <li>Exceptions and incomplete link URLs recovered when
3148 loading a features file containing HTML tags in feature
3152 <em>Application</em>
3154 <li>Annotations corrupted after BioJS export and
3156 <li>Incorrect sequence limits after Fetch DB References
3157 with 'trim retrieved sequences'</li>
3158 <li>Incorrect warning about deleting all data when
3159 deleting selected columns</li>
3160 <li>Patch to build system for shipping properly signed
3161 JNLP templates for webstart launch</li>
3162 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3163 unreleased structures for download or viewing</li>
3164 <li>Tab/space/return keystroke operation of EMBL-PDBe
3165 fetcher/viewer dialogs works correctly</li>
3166 <li>Disabled 'minimise' button on Jalview windows
3167 running on OSX to workaround redraw hang bug</li>
3168 <li>Split cDNA/Protein view position and geometry not
3169 recovered from jalview project</li>
3170 <li>Initial enabled/disabled state of annotation menu
3171 sorter 'show autocalculated first/last' corresponds to
3173 <li>Restoring of Clustal, RNA Helices and T-Coffee
3174 color schemes from BioJSON</li>
3178 <li>Reorder sequences mirrored in cDNA/Protein split
3180 <li>Applet with Jmol examples not loading correctly</li>
3186 <td><div align="center">
3187 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3189 <td><em>General</em>
3191 <li>Linked visualisation and analysis of DNA and Protein
3194 <li>Translated cDNA alignments shown as split protein
3195 and DNA alignment views</li>
3196 <li>Codon consensus annotation for linked protein and
3197 cDNA alignment views</li>
3198 <li>Link cDNA or Protein product sequences by loading
3199 them onto Protein or cDNA alignments</li>
3200 <li>Reconstruct linked cDNA alignment from aligned
3201 protein sequences</li>
3204 <li>Jmol integration updated to Jmol v14.2.14</li>
3205 <li>Import and export of Jalview alignment views as <a
3206 href="features/bioJsonFormat.html">BioJSON</a></li>
3207 <li>New alignment annotation file statements for
3208 reference sequences and marking hidden columns</li>
3209 <li>Reference sequence based alignment shading to
3210 highlight variation</li>
3211 <li>Select or hide columns according to alignment
3213 <li>Find option for locating sequences by description</li>
3214 <li>Conserved physicochemical properties shown in amino
3215 acid conservation row</li>
3216 <li>Alignments can be sorted by number of RNA helices</li>
3217 </ul> <em>Application</em>
3219 <li>New cDNA/Protein analysis capabilities
3221 <li>Get Cross-References should open a Split Frame
3222 view with cDNA/Protein</li>
3223 <li>Detect when nucleotide sequences and protein
3224 sequences are placed in the same alignment</li>
3225 <li>Split cDNA/Protein views are saved in Jalview
3230 <li>Use REST API to talk to Chimera</li>
3231 <li>Selected regions in Chimera are highlighted in linked
3232 Jalview windows</li>
3234 <li>VARNA RNA viewer updated to v3.93</li>
3235 <li>VARNA views are saved in Jalview Projects</li>
3236 <li>Pseudoknots displayed as Jalview RNA annotation can
3237 be shown in VARNA</li>
3239 <li>Make groups for selection uses marked columns as well
3240 as the active selected region</li>
3242 <li>Calculate UPGMA and NJ trees using sequence feature
3244 <li>New Export options
3246 <li>New Export Settings dialog to control hidden
3247 region export in flat file generation</li>
3249 <li>Export alignment views for display with the <a
3250 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3252 <li>Export scrollable SVG in HTML page</li>
3253 <li>Optional embedding of BioJSON data when exporting
3254 alignment figures to HTML</li>
3256 <li>3D structure retrieval and display
3258 <li>Free text and structured queries with the PDBe
3260 <li>PDBe Search API based discovery and selection of
3261 PDB structures for a sequence set</li>
3265 <li>JPred4 employed for protein secondary structure
3267 <li>Hide Insertions menu option to hide unaligned columns
3268 for one or a group of sequences</li>
3269 <li>Automatically hide insertions in alignments imported
3270 from the JPred4 web server</li>
3271 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3272 system on OSX<br />LGPL libraries courtesy of <a
3273 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3275 <li>changed 'View nucleotide structure' submenu to 'View
3276 VARNA 2D Structure'</li>
3277 <li>change "View protein structure" menu option to "3D
3280 </ul> <em>Applet</em>
3282 <li>New layout for applet example pages</li>
3283 <li>New parameters to enable SplitFrame view
3284 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3285 <li>New example demonstrating linked viewing of cDNA and
3286 Protein alignments</li>
3287 </ul> <em>Development and deployment</em>
3289 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3290 <li>Include installation type and git revision in build
3291 properties and console log output</li>
3292 <li>Jalview Github organisation, and new github site for
3293 storing BioJsMSA Templates</li>
3294 <li>Jalview's unit tests now managed with TestNG</li>
3297 <!-- <em>General</em>
3299 </ul> --> <!-- issues resolved --> <em>Application</em>
3301 <li>Escape should close any open find dialogs</li>
3302 <li>Typo in select-by-features status report</li>
3303 <li>Consensus RNA secondary secondary structure
3304 predictions are not highlighted in amber</li>
3305 <li>Missing gap character in v2.7 example file means
3306 alignment appears unaligned when pad-gaps is not enabled</li>
3307 <li>First switch to RNA Helices colouring doesn't colour
3308 associated structure views</li>
3309 <li>ID width preference option is greyed out when auto
3310 width checkbox not enabled</li>
3311 <li>Stopped a warning dialog from being shown when
3312 creating user defined colours</li>
3313 <li>'View Mapping' in structure viewer shows sequence
3314 mappings for just that viewer's sequences</li>
3315 <li>Workaround for superposing PDB files containing
3316 multiple models in Chimera</li>
3317 <li>Report sequence position in status bar when hovering
3318 over Jmol structure</li>
3319 <li>Cannot output gaps as '.' symbols with Selection ->
3320 output to text box</li>
3321 <li>Flat file exports of alignments with hidden columns
3322 have incorrect sequence start/end</li>
3323 <li>'Aligning' a second chain to a Chimera structure from
3325 <li>Colour schemes applied to structure viewers don't
3326 work for nucleotide</li>
3327 <li>Loading/cut'n'pasting an empty or invalid file leads
3328 to a grey/invisible alignment window</li>
3329 <li>Exported Jpred annotation from a sequence region
3330 imports to different position</li>
3331 <li>Space at beginning of sequence feature tooltips shown
3332 on some platforms</li>
3333 <li>Chimera viewer 'View | Show Chain' menu is not
3335 <li>'New View' fails with a Null Pointer Exception in
3336 console if Chimera has been opened</li>
3337 <li>Mouseover to Chimera not working</li>
3338 <li>Miscellaneous ENA XML feature qualifiers not
3340 <li>NPE in annotation renderer after 'Extract Scores'</li>
3341 <li>If two structures in one Chimera window, mouseover of
3342 either sequence shows on first structure</li>
3343 <li>'Show annotations' options should not make
3344 non-positional annotations visible</li>
3345 <li>Subsequence secondary structure annotation not shown
3346 in right place after 'view flanking regions'</li>
3347 <li>File Save As type unset when current file format is
3349 <li>Save as '.jar' option removed for saving Jalview
3351 <li>Colour by Sequence colouring in Chimera more
3353 <li>Cannot 'add reference annotation' for a sequence in
3354 several views on same alignment</li>
3355 <li>Cannot show linked products for EMBL / ENA records</li>
3356 <li>Jalview's tooltip wraps long texts containing no
3358 </ul> <em>Applet</em>
3360 <li>Jmol to JalviewLite mouseover/link not working</li>
3361 <li>JalviewLite can't import sequences with ID
3362 descriptions containing angle brackets</li>
3363 </ul> <em>General</em>
3365 <li>Cannot export and reimport RNA secondary structure
3366 via jalview annotation file</li>
3367 <li>Random helix colour palette for colour by annotation
3368 with RNA secondary structure</li>
3369 <li>Mouseover to cDNA from STOP residue in protein
3370 translation doesn't work.</li>
3371 <li>hints when using the select by annotation dialog box</li>
3372 <li>Jmol alignment incorrect if PDB file has alternate CA
3374 <li>FontChooser message dialog appears to hang after
3375 choosing 1pt font</li>
3376 <li>Peptide secondary structure incorrectly imported from
3377 annotation file when annotation display text includes 'e' or
3379 <li>Cannot set colour of new feature type whilst creating
3381 <li>cDNA translation alignment should not be sequence
3382 order dependent</li>
3383 <li>'Show unconserved' doesn't work for lower case
3385 <li>Nucleotide ambiguity codes involving R not recognised</li>
3386 </ul> <em>Deployment and Documentation</em>
3388 <li>Applet example pages appear different to the rest of
3389 www.jalview.org</li>
3390 </ul> <em>Application Known issues</em>
3392 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3393 <li>Misleading message appears after trying to delete
3395 <li>Jalview icon not shown in dock after InstallAnywhere
3396 version launches</li>
3397 <li>Fetching EMBL reference for an RNA sequence results
3398 fails with a sequence mismatch</li>
3399 <li>Corrupted or unreadable alignment display when
3400 scrolling alignment to right</li>
3401 <li>ArrayIndexOutOfBoundsException thrown when remove
3402 empty columns called on alignment with ragged gapped ends</li>
3403 <li>auto calculated alignment annotation rows do not get
3404 placed above or below non-autocalculated rows</li>
3405 <li>Jalview dekstop becomes sluggish at full screen in
3406 ultra-high resolution</li>
3407 <li>Cannot disable consensus calculation independently of
3408 quality and conservation</li>
3409 <li>Mouseover highlighting between cDNA and protein can
3410 become sluggish with more than one splitframe shown</li>
3411 </ul> <em>Applet Known Issues</em>
3413 <li>Core PDB parsing code requires Jmol</li>
3414 <li>Sequence canvas panel goes white when alignment
3415 window is being resized</li>
3421 <td><div align="center">
3422 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3424 <td><em>General</em>
3426 <li>Updated Java code signing certificate donated by
3428 <li>Features and annotation preserved when performing
3429 pairwise alignment</li>
3430 <li>RNA pseudoknot annotation can be
3431 imported/exported/displayed</li>
3432 <li>'colour by annotation' can colour by RNA and
3433 protein secondary structure</li>
3434 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3435 post-hoc with 2.9 release</em>)
3438 </ul> <em>Application</em>
3440 <li>Extract and display secondary structure for sequences
3441 with 3D structures</li>
3442 <li>Support for parsing RNAML</li>
3443 <li>Annotations menu for layout
3445 <li>sort sequence annotation rows by alignment</li>
3446 <li>place sequence annotation above/below alignment
3449 <li>Output in Stockholm format</li>
3450 <li>Internationalisation: improved Spanish (es)
3452 <li>Structure viewer preferences tab</li>
3453 <li>Disorder and Secondary Structure annotation tracks
3454 shared between alignments</li>
3455 <li>UCSF Chimera launch and linked highlighting from
3457 <li>Show/hide all sequence associated annotation rows for
3458 all or current selection</li>
3459 <li>disorder and secondary structure predictions
3460 available as dataset annotation</li>
3461 <li>Per-sequence rna helices colouring</li>
3464 <li>Sequence database accessions imported when fetching
3465 alignments from Rfam</li>
3466 <li>update VARNA version to 3.91</li>
3468 <li>New groovy scripts for exporting aligned positions,
3469 conservation values, and calculating sum of pairs scores.</li>
3470 <li>Command line argument to set default JABAWS server</li>
3471 <li>include installation type in build properties and
3472 console log output</li>
3473 <li>Updated Jalview project format to preserve dataset
3477 <!-- issues resolved --> <em>Application</em>
3479 <li>Distinguish alignment and sequence associated RNA
3480 structure in structure->view->VARNA</li>
3481 <li>Raise dialog box if user deletes all sequences in an
3483 <li>Pressing F1 results in documentation opening twice</li>
3484 <li>Sequence feature tooltip is wrapped</li>
3485 <li>Double click on sequence associated annotation
3486 selects only first column</li>
3487 <li>Redundancy removal doesn't result in unlinked
3488 leaves shown in tree</li>
3489 <li>Undos after several redundancy removals don't undo
3491 <li>Hide sequence doesn't hide associated annotation</li>
3492 <li>User defined colours dialog box too big to fit on
3493 screen and buttons not visible</li>
3494 <li>author list isn't updated if already written to
3495 Jalview properties</li>
3496 <li>Popup menu won't open after retrieving sequence
3498 <li>File open window for associate PDB doesn't open</li>
3499 <li>Left-then-right click on a sequence id opens a
3500 browser search window</li>
3501 <li>Cannot open sequence feature shading/sort popup menu
3502 in feature settings dialog</li>
3503 <li>better tooltip placement for some areas of Jalview
3505 <li>Allow addition of JABAWS Server which doesn't
3506 pass validation</li>
3507 <li>Web services parameters dialog box is too large to
3509 <li>Muscle nucleotide alignment preset obscured by
3511 <li>JABAWS preset submenus don't contain newly
3512 defined user preset</li>
3513 <li>MSA web services warns user if they were launched
3514 with invalid input</li>
3515 <li>Jalview cannot contact DAS Registy when running on
3518 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3519 'Superpose with' submenu not shown when new view
3523 </ul> <!-- <em>Applet</em>
3525 </ul> <em>General</em>
3527 </ul>--> <em>Deployment and Documentation</em>
3529 <li>2G and 1G options in launchApp have no effect on
3530 memory allocation</li>
3531 <li>launchApp service doesn't automatically open
3532 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3534 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3535 InstallAnywhere reports cannot find valid JVM when Java
3536 1.7_055 is available
3538 </ul> <em>Application Known issues</em>
3541 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3542 corrupted or unreadable alignment display when scrolling
3546 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3547 retrieval fails but progress bar continues for DAS retrieval
3548 with large number of ID
3551 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3552 flatfile output of visible region has incorrect sequence
3556 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3557 rna structure consensus doesn't update when secondary
3558 structure tracks are rearranged
3561 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3562 invalid rna structure positional highlighting does not
3563 highlight position of invalid base pairs
3566 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3567 out of memory errors are not raised when saving Jalview
3568 project from alignment window file menu
3571 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3572 Switching to RNA Helices colouring doesn't propagate to
3576 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3577 colour by RNA Helices not enabled when user created
3578 annotation added to alignment
3581 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3582 Jalview icon not shown on dock in Mountain Lion/Webstart
3584 </ul> <em>Applet Known Issues</em>
3587 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3588 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3591 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3592 Jalview and Jmol example not compatible with IE9
3595 <li>Sort by annotation score doesn't reverse order
3601 <td><div align="center">
3602 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3605 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3608 <li>Internationalisation of user interface (usually
3609 called i18n support) and translation for Spanish locale</li>
3610 <li>Define/Undefine group on current selection with
3611 Ctrl-G/Shift Ctrl-G</li>
3612 <li>Improved group creation/removal options in
3613 alignment/sequence Popup menu</li>
3614 <li>Sensible precision for symbol distribution
3615 percentages shown in logo tooltip.</li>
3616 <li>Annotation panel height set according to amount of
3617 annotation when alignment first opened</li>
3618 </ul> <em>Application</em>
3620 <li>Interactive consensus RNA secondary structure
3621 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3622 <li>Select columns containing particular features from
3623 Feature Settings dialog</li>
3624 <li>View all 'representative' PDB structures for selected
3626 <li>Update Jalview project format:
3628 <li>New file extension for Jalview projects '.jvp'</li>
3629 <li>Preserve sequence and annotation dataset (to
3630 store secondary structure annotation,etc)</li>
3631 <li>Per group and alignment annotation and RNA helix
3635 <li>New similarity measures for PCA and Tree calculation
3637 <li>Experimental support for retrieval and viewing of
3638 flanking regions for an alignment</li>
3642 <!-- issues resolved --> <em>Application</em>
3644 <li>logo keeps spinning and status remains at queued or
3645 running after job is cancelled</li>
3646 <li>cannot export features from alignments imported from
3647 Jalview/VAMSAS projects</li>
3648 <li>Buggy slider for web service parameters that take
3650 <li>Newly created RNA secondary structure line doesn't
3651 have 'display all symbols' flag set</li>
3652 <li>T-COFFEE alignment score shading scheme and other
3653 annotation shading not saved in Jalview project</li>
3654 <li>Local file cannot be loaded in freshly downloaded
3656 <li>Jalview icon not shown on dock in Mountain
3658 <li>Load file from desktop file browser fails</li>
3659 <li>Occasional NPE thrown when calculating large trees</li>
3660 <li>Cannot reorder or slide sequences after dragging an
3661 alignment onto desktop</li>
3662 <li>Colour by annotation dialog throws NPE after using
3663 'extract scores' function</li>
3664 <li>Loading/cut'n'pasting an empty file leads to a grey
3665 alignment window</li>
3666 <li>Disorder thresholds rendered incorrectly after
3667 performing IUPred disorder prediction</li>
3668 <li>Multiple group annotated consensus rows shown when
3669 changing 'normalise logo' display setting</li>
3670 <li>Find shows blank dialog after 'finished searching' if
3671 nothing matches query</li>
3672 <li>Null Pointer Exceptions raised when sorting by
3673 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3675 <li>Errors in Jmol console when structures in alignment
3676 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3678 <li>Not all working JABAWS services are shown in
3680 <li>JAVAWS version of Jalview fails to launch with
3681 'invalid literal/length code'</li>
3682 <li>Annotation/RNA Helix colourschemes cannot be applied
3683 to alignment with groups (actually fixed in 2.8.0b1)</li>
3684 <li>RNA Helices and T-Coffee Scores available as default
3687 </ul> <em>Applet</em>
3689 <li>Remove group option is shown even when selection is
3691 <li>Apply to all groups ticked but colourscheme changes
3692 don't affect groups</li>
3693 <li>Documented RNA Helices and T-Coffee Scores as valid
3694 colourscheme name</li>
3695 <li>Annotation labels drawn on sequence IDs when
3696 Annotation panel is not displayed</li>
3697 <li>Increased font size for dropdown menus on OSX and
3698 embedded windows</li>
3699 </ul> <em>Other</em>
3701 <li>Consensus sequence for alignments/groups with a
3702 single sequence were not calculated</li>
3703 <li>annotation files that contain only groups imported as
3704 annotation and junk sequences</li>
3705 <li>Fasta files with sequences containing '*' incorrectly
3706 recognised as PFAM or BLC</li>
3707 <li>conservation/PID slider apply all groups option
3708 doesn't affect background (2.8.0b1)
3710 <li>redundancy highlighting is erratic at 0% and 100%</li>
3711 <li>Remove gapped columns fails for sequences with ragged
3713 <li>AMSA annotation row with leading spaces is not
3714 registered correctly on import</li>
3715 <li>Jalview crashes when selecting PCA analysis for
3716 certain alignments</li>
3717 <li>Opening the colour by annotation dialog for an
3718 existing annotation based 'use original colours'
3719 colourscheme loses original colours setting</li>
3724 <td><div align="center">
3725 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3726 <em>30/1/2014</em></strong>
3730 <li>Trusted certificates for JalviewLite applet and
3731 Jalview Desktop application<br />Certificate was donated by
3732 <a href="https://www.certum.eu">Certum</a> to the Jalview
3733 open source project).
3735 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3736 <li>Output in Stockholm format</li>
3737 <li>Allow import of data from gzipped files</li>
3738 <li>Export/import group and sequence associated line
3739 graph thresholds</li>
3740 <li>Nucleotide substitution matrix that supports RNA and
3741 ambiguity codes</li>
3742 <li>Allow disorder predictions to be made on the current
3743 selection (or visible selection) in the same way that JPred
3745 <li>Groovy scripting for headless Jalview operation</li>
3746 </ul> <em>Other improvements</em>
3748 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3749 <li>COMBINE statement uses current SEQUENCE_REF and
3750 GROUP_REF scope to group annotation rows</li>
3751 <li>Support '' style escaping of quotes in Newick
3753 <li>Group options for JABAWS service by command line name</li>
3754 <li>Empty tooltip shown for JABA service options with a
3755 link but no description</li>
3756 <li>Select primary source when selecting authority in
3757 database fetcher GUI</li>
3758 <li>Add .mfa to FASTA file extensions recognised by
3760 <li>Annotation label tooltip text wrap</li>
3765 <li>Slow scrolling when lots of annotation rows are
3767 <li>Lots of NPE (and slowness) after creating RNA
3768 secondary structure annotation line</li>
3769 <li>Sequence database accessions not imported when
3770 fetching alignments from Rfam</li>
3771 <li>Incorrect SHMR submission for sequences with
3773 <li>View all structures does not always superpose
3775 <li>Option widgets in service parameters not updated to
3776 reflect user or preset settings</li>
3777 <li>Null pointer exceptions for some services without
3778 presets or adjustable parameters</li>
3779 <li>Discover PDB IDs entry in structure menu doesn't
3780 discover PDB xRefs</li>
3781 <li>Exception encountered while trying to retrieve
3782 features with DAS</li>
3783 <li>Lowest value in annotation row isn't coloured
3784 when colour by annotation (per sequence) is coloured</li>
3785 <li>Keyboard mode P jumps to start of gapped region when
3786 residue follows a gap</li>
3787 <li>Jalview appears to hang importing an alignment with
3788 Wrap as default or after enabling Wrap</li>
3789 <li>'Right click to add annotations' message
3790 shown in wrap mode when no annotations present</li>
3791 <li>Disorder predictions fail with NPE if no automatic
3792 annotation already exists on alignment</li>
3793 <li>oninit javascript function should be called after
3794 initialisation completes</li>
3795 <li>Remove redundancy after disorder prediction corrupts
3796 alignment window display</li>
3797 <li>Example annotation file in documentation is invalid</li>
3798 <li>Grouped line graph annotation rows are not exported
3799 to annotation file</li>
3800 <li>Multi-harmony analysis cannot be run when only two
3802 <li>Cannot create multiple groups of line graphs with
3803 several 'combine' statements in annotation file</li>
3804 <li>Pressing return several times causes Number Format
3805 exceptions in keyboard mode</li>
3806 <li>Multi-harmony (SHMMR) method doesn't submit
3807 correct partitions for input data</li>
3808 <li>Translation from DNA to Amino Acids fails</li>
3809 <li>Jalview fail to load newick tree with quoted label</li>
3810 <li>--headless flag isn't understood</li>
3811 <li>ClassCastException when generating EPS in headless
3813 <li>Adjusting sequence-associated shading threshold only
3814 changes one row's threshold</li>
3815 <li>Preferences and Feature settings panel panel
3816 doesn't open</li>
3817 <li>hide consensus histogram also hides conservation and
3818 quality histograms</li>
3823 <td><div align="center">
3824 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3826 <td><em>Application</em>
3828 <li>Support for JABAWS 2.0 Services (AACon alignment
3829 conservation, protein disorder and Clustal Omega)</li>
3830 <li>JABAWS server status indicator in Web Services
3832 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3833 in Jalview alignment window</li>
3834 <li>Updated Jalview build and deploy framework for OSX
3835 mountain lion, windows 7, and 8</li>
3836 <li>Nucleotide substitution matrix for PCA that supports
3837 RNA and ambiguity codes</li>
3839 <li>Improved sequence database retrieval GUI</li>
3840 <li>Support fetching and database reference look up
3841 against multiple DAS sources (Fetch all from in 'fetch db
3843 <li>Jalview project improvements
3845 <li>Store and retrieve the 'belowAlignment'
3846 flag for annotation</li>
3847 <li>calcId attribute to group annotation rows on the
3849 <li>Store AACon calculation settings for a view in
3850 Jalview project</li>
3854 <li>horizontal scrolling gesture support</li>
3855 <li>Visual progress indicator when PCA calculation is
3857 <li>Simpler JABA web services menus</li>
3858 <li>visual indication that web service results are still
3859 being retrieved from server</li>
3860 <li>Serialise the dialogs that are shown when Jalview
3861 starts up for first time</li>
3862 <li>Jalview user agent string for interacting with HTTP
3864 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3866 <li>Examples directory and Groovy library included in
3867 InstallAnywhere distribution</li>
3868 </ul> <em>Applet</em>
3870 <li>RNA alignment and secondary structure annotation
3871 visualization applet example</li>
3872 </ul> <em>General</em>
3874 <li>Normalise option for consensus sequence logo</li>
3875 <li>Reset button in PCA window to return dimensions to
3877 <li>Allow seqspace or Jalview variant of alignment PCA
3879 <li>PCA with either nucleic acid and protein substitution
3881 <li>Allow windows containing HTML reports to be exported
3883 <li>Interactive display and editing of RNA secondary
3884 structure contacts</li>
3885 <li>RNA Helix Alignment Colouring</li>
3886 <li>RNA base pair logo consensus</li>
3887 <li>Parse sequence associated secondary structure
3888 information in Stockholm files</li>
3889 <li>HTML Export database accessions and annotation
3890 information presented in tooltip for sequences</li>
3891 <li>Import secondary structure from LOCARNA clustalw
3892 style RNA alignment files</li>
3893 <li>import and visualise T-COFFEE quality scores for an
3895 <li>'colour by annotation' per sequence option to
3896 shade each sequence according to its associated alignment
3898 <li>New Jalview Logo</li>
3899 </ul> <em>Documentation and Development</em>
3901 <li>documentation for score matrices used in Jalview</li>
3902 <li>New Website!</li>
3904 <td><em>Application</em>
3906 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3907 wsdbfetch REST service</li>
3908 <li>Stop windows being moved outside desktop on OSX</li>
3909 <li>Filetype associations not installed for webstart
3911 <li>Jalview does not always retrieve progress of a JABAWS
3912 job execution in full once it is complete</li>
3913 <li>revise SHMR RSBS definition to ensure alignment is
3914 uploaded via ali_file parameter</li>
3915 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3916 <li>View all structures superposed fails with exception</li>
3917 <li>Jnet job queues forever if a very short sequence is
3918 submitted for prediction</li>
3919 <li>Cut and paste menu not opened when mouse clicked on
3921 <li>Putting fractional value into integer text box in
3922 alignment parameter dialog causes Jalview to hang</li>
3923 <li>Structure view highlighting doesn't work on
3925 <li>View all structures fails with exception shown in
3927 <li>Characters in filename associated with PDBEntry not
3928 escaped in a platform independent way</li>
3929 <li>Jalview desktop fails to launch with exception when
3931 <li>Tree calculation reports 'you must have 2 or more
3932 sequences selected' when selection is empty</li>
3933 <li>Jalview desktop fails to launch with jar signature
3934 failure when java web start temporary file caching is
3936 <li>DAS Sequence retrieval with range qualification
3937 results in sequence xref which includes range qualification</li>
3938 <li>Errors during processing of command line arguments
3939 cause progress bar (JAL-898) to be removed</li>
3940 <li>Replace comma for semi-colon option not disabled for
3941 DAS sources in sequence fetcher</li>
3942 <li>Cannot close news reader when JABAWS server warning
3943 dialog is shown</li>
3944 <li>Option widgets not updated to reflect user settings</li>
3945 <li>Edited sequence not submitted to web service</li>
3946 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3947 <li>InstallAnywhere installer doesn't unpack and run
3948 on OSX Mountain Lion</li>
3949 <li>Annotation panel not given a scroll bar when
3950 sequences with alignment annotation are pasted into the
3952 <li>Sequence associated annotation rows not associated
3953 when loaded from Jalview project</li>
3954 <li>Browser launch fails with NPE on java 1.7</li>
3955 <li>JABAWS alignment marked as finished when job was
3956 cancelled or job failed due to invalid input</li>
3957 <li>NPE with v2.7 example when clicking on Tree
3958 associated with all views</li>
3959 <li>Exceptions when copy/paste sequences with grouped
3960 annotation rows to new window</li>
3961 </ul> <em>Applet</em>
3963 <li>Sequence features are momentarily displayed before
3964 they are hidden using hidefeaturegroups applet parameter</li>
3965 <li>loading features via javascript API automatically
3966 enables feature display</li>
3967 <li>scrollToColumnIn javascript API method doesn't
3969 </ul> <em>General</em>
3971 <li>Redundancy removal fails for rna alignment</li>
3972 <li>PCA calculation fails when sequence has been selected
3973 and then deselected</li>
3974 <li>PCA window shows grey box when first opened on OSX</li>
3975 <li>Letters coloured pink in sequence logo when alignment
3976 coloured with clustalx</li>
3977 <li>Choosing fonts without letter symbols defined causes
3978 exceptions and redraw errors</li>
3979 <li>Initial PCA plot view is not same as manually
3980 reconfigured view</li>
3981 <li>Grouped annotation graph label has incorrect line
3983 <li>Grouped annotation graph label display is corrupted
3984 for lots of labels</li>
3989 <div align="center">
3990 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3993 <td><em>Application</em>
3995 <li>Jalview Desktop News Reader</li>
3996 <li>Tweaked default layout of web services menu</li>
3997 <li>View/alignment association menu to enable user to
3998 easily specify which alignment a multi-structure view takes
3999 its colours/correspondences from</li>
4000 <li>Allow properties file location to be specified as URL</li>
4001 <li>Extend Jalview project to preserve associations
4002 between many alignment views and a single Jmol display</li>
4003 <li>Store annotation row height in Jalview project file</li>
4004 <li>Annotation row column label formatting attributes
4005 stored in project file</li>
4006 <li>Annotation row order for auto-calculated annotation
4007 rows preserved in Jalview project file</li>
4008 <li>Visual progress indication when Jalview state is
4009 saved using Desktop window menu</li>
4010 <li>Visual indication that command line arguments are
4011 still being processed</li>
4012 <li>Groovy script execution from URL</li>
4013 <li>Colour by annotation default min and max colours in
4015 <li>Automatically associate PDB files dragged onto an
4016 alignment with sequences that have high similarity and
4018 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4019 <li>'view structures' option to open many
4020 structures in same window</li>
4021 <li>Sort associated views menu option for tree panel</li>
4022 <li>Group all JABA and non-JABA services for a particular
4023 analysis function in its own submenu</li>
4024 </ul> <em>Applet</em>
4026 <li>Userdefined and autogenerated annotation rows for
4028 <li>Adjustment of alignment annotation pane height</li>
4029 <li>Annotation scrollbar for annotation panel</li>
4030 <li>Drag to reorder annotation rows in annotation panel</li>
4031 <li>'automaticScrolling' parameter</li>
4032 <li>Allow sequences with partial ID string matches to be
4033 annotated from GFF/Jalview features files</li>
4034 <li>Sequence logo annotation row in applet</li>
4035 <li>Absolute paths relative to host server in applet
4036 parameters are treated as such</li>
4037 <li>New in the JalviewLite javascript API:
4039 <li>JalviewLite.js javascript library</li>
4040 <li>Javascript callbacks for
4042 <li>Applet initialisation</li>
4043 <li>Sequence/alignment mouse-overs and selections</li>
4046 <li>scrollTo row and column alignment scrolling
4048 <li>Select sequence/alignment regions from javascript</li>
4049 <li>javascript structure viewer harness to pass
4050 messages between Jmol and Jalview when running as
4051 distinct applets</li>
4052 <li>sortBy method</li>
4053 <li>Set of applet and application examples shipped
4054 with documentation</li>
4055 <li>New example to demonstrate JalviewLite and Jmol
4056 javascript message exchange</li>
4058 </ul> <em>General</em>
4060 <li>Enable Jmol displays to be associated with multiple
4061 multiple alignments</li>
4062 <li>Option to automatically sort alignment with new tree</li>
4063 <li>User configurable link to enable redirects to a
4064 www.Jalview.org mirror</li>
4065 <li>Jmol colours option for Jmol displays</li>
4066 <li>Configurable newline string when writing alignment
4067 and other flat files</li>
4068 <li>Allow alignment annotation description lines to
4069 contain html tags</li>
4070 </ul> <em>Documentation and Development</em>
4072 <li>Add groovy test harness for bulk load testing to
4074 <li>Groovy script to load and align a set of sequences
4075 using a web service before displaying the result in the
4076 Jalview desktop</li>
4077 <li>Restructured javascript and applet api documentation</li>
4078 <li>Ant target to publish example html files with applet
4080 <li>Netbeans project for building Jalview from source</li>
4081 <li>ant task to create online javadoc for Jalview source</li>
4083 <td><em>Application</em>
4085 <li>User defined colourscheme throws exception when
4086 current built in colourscheme is saved as new scheme</li>
4087 <li>AlignFrame->Save in application pops up save
4088 dialog for valid filename/format</li>
4089 <li>Cannot view associated structure for UniProt sequence</li>
4090 <li>PDB file association breaks for UniProt sequence
4092 <li>Associate PDB from file dialog does not tell you
4093 which sequence is to be associated with the file</li>
4094 <li>Find All raises null pointer exception when query
4095 only matches sequence IDs</li>
4096 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4097 <li>Jalview project with Jmol views created with Jalview
4098 2.4 cannot be loaded</li>
4099 <li>Filetype associations not installed for webstart
4101 <li>Two or more chains in a single PDB file associated
4102 with sequences in different alignments do not get coloured
4103 by their associated sequence</li>
4104 <li>Visibility status of autocalculated annotation row
4105 not preserved when project is loaded</li>
4106 <li>Annotation row height and visibility attributes not
4107 stored in Jalview project</li>
4108 <li>Tree bootstraps are not preserved when saved as a
4109 Jalview project</li>
4110 <li>Envision2 workflow tooltips are corrupted</li>
4111 <li>Enabling show group conservation also enables colour
4112 by conservation</li>
4113 <li>Duplicate group associated conservation or consensus
4114 created on new view</li>
4115 <li>Annotation scrollbar not displayed after 'show
4116 all hidden annotation rows' option selected</li>
4117 <li>Alignment quality not updated after alignment
4118 annotation row is hidden then shown</li>
4119 <li>Preserve colouring of structures coloured by
4120 sequences in pre Jalview 2.7 projects</li>
4121 <li>Web service job parameter dialog is not laid out
4123 <li>Web services menu not refreshed after 'reset
4124 services' button is pressed in preferences</li>
4125 <li>Annotation off by one in Jalview v2_3 example project</li>
4126 <li>Structures imported from file and saved in project
4127 get name like jalview_pdb1234.txt when reloaded</li>
4128 <li>Jalview does not always retrieve progress of a JABAWS
4129 job execution in full once it is complete</li>
4130 </ul> <em>Applet</em>
4132 <li>Alignment height set incorrectly when lots of
4133 annotation rows are displayed</li>
4134 <li>Relative URLs in feature HTML text not resolved to
4136 <li>View follows highlighting does not work for positions
4138 <li><= shown as = in tooltip</li>
4139 <li>Export features raises exception when no features
4141 <li>Separator string used for serialising lists of IDs
4142 for javascript api is modified when separator string
4143 provided as parameter</li>
4144 <li>Null pointer exception when selecting tree leaves for
4145 alignment with no existing selection</li>
4146 <li>Relative URLs for datasources assumed to be relative
4147 to applet's codebase</li>
4148 <li>Status bar not updated after finished searching and
4149 search wraps around to first result</li>
4150 <li>StructureSelectionManager instance shared between
4151 several Jalview applets causes race conditions and memory
4153 <li>Hover tooltip and mouseover of position on structure
4154 not sent from Jmol in applet</li>
4155 <li>Certain sequences of javascript method calls to
4156 applet API fatally hang browser</li>
4157 </ul> <em>General</em>
4159 <li>View follows structure mouseover scrolls beyond
4160 position with wrapped view and hidden regions</li>
4161 <li>Find sequence position moves to wrong residue
4162 with/without hidden columns</li>
4163 <li>Sequence length given in alignment properties window
4165 <li>InvalidNumberFormat exceptions thrown when trying to
4166 import PDB like structure files</li>
4167 <li>Positional search results are only highlighted
4168 between user-supplied sequence start/end bounds</li>
4169 <li>End attribute of sequence is not validated</li>
4170 <li>Find dialog only finds first sequence containing a
4171 given sequence position</li>
4172 <li>Sequence numbering not preserved in MSF alignment
4174 <li>Jalview PDB file reader does not extract sequence
4175 from nucleotide chains correctly</li>
4176 <li>Structure colours not updated when tree partition
4177 changed in alignment</li>
4178 <li>Sequence associated secondary structure not correctly
4179 parsed in interleaved stockholm</li>
4180 <li>Colour by annotation dialog does not restore current
4182 <li>Hiding (nearly) all sequences doesn't work
4184 <li>Sequences containing lowercase letters are not
4185 properly associated with their pdb files</li>
4186 </ul> <em>Documentation and Development</em>
4188 <li>schemas/JalviewWsParamSet.xsd corrupted by
4189 ApplyCopyright tool</li>
4194 <div align="center">
4195 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4198 <td><em>Application</em>
4200 <li>New warning dialog when the Jalview Desktop cannot
4201 contact web services</li>
4202 <li>JABA service parameters for a preset are shown in
4203 service job window</li>
4204 <li>JABA Service menu entries reworded</li>
4208 <li>Modeller PIR IO broken - cannot correctly import a
4209 pir file emitted by Jalview</li>
4210 <li>Existing feature settings transferred to new
4211 alignment view created from cut'n'paste</li>
4212 <li>Improved test for mixed amino/nucleotide chains when
4213 parsing PDB files</li>
4214 <li>Consensus and conservation annotation rows
4215 occasionally become blank for all new windows</li>
4216 <li>Exception raised when right clicking above sequences
4217 in wrapped view mode</li>
4218 </ul> <em>Application</em>
4220 <li>multiple multiply aligned structure views cause cpu
4221 usage to hit 100% and computer to hang</li>
4222 <li>Web Service parameter layout breaks for long user
4223 parameter names</li>
4224 <li>Jaba service discovery hangs desktop if Jaba server
4231 <div align="center">
4232 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4235 <td><em>Application</em>
4237 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4238 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4241 <li>Web Services preference tab</li>
4242 <li>Analysis parameters dialog box and user defined
4244 <li>Improved speed and layout of Envision2 service menu</li>
4245 <li>Superpose structures using associated sequence
4247 <li>Export coordinates and projection as CSV from PCA
4249 </ul> <em>Applet</em>
4251 <li>enable javascript: execution by the applet via the
4252 link out mechanism</li>
4253 </ul> <em>Other</em>
4255 <li>Updated the Jmol Jalview interface to work with Jmol
4257 <li>The Jalview Desktop and JalviewLite applet now
4258 require Java 1.5</li>
4259 <li>Allow Jalview feature colour specification for GFF
4260 sequence annotation files</li>
4261 <li>New 'colour by label' keword in Jalview feature file
4262 type colour specification</li>
4263 <li>New Jalview Desktop Groovy API method that allows a
4264 script to check if it being run in an interactive session or
4265 in a batch operation from the Jalview command line</li>
4269 <li>clustalx colourscheme colours Ds preferentially when
4270 both D+E are present in over 50% of the column</li>
4271 </ul> <em>Application</em>
4273 <li>typo in AlignmentFrame->View->Hide->all but
4274 selected Regions menu item</li>
4275 <li>sequence fetcher replaces ',' for ';' when the ',' is
4276 part of a valid accession ID</li>
4277 <li>fatal OOM if object retrieved by sequence fetcher
4278 runs out of memory</li>
4279 <li>unhandled Out of Memory Error when viewing pca
4280 analysis results</li>
4281 <li>InstallAnywhere builds fail to launch on OS X java
4282 10.5 update 4 (due to apple Java 1.6 update)</li>
4283 <li>Installanywhere Jalview silently fails to launch</li>
4284 </ul> <em>Applet</em>
4286 <li>Jalview.getFeatureGroups() raises an
4287 ArrayIndexOutOfBoundsException if no feature groups are
4294 <div align="center">
4295 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4301 <li>Alignment prettyprinter doesn't cope with long
4303 <li>clustalx colourscheme colours Ds preferentially when
4304 both D+E are present in over 50% of the column</li>
4305 <li>nucleic acid structures retrieved from PDB do not
4306 import correctly</li>
4307 <li>More columns get selected than were clicked on when a
4308 number of columns are hidden</li>
4309 <li>annotation label popup menu not providing correct
4310 add/hide/show options when rows are hidden or none are
4312 <li>Stockholm format shown in list of readable formats,
4313 and parser copes better with alignments from RFAM.</li>
4314 <li>CSV output of consensus only includes the percentage
4315 of all symbols if sequence logo display is enabled</li>
4317 </ul> <em>Applet</em>
4319 <li>annotation panel disappears when annotation is
4321 </ul> <em>Application</em>
4323 <li>Alignment view not redrawn properly when new
4324 alignment opened where annotation panel is visible but no
4325 annotations are present on alignment</li>
4326 <li>pasted region containing hidden columns is
4327 incorrectly displayed in new alignment window</li>
4328 <li>Jalview slow to complete operations when stdout is
4329 flooded (fix is to close the Jalview console)</li>
4330 <li>typo in AlignmentFrame->View->Hide->all but
4331 selected Rregions menu item.</li>
4332 <li>inconsistent group submenu and Format submenu entry
4333 'Un' or 'Non'conserved</li>
4334 <li>Sequence feature settings are being shared by
4335 multiple distinct alignments</li>
4336 <li>group annotation not recreated when tree partition is
4338 <li>double click on group annotation to select sequences
4339 does not propagate to associated trees</li>
4340 <li>Mac OSX specific issues:
4342 <li>exception raised when mouse clicked on desktop
4343 window background</li>
4344 <li>Desktop menu placed on menu bar and application
4345 name set correctly</li>
4346 <li>sequence feature settings not wide enough for the
4347 save feature colourscheme button</li>
4356 <div align="center">
4357 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4360 <td><em>New Capabilities</em>
4362 <li>URL links generated from description line for
4363 regular-expression based URL links (applet and application)
4365 <li>Non-positional feature URL links are shown in link
4367 <li>Linked viewing of nucleic acid sequences and
4369 <li>Automatic Scrolling option in View menu to display
4370 the currently highlighted region of an alignment.</li>
4371 <li>Order an alignment by sequence length, or using the
4372 average score or total feature count for each sequence.</li>
4373 <li>Shading features by score or associated description</li>
4374 <li>Subdivide alignment and groups based on identity of
4375 selected subsequence (Make Groups from Selection).</li>
4376 <li>New hide/show options including Shift+Control+H to
4377 hide everything but the currently selected region.</li>
4378 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4379 </ul> <em>Application</em>
4381 <li>Fetch DB References capabilities and UI expanded to
4382 support retrieval from DAS sequence sources</li>
4383 <li>Local DAS Sequence sources can be added via the
4384 command line or via the Add local source dialog box.</li>
4385 <li>DAS Dbref and DbxRef feature types are parsed as
4386 database references and protein_name is parsed as
4387 description line (BioSapiens terms).</li>
4388 <li>Enable or disable non-positional feature and database
4389 references in sequence ID tooltip from View menu in
4391 <!-- <li>New hidden columns and rows and representatives capabilities
4392 in annotations file (in progress - not yet fully implemented)</li> -->
4393 <li>Group-associated consensus, sequence logos and
4394 conservation plots</li>
4395 <li>Symbol distributions for each column can be exported
4396 and visualized as sequence logos</li>
4397 <li>Optionally scale multi-character column labels to fit
4398 within each column of annotation row<!-- todo for applet -->
4400 <li>Optional automatic sort of associated alignment view
4401 when a new tree is opened.</li>
4402 <li>Jalview Java Console</li>
4403 <li>Better placement of desktop window when moving
4404 between different screens.</li>
4405 <li>New preference items for sequence ID tooltip and
4406 consensus annotation</li>
4407 <li>Client to submit sequences and IDs to Envision2
4409 <li><em>Vamsas Capabilities</em>
4411 <li>Improved VAMSAS synchronization (Jalview archive
4412 used to preserve views, structures, and tree display
4414 <li>Import of vamsas documents from disk or URL via
4416 <li>Sharing of selected regions between views and
4417 with other VAMSAS applications (Experimental feature!)</li>
4418 <li>Updated API to VAMSAS version 0.2</li>
4420 </ul> <em>Applet</em>
4422 <li>Middle button resizes annotation row height</li>
4425 <li>sortByTree (true/false) - automatically sort the
4426 associated alignment view by the tree when a new tree is
4428 <li>showTreeBootstraps (true/false) - show or hide
4429 branch bootstraps (default is to show them if available)</li>
4430 <li>showTreeDistances (true/false) - show or hide
4431 branch lengths (default is to show them if available)</li>
4432 <li>showUnlinkedTreeNodes (true/false) - indicate if
4433 unassociated nodes should be highlighted in the tree
4435 <li>heightScale and widthScale (1.0 or more) -
4436 increase the height or width of a cell in the alignment
4437 grid relative to the current font size.</li>
4440 <li>Non-positional features displayed in sequence ID
4442 </ul> <em>Other</em>
4444 <li>Features format: graduated colour definitions and
4445 specification of feature scores</li>
4446 <li>Alignment Annotations format: new keywords for group
4447 associated annotation (GROUP_REF) and annotation row display
4448 properties (ROW_PROPERTIES)</li>
4449 <li>XML formats extended to support graduated feature
4450 colourschemes, group associated annotation, and profile
4451 visualization settings.</li></td>
4454 <li>Source field in GFF files parsed as feature source
4455 rather than description</li>
4456 <li>Non-positional features are now included in sequence
4457 feature and gff files (controlled via non-positional feature
4458 visibility in tooltip).</li>
4459 <li>URL links generated for all feature links (bugfix)</li>
4460 <li>Added URL embedding instructions to features file
4462 <li>Codons containing ambiguous nucleotides translated as
4463 'X' in peptide product</li>
4464 <li>Match case switch in find dialog box works for both
4465 sequence ID and sequence string and query strings do not
4466 have to be in upper case to match case-insensitively.</li>
4467 <li>AMSA files only contain first column of
4468 multi-character column annotation labels</li>
4469 <li>Jalview Annotation File generation/parsing consistent
4470 with documentation (e.g. Stockholm annotation can be
4471 exported and re-imported)</li>
4472 <li>PDB files without embedded PDB IDs given a friendly
4474 <li>Find incrementally searches ID string matches as well
4475 as subsequence matches, and correctly reports total number
4479 <li>Better handling of exceptions during sequence
4481 <li>Dasobert generated non-positional feature URL
4482 link text excludes the start_end suffix</li>
4483 <li>DAS feature and source retrieval buttons disabled
4484 when fetch or registry operations in progress.</li>
4485 <li>PDB files retrieved from URLs are cached properly</li>
4486 <li>Sequence description lines properly shared via
4488 <li>Sequence fetcher fetches multiple records for all
4490 <li>Ensured that command line das feature retrieval
4491 completes before alignment figures are generated.</li>
4492 <li>Reduced time taken when opening file browser for
4494 <li>isAligned check prior to calculating tree, PCA or
4495 submitting an MSA to JNet now excludes hidden sequences.</li>
4496 <li>User defined group colours properly recovered
4497 from Jalview projects.</li>
4506 <div align="center">
4507 <strong>2.4.0.b2</strong><br> 28/10/2009
4512 <li>Experimental support for google analytics usage
4514 <li>Jalview privacy settings (user preferences and docs).</li>
4519 <li>Race condition in applet preventing startup in
4521 <li>Exception when feature created from selection beyond
4522 length of sequence.</li>
4523 <li>Allow synthetic PDB files to be imported gracefully</li>
4524 <li>Sequence associated annotation rows associate with
4525 all sequences with a given id</li>
4526 <li>Find function matches case-insensitively for sequence
4527 ID string searches</li>
4528 <li>Non-standard characters do not cause pairwise
4529 alignment to fail with exception</li>
4530 </ul> <em>Application Issues</em>
4532 <li>Sequences are now validated against EMBL database</li>
4533 <li>Sequence fetcher fetches multiple records for all
4535 </ul> <em>InstallAnywhere Issues</em>
4537 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4538 issue with installAnywhere mechanism)</li>
4539 <li>Command line launching of JARs from InstallAnywhere
4540 version (java class versioning error fixed)</li>
4547 <div align="center">
4548 <strong>2.4</strong><br> 27/8/2008
4551 <td><em>User Interface</em>
4553 <li>Linked highlighting of codon and amino acid from
4554 translation and protein products</li>
4555 <li>Linked highlighting of structure associated with
4556 residue mapping to codon position</li>
4557 <li>Sequence Fetcher provides example accession numbers
4558 and 'clear' button</li>
4559 <li>MemoryMonitor added as an option under Desktop's
4561 <li>Extract score function to parse whitespace separated
4562 numeric data in description line</li>
4563 <li>Column labels in alignment annotation can be centred.</li>
4564 <li>Tooltip for sequence associated annotation give name
4566 </ul> <em>Web Services and URL fetching</em>
4568 <li>JPred3 web service</li>
4569 <li>Prototype sequence search client (no public services
4571 <li>Fetch either seed alignment or full alignment from
4573 <li>URL Links created for matching database cross
4574 references as well as sequence ID</li>
4575 <li>URL Links can be created using regular-expressions</li>
4576 </ul> <em>Sequence Database Connectivity</em>
4578 <li>Retrieval of cross-referenced sequences from other
4580 <li>Generalised database reference retrieval and
4581 validation to all fetchable databases</li>
4582 <li>Fetch sequences from DAS sources supporting the
4583 sequence command</li>
4584 </ul> <em>Import and Export</em>
4585 <li>export annotation rows as CSV for spreadsheet import</li>
4586 <li>Jalview projects record alignment dataset associations,
4587 EMBL products, and cDNA sequence mappings</li>
4588 <li>Sequence Group colour can be specified in Annotation
4590 <li>Ad-hoc colouring of group in Annotation File using RGB
4591 triplet as name of colourscheme</li>
4592 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4594 <li>treenode binding for VAMSAS tree exchange</li>
4595 <li>local editing and update of sequences in VAMSAS
4596 alignments (experimental)</li>
4597 <li>Create new or select existing session to join</li>
4598 <li>load and save of vamsas documents</li>
4599 </ul> <em>Application command line</em>
4601 <li>-tree parameter to open trees (introduced for passing
4603 <li>-fetchfrom command line argument to specify nicknames
4604 of DAS servers to query for alignment features</li>
4605 <li>-dasserver command line argument to add new servers
4606 that are also automatically queried for features</li>
4607 <li>-groovy command line argument executes a given groovy
4608 script after all input data has been loaded and parsed</li>
4609 </ul> <em>Applet-Application data exchange</em>
4611 <li>Trees passed as applet parameters can be passed to
4612 application (when using "View in full
4613 application")</li>
4614 </ul> <em>Applet Parameters</em>
4616 <li>feature group display control parameter</li>
4617 <li>debug parameter</li>
4618 <li>showbutton parameter</li>
4619 </ul> <em>Applet API methods</em>
4621 <li>newView public method</li>
4622 <li>Window (current view) specific get/set public methods</li>
4623 <li>Feature display control methods</li>
4624 <li>get list of currently selected sequences</li>
4625 </ul> <em>New Jalview distribution features</em>
4627 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4628 <li>RELEASE file gives build properties for the latest
4629 Jalview release.</li>
4630 <li>Java 1.1 Applet build made easier and donotobfuscate
4631 property controls execution of obfuscator</li>
4632 <li>Build target for generating source distribution</li>
4633 <li>Debug flag for javacc</li>
4634 <li>.jalview_properties file is documented (slightly) in
4635 jalview.bin.Cache</li>
4636 <li>Continuous Build Integration for stable and
4637 development version of Application, Applet and source
4642 <li>selected region output includes visible annotations
4643 (for certain formats)</li>
4644 <li>edit label/displaychar contains existing label/char
4646 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4647 <li>shorter peptide product names from EMBL records</li>
4648 <li>Newick string generator makes compact representations</li>
4649 <li>bootstrap values parsed correctly for tree files with
4651 <li>pathological filechooser bug avoided by not allowing
4652 filenames containing a ':'</li>
4653 <li>Fixed exception when parsing GFF files containing
4654 global sequence features</li>
4655 <li>Alignment datasets are finalized only when number of
4656 references from alignment sequences goes to zero</li>
4657 <li>Close of tree branch colour box without colour
4658 selection causes cascading exceptions</li>
4659 <li>occasional negative imgwidth exceptions</li>
4660 <li>better reporting of non-fatal warnings to user when
4661 file parsing fails.</li>
4662 <li>Save works when Jalview project is default format</li>
4663 <li>Save as dialog opened if current alignment format is
4664 not a valid output format</li>
4665 <li>UniProt canonical names introduced for both das and
4667 <li>Histidine should be midblue (not pink!) in Zappo</li>
4668 <li>error messages passed up and output when data read
4670 <li>edit undo recovers previous dataset sequence when
4671 sequence is edited</li>
4672 <li>allow PDB files without pdb ID HEADER lines (like
4673 those generated by MODELLER) to be read in properly</li>
4674 <li>allow reading of JPred concise files as a normal
4676 <li>Stockholm annotation parsing and alignment properties
4677 import fixed for PFAM records</li>
4678 <li>Structure view windows have correct name in Desktop
4680 <li>annotation consisting of sequence associated scores
4681 can be read and written correctly to annotation file</li>
4682 <li>Aligned cDNA translation to aligned peptide works
4684 <li>Fixed display of hidden sequence markers and
4685 non-italic font for representatives in Applet</li>
4686 <li>Applet Menus are always embedded in applet window on
4688 <li>Newly shown features appear at top of stack (in
4690 <li>Annotations added via parameter not drawn properly
4691 due to null pointer exceptions</li>
4692 <li>Secondary structure lines are drawn starting from
4693 first column of alignment</li>
4694 <li>UniProt XML import updated for new schema release in
4696 <li>Sequence feature to sequence ID match for Features
4697 file is case-insensitive</li>
4698 <li>Sequence features read from Features file appended to
4699 all sequences with matching IDs</li>
4700 <li>PDB structure coloured correctly for associated views
4701 containing a sub-sequence</li>
4702 <li>PDB files can be retrieved by applet from Jar files</li>
4703 <li>feature and annotation file applet parameters
4704 referring to different directories are retrieved correctly</li>
4705 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4706 <li>Fixed application hang whilst waiting for
4707 splash-screen version check to complete</li>
4708 <li>Applet properly URLencodes input parameter values
4709 when passing them to the launchApp service</li>
4710 <li>display name and local features preserved in results
4711 retrieved from web service</li>
4712 <li>Visual delay indication for sequence retrieval and
4713 sequence fetcher initialisation</li>
4714 <li>updated Application to use DAS 1.53e version of
4715 dasobert DAS client</li>
4716 <li>Re-instated Full AMSA support and .amsa file
4718 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4726 <div align="center">
4727 <strong>2.3</strong><br> 9/5/07
4732 <li>Jmol 11.0.2 integration</li>
4733 <li>PDB views stored in Jalview XML files</li>
4734 <li>Slide sequences</li>
4735 <li>Edit sequence in place</li>
4736 <li>EMBL CDS features</li>
4737 <li>DAS Feature mapping</li>
4738 <li>Feature ordering</li>
4739 <li>Alignment Properties</li>
4740 <li>Annotation Scores</li>
4741 <li>Sort by scores</li>
4742 <li>Feature/annotation editing in applet</li>
4747 <li>Headless state operation in 2.2.1</li>
4748 <li>Incorrect and unstable DNA pairwise alignment</li>
4749 <li>Cut and paste of sequences with annotation</li>
4750 <li>Feature group display state in XML</li>
4751 <li>Feature ordering in XML</li>
4752 <li>blc file iteration selection using filename # suffix</li>
4753 <li>Stockholm alignment properties</li>
4754 <li>Stockhom alignment secondary structure annotation</li>
4755 <li>2.2.1 applet had no feature transparency</li>
4756 <li>Number pad keys can be used in cursor mode</li>
4757 <li>Structure Viewer mirror image resolved</li>
4764 <div align="center">
4765 <strong>2.2.1</strong><br> 12/2/07
4770 <li>Non standard characters can be read and displayed
4771 <li>Annotations/Features can be imported/exported to the
4773 <li>Applet allows editing of sequence/annotation/group
4774 name & description
4775 <li>Preference setting to display sequence name in
4777 <li>Annotation file format extended to allow
4778 Sequence_groups to be defined
4779 <li>Default opening of alignment overview panel can be
4780 specified in preferences
4781 <li>PDB residue numbering annotation added to associated
4787 <li>Applet crash under certain Linux OS with Java 1.6
4789 <li>Annotation file export / import bugs fixed
4790 <li>PNG / EPS image output bugs fixed
4796 <div align="center">
4797 <strong>2.2</strong><br> 27/11/06
4802 <li>Multiple views on alignment
4803 <li>Sequence feature editing
4804 <li>"Reload" alignment
4805 <li>"Save" to current filename
4806 <li>Background dependent text colour
4807 <li>Right align sequence ids
4808 <li>User-defined lower case residue colours
4811 <li>Menu item accelerator keys
4812 <li>Control-V pastes to current alignment
4813 <li>Cancel button for DAS Feature Fetching
4814 <li>PCA and PDB Viewers zoom via mouse roller
4815 <li>User-defined sub-tree colours and sub-tree selection
4817 <li>'New Window' button on the 'Output to Text box'
4822 <li>New memory efficient Undo/Redo System
4823 <li>Optimised symbol lookups and conservation/consensus
4825 <li>Region Conservation/Consensus recalculated after
4827 <li>Fixed Remove Empty Columns Bug (empty columns at end
4829 <li>Slowed DAS Feature Fetching for increased robustness.
4831 <li>Made angle brackets in ASCII feature descriptions
4833 <li>Re-instated Zoom function for PCA
4834 <li>Sequence descriptions conserved in web service
4836 <li>UniProt ID discoverer uses any word separated by
4838 <li>WsDbFetch query/result association resolved
4839 <li>Tree leaf to sequence mapping improved
4840 <li>Smooth fonts switch moved to FontChooser dialog box.
4847 <div align="center">
4848 <strong>2.1.1</strong><br> 12/9/06
4853 <li>Copy consensus sequence to clipboard</li>
4858 <li>Image output - rightmost residues are rendered if
4859 sequence id panel has been resized</li>
4860 <li>Image output - all offscreen group boundaries are
4862 <li>Annotation files with sequence references - all
4863 elements in file are relative to sequence position</li>
4864 <li>Mac Applet users can use Alt key for group editing</li>
4870 <div align="center">
4871 <strong>2.1</strong><br> 22/8/06
4876 <li>MAFFT Multiple Alignment in default Web Service list</li>
4877 <li>DAS Feature fetching</li>
4878 <li>Hide sequences and columns</li>
4879 <li>Export Annotations and Features</li>
4880 <li>GFF file reading / writing</li>
4881 <li>Associate structures with sequences from local PDB
4883 <li>Add sequences to exisiting alignment</li>
4884 <li>Recently opened files / URL lists</li>
4885 <li>Applet can launch the full application</li>
4886 <li>Applet has transparency for features (Java 1.2
4888 <li>Applet has user defined colours parameter</li>
4889 <li>Applet can load sequences from parameter
4890 "sequence<em>x</em>"
4896 <li>Redundancy Panel reinstalled in the Applet</li>
4897 <li>Monospaced font - EPS / rescaling bug fixed</li>
4898 <li>Annotation files with sequence references bug fixed</li>
4904 <div align="center">
4905 <strong>2.08.1</strong><br> 2/5/06
4910 <li>Change case of selected region from Popup menu</li>
4911 <li>Choose to match case when searching</li>
4912 <li>Middle mouse button and mouse movement can compress /
4913 expand the visible width and height of the alignment</li>
4918 <li>Annotation Panel displays complete JNet results</li>
4924 <div align="center">
4925 <strong>2.08b</strong><br> 18/4/06
4931 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4932 <li>Righthand label on wrapped alignments shows correct
4939 <div align="center">
4940 <strong>2.08</strong><br> 10/4/06
4945 <li>Editing can be locked to the selection area</li>
4946 <li>Keyboard editing</li>
4947 <li>Create sequence features from searches</li>
4948 <li>Precalculated annotations can be loaded onto
4950 <li>Features file allows grouping of features</li>
4951 <li>Annotation Colouring scheme added</li>
4952 <li>Smooth fonts off by default - Faster rendering</li>
4953 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4958 <li>Drag & Drop fixed on Linux</li>
4959 <li>Jalview Archive file faster to load/save, sequence
4960 descriptions saved.</li>
4966 <div align="center">
4967 <strong>2.07</strong><br> 12/12/05
4972 <li>PDB Structure Viewer enhanced</li>
4973 <li>Sequence Feature retrieval and display enhanced</li>
4974 <li>Choose to output sequence start-end after sequence
4975 name for file output</li>
4976 <li>Sequence Fetcher WSDBFetch@EBI</li>
4977 <li>Applet can read feature files, PDB files and can be
4978 used for HTML form input</li>
4983 <li>HTML output writes groups and features</li>
4984 <li>Group editing is Control and mouse click</li>
4985 <li>File IO bugs</li>
4991 <div align="center">
4992 <strong>2.06</strong><br> 28/9/05
4997 <li>View annotations in wrapped mode</li>
4998 <li>More options for PCA viewer</li>
5003 <li>GUI bugs resolved</li>
5004 <li>Runs with -nodisplay from command line</li>
5010 <div align="center">
5011 <strong>2.05b</strong><br> 15/9/05
5016 <li>Choose EPS export as lineart or text</li>
5017 <li>Jar files are executable</li>
5018 <li>Can read in Uracil - maps to unknown residue</li>
5023 <li>Known OutOfMemory errors give warning message</li>
5024 <li>Overview window calculated more efficiently</li>
5025 <li>Several GUI bugs resolved</li>
5031 <div align="center">
5032 <strong>2.05</strong><br> 30/8/05
5037 <li>Edit and annotate in "Wrapped" view</li>
5042 <li>Several GUI bugs resolved</li>
5048 <div align="center">
5049 <strong>2.04</strong><br> 24/8/05
5054 <li>Hold down mouse wheel & scroll to change font
5060 <li>Improved JPred client reliability</li>
5061 <li>Improved loading of Jalview files</li>
5067 <div align="center">
5068 <strong>2.03</strong><br> 18/8/05
5073 <li>Set Proxy server name and port in preferences</li>
5074 <li>Multiple URL links from sequence ids</li>
5075 <li>User Defined Colours can have a scheme name and added
5077 <li>Choose to ignore gaps in consensus calculation</li>
5078 <li>Unix users can set default web browser</li>
5079 <li>Runs without GUI for batch processing</li>
5080 <li>Dynamically generated Web Service Menus</li>
5085 <li>InstallAnywhere download for Sparc Solaris</li>
5091 <div align="center">
5092 <strong>2.02</strong><br> 18/7/05
5098 <li>Copy & Paste order of sequences maintains
5099 alignment order.</li>
5105 <div align="center">
5106 <strong>2.01</strong><br> 12/7/05
5111 <li>Use delete key for deleting selection.</li>
5112 <li>Use Mouse wheel to scroll sequences.</li>
5113 <li>Help file updated to describe how to add alignment
5115 <li>Version and build date written to build properties
5117 <li>InstallAnywhere installation will check for updates
5118 at launch of Jalview.</li>
5123 <li>Delete gaps bug fixed.</li>
5124 <li>FileChooser sorts columns.</li>
5125 <li>Can remove groups one by one.</li>
5126 <li>Filechooser icons installed.</li>
5127 <li>Finder ignores return character when searching.
5128 Return key will initiate a search.<br>
5135 <div align="center">
5136 <strong>2.0</strong><br> 20/6/05
5141 <li>New codebase</li>