3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
61 <em>29/10/2020</em></strong></td>
62 <td align="left" valign="top">
67 <td align="left" valign="top">
70 <!-- JAL-3765 -->Find doesn't always highlight all matching
71 positions in a sequence (bug introduced in 2.11.1.2)
74 <!-- JAL-3760 -->Alignments containing one or more protein
75 sequences can be classed as nucleotide
78 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
79 sequences after alignment of protein products (known defect
80 first reported for 2.11.1.0)
83 <!-- JAL-3725 -->No tooltip or popup menu for genomic features
84 outwith CDS shown overlaid on protein
87 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
88 correctly mapped by Jalview (e.g. affects viral CDS with
89 ribosomal slippage, since 2.9.0)
92 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
96 <!-- JAL-3700 -->Selections in CDS sequence panel don't
97 always select corresponding protein sequences
101 <em>Make groups from selection</em> for a column selection
102 doesn't always ignore hidden columns
104 </ul> <em>Installer</em>
107 <!-- JAL-3611 -->Space character in Jalview install path on
108 Windows prevents install4j launching getdown
110 </ul> <em>Development</em>
113 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
114 version numbers in doc/building.md
120 <td width="60" align="center" nowrap><strong><a
121 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
122 <em>25/09/2020</em></strong></td>
123 <td align="left" valign="top">
127 <td align="left" valign="top">
130 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
131 "Encountered problems opening
132 https://www.jalview.org/examples/exampleFile_2_7.jvp"
138 <td width="60" align="center" nowrap><strong><a
139 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
140 <em>17/09/2020</em></strong></td>
141 <td align="left" valign="top">
144 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
145 residue in cursor mode
148 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
149 HTSJDK from 2.12 to 2.23
152 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
153 optimisations and improvements suggested by Bob Hanson and
154 improved compatibility with JalviewJS
157 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
158 alignments from Pfam and Rfam
161 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
162 import (no longer based on .gz extension)
165 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
168 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
169 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
173 <!-- JAL-3667 -->Improved warning messages, debug logging
174 and fixed Retry action when Jalview encounters errors when
175 saving or making backup files.
178 <!-- JAL-3676 -->Enhanced Jalview Java Console:
180 <li>Jalview's logging level can be configured</li>
181 <li>Copy to Clipboard Buttion</li>
185 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
186 when running on Linux (Requires Java 11+)
188 </ul> <em>Launching Jalview</em>
191 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
192 through a system property
195 <!-- JAL-3477 -->Improved built-in documentation and command
196 line help for configuring Jalview's memory
200 <td align="left" valign="top">
203 <!-- JAL-3691 -->Conservation and Quality tracks are shown
204 but not calculated and no protein or DNA score models are
205 available for tree/PCA calculation when launched with
206 Turkish language locale
209 <!-- JAL-3493 -->Escape does not clear highlights on the
210 alignment (Since Jalview 2.10.3)
213 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
214 doesn't slide selected sequences, just sequence under cursor
217 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
218 sequence under the cursor
221 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
222 multiple EMBL gene products shown forĀ a single contig
225 <!-- JAL-3696 -->Errors encountered when processing variants
226 from VCF files yield "Error processing VCF: Format specifier
230 <!-- JAL-3697 -->Count of features not shown can be wrong
231 when there are both local and complementary features mapped
232 to the position under the cursor
235 <!-- JAL-3673 -->Sequence ID for reference sequence is
236 clipped when Right align Sequence IDs enabled
239 <!-- JAL-2983 -->Slider with negative range values not
240 rendered correctly in VAqua4 (Since 2.10.4)
243 <!-- JAL-3685 -->Single quotes not displayed correctly in
244 internationalised text for some messages and log output
247 <!-- JAL-3490 -->Find doesn't report matches that span
248 hidden gapped columns
251 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
252 panels, Alignment viewport and annotation renderer.
255 <!-- JAL-3561 -->Jalview ignores file format parameter
256 specifying output format when exporting an alignment via the
260 <!-- JAL-3667 -->Windows 10: For a minority of users, if
261 backups are not enabled, Jalview sometimes fails to
262 overwrite an existing file and raises a warning dialog. (in
263 2.11.0, and 2.11.1.0, the workaround is to try to save the
264 file again, and if that fails, delete the original file and
268 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
272 <!-- JAL-3741 -->References to http://www.jalview.org in
273 program and documentation
275 </ul> <em>Launching Jalview</em>
278 <!-- JAL-3718 -->Jalview application fails when launched the
279 first time for a version that has different jars to the
280 previous launched version.
282 </ul> <em>Developing Jalview</em>
285 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
286 data, causing cloverReport gradle task to fail with an
290 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
291 monitor the release channel
293 </ul> <em>New Known defects</em>
296 <!-- JAL-3748 -->CDS shown in result of submitting proteins
297 in a CDS/Protein alignment to a web service is wrong when
298 proteins share a common transcript sequence (e.g.
299 genome of RNA viruses)
302 <!-- JAL-3576 -->Co-located features exported and re-imported
303 are ordered differently when shown on alignment and in
304 tooltips. (Also affects v2.11.1.0)
307 <!-- JAL-3702 -->Drag and drop of alignment file onto
308 alignment window when in a HiDPI scaled mode in Linux only
309 works for the top left quadrant of the alignment window
312 <!-- JAL-3701 -->Stale build data in jalview standalone jar
313 builds (only affects 2.11.1.1 branch)
316 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
317 when alignment view restored from project (since Jalview 2.11.0)
320 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
321 protein products for certain ENA records are repeatedly
322 shown via Calculate->Show Cross Refs
328 <td width="60" align="center" nowrap><strong><a
329 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
330 <em>22/04/2020</em></strong></td>
331 <td align="left" valign="top">
334 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
335 'virtual' codon features shown on protein (or vice versa)
336 for display in alignments, on structure views (including
337 transfer to UCSF chimera), in feature reports and for
341 <!-- JAL-3121 -->Feature attributes from VCF files can be
342 exported and re-imported as GFF3 files
345 <!-- JAL-3376 -->Capture VCF "fixed column" values
346 POS, ID, QUAL, FILTER as Feature Attributes
349 <!-- JAL-3375 -->More robust VCF numeric data field
350 validation while parsing
353 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
357 <!-- JAL-3535 -->Feature Settings dialog title includes name
361 <!-- JAL-3538 -->Font anti-aliasing in alignment views
365 <!-- JAL-3468 -->Very long feature descriptions truncated in
369 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
370 with no feature types visible
373 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
375 </ul><em>Jalview Installer</em>
378 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
379 in console (may be null when Jalview launched as executable jar or via conda)
382 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
385 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
388 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
390 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
391 </ul> <em>Release processes</em>
394 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
397 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
399 </ul> <em>Build System</em>
402 <!-- JAL-3510 -->Clover updated to 4.4.1
405 <!-- JAL-3513 -->Test code included in Clover coverage
409 <em>Groovy Scripts</em>
412 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
413 to stdout containing the consensus sequence for each
414 alignment in a Jalview session
417 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
418 genomic sequence_variant annotation from CDS as
419 missense_variant or synonymous_variant on protein products.
423 <td align="left" valign="top">
426 <!-- JAL-3581 -->Hidden sequence markers still visible when
427 'Show hidden markers' option is not ticked
430 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
431 PNG output when 'Automatically set ID width' is set in
432 jalview preferences or properties file
435 <!-- JAL-3571 -->Feature Editor dialog can be opened when
436 'Show Sequence Features' option is not ticked
439 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
440 buttons in Feature Settings dialog are clicked when no
444 <!-- JAL-3412 -->ID margins for CDS and Protein views not
445 equal when split frame is first opened
448 <!-- JAL-3296 -->Sequence position numbers in status bar not
449 correct after editing a sequence's start position
452 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
453 with annotation and exceptions thrown when only a few
454 columns shown in wrapped mode
457 <!-- JAL-3386 -->Sequence IDs missing in headless export of
458 wrapped alignment figure with annotations
461 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
462 ID fails with ClassCastException
465 <!-- JAL-3389 -->Chimera session not restored from Jalview
469 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
470 feature settings dialog also selects columns
473 <!-- JAL-3473 -->SpinnerNumberModel causes
474 IllegalArgumentException in some circumstances
477 <!-- JAL-3534 -->Multiple feature settings dialogs can be
481 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
482 alignment window is closed
485 <!-- JAL-3406 -->Credits missing some authors in Jalview
486 help documentation for 2.11.0 release
489 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
490 includes Pfam ID as sequence's accession rather than its
493 </ul> <em>Java 11 Compatibility issues</em>
496 <!-- JAL-2987 -->OSX - Can't view some search results in
497 PDB/Uniprot search panel
499 </ul> <em>Installer</em>
502 <!-- JAL-3447 -->Jalview should not create file associations
503 for 3D structure files (.pdb, .mmcif. .cif)
505 </ul> <em>Repository and Source Release</em>
508 <!-- JAL-3474 -->removed obsolete .cvsignore files from
512 <!-- JAL-3541 -->Clover report generation running out of
515 </ul> <em>New Known Issues</em>
518 <!-- JAL-3523 -->OSX - Current working directory not
519 preserved when Jalview.app launched with parameters from
523 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
524 clipped in headless figure export when Right Align option
528 <!-- JAL-3542 -->Jalview Installation type always reports
529 'Source' in console output
532 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
533 bamboo server but run fine locally.
539 <td width="60" align="center" nowrap>
540 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
541 <em>04/07/2019</em></strong>
543 <td align="left" valign="top">
546 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
547 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
548 source project) rather than InstallAnywhere
551 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
552 settings, receive over the air updates and launch specific
553 versions via (<a href="https://github.com/threerings/getdown">Three
557 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
558 formats supported by Jalview (including .jvp project files)
561 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
562 arguments and switch between different getdown channels
565 <!-- JAL-3141 -->Backup files created when saving Jalview project
570 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
571 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
573 <!-- JAL-2620 -->Alternative genetic code tables for
574 'Translate as cDNA'</li>
576 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
577 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
580 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
581 implementation that allows updates) used for Sequence Feature collections</li>
583 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
584 features can be filtered and shaded according to any
585 associated attributes (e.g. variant attributes from VCF
586 file, or key-value pairs imported from column 9 of GFF
590 <!-- JAL-2879 -->Feature Attributes and shading schemes
591 stored and restored from Jalview Projects
594 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
595 recognise variant features
598 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
599 sequences (also coloured red by default)
602 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
606 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
607 algorithm (Z-sort/transparency and filter aware)
610 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
616 <!-- JAL-3205 -->Symmetric score matrices for faster
617 tree and PCA calculations
619 <li><strong>Principal Components Analysis Viewer</strong>
622 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
623 and Viewer state saved in Jalview Project
625 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
628 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
632 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
637 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
639 <li><strong>Speed and Efficiency</strong>
642 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
643 multiple groups when working with large alignments
646 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
650 <li><strong>User Interface</strong>
653 <!-- JAL-2933 -->Finder panel remembers last position in each
657 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
658 what is shown)<br />Only visible regions of alignment are shown by
659 default (can be changed in user preferences)
662 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
663 to the Overwrite Dialog
666 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
670 <!-- JAL-1244 -->Status bar shows bounds when dragging a
671 selection region, and gap count when inserting or deleting gaps
674 <!-- JAL-3132 -->Status bar updates over sequence and annotation
678 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
682 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
686 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
689 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
693 <!-- JAL-3181 -->Consistent ordering of links in sequence id
697 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
699 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
703 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
704 <li><strong>Java 11 Support (not yet on general release)</strong>
707 <!-- -->OSX GUI integrations for App menu's 'About' entry and
712 <em>Deprecations</em>
714 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
715 capabilities removed from the Jalview Desktop
717 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
718 unmarshalling has been replaced by JAXB for Jalview projects
719 and XML based data retrieval clients</li>
720 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
721 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
722 </ul> <em>Documentation</em>
724 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
725 not supported in EPS figure export
727 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
728 </ul> <em>Development and Release Processes</em>
731 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
734 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
736 <!-- JAL-3225 -->Eclipse project configuration managed with
740 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
741 Bamboo continuous integration for unattended Test Suite
745 <!-- JAL-2864 -->Memory test suite to detect leaks in common
749 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
753 <!-- JAL-3248 -->Developer documentation migrated to
754 markdown (with HTML rendering)
757 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
760 <!-- JAL-3289 -->New URLs for publishing development
765 <td align="left" valign="top">
768 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
771 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
772 superposition in Jmol fail on Windows
775 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
776 structures for sequences with lots of PDB structures
779 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
783 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
784 project involving multiple views
787 <!-- JAL-3164 -->Overview for complementary view in a linked
788 CDS/Protein alignment is not updated when Hide Columns by
789 Annotation dialog hides columns
792 <!-- JAL-3158 -->Selection highlighting in the complement of a
793 CDS/Protein alignment stops working after making a selection in
794 one view, then making another selection in the other view
797 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
801 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
802 Settings and Jalview Preferences panels
805 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
806 overview with large alignments
809 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
810 region if columns were selected by dragging right-to-left and the
811 mouse moved to the left of the first column
814 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
815 hidden column marker via scale popup menu
818 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
819 doesn't tell users the invalid URL
822 <!-- JAL-2816 -->Tooltips displayed for features filtered by
826 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
827 show cross references or Fetch Database References are shown in
831 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
832 peptide sequence (computed variant shown as p.Res.null)
835 <!-- JAL-2060 -->'Graduated colour' option not offered for
836 manually created features (where feature score is Float.NaN)
839 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
840 when columns are hidden
843 <!-- JAL-3082 -->Regular expression error for '(' in Select
844 Columns by Annotation description
847 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
848 out of Scale or Annotation Panel
851 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
855 <!-- JAL-3074 -->Left/right drag in annotation can scroll
859 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
863 <!-- JAL-3002 -->Column display is out by one after Page Down,
864 Page Up in wrapped mode
867 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
870 <!-- JAL-2932 -->Finder searches in minimised alignments
873 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
874 on opening an alignment
877 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
881 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
882 different groups in the alignment are selected
885 <!-- JAL-2717 -->Internationalised colour scheme names not shown
889 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
893 <!-- JAL-3125 -->Value input for graduated feature colour
894 threshold gets 'unrounded'
897 <!-- JAL-2982 -->PCA image export doesn't respect background
901 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
904 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
907 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
911 <!-- JAL-2964 -->Associate Tree with All Views not restored from
915 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
916 shown in complementary view
919 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
920 without normalisation
923 <!-- JAL-3021 -->Sequence Details report should open positioned at top
927 <!-- JAL-914 -->Help page can be opened twice
930 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
932 </ul> <em>Editing</em>
935 <!-- JAL-2822 -->Start and End should be updated when sequence
936 data at beginning or end of alignment added/removed via 'Edit'
940 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
941 relocate sequence features correctly when start of sequence is
942 removed (Known defect since 2.10)
945 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
946 dialog corrupts dataset sequence
949 <!-- JAL-868 -->Structure colours not updated when associated tree
950 repartitions the alignment view (Regression in 2.10.5)
952 </ul> <em>Datamodel</em>
955 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
956 sequence's End is greater than its length
958 </ul> <em>Bugs fixed for Java 11 Support (not yet on
959 general release)</em>
962 <!-- JAL-3288 -->Menus work properly in split-screen
964 </ul> <em>New Known Defects</em>
967 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
970 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
971 regions of protein alignment.
974 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
975 is restored from a Jalview 2.11 project
978 <!-- JAL-3213 -->Alignment panel height can be too small after
982 <!-- JAL-3240 -->Display is incorrect after removing gapped
983 columns within hidden columns
986 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
987 window after dragging left to select columns to left of visible
991 <!-- JAL-2876 -->Features coloured according to their description
992 string and thresholded by score in earlier versions of Jalview are
993 not shown as thresholded features in 2.11. To workaround please
994 create a Score filter instead.
997 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
999 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1002 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1003 alignments with multiple views can close views unexpectedly
1006 <em>Java 11 Specific defects</em>
1009 <!-- JAL-3235 -->Jalview Properties file is not sorted
1010 alphabetically when saved
1016 <td width="60" nowrap>
1017 <div align="center">
1018 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1021 <td><div align="left">
1025 <!-- JAL-3101 -->Default memory for Jalview webstart and
1026 InstallAnywhere increased to 1G.
1029 <!-- JAL-247 -->Hidden sequence markers and representative
1030 sequence bolding included when exporting alignment as EPS,
1031 SVG, PNG or HTML. <em>Display is configured via the
1032 Format menu, or for command-line use via a Jalview
1033 properties file.</em>
1036 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1037 API and sequence data now imported as JSON.
1040 <!-- JAL-3065 -->Change in recommended way of starting
1041 Jalview via a Java command line: add jars in lib directory
1042 to CLASSPATH, rather than via the deprecated java.ext.dirs
1046 <em>Development</em>
1049 <!-- JAL-3047 -->Support added to execute test suite
1050 instrumented with <a href="http://openclover.org/">Open
1055 <td><div align="left">
1059 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1060 row shown in Feredoxin Structure alignment view of example
1064 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1065 annotation displayed.
1068 <!-- JAL-3107 -->Group conservation/consensus not shown
1069 for newly created group when 'Apply to all groups'
1073 <!-- JAL-3087 -->Corrupted display when switching to
1074 wrapped mode when sequence panel's vertical scrollbar is
1078 <!-- JAL-3003 -->Alignment is black in exported EPS file
1079 when sequences are selected in exported view.</em>
1082 <!-- JAL-3059 -->Groups with different coloured borders
1083 aren't rendered with correct colour.
1086 <!-- JAL-3092 -->Jalview could hang when importing certain
1087 types of knotted RNA secondary structure.
1090 <!-- JAL-3095 -->Sequence highlight and selection in
1091 trimmed VARNA 2D structure is incorrect for sequences that
1095 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1096 annotation when columns are inserted into an alignment,
1097 and when exporting as Stockholm flatfile.
1100 <!-- JAL-3053 -->Jalview annotation rows containing upper
1101 and lower-case 'E' and 'H' do not automatically get
1102 treated as RNA secondary structure.
1105 <!-- JAL-3106 -->.jvp should be used as default extension
1106 (not .jar) when saving a Jalview project file.
1109 <!-- JAL-3105 -->Mac Users: closing a window correctly
1110 transfers focus to previous window on OSX
1113 <em>Java 10 Issues Resolved</em>
1116 <!-- JAL-2988 -->OSX - Can't save new files via the File
1117 or export menus by typing in a name into the Save dialog
1121 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1122 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1123 'look and feel' which has improved compatibility with the
1124 latest version of OSX.
1131 <td width="60" nowrap>
1132 <div align="center">
1133 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1134 <em>7/06/2018</em></strong>
1137 <td><div align="left">
1141 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1142 annotation retrieved from Uniprot
1145 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1146 onto the Jalview Desktop
1150 <td><div align="left">
1154 <!-- JAL-3017 -->Cannot import features with multiple
1155 variant elements (blocks import of some Uniprot records)
1158 <!-- JAL-2997 -->Clustal files with sequence positions in
1159 right-hand column parsed correctly
1162 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1163 not alignment area in exported graphic
1166 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1167 window has input focus
1170 <!-- JAL-2992 -->Annotation panel set too high when
1171 annotation added to view (Windows)
1174 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1175 network connectivity is poor
1178 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1179 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1180 the currently open URL and links from a page viewed in
1181 Firefox or Chrome on Windows is now fully supported. If
1182 you are using Edge, only links in the page can be
1183 dragged, and with Internet Explorer, only the currently
1184 open URL in the browser can be dropped onto Jalview.</em>
1187 <em>New Known Defects</em>
1189 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1194 <td width="60" nowrap>
1195 <div align="center">
1196 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1199 <td><div align="left">
1203 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1204 for disabling automatic superposition of multiple
1205 structures and open structures in existing views
1208 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1209 ID and annotation area margins can be click-dragged to
1213 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1217 <!-- JAL-2759 -->Improved performance for large alignments
1218 and lots of hidden columns
1221 <!-- JAL-2593 -->Improved performance when rendering lots
1222 of features (particularly when transparency is disabled)
1225 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1226 exchange of Jalview features and Chimera attributes made
1232 <td><div align="left">
1235 <!-- JAL-2899 -->Structure and Overview aren't updated
1236 when Colour By Annotation threshold slider is adjusted
1239 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1240 overlapping alignment panel
1243 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1247 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1248 improved: CDS not handled correctly if transcript has no
1252 <!-- JAL-2321 -->Secondary structure and temperature
1253 factor annotation not added to sequence when local PDB
1254 file associated with it by drag'n'drop or structure
1258 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1259 dialog doesn't import PDB files dropped on an alignment
1262 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1263 scroll bar doesn't work for some CDS/Protein views
1266 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1267 Java 1.8u153 onwards and Java 1.9u4+.
1270 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1271 columns in annotation row
1274 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1275 honored in batch mode
1278 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1279 for structures added to existing Jmol view
1282 <!-- JAL-2223 -->'View Mappings' includes duplicate
1283 entries after importing project with multiple views
1286 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1287 protein sequences via SIFTS from associated PDB entries
1288 with negative residue numbers or missing residues fails
1291 <!-- JAL-2952 -->Exception when shading sequence with negative
1292 Temperature Factor values from annotated PDB files (e.g.
1293 as generated by CONSURF)
1296 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1297 tooltip doesn't include a text description of mutation
1300 <!-- JAL-2922 -->Invert displayed features very slow when
1301 structure and/or overview windows are also shown
1304 <!-- JAL-2954 -->Selecting columns from highlighted regions
1305 very slow for alignments with large numbers of sequences
1308 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1309 with 'StringIndexOutOfBounds'
1312 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1313 platforms running Java 10
1316 <!-- JAL-2960 -->Adding a structure to existing structure
1317 view appears to do nothing because the view is hidden behind the alignment view
1323 <!-- JAL-2926 -->Copy consensus sequence option in applet
1324 should copy the group consensus when popup is opened on it
1330 <!-- JAL-2913 -->Fixed ID width preference is not respected
1333 <em>New Known Defects</em>
1336 <!-- JAL-2973 --> Exceptions occasionally raised when
1337 editing a large alignment and overview is displayed
1340 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1341 repeatedly after a series of edits even when the overview
1342 is no longer reflecting updates
1345 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1346 structures for protein subsequence (if 'Trim Retrieved
1347 Sequences' enabled) or Ensembl isoforms (Workaround in
1348 2.10.4 is to fail back to N&W mapping)
1351 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1352 option gives blank output
1359 <td width="60" nowrap>
1360 <div align="center">
1361 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1364 <td><div align="left">
1365 <ul><li>Updated Certum Codesigning Certificate
1366 (Valid till 30th November 2018)</li></ul></div></td>
1367 <td><div align="left">
1368 <em>Desktop</em><ul>
1370 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1371 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1372 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1373 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1374 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1375 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1376 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1382 <td width="60" nowrap>
1383 <div align="center">
1384 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1387 <td><div align="left">
1391 <!-- JAL-2446 -->Faster and more efficient management and
1392 rendering of sequence features
1395 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1396 429 rate limit request hander
1399 <!-- JAL-2773 -->Structure views don't get updated unless
1400 their colours have changed
1403 <!-- JAL-2495 -->All linked sequences are highlighted for
1404 a structure mousover (Jmol) or selection (Chimera)
1407 <!-- JAL-2790 -->'Cancel' button in progress bar for
1408 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1411 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1412 view from Ensembl locus cross-references
1415 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1419 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1420 feature can be disabled
1423 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1424 PDB easier retrieval of sequences for lists of IDs
1427 <!-- JAL-2758 -->Short names for sequences retrieved from
1433 <li>Groovy interpreter updated to 2.4.12</li>
1434 <li>Example groovy script for generating a matrix of
1435 percent identity scores for current alignment.</li>
1437 <em>Testing and Deployment</em>
1440 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1444 <td><div align="left">
1448 <!-- JAL-2643 -->Pressing tab after updating the colour
1449 threshold text field doesn't trigger an update to the
1453 <!-- JAL-2682 -->Race condition when parsing sequence ID
1457 <!-- JAL-2608 -->Overview windows are also closed when
1458 alignment window is closed
1461 <!-- JAL-2548 -->Export of features doesn't always respect
1465 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1466 takes a long time in Cursor mode
1472 <!-- JAL-2777 -->Structures with whitespace chainCode
1473 cannot be viewed in Chimera
1476 <!-- JAL-2728 -->Protein annotation panel too high in
1480 <!-- JAL-2757 -->Can't edit the query after the server
1481 error warning icon is shown in Uniprot and PDB Free Text
1485 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1488 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1491 <!-- JAL-2739 -->Hidden column marker in last column not
1492 rendered when switching back from Wrapped to normal view
1495 <!-- JAL-2768 -->Annotation display corrupted when
1496 scrolling right in unwapped alignment view
1499 <!-- JAL-2542 -->Existing features on subsequence
1500 incorrectly relocated when full sequence retrieved from
1504 <!-- JAL-2733 -->Last reported memory still shown when
1505 Desktop->Show Memory is unticked (OSX only)
1508 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1509 features of same type and group to be selected for
1513 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1514 alignments when hidden columns are present
1517 <!-- JAL-2392 -->Jalview freezes when loading and
1518 displaying several structures
1521 <!-- JAL-2732 -->Black outlines left after resizing or
1525 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1526 within the Jalview desktop on OSX
1529 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1530 when in wrapped alignment mode
1533 <!-- JAL-2636 -->Scale mark not shown when close to right
1534 hand end of alignment
1537 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1538 each selected sequence do not have correct start/end
1542 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1543 after canceling the Alignment Window's Font dialog
1546 <!-- JAL-2036 -->Show cross-references not enabled after
1547 restoring project until a new view is created
1550 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1551 URL links appears when only default EMBL-EBI link is
1552 configured (since 2.10.2b2)
1555 <!-- JAL-2775 -->Overview redraws whole window when box
1556 position is adjusted
1559 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1560 in a multi-chain structure when viewing alignment
1561 involving more than one chain (since 2.10)
1564 <!-- JAL-2811 -->Double residue highlights in cursor mode
1565 if new selection moves alignment window
1568 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1569 arrow key in cursor mode to pass hidden column marker
1572 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1573 that produces correctly annotated transcripts and products
1576 <!-- JAL-2776 -->Toggling a feature group after first time
1577 doesn't update associated structure view
1580 <em>Applet</em><br />
1583 <!-- JAL-2687 -->Concurrent modification exception when
1584 closing alignment panel
1587 <em>BioJSON</em><br />
1590 <!-- JAL-2546 -->BioJSON export does not preserve
1591 non-positional features
1594 <em>New Known Issues</em>
1597 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1598 sequence features correctly (for many previous versions of
1602 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1603 using cursor in wrapped panel other than top
1606 <!-- JAL-2791 -->Select columns containing feature ignores
1607 graduated colour threshold
1610 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1611 always preserve numbering and sequence features
1614 <em>Known Java 9 Issues</em>
1617 <!-- JAL-2902 -->Groovy Console very slow to open and is
1618 not responsive when entering characters (Webstart, Java
1625 <td width="60" nowrap>
1626 <div align="center">
1627 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1628 <em>2/10/2017</em></strong>
1631 <td><div align="left">
1632 <em>New features in Jalview Desktop</em>
1635 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1637 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1641 <td><div align="left">
1645 <td width="60" nowrap>
1646 <div align="center">
1647 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1648 <em>7/9/2017</em></strong>
1651 <td><div align="left">
1655 <!-- JAL-2588 -->Show gaps in overview window by colouring
1656 in grey (sequences used to be coloured grey, and gaps were
1660 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1664 <!-- JAL-2587 -->Overview updates immediately on increase
1665 in size and progress bar shown as higher resolution
1666 overview is recalculated
1671 <td><div align="left">
1675 <!-- JAL-2664 -->Overview window redraws every hidden
1676 column region row by row
1679 <!-- JAL-2681 -->duplicate protein sequences shown after
1680 retrieving Ensembl crossrefs for sequences from Uniprot
1683 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1684 format setting is unticked
1687 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1688 if group has show boxes format setting unticked
1691 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1692 autoscrolling whilst dragging current selection group to
1693 include sequences and columns not currently displayed
1696 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1697 assemblies are imported via CIF file
1700 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1701 displayed when threshold or conservation colouring is also
1705 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1709 <!-- JAL-2673 -->Jalview continues to scroll after
1710 dragging a selected region off the visible region of the
1714 <!-- JAL-2724 -->Cannot apply annotation based
1715 colourscheme to all groups in a view
1718 <!-- JAL-2511 -->IDs don't line up with sequences
1719 initially after font size change using the Font chooser or
1726 <td width="60" nowrap>
1727 <div align="center">
1728 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1731 <td><div align="left">
1732 <em>Calculations</em>
1736 <!-- JAL-1933 -->Occupancy annotation row shows number of
1737 ungapped positions in each column of the alignment.
1740 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1741 a calculation dialog box
1744 <!-- JAL-2379 -->Revised implementation of PCA for speed
1745 and memory efficiency (~30x faster)
1748 <!-- JAL-2403 -->Revised implementation of sequence
1749 similarity scores as used by Tree, PCA, Shading Consensus
1750 and other calculations
1753 <!-- JAL-2416 -->Score matrices are stored as resource
1754 files within the Jalview codebase
1757 <!-- JAL-2500 -->Trees computed on Sequence Feature
1758 Similarity may have different topology due to increased
1765 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1766 model for alignments and groups
1769 <!-- JAL-384 -->Custom shading schemes created via groovy
1776 <!-- JAL-2526 -->Efficiency improvements for interacting
1777 with alignment and overview windows
1780 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1784 <!-- JAL-2388 -->Hidden columns and sequences can be
1788 <!-- JAL-2611 -->Click-drag in visible area allows fine
1789 adjustment of visible position
1793 <em>Data import/export</em>
1796 <!-- JAL-2535 -->Posterior probability annotation from
1797 Stockholm files imported as sequence associated annotation
1800 <!-- JAL-2507 -->More robust per-sequence positional
1801 annotation input/output via stockholm flatfile
1804 <!-- JAL-2533 -->Sequence names don't include file
1805 extension when importing structure files without embedded
1806 names or PDB accessions
1809 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1810 format sequence substitution matrices
1813 <em>User Interface</em>
1816 <!-- JAL-2447 --> Experimental Features Checkbox in
1817 Desktop's Tools menu to hide or show untested features in
1821 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1822 via Overview or sequence motif search operations
1825 <!-- JAL-2547 -->Amend sequence features dialog box can be
1826 opened by double clicking gaps within sequence feature
1830 <!-- JAL-1476 -->Status bar message shown when not enough
1831 aligned positions were available to create a 3D structure
1835 <em>3D Structure</em>
1838 <!-- JAL-2430 -->Hidden regions in alignment views are not
1839 coloured in linked structure views
1842 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1843 file-based command exchange
1846 <!-- JAL-2375 -->Structure chooser automatically shows
1847 Cached Structures rather than querying the PDBe if
1848 structures are already available for sequences
1851 <!-- JAL-2520 -->Structures imported via URL are cached in
1852 the Jalview project rather than downloaded again when the
1853 project is reopened.
1856 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1857 to transfer Chimera's structure attributes as Jalview
1858 features, and vice-versa (<strong>Experimental
1862 <em>Web Services</em>
1865 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1868 <!-- JAL-2335 -->Filter non-standard amino acids and
1869 nucleotides when submitting to AACon and other MSA
1873 <!-- JAL-2316, -->URLs for viewing database
1874 cross-references provided by identifiers.org and the
1875 EMBL-EBI's MIRIAM DB
1882 <!-- JAL-2344 -->FileFormatI interface for describing and
1883 identifying file formats (instead of String constants)
1886 <!-- JAL-2228 -->FeatureCounter script refactored for
1887 efficiency when counting all displayed features (not
1888 backwards compatible with 2.10.1)
1891 <em>Example files</em>
1894 <!-- JAL-2631 -->Graduated feature colour style example
1895 included in the example feature file
1898 <em>Documentation</em>
1901 <!-- JAL-2339 -->Release notes reformatted for readability
1902 with the built-in Java help viewer
1905 <!-- JAL-1644 -->Find documentation updated with 'search
1906 sequence description' option
1912 <!-- JAL-2485, -->External service integration tests for
1913 Uniprot REST Free Text Search Client
1916 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1919 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1924 <td><div align="left">
1925 <em>Calculations</em>
1928 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1929 matrix - C->R should be '-3'<br />Old matrix restored
1930 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1932 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1933 Jalview's treatment of gaps in PCA and substitution matrix
1934 based Tree calculations.<br /> <br />In earlier versions
1935 of Jalview, gaps matching gaps were penalised, and gaps
1936 matching non-gaps penalised even more. In the PCA
1937 calculation, gaps were actually treated as non-gaps - so
1938 different costs were applied, which meant Jalview's PCAs
1939 were different to those produced by SeqSpace.<br />Jalview
1940 now treats gaps in the same way as SeqSpace (ie it scores
1941 them as 0). <br /> <br />Enter the following in the
1942 Groovy console to restore pre-2.10.2 behaviour:<br />
1943 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1944 // for 2.10.1 mode <br />
1945 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1946 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1947 these settings will affect all subsequent tree and PCA
1948 calculations (not recommended)</em></li>
1950 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1951 scaling of branch lengths for trees computed using
1952 Sequence Feature Similarity.
1955 <!-- JAL-2377 -->PCA calculation could hang when
1956 generating output report when working with highly
1957 redundant alignments
1960 <!-- JAL-2544 --> Sort by features includes features to
1961 right of selected region when gaps present on right-hand
1965 <em>User Interface</em>
1968 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1969 doesn't reselect a specific sequence's associated
1970 annotation after it was used for colouring a view
1973 <!-- JAL-2419 -->Current selection lost if popup menu
1974 opened on a region of alignment without groups
1977 <!-- JAL-2374 -->Popup menu not always shown for regions
1978 of an alignment with overlapping groups
1981 <!-- JAL-2310 -->Finder double counts if both a sequence's
1982 name and description match
1985 <!-- JAL-2370 -->Hiding column selection containing two
1986 hidden regions results in incorrect hidden regions
1989 <!-- JAL-2386 -->'Apply to all groups' setting when
1990 changing colour does not apply Conservation slider value
1994 <!-- JAL-2373 -->Percentage identity and conservation menu
1995 items do not show a tick or allow shading to be disabled
1998 <!-- JAL-2385 -->Conservation shading or PID threshold
1999 lost when base colourscheme changed if slider not visible
2002 <!-- JAL-2547 -->Sequence features shown in tooltip for
2003 gaps before start of features
2006 <!-- JAL-2623 -->Graduated feature colour threshold not
2007 restored to UI when feature colour is edited
2010 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2011 a time when scrolling vertically in wrapped mode.
2014 <!-- JAL-2630 -->Structure and alignment overview update
2015 as graduate feature colour settings are modified via the
2019 <!-- JAL-2034 -->Overview window doesn't always update
2020 when a group defined on the alignment is resized
2023 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2024 wrapped view result in positional status updates
2028 <!-- JAL-2563 -->Status bar doesn't show position for
2029 ambiguous amino acid and nucleotide symbols
2032 <!-- JAL-2602 -->Copy consensus sequence failed if
2033 alignment included gapped columns
2036 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2037 widgets don't permanently disappear
2040 <!-- JAL-2503 -->Cannot select or filter quantitative
2041 annotation that are shown only as column labels (e.g.
2042 T-Coffee column reliability scores)
2045 <!-- JAL-2594 -->Exception thrown if trying to create a
2046 sequence feature on gaps only
2049 <!-- JAL-2504 -->Features created with 'New feature'
2050 button from a Find inherit previously defined feature type
2051 rather than the Find query string
2054 <!-- JAL-2423 -->incorrect title in output window when
2055 exporting tree calculated in Jalview
2058 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2059 and then revealing them reorders sequences on the
2063 <!-- JAL-964 -->Group panel in sequence feature settings
2064 doesn't update to reflect available set of groups after
2065 interactively adding or modifying features
2068 <!-- JAL-2225 -->Sequence Database chooser unusable on
2072 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2073 only excluded gaps in current sequence and ignored
2080 <!-- JAL-2421 -->Overview window visible region moves
2081 erratically when hidden rows or columns are present
2084 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2085 Structure Viewer's colour menu don't correspond to
2089 <!-- JAL-2405 -->Protein specific colours only offered in
2090 colour and group colour menu for protein alignments
2093 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2094 reflect currently selected view or group's shading
2098 <!-- JAL-2624 -->Feature colour thresholds not respected
2099 when rendered on overview and structures when opacity at
2103 <!-- JAL-2589 -->User defined gap colour not shown in
2104 overview when features overlaid on alignment
2107 <!-- JAL-2567 -->Feature settings for different views not
2108 recovered correctly from Jalview project file
2111 <!-- JAL-2256 -->Feature colours in overview when first opened
2112 (automatically via preferences) are different to the main
2116 <em>Data import/export</em>
2119 <!-- JAL-2576 -->Very large alignments take a long time to
2123 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2124 added after a sequence was imported are not written to
2128 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2129 when importing RNA secondary structure via Stockholm
2132 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2133 not shown in correct direction for simple pseudoknots
2136 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2137 with lightGray or darkGray via features file (but can
2141 <!-- JAL-2383 -->Above PID colour threshold not recovered
2142 when alignment view imported from project
2145 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2146 structure and sequences extracted from structure files
2147 imported via URL and viewed in Jmol
2150 <!-- JAL-2520 -->Structures loaded via URL are saved in
2151 Jalview Projects rather than fetched via URL again when
2152 the project is loaded and the structure viewed
2155 <em>Web Services</em>
2158 <!-- JAL-2519 -->EnsemblGenomes example failing after
2159 release of Ensembl v.88
2162 <!-- JAL-2366 -->Proxy server address and port always
2163 appear enabled in Preferences->Connections
2166 <!-- JAL-2461 -->DAS registry not found exceptions
2167 removed from console output
2170 <!-- JAL-2582 -->Cannot retrieve protein products from
2171 Ensembl by Peptide ID
2174 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2175 created from SIFTs, and spurious 'Couldn't open structure
2176 in Chimera' errors raised after April 2017 update (problem
2177 due to 'null' string rather than empty string used for
2178 residues with no corresponding PDB mapping).
2181 <em>Application UI</em>
2184 <!-- JAL-2361 -->User Defined Colours not added to Colour
2188 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2189 case' residues (button in colourscheme editor debugged and
2190 new documentation and tooltips added)
2193 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2194 doesn't restore group-specific text colour thresholds
2197 <!-- JAL-2243 -->Feature settings panel does not update as
2198 new features are added to alignment
2201 <!-- JAL-2532 -->Cancel in feature settings reverts
2202 changes to feature colours via the Amend features dialog
2205 <!-- JAL-2506 -->Null pointer exception when attempting to
2206 edit graduated feature colour via amend features dialog
2210 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2211 selection menu changes colours of alignment views
2214 <!-- JAL-2426 -->Spurious exceptions in console raised
2215 from alignment calculation workers after alignment has
2219 <!-- JAL-1608 -->Typo in selection popup menu - Create
2220 groups now 'Create Group'
2223 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2224 Create/Undefine group doesn't always work
2227 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2228 shown again after pressing 'Cancel'
2231 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2232 adjusts start position in wrap mode
2235 <!-- JAL-2563 -->Status bar doesn't show positions for
2236 ambiguous amino acids
2239 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2240 CDS/Protein view after CDS sequences added for aligned
2244 <!-- JAL-2592 -->User defined colourschemes called 'User
2245 Defined' don't appear in Colours menu
2251 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2252 score models doesn't always result in an updated PCA plot
2255 <!-- JAL-2442 -->Features not rendered as transparent on
2256 overview or linked structure view
2259 <!-- JAL-2372 -->Colour group by conservation doesn't
2263 <!-- JAL-2517 -->Hitting Cancel after applying
2264 user-defined colourscheme doesn't restore original
2271 <!-- JAL-2314 -->Unit test failure:
2272 jalview.ws.jabaws.RNAStructExportImport setup fails
2275 <!-- JAL-2307 -->Unit test failure:
2276 jalview.ws.sifts.SiftsClientTest due to compatibility
2277 problems with deep array comparison equality asserts in
2278 successive versions of TestNG
2281 <!-- JAL-2479 -->Relocated StructureChooserTest and
2282 ParameterUtilsTest Unit tests to Network suite
2285 <em>New Known Issues</em>
2288 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2289 phase after a sequence motif find operation
2292 <!-- JAL-2550 -->Importing annotation file with rows
2293 containing just upper and lower case letters are
2294 interpreted as WUSS RNA secondary structure symbols
2297 <!-- JAL-2590 -->Cannot load and display Newick trees
2298 reliably from eggnog Ortholog database
2301 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2302 containing features of type Highlight' when 'B' is pressed
2303 to mark columns containing highlighted regions.
2306 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2307 doesn't always add secondary structure annotation.
2312 <td width="60" nowrap>
2313 <div align="center">
2314 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2317 <td><div align="left">
2321 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2322 for all consensus calculations
2325 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2328 <li>Updated Jalview's Certum code signing certificate
2331 <em>Application</em>
2334 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2335 set of database cross-references, sorted alphabetically
2338 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2339 from database cross references. Users with custom links
2340 will receive a <a href="webServices/urllinks.html#warning">warning
2341 dialog</a> asking them to update their preferences.
2344 <!-- JAL-2287-->Cancel button and escape listener on
2345 dialog warning user about disconnecting Jalview from a
2349 <!-- JAL-2320-->Jalview's Chimera control window closes if
2350 the Chimera it is connected to is shut down
2353 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2354 columns menu item to mark columns containing highlighted
2355 regions (e.g. from structure selections or results of a
2359 <!-- JAL-2284-->Command line option for batch-generation
2360 of HTML pages rendering alignment data with the BioJS
2370 <!-- JAL-2286 -->Columns with more than one modal residue
2371 are not coloured or thresholded according to percent
2372 identity (first observed in Jalview 2.8.2)
2375 <!-- JAL-2301 -->Threonine incorrectly reported as not
2379 <!-- JAL-2318 -->Updates to documentation pages (above PID
2380 threshold, amino acid properties)
2383 <!-- JAL-2292 -->Lower case residues in sequences are not
2384 reported as mapped to residues in a structure file in the
2388 <!--JAL-2324 -->Identical features with non-numeric scores
2389 could be added multiple times to a sequence
2392 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2393 bond features shown as two highlighted residues rather
2394 than a range in linked structure views, and treated
2395 correctly when selecting and computing trees from features
2398 <!-- JAL-2281-->Custom URL links for database
2399 cross-references are matched to database name regardless
2404 <em>Application</em>
2407 <!-- JAL-2282-->Custom URL links for specific database
2408 names without regular expressions also offer links from
2412 <!-- JAL-2315-->Removing a single configured link in the
2413 URL links pane in Connections preferences doesn't actually
2414 update Jalview configuration
2417 <!-- JAL-2272-->CTRL-Click on a selected region to open
2418 the alignment area popup menu doesn't work on El-Capitan
2421 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2422 files with similarly named sequences if dropped onto the
2426 <!-- JAL-2312 -->Additional mappings are shown for PDB
2427 entries where more chains exist in the PDB accession than
2428 are reported in the SIFTS file
2431 <!-- JAL-2317-->Certain structures do not get mapped to
2432 the structure view when displayed with Chimera
2435 <!-- JAL-2317-->No chains shown in the Chimera view
2436 panel's View->Show Chains submenu
2439 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2440 work for wrapped alignment views
2443 <!--JAL-2197 -->Rename UI components for running JPred
2444 predictions from 'JNet' to 'JPred'
2447 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2448 corrupted when annotation panel vertical scroll is not at
2449 first annotation row
2452 <!--JAL-2332 -->Attempting to view structure for Hen
2453 lysozyme results in a PDB Client error dialog box
2456 <!-- JAL-2319 -->Structure View's mapping report switched
2457 ranges for PDB and sequence for SIFTS
2460 SIFTS 'Not_Observed' residues mapped to non-existant
2464 <!-- <em>New Known Issues</em>
2471 <td width="60" nowrap>
2472 <div align="center">
2473 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2474 <em>25/10/2016</em></strong>
2477 <td><em>Application</em>
2479 <li>3D Structure chooser opens with 'Cached structures'
2480 view if structures already loaded</li>
2481 <li>Progress bar reports models as they are loaded to
2482 structure views</li>
2488 <li>Colour by conservation always enabled and no tick
2489 shown in menu when BLOSUM or PID shading applied</li>
2490 <li>FER1_ARATH and FER2_ARATH labels were switched in
2491 example sequences/projects/trees</li>
2493 <em>Application</em>
2495 <li>Jalview projects with views of local PDB structure
2496 files saved on Windows cannot be opened on OSX</li>
2497 <li>Multiple structure views can be opened and superposed
2498 without timeout for structures with multiple models or
2499 multiple sequences in alignment</li>
2500 <li>Cannot import or associated local PDB files without a
2501 PDB ID HEADER line</li>
2502 <li>RMSD is not output in Jmol console when superposition
2504 <li>Drag and drop of URL from Browser fails for Linux and
2505 OSX versions earlier than El Capitan</li>
2506 <li>ENA client ignores invalid content from ENA server</li>
2507 <li>Exceptions are not raised in console when ENA client
2508 attempts to fetch non-existent IDs via Fetch DB Refs UI
2510 <li>Exceptions are not raised in console when a new view
2511 is created on the alignment</li>
2512 <li>OSX right-click fixed for group selections: CMD-click
2513 to insert/remove gaps in groups and CTRL-click to open group
2516 <em>Build and deployment</em>
2518 <li>URL link checker now copes with multi-line anchor
2521 <em>New Known Issues</em>
2523 <li>Drag and drop from URL links in browsers do not work
2530 <td width="60" nowrap>
2531 <div align="center">
2532 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2535 <td><em>General</em>
2538 <!-- JAL-2124 -->Updated Spanish translations.
2541 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2542 for importing structure data to Jalview. Enables mmCIF and
2546 <!-- JAL-192 --->Alignment ruler shows positions relative to
2550 <!-- JAL-2202 -->Position/residue shown in status bar when
2551 mousing over sequence associated annotation
2554 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2558 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2559 '()', canonical '[]' and invalid '{}' base pair populations
2563 <!-- JAL-2092 -->Feature settings popup menu options for
2564 showing or hiding columns containing a feature
2567 <!-- JAL-1557 -->Edit selected group by double clicking on
2568 group and sequence associated annotation labels
2571 <!-- JAL-2236 -->Sequence name added to annotation label in
2572 select/hide columns by annotation and colour by annotation
2576 </ul> <em>Application</em>
2579 <!-- JAL-2050-->Automatically hide introns when opening a
2580 gene/transcript view
2583 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2587 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2588 structure mappings with the EMBL-EBI PDBe SIFTS database
2591 <!-- JAL-2079 -->Updated download sites used for Rfam and
2592 Pfam sources to xfam.org
2595 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2598 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2599 over sequences in Jalview
2602 <!-- JAL-2027-->Support for reverse-complement coding
2603 regions in ENA and EMBL
2606 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2607 for record retrieval via ENA rest API
2610 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2614 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2615 groovy script execution
2618 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2619 alignment window's Calculate menu
2622 <!-- JAL-1812 -->Allow groovy scripts that call
2623 Jalview.getAlignFrames() to run in headless mode
2626 <!-- JAL-2068 -->Support for creating new alignment
2627 calculation workers from groovy scripts
2630 <!-- JAL-1369 --->Store/restore reference sequence in
2634 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2635 associations are now saved/restored from project
2638 <!-- JAL-1993 -->Database selection dialog always shown
2639 before sequence fetcher is opened
2642 <!-- JAL-2183 -->Double click on an entry in Jalview's
2643 database chooser opens a sequence fetcher
2646 <!-- JAL-1563 -->Free-text search client for UniProt using
2647 the UniProt REST API
2650 <!-- JAL-2168 -->-nonews command line parameter to prevent
2651 the news reader opening
2654 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2655 querying stored in preferences
2658 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2662 <!-- JAL-1977-->Tooltips shown on database chooser
2665 <!-- JAL-391 -->Reverse complement function in calculate
2666 menu for nucleotide sequences
2669 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2670 and feature counts preserves alignment ordering (and
2671 debugged for complex feature sets).
2674 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2675 viewing structures with Jalview 2.10
2678 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2679 genome, transcript CCDS and gene ids via the Ensembl and
2680 Ensembl Genomes REST API
2683 <!-- JAL-2049 -->Protein sequence variant annotation
2684 computed for 'sequence_variant' annotation on CDS regions
2688 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2692 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2693 Ref Fetcher fails to match, or otherwise updates sequence
2694 data from external database records.
2697 <!-- JAL-2154 -->Revised Jalview Project format for
2698 efficient recovery of sequence coding and alignment
2699 annotation relationships.
2701 </ul> <!-- <em>Applet</em>
2712 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2716 <!-- JAL-2018-->Export features in Jalview format (again)
2717 includes graduated colourschemes
2720 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2721 working with big alignments and lots of hidden columns
2724 <!-- JAL-2053-->Hidden column markers not always rendered
2725 at right of alignment window
2728 <!-- JAL-2067 -->Tidied up links in help file table of
2732 <!-- JAL-2072 -->Feature based tree calculation not shown
2736 <!-- JAL-2075 -->Hidden columns ignored during feature
2737 based tree calculation
2740 <!-- JAL-2065 -->Alignment view stops updating when show
2741 unconserved enabled for group on alignment
2744 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2748 <!-- JAL-2146 -->Alignment column in status incorrectly
2749 shown as "Sequence position" when mousing over
2753 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2754 hidden columns present
2757 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2758 user created annotation added to alignment
2761 <!-- JAL-1841 -->RNA Structure consensus only computed for
2762 '()' base pair annotation
2765 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2766 in zero scores for all base pairs in RNA Structure
2770 <!-- JAL-2174-->Extend selection with columns containing
2774 <!-- JAL-2275 -->Pfam format writer puts extra space at
2775 beginning of sequence
2778 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2782 <!-- JAL-2238 -->Cannot create groups on an alignment from
2783 from a tree when t-coffee scores are shown
2786 <!-- JAL-1836,1967 -->Cannot import and view PDB
2787 structures with chains containing negative resnums (4q4h)
2790 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2794 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2795 to Clustal, PIR and PileUp output
2798 <!-- JAL-2008 -->Reordering sequence features that are
2799 not visible causes alignment window to repaint
2802 <!-- JAL-2006 -->Threshold sliders don't work in
2803 graduated colour and colour by annotation row for e-value
2804 scores associated with features and annotation rows
2807 <!-- JAL-1797 -->amino acid physicochemical conservation
2808 calculation should be case independent
2811 <!-- JAL-2173 -->Remove annotation also updates hidden
2815 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2816 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2817 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2820 <!-- JAL-2065 -->Null pointer exceptions and redraw
2821 problems when reference sequence defined and 'show
2822 non-conserved' enabled
2825 <!-- JAL-1306 -->Quality and Conservation are now shown on
2826 load even when Consensus calculation is disabled
2829 <!-- JAL-1932 -->Remove right on penultimate column of
2830 alignment does nothing
2833 <em>Application</em>
2836 <!-- JAL-1552-->URLs and links can't be imported by
2837 drag'n'drop on OSX when launched via webstart (note - not
2838 yet fixed for El Capitan)
2841 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2842 output when running on non-gb/us i18n platforms
2845 <!-- JAL-1944 -->Error thrown when exporting a view with
2846 hidden sequences as flat-file alignment
2849 <!-- JAL-2030-->InstallAnywhere distribution fails when
2853 <!-- JAL-2080-->Jalview very slow to launch via webstart
2854 (also hotfix for 2.9.0b2)
2857 <!-- JAL-2085 -->Cannot save project when view has a
2858 reference sequence defined
2861 <!-- JAL-1011 -->Columns are suddenly selected in other
2862 alignments and views when revealing hidden columns
2865 <!-- JAL-1989 -->Hide columns not mirrored in complement
2866 view in a cDNA/Protein splitframe
2869 <!-- JAL-1369 -->Cannot save/restore representative
2870 sequence from project when only one sequence is
2874 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2875 in Structure Chooser
2878 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2879 structure consensus didn't refresh annotation panel
2882 <!-- JAL-1962 -->View mapping in structure view shows
2883 mappings between sequence and all chains in a PDB file
2886 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2887 dialogs format columns correctly, don't display array
2888 data, sort columns according to type
2891 <!-- JAL-1975 -->Export complete shown after destination
2892 file chooser is cancelled during an image export
2895 <!-- JAL-2025 -->Error when querying PDB Service with
2896 sequence name containing special characters
2899 <!-- JAL-2024 -->Manual PDB structure querying should be
2903 <!-- JAL-2104 -->Large tooltips with broken HTML
2904 formatting don't wrap
2907 <!-- JAL-1128 -->Figures exported from wrapped view are
2908 truncated so L looks like I in consensus annotation
2911 <!-- JAL-2003 -->Export features should only export the
2912 currently displayed features for the current selection or
2916 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2917 after fetching cross-references, and restoring from
2921 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2922 followed in the structure viewer
2925 <!-- JAL-2163 -->Titles for individual alignments in
2926 splitframe not restored from project
2929 <!-- JAL-2145 -->missing autocalculated annotation at
2930 trailing end of protein alignment in transcript/product
2931 splitview when pad-gaps not enabled by default
2934 <!-- JAL-1797 -->amino acid physicochemical conservation
2938 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2939 article has been read (reopened issue due to
2940 internationalisation problems)
2943 <!-- JAL-1960 -->Only offer PDB structures in structure
2944 viewer based on sequence name, PDB and UniProt
2949 <!-- JAL-1976 -->No progress bar shown during export of
2953 <!-- JAL-2213 -->Structures not always superimposed after
2954 multiple structures are shown for one or more sequences.
2957 <!-- JAL-1370 -->Reference sequence characters should not
2958 be replaced with '.' when 'Show unconserved' format option
2962 <!-- JAL-1823 -->Cannot specify chain code when entering
2963 specific PDB id for sequence
2966 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2967 'Export hidden sequences' is enabled, but 'export hidden
2968 columns' is disabled.
2971 <!--JAL-2026-->Best Quality option in structure chooser
2972 selects lowest rather than highest resolution structures
2976 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2977 to sequence mapping in 'View Mappings' report
2980 <!-- JAL-2284 -->Unable to read old Jalview projects that
2981 contain non-XML data added after Jalvew wrote project.
2984 <!-- JAL-2118 -->Newly created annotation row reorders
2985 after clicking on it to create new annotation for a
2989 <!-- JAL-1980 -->Null Pointer Exception raised when
2990 pressing Add on an orphaned cut'n'paste window.
2992 <!-- may exclude, this is an external service stability issue JAL-1941
2993 -- > RNA 3D structure not added via DSSR service</li> -->
2998 <!-- JAL-2151 -->Incorrect columns are selected when
2999 hidden columns present before start of sequence
3002 <!-- JAL-1986 -->Missing dependencies on applet pages
3006 <!-- JAL-1947 -->Overview pixel size changes when
3007 sequences are hidden in applet
3010 <!-- JAL-1996 -->Updated instructions for applet
3011 deployment on examples pages.
3018 <td width="60" nowrap>
3019 <div align="center">
3020 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3021 <em>16/10/2015</em></strong>
3024 <td><em>General</em>
3026 <li>Time stamps for signed Jalview application and applet
3031 <em>Application</em>
3033 <li>Duplicate group consensus and conservation rows
3034 shown when tree is partitioned</li>
3035 <li>Erratic behaviour when tree partitions made with
3036 multiple cDNA/Protein split views</li>
3042 <td width="60" nowrap>
3043 <div align="center">
3044 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3045 <em>8/10/2015</em></strong>
3048 <td><em>General</em>
3050 <li>Updated Spanish translations of localized text for
3052 </ul> <em>Application</em>
3054 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3055 <li>Signed OSX InstallAnywhere installer<br></li>
3056 <li>Support for per-sequence based annotations in BioJSON</li>
3057 </ul> <em>Applet</em>
3059 <li>Split frame example added to applet examples page</li>
3060 </ul> <em>Build and Deployment</em>
3063 <!-- JAL-1888 -->New ant target for running Jalview's test
3071 <li>Mapping of cDNA to protein in split frames
3072 incorrect when sequence start > 1</li>
3073 <li>Broken images in filter column by annotation dialog
3075 <li>Feature colours not parsed from features file</li>
3076 <li>Exceptions and incomplete link URLs recovered when
3077 loading a features file containing HTML tags in feature
3081 <em>Application</em>
3083 <li>Annotations corrupted after BioJS export and
3085 <li>Incorrect sequence limits after Fetch DB References
3086 with 'trim retrieved sequences'</li>
3087 <li>Incorrect warning about deleting all data when
3088 deleting selected columns</li>
3089 <li>Patch to build system for shipping properly signed
3090 JNLP templates for webstart launch</li>
3091 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3092 unreleased structures for download or viewing</li>
3093 <li>Tab/space/return keystroke operation of EMBL-PDBe
3094 fetcher/viewer dialogs works correctly</li>
3095 <li>Disabled 'minimise' button on Jalview windows
3096 running on OSX to workaround redraw hang bug</li>
3097 <li>Split cDNA/Protein view position and geometry not
3098 recovered from jalview project</li>
3099 <li>Initial enabled/disabled state of annotation menu
3100 sorter 'show autocalculated first/last' corresponds to
3102 <li>Restoring of Clustal, RNA Helices and T-Coffee
3103 color schemes from BioJSON</li>
3107 <li>Reorder sequences mirrored in cDNA/Protein split
3109 <li>Applet with Jmol examples not loading correctly</li>
3115 <td><div align="center">
3116 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3118 <td><em>General</em>
3120 <li>Linked visualisation and analysis of DNA and Protein
3123 <li>Translated cDNA alignments shown as split protein
3124 and DNA alignment views</li>
3125 <li>Codon consensus annotation for linked protein and
3126 cDNA alignment views</li>
3127 <li>Link cDNA or Protein product sequences by loading
3128 them onto Protein or cDNA alignments</li>
3129 <li>Reconstruct linked cDNA alignment from aligned
3130 protein sequences</li>
3133 <li>Jmol integration updated to Jmol v14.2.14</li>
3134 <li>Import and export of Jalview alignment views as <a
3135 href="features/bioJsonFormat.html">BioJSON</a></li>
3136 <li>New alignment annotation file statements for
3137 reference sequences and marking hidden columns</li>
3138 <li>Reference sequence based alignment shading to
3139 highlight variation</li>
3140 <li>Select or hide columns according to alignment
3142 <li>Find option for locating sequences by description</li>
3143 <li>Conserved physicochemical properties shown in amino
3144 acid conservation row</li>
3145 <li>Alignments can be sorted by number of RNA helices</li>
3146 </ul> <em>Application</em>
3148 <li>New cDNA/Protein analysis capabilities
3150 <li>Get Cross-References should open a Split Frame
3151 view with cDNA/Protein</li>
3152 <li>Detect when nucleotide sequences and protein
3153 sequences are placed in the same alignment</li>
3154 <li>Split cDNA/Protein views are saved in Jalview
3159 <li>Use REST API to talk to Chimera</li>
3160 <li>Selected regions in Chimera are highlighted in linked
3161 Jalview windows</li>
3163 <li>VARNA RNA viewer updated to v3.93</li>
3164 <li>VARNA views are saved in Jalview Projects</li>
3165 <li>Pseudoknots displayed as Jalview RNA annotation can
3166 be shown in VARNA</li>
3168 <li>Make groups for selection uses marked columns as well
3169 as the active selected region</li>
3171 <li>Calculate UPGMA and NJ trees using sequence feature
3173 <li>New Export options
3175 <li>New Export Settings dialog to control hidden
3176 region export in flat file generation</li>
3178 <li>Export alignment views for display with the <a
3179 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3181 <li>Export scrollable SVG in HTML page</li>
3182 <li>Optional embedding of BioJSON data when exporting
3183 alignment figures to HTML</li>
3185 <li>3D structure retrieval and display
3187 <li>Free text and structured queries with the PDBe
3189 <li>PDBe Search API based discovery and selection of
3190 PDB structures for a sequence set</li>
3194 <li>JPred4 employed for protein secondary structure
3196 <li>Hide Insertions menu option to hide unaligned columns
3197 for one or a group of sequences</li>
3198 <li>Automatically hide insertions in alignments imported
3199 from the JPred4 web server</li>
3200 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3201 system on OSX<br />LGPL libraries courtesy of <a
3202 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3204 <li>changed 'View nucleotide structure' submenu to 'View
3205 VARNA 2D Structure'</li>
3206 <li>change "View protein structure" menu option to "3D
3209 </ul> <em>Applet</em>
3211 <li>New layout for applet example pages</li>
3212 <li>New parameters to enable SplitFrame view
3213 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3214 <li>New example demonstrating linked viewing of cDNA and
3215 Protein alignments</li>
3216 </ul> <em>Development and deployment</em>
3218 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3219 <li>Include installation type and git revision in build
3220 properties and console log output</li>
3221 <li>Jalview Github organisation, and new github site for
3222 storing BioJsMSA Templates</li>
3223 <li>Jalview's unit tests now managed with TestNG</li>
3226 <!-- <em>General</em>
3228 </ul> --> <!-- issues resolved --> <em>Application</em>
3230 <li>Escape should close any open find dialogs</li>
3231 <li>Typo in select-by-features status report</li>
3232 <li>Consensus RNA secondary secondary structure
3233 predictions are not highlighted in amber</li>
3234 <li>Missing gap character in v2.7 example file means
3235 alignment appears unaligned when pad-gaps is not enabled</li>
3236 <li>First switch to RNA Helices colouring doesn't colour
3237 associated structure views</li>
3238 <li>ID width preference option is greyed out when auto
3239 width checkbox not enabled</li>
3240 <li>Stopped a warning dialog from being shown when
3241 creating user defined colours</li>
3242 <li>'View Mapping' in structure viewer shows sequence
3243 mappings for just that viewer's sequences</li>
3244 <li>Workaround for superposing PDB files containing
3245 multiple models in Chimera</li>
3246 <li>Report sequence position in status bar when hovering
3247 over Jmol structure</li>
3248 <li>Cannot output gaps as '.' symbols with Selection ->
3249 output to text box</li>
3250 <li>Flat file exports of alignments with hidden columns
3251 have incorrect sequence start/end</li>
3252 <li>'Aligning' a second chain to a Chimera structure from
3254 <li>Colour schemes applied to structure viewers don't
3255 work for nucleotide</li>
3256 <li>Loading/cut'n'pasting an empty or invalid file leads
3257 to a grey/invisible alignment window</li>
3258 <li>Exported Jpred annotation from a sequence region
3259 imports to different position</li>
3260 <li>Space at beginning of sequence feature tooltips shown
3261 on some platforms</li>
3262 <li>Chimera viewer 'View | Show Chain' menu is not
3264 <li>'New View' fails with a Null Pointer Exception in
3265 console if Chimera has been opened</li>
3266 <li>Mouseover to Chimera not working</li>
3267 <li>Miscellaneous ENA XML feature qualifiers not
3269 <li>NPE in annotation renderer after 'Extract Scores'</li>
3270 <li>If two structures in one Chimera window, mouseover of
3271 either sequence shows on first structure</li>
3272 <li>'Show annotations' options should not make
3273 non-positional annotations visible</li>
3274 <li>Subsequence secondary structure annotation not shown
3275 in right place after 'view flanking regions'</li>
3276 <li>File Save As type unset when current file format is
3278 <li>Save as '.jar' option removed for saving Jalview
3280 <li>Colour by Sequence colouring in Chimera more
3282 <li>Cannot 'add reference annotation' for a sequence in
3283 several views on same alignment</li>
3284 <li>Cannot show linked products for EMBL / ENA records</li>
3285 <li>Jalview's tooltip wraps long texts containing no
3287 </ul> <em>Applet</em>
3289 <li>Jmol to JalviewLite mouseover/link not working</li>
3290 <li>JalviewLite can't import sequences with ID
3291 descriptions containing angle brackets</li>
3292 </ul> <em>General</em>
3294 <li>Cannot export and reimport RNA secondary structure
3295 via jalview annotation file</li>
3296 <li>Random helix colour palette for colour by annotation
3297 with RNA secondary structure</li>
3298 <li>Mouseover to cDNA from STOP residue in protein
3299 translation doesn't work.</li>
3300 <li>hints when using the select by annotation dialog box</li>
3301 <li>Jmol alignment incorrect if PDB file has alternate CA
3303 <li>FontChooser message dialog appears to hang after
3304 choosing 1pt font</li>
3305 <li>Peptide secondary structure incorrectly imported from
3306 annotation file when annotation display text includes 'e' or
3308 <li>Cannot set colour of new feature type whilst creating
3310 <li>cDNA translation alignment should not be sequence
3311 order dependent</li>
3312 <li>'Show unconserved' doesn't work for lower case
3314 <li>Nucleotide ambiguity codes involving R not recognised</li>
3315 </ul> <em>Deployment and Documentation</em>
3317 <li>Applet example pages appear different to the rest of
3318 www.jalview.org</li>
3319 </ul> <em>Application Known issues</em>
3321 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3322 <li>Misleading message appears after trying to delete
3324 <li>Jalview icon not shown in dock after InstallAnywhere
3325 version launches</li>
3326 <li>Fetching EMBL reference for an RNA sequence results
3327 fails with a sequence mismatch</li>
3328 <li>Corrupted or unreadable alignment display when
3329 scrolling alignment to right</li>
3330 <li>ArrayIndexOutOfBoundsException thrown when remove
3331 empty columns called on alignment with ragged gapped ends</li>
3332 <li>auto calculated alignment annotation rows do not get
3333 placed above or below non-autocalculated rows</li>
3334 <li>Jalview dekstop becomes sluggish at full screen in
3335 ultra-high resolution</li>
3336 <li>Cannot disable consensus calculation independently of
3337 quality and conservation</li>
3338 <li>Mouseover highlighting between cDNA and protein can
3339 become sluggish with more than one splitframe shown</li>
3340 </ul> <em>Applet Known Issues</em>
3342 <li>Core PDB parsing code requires Jmol</li>
3343 <li>Sequence canvas panel goes white when alignment
3344 window is being resized</li>
3350 <td><div align="center">
3351 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3353 <td><em>General</em>
3355 <li>Updated Java code signing certificate donated by
3357 <li>Features and annotation preserved when performing
3358 pairwise alignment</li>
3359 <li>RNA pseudoknot annotation can be
3360 imported/exported/displayed</li>
3361 <li>'colour by annotation' can colour by RNA and
3362 protein secondary structure</li>
3363 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3364 post-hoc with 2.9 release</em>)
3367 </ul> <em>Application</em>
3369 <li>Extract and display secondary structure for sequences
3370 with 3D structures</li>
3371 <li>Support for parsing RNAML</li>
3372 <li>Annotations menu for layout
3374 <li>sort sequence annotation rows by alignment</li>
3375 <li>place sequence annotation above/below alignment
3378 <li>Output in Stockholm format</li>
3379 <li>Internationalisation: improved Spanish (es)
3381 <li>Structure viewer preferences tab</li>
3382 <li>Disorder and Secondary Structure annotation tracks
3383 shared between alignments</li>
3384 <li>UCSF Chimera launch and linked highlighting from
3386 <li>Show/hide all sequence associated annotation rows for
3387 all or current selection</li>
3388 <li>disorder and secondary structure predictions
3389 available as dataset annotation</li>
3390 <li>Per-sequence rna helices colouring</li>
3393 <li>Sequence database accessions imported when fetching
3394 alignments from Rfam</li>
3395 <li>update VARNA version to 3.91</li>
3397 <li>New groovy scripts for exporting aligned positions,
3398 conservation values, and calculating sum of pairs scores.</li>
3399 <li>Command line argument to set default JABAWS server</li>
3400 <li>include installation type in build properties and
3401 console log output</li>
3402 <li>Updated Jalview project format to preserve dataset
3406 <!-- issues resolved --> <em>Application</em>
3408 <li>Distinguish alignment and sequence associated RNA
3409 structure in structure->view->VARNA</li>
3410 <li>Raise dialog box if user deletes all sequences in an
3412 <li>Pressing F1 results in documentation opening twice</li>
3413 <li>Sequence feature tooltip is wrapped</li>
3414 <li>Double click on sequence associated annotation
3415 selects only first column</li>
3416 <li>Redundancy removal doesn't result in unlinked
3417 leaves shown in tree</li>
3418 <li>Undos after several redundancy removals don't undo
3420 <li>Hide sequence doesn't hide associated annotation</li>
3421 <li>User defined colours dialog box too big to fit on
3422 screen and buttons not visible</li>
3423 <li>author list isn't updated if already written to
3424 Jalview properties</li>
3425 <li>Popup menu won't open after retrieving sequence
3427 <li>File open window for associate PDB doesn't open</li>
3428 <li>Left-then-right click on a sequence id opens a
3429 browser search window</li>
3430 <li>Cannot open sequence feature shading/sort popup menu
3431 in feature settings dialog</li>
3432 <li>better tooltip placement for some areas of Jalview
3434 <li>Allow addition of JABAWS Server which doesn't
3435 pass validation</li>
3436 <li>Web services parameters dialog box is too large to
3438 <li>Muscle nucleotide alignment preset obscured by
3440 <li>JABAWS preset submenus don't contain newly
3441 defined user preset</li>
3442 <li>MSA web services warns user if they were launched
3443 with invalid input</li>
3444 <li>Jalview cannot contact DAS Registy when running on
3447 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3448 'Superpose with' submenu not shown when new view
3452 </ul> <!-- <em>Applet</em>
3454 </ul> <em>General</em>
3456 </ul>--> <em>Deployment and Documentation</em>
3458 <li>2G and 1G options in launchApp have no effect on
3459 memory allocation</li>
3460 <li>launchApp service doesn't automatically open
3461 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3463 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3464 InstallAnywhere reports cannot find valid JVM when Java
3465 1.7_055 is available
3467 </ul> <em>Application Known issues</em>
3470 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3471 corrupted or unreadable alignment display when scrolling
3475 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3476 retrieval fails but progress bar continues for DAS retrieval
3477 with large number of ID
3480 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3481 flatfile output of visible region has incorrect sequence
3485 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3486 rna structure consensus doesn't update when secondary
3487 structure tracks are rearranged
3490 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3491 invalid rna structure positional highlighting does not
3492 highlight position of invalid base pairs
3495 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3496 out of memory errors are not raised when saving Jalview
3497 project from alignment window file menu
3500 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3501 Switching to RNA Helices colouring doesn't propagate to
3505 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3506 colour by RNA Helices not enabled when user created
3507 annotation added to alignment
3510 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3511 Jalview icon not shown on dock in Mountain Lion/Webstart
3513 </ul> <em>Applet Known Issues</em>
3516 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3517 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3520 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3521 Jalview and Jmol example not compatible with IE9
3524 <li>Sort by annotation score doesn't reverse order
3530 <td><div align="center">
3531 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3534 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3537 <li>Internationalisation of user interface (usually
3538 called i18n support) and translation for Spanish locale</li>
3539 <li>Define/Undefine group on current selection with
3540 Ctrl-G/Shift Ctrl-G</li>
3541 <li>Improved group creation/removal options in
3542 alignment/sequence Popup menu</li>
3543 <li>Sensible precision for symbol distribution
3544 percentages shown in logo tooltip.</li>
3545 <li>Annotation panel height set according to amount of
3546 annotation when alignment first opened</li>
3547 </ul> <em>Application</em>
3549 <li>Interactive consensus RNA secondary structure
3550 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3551 <li>Select columns containing particular features from
3552 Feature Settings dialog</li>
3553 <li>View all 'representative' PDB structures for selected
3555 <li>Update Jalview project format:
3557 <li>New file extension for Jalview projects '.jvp'</li>
3558 <li>Preserve sequence and annotation dataset (to
3559 store secondary structure annotation,etc)</li>
3560 <li>Per group and alignment annotation and RNA helix
3564 <li>New similarity measures for PCA and Tree calculation
3566 <li>Experimental support for retrieval and viewing of
3567 flanking regions for an alignment</li>
3571 <!-- issues resolved --> <em>Application</em>
3573 <li>logo keeps spinning and status remains at queued or
3574 running after job is cancelled</li>
3575 <li>cannot export features from alignments imported from
3576 Jalview/VAMSAS projects</li>
3577 <li>Buggy slider for web service parameters that take
3579 <li>Newly created RNA secondary structure line doesn't
3580 have 'display all symbols' flag set</li>
3581 <li>T-COFFEE alignment score shading scheme and other
3582 annotation shading not saved in Jalview project</li>
3583 <li>Local file cannot be loaded in freshly downloaded
3585 <li>Jalview icon not shown on dock in Mountain
3587 <li>Load file from desktop file browser fails</li>
3588 <li>Occasional NPE thrown when calculating large trees</li>
3589 <li>Cannot reorder or slide sequences after dragging an
3590 alignment onto desktop</li>
3591 <li>Colour by annotation dialog throws NPE after using
3592 'extract scores' function</li>
3593 <li>Loading/cut'n'pasting an empty file leads to a grey
3594 alignment window</li>
3595 <li>Disorder thresholds rendered incorrectly after
3596 performing IUPred disorder prediction</li>
3597 <li>Multiple group annotated consensus rows shown when
3598 changing 'normalise logo' display setting</li>
3599 <li>Find shows blank dialog after 'finished searching' if
3600 nothing matches query</li>
3601 <li>Null Pointer Exceptions raised when sorting by
3602 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3604 <li>Errors in Jmol console when structures in alignment
3605 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3607 <li>Not all working JABAWS services are shown in
3609 <li>JAVAWS version of Jalview fails to launch with
3610 'invalid literal/length code'</li>
3611 <li>Annotation/RNA Helix colourschemes cannot be applied
3612 to alignment with groups (actually fixed in 2.8.0b1)</li>
3613 <li>RNA Helices and T-Coffee Scores available as default
3616 </ul> <em>Applet</em>
3618 <li>Remove group option is shown even when selection is
3620 <li>Apply to all groups ticked but colourscheme changes
3621 don't affect groups</li>
3622 <li>Documented RNA Helices and T-Coffee Scores as valid
3623 colourscheme name</li>
3624 <li>Annotation labels drawn on sequence IDs when
3625 Annotation panel is not displayed</li>
3626 <li>Increased font size for dropdown menus on OSX and
3627 embedded windows</li>
3628 </ul> <em>Other</em>
3630 <li>Consensus sequence for alignments/groups with a
3631 single sequence were not calculated</li>
3632 <li>annotation files that contain only groups imported as
3633 annotation and junk sequences</li>
3634 <li>Fasta files with sequences containing '*' incorrectly
3635 recognised as PFAM or BLC</li>
3636 <li>conservation/PID slider apply all groups option
3637 doesn't affect background (2.8.0b1)
3639 <li>redundancy highlighting is erratic at 0% and 100%</li>
3640 <li>Remove gapped columns fails for sequences with ragged
3642 <li>AMSA annotation row with leading spaces is not
3643 registered correctly on import</li>
3644 <li>Jalview crashes when selecting PCA analysis for
3645 certain alignments</li>
3646 <li>Opening the colour by annotation dialog for an
3647 existing annotation based 'use original colours'
3648 colourscheme loses original colours setting</li>
3653 <td><div align="center">
3654 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3655 <em>30/1/2014</em></strong>
3659 <li>Trusted certificates for JalviewLite applet and
3660 Jalview Desktop application<br />Certificate was donated by
3661 <a href="https://www.certum.eu">Certum</a> to the Jalview
3662 open source project).
3664 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3665 <li>Output in Stockholm format</li>
3666 <li>Allow import of data from gzipped files</li>
3667 <li>Export/import group and sequence associated line
3668 graph thresholds</li>
3669 <li>Nucleotide substitution matrix that supports RNA and
3670 ambiguity codes</li>
3671 <li>Allow disorder predictions to be made on the current
3672 selection (or visible selection) in the same way that JPred
3674 <li>Groovy scripting for headless Jalview operation</li>
3675 </ul> <em>Other improvements</em>
3677 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3678 <li>COMBINE statement uses current SEQUENCE_REF and
3679 GROUP_REF scope to group annotation rows</li>
3680 <li>Support '' style escaping of quotes in Newick
3682 <li>Group options for JABAWS service by command line name</li>
3683 <li>Empty tooltip shown for JABA service options with a
3684 link but no description</li>
3685 <li>Select primary source when selecting authority in
3686 database fetcher GUI</li>
3687 <li>Add .mfa to FASTA file extensions recognised by
3689 <li>Annotation label tooltip text wrap</li>
3694 <li>Slow scrolling when lots of annotation rows are
3696 <li>Lots of NPE (and slowness) after creating RNA
3697 secondary structure annotation line</li>
3698 <li>Sequence database accessions not imported when
3699 fetching alignments from Rfam</li>
3700 <li>Incorrect SHMR submission for sequences with
3702 <li>View all structures does not always superpose
3704 <li>Option widgets in service parameters not updated to
3705 reflect user or preset settings</li>
3706 <li>Null pointer exceptions for some services without
3707 presets or adjustable parameters</li>
3708 <li>Discover PDB IDs entry in structure menu doesn't
3709 discover PDB xRefs</li>
3710 <li>Exception encountered while trying to retrieve
3711 features with DAS</li>
3712 <li>Lowest value in annotation row isn't coloured
3713 when colour by annotation (per sequence) is coloured</li>
3714 <li>Keyboard mode P jumps to start of gapped region when
3715 residue follows a gap</li>
3716 <li>Jalview appears to hang importing an alignment with
3717 Wrap as default or after enabling Wrap</li>
3718 <li>'Right click to add annotations' message
3719 shown in wrap mode when no annotations present</li>
3720 <li>Disorder predictions fail with NPE if no automatic
3721 annotation already exists on alignment</li>
3722 <li>oninit javascript function should be called after
3723 initialisation completes</li>
3724 <li>Remove redundancy after disorder prediction corrupts
3725 alignment window display</li>
3726 <li>Example annotation file in documentation is invalid</li>
3727 <li>Grouped line graph annotation rows are not exported
3728 to annotation file</li>
3729 <li>Multi-harmony analysis cannot be run when only two
3731 <li>Cannot create multiple groups of line graphs with
3732 several 'combine' statements in annotation file</li>
3733 <li>Pressing return several times causes Number Format
3734 exceptions in keyboard mode</li>
3735 <li>Multi-harmony (SHMMR) method doesn't submit
3736 correct partitions for input data</li>
3737 <li>Translation from DNA to Amino Acids fails</li>
3738 <li>Jalview fail to load newick tree with quoted label</li>
3739 <li>--headless flag isn't understood</li>
3740 <li>ClassCastException when generating EPS in headless
3742 <li>Adjusting sequence-associated shading threshold only
3743 changes one row's threshold</li>
3744 <li>Preferences and Feature settings panel panel
3745 doesn't open</li>
3746 <li>hide consensus histogram also hides conservation and
3747 quality histograms</li>
3752 <td><div align="center">
3753 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3755 <td><em>Application</em>
3757 <li>Support for JABAWS 2.0 Services (AACon alignment
3758 conservation, protein disorder and Clustal Omega)</li>
3759 <li>JABAWS server status indicator in Web Services
3761 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3762 in Jalview alignment window</li>
3763 <li>Updated Jalview build and deploy framework for OSX
3764 mountain lion, windows 7, and 8</li>
3765 <li>Nucleotide substitution matrix for PCA that supports
3766 RNA and ambiguity codes</li>
3768 <li>Improved sequence database retrieval GUI</li>
3769 <li>Support fetching and database reference look up
3770 against multiple DAS sources (Fetch all from in 'fetch db
3772 <li>Jalview project improvements
3774 <li>Store and retrieve the 'belowAlignment'
3775 flag for annotation</li>
3776 <li>calcId attribute to group annotation rows on the
3778 <li>Store AACon calculation settings for a view in
3779 Jalview project</li>
3783 <li>horizontal scrolling gesture support</li>
3784 <li>Visual progress indicator when PCA calculation is
3786 <li>Simpler JABA web services menus</li>
3787 <li>visual indication that web service results are still
3788 being retrieved from server</li>
3789 <li>Serialise the dialogs that are shown when Jalview
3790 starts up for first time</li>
3791 <li>Jalview user agent string for interacting with HTTP
3793 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3795 <li>Examples directory and Groovy library included in
3796 InstallAnywhere distribution</li>
3797 </ul> <em>Applet</em>
3799 <li>RNA alignment and secondary structure annotation
3800 visualization applet example</li>
3801 </ul> <em>General</em>
3803 <li>Normalise option for consensus sequence logo</li>
3804 <li>Reset button in PCA window to return dimensions to
3806 <li>Allow seqspace or Jalview variant of alignment PCA
3808 <li>PCA with either nucleic acid and protein substitution
3810 <li>Allow windows containing HTML reports to be exported
3812 <li>Interactive display and editing of RNA secondary
3813 structure contacts</li>
3814 <li>RNA Helix Alignment Colouring</li>
3815 <li>RNA base pair logo consensus</li>
3816 <li>Parse sequence associated secondary structure
3817 information in Stockholm files</li>
3818 <li>HTML Export database accessions and annotation
3819 information presented in tooltip for sequences</li>
3820 <li>Import secondary structure from LOCARNA clustalw
3821 style RNA alignment files</li>
3822 <li>import and visualise T-COFFEE quality scores for an
3824 <li>'colour by annotation' per sequence option to
3825 shade each sequence according to its associated alignment
3827 <li>New Jalview Logo</li>
3828 </ul> <em>Documentation and Development</em>
3830 <li>documentation for score matrices used in Jalview</li>
3831 <li>New Website!</li>
3833 <td><em>Application</em>
3835 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3836 wsdbfetch REST service</li>
3837 <li>Stop windows being moved outside desktop on OSX</li>
3838 <li>Filetype associations not installed for webstart
3840 <li>Jalview does not always retrieve progress of a JABAWS
3841 job execution in full once it is complete</li>
3842 <li>revise SHMR RSBS definition to ensure alignment is
3843 uploaded via ali_file parameter</li>
3844 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3845 <li>View all structures superposed fails with exception</li>
3846 <li>Jnet job queues forever if a very short sequence is
3847 submitted for prediction</li>
3848 <li>Cut and paste menu not opened when mouse clicked on
3850 <li>Putting fractional value into integer text box in
3851 alignment parameter dialog causes Jalview to hang</li>
3852 <li>Structure view highlighting doesn't work on
3854 <li>View all structures fails with exception shown in
3856 <li>Characters in filename associated with PDBEntry not
3857 escaped in a platform independent way</li>
3858 <li>Jalview desktop fails to launch with exception when
3860 <li>Tree calculation reports 'you must have 2 or more
3861 sequences selected' when selection is empty</li>
3862 <li>Jalview desktop fails to launch with jar signature
3863 failure when java web start temporary file caching is
3865 <li>DAS Sequence retrieval with range qualification
3866 results in sequence xref which includes range qualification</li>
3867 <li>Errors during processing of command line arguments
3868 cause progress bar (JAL-898) to be removed</li>
3869 <li>Replace comma for semi-colon option not disabled for
3870 DAS sources in sequence fetcher</li>
3871 <li>Cannot close news reader when JABAWS server warning
3872 dialog is shown</li>
3873 <li>Option widgets not updated to reflect user settings</li>
3874 <li>Edited sequence not submitted to web service</li>
3875 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3876 <li>InstallAnywhere installer doesn't unpack and run
3877 on OSX Mountain Lion</li>
3878 <li>Annotation panel not given a scroll bar when
3879 sequences with alignment annotation are pasted into the
3881 <li>Sequence associated annotation rows not associated
3882 when loaded from Jalview project</li>
3883 <li>Browser launch fails with NPE on java 1.7</li>
3884 <li>JABAWS alignment marked as finished when job was
3885 cancelled or job failed due to invalid input</li>
3886 <li>NPE with v2.7 example when clicking on Tree
3887 associated with all views</li>
3888 <li>Exceptions when copy/paste sequences with grouped
3889 annotation rows to new window</li>
3890 </ul> <em>Applet</em>
3892 <li>Sequence features are momentarily displayed before
3893 they are hidden using hidefeaturegroups applet parameter</li>
3894 <li>loading features via javascript API automatically
3895 enables feature display</li>
3896 <li>scrollToColumnIn javascript API method doesn't
3898 </ul> <em>General</em>
3900 <li>Redundancy removal fails for rna alignment</li>
3901 <li>PCA calculation fails when sequence has been selected
3902 and then deselected</li>
3903 <li>PCA window shows grey box when first opened on OSX</li>
3904 <li>Letters coloured pink in sequence logo when alignment
3905 coloured with clustalx</li>
3906 <li>Choosing fonts without letter symbols defined causes
3907 exceptions and redraw errors</li>
3908 <li>Initial PCA plot view is not same as manually
3909 reconfigured view</li>
3910 <li>Grouped annotation graph label has incorrect line
3912 <li>Grouped annotation graph label display is corrupted
3913 for lots of labels</li>
3918 <div align="center">
3919 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3922 <td><em>Application</em>
3924 <li>Jalview Desktop News Reader</li>
3925 <li>Tweaked default layout of web services menu</li>
3926 <li>View/alignment association menu to enable user to
3927 easily specify which alignment a multi-structure view takes
3928 its colours/correspondences from</li>
3929 <li>Allow properties file location to be specified as URL</li>
3930 <li>Extend Jalview project to preserve associations
3931 between many alignment views and a single Jmol display</li>
3932 <li>Store annotation row height in Jalview project file</li>
3933 <li>Annotation row column label formatting attributes
3934 stored in project file</li>
3935 <li>Annotation row order for auto-calculated annotation
3936 rows preserved in Jalview project file</li>
3937 <li>Visual progress indication when Jalview state is
3938 saved using Desktop window menu</li>
3939 <li>Visual indication that command line arguments are
3940 still being processed</li>
3941 <li>Groovy script execution from URL</li>
3942 <li>Colour by annotation default min and max colours in
3944 <li>Automatically associate PDB files dragged onto an
3945 alignment with sequences that have high similarity and
3947 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3948 <li>'view structures' option to open many
3949 structures in same window</li>
3950 <li>Sort associated views menu option for tree panel</li>
3951 <li>Group all JABA and non-JABA services for a particular
3952 analysis function in its own submenu</li>
3953 </ul> <em>Applet</em>
3955 <li>Userdefined and autogenerated annotation rows for
3957 <li>Adjustment of alignment annotation pane height</li>
3958 <li>Annotation scrollbar for annotation panel</li>
3959 <li>Drag to reorder annotation rows in annotation panel</li>
3960 <li>'automaticScrolling' parameter</li>
3961 <li>Allow sequences with partial ID string matches to be
3962 annotated from GFF/Jalview features files</li>
3963 <li>Sequence logo annotation row in applet</li>
3964 <li>Absolute paths relative to host server in applet
3965 parameters are treated as such</li>
3966 <li>New in the JalviewLite javascript API:
3968 <li>JalviewLite.js javascript library</li>
3969 <li>Javascript callbacks for
3971 <li>Applet initialisation</li>
3972 <li>Sequence/alignment mouse-overs and selections</li>
3975 <li>scrollTo row and column alignment scrolling
3977 <li>Select sequence/alignment regions from javascript</li>
3978 <li>javascript structure viewer harness to pass
3979 messages between Jmol and Jalview when running as
3980 distinct applets</li>
3981 <li>sortBy method</li>
3982 <li>Set of applet and application examples shipped
3983 with documentation</li>
3984 <li>New example to demonstrate JalviewLite and Jmol
3985 javascript message exchange</li>
3987 </ul> <em>General</em>
3989 <li>Enable Jmol displays to be associated with multiple
3990 multiple alignments</li>
3991 <li>Option to automatically sort alignment with new tree</li>
3992 <li>User configurable link to enable redirects to a
3993 www.Jalview.org mirror</li>
3994 <li>Jmol colours option for Jmol displays</li>
3995 <li>Configurable newline string when writing alignment
3996 and other flat files</li>
3997 <li>Allow alignment annotation description lines to
3998 contain html tags</li>
3999 </ul> <em>Documentation and Development</em>
4001 <li>Add groovy test harness for bulk load testing to
4003 <li>Groovy script to load and align a set of sequences
4004 using a web service before displaying the result in the
4005 Jalview desktop</li>
4006 <li>Restructured javascript and applet api documentation</li>
4007 <li>Ant target to publish example html files with applet
4009 <li>Netbeans project for building Jalview from source</li>
4010 <li>ant task to create online javadoc for Jalview source</li>
4012 <td><em>Application</em>
4014 <li>User defined colourscheme throws exception when
4015 current built in colourscheme is saved as new scheme</li>
4016 <li>AlignFrame->Save in application pops up save
4017 dialog for valid filename/format</li>
4018 <li>Cannot view associated structure for UniProt sequence</li>
4019 <li>PDB file association breaks for UniProt sequence
4021 <li>Associate PDB from file dialog does not tell you
4022 which sequence is to be associated with the file</li>
4023 <li>Find All raises null pointer exception when query
4024 only matches sequence IDs</li>
4025 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4026 <li>Jalview project with Jmol views created with Jalview
4027 2.4 cannot be loaded</li>
4028 <li>Filetype associations not installed for webstart
4030 <li>Two or more chains in a single PDB file associated
4031 with sequences in different alignments do not get coloured
4032 by their associated sequence</li>
4033 <li>Visibility status of autocalculated annotation row
4034 not preserved when project is loaded</li>
4035 <li>Annotation row height and visibility attributes not
4036 stored in Jalview project</li>
4037 <li>Tree bootstraps are not preserved when saved as a
4038 Jalview project</li>
4039 <li>Envision2 workflow tooltips are corrupted</li>
4040 <li>Enabling show group conservation also enables colour
4041 by conservation</li>
4042 <li>Duplicate group associated conservation or consensus
4043 created on new view</li>
4044 <li>Annotation scrollbar not displayed after 'show
4045 all hidden annotation rows' option selected</li>
4046 <li>Alignment quality not updated after alignment
4047 annotation row is hidden then shown</li>
4048 <li>Preserve colouring of structures coloured by
4049 sequences in pre Jalview 2.7 projects</li>
4050 <li>Web service job parameter dialog is not laid out
4052 <li>Web services menu not refreshed after 'reset
4053 services' button is pressed in preferences</li>
4054 <li>Annotation off by one in Jalview v2_3 example project</li>
4055 <li>Structures imported from file and saved in project
4056 get name like jalview_pdb1234.txt when reloaded</li>
4057 <li>Jalview does not always retrieve progress of a JABAWS
4058 job execution in full once it is complete</li>
4059 </ul> <em>Applet</em>
4061 <li>Alignment height set incorrectly when lots of
4062 annotation rows are displayed</li>
4063 <li>Relative URLs in feature HTML text not resolved to
4065 <li>View follows highlighting does not work for positions
4067 <li><= shown as = in tooltip</li>
4068 <li>Export features raises exception when no features
4070 <li>Separator string used for serialising lists of IDs
4071 for javascript api is modified when separator string
4072 provided as parameter</li>
4073 <li>Null pointer exception when selecting tree leaves for
4074 alignment with no existing selection</li>
4075 <li>Relative URLs for datasources assumed to be relative
4076 to applet's codebase</li>
4077 <li>Status bar not updated after finished searching and
4078 search wraps around to first result</li>
4079 <li>StructureSelectionManager instance shared between
4080 several Jalview applets causes race conditions and memory
4082 <li>Hover tooltip and mouseover of position on structure
4083 not sent from Jmol in applet</li>
4084 <li>Certain sequences of javascript method calls to
4085 applet API fatally hang browser</li>
4086 </ul> <em>General</em>
4088 <li>View follows structure mouseover scrolls beyond
4089 position with wrapped view and hidden regions</li>
4090 <li>Find sequence position moves to wrong residue
4091 with/without hidden columns</li>
4092 <li>Sequence length given in alignment properties window
4094 <li>InvalidNumberFormat exceptions thrown when trying to
4095 import PDB like structure files</li>
4096 <li>Positional search results are only highlighted
4097 between user-supplied sequence start/end bounds</li>
4098 <li>End attribute of sequence is not validated</li>
4099 <li>Find dialog only finds first sequence containing a
4100 given sequence position</li>
4101 <li>Sequence numbering not preserved in MSF alignment
4103 <li>Jalview PDB file reader does not extract sequence
4104 from nucleotide chains correctly</li>
4105 <li>Structure colours not updated when tree partition
4106 changed in alignment</li>
4107 <li>Sequence associated secondary structure not correctly
4108 parsed in interleaved stockholm</li>
4109 <li>Colour by annotation dialog does not restore current
4111 <li>Hiding (nearly) all sequences doesn't work
4113 <li>Sequences containing lowercase letters are not
4114 properly associated with their pdb files</li>
4115 </ul> <em>Documentation and Development</em>
4117 <li>schemas/JalviewWsParamSet.xsd corrupted by
4118 ApplyCopyright tool</li>
4123 <div align="center">
4124 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4127 <td><em>Application</em>
4129 <li>New warning dialog when the Jalview Desktop cannot
4130 contact web services</li>
4131 <li>JABA service parameters for a preset are shown in
4132 service job window</li>
4133 <li>JABA Service menu entries reworded</li>
4137 <li>Modeller PIR IO broken - cannot correctly import a
4138 pir file emitted by Jalview</li>
4139 <li>Existing feature settings transferred to new
4140 alignment view created from cut'n'paste</li>
4141 <li>Improved test for mixed amino/nucleotide chains when
4142 parsing PDB files</li>
4143 <li>Consensus and conservation annotation rows
4144 occasionally become blank for all new windows</li>
4145 <li>Exception raised when right clicking above sequences
4146 in wrapped view mode</li>
4147 </ul> <em>Application</em>
4149 <li>multiple multiply aligned structure views cause cpu
4150 usage to hit 100% and computer to hang</li>
4151 <li>Web Service parameter layout breaks for long user
4152 parameter names</li>
4153 <li>Jaba service discovery hangs desktop if Jaba server
4160 <div align="center">
4161 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4164 <td><em>Application</em>
4166 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4167 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4170 <li>Web Services preference tab</li>
4171 <li>Analysis parameters dialog box and user defined
4173 <li>Improved speed and layout of Envision2 service menu</li>
4174 <li>Superpose structures using associated sequence
4176 <li>Export coordinates and projection as CSV from PCA
4178 </ul> <em>Applet</em>
4180 <li>enable javascript: execution by the applet via the
4181 link out mechanism</li>
4182 </ul> <em>Other</em>
4184 <li>Updated the Jmol Jalview interface to work with Jmol
4186 <li>The Jalview Desktop and JalviewLite applet now
4187 require Java 1.5</li>
4188 <li>Allow Jalview feature colour specification for GFF
4189 sequence annotation files</li>
4190 <li>New 'colour by label' keword in Jalview feature file
4191 type colour specification</li>
4192 <li>New Jalview Desktop Groovy API method that allows a
4193 script to check if it being run in an interactive session or
4194 in a batch operation from the Jalview command line</li>
4198 <li>clustalx colourscheme colours Ds preferentially when
4199 both D+E are present in over 50% of the column</li>
4200 </ul> <em>Application</em>
4202 <li>typo in AlignmentFrame->View->Hide->all but
4203 selected Regions menu item</li>
4204 <li>sequence fetcher replaces ',' for ';' when the ',' is
4205 part of a valid accession ID</li>
4206 <li>fatal OOM if object retrieved by sequence fetcher
4207 runs out of memory</li>
4208 <li>unhandled Out of Memory Error when viewing pca
4209 analysis results</li>
4210 <li>InstallAnywhere builds fail to launch on OS X java
4211 10.5 update 4 (due to apple Java 1.6 update)</li>
4212 <li>Installanywhere Jalview silently fails to launch</li>
4213 </ul> <em>Applet</em>
4215 <li>Jalview.getFeatureGroups() raises an
4216 ArrayIndexOutOfBoundsException if no feature groups are
4223 <div align="center">
4224 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4230 <li>Alignment prettyprinter doesn't cope with long
4232 <li>clustalx colourscheme colours Ds preferentially when
4233 both D+E are present in over 50% of the column</li>
4234 <li>nucleic acid structures retrieved from PDB do not
4235 import correctly</li>
4236 <li>More columns get selected than were clicked on when a
4237 number of columns are hidden</li>
4238 <li>annotation label popup menu not providing correct
4239 add/hide/show options when rows are hidden or none are
4241 <li>Stockholm format shown in list of readable formats,
4242 and parser copes better with alignments from RFAM.</li>
4243 <li>CSV output of consensus only includes the percentage
4244 of all symbols if sequence logo display is enabled</li>
4246 </ul> <em>Applet</em>
4248 <li>annotation panel disappears when annotation is
4250 </ul> <em>Application</em>
4252 <li>Alignment view not redrawn properly when new
4253 alignment opened where annotation panel is visible but no
4254 annotations are present on alignment</li>
4255 <li>pasted region containing hidden columns is
4256 incorrectly displayed in new alignment window</li>
4257 <li>Jalview slow to complete operations when stdout is
4258 flooded (fix is to close the Jalview console)</li>
4259 <li>typo in AlignmentFrame->View->Hide->all but
4260 selected Rregions menu item.</li>
4261 <li>inconsistent group submenu and Format submenu entry
4262 'Un' or 'Non'conserved</li>
4263 <li>Sequence feature settings are being shared by
4264 multiple distinct alignments</li>
4265 <li>group annotation not recreated when tree partition is
4267 <li>double click on group annotation to select sequences
4268 does not propagate to associated trees</li>
4269 <li>Mac OSX specific issues:
4271 <li>exception raised when mouse clicked on desktop
4272 window background</li>
4273 <li>Desktop menu placed on menu bar and application
4274 name set correctly</li>
4275 <li>sequence feature settings not wide enough for the
4276 save feature colourscheme button</li>
4285 <div align="center">
4286 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4289 <td><em>New Capabilities</em>
4291 <li>URL links generated from description line for
4292 regular-expression based URL links (applet and application)
4294 <li>Non-positional feature URL links are shown in link
4296 <li>Linked viewing of nucleic acid sequences and
4298 <li>Automatic Scrolling option in View menu to display
4299 the currently highlighted region of an alignment.</li>
4300 <li>Order an alignment by sequence length, or using the
4301 average score or total feature count for each sequence.</li>
4302 <li>Shading features by score or associated description</li>
4303 <li>Subdivide alignment and groups based on identity of
4304 selected subsequence (Make Groups from Selection).</li>
4305 <li>New hide/show options including Shift+Control+H to
4306 hide everything but the currently selected region.</li>
4307 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4308 </ul> <em>Application</em>
4310 <li>Fetch DB References capabilities and UI expanded to
4311 support retrieval from DAS sequence sources</li>
4312 <li>Local DAS Sequence sources can be added via the
4313 command line or via the Add local source dialog box.</li>
4314 <li>DAS Dbref and DbxRef feature types are parsed as
4315 database references and protein_name is parsed as
4316 description line (BioSapiens terms).</li>
4317 <li>Enable or disable non-positional feature and database
4318 references in sequence ID tooltip from View menu in
4320 <!-- <li>New hidden columns and rows and representatives capabilities
4321 in annotations file (in progress - not yet fully implemented)</li> -->
4322 <li>Group-associated consensus, sequence logos and
4323 conservation plots</li>
4324 <li>Symbol distributions for each column can be exported
4325 and visualized as sequence logos</li>
4326 <li>Optionally scale multi-character column labels to fit
4327 within each column of annotation row<!-- todo for applet -->
4329 <li>Optional automatic sort of associated alignment view
4330 when a new tree is opened.</li>
4331 <li>Jalview Java Console</li>
4332 <li>Better placement of desktop window when moving
4333 between different screens.</li>
4334 <li>New preference items for sequence ID tooltip and
4335 consensus annotation</li>
4336 <li>Client to submit sequences and IDs to Envision2
4338 <li><em>Vamsas Capabilities</em>
4340 <li>Improved VAMSAS synchronization (Jalview archive
4341 used to preserve views, structures, and tree display
4343 <li>Import of vamsas documents from disk or URL via
4345 <li>Sharing of selected regions between views and
4346 with other VAMSAS applications (Experimental feature!)</li>
4347 <li>Updated API to VAMSAS version 0.2</li>
4349 </ul> <em>Applet</em>
4351 <li>Middle button resizes annotation row height</li>
4354 <li>sortByTree (true/false) - automatically sort the
4355 associated alignment view by the tree when a new tree is
4357 <li>showTreeBootstraps (true/false) - show or hide
4358 branch bootstraps (default is to show them if available)</li>
4359 <li>showTreeDistances (true/false) - show or hide
4360 branch lengths (default is to show them if available)</li>
4361 <li>showUnlinkedTreeNodes (true/false) - indicate if
4362 unassociated nodes should be highlighted in the tree
4364 <li>heightScale and widthScale (1.0 or more) -
4365 increase the height or width of a cell in the alignment
4366 grid relative to the current font size.</li>
4369 <li>Non-positional features displayed in sequence ID
4371 </ul> <em>Other</em>
4373 <li>Features format: graduated colour definitions and
4374 specification of feature scores</li>
4375 <li>Alignment Annotations format: new keywords for group
4376 associated annotation (GROUP_REF) and annotation row display
4377 properties (ROW_PROPERTIES)</li>
4378 <li>XML formats extended to support graduated feature
4379 colourschemes, group associated annotation, and profile
4380 visualization settings.</li></td>
4383 <li>Source field in GFF files parsed as feature source
4384 rather than description</li>
4385 <li>Non-positional features are now included in sequence
4386 feature and gff files (controlled via non-positional feature
4387 visibility in tooltip).</li>
4388 <li>URL links generated for all feature links (bugfix)</li>
4389 <li>Added URL embedding instructions to features file
4391 <li>Codons containing ambiguous nucleotides translated as
4392 'X' in peptide product</li>
4393 <li>Match case switch in find dialog box works for both
4394 sequence ID and sequence string and query strings do not
4395 have to be in upper case to match case-insensitively.</li>
4396 <li>AMSA files only contain first column of
4397 multi-character column annotation labels</li>
4398 <li>Jalview Annotation File generation/parsing consistent
4399 with documentation (e.g. Stockholm annotation can be
4400 exported and re-imported)</li>
4401 <li>PDB files without embedded PDB IDs given a friendly
4403 <li>Find incrementally searches ID string matches as well
4404 as subsequence matches, and correctly reports total number
4408 <li>Better handling of exceptions during sequence
4410 <li>Dasobert generated non-positional feature URL
4411 link text excludes the start_end suffix</li>
4412 <li>DAS feature and source retrieval buttons disabled
4413 when fetch or registry operations in progress.</li>
4414 <li>PDB files retrieved from URLs are cached properly</li>
4415 <li>Sequence description lines properly shared via
4417 <li>Sequence fetcher fetches multiple records for all
4419 <li>Ensured that command line das feature retrieval
4420 completes before alignment figures are generated.</li>
4421 <li>Reduced time taken when opening file browser for
4423 <li>isAligned check prior to calculating tree, PCA or
4424 submitting an MSA to JNet now excludes hidden sequences.</li>
4425 <li>User defined group colours properly recovered
4426 from Jalview projects.</li>
4435 <div align="center">
4436 <strong>2.4.0.b2</strong><br> 28/10/2009
4441 <li>Experimental support for google analytics usage
4443 <li>Jalview privacy settings (user preferences and docs).</li>
4448 <li>Race condition in applet preventing startup in
4450 <li>Exception when feature created from selection beyond
4451 length of sequence.</li>
4452 <li>Allow synthetic PDB files to be imported gracefully</li>
4453 <li>Sequence associated annotation rows associate with
4454 all sequences with a given id</li>
4455 <li>Find function matches case-insensitively for sequence
4456 ID string searches</li>
4457 <li>Non-standard characters do not cause pairwise
4458 alignment to fail with exception</li>
4459 </ul> <em>Application Issues</em>
4461 <li>Sequences are now validated against EMBL database</li>
4462 <li>Sequence fetcher fetches multiple records for all
4464 </ul> <em>InstallAnywhere Issues</em>
4466 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4467 issue with installAnywhere mechanism)</li>
4468 <li>Command line launching of JARs from InstallAnywhere
4469 version (java class versioning error fixed)</li>
4476 <div align="center">
4477 <strong>2.4</strong><br> 27/8/2008
4480 <td><em>User Interface</em>
4482 <li>Linked highlighting of codon and amino acid from
4483 translation and protein products</li>
4484 <li>Linked highlighting of structure associated with
4485 residue mapping to codon position</li>
4486 <li>Sequence Fetcher provides example accession numbers
4487 and 'clear' button</li>
4488 <li>MemoryMonitor added as an option under Desktop's
4490 <li>Extract score function to parse whitespace separated
4491 numeric data in description line</li>
4492 <li>Column labels in alignment annotation can be centred.</li>
4493 <li>Tooltip for sequence associated annotation give name
4495 </ul> <em>Web Services and URL fetching</em>
4497 <li>JPred3 web service</li>
4498 <li>Prototype sequence search client (no public services
4500 <li>Fetch either seed alignment or full alignment from
4502 <li>URL Links created for matching database cross
4503 references as well as sequence ID</li>
4504 <li>URL Links can be created using regular-expressions</li>
4505 </ul> <em>Sequence Database Connectivity</em>
4507 <li>Retrieval of cross-referenced sequences from other
4509 <li>Generalised database reference retrieval and
4510 validation to all fetchable databases</li>
4511 <li>Fetch sequences from DAS sources supporting the
4512 sequence command</li>
4513 </ul> <em>Import and Export</em>
4514 <li>export annotation rows as CSV for spreadsheet import</li>
4515 <li>Jalview projects record alignment dataset associations,
4516 EMBL products, and cDNA sequence mappings</li>
4517 <li>Sequence Group colour can be specified in Annotation
4519 <li>Ad-hoc colouring of group in Annotation File using RGB
4520 triplet as name of colourscheme</li>
4521 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4523 <li>treenode binding for VAMSAS tree exchange</li>
4524 <li>local editing and update of sequences in VAMSAS
4525 alignments (experimental)</li>
4526 <li>Create new or select existing session to join</li>
4527 <li>load and save of vamsas documents</li>
4528 </ul> <em>Application command line</em>
4530 <li>-tree parameter to open trees (introduced for passing
4532 <li>-fetchfrom command line argument to specify nicknames
4533 of DAS servers to query for alignment features</li>
4534 <li>-dasserver command line argument to add new servers
4535 that are also automatically queried for features</li>
4536 <li>-groovy command line argument executes a given groovy
4537 script after all input data has been loaded and parsed</li>
4538 </ul> <em>Applet-Application data exchange</em>
4540 <li>Trees passed as applet parameters can be passed to
4541 application (when using "View in full
4542 application")</li>
4543 </ul> <em>Applet Parameters</em>
4545 <li>feature group display control parameter</li>
4546 <li>debug parameter</li>
4547 <li>showbutton parameter</li>
4548 </ul> <em>Applet API methods</em>
4550 <li>newView public method</li>
4551 <li>Window (current view) specific get/set public methods</li>
4552 <li>Feature display control methods</li>
4553 <li>get list of currently selected sequences</li>
4554 </ul> <em>New Jalview distribution features</em>
4556 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4557 <li>RELEASE file gives build properties for the latest
4558 Jalview release.</li>
4559 <li>Java 1.1 Applet build made easier and donotobfuscate
4560 property controls execution of obfuscator</li>
4561 <li>Build target for generating source distribution</li>
4562 <li>Debug flag for javacc</li>
4563 <li>.jalview_properties file is documented (slightly) in
4564 jalview.bin.Cache</li>
4565 <li>Continuous Build Integration for stable and
4566 development version of Application, Applet and source
4571 <li>selected region output includes visible annotations
4572 (for certain formats)</li>
4573 <li>edit label/displaychar contains existing label/char
4575 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4576 <li>shorter peptide product names from EMBL records</li>
4577 <li>Newick string generator makes compact representations</li>
4578 <li>bootstrap values parsed correctly for tree files with
4580 <li>pathological filechooser bug avoided by not allowing
4581 filenames containing a ':'</li>
4582 <li>Fixed exception when parsing GFF files containing
4583 global sequence features</li>
4584 <li>Alignment datasets are finalized only when number of
4585 references from alignment sequences goes to zero</li>
4586 <li>Close of tree branch colour box without colour
4587 selection causes cascading exceptions</li>
4588 <li>occasional negative imgwidth exceptions</li>
4589 <li>better reporting of non-fatal warnings to user when
4590 file parsing fails.</li>
4591 <li>Save works when Jalview project is default format</li>
4592 <li>Save as dialog opened if current alignment format is
4593 not a valid output format</li>
4594 <li>UniProt canonical names introduced for both das and
4596 <li>Histidine should be midblue (not pink!) in Zappo</li>
4597 <li>error messages passed up and output when data read
4599 <li>edit undo recovers previous dataset sequence when
4600 sequence is edited</li>
4601 <li>allow PDB files without pdb ID HEADER lines (like
4602 those generated by MODELLER) to be read in properly</li>
4603 <li>allow reading of JPred concise files as a normal
4605 <li>Stockholm annotation parsing and alignment properties
4606 import fixed for PFAM records</li>
4607 <li>Structure view windows have correct name in Desktop
4609 <li>annotation consisting of sequence associated scores
4610 can be read and written correctly to annotation file</li>
4611 <li>Aligned cDNA translation to aligned peptide works
4613 <li>Fixed display of hidden sequence markers and
4614 non-italic font for representatives in Applet</li>
4615 <li>Applet Menus are always embedded in applet window on
4617 <li>Newly shown features appear at top of stack (in
4619 <li>Annotations added via parameter not drawn properly
4620 due to null pointer exceptions</li>
4621 <li>Secondary structure lines are drawn starting from
4622 first column of alignment</li>
4623 <li>UniProt XML import updated for new schema release in
4625 <li>Sequence feature to sequence ID match for Features
4626 file is case-insensitive</li>
4627 <li>Sequence features read from Features file appended to
4628 all sequences with matching IDs</li>
4629 <li>PDB structure coloured correctly for associated views
4630 containing a sub-sequence</li>
4631 <li>PDB files can be retrieved by applet from Jar files</li>
4632 <li>feature and annotation file applet parameters
4633 referring to different directories are retrieved correctly</li>
4634 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4635 <li>Fixed application hang whilst waiting for
4636 splash-screen version check to complete</li>
4637 <li>Applet properly URLencodes input parameter values
4638 when passing them to the launchApp service</li>
4639 <li>display name and local features preserved in results
4640 retrieved from web service</li>
4641 <li>Visual delay indication for sequence retrieval and
4642 sequence fetcher initialisation</li>
4643 <li>updated Application to use DAS 1.53e version of
4644 dasobert DAS client</li>
4645 <li>Re-instated Full AMSA support and .amsa file
4647 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4655 <div align="center">
4656 <strong>2.3</strong><br> 9/5/07
4661 <li>Jmol 11.0.2 integration</li>
4662 <li>PDB views stored in Jalview XML files</li>
4663 <li>Slide sequences</li>
4664 <li>Edit sequence in place</li>
4665 <li>EMBL CDS features</li>
4666 <li>DAS Feature mapping</li>
4667 <li>Feature ordering</li>
4668 <li>Alignment Properties</li>
4669 <li>Annotation Scores</li>
4670 <li>Sort by scores</li>
4671 <li>Feature/annotation editing in applet</li>
4676 <li>Headless state operation in 2.2.1</li>
4677 <li>Incorrect and unstable DNA pairwise alignment</li>
4678 <li>Cut and paste of sequences with annotation</li>
4679 <li>Feature group display state in XML</li>
4680 <li>Feature ordering in XML</li>
4681 <li>blc file iteration selection using filename # suffix</li>
4682 <li>Stockholm alignment properties</li>
4683 <li>Stockhom alignment secondary structure annotation</li>
4684 <li>2.2.1 applet had no feature transparency</li>
4685 <li>Number pad keys can be used in cursor mode</li>
4686 <li>Structure Viewer mirror image resolved</li>
4693 <div align="center">
4694 <strong>2.2.1</strong><br> 12/2/07
4699 <li>Non standard characters can be read and displayed
4700 <li>Annotations/Features can be imported/exported to the
4702 <li>Applet allows editing of sequence/annotation/group
4703 name & description
4704 <li>Preference setting to display sequence name in
4706 <li>Annotation file format extended to allow
4707 Sequence_groups to be defined
4708 <li>Default opening of alignment overview panel can be
4709 specified in preferences
4710 <li>PDB residue numbering annotation added to associated
4716 <li>Applet crash under certain Linux OS with Java 1.6
4718 <li>Annotation file export / import bugs fixed
4719 <li>PNG / EPS image output bugs fixed
4725 <div align="center">
4726 <strong>2.2</strong><br> 27/11/06
4731 <li>Multiple views on alignment
4732 <li>Sequence feature editing
4733 <li>"Reload" alignment
4734 <li>"Save" to current filename
4735 <li>Background dependent text colour
4736 <li>Right align sequence ids
4737 <li>User-defined lower case residue colours
4740 <li>Menu item accelerator keys
4741 <li>Control-V pastes to current alignment
4742 <li>Cancel button for DAS Feature Fetching
4743 <li>PCA and PDB Viewers zoom via mouse roller
4744 <li>User-defined sub-tree colours and sub-tree selection
4746 <li>'New Window' button on the 'Output to Text box'
4751 <li>New memory efficient Undo/Redo System
4752 <li>Optimised symbol lookups and conservation/consensus
4754 <li>Region Conservation/Consensus recalculated after
4756 <li>Fixed Remove Empty Columns Bug (empty columns at end
4758 <li>Slowed DAS Feature Fetching for increased robustness.
4760 <li>Made angle brackets in ASCII feature descriptions
4762 <li>Re-instated Zoom function for PCA
4763 <li>Sequence descriptions conserved in web service
4765 <li>UniProt ID discoverer uses any word separated by
4767 <li>WsDbFetch query/result association resolved
4768 <li>Tree leaf to sequence mapping improved
4769 <li>Smooth fonts switch moved to FontChooser dialog box.
4776 <div align="center">
4777 <strong>2.1.1</strong><br> 12/9/06
4782 <li>Copy consensus sequence to clipboard</li>
4787 <li>Image output - rightmost residues are rendered if
4788 sequence id panel has been resized</li>
4789 <li>Image output - all offscreen group boundaries are
4791 <li>Annotation files with sequence references - all
4792 elements in file are relative to sequence position</li>
4793 <li>Mac Applet users can use Alt key for group editing</li>
4799 <div align="center">
4800 <strong>2.1</strong><br> 22/8/06
4805 <li>MAFFT Multiple Alignment in default Web Service list</li>
4806 <li>DAS Feature fetching</li>
4807 <li>Hide sequences and columns</li>
4808 <li>Export Annotations and Features</li>
4809 <li>GFF file reading / writing</li>
4810 <li>Associate structures with sequences from local PDB
4812 <li>Add sequences to exisiting alignment</li>
4813 <li>Recently opened files / URL lists</li>
4814 <li>Applet can launch the full application</li>
4815 <li>Applet has transparency for features (Java 1.2
4817 <li>Applet has user defined colours parameter</li>
4818 <li>Applet can load sequences from parameter
4819 "sequence<em>x</em>"
4825 <li>Redundancy Panel reinstalled in the Applet</li>
4826 <li>Monospaced font - EPS / rescaling bug fixed</li>
4827 <li>Annotation files with sequence references bug fixed</li>
4833 <div align="center">
4834 <strong>2.08.1</strong><br> 2/5/06
4839 <li>Change case of selected region from Popup menu</li>
4840 <li>Choose to match case when searching</li>
4841 <li>Middle mouse button and mouse movement can compress /
4842 expand the visible width and height of the alignment</li>
4847 <li>Annotation Panel displays complete JNet results</li>
4853 <div align="center">
4854 <strong>2.08b</strong><br> 18/4/06
4860 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4861 <li>Righthand label on wrapped alignments shows correct
4868 <div align="center">
4869 <strong>2.08</strong><br> 10/4/06
4874 <li>Editing can be locked to the selection area</li>
4875 <li>Keyboard editing</li>
4876 <li>Create sequence features from searches</li>
4877 <li>Precalculated annotations can be loaded onto
4879 <li>Features file allows grouping of features</li>
4880 <li>Annotation Colouring scheme added</li>
4881 <li>Smooth fonts off by default - Faster rendering</li>
4882 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4887 <li>Drag & Drop fixed on Linux</li>
4888 <li>Jalview Archive file faster to load/save, sequence
4889 descriptions saved.</li>
4895 <div align="center">
4896 <strong>2.07</strong><br> 12/12/05
4901 <li>PDB Structure Viewer enhanced</li>
4902 <li>Sequence Feature retrieval and display enhanced</li>
4903 <li>Choose to output sequence start-end after sequence
4904 name for file output</li>
4905 <li>Sequence Fetcher WSDBFetch@EBI</li>
4906 <li>Applet can read feature files, PDB files and can be
4907 used for HTML form input</li>
4912 <li>HTML output writes groups and features</li>
4913 <li>Group editing is Control and mouse click</li>
4914 <li>File IO bugs</li>
4920 <div align="center">
4921 <strong>2.06</strong><br> 28/9/05
4926 <li>View annotations in wrapped mode</li>
4927 <li>More options for PCA viewer</li>
4932 <li>GUI bugs resolved</li>
4933 <li>Runs with -nodisplay from command line</li>
4939 <div align="center">
4940 <strong>2.05b</strong><br> 15/9/05
4945 <li>Choose EPS export as lineart or text</li>
4946 <li>Jar files are executable</li>
4947 <li>Can read in Uracil - maps to unknown residue</li>
4952 <li>Known OutOfMemory errors give warning message</li>
4953 <li>Overview window calculated more efficiently</li>
4954 <li>Several GUI bugs resolved</li>
4960 <div align="center">
4961 <strong>2.05</strong><br> 30/8/05
4966 <li>Edit and annotate in "Wrapped" view</li>
4971 <li>Several GUI bugs resolved</li>
4977 <div align="center">
4978 <strong>2.04</strong><br> 24/8/05
4983 <li>Hold down mouse wheel & scroll to change font
4989 <li>Improved JPred client reliability</li>
4990 <li>Improved loading of Jalview files</li>
4996 <div align="center">
4997 <strong>2.03</strong><br> 18/8/05
5002 <li>Set Proxy server name and port in preferences</li>
5003 <li>Multiple URL links from sequence ids</li>
5004 <li>User Defined Colours can have a scheme name and added
5006 <li>Choose to ignore gaps in consensus calculation</li>
5007 <li>Unix users can set default web browser</li>
5008 <li>Runs without GUI for batch processing</li>
5009 <li>Dynamically generated Web Service Menus</li>
5014 <li>InstallAnywhere download for Sparc Solaris</li>
5020 <div align="center">
5021 <strong>2.02</strong><br> 18/7/05
5027 <li>Copy & Paste order of sequences maintains
5028 alignment order.</li>
5034 <div align="center">
5035 <strong>2.01</strong><br> 12/7/05
5040 <li>Use delete key for deleting selection.</li>
5041 <li>Use Mouse wheel to scroll sequences.</li>
5042 <li>Help file updated to describe how to add alignment
5044 <li>Version and build date written to build properties
5046 <li>InstallAnywhere installation will check for updates
5047 at launch of Jalview.</li>
5052 <li>Delete gaps bug fixed.</li>
5053 <li>FileChooser sorts columns.</li>
5054 <li>Can remove groups one by one.</li>
5055 <li>Filechooser icons installed.</li>
5056 <li>Finder ignores return character when searching.
5057 Return key will initiate a search.<br>
5064 <div align="center">
5065 <strong>2.0</strong><br> 20/6/05
5070 <li>New codebase</li>