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><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>29/09/2021</em></strong></td>
63 <td align="left" valign="top">
69 <li>Updated building instructions</li>
74 <!-- JAL-3840 -->Occupancy calculation is incorrect for
75 alignment columns with over -1+2^32 gaps (breaking filtering
79 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
80 scale factors being set with buggy window-managers (linux
83 </ul> <em>Development</em>
85 <li>Fixed non-fatal gradle errors during build</li>
90 <td width="60" align="center" nowrap><strong><a
91 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
92 <em>09/03/2021</em></strong></td>
93 <td align="left" valign="top"><em>Improved control of
94 Jalview's use of network services via jalview_properties</em>
97 <!-- JAL-3814 -->New .jalview_properties token controlling
98 launch of the news browser (like -nonews argument)
101 <!-- JAL-3813 -->New .jalview_properties token controlling
102 download of linkout URLs from
103 www.jalview.org/services/identifiers
106 <!-- JAL-3812 -->New .jalview_properties token controlling
107 download of BIOJSHTML templates
110 <!-- JAL-3811 -->New 'Discover Web Services' option to
111 trigger a one off JABAWS discovery if autodiscovery was
115 <td align="left" valign="top">
118 <!-- JAL-3818 -->Intermittent deadlock opening structure in
121 </ul> <em>New Known defects</em>
124 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
125 always restored from project (since 2.10.3)
128 <!-- JAL-3806 -->Selections from tree built from CDS aren't
129 propagated to Protein alignment (since 2.11.1.3)
135 <td width="60" align="center" nowrap><strong><a
136 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
137 <em>29/10/2020</em></strong></td>
138 <td align="left" valign="top">
143 <td align="left" valign="top">
146 <!-- JAL-3765 -->Find doesn't always highlight all matching
147 positions in a sequence (bug introduced in 2.11.1.2)
150 <!-- JAL-3760 -->Alignments containing one or more protein
151 sequences can be classed as nucleotide
154 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
155 sequences after alignment of protein products (known defect
156 first reported for 2.11.1.0)
159 <!-- JAL-3725 -->No tooltip or popup menu for genomic
160 features outwith CDS shown overlaid on protein
163 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
164 correctly mapped by Jalview (e.g. affects viral CDS with
165 ribosomal slippage, since 2.9.0)
168 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
172 <!-- JAL-3700 -->Selections in CDS sequence panel don't
173 always select corresponding protein sequences
176 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
177 column selection doesn't always ignore hidden columns
179 </ul> <em>Installer</em>
182 <!-- JAL-3611 -->Space character in Jalview install path on
183 Windows prevents install4j launching getdown
185 </ul> <em>Development</em>
188 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
189 version numbers in doc/building.md
195 <td width="60" align="center" nowrap><strong><a
196 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
197 <em>25/09/2020</em></strong></td>
198 <td align="left" valign="top">
202 <td align="left" valign="top">
205 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
206 "Encountered problems opening
207 https://www.jalview.org/examples/exampleFile_2_7.jvp"
213 <td width="60" align="center" nowrap><strong><a
214 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
215 <em>17/09/2020</em></strong></td>
216 <td align="left" valign="top">
219 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
220 residue in cursor mode
223 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
224 HTSJDK from 2.12 to 2.23
227 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
228 optimisations and improvements suggested by Bob Hanson and
229 improved compatibility with JalviewJS
232 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
233 alignments from Pfam and Rfam
236 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
237 import (no longer based on .gz extension)
240 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
243 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
244 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
248 <!-- JAL-3667 -->Improved warning messages, debug logging
249 and fixed Retry action when Jalview encounters errors when
250 saving or making backup files.
253 <!-- JAL-3676 -->Enhanced Jalview Java Console:
255 <li>Jalview's logging level can be configured</li>
256 <li>Copy to Clipboard Buttion</li>
260 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
261 when running on Linux (Requires Java 11+)
263 </ul> <em>Launching Jalview</em>
266 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
267 through a system property
270 <!-- JAL-3477 -->Improved built-in documentation and command
271 line help for configuring Jalview's memory
275 <td align="left" valign="top">
278 <!-- JAL-3691 -->Conservation and Quality tracks are shown
279 but not calculated and no protein or DNA score models are
280 available for tree/PCA calculation when launched with
281 Turkish language locale
284 <!-- JAL-3493 -->Escape does not clear highlights on the
285 alignment (Since Jalview 2.10.3)
288 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
289 doesn't slide selected sequences, just sequence under cursor
292 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
293 sequence under the cursor
296 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
297 multiple EMBL gene products shown for a single contig
300 <!-- JAL-3696 -->Errors encountered when processing variants
301 from VCF files yield "Error processing VCF: Format specifier
305 <!-- JAL-3697 -->Count of features not shown can be wrong
306 when there are both local and complementary features mapped
307 to the position under the cursor
310 <!-- JAL-3673 -->Sequence ID for reference sequence is
311 clipped when Right align Sequence IDs enabled
314 <!-- JAL-2983 -->Slider with negative range values not
315 rendered correctly in VAqua4 (Since 2.10.4)
318 <!-- JAL-3685 -->Single quotes not displayed correctly in
319 internationalised text for some messages and log output
322 <!-- JAL-3490 -->Find doesn't report matches that span
323 hidden gapped columns
326 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
327 panels, Alignment viewport and annotation renderer.
330 <!-- JAL-3561 -->Jalview ignores file format parameter
331 specifying output format when exporting an alignment via the
335 <!-- JAL-3667 -->Windows 10: For a minority of users, if
336 backups are not enabled, Jalview sometimes fails to
337 overwrite an existing file and raises a warning dialog. (in
338 2.11.0, and 2.11.1.0, the workaround is to try to save the
339 file again, and if that fails, delete the original file and
343 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
347 <!-- JAL-3741 -->References to http://www.jalview.org in
348 program and documentation
350 </ul> <em>Launching Jalview</em>
353 <!-- JAL-3718 -->Jalview application fails when launched the
354 first time for a version that has different jars to the
355 previous launched version.
357 </ul> <em>Developing Jalview</em>
360 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
361 data, causing cloverReport gradle task to fail with an
365 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
366 monitor the release channel
368 </ul> <em>New Known defects</em>
371 <!-- JAL-3748 -->CDS shown in result of submitting proteins
372 in a CDS/Protein alignment to a web service is wrong when
373 proteins share a common transcript sequence (e.g.
374 genome of RNA viruses)
377 <!-- JAL-3576 -->Co-located features exported and re-imported
378 are ordered differently when shown on alignment and in
379 tooltips. (Also affects v2.11.1.0)
382 <!-- JAL-3702 -->Drag and drop of alignment file onto
383 alignment window when in a HiDPI scaled mode in Linux only
384 works for the top left quadrant of the alignment window
387 <!-- JAL-3701 -->Stale build data in jalview standalone jar
388 builds (only affects 2.11.1.1 branch)
391 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
392 when alignment view restored from project (since Jalview 2.11.0)
395 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
396 protein products for certain ENA records are repeatedly
397 shown via Calculate->Show Cross Refs
403 <td width="60" align="center" nowrap><strong><a
404 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
405 <em>22/04/2020</em></strong></td>
406 <td align="left" valign="top">
409 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
410 'virtual' codon features shown on protein (or vice versa)
411 for display in alignments, on structure views (including
412 transfer to UCSF chimera), in feature reports and for
416 <!-- JAL-3121 -->Feature attributes from VCF files can be
417 exported and re-imported as GFF3 files
420 <!-- JAL-3376 -->Capture VCF "fixed column" values
421 POS, ID, QUAL, FILTER as Feature Attributes
424 <!-- JAL-3375 -->More robust VCF numeric data field
425 validation while parsing
428 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
432 <!-- JAL-3535 -->Feature Settings dialog title includes name
436 <!-- JAL-3538 -->Font anti-aliasing in alignment views
440 <!-- JAL-3468 -->Very long feature descriptions truncated in
444 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
445 with no feature types visible
448 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
450 </ul><em>Jalview Installer</em>
453 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
454 in console (may be null when Jalview launched as executable jar or via conda)
457 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
460 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
463 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
465 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
466 </ul> <em>Release processes</em>
469 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
472 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
474 </ul> <em>Build System</em>
477 <!-- JAL-3510 -->Clover updated to 4.4.1
480 <!-- JAL-3513 -->Test code included in Clover coverage
484 <em>Groovy Scripts</em>
487 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
488 to stdout containing the consensus sequence for each
489 alignment in a Jalview session
492 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
493 genomic sequence_variant annotation from CDS as
494 missense_variant or synonymous_variant on protein products.
498 <td align="left" valign="top">
501 <!-- JAL-3581 -->Hidden sequence markers still visible when
502 'Show hidden markers' option is not ticked
505 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
506 PNG output when 'Automatically set ID width' is set in
507 jalview preferences or properties file
510 <!-- JAL-3571 -->Feature Editor dialog can be opened when
511 'Show Sequence Features' option is not ticked
514 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
515 buttons in Feature Settings dialog are clicked when no
519 <!-- JAL-3412 -->ID margins for CDS and Protein views not
520 equal when split frame is first opened
523 <!-- JAL-3296 -->Sequence position numbers in status bar not
524 correct after editing a sequence's start position
527 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
528 with annotation and exceptions thrown when only a few
529 columns shown in wrapped mode
532 <!-- JAL-3386 -->Sequence IDs missing in headless export of
533 wrapped alignment figure with annotations
536 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
537 ID fails with ClassCastException
540 <!-- JAL-3389 -->Chimera session not restored from Jalview
544 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
545 feature settings dialog also selects columns
548 <!-- JAL-3473 -->SpinnerNumberModel causes
549 IllegalArgumentException in some circumstances
552 <!-- JAL-3534 -->Multiple feature settings dialogs can be
556 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
557 alignment window is closed
560 <!-- JAL-3406 -->Credits missing some authors in Jalview
561 help documentation for 2.11.0 release
564 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
565 includes Pfam ID as sequence's accession rather than its
568 </ul> <em>Java 11 Compatibility issues</em>
571 <!-- JAL-2987 -->OSX - Can't view some search results in
572 PDB/Uniprot search panel
574 </ul> <em>Installer</em>
577 <!-- JAL-3447 -->Jalview should not create file associations
578 for 3D structure files (.pdb, .mmcif. .cif)
580 </ul> <em>Repository and Source Release</em>
583 <!-- JAL-3474 -->removed obsolete .cvsignore files from
587 <!-- JAL-3541 -->Clover report generation running out of
590 </ul> <em>New Known Issues</em>
593 <!-- JAL-3523 -->OSX - Current working directory not
594 preserved when Jalview.app launched with parameters from
598 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
599 clipped in headless figure export when Right Align option
603 <!-- JAL-3542 -->Jalview Installation type always reports
604 'Source' in console output
607 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
608 bamboo server but run fine locally.
614 <td width="60" align="center" nowrap>
615 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
616 <em>04/07/2019</em></strong>
618 <td align="left" valign="top">
621 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
622 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
623 source project) rather than InstallAnywhere
626 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
627 settings, receive over the air updates and launch specific
628 versions via (<a href="https://github.com/threerings/getdown">Three
632 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
633 formats supported by Jalview (including .jvp project files)
636 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
637 arguments and switch between different getdown channels
640 <!-- JAL-3141 -->Backup files created when saving Jalview project
645 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
646 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
648 <!-- JAL-2620 -->Alternative genetic code tables for
649 'Translate as cDNA'</li>
651 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
652 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
655 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
656 implementation that allows updates) used for Sequence Feature collections</li>
658 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
659 features can be filtered and shaded according to any
660 associated attributes (e.g. variant attributes from VCF
661 file, or key-value pairs imported from column 9 of GFF
665 <!-- JAL-2879 -->Feature Attributes and shading schemes
666 stored and restored from Jalview Projects
669 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
670 recognise variant features
673 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
674 sequences (also coloured red by default)
677 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
681 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
682 algorithm (Z-sort/transparency and filter aware)
685 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
691 <!-- JAL-3205 -->Symmetric score matrices for faster
692 tree and PCA calculations
694 <li><strong>Principal Components Analysis Viewer</strong>
697 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
698 and Viewer state saved in Jalview Project
700 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
703 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
707 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
712 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
714 <li><strong>Speed and Efficiency</strong>
717 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
718 multiple groups when working with large alignments
721 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
725 <li><strong>User Interface</strong>
728 <!-- JAL-2933 -->Finder panel remembers last position in each
732 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
733 what is shown)<br />Only visible regions of alignment are shown by
734 default (can be changed in user preferences)
737 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
738 to the Overwrite Dialog
741 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
745 <!-- JAL-1244 -->Status bar shows bounds when dragging a
746 selection region, and gap count when inserting or deleting gaps
749 <!-- JAL-3132 -->Status bar updates over sequence and annotation
753 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
757 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
761 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
764 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
768 <!-- JAL-3181 -->Consistent ordering of links in sequence id
772 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
774 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
778 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
779 <li><strong>Java 11 Support (not yet on general release)</strong>
782 <!-- -->OSX GUI integrations for App menu's 'About' entry and
787 <em>Deprecations</em>
789 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
790 capabilities removed from the Jalview Desktop
792 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
793 unmarshalling has been replaced by JAXB for Jalview projects
794 and XML based data retrieval clients</li>
795 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
796 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
797 </ul> <em>Documentation</em>
799 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
800 not supported in EPS figure export
802 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
803 </ul> <em>Development and Release Processes</em>
806 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
809 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
811 <!-- JAL-3225 -->Eclipse project configuration managed with
815 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
816 Bamboo continuous integration for unattended Test Suite
820 <!-- JAL-2864 -->Memory test suite to detect leaks in common
824 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
828 <!-- JAL-3248 -->Developer documentation migrated to
829 markdown (with HTML rendering)
832 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
835 <!-- JAL-3289 -->New URLs for publishing development
840 <td align="left" valign="top">
843 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
846 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
847 superposition in Jmol fail on Windows
850 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
851 structures for sequences with lots of PDB structures
854 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
858 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
859 project involving multiple views
862 <!-- JAL-3164 -->Overview for complementary view in a linked
863 CDS/Protein alignment is not updated when Hide Columns by
864 Annotation dialog hides columns
867 <!-- JAL-3158 -->Selection highlighting in the complement of a
868 CDS/Protein alignment stops working after making a selection in
869 one view, then making another selection in the other view
872 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
876 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
877 Settings and Jalview Preferences panels
880 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
881 overview with large alignments
884 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
885 region if columns were selected by dragging right-to-left and the
886 mouse moved to the left of the first column
889 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
890 hidden column marker via scale popup menu
893 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
894 doesn't tell users the invalid URL
897 <!-- JAL-2816 -->Tooltips displayed for features filtered by
901 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
902 show cross references or Fetch Database References are shown in
906 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
907 peptide sequence (computed variant shown as p.Res.null)
910 <!-- JAL-2060 -->'Graduated colour' option not offered for
911 manually created features (where feature score is Float.NaN)
914 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
915 when columns are hidden
918 <!-- JAL-3082 -->Regular expression error for '(' in Select
919 Columns by Annotation description
922 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
923 out of Scale or Annotation Panel
926 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
930 <!-- JAL-3074 -->Left/right drag in annotation can scroll
934 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
938 <!-- JAL-3002 -->Column display is out by one after Page Down,
939 Page Up in wrapped mode
942 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
945 <!-- JAL-2932 -->Finder searches in minimised alignments
948 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
949 on opening an alignment
952 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
956 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
957 different groups in the alignment are selected
960 <!-- JAL-2717 -->Internationalised colour scheme names not shown
964 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
968 <!-- JAL-3125 -->Value input for graduated feature colour
969 threshold gets 'unrounded'
972 <!-- JAL-2982 -->PCA image export doesn't respect background
976 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
979 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
982 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
986 <!-- JAL-2964 -->Associate Tree with All Views not restored from
990 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
991 shown in complementary view
994 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
995 without normalisation
998 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1002 <!-- JAL-914 -->Help page can be opened twice
1005 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1007 </ul> <em>Editing</em>
1010 <!-- JAL-2822 -->Start and End should be updated when sequence
1011 data at beginning or end of alignment added/removed via 'Edit'
1015 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1016 relocate sequence features correctly when start of sequence is
1017 removed (Known defect since 2.10)
1020 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1021 dialog corrupts dataset sequence
1024 <!-- JAL-868 -->Structure colours not updated when associated tree
1025 repartitions the alignment view (Regression in 2.10.5)
1027 </ul> <em>Datamodel</em>
1030 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1031 sequence's End is greater than its length
1033 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1034 general release)</em>
1037 <!-- JAL-3288 -->Menus work properly in split-screen
1039 </ul> <em>New Known Defects</em>
1042 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1045 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1046 regions of protein alignment.
1049 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1050 is restored from a Jalview 2.11 project
1053 <!-- JAL-3213 -->Alignment panel height can be too small after
1057 <!-- JAL-3240 -->Display is incorrect after removing gapped
1058 columns within hidden columns
1061 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1062 window after dragging left to select columns to left of visible
1066 <!-- JAL-2876 -->Features coloured according to their description
1067 string and thresholded by score in earlier versions of Jalview are
1068 not shown as thresholded features in 2.11. To workaround please
1069 create a Score filter instead.
1072 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1074 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1077 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1078 alignments with multiple views can close views unexpectedly
1081 <em>Java 11 Specific defects</em>
1084 <!-- JAL-3235 -->Jalview Properties file is not sorted
1085 alphabetically when saved
1091 <td width="60" nowrap>
1092 <div align="center">
1093 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1096 <td><div align="left">
1100 <!-- JAL-3101 -->Default memory for Jalview webstart and
1101 InstallAnywhere increased to 1G.
1104 <!-- JAL-247 -->Hidden sequence markers and representative
1105 sequence bolding included when exporting alignment as EPS,
1106 SVG, PNG or HTML. <em>Display is configured via the
1107 Format menu, or for command-line use via a Jalview
1108 properties file.</em>
1111 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1112 API and sequence data now imported as JSON.
1115 <!-- JAL-3065 -->Change in recommended way of starting
1116 Jalview via a Java command line: add jars in lib directory
1117 to CLASSPATH, rather than via the deprecated java.ext.dirs
1121 <em>Development</em>
1124 <!-- JAL-3047 -->Support added to execute test suite
1125 instrumented with <a href="http://openclover.org/">Open
1130 <td><div align="left">
1134 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1135 row shown in Feredoxin Structure alignment view of example
1139 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1140 annotation displayed.
1143 <!-- JAL-3107 -->Group conservation/consensus not shown
1144 for newly created group when 'Apply to all groups'
1148 <!-- JAL-3087 -->Corrupted display when switching to
1149 wrapped mode when sequence panel's vertical scrollbar is
1153 <!-- JAL-3003 -->Alignment is black in exported EPS file
1154 when sequences are selected in exported view.</em>
1157 <!-- JAL-3059 -->Groups with different coloured borders
1158 aren't rendered with correct colour.
1161 <!-- JAL-3092 -->Jalview could hang when importing certain
1162 types of knotted RNA secondary structure.
1165 <!-- JAL-3095 -->Sequence highlight and selection in
1166 trimmed VARNA 2D structure is incorrect for sequences that
1170 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1171 annotation when columns are inserted into an alignment,
1172 and when exporting as Stockholm flatfile.
1175 <!-- JAL-3053 -->Jalview annotation rows containing upper
1176 and lower-case 'E' and 'H' do not automatically get
1177 treated as RNA secondary structure.
1180 <!-- JAL-3106 -->.jvp should be used as default extension
1181 (not .jar) when saving a Jalview project file.
1184 <!-- JAL-3105 -->Mac Users: closing a window correctly
1185 transfers focus to previous window on OSX
1188 <em>Java 10 Issues Resolved</em>
1191 <!-- JAL-2988 -->OSX - Can't save new files via the File
1192 or export menus by typing in a name into the Save dialog
1196 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1197 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1198 'look and feel' which has improved compatibility with the
1199 latest version of OSX.
1206 <td width="60" nowrap>
1207 <div align="center">
1208 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1209 <em>7/06/2018</em></strong>
1212 <td><div align="left">
1216 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1217 annotation retrieved from Uniprot
1220 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1221 onto the Jalview Desktop
1225 <td><div align="left">
1229 <!-- JAL-3017 -->Cannot import features with multiple
1230 variant elements (blocks import of some Uniprot records)
1233 <!-- JAL-2997 -->Clustal files with sequence positions in
1234 right-hand column parsed correctly
1237 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1238 not alignment area in exported graphic
1241 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1242 window has input focus
1245 <!-- JAL-2992 -->Annotation panel set too high when
1246 annotation added to view (Windows)
1249 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1250 network connectivity is poor
1253 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1254 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1255 the currently open URL and links from a page viewed in
1256 Firefox or Chrome on Windows is now fully supported. If
1257 you are using Edge, only links in the page can be
1258 dragged, and with Internet Explorer, only the currently
1259 open URL in the browser can be dropped onto Jalview.</em>
1262 <em>New Known Defects</em>
1264 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1269 <td width="60" nowrap>
1270 <div align="center">
1271 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1274 <td><div align="left">
1278 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1279 for disabling automatic superposition of multiple
1280 structures and open structures in existing views
1283 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1284 ID and annotation area margins can be click-dragged to
1288 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1292 <!-- JAL-2759 -->Improved performance for large alignments
1293 and lots of hidden columns
1296 <!-- JAL-2593 -->Improved performance when rendering lots
1297 of features (particularly when transparency is disabled)
1300 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1301 exchange of Jalview features and Chimera attributes made
1307 <td><div align="left">
1310 <!-- JAL-2899 -->Structure and Overview aren't updated
1311 when Colour By Annotation threshold slider is adjusted
1314 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1315 overlapping alignment panel
1318 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1322 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1323 improved: CDS not handled correctly if transcript has no
1327 <!-- JAL-2321 -->Secondary structure and temperature
1328 factor annotation not added to sequence when local PDB
1329 file associated with it by drag'n'drop or structure
1333 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1334 dialog doesn't import PDB files dropped on an alignment
1337 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1338 scroll bar doesn't work for some CDS/Protein views
1341 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1342 Java 1.8u153 onwards and Java 1.9u4+.
1345 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1346 columns in annotation row
1349 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1350 honored in batch mode
1353 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1354 for structures added to existing Jmol view
1357 <!-- JAL-2223 -->'View Mappings' includes duplicate
1358 entries after importing project with multiple views
1361 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1362 protein sequences via SIFTS from associated PDB entries
1363 with negative residue numbers or missing residues fails
1366 <!-- JAL-2952 -->Exception when shading sequence with negative
1367 Temperature Factor values from annotated PDB files (e.g.
1368 as generated by CONSURF)
1371 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1372 tooltip doesn't include a text description of mutation
1375 <!-- JAL-2922 -->Invert displayed features very slow when
1376 structure and/or overview windows are also shown
1379 <!-- JAL-2954 -->Selecting columns from highlighted regions
1380 very slow for alignments with large numbers of sequences
1383 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1384 with 'StringIndexOutOfBounds'
1387 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1388 platforms running Java 10
1391 <!-- JAL-2960 -->Adding a structure to existing structure
1392 view appears to do nothing because the view is hidden behind the alignment view
1398 <!-- JAL-2926 -->Copy consensus sequence option in applet
1399 should copy the group consensus when popup is opened on it
1405 <!-- JAL-2913 -->Fixed ID width preference is not respected
1408 <em>New Known Defects</em>
1411 <!-- JAL-2973 --> Exceptions occasionally raised when
1412 editing a large alignment and overview is displayed
1415 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1416 repeatedly after a series of edits even when the overview
1417 is no longer reflecting updates
1420 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1421 structures for protein subsequence (if 'Trim Retrieved
1422 Sequences' enabled) or Ensembl isoforms (Workaround in
1423 2.10.4 is to fail back to N&W mapping)
1426 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1427 option gives blank output
1434 <td width="60" nowrap>
1435 <div align="center">
1436 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1439 <td><div align="left">
1440 <ul><li>Updated Certum Codesigning Certificate
1441 (Valid till 30th November 2018)</li></ul></div></td>
1442 <td><div align="left">
1443 <em>Desktop</em><ul>
1445 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1446 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1447 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1448 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1449 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1450 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1451 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1457 <td width="60" nowrap>
1458 <div align="center">
1459 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1462 <td><div align="left">
1466 <!-- JAL-2446 -->Faster and more efficient management and
1467 rendering of sequence features
1470 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1471 429 rate limit request hander
1474 <!-- JAL-2773 -->Structure views don't get updated unless
1475 their colours have changed
1478 <!-- JAL-2495 -->All linked sequences are highlighted for
1479 a structure mousover (Jmol) or selection (Chimera)
1482 <!-- JAL-2790 -->'Cancel' button in progress bar for
1483 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1486 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1487 view from Ensembl locus cross-references
1490 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1494 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1495 feature can be disabled
1498 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1499 PDB easier retrieval of sequences for lists of IDs
1502 <!-- JAL-2758 -->Short names for sequences retrieved from
1508 <li>Groovy interpreter updated to 2.4.12</li>
1509 <li>Example groovy script for generating a matrix of
1510 percent identity scores for current alignment.</li>
1512 <em>Testing and Deployment</em>
1515 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1519 <td><div align="left">
1523 <!-- JAL-2643 -->Pressing tab after updating the colour
1524 threshold text field doesn't trigger an update to the
1528 <!-- JAL-2682 -->Race condition when parsing sequence ID
1532 <!-- JAL-2608 -->Overview windows are also closed when
1533 alignment window is closed
1536 <!-- JAL-2548 -->Export of features doesn't always respect
1540 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1541 takes a long time in Cursor mode
1547 <!-- JAL-2777 -->Structures with whitespace chainCode
1548 cannot be viewed in Chimera
1551 <!-- JAL-2728 -->Protein annotation panel too high in
1555 <!-- JAL-2757 -->Can't edit the query after the server
1556 error warning icon is shown in Uniprot and PDB Free Text
1560 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1563 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1566 <!-- JAL-2739 -->Hidden column marker in last column not
1567 rendered when switching back from Wrapped to normal view
1570 <!-- JAL-2768 -->Annotation display corrupted when
1571 scrolling right in unwapped alignment view
1574 <!-- JAL-2542 -->Existing features on subsequence
1575 incorrectly relocated when full sequence retrieved from
1579 <!-- JAL-2733 -->Last reported memory still shown when
1580 Desktop->Show Memory is unticked (OSX only)
1583 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1584 features of same type and group to be selected for
1588 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1589 alignments when hidden columns are present
1592 <!-- JAL-2392 -->Jalview freezes when loading and
1593 displaying several structures
1596 <!-- JAL-2732 -->Black outlines left after resizing or
1600 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1601 within the Jalview desktop on OSX
1604 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1605 when in wrapped alignment mode
1608 <!-- JAL-2636 -->Scale mark not shown when close to right
1609 hand end of alignment
1612 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1613 each selected sequence do not have correct start/end
1617 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1618 after canceling the Alignment Window's Font dialog
1621 <!-- JAL-2036 -->Show cross-references not enabled after
1622 restoring project until a new view is created
1625 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1626 URL links appears when only default EMBL-EBI link is
1627 configured (since 2.10.2b2)
1630 <!-- JAL-2775 -->Overview redraws whole window when box
1631 position is adjusted
1634 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1635 in a multi-chain structure when viewing alignment
1636 involving more than one chain (since 2.10)
1639 <!-- JAL-2811 -->Double residue highlights in cursor mode
1640 if new selection moves alignment window
1643 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1644 arrow key in cursor mode to pass hidden column marker
1647 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1648 that produces correctly annotated transcripts and products
1651 <!-- JAL-2776 -->Toggling a feature group after first time
1652 doesn't update associated structure view
1655 <em>Applet</em><br />
1658 <!-- JAL-2687 -->Concurrent modification exception when
1659 closing alignment panel
1662 <em>BioJSON</em><br />
1665 <!-- JAL-2546 -->BioJSON export does not preserve
1666 non-positional features
1669 <em>New Known Issues</em>
1672 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1673 sequence features correctly (for many previous versions of
1677 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1678 using cursor in wrapped panel other than top
1681 <!-- JAL-2791 -->Select columns containing feature ignores
1682 graduated colour threshold
1685 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1686 always preserve numbering and sequence features
1689 <em>Known Java 9 Issues</em>
1692 <!-- JAL-2902 -->Groovy Console very slow to open and is
1693 not responsive when entering characters (Webstart, Java
1700 <td width="60" nowrap>
1701 <div align="center">
1702 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1703 <em>2/10/2017</em></strong>
1706 <td><div align="left">
1707 <em>New features in Jalview Desktop</em>
1710 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1712 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1716 <td><div align="left">
1720 <td width="60" nowrap>
1721 <div align="center">
1722 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1723 <em>7/9/2017</em></strong>
1726 <td><div align="left">
1730 <!-- JAL-2588 -->Show gaps in overview window by colouring
1731 in grey (sequences used to be coloured grey, and gaps were
1735 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1739 <!-- JAL-2587 -->Overview updates immediately on increase
1740 in size and progress bar shown as higher resolution
1741 overview is recalculated
1746 <td><div align="left">
1750 <!-- JAL-2664 -->Overview window redraws every hidden
1751 column region row by row
1754 <!-- JAL-2681 -->duplicate protein sequences shown after
1755 retrieving Ensembl crossrefs for sequences from Uniprot
1758 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1759 format setting is unticked
1762 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1763 if group has show boxes format setting unticked
1766 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1767 autoscrolling whilst dragging current selection group to
1768 include sequences and columns not currently displayed
1771 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1772 assemblies are imported via CIF file
1775 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1776 displayed when threshold or conservation colouring is also
1780 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1784 <!-- JAL-2673 -->Jalview continues to scroll after
1785 dragging a selected region off the visible region of the
1789 <!-- JAL-2724 -->Cannot apply annotation based
1790 colourscheme to all groups in a view
1793 <!-- JAL-2511 -->IDs don't line up with sequences
1794 initially after font size change using the Font chooser or
1801 <td width="60" nowrap>
1802 <div align="center">
1803 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1806 <td><div align="left">
1807 <em>Calculations</em>
1811 <!-- JAL-1933 -->Occupancy annotation row shows number of
1812 ungapped positions in each column of the alignment.
1815 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1816 a calculation dialog box
1819 <!-- JAL-2379 -->Revised implementation of PCA for speed
1820 and memory efficiency (~30x faster)
1823 <!-- JAL-2403 -->Revised implementation of sequence
1824 similarity scores as used by Tree, PCA, Shading Consensus
1825 and other calculations
1828 <!-- JAL-2416 -->Score matrices are stored as resource
1829 files within the Jalview codebase
1832 <!-- JAL-2500 -->Trees computed on Sequence Feature
1833 Similarity may have different topology due to increased
1840 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1841 model for alignments and groups
1844 <!-- JAL-384 -->Custom shading schemes created via groovy
1851 <!-- JAL-2526 -->Efficiency improvements for interacting
1852 with alignment and overview windows
1855 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1859 <!-- JAL-2388 -->Hidden columns and sequences can be
1863 <!-- JAL-2611 -->Click-drag in visible area allows fine
1864 adjustment of visible position
1868 <em>Data import/export</em>
1871 <!-- JAL-2535 -->Posterior probability annotation from
1872 Stockholm files imported as sequence associated annotation
1875 <!-- JAL-2507 -->More robust per-sequence positional
1876 annotation input/output via stockholm flatfile
1879 <!-- JAL-2533 -->Sequence names don't include file
1880 extension when importing structure files without embedded
1881 names or PDB accessions
1884 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1885 format sequence substitution matrices
1888 <em>User Interface</em>
1891 <!-- JAL-2447 --> Experimental Features Checkbox in
1892 Desktop's Tools menu to hide or show untested features in
1896 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1897 via Overview or sequence motif search operations
1900 <!-- JAL-2547 -->Amend sequence features dialog box can be
1901 opened by double clicking gaps within sequence feature
1905 <!-- JAL-1476 -->Status bar message shown when not enough
1906 aligned positions were available to create a 3D structure
1910 <em>3D Structure</em>
1913 <!-- JAL-2430 -->Hidden regions in alignment views are not
1914 coloured in linked structure views
1917 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1918 file-based command exchange
1921 <!-- JAL-2375 -->Structure chooser automatically shows
1922 Cached Structures rather than querying the PDBe if
1923 structures are already available for sequences
1926 <!-- JAL-2520 -->Structures imported via URL are cached in
1927 the Jalview project rather than downloaded again when the
1928 project is reopened.
1931 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1932 to transfer Chimera's structure attributes as Jalview
1933 features, and vice-versa (<strong>Experimental
1937 <em>Web Services</em>
1940 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1943 <!-- JAL-2335 -->Filter non-standard amino acids and
1944 nucleotides when submitting to AACon and other MSA
1948 <!-- JAL-2316, -->URLs for viewing database
1949 cross-references provided by identifiers.org and the
1950 EMBL-EBI's MIRIAM DB
1957 <!-- JAL-2344 -->FileFormatI interface for describing and
1958 identifying file formats (instead of String constants)
1961 <!-- JAL-2228 -->FeatureCounter script refactored for
1962 efficiency when counting all displayed features (not
1963 backwards compatible with 2.10.1)
1966 <em>Example files</em>
1969 <!-- JAL-2631 -->Graduated feature colour style example
1970 included in the example feature file
1973 <em>Documentation</em>
1976 <!-- JAL-2339 -->Release notes reformatted for readability
1977 with the built-in Java help viewer
1980 <!-- JAL-1644 -->Find documentation updated with 'search
1981 sequence description' option
1987 <!-- JAL-2485, -->External service integration tests for
1988 Uniprot REST Free Text Search Client
1991 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1994 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1999 <td><div align="left">
2000 <em>Calculations</em>
2003 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2004 matrix - C->R should be '-3'<br />Old matrix restored
2005 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2007 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2008 Jalview's treatment of gaps in PCA and substitution matrix
2009 based Tree calculations.<br /> <br />In earlier versions
2010 of Jalview, gaps matching gaps were penalised, and gaps
2011 matching non-gaps penalised even more. In the PCA
2012 calculation, gaps were actually treated as non-gaps - so
2013 different costs were applied, which meant Jalview's PCAs
2014 were different to those produced by SeqSpace.<br />Jalview
2015 now treats gaps in the same way as SeqSpace (ie it scores
2016 them as 0). <br /> <br />Enter the following in the
2017 Groovy console to restore pre-2.10.2 behaviour:<br />
2018 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2019 // for 2.10.1 mode <br />
2020 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2021 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2022 these settings will affect all subsequent tree and PCA
2023 calculations (not recommended)</em></li>
2025 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2026 scaling of branch lengths for trees computed using
2027 Sequence Feature Similarity.
2030 <!-- JAL-2377 -->PCA calculation could hang when
2031 generating output report when working with highly
2032 redundant alignments
2035 <!-- JAL-2544 --> Sort by features includes features to
2036 right of selected region when gaps present on right-hand
2040 <em>User Interface</em>
2043 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2044 doesn't reselect a specific sequence's associated
2045 annotation after it was used for colouring a view
2048 <!-- JAL-2419 -->Current selection lost if popup menu
2049 opened on a region of alignment without groups
2052 <!-- JAL-2374 -->Popup menu not always shown for regions
2053 of an alignment with overlapping groups
2056 <!-- JAL-2310 -->Finder double counts if both a sequence's
2057 name and description match
2060 <!-- JAL-2370 -->Hiding column selection containing two
2061 hidden regions results in incorrect hidden regions
2064 <!-- JAL-2386 -->'Apply to all groups' setting when
2065 changing colour does not apply Conservation slider value
2069 <!-- JAL-2373 -->Percentage identity and conservation menu
2070 items do not show a tick or allow shading to be disabled
2073 <!-- JAL-2385 -->Conservation shading or PID threshold
2074 lost when base colourscheme changed if slider not visible
2077 <!-- JAL-2547 -->Sequence features shown in tooltip for
2078 gaps before start of features
2081 <!-- JAL-2623 -->Graduated feature colour threshold not
2082 restored to UI when feature colour is edited
2085 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2086 a time when scrolling vertically in wrapped mode.
2089 <!-- JAL-2630 -->Structure and alignment overview update
2090 as graduate feature colour settings are modified via the
2094 <!-- JAL-2034 -->Overview window doesn't always update
2095 when a group defined on the alignment is resized
2098 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2099 wrapped view result in positional status updates
2103 <!-- JAL-2563 -->Status bar doesn't show position for
2104 ambiguous amino acid and nucleotide symbols
2107 <!-- JAL-2602 -->Copy consensus sequence failed if
2108 alignment included gapped columns
2111 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2112 widgets don't permanently disappear
2115 <!-- JAL-2503 -->Cannot select or filter quantitative
2116 annotation that are shown only as column labels (e.g.
2117 T-Coffee column reliability scores)
2120 <!-- JAL-2594 -->Exception thrown if trying to create a
2121 sequence feature on gaps only
2124 <!-- JAL-2504 -->Features created with 'New feature'
2125 button from a Find inherit previously defined feature type
2126 rather than the Find query string
2129 <!-- JAL-2423 -->incorrect title in output window when
2130 exporting tree calculated in Jalview
2133 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2134 and then revealing them reorders sequences on the
2138 <!-- JAL-964 -->Group panel in sequence feature settings
2139 doesn't update to reflect available set of groups after
2140 interactively adding or modifying features
2143 <!-- JAL-2225 -->Sequence Database chooser unusable on
2147 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2148 only excluded gaps in current sequence and ignored
2155 <!-- JAL-2421 -->Overview window visible region moves
2156 erratically when hidden rows or columns are present
2159 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2160 Structure Viewer's colour menu don't correspond to
2164 <!-- JAL-2405 -->Protein specific colours only offered in
2165 colour and group colour menu for protein alignments
2168 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2169 reflect currently selected view or group's shading
2173 <!-- JAL-2624 -->Feature colour thresholds not respected
2174 when rendered on overview and structures when opacity at
2178 <!-- JAL-2589 -->User defined gap colour not shown in
2179 overview when features overlaid on alignment
2182 <!-- JAL-2567 -->Feature settings for different views not
2183 recovered correctly from Jalview project file
2186 <!-- JAL-2256 -->Feature colours in overview when first opened
2187 (automatically via preferences) are different to the main
2191 <em>Data import/export</em>
2194 <!-- JAL-2576 -->Very large alignments take a long time to
2198 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2199 added after a sequence was imported are not written to
2203 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2204 when importing RNA secondary structure via Stockholm
2207 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2208 not shown in correct direction for simple pseudoknots
2211 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2212 with lightGray or darkGray via features file (but can
2216 <!-- JAL-2383 -->Above PID colour threshold not recovered
2217 when alignment view imported from project
2220 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2221 structure and sequences extracted from structure files
2222 imported via URL and viewed in Jmol
2225 <!-- JAL-2520 -->Structures loaded via URL are saved in
2226 Jalview Projects rather than fetched via URL again when
2227 the project is loaded and the structure viewed
2230 <em>Web Services</em>
2233 <!-- JAL-2519 -->EnsemblGenomes example failing after
2234 release of Ensembl v.88
2237 <!-- JAL-2366 -->Proxy server address and port always
2238 appear enabled in Preferences->Connections
2241 <!-- JAL-2461 -->DAS registry not found exceptions
2242 removed from console output
2245 <!-- JAL-2582 -->Cannot retrieve protein products from
2246 Ensembl by Peptide ID
2249 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2250 created from SIFTs, and spurious 'Couldn't open structure
2251 in Chimera' errors raised after April 2017 update (problem
2252 due to 'null' string rather than empty string used for
2253 residues with no corresponding PDB mapping).
2256 <em>Application UI</em>
2259 <!-- JAL-2361 -->User Defined Colours not added to Colour
2263 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2264 case' residues (button in colourscheme editor debugged and
2265 new documentation and tooltips added)
2268 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2269 doesn't restore group-specific text colour thresholds
2272 <!-- JAL-2243 -->Feature settings panel does not update as
2273 new features are added to alignment
2276 <!-- JAL-2532 -->Cancel in feature settings reverts
2277 changes to feature colours via the Amend features dialog
2280 <!-- JAL-2506 -->Null pointer exception when attempting to
2281 edit graduated feature colour via amend features dialog
2285 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2286 selection menu changes colours of alignment views
2289 <!-- JAL-2426 -->Spurious exceptions in console raised
2290 from alignment calculation workers after alignment has
2294 <!-- JAL-1608 -->Typo in selection popup menu - Create
2295 groups now 'Create Group'
2298 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2299 Create/Undefine group doesn't always work
2302 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2303 shown again after pressing 'Cancel'
2306 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2307 adjusts start position in wrap mode
2310 <!-- JAL-2563 -->Status bar doesn't show positions for
2311 ambiguous amino acids
2314 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2315 CDS/Protein view after CDS sequences added for aligned
2319 <!-- JAL-2592 -->User defined colourschemes called 'User
2320 Defined' don't appear in Colours menu
2326 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2327 score models doesn't always result in an updated PCA plot
2330 <!-- JAL-2442 -->Features not rendered as transparent on
2331 overview or linked structure view
2334 <!-- JAL-2372 -->Colour group by conservation doesn't
2338 <!-- JAL-2517 -->Hitting Cancel after applying
2339 user-defined colourscheme doesn't restore original
2346 <!-- JAL-2314 -->Unit test failure:
2347 jalview.ws.jabaws.RNAStructExportImport setup fails
2350 <!-- JAL-2307 -->Unit test failure:
2351 jalview.ws.sifts.SiftsClientTest due to compatibility
2352 problems with deep array comparison equality asserts in
2353 successive versions of TestNG
2356 <!-- JAL-2479 -->Relocated StructureChooserTest and
2357 ParameterUtilsTest Unit tests to Network suite
2360 <em>New Known Issues</em>
2363 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2364 phase after a sequence motif find operation
2367 <!-- JAL-2550 -->Importing annotation file with rows
2368 containing just upper and lower case letters are
2369 interpreted as WUSS RNA secondary structure symbols
2372 <!-- JAL-2590 -->Cannot load and display Newick trees
2373 reliably from eggnog Ortholog database
2376 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2377 containing features of type Highlight' when 'B' is pressed
2378 to mark columns containing highlighted regions.
2381 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2382 doesn't always add secondary structure annotation.
2387 <td width="60" nowrap>
2388 <div align="center">
2389 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2392 <td><div align="left">
2396 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2397 for all consensus calculations
2400 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2403 <li>Updated Jalview's Certum code signing certificate
2406 <em>Application</em>
2409 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2410 set of database cross-references, sorted alphabetically
2413 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2414 from database cross references. Users with custom links
2415 will receive a <a href="webServices/urllinks.html#warning">warning
2416 dialog</a> asking them to update their preferences.
2419 <!-- JAL-2287-->Cancel button and escape listener on
2420 dialog warning user about disconnecting Jalview from a
2424 <!-- JAL-2320-->Jalview's Chimera control window closes if
2425 the Chimera it is connected to is shut down
2428 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2429 columns menu item to mark columns containing highlighted
2430 regions (e.g. from structure selections or results of a
2434 <!-- JAL-2284-->Command line option for batch-generation
2435 of HTML pages rendering alignment data with the BioJS
2445 <!-- JAL-2286 -->Columns with more than one modal residue
2446 are not coloured or thresholded according to percent
2447 identity (first observed in Jalview 2.8.2)
2450 <!-- JAL-2301 -->Threonine incorrectly reported as not
2454 <!-- JAL-2318 -->Updates to documentation pages (above PID
2455 threshold, amino acid properties)
2458 <!-- JAL-2292 -->Lower case residues in sequences are not
2459 reported as mapped to residues in a structure file in the
2463 <!--JAL-2324 -->Identical features with non-numeric scores
2464 could be added multiple times to a sequence
2467 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2468 bond features shown as two highlighted residues rather
2469 than a range in linked structure views, and treated
2470 correctly when selecting and computing trees from features
2473 <!-- JAL-2281-->Custom URL links for database
2474 cross-references are matched to database name regardless
2479 <em>Application</em>
2482 <!-- JAL-2282-->Custom URL links for specific database
2483 names without regular expressions also offer links from
2487 <!-- JAL-2315-->Removing a single configured link in the
2488 URL links pane in Connections preferences doesn't actually
2489 update Jalview configuration
2492 <!-- JAL-2272-->CTRL-Click on a selected region to open
2493 the alignment area popup menu doesn't work on El-Capitan
2496 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2497 files with similarly named sequences if dropped onto the
2501 <!-- JAL-2312 -->Additional mappings are shown for PDB
2502 entries where more chains exist in the PDB accession than
2503 are reported in the SIFTS file
2506 <!-- JAL-2317-->Certain structures do not get mapped to
2507 the structure view when displayed with Chimera
2510 <!-- JAL-2317-->No chains shown in the Chimera view
2511 panel's View->Show Chains submenu
2514 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2515 work for wrapped alignment views
2518 <!--JAL-2197 -->Rename UI components for running JPred
2519 predictions from 'JNet' to 'JPred'
2522 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2523 corrupted when annotation panel vertical scroll is not at
2524 first annotation row
2527 <!--JAL-2332 -->Attempting to view structure for Hen
2528 lysozyme results in a PDB Client error dialog box
2531 <!-- JAL-2319 -->Structure View's mapping report switched
2532 ranges for PDB and sequence for SIFTS
2535 SIFTS 'Not_Observed' residues mapped to non-existant
2539 <!-- <em>New Known Issues</em>
2546 <td width="60" nowrap>
2547 <div align="center">
2548 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2549 <em>25/10/2016</em></strong>
2552 <td><em>Application</em>
2554 <li>3D Structure chooser opens with 'Cached structures'
2555 view if structures already loaded</li>
2556 <li>Progress bar reports models as they are loaded to
2557 structure views</li>
2563 <li>Colour by conservation always enabled and no tick
2564 shown in menu when BLOSUM or PID shading applied</li>
2565 <li>FER1_ARATH and FER2_ARATH labels were switched in
2566 example sequences/projects/trees</li>
2568 <em>Application</em>
2570 <li>Jalview projects with views of local PDB structure
2571 files saved on Windows cannot be opened on OSX</li>
2572 <li>Multiple structure views can be opened and superposed
2573 without timeout for structures with multiple models or
2574 multiple sequences in alignment</li>
2575 <li>Cannot import or associated local PDB files without a
2576 PDB ID HEADER line</li>
2577 <li>RMSD is not output in Jmol console when superposition
2579 <li>Drag and drop of URL from Browser fails for Linux and
2580 OSX versions earlier than El Capitan</li>
2581 <li>ENA client ignores invalid content from ENA server</li>
2582 <li>Exceptions are not raised in console when ENA client
2583 attempts to fetch non-existent IDs via Fetch DB Refs UI
2585 <li>Exceptions are not raised in console when a new view
2586 is created on the alignment</li>
2587 <li>OSX right-click fixed for group selections: CMD-click
2588 to insert/remove gaps in groups and CTRL-click to open group
2591 <em>Build and deployment</em>
2593 <li>URL link checker now copes with multi-line anchor
2596 <em>New Known Issues</em>
2598 <li>Drag and drop from URL links in browsers do not work
2605 <td width="60" nowrap>
2606 <div align="center">
2607 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2610 <td><em>General</em>
2613 <!-- JAL-2124 -->Updated Spanish translations.
2616 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2617 for importing structure data to Jalview. Enables mmCIF and
2621 <!-- JAL-192 --->Alignment ruler shows positions relative to
2625 <!-- JAL-2202 -->Position/residue shown in status bar when
2626 mousing over sequence associated annotation
2629 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2633 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2634 '()', canonical '[]' and invalid '{}' base pair populations
2638 <!-- JAL-2092 -->Feature settings popup menu options for
2639 showing or hiding columns containing a feature
2642 <!-- JAL-1557 -->Edit selected group by double clicking on
2643 group and sequence associated annotation labels
2646 <!-- JAL-2236 -->Sequence name added to annotation label in
2647 select/hide columns by annotation and colour by annotation
2651 </ul> <em>Application</em>
2654 <!-- JAL-2050-->Automatically hide introns when opening a
2655 gene/transcript view
2658 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2662 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2663 structure mappings with the EMBL-EBI PDBe SIFTS database
2666 <!-- JAL-2079 -->Updated download sites used for Rfam and
2667 Pfam sources to xfam.org
2670 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2673 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2674 over sequences in Jalview
2677 <!-- JAL-2027-->Support for reverse-complement coding
2678 regions in ENA and EMBL
2681 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2682 for record retrieval via ENA rest API
2685 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2689 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2690 groovy script execution
2693 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2694 alignment window's Calculate menu
2697 <!-- JAL-1812 -->Allow groovy scripts that call
2698 Jalview.getAlignFrames() to run in headless mode
2701 <!-- JAL-2068 -->Support for creating new alignment
2702 calculation workers from groovy scripts
2705 <!-- JAL-1369 --->Store/restore reference sequence in
2709 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2710 associations are now saved/restored from project
2713 <!-- JAL-1993 -->Database selection dialog always shown
2714 before sequence fetcher is opened
2717 <!-- JAL-2183 -->Double click on an entry in Jalview's
2718 database chooser opens a sequence fetcher
2721 <!-- JAL-1563 -->Free-text search client for UniProt using
2722 the UniProt REST API
2725 <!-- JAL-2168 -->-nonews command line parameter to prevent
2726 the news reader opening
2729 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2730 querying stored in preferences
2733 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2737 <!-- JAL-1977-->Tooltips shown on database chooser
2740 <!-- JAL-391 -->Reverse complement function in calculate
2741 menu for nucleotide sequences
2744 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2745 and feature counts preserves alignment ordering (and
2746 debugged for complex feature sets).
2749 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2750 viewing structures with Jalview 2.10
2753 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2754 genome, transcript CCDS and gene ids via the Ensembl and
2755 Ensembl Genomes REST API
2758 <!-- JAL-2049 -->Protein sequence variant annotation
2759 computed for 'sequence_variant' annotation on CDS regions
2763 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2767 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2768 Ref Fetcher fails to match, or otherwise updates sequence
2769 data from external database records.
2772 <!-- JAL-2154 -->Revised Jalview Project format for
2773 efficient recovery of sequence coding and alignment
2774 annotation relationships.
2776 </ul> <!-- <em>Applet</em>
2787 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2791 <!-- JAL-2018-->Export features in Jalview format (again)
2792 includes graduated colourschemes
2795 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2796 working with big alignments and lots of hidden columns
2799 <!-- JAL-2053-->Hidden column markers not always rendered
2800 at right of alignment window
2803 <!-- JAL-2067 -->Tidied up links in help file table of
2807 <!-- JAL-2072 -->Feature based tree calculation not shown
2811 <!-- JAL-2075 -->Hidden columns ignored during feature
2812 based tree calculation
2815 <!-- JAL-2065 -->Alignment view stops updating when show
2816 unconserved enabled for group on alignment
2819 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2823 <!-- JAL-2146 -->Alignment column in status incorrectly
2824 shown as "Sequence position" when mousing over
2828 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2829 hidden columns present
2832 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2833 user created annotation added to alignment
2836 <!-- JAL-1841 -->RNA Structure consensus only computed for
2837 '()' base pair annotation
2840 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2841 in zero scores for all base pairs in RNA Structure
2845 <!-- JAL-2174-->Extend selection with columns containing
2849 <!-- JAL-2275 -->Pfam format writer puts extra space at
2850 beginning of sequence
2853 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2857 <!-- JAL-2238 -->Cannot create groups on an alignment from
2858 from a tree when t-coffee scores are shown
2861 <!-- JAL-1836,1967 -->Cannot import and view PDB
2862 structures with chains containing negative resnums (4q4h)
2865 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2869 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2870 to Clustal, PIR and PileUp output
2873 <!-- JAL-2008 -->Reordering sequence features that are
2874 not visible causes alignment window to repaint
2877 <!-- JAL-2006 -->Threshold sliders don't work in
2878 graduated colour and colour by annotation row for e-value
2879 scores associated with features and annotation rows
2882 <!-- JAL-1797 -->amino acid physicochemical conservation
2883 calculation should be case independent
2886 <!-- JAL-2173 -->Remove annotation also updates hidden
2890 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2891 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2892 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2895 <!-- JAL-2065 -->Null pointer exceptions and redraw
2896 problems when reference sequence defined and 'show
2897 non-conserved' enabled
2900 <!-- JAL-1306 -->Quality and Conservation are now shown on
2901 load even when Consensus calculation is disabled
2904 <!-- JAL-1932 -->Remove right on penultimate column of
2905 alignment does nothing
2908 <em>Application</em>
2911 <!-- JAL-1552-->URLs and links can't be imported by
2912 drag'n'drop on OSX when launched via webstart (note - not
2913 yet fixed for El Capitan)
2916 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2917 output when running on non-gb/us i18n platforms
2920 <!-- JAL-1944 -->Error thrown when exporting a view with
2921 hidden sequences as flat-file alignment
2924 <!-- JAL-2030-->InstallAnywhere distribution fails when
2928 <!-- JAL-2080-->Jalview very slow to launch via webstart
2929 (also hotfix for 2.9.0b2)
2932 <!-- JAL-2085 -->Cannot save project when view has a
2933 reference sequence defined
2936 <!-- JAL-1011 -->Columns are suddenly selected in other
2937 alignments and views when revealing hidden columns
2940 <!-- JAL-1989 -->Hide columns not mirrored in complement
2941 view in a cDNA/Protein splitframe
2944 <!-- JAL-1369 -->Cannot save/restore representative
2945 sequence from project when only one sequence is
2949 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2950 in Structure Chooser
2953 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2954 structure consensus didn't refresh annotation panel
2957 <!-- JAL-1962 -->View mapping in structure view shows
2958 mappings between sequence and all chains in a PDB file
2961 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2962 dialogs format columns correctly, don't display array
2963 data, sort columns according to type
2966 <!-- JAL-1975 -->Export complete shown after destination
2967 file chooser is cancelled during an image export
2970 <!-- JAL-2025 -->Error when querying PDB Service with
2971 sequence name containing special characters
2974 <!-- JAL-2024 -->Manual PDB structure querying should be
2978 <!-- JAL-2104 -->Large tooltips with broken HTML
2979 formatting don't wrap
2982 <!-- JAL-1128 -->Figures exported from wrapped view are
2983 truncated so L looks like I in consensus annotation
2986 <!-- JAL-2003 -->Export features should only export the
2987 currently displayed features for the current selection or
2991 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2992 after fetching cross-references, and restoring from
2996 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2997 followed in the structure viewer
3000 <!-- JAL-2163 -->Titles for individual alignments in
3001 splitframe not restored from project
3004 <!-- JAL-2145 -->missing autocalculated annotation at
3005 trailing end of protein alignment in transcript/product
3006 splitview when pad-gaps not enabled by default
3009 <!-- JAL-1797 -->amino acid physicochemical conservation
3013 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3014 article has been read (reopened issue due to
3015 internationalisation problems)
3018 <!-- JAL-1960 -->Only offer PDB structures in structure
3019 viewer based on sequence name, PDB and UniProt
3024 <!-- JAL-1976 -->No progress bar shown during export of
3028 <!-- JAL-2213 -->Structures not always superimposed after
3029 multiple structures are shown for one or more sequences.
3032 <!-- JAL-1370 -->Reference sequence characters should not
3033 be replaced with '.' when 'Show unconserved' format option
3037 <!-- JAL-1823 -->Cannot specify chain code when entering
3038 specific PDB id for sequence
3041 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3042 'Export hidden sequences' is enabled, but 'export hidden
3043 columns' is disabled.
3046 <!--JAL-2026-->Best Quality option in structure chooser
3047 selects lowest rather than highest resolution structures
3051 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3052 to sequence mapping in 'View Mappings' report
3055 <!-- JAL-2284 -->Unable to read old Jalview projects that
3056 contain non-XML data added after Jalvew wrote project.
3059 <!-- JAL-2118 -->Newly created annotation row reorders
3060 after clicking on it to create new annotation for a
3064 <!-- JAL-1980 -->Null Pointer Exception raised when
3065 pressing Add on an orphaned cut'n'paste window.
3067 <!-- may exclude, this is an external service stability issue JAL-1941
3068 -- > RNA 3D structure not added via DSSR service</li> -->
3073 <!-- JAL-2151 -->Incorrect columns are selected when
3074 hidden columns present before start of sequence
3077 <!-- JAL-1986 -->Missing dependencies on applet pages
3081 <!-- JAL-1947 -->Overview pixel size changes when
3082 sequences are hidden in applet
3085 <!-- JAL-1996 -->Updated instructions for applet
3086 deployment on examples pages.
3093 <td width="60" nowrap>
3094 <div align="center">
3095 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3096 <em>16/10/2015</em></strong>
3099 <td><em>General</em>
3101 <li>Time stamps for signed Jalview application and applet
3106 <em>Application</em>
3108 <li>Duplicate group consensus and conservation rows
3109 shown when tree is partitioned</li>
3110 <li>Erratic behaviour when tree partitions made with
3111 multiple cDNA/Protein split views</li>
3117 <td width="60" nowrap>
3118 <div align="center">
3119 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3120 <em>8/10/2015</em></strong>
3123 <td><em>General</em>
3125 <li>Updated Spanish translations of localized text for
3127 </ul> <em>Application</em>
3129 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3130 <li>Signed OSX InstallAnywhere installer<br></li>
3131 <li>Support for per-sequence based annotations in BioJSON</li>
3132 </ul> <em>Applet</em>
3134 <li>Split frame example added to applet examples page</li>
3135 </ul> <em>Build and Deployment</em>
3138 <!-- JAL-1888 -->New ant target for running Jalview's test
3146 <li>Mapping of cDNA to protein in split frames
3147 incorrect when sequence start > 1</li>
3148 <li>Broken images in filter column by annotation dialog
3150 <li>Feature colours not parsed from features file</li>
3151 <li>Exceptions and incomplete link URLs recovered when
3152 loading a features file containing HTML tags in feature
3156 <em>Application</em>
3158 <li>Annotations corrupted after BioJS export and
3160 <li>Incorrect sequence limits after Fetch DB References
3161 with 'trim retrieved sequences'</li>
3162 <li>Incorrect warning about deleting all data when
3163 deleting selected columns</li>
3164 <li>Patch to build system for shipping properly signed
3165 JNLP templates for webstart launch</li>
3166 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3167 unreleased structures for download or viewing</li>
3168 <li>Tab/space/return keystroke operation of EMBL-PDBe
3169 fetcher/viewer dialogs works correctly</li>
3170 <li>Disabled 'minimise' button on Jalview windows
3171 running on OSX to workaround redraw hang bug</li>
3172 <li>Split cDNA/Protein view position and geometry not
3173 recovered from jalview project</li>
3174 <li>Initial enabled/disabled state of annotation menu
3175 sorter 'show autocalculated first/last' corresponds to
3177 <li>Restoring of Clustal, RNA Helices and T-Coffee
3178 color schemes from BioJSON</li>
3182 <li>Reorder sequences mirrored in cDNA/Protein split
3184 <li>Applet with Jmol examples not loading correctly</li>
3190 <td><div align="center">
3191 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3193 <td><em>General</em>
3195 <li>Linked visualisation and analysis of DNA and Protein
3198 <li>Translated cDNA alignments shown as split protein
3199 and DNA alignment views</li>
3200 <li>Codon consensus annotation for linked protein and
3201 cDNA alignment views</li>
3202 <li>Link cDNA or Protein product sequences by loading
3203 them onto Protein or cDNA alignments</li>
3204 <li>Reconstruct linked cDNA alignment from aligned
3205 protein sequences</li>
3208 <li>Jmol integration updated to Jmol v14.2.14</li>
3209 <li>Import and export of Jalview alignment views as <a
3210 href="features/bioJsonFormat.html">BioJSON</a></li>
3211 <li>New alignment annotation file statements for
3212 reference sequences and marking hidden columns</li>
3213 <li>Reference sequence based alignment shading to
3214 highlight variation</li>
3215 <li>Select or hide columns according to alignment
3217 <li>Find option for locating sequences by description</li>
3218 <li>Conserved physicochemical properties shown in amino
3219 acid conservation row</li>
3220 <li>Alignments can be sorted by number of RNA helices</li>
3221 </ul> <em>Application</em>
3223 <li>New cDNA/Protein analysis capabilities
3225 <li>Get Cross-References should open a Split Frame
3226 view with cDNA/Protein</li>
3227 <li>Detect when nucleotide sequences and protein
3228 sequences are placed in the same alignment</li>
3229 <li>Split cDNA/Protein views are saved in Jalview
3234 <li>Use REST API to talk to Chimera</li>
3235 <li>Selected regions in Chimera are highlighted in linked
3236 Jalview windows</li>
3238 <li>VARNA RNA viewer updated to v3.93</li>
3239 <li>VARNA views are saved in Jalview Projects</li>
3240 <li>Pseudoknots displayed as Jalview RNA annotation can
3241 be shown in VARNA</li>
3243 <li>Make groups for selection uses marked columns as well
3244 as the active selected region</li>
3246 <li>Calculate UPGMA and NJ trees using sequence feature
3248 <li>New Export options
3250 <li>New Export Settings dialog to control hidden
3251 region export in flat file generation</li>
3253 <li>Export alignment views for display with the <a
3254 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3256 <li>Export scrollable SVG in HTML page</li>
3257 <li>Optional embedding of BioJSON data when exporting
3258 alignment figures to HTML</li>
3260 <li>3D structure retrieval and display
3262 <li>Free text and structured queries with the PDBe
3264 <li>PDBe Search API based discovery and selection of
3265 PDB structures for a sequence set</li>
3269 <li>JPred4 employed for protein secondary structure
3271 <li>Hide Insertions menu option to hide unaligned columns
3272 for one or a group of sequences</li>
3273 <li>Automatically hide insertions in alignments imported
3274 from the JPred4 web server</li>
3275 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3276 system on OSX<br />LGPL libraries courtesy of <a
3277 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3279 <li>changed 'View nucleotide structure' submenu to 'View
3280 VARNA 2D Structure'</li>
3281 <li>change "View protein structure" menu option to "3D
3284 </ul> <em>Applet</em>
3286 <li>New layout for applet example pages</li>
3287 <li>New parameters to enable SplitFrame view
3288 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3289 <li>New example demonstrating linked viewing of cDNA and
3290 Protein alignments</li>
3291 </ul> <em>Development and deployment</em>
3293 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3294 <li>Include installation type and git revision in build
3295 properties and console log output</li>
3296 <li>Jalview Github organisation, and new github site for
3297 storing BioJsMSA Templates</li>
3298 <li>Jalview's unit tests now managed with TestNG</li>
3301 <!-- <em>General</em>
3303 </ul> --> <!-- issues resolved --> <em>Application</em>
3305 <li>Escape should close any open find dialogs</li>
3306 <li>Typo in select-by-features status report</li>
3307 <li>Consensus RNA secondary secondary structure
3308 predictions are not highlighted in amber</li>
3309 <li>Missing gap character in v2.7 example file means
3310 alignment appears unaligned when pad-gaps is not enabled</li>
3311 <li>First switch to RNA Helices colouring doesn't colour
3312 associated structure views</li>
3313 <li>ID width preference option is greyed out when auto
3314 width checkbox not enabled</li>
3315 <li>Stopped a warning dialog from being shown when
3316 creating user defined colours</li>
3317 <li>'View Mapping' in structure viewer shows sequence
3318 mappings for just that viewer's sequences</li>
3319 <li>Workaround for superposing PDB files containing
3320 multiple models in Chimera</li>
3321 <li>Report sequence position in status bar when hovering
3322 over Jmol structure</li>
3323 <li>Cannot output gaps as '.' symbols with Selection ->
3324 output to text box</li>
3325 <li>Flat file exports of alignments with hidden columns
3326 have incorrect sequence start/end</li>
3327 <li>'Aligning' a second chain to a Chimera structure from
3329 <li>Colour schemes applied to structure viewers don't
3330 work for nucleotide</li>
3331 <li>Loading/cut'n'pasting an empty or invalid file leads
3332 to a grey/invisible alignment window</li>
3333 <li>Exported Jpred annotation from a sequence region
3334 imports to different position</li>
3335 <li>Space at beginning of sequence feature tooltips shown
3336 on some platforms</li>
3337 <li>Chimera viewer 'View | Show Chain' menu is not
3339 <li>'New View' fails with a Null Pointer Exception in
3340 console if Chimera has been opened</li>
3341 <li>Mouseover to Chimera not working</li>
3342 <li>Miscellaneous ENA XML feature qualifiers not
3344 <li>NPE in annotation renderer after 'Extract Scores'</li>
3345 <li>If two structures in one Chimera window, mouseover of
3346 either sequence shows on first structure</li>
3347 <li>'Show annotations' options should not make
3348 non-positional annotations visible</li>
3349 <li>Subsequence secondary structure annotation not shown
3350 in right place after 'view flanking regions'</li>
3351 <li>File Save As type unset when current file format is
3353 <li>Save as '.jar' option removed for saving Jalview
3355 <li>Colour by Sequence colouring in Chimera more
3357 <li>Cannot 'add reference annotation' for a sequence in
3358 several views on same alignment</li>
3359 <li>Cannot show linked products for EMBL / ENA records</li>
3360 <li>Jalview's tooltip wraps long texts containing no
3362 </ul> <em>Applet</em>
3364 <li>Jmol to JalviewLite mouseover/link not working</li>
3365 <li>JalviewLite can't import sequences with ID
3366 descriptions containing angle brackets</li>
3367 </ul> <em>General</em>
3369 <li>Cannot export and reimport RNA secondary structure
3370 via jalview annotation file</li>
3371 <li>Random helix colour palette for colour by annotation
3372 with RNA secondary structure</li>
3373 <li>Mouseover to cDNA from STOP residue in protein
3374 translation doesn't work.</li>
3375 <li>hints when using the select by annotation dialog box</li>
3376 <li>Jmol alignment incorrect if PDB file has alternate CA
3378 <li>FontChooser message dialog appears to hang after
3379 choosing 1pt font</li>
3380 <li>Peptide secondary structure incorrectly imported from
3381 annotation file when annotation display text includes 'e' or
3383 <li>Cannot set colour of new feature type whilst creating
3385 <li>cDNA translation alignment should not be sequence
3386 order dependent</li>
3387 <li>'Show unconserved' doesn't work for lower case
3389 <li>Nucleotide ambiguity codes involving R not recognised</li>
3390 </ul> <em>Deployment and Documentation</em>
3392 <li>Applet example pages appear different to the rest of
3393 www.jalview.org</li>
3394 </ul> <em>Application Known issues</em>
3396 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3397 <li>Misleading message appears after trying to delete
3399 <li>Jalview icon not shown in dock after InstallAnywhere
3400 version launches</li>
3401 <li>Fetching EMBL reference for an RNA sequence results
3402 fails with a sequence mismatch</li>
3403 <li>Corrupted or unreadable alignment display when
3404 scrolling alignment to right</li>
3405 <li>ArrayIndexOutOfBoundsException thrown when remove
3406 empty columns called on alignment with ragged gapped ends</li>
3407 <li>auto calculated alignment annotation rows do not get
3408 placed above or below non-autocalculated rows</li>
3409 <li>Jalview dekstop becomes sluggish at full screen in
3410 ultra-high resolution</li>
3411 <li>Cannot disable consensus calculation independently of
3412 quality and conservation</li>
3413 <li>Mouseover highlighting between cDNA and protein can
3414 become sluggish with more than one splitframe shown</li>
3415 </ul> <em>Applet Known Issues</em>
3417 <li>Core PDB parsing code requires Jmol</li>
3418 <li>Sequence canvas panel goes white when alignment
3419 window is being resized</li>
3425 <td><div align="center">
3426 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3428 <td><em>General</em>
3430 <li>Updated Java code signing certificate donated by
3432 <li>Features and annotation preserved when performing
3433 pairwise alignment</li>
3434 <li>RNA pseudoknot annotation can be
3435 imported/exported/displayed</li>
3436 <li>'colour by annotation' can colour by RNA and
3437 protein secondary structure</li>
3438 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3439 post-hoc with 2.9 release</em>)
3442 </ul> <em>Application</em>
3444 <li>Extract and display secondary structure for sequences
3445 with 3D structures</li>
3446 <li>Support for parsing RNAML</li>
3447 <li>Annotations menu for layout
3449 <li>sort sequence annotation rows by alignment</li>
3450 <li>place sequence annotation above/below alignment
3453 <li>Output in Stockholm format</li>
3454 <li>Internationalisation: improved Spanish (es)
3456 <li>Structure viewer preferences tab</li>
3457 <li>Disorder and Secondary Structure annotation tracks
3458 shared between alignments</li>
3459 <li>UCSF Chimera launch and linked highlighting from
3461 <li>Show/hide all sequence associated annotation rows for
3462 all or current selection</li>
3463 <li>disorder and secondary structure predictions
3464 available as dataset annotation</li>
3465 <li>Per-sequence rna helices colouring</li>
3468 <li>Sequence database accessions imported when fetching
3469 alignments from Rfam</li>
3470 <li>update VARNA version to 3.91</li>
3472 <li>New groovy scripts for exporting aligned positions,
3473 conservation values, and calculating sum of pairs scores.</li>
3474 <li>Command line argument to set default JABAWS server</li>
3475 <li>include installation type in build properties and
3476 console log output</li>
3477 <li>Updated Jalview project format to preserve dataset
3481 <!-- issues resolved --> <em>Application</em>
3483 <li>Distinguish alignment and sequence associated RNA
3484 structure in structure->view->VARNA</li>
3485 <li>Raise dialog box if user deletes all sequences in an
3487 <li>Pressing F1 results in documentation opening twice</li>
3488 <li>Sequence feature tooltip is wrapped</li>
3489 <li>Double click on sequence associated annotation
3490 selects only first column</li>
3491 <li>Redundancy removal doesn't result in unlinked
3492 leaves shown in tree</li>
3493 <li>Undos after several redundancy removals don't undo
3495 <li>Hide sequence doesn't hide associated annotation</li>
3496 <li>User defined colours dialog box too big to fit on
3497 screen and buttons not visible</li>
3498 <li>author list isn't updated if already written to
3499 Jalview properties</li>
3500 <li>Popup menu won't open after retrieving sequence
3502 <li>File open window for associate PDB doesn't open</li>
3503 <li>Left-then-right click on a sequence id opens a
3504 browser search window</li>
3505 <li>Cannot open sequence feature shading/sort popup menu
3506 in feature settings dialog</li>
3507 <li>better tooltip placement for some areas of Jalview
3509 <li>Allow addition of JABAWS Server which doesn't
3510 pass validation</li>
3511 <li>Web services parameters dialog box is too large to
3513 <li>Muscle nucleotide alignment preset obscured by
3515 <li>JABAWS preset submenus don't contain newly
3516 defined user preset</li>
3517 <li>MSA web services warns user if they were launched
3518 with invalid input</li>
3519 <li>Jalview cannot contact DAS Registy when running on
3522 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3523 'Superpose with' submenu not shown when new view
3527 </ul> <!-- <em>Applet</em>
3529 </ul> <em>General</em>
3531 </ul>--> <em>Deployment and Documentation</em>
3533 <li>2G and 1G options in launchApp have no effect on
3534 memory allocation</li>
3535 <li>launchApp service doesn't automatically open
3536 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3538 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3539 InstallAnywhere reports cannot find valid JVM when Java
3540 1.7_055 is available
3542 </ul> <em>Application Known issues</em>
3545 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3546 corrupted or unreadable alignment display when scrolling
3550 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3551 retrieval fails but progress bar continues for DAS retrieval
3552 with large number of ID
3555 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3556 flatfile output of visible region has incorrect sequence
3560 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3561 rna structure consensus doesn't update when secondary
3562 structure tracks are rearranged
3565 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3566 invalid rna structure positional highlighting does not
3567 highlight position of invalid base pairs
3570 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3571 out of memory errors are not raised when saving Jalview
3572 project from alignment window file menu
3575 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3576 Switching to RNA Helices colouring doesn't propagate to
3580 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3581 colour by RNA Helices not enabled when user created
3582 annotation added to alignment
3585 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3586 Jalview icon not shown on dock in Mountain Lion/Webstart
3588 </ul> <em>Applet Known Issues</em>
3591 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3592 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3595 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3596 Jalview and Jmol example not compatible with IE9
3599 <li>Sort by annotation score doesn't reverse order
3605 <td><div align="center">
3606 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3609 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3612 <li>Internationalisation of user interface (usually
3613 called i18n support) and translation for Spanish locale</li>
3614 <li>Define/Undefine group on current selection with
3615 Ctrl-G/Shift Ctrl-G</li>
3616 <li>Improved group creation/removal options in
3617 alignment/sequence Popup menu</li>
3618 <li>Sensible precision for symbol distribution
3619 percentages shown in logo tooltip.</li>
3620 <li>Annotation panel height set according to amount of
3621 annotation when alignment first opened</li>
3622 </ul> <em>Application</em>
3624 <li>Interactive consensus RNA secondary structure
3625 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3626 <li>Select columns containing particular features from
3627 Feature Settings dialog</li>
3628 <li>View all 'representative' PDB structures for selected
3630 <li>Update Jalview project format:
3632 <li>New file extension for Jalview projects '.jvp'</li>
3633 <li>Preserve sequence and annotation dataset (to
3634 store secondary structure annotation,etc)</li>
3635 <li>Per group and alignment annotation and RNA helix
3639 <li>New similarity measures for PCA and Tree calculation
3641 <li>Experimental support for retrieval and viewing of
3642 flanking regions for an alignment</li>
3646 <!-- issues resolved --> <em>Application</em>
3648 <li>logo keeps spinning and status remains at queued or
3649 running after job is cancelled</li>
3650 <li>cannot export features from alignments imported from
3651 Jalview/VAMSAS projects</li>
3652 <li>Buggy slider for web service parameters that take
3654 <li>Newly created RNA secondary structure line doesn't
3655 have 'display all symbols' flag set</li>
3656 <li>T-COFFEE alignment score shading scheme and other
3657 annotation shading not saved in Jalview project</li>
3658 <li>Local file cannot be loaded in freshly downloaded
3660 <li>Jalview icon not shown on dock in Mountain
3662 <li>Load file from desktop file browser fails</li>
3663 <li>Occasional NPE thrown when calculating large trees</li>
3664 <li>Cannot reorder or slide sequences after dragging an
3665 alignment onto desktop</li>
3666 <li>Colour by annotation dialog throws NPE after using
3667 'extract scores' function</li>
3668 <li>Loading/cut'n'pasting an empty file leads to a grey
3669 alignment window</li>
3670 <li>Disorder thresholds rendered incorrectly after
3671 performing IUPred disorder prediction</li>
3672 <li>Multiple group annotated consensus rows shown when
3673 changing 'normalise logo' display setting</li>
3674 <li>Find shows blank dialog after 'finished searching' if
3675 nothing matches query</li>
3676 <li>Null Pointer Exceptions raised when sorting by
3677 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3679 <li>Errors in Jmol console when structures in alignment
3680 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3682 <li>Not all working JABAWS services are shown in
3684 <li>JAVAWS version of Jalview fails to launch with
3685 'invalid literal/length code'</li>
3686 <li>Annotation/RNA Helix colourschemes cannot be applied
3687 to alignment with groups (actually fixed in 2.8.0b1)</li>
3688 <li>RNA Helices and T-Coffee Scores available as default
3691 </ul> <em>Applet</em>
3693 <li>Remove group option is shown even when selection is
3695 <li>Apply to all groups ticked but colourscheme changes
3696 don't affect groups</li>
3697 <li>Documented RNA Helices and T-Coffee Scores as valid
3698 colourscheme name</li>
3699 <li>Annotation labels drawn on sequence IDs when
3700 Annotation panel is not displayed</li>
3701 <li>Increased font size for dropdown menus on OSX and
3702 embedded windows</li>
3703 </ul> <em>Other</em>
3705 <li>Consensus sequence for alignments/groups with a
3706 single sequence were not calculated</li>
3707 <li>annotation files that contain only groups imported as
3708 annotation and junk sequences</li>
3709 <li>Fasta files with sequences containing '*' incorrectly
3710 recognised as PFAM or BLC</li>
3711 <li>conservation/PID slider apply all groups option
3712 doesn't affect background (2.8.0b1)
3714 <li>redundancy highlighting is erratic at 0% and 100%</li>
3715 <li>Remove gapped columns fails for sequences with ragged
3717 <li>AMSA annotation row with leading spaces is not
3718 registered correctly on import</li>
3719 <li>Jalview crashes when selecting PCA analysis for
3720 certain alignments</li>
3721 <li>Opening the colour by annotation dialog for an
3722 existing annotation based 'use original colours'
3723 colourscheme loses original colours setting</li>
3728 <td><div align="center">
3729 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3730 <em>30/1/2014</em></strong>
3734 <li>Trusted certificates for JalviewLite applet and
3735 Jalview Desktop application<br />Certificate was donated by
3736 <a href="https://www.certum.eu">Certum</a> to the Jalview
3737 open source project).
3739 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3740 <li>Output in Stockholm format</li>
3741 <li>Allow import of data from gzipped files</li>
3742 <li>Export/import group and sequence associated line
3743 graph thresholds</li>
3744 <li>Nucleotide substitution matrix that supports RNA and
3745 ambiguity codes</li>
3746 <li>Allow disorder predictions to be made on the current
3747 selection (or visible selection) in the same way that JPred
3749 <li>Groovy scripting for headless Jalview operation</li>
3750 </ul> <em>Other improvements</em>
3752 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3753 <li>COMBINE statement uses current SEQUENCE_REF and
3754 GROUP_REF scope to group annotation rows</li>
3755 <li>Support '' style escaping of quotes in Newick
3757 <li>Group options for JABAWS service by command line name</li>
3758 <li>Empty tooltip shown for JABA service options with a
3759 link but no description</li>
3760 <li>Select primary source when selecting authority in
3761 database fetcher GUI</li>
3762 <li>Add .mfa to FASTA file extensions recognised by
3764 <li>Annotation label tooltip text wrap</li>
3769 <li>Slow scrolling when lots of annotation rows are
3771 <li>Lots of NPE (and slowness) after creating RNA
3772 secondary structure annotation line</li>
3773 <li>Sequence database accessions not imported when
3774 fetching alignments from Rfam</li>
3775 <li>Incorrect SHMR submission for sequences with
3777 <li>View all structures does not always superpose
3779 <li>Option widgets in service parameters not updated to
3780 reflect user or preset settings</li>
3781 <li>Null pointer exceptions for some services without
3782 presets or adjustable parameters</li>
3783 <li>Discover PDB IDs entry in structure menu doesn't
3784 discover PDB xRefs</li>
3785 <li>Exception encountered while trying to retrieve
3786 features with DAS</li>
3787 <li>Lowest value in annotation row isn't coloured
3788 when colour by annotation (per sequence) is coloured</li>
3789 <li>Keyboard mode P jumps to start of gapped region when
3790 residue follows a gap</li>
3791 <li>Jalview appears to hang importing an alignment with
3792 Wrap as default or after enabling Wrap</li>
3793 <li>'Right click to add annotations' message
3794 shown in wrap mode when no annotations present</li>
3795 <li>Disorder predictions fail with NPE if no automatic
3796 annotation already exists on alignment</li>
3797 <li>oninit javascript function should be called after
3798 initialisation completes</li>
3799 <li>Remove redundancy after disorder prediction corrupts
3800 alignment window display</li>
3801 <li>Example annotation file in documentation is invalid</li>
3802 <li>Grouped line graph annotation rows are not exported
3803 to annotation file</li>
3804 <li>Multi-harmony analysis cannot be run when only two
3806 <li>Cannot create multiple groups of line graphs with
3807 several 'combine' statements in annotation file</li>
3808 <li>Pressing return several times causes Number Format
3809 exceptions in keyboard mode</li>
3810 <li>Multi-harmony (SHMMR) method doesn't submit
3811 correct partitions for input data</li>
3812 <li>Translation from DNA to Amino Acids fails</li>
3813 <li>Jalview fail to load newick tree with quoted label</li>
3814 <li>--headless flag isn't understood</li>
3815 <li>ClassCastException when generating EPS in headless
3817 <li>Adjusting sequence-associated shading threshold only
3818 changes one row's threshold</li>
3819 <li>Preferences and Feature settings panel panel
3820 doesn't open</li>
3821 <li>hide consensus histogram also hides conservation and
3822 quality histograms</li>
3827 <td><div align="center">
3828 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3830 <td><em>Application</em>
3832 <li>Support for JABAWS 2.0 Services (AACon alignment
3833 conservation, protein disorder and Clustal Omega)</li>
3834 <li>JABAWS server status indicator in Web Services
3836 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3837 in Jalview alignment window</li>
3838 <li>Updated Jalview build and deploy framework for OSX
3839 mountain lion, windows 7, and 8</li>
3840 <li>Nucleotide substitution matrix for PCA that supports
3841 RNA and ambiguity codes</li>
3843 <li>Improved sequence database retrieval GUI</li>
3844 <li>Support fetching and database reference look up
3845 against multiple DAS sources (Fetch all from in 'fetch db
3847 <li>Jalview project improvements
3849 <li>Store and retrieve the 'belowAlignment'
3850 flag for annotation</li>
3851 <li>calcId attribute to group annotation rows on the
3853 <li>Store AACon calculation settings for a view in
3854 Jalview project</li>
3858 <li>horizontal scrolling gesture support</li>
3859 <li>Visual progress indicator when PCA calculation is
3861 <li>Simpler JABA web services menus</li>
3862 <li>visual indication that web service results are still
3863 being retrieved from server</li>
3864 <li>Serialise the dialogs that are shown when Jalview
3865 starts up for first time</li>
3866 <li>Jalview user agent string for interacting with HTTP
3868 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3870 <li>Examples directory and Groovy library included in
3871 InstallAnywhere distribution</li>
3872 </ul> <em>Applet</em>
3874 <li>RNA alignment and secondary structure annotation
3875 visualization applet example</li>
3876 </ul> <em>General</em>
3878 <li>Normalise option for consensus sequence logo</li>
3879 <li>Reset button in PCA window to return dimensions to
3881 <li>Allow seqspace or Jalview variant of alignment PCA
3883 <li>PCA with either nucleic acid and protein substitution
3885 <li>Allow windows containing HTML reports to be exported
3887 <li>Interactive display and editing of RNA secondary
3888 structure contacts</li>
3889 <li>RNA Helix Alignment Colouring</li>
3890 <li>RNA base pair logo consensus</li>
3891 <li>Parse sequence associated secondary structure
3892 information in Stockholm files</li>
3893 <li>HTML Export database accessions and annotation
3894 information presented in tooltip for sequences</li>
3895 <li>Import secondary structure from LOCARNA clustalw
3896 style RNA alignment files</li>
3897 <li>import and visualise T-COFFEE quality scores for an
3899 <li>'colour by annotation' per sequence option to
3900 shade each sequence according to its associated alignment
3902 <li>New Jalview Logo</li>
3903 </ul> <em>Documentation and Development</em>
3905 <li>documentation for score matrices used in Jalview</li>
3906 <li>New Website!</li>
3908 <td><em>Application</em>
3910 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3911 wsdbfetch REST service</li>
3912 <li>Stop windows being moved outside desktop on OSX</li>
3913 <li>Filetype associations not installed for webstart
3915 <li>Jalview does not always retrieve progress of a JABAWS
3916 job execution in full once it is complete</li>
3917 <li>revise SHMR RSBS definition to ensure alignment is
3918 uploaded via ali_file parameter</li>
3919 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3920 <li>View all structures superposed fails with exception</li>
3921 <li>Jnet job queues forever if a very short sequence is
3922 submitted for prediction</li>
3923 <li>Cut and paste menu not opened when mouse clicked on
3925 <li>Putting fractional value into integer text box in
3926 alignment parameter dialog causes Jalview to hang</li>
3927 <li>Structure view highlighting doesn't work on
3929 <li>View all structures fails with exception shown in
3931 <li>Characters in filename associated with PDBEntry not
3932 escaped in a platform independent way</li>
3933 <li>Jalview desktop fails to launch with exception when
3935 <li>Tree calculation reports 'you must have 2 or more
3936 sequences selected' when selection is empty</li>
3937 <li>Jalview desktop fails to launch with jar signature
3938 failure when java web start temporary file caching is
3940 <li>DAS Sequence retrieval with range qualification
3941 results in sequence xref which includes range qualification</li>
3942 <li>Errors during processing of command line arguments
3943 cause progress bar (JAL-898) to be removed</li>
3944 <li>Replace comma for semi-colon option not disabled for
3945 DAS sources in sequence fetcher</li>
3946 <li>Cannot close news reader when JABAWS server warning
3947 dialog is shown</li>
3948 <li>Option widgets not updated to reflect user settings</li>
3949 <li>Edited sequence not submitted to web service</li>
3950 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3951 <li>InstallAnywhere installer doesn't unpack and run
3952 on OSX Mountain Lion</li>
3953 <li>Annotation panel not given a scroll bar when
3954 sequences with alignment annotation are pasted into the
3956 <li>Sequence associated annotation rows not associated
3957 when loaded from Jalview project</li>
3958 <li>Browser launch fails with NPE on java 1.7</li>
3959 <li>JABAWS alignment marked as finished when job was
3960 cancelled or job failed due to invalid input</li>
3961 <li>NPE with v2.7 example when clicking on Tree
3962 associated with all views</li>
3963 <li>Exceptions when copy/paste sequences with grouped
3964 annotation rows to new window</li>
3965 </ul> <em>Applet</em>
3967 <li>Sequence features are momentarily displayed before
3968 they are hidden using hidefeaturegroups applet parameter</li>
3969 <li>loading features via javascript API automatically
3970 enables feature display</li>
3971 <li>scrollToColumnIn javascript API method doesn't
3973 </ul> <em>General</em>
3975 <li>Redundancy removal fails for rna alignment</li>
3976 <li>PCA calculation fails when sequence has been selected
3977 and then deselected</li>
3978 <li>PCA window shows grey box when first opened on OSX</li>
3979 <li>Letters coloured pink in sequence logo when alignment
3980 coloured with clustalx</li>
3981 <li>Choosing fonts without letter symbols defined causes
3982 exceptions and redraw errors</li>
3983 <li>Initial PCA plot view is not same as manually
3984 reconfigured view</li>
3985 <li>Grouped annotation graph label has incorrect line
3987 <li>Grouped annotation graph label display is corrupted
3988 for lots of labels</li>
3993 <div align="center">
3994 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3997 <td><em>Application</em>
3999 <li>Jalview Desktop News Reader</li>
4000 <li>Tweaked default layout of web services menu</li>
4001 <li>View/alignment association menu to enable user to
4002 easily specify which alignment a multi-structure view takes
4003 its colours/correspondences from</li>
4004 <li>Allow properties file location to be specified as URL</li>
4005 <li>Extend Jalview project to preserve associations
4006 between many alignment views and a single Jmol display</li>
4007 <li>Store annotation row height in Jalview project file</li>
4008 <li>Annotation row column label formatting attributes
4009 stored in project file</li>
4010 <li>Annotation row order for auto-calculated annotation
4011 rows preserved in Jalview project file</li>
4012 <li>Visual progress indication when Jalview state is
4013 saved using Desktop window menu</li>
4014 <li>Visual indication that command line arguments are
4015 still being processed</li>
4016 <li>Groovy script execution from URL</li>
4017 <li>Colour by annotation default min and max colours in
4019 <li>Automatically associate PDB files dragged onto an
4020 alignment with sequences that have high similarity and
4022 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4023 <li>'view structures' option to open many
4024 structures in same window</li>
4025 <li>Sort associated views menu option for tree panel</li>
4026 <li>Group all JABA and non-JABA services for a particular
4027 analysis function in its own submenu</li>
4028 </ul> <em>Applet</em>
4030 <li>Userdefined and autogenerated annotation rows for
4032 <li>Adjustment of alignment annotation pane height</li>
4033 <li>Annotation scrollbar for annotation panel</li>
4034 <li>Drag to reorder annotation rows in annotation panel</li>
4035 <li>'automaticScrolling' parameter</li>
4036 <li>Allow sequences with partial ID string matches to be
4037 annotated from GFF/Jalview features files</li>
4038 <li>Sequence logo annotation row in applet</li>
4039 <li>Absolute paths relative to host server in applet
4040 parameters are treated as such</li>
4041 <li>New in the JalviewLite javascript API:
4043 <li>JalviewLite.js javascript library</li>
4044 <li>Javascript callbacks for
4046 <li>Applet initialisation</li>
4047 <li>Sequence/alignment mouse-overs and selections</li>
4050 <li>scrollTo row and column alignment scrolling
4052 <li>Select sequence/alignment regions from javascript</li>
4053 <li>javascript structure viewer harness to pass
4054 messages between Jmol and Jalview when running as
4055 distinct applets</li>
4056 <li>sortBy method</li>
4057 <li>Set of applet and application examples shipped
4058 with documentation</li>
4059 <li>New example to demonstrate JalviewLite and Jmol
4060 javascript message exchange</li>
4062 </ul> <em>General</em>
4064 <li>Enable Jmol displays to be associated with multiple
4065 multiple alignments</li>
4066 <li>Option to automatically sort alignment with new tree</li>
4067 <li>User configurable link to enable redirects to a
4068 www.Jalview.org mirror</li>
4069 <li>Jmol colours option for Jmol displays</li>
4070 <li>Configurable newline string when writing alignment
4071 and other flat files</li>
4072 <li>Allow alignment annotation description lines to
4073 contain html tags</li>
4074 </ul> <em>Documentation and Development</em>
4076 <li>Add groovy test harness for bulk load testing to
4078 <li>Groovy script to load and align a set of sequences
4079 using a web service before displaying the result in the
4080 Jalview desktop</li>
4081 <li>Restructured javascript and applet api documentation</li>
4082 <li>Ant target to publish example html files with applet
4084 <li>Netbeans project for building Jalview from source</li>
4085 <li>ant task to create online javadoc for Jalview source</li>
4087 <td><em>Application</em>
4089 <li>User defined colourscheme throws exception when
4090 current built in colourscheme is saved as new scheme</li>
4091 <li>AlignFrame->Save in application pops up save
4092 dialog for valid filename/format</li>
4093 <li>Cannot view associated structure for UniProt sequence</li>
4094 <li>PDB file association breaks for UniProt sequence
4096 <li>Associate PDB from file dialog does not tell you
4097 which sequence is to be associated with the file</li>
4098 <li>Find All raises null pointer exception when query
4099 only matches sequence IDs</li>
4100 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4101 <li>Jalview project with Jmol views created with Jalview
4102 2.4 cannot be loaded</li>
4103 <li>Filetype associations not installed for webstart
4105 <li>Two or more chains in a single PDB file associated
4106 with sequences in different alignments do not get coloured
4107 by their associated sequence</li>
4108 <li>Visibility status of autocalculated annotation row
4109 not preserved when project is loaded</li>
4110 <li>Annotation row height and visibility attributes not
4111 stored in Jalview project</li>
4112 <li>Tree bootstraps are not preserved when saved as a
4113 Jalview project</li>
4114 <li>Envision2 workflow tooltips are corrupted</li>
4115 <li>Enabling show group conservation also enables colour
4116 by conservation</li>
4117 <li>Duplicate group associated conservation or consensus
4118 created on new view</li>
4119 <li>Annotation scrollbar not displayed after 'show
4120 all hidden annotation rows' option selected</li>
4121 <li>Alignment quality not updated after alignment
4122 annotation row is hidden then shown</li>
4123 <li>Preserve colouring of structures coloured by
4124 sequences in pre Jalview 2.7 projects</li>
4125 <li>Web service job parameter dialog is not laid out
4127 <li>Web services menu not refreshed after 'reset
4128 services' button is pressed in preferences</li>
4129 <li>Annotation off by one in Jalview v2_3 example project</li>
4130 <li>Structures imported from file and saved in project
4131 get name like jalview_pdb1234.txt when reloaded</li>
4132 <li>Jalview does not always retrieve progress of a JABAWS
4133 job execution in full once it is complete</li>
4134 </ul> <em>Applet</em>
4136 <li>Alignment height set incorrectly when lots of
4137 annotation rows are displayed</li>
4138 <li>Relative URLs in feature HTML text not resolved to
4140 <li>View follows highlighting does not work for positions
4142 <li><= shown as = in tooltip</li>
4143 <li>Export features raises exception when no features
4145 <li>Separator string used for serialising lists of IDs
4146 for javascript api is modified when separator string
4147 provided as parameter</li>
4148 <li>Null pointer exception when selecting tree leaves for
4149 alignment with no existing selection</li>
4150 <li>Relative URLs for datasources assumed to be relative
4151 to applet's codebase</li>
4152 <li>Status bar not updated after finished searching and
4153 search wraps around to first result</li>
4154 <li>StructureSelectionManager instance shared between
4155 several Jalview applets causes race conditions and memory
4157 <li>Hover tooltip and mouseover of position on structure
4158 not sent from Jmol in applet</li>
4159 <li>Certain sequences of javascript method calls to
4160 applet API fatally hang browser</li>
4161 </ul> <em>General</em>
4163 <li>View follows structure mouseover scrolls beyond
4164 position with wrapped view and hidden regions</li>
4165 <li>Find sequence position moves to wrong residue
4166 with/without hidden columns</li>
4167 <li>Sequence length given in alignment properties window
4169 <li>InvalidNumberFormat exceptions thrown when trying to
4170 import PDB like structure files</li>
4171 <li>Positional search results are only highlighted
4172 between user-supplied sequence start/end bounds</li>
4173 <li>End attribute of sequence is not validated</li>
4174 <li>Find dialog only finds first sequence containing a
4175 given sequence position</li>
4176 <li>Sequence numbering not preserved in MSF alignment
4178 <li>Jalview PDB file reader does not extract sequence
4179 from nucleotide chains correctly</li>
4180 <li>Structure colours not updated when tree partition
4181 changed in alignment</li>
4182 <li>Sequence associated secondary structure not correctly
4183 parsed in interleaved stockholm</li>
4184 <li>Colour by annotation dialog does not restore current
4186 <li>Hiding (nearly) all sequences doesn't work
4188 <li>Sequences containing lowercase letters are not
4189 properly associated with their pdb files</li>
4190 </ul> <em>Documentation and Development</em>
4192 <li>schemas/JalviewWsParamSet.xsd corrupted by
4193 ApplyCopyright tool</li>
4198 <div align="center">
4199 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4202 <td><em>Application</em>
4204 <li>New warning dialog when the Jalview Desktop cannot
4205 contact web services</li>
4206 <li>JABA service parameters for a preset are shown in
4207 service job window</li>
4208 <li>JABA Service menu entries reworded</li>
4212 <li>Modeller PIR IO broken - cannot correctly import a
4213 pir file emitted by Jalview</li>
4214 <li>Existing feature settings transferred to new
4215 alignment view created from cut'n'paste</li>
4216 <li>Improved test for mixed amino/nucleotide chains when
4217 parsing PDB files</li>
4218 <li>Consensus and conservation annotation rows
4219 occasionally become blank for all new windows</li>
4220 <li>Exception raised when right clicking above sequences
4221 in wrapped view mode</li>
4222 </ul> <em>Application</em>
4224 <li>multiple multiply aligned structure views cause cpu
4225 usage to hit 100% and computer to hang</li>
4226 <li>Web Service parameter layout breaks for long user
4227 parameter names</li>
4228 <li>Jaba service discovery hangs desktop if Jaba server
4235 <div align="center">
4236 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4239 <td><em>Application</em>
4241 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4242 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4245 <li>Web Services preference tab</li>
4246 <li>Analysis parameters dialog box and user defined
4248 <li>Improved speed and layout of Envision2 service menu</li>
4249 <li>Superpose structures using associated sequence
4251 <li>Export coordinates and projection as CSV from PCA
4253 </ul> <em>Applet</em>
4255 <li>enable javascript: execution by the applet via the
4256 link out mechanism</li>
4257 </ul> <em>Other</em>
4259 <li>Updated the Jmol Jalview interface to work with Jmol
4261 <li>The Jalview Desktop and JalviewLite applet now
4262 require Java 1.5</li>
4263 <li>Allow Jalview feature colour specification for GFF
4264 sequence annotation files</li>
4265 <li>New 'colour by label' keword in Jalview feature file
4266 type colour specification</li>
4267 <li>New Jalview Desktop Groovy API method that allows a
4268 script to check if it being run in an interactive session or
4269 in a batch operation from the Jalview command line</li>
4273 <li>clustalx colourscheme colours Ds preferentially when
4274 both D+E are present in over 50% of the column</li>
4275 </ul> <em>Application</em>
4277 <li>typo in AlignmentFrame->View->Hide->all but
4278 selected Regions menu item</li>
4279 <li>sequence fetcher replaces ',' for ';' when the ',' is
4280 part of a valid accession ID</li>
4281 <li>fatal OOM if object retrieved by sequence fetcher
4282 runs out of memory</li>
4283 <li>unhandled Out of Memory Error when viewing pca
4284 analysis results</li>
4285 <li>InstallAnywhere builds fail to launch on OS X java
4286 10.5 update 4 (due to apple Java 1.6 update)</li>
4287 <li>Installanywhere Jalview silently fails to launch</li>
4288 </ul> <em>Applet</em>
4290 <li>Jalview.getFeatureGroups() raises an
4291 ArrayIndexOutOfBoundsException if no feature groups are
4298 <div align="center">
4299 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4305 <li>Alignment prettyprinter doesn't cope with long
4307 <li>clustalx colourscheme colours Ds preferentially when
4308 both D+E are present in over 50% of the column</li>
4309 <li>nucleic acid structures retrieved from PDB do not
4310 import correctly</li>
4311 <li>More columns get selected than were clicked on when a
4312 number of columns are hidden</li>
4313 <li>annotation label popup menu not providing correct
4314 add/hide/show options when rows are hidden or none are
4316 <li>Stockholm format shown in list of readable formats,
4317 and parser copes better with alignments from RFAM.</li>
4318 <li>CSV output of consensus only includes the percentage
4319 of all symbols if sequence logo display is enabled</li>
4321 </ul> <em>Applet</em>
4323 <li>annotation panel disappears when annotation is
4325 </ul> <em>Application</em>
4327 <li>Alignment view not redrawn properly when new
4328 alignment opened where annotation panel is visible but no
4329 annotations are present on alignment</li>
4330 <li>pasted region containing hidden columns is
4331 incorrectly displayed in new alignment window</li>
4332 <li>Jalview slow to complete operations when stdout is
4333 flooded (fix is to close the Jalview console)</li>
4334 <li>typo in AlignmentFrame->View->Hide->all but
4335 selected Rregions menu item.</li>
4336 <li>inconsistent group submenu and Format submenu entry
4337 'Un' or 'Non'conserved</li>
4338 <li>Sequence feature settings are being shared by
4339 multiple distinct alignments</li>
4340 <li>group annotation not recreated when tree partition is
4342 <li>double click on group annotation to select sequences
4343 does not propagate to associated trees</li>
4344 <li>Mac OSX specific issues:
4346 <li>exception raised when mouse clicked on desktop
4347 window background</li>
4348 <li>Desktop menu placed on menu bar and application
4349 name set correctly</li>
4350 <li>sequence feature settings not wide enough for the
4351 save feature colourscheme button</li>
4360 <div align="center">
4361 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4364 <td><em>New Capabilities</em>
4366 <li>URL links generated from description line for
4367 regular-expression based URL links (applet and application)
4369 <li>Non-positional feature URL links are shown in link
4371 <li>Linked viewing of nucleic acid sequences and
4373 <li>Automatic Scrolling option in View menu to display
4374 the currently highlighted region of an alignment.</li>
4375 <li>Order an alignment by sequence length, or using the
4376 average score or total feature count for each sequence.</li>
4377 <li>Shading features by score or associated description</li>
4378 <li>Subdivide alignment and groups based on identity of
4379 selected subsequence (Make Groups from Selection).</li>
4380 <li>New hide/show options including Shift+Control+H to
4381 hide everything but the currently selected region.</li>
4382 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4383 </ul> <em>Application</em>
4385 <li>Fetch DB References capabilities and UI expanded to
4386 support retrieval from DAS sequence sources</li>
4387 <li>Local DAS Sequence sources can be added via the
4388 command line or via the Add local source dialog box.</li>
4389 <li>DAS Dbref and DbxRef feature types are parsed as
4390 database references and protein_name is parsed as
4391 description line (BioSapiens terms).</li>
4392 <li>Enable or disable non-positional feature and database
4393 references in sequence ID tooltip from View menu in
4395 <!-- <li>New hidden columns and rows and representatives capabilities
4396 in annotations file (in progress - not yet fully implemented)</li> -->
4397 <li>Group-associated consensus, sequence logos and
4398 conservation plots</li>
4399 <li>Symbol distributions for each column can be exported
4400 and visualized as sequence logos</li>
4401 <li>Optionally scale multi-character column labels to fit
4402 within each column of annotation row<!-- todo for applet -->
4404 <li>Optional automatic sort of associated alignment view
4405 when a new tree is opened.</li>
4406 <li>Jalview Java Console</li>
4407 <li>Better placement of desktop window when moving
4408 between different screens.</li>
4409 <li>New preference items for sequence ID tooltip and
4410 consensus annotation</li>
4411 <li>Client to submit sequences and IDs to Envision2
4413 <li><em>Vamsas Capabilities</em>
4415 <li>Improved VAMSAS synchronization (Jalview archive
4416 used to preserve views, structures, and tree display
4418 <li>Import of vamsas documents from disk or URL via
4420 <li>Sharing of selected regions between views and
4421 with other VAMSAS applications (Experimental feature!)</li>
4422 <li>Updated API to VAMSAS version 0.2</li>
4424 </ul> <em>Applet</em>
4426 <li>Middle button resizes annotation row height</li>
4429 <li>sortByTree (true/false) - automatically sort the
4430 associated alignment view by the tree when a new tree is
4432 <li>showTreeBootstraps (true/false) - show or hide
4433 branch bootstraps (default is to show them if available)</li>
4434 <li>showTreeDistances (true/false) - show or hide
4435 branch lengths (default is to show them if available)</li>
4436 <li>showUnlinkedTreeNodes (true/false) - indicate if
4437 unassociated nodes should be highlighted in the tree
4439 <li>heightScale and widthScale (1.0 or more) -
4440 increase the height or width of a cell in the alignment
4441 grid relative to the current font size.</li>
4444 <li>Non-positional features displayed in sequence ID
4446 </ul> <em>Other</em>
4448 <li>Features format: graduated colour definitions and
4449 specification of feature scores</li>
4450 <li>Alignment Annotations format: new keywords for group
4451 associated annotation (GROUP_REF) and annotation row display
4452 properties (ROW_PROPERTIES)</li>
4453 <li>XML formats extended to support graduated feature
4454 colourschemes, group associated annotation, and profile
4455 visualization settings.</li></td>
4458 <li>Source field in GFF files parsed as feature source
4459 rather than description</li>
4460 <li>Non-positional features are now included in sequence
4461 feature and gff files (controlled via non-positional feature
4462 visibility in tooltip).</li>
4463 <li>URL links generated for all feature links (bugfix)</li>
4464 <li>Added URL embedding instructions to features file
4466 <li>Codons containing ambiguous nucleotides translated as
4467 'X' in peptide product</li>
4468 <li>Match case switch in find dialog box works for both
4469 sequence ID and sequence string and query strings do not
4470 have to be in upper case to match case-insensitively.</li>
4471 <li>AMSA files only contain first column of
4472 multi-character column annotation labels</li>
4473 <li>Jalview Annotation File generation/parsing consistent
4474 with documentation (e.g. Stockholm annotation can be
4475 exported and re-imported)</li>
4476 <li>PDB files without embedded PDB IDs given a friendly
4478 <li>Find incrementally searches ID string matches as well
4479 as subsequence matches, and correctly reports total number
4483 <li>Better handling of exceptions during sequence
4485 <li>Dasobert generated non-positional feature URL
4486 link text excludes the start_end suffix</li>
4487 <li>DAS feature and source retrieval buttons disabled
4488 when fetch or registry operations in progress.</li>
4489 <li>PDB files retrieved from URLs are cached properly</li>
4490 <li>Sequence description lines properly shared via
4492 <li>Sequence fetcher fetches multiple records for all
4494 <li>Ensured that command line das feature retrieval
4495 completes before alignment figures are generated.</li>
4496 <li>Reduced time taken when opening file browser for
4498 <li>isAligned check prior to calculating tree, PCA or
4499 submitting an MSA to JNet now excludes hidden sequences.</li>
4500 <li>User defined group colours properly recovered
4501 from Jalview projects.</li>
4510 <div align="center">
4511 <strong>2.4.0.b2</strong><br> 28/10/2009
4516 <li>Experimental support for google analytics usage
4518 <li>Jalview privacy settings (user preferences and docs).</li>
4523 <li>Race condition in applet preventing startup in
4525 <li>Exception when feature created from selection beyond
4526 length of sequence.</li>
4527 <li>Allow synthetic PDB files to be imported gracefully</li>
4528 <li>Sequence associated annotation rows associate with
4529 all sequences with a given id</li>
4530 <li>Find function matches case-insensitively for sequence
4531 ID string searches</li>
4532 <li>Non-standard characters do not cause pairwise
4533 alignment to fail with exception</li>
4534 </ul> <em>Application Issues</em>
4536 <li>Sequences are now validated against EMBL database</li>
4537 <li>Sequence fetcher fetches multiple records for all
4539 </ul> <em>InstallAnywhere Issues</em>
4541 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4542 issue with installAnywhere mechanism)</li>
4543 <li>Command line launching of JARs from InstallAnywhere
4544 version (java class versioning error fixed)</li>
4551 <div align="center">
4552 <strong>2.4</strong><br> 27/8/2008
4555 <td><em>User Interface</em>
4557 <li>Linked highlighting of codon and amino acid from
4558 translation and protein products</li>
4559 <li>Linked highlighting of structure associated with
4560 residue mapping to codon position</li>
4561 <li>Sequence Fetcher provides example accession numbers
4562 and 'clear' button</li>
4563 <li>MemoryMonitor added as an option under Desktop's
4565 <li>Extract score function to parse whitespace separated
4566 numeric data in description line</li>
4567 <li>Column labels in alignment annotation can be centred.</li>
4568 <li>Tooltip for sequence associated annotation give name
4570 </ul> <em>Web Services and URL fetching</em>
4572 <li>JPred3 web service</li>
4573 <li>Prototype sequence search client (no public services
4575 <li>Fetch either seed alignment or full alignment from
4577 <li>URL Links created for matching database cross
4578 references as well as sequence ID</li>
4579 <li>URL Links can be created using regular-expressions</li>
4580 </ul> <em>Sequence Database Connectivity</em>
4582 <li>Retrieval of cross-referenced sequences from other
4584 <li>Generalised database reference retrieval and
4585 validation to all fetchable databases</li>
4586 <li>Fetch sequences from DAS sources supporting the
4587 sequence command</li>
4588 </ul> <em>Import and Export</em>
4589 <li>export annotation rows as CSV for spreadsheet import</li>
4590 <li>Jalview projects record alignment dataset associations,
4591 EMBL products, and cDNA sequence mappings</li>
4592 <li>Sequence Group colour can be specified in Annotation
4594 <li>Ad-hoc colouring of group in Annotation File using RGB
4595 triplet as name of colourscheme</li>
4596 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4598 <li>treenode binding for VAMSAS tree exchange</li>
4599 <li>local editing and update of sequences in VAMSAS
4600 alignments (experimental)</li>
4601 <li>Create new or select existing session to join</li>
4602 <li>load and save of vamsas documents</li>
4603 </ul> <em>Application command line</em>
4605 <li>-tree parameter to open trees (introduced for passing
4607 <li>-fetchfrom command line argument to specify nicknames
4608 of DAS servers to query for alignment features</li>
4609 <li>-dasserver command line argument to add new servers
4610 that are also automatically queried for features</li>
4611 <li>-groovy command line argument executes a given groovy
4612 script after all input data has been loaded and parsed</li>
4613 </ul> <em>Applet-Application data exchange</em>
4615 <li>Trees passed as applet parameters can be passed to
4616 application (when using "View in full
4617 application")</li>
4618 </ul> <em>Applet Parameters</em>
4620 <li>feature group display control parameter</li>
4621 <li>debug parameter</li>
4622 <li>showbutton parameter</li>
4623 </ul> <em>Applet API methods</em>
4625 <li>newView public method</li>
4626 <li>Window (current view) specific get/set public methods</li>
4627 <li>Feature display control methods</li>
4628 <li>get list of currently selected sequences</li>
4629 </ul> <em>New Jalview distribution features</em>
4631 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4632 <li>RELEASE file gives build properties for the latest
4633 Jalview release.</li>
4634 <li>Java 1.1 Applet build made easier and donotobfuscate
4635 property controls execution of obfuscator</li>
4636 <li>Build target for generating source distribution</li>
4637 <li>Debug flag for javacc</li>
4638 <li>.jalview_properties file is documented (slightly) in
4639 jalview.bin.Cache</li>
4640 <li>Continuous Build Integration for stable and
4641 development version of Application, Applet and source
4646 <li>selected region output includes visible annotations
4647 (for certain formats)</li>
4648 <li>edit label/displaychar contains existing label/char
4650 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4651 <li>shorter peptide product names from EMBL records</li>
4652 <li>Newick string generator makes compact representations</li>
4653 <li>bootstrap values parsed correctly for tree files with
4655 <li>pathological filechooser bug avoided by not allowing
4656 filenames containing a ':'</li>
4657 <li>Fixed exception when parsing GFF files containing
4658 global sequence features</li>
4659 <li>Alignment datasets are finalized only when number of
4660 references from alignment sequences goes to zero</li>
4661 <li>Close of tree branch colour box without colour
4662 selection causes cascading exceptions</li>
4663 <li>occasional negative imgwidth exceptions</li>
4664 <li>better reporting of non-fatal warnings to user when
4665 file parsing fails.</li>
4666 <li>Save works when Jalview project is default format</li>
4667 <li>Save as dialog opened if current alignment format is
4668 not a valid output format</li>
4669 <li>UniProt canonical names introduced for both das and
4671 <li>Histidine should be midblue (not pink!) in Zappo</li>
4672 <li>error messages passed up and output when data read
4674 <li>edit undo recovers previous dataset sequence when
4675 sequence is edited</li>
4676 <li>allow PDB files without pdb ID HEADER lines (like
4677 those generated by MODELLER) to be read in properly</li>
4678 <li>allow reading of JPred concise files as a normal
4680 <li>Stockholm annotation parsing and alignment properties
4681 import fixed for PFAM records</li>
4682 <li>Structure view windows have correct name in Desktop
4684 <li>annotation consisting of sequence associated scores
4685 can be read and written correctly to annotation file</li>
4686 <li>Aligned cDNA translation to aligned peptide works
4688 <li>Fixed display of hidden sequence markers and
4689 non-italic font for representatives in Applet</li>
4690 <li>Applet Menus are always embedded in applet window on
4692 <li>Newly shown features appear at top of stack (in
4694 <li>Annotations added via parameter not drawn properly
4695 due to null pointer exceptions</li>
4696 <li>Secondary structure lines are drawn starting from
4697 first column of alignment</li>
4698 <li>UniProt XML import updated for new schema release in
4700 <li>Sequence feature to sequence ID match for Features
4701 file is case-insensitive</li>
4702 <li>Sequence features read from Features file appended to
4703 all sequences with matching IDs</li>
4704 <li>PDB structure coloured correctly for associated views
4705 containing a sub-sequence</li>
4706 <li>PDB files can be retrieved by applet from Jar files</li>
4707 <li>feature and annotation file applet parameters
4708 referring to different directories are retrieved correctly</li>
4709 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4710 <li>Fixed application hang whilst waiting for
4711 splash-screen version check to complete</li>
4712 <li>Applet properly URLencodes input parameter values
4713 when passing them to the launchApp service</li>
4714 <li>display name and local features preserved in results
4715 retrieved from web service</li>
4716 <li>Visual delay indication for sequence retrieval and
4717 sequence fetcher initialisation</li>
4718 <li>updated Application to use DAS 1.53e version of
4719 dasobert DAS client</li>
4720 <li>Re-instated Full AMSA support and .amsa file
4722 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4730 <div align="center">
4731 <strong>2.3</strong><br> 9/5/07
4736 <li>Jmol 11.0.2 integration</li>
4737 <li>PDB views stored in Jalview XML files</li>
4738 <li>Slide sequences</li>
4739 <li>Edit sequence in place</li>
4740 <li>EMBL CDS features</li>
4741 <li>DAS Feature mapping</li>
4742 <li>Feature ordering</li>
4743 <li>Alignment Properties</li>
4744 <li>Annotation Scores</li>
4745 <li>Sort by scores</li>
4746 <li>Feature/annotation editing in applet</li>
4751 <li>Headless state operation in 2.2.1</li>
4752 <li>Incorrect and unstable DNA pairwise alignment</li>
4753 <li>Cut and paste of sequences with annotation</li>
4754 <li>Feature group display state in XML</li>
4755 <li>Feature ordering in XML</li>
4756 <li>blc file iteration selection using filename # suffix</li>
4757 <li>Stockholm alignment properties</li>
4758 <li>Stockhom alignment secondary structure annotation</li>
4759 <li>2.2.1 applet had no feature transparency</li>
4760 <li>Number pad keys can be used in cursor mode</li>
4761 <li>Structure Viewer mirror image resolved</li>
4768 <div align="center">
4769 <strong>2.2.1</strong><br> 12/2/07
4774 <li>Non standard characters can be read and displayed
4775 <li>Annotations/Features can be imported/exported to the
4777 <li>Applet allows editing of sequence/annotation/group
4778 name & description
4779 <li>Preference setting to display sequence name in
4781 <li>Annotation file format extended to allow
4782 Sequence_groups to be defined
4783 <li>Default opening of alignment overview panel can be
4784 specified in preferences
4785 <li>PDB residue numbering annotation added to associated
4791 <li>Applet crash under certain Linux OS with Java 1.6
4793 <li>Annotation file export / import bugs fixed
4794 <li>PNG / EPS image output bugs fixed
4800 <div align="center">
4801 <strong>2.2</strong><br> 27/11/06
4806 <li>Multiple views on alignment
4807 <li>Sequence feature editing
4808 <li>"Reload" alignment
4809 <li>"Save" to current filename
4810 <li>Background dependent text colour
4811 <li>Right align sequence ids
4812 <li>User-defined lower case residue colours
4815 <li>Menu item accelerator keys
4816 <li>Control-V pastes to current alignment
4817 <li>Cancel button for DAS Feature Fetching
4818 <li>PCA and PDB Viewers zoom via mouse roller
4819 <li>User-defined sub-tree colours and sub-tree selection
4821 <li>'New Window' button on the 'Output to Text box'
4826 <li>New memory efficient Undo/Redo System
4827 <li>Optimised symbol lookups and conservation/consensus
4829 <li>Region Conservation/Consensus recalculated after
4831 <li>Fixed Remove Empty Columns Bug (empty columns at end
4833 <li>Slowed DAS Feature Fetching for increased robustness.
4835 <li>Made angle brackets in ASCII feature descriptions
4837 <li>Re-instated Zoom function for PCA
4838 <li>Sequence descriptions conserved in web service
4840 <li>UniProt ID discoverer uses any word separated by
4842 <li>WsDbFetch query/result association resolved
4843 <li>Tree leaf to sequence mapping improved
4844 <li>Smooth fonts switch moved to FontChooser dialog box.
4851 <div align="center">
4852 <strong>2.1.1</strong><br> 12/9/06
4857 <li>Copy consensus sequence to clipboard</li>
4862 <li>Image output - rightmost residues are rendered if
4863 sequence id panel has been resized</li>
4864 <li>Image output - all offscreen group boundaries are
4866 <li>Annotation files with sequence references - all
4867 elements in file are relative to sequence position</li>
4868 <li>Mac Applet users can use Alt key for group editing</li>
4874 <div align="center">
4875 <strong>2.1</strong><br> 22/8/06
4880 <li>MAFFT Multiple Alignment in default Web Service list</li>
4881 <li>DAS Feature fetching</li>
4882 <li>Hide sequences and columns</li>
4883 <li>Export Annotations and Features</li>
4884 <li>GFF file reading / writing</li>
4885 <li>Associate structures with sequences from local PDB
4887 <li>Add sequences to exisiting alignment</li>
4888 <li>Recently opened files / URL lists</li>
4889 <li>Applet can launch the full application</li>
4890 <li>Applet has transparency for features (Java 1.2
4892 <li>Applet has user defined colours parameter</li>
4893 <li>Applet can load sequences from parameter
4894 "sequence<em>x</em>"
4900 <li>Redundancy Panel reinstalled in the Applet</li>
4901 <li>Monospaced font - EPS / rescaling bug fixed</li>
4902 <li>Annotation files with sequence references bug fixed</li>
4908 <div align="center">
4909 <strong>2.08.1</strong><br> 2/5/06
4914 <li>Change case of selected region from Popup menu</li>
4915 <li>Choose to match case when searching</li>
4916 <li>Middle mouse button and mouse movement can compress /
4917 expand the visible width and height of the alignment</li>
4922 <li>Annotation Panel displays complete JNet results</li>
4928 <div align="center">
4929 <strong>2.08b</strong><br> 18/4/06
4935 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4936 <li>Righthand label on wrapped alignments shows correct
4943 <div align="center">
4944 <strong>2.08</strong><br> 10/4/06
4949 <li>Editing can be locked to the selection area</li>
4950 <li>Keyboard editing</li>
4951 <li>Create sequence features from searches</li>
4952 <li>Precalculated annotations can be loaded onto
4954 <li>Features file allows grouping of features</li>
4955 <li>Annotation Colouring scheme added</li>
4956 <li>Smooth fonts off by default - Faster rendering</li>
4957 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4962 <li>Drag & Drop fixed on Linux</li>
4963 <li>Jalview Archive file faster to load/save, sequence
4964 descriptions saved.</li>
4970 <div align="center">
4971 <strong>2.07</strong><br> 12/12/05
4976 <li>PDB Structure Viewer enhanced</li>
4977 <li>Sequence Feature retrieval and display enhanced</li>
4978 <li>Choose to output sequence start-end after sequence
4979 name for file output</li>
4980 <li>Sequence Fetcher WSDBFetch@EBI</li>
4981 <li>Applet can read feature files, PDB files and can be
4982 used for HTML form input</li>
4987 <li>HTML output writes groups and features</li>
4988 <li>Group editing is Control and mouse click</li>
4989 <li>File IO bugs</li>
4995 <div align="center">
4996 <strong>2.06</strong><br> 28/9/05
5001 <li>View annotations in wrapped mode</li>
5002 <li>More options for PCA viewer</li>
5007 <li>GUI bugs resolved</li>
5008 <li>Runs with -nodisplay from command line</li>
5014 <div align="center">
5015 <strong>2.05b</strong><br> 15/9/05
5020 <li>Choose EPS export as lineart or text</li>
5021 <li>Jar files are executable</li>
5022 <li>Can read in Uracil - maps to unknown residue</li>
5027 <li>Known OutOfMemory errors give warning message</li>
5028 <li>Overview window calculated more efficiently</li>
5029 <li>Several GUI bugs resolved</li>
5035 <div align="center">
5036 <strong>2.05</strong><br> 30/8/05
5041 <li>Edit and annotate in "Wrapped" view</li>
5046 <li>Several GUI bugs resolved</li>
5052 <div align="center">
5053 <strong>2.04</strong><br> 24/8/05
5058 <li>Hold down mouse wheel & scroll to change font
5064 <li>Improved JPred client reliability</li>
5065 <li>Improved loading of Jalview files</li>
5071 <div align="center">
5072 <strong>2.03</strong><br> 18/8/05
5077 <li>Set Proxy server name and port in preferences</li>
5078 <li>Multiple URL links from sequence ids</li>
5079 <li>User Defined Colours can have a scheme name and added
5081 <li>Choose to ignore gaps in consensus calculation</li>
5082 <li>Unix users can set default web browser</li>
5083 <li>Runs without GUI for batch processing</li>
5084 <li>Dynamically generated Web Service Menus</li>
5089 <li>InstallAnywhere download for Sparc Solaris</li>
5095 <div align="center">
5096 <strong>2.02</strong><br> 18/7/05
5102 <li>Copy & Paste order of sequences maintains
5103 alignment order.</li>
5109 <div align="center">
5110 <strong>2.01</strong><br> 12/7/05
5115 <li>Use delete key for deleting selection.</li>
5116 <li>Use Mouse wheel to scroll sequences.</li>
5117 <li>Help file updated to describe how to add alignment
5119 <li>Version and build date written to build properties
5121 <li>InstallAnywhere installation will check for updates
5122 at launch of Jalview.</li>
5127 <li>Delete gaps bug fixed.</li>
5128 <li>FileChooser sorts columns.</li>
5129 <li>Can remove groups one by one.</li>
5130 <li>Filechooser icons installed.</li>
5131 <li>Finder ignores return character when searching.
5132 Return key will initiate a search.<br>
5139 <div align="center">
5140 <strong>2.0</strong><br> 20/6/05
5145 <li>New codebase</li>
git://source.jalview.org / jalview.git / blob