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
99 </ul> <em>Installer</em>
102 <!-- JAL-3611 -->Space character in Jalview install path on
103 Windows prevents install4j launching getdown
105 </ul> <em>Development</em>
108 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
109 version numbers in doc/building.md
115 <td width="60" align="center" nowrap><strong><a
116 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
117 <em>25/09/2020</em></strong></td>
118 <td align="left" valign="top">
122 <td align="left" valign="top">
125 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
126 "Encountered problems opening
127 https://www.jalview.org/examples/exampleFile_2_7.jvp"
133 <td width="60" align="center" nowrap><strong><a
134 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
135 <em>17/09/2020</em></strong></td>
136 <td align="left" valign="top">
139 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
140 residue in cursor mode
143 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
144 HTSJDK from 2.12 to 2.23
147 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
148 optimisations and improvements suggested by Bob Hanson and
149 improved compatibility with JalviewJS
152 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
153 alignments from Pfam and Rfam
156 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
157 import (no longer based on .gz extension)
160 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
163 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
164 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
168 <!-- JAL-3667 -->Improved warning messages, debug logging
169 and fixed Retry action when Jalview encounters errors when
170 saving or making backup files.
173 <!-- JAL-3676 -->Enhanced Jalview Java Console:
175 <li>Jalview's logging level can be configured</li>
176 <li>Copy to Clipboard Buttion</li>
180 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
181 when running on Linux (Requires Java 11+)
183 </ul> <em>Launching Jalview</em>
186 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
187 through a system property
190 <!-- JAL-3477 -->Improved built-in documentation and command
191 line help for configuring Jalview's memory
195 <td align="left" valign="top">
198 <!-- JAL-3691 -->Conservation and Quality tracks are shown
199 but not calculated and no protein or DNA score models are
200 available for tree/PCA calculation when launched with
201 Turkish language locale
204 <!-- JAL-3493 -->Escape does not clear highlights on the
205 alignment (Since Jalview 2.10.3)
208 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
209 doesn't slide selected sequences, just sequence under cursor
212 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
213 sequence under the cursor
216 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
217 multiple EMBL gene products shown forĀ a single contig
220 <!-- JAL-3696 -->Errors encountered when processing variants
221 from VCF files yield "Error processing VCF: Format specifier
225 <!-- JAL-3697 -->Count of features not shown can be wrong
226 when there are both local and complementary features mapped
227 to the position under the cursor
230 <!-- JAL-3673 -->Sequence ID for reference sequence is
231 clipped when Right align Sequence IDs enabled
234 <!-- JAL-2983 -->Slider with negative range values not
235 rendered correctly in VAqua4 (Since 2.10.4)
238 <!-- JAL-3685 -->Single quotes not displayed correctly in
239 internationalised text for some messages and log output
242 <!-- JAL-3490 -->Find doesn't report matches that span
243 hidden gapped columns
246 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
247 panels, Alignment viewport and annotation renderer.
250 <!-- JAL-3561 -->Jalview ignores file format parameter
251 specifying output format when exporting an alignment via the
255 <!-- JAL-3667 -->Windows 10: For a minority of users, if
256 backups are not enabled, Jalview sometimes fails to
257 overwrite an existing file and raises a warning dialog. (in
258 2.11.0, and 2.11.1.0, the workaround is to try to save the
259 file again, and if that fails, delete the original file and
263 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
267 <!-- JAL-3741 -->References to http://www.jalview.org in
268 program and documentation
270 </ul> <em>Launching Jalview</em>
273 <!-- JAL-3718 -->Jalview application fails when launched the
274 first time for a version that has different jars to the
275 previous launched version.
277 </ul> <em>Developing Jalview</em>
280 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
281 data, causing cloverReport gradle task to fail with an
285 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
286 monitor the release channel
288 </ul> <em>New Known defects</em>
291 <!-- JAL-3748 -->CDS shown in result of submitting proteins
292 in a CDS/Protein alignment to a web service is wrong when
293 proteins share a common transcript sequence (e.g.
294 genome of RNA viruses)
297 <!-- JAL-3576 -->Co-located features exported and re-imported
298 are ordered differently when shown on alignment and in
299 tooltips. (Also affects v2.11.1.0)
302 <!-- JAL-3702 -->Drag and drop of alignment file onto
303 alignment window when in a HiDPI scaled mode in Linux only
304 works for the top left quadrant of the alignment window
307 <!-- JAL-3701 -->Stale build data in jalview standalone jar
308 builds (only affects 2.11.1.1 branch)
311 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
312 when alignment view restored from project (since Jalview 2.11.0)
315 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
316 protein products for certain ENA records are repeatedly
317 shown via Calculate->Show Cross Refs
323 <td width="60" align="center" nowrap><strong><a
324 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
325 <em>22/04/2020</em></strong></td>
326 <td align="left" valign="top">
329 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
330 'virtual' codon features shown on protein (or vice versa)
331 for display in alignments, on structure views (including
332 transfer to UCSF chimera), in feature reports and for
336 <!-- JAL-3121 -->Feature attributes from VCF files can be
337 exported and re-imported as GFF3 files
340 <!-- JAL-3376 -->Capture VCF "fixed column" values
341 POS, ID, QUAL, FILTER as Feature Attributes
344 <!-- JAL-3375 -->More robust VCF numeric data field
345 validation while parsing
348 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
352 <!-- JAL-3535 -->Feature Settings dialog title includes name
356 <!-- JAL-3538 -->Font anti-aliasing in alignment views
360 <!-- JAL-3468 -->Very long feature descriptions truncated in
364 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
365 with no feature types visible
368 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
370 </ul><em>Jalview Installer</em>
373 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
374 in console (may be null when Jalview launched as executable jar or via conda)
377 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
380 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
383 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
385 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
386 </ul> <em>Release processes</em>
389 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
392 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
394 </ul> <em>Build System</em>
397 <!-- JAL-3510 -->Clover updated to 4.4.1
400 <!-- JAL-3513 -->Test code included in Clover coverage
404 <em>Groovy Scripts</em>
407 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
408 to stdout containing the consensus sequence for each
409 alignment in a Jalview session
412 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
413 genomic sequence_variant annotation from CDS as
414 missense_variant or synonymous_variant on protein products.
418 <td align="left" valign="top">
421 <!-- JAL-3581 -->Hidden sequence markers still visible when
422 'Show hidden markers' option is not ticked
425 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
426 PNG output when 'Automatically set ID width' is set in
427 jalview preferences or properties file
430 <!-- JAL-3571 -->Feature Editor dialog can be opened when
431 'Show Sequence Features' option is not ticked
434 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
435 buttons in Feature Settings dialog are clicked when no
439 <!-- JAL-3412 -->ID margins for CDS and Protein views not
440 equal when split frame is first opened
443 <!-- JAL-3296 -->Sequence position numbers in status bar not
444 correct after editing a sequence's start position
447 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
448 with annotation and exceptions thrown when only a few
449 columns shown in wrapped mode
452 <!-- JAL-3386 -->Sequence IDs missing in headless export of
453 wrapped alignment figure with annotations
456 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
457 ID fails with ClassCastException
460 <!-- JAL-3389 -->Chimera session not restored from Jalview
464 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
465 feature settings dialog also selects columns
468 <!-- JAL-3473 -->SpinnerNumberModel causes
469 IllegalArgumentException in some circumstances
472 <!-- JAL-3534 -->Multiple feature settings dialogs can be
476 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
477 alignment window is closed
480 <!-- JAL-3406 -->Credits missing some authors in Jalview
481 help documentation for 2.11.0 release
484 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
485 includes Pfam ID as sequence's accession rather than its
488 </ul> <em>Java 11 Compatibility issues</em>
491 <!-- JAL-2987 -->OSX - Can't view some search results in
492 PDB/Uniprot search panel
494 </ul> <em>Installer</em>
497 <!-- JAL-3447 -->Jalview should not create file associations
498 for 3D structure files (.pdb, .mmcif. .cif)
500 </ul> <em>Repository and Source Release</em>
503 <!-- JAL-3474 -->removed obsolete .cvsignore files from
507 <!-- JAL-3541 -->Clover report generation running out of
510 </ul> <em>New Known Issues</em>
513 <!-- JAL-3523 -->OSX - Current working directory not
514 preserved when Jalview.app launched with parameters from
518 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
519 clipped in headless figure export when Right Align option
523 <!-- JAL-3542 -->Jalview Installation type always reports
524 'Source' in console output
527 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
528 bamboo server but run fine locally.
534 <td width="60" align="center" nowrap>
535 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
536 <em>04/07/2019</em></strong>
538 <td align="left" valign="top">
541 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
542 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
543 source project) rather than InstallAnywhere
546 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
547 settings, receive over the air updates and launch specific
548 versions via (<a href="https://github.com/threerings/getdown">Three
552 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
553 formats supported by Jalview (including .jvp project files)
556 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
557 arguments and switch between different getdown channels
560 <!-- JAL-3141 -->Backup files created when saving Jalview project
565 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
566 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
568 <!-- JAL-2620 -->Alternative genetic code tables for
569 'Translate as cDNA'</li>
571 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
572 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
575 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
576 implementation that allows updates) used for Sequence Feature collections</li>
578 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
579 features can be filtered and shaded according to any
580 associated attributes (e.g. variant attributes from VCF
581 file, or key-value pairs imported from column 9 of GFF
585 <!-- JAL-2879 -->Feature Attributes and shading schemes
586 stored and restored from Jalview Projects
589 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
590 recognise variant features
593 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
594 sequences (also coloured red by default)
597 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
601 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
602 algorithm (Z-sort/transparency and filter aware)
605 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
611 <!-- JAL-3205 -->Symmetric score matrices for faster
612 tree and PCA calculations
614 <li><strong>Principal Components Analysis Viewer</strong>
617 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
618 and Viewer state saved in Jalview Project
620 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
623 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
627 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
632 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
634 <li><strong>Speed and Efficiency</strong>
637 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
638 multiple groups when working with large alignments
641 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
645 <li><strong>User Interface</strong>
648 <!-- JAL-2933 -->Finder panel remembers last position in each
652 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
653 what is shown)<br />Only visible regions of alignment are shown by
654 default (can be changed in user preferences)
657 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
658 to the Overwrite Dialog
661 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
665 <!-- JAL-1244 -->Status bar shows bounds when dragging a
666 selection region, and gap count when inserting or deleting gaps
669 <!-- JAL-3132 -->Status bar updates over sequence and annotation
673 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
677 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
681 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
684 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
688 <!-- JAL-3181 -->Consistent ordering of links in sequence id
692 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
694 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
698 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
699 <li><strong>Java 11 Support (not yet on general release)</strong>
702 <!-- -->OSX GUI integrations for App menu's 'About' entry and
707 <em>Deprecations</em>
709 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
710 capabilities removed from the Jalview Desktop
712 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
713 unmarshalling has been replaced by JAXB for Jalview projects
714 and XML based data retrieval clients</li>
715 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
716 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
717 </ul> <em>Documentation</em>
719 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
720 not supported in EPS figure export
722 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
723 </ul> <em>Development and Release Processes</em>
726 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
729 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
731 <!-- JAL-3225 -->Eclipse project configuration managed with
735 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
736 Bamboo continuous integration for unattended Test Suite
740 <!-- JAL-2864 -->Memory test suite to detect leaks in common
744 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
748 <!-- JAL-3248 -->Developer documentation migrated to
749 markdown (with HTML rendering)
752 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
755 <!-- JAL-3289 -->New URLs for publishing development
760 <td align="left" valign="top">
763 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
766 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
767 superposition in Jmol fail on Windows
770 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
771 structures for sequences with lots of PDB structures
774 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
778 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
779 project involving multiple views
782 <!-- JAL-3164 -->Overview for complementary view in a linked
783 CDS/Protein alignment is not updated when Hide Columns by
784 Annotation dialog hides columns
787 <!-- JAL-3158 -->Selection highlighting in the complement of a
788 CDS/Protein alignment stops working after making a selection in
789 one view, then making another selection in the other view
792 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
796 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
797 Settings and Jalview Preferences panels
800 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
801 overview with large alignments
804 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
805 region if columns were selected by dragging right-to-left and the
806 mouse moved to the left of the first column
809 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
810 hidden column marker via scale popup menu
813 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
814 doesn't tell users the invalid URL
817 <!-- JAL-2816 -->Tooltips displayed for features filtered by
821 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
822 show cross references or Fetch Database References are shown in
826 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
827 peptide sequence (computed variant shown as p.Res.null)
830 <!-- JAL-2060 -->'Graduated colour' option not offered for
831 manually created features (where feature score is Float.NaN)
834 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
835 when columns are hidden
838 <!-- JAL-3082 -->Regular expression error for '(' in Select
839 Columns by Annotation description
842 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
843 out of Scale or Annotation Panel
846 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
850 <!-- JAL-3074 -->Left/right drag in annotation can scroll
854 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
858 <!-- JAL-3002 -->Column display is out by one after Page Down,
859 Page Up in wrapped mode
862 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
865 <!-- JAL-2932 -->Finder searches in minimised alignments
868 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
869 on opening an alignment
872 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
876 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
877 different groups in the alignment are selected
880 <!-- JAL-2717 -->Internationalised colour scheme names not shown
884 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
888 <!-- JAL-3125 -->Value input for graduated feature colour
889 threshold gets 'unrounded'
892 <!-- JAL-2982 -->PCA image export doesn't respect background
896 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
899 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
902 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
906 <!-- JAL-2964 -->Associate Tree with All Views not restored from
910 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
911 shown in complementary view
914 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
915 without normalisation
918 <!-- JAL-3021 -->Sequence Details report should open positioned at top
922 <!-- JAL-914 -->Help page can be opened twice
925 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
927 </ul> <em>Editing</em>
930 <!-- JAL-2822 -->Start and End should be updated when sequence
931 data at beginning or end of alignment added/removed via 'Edit'
935 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
936 relocate sequence features correctly when start of sequence is
937 removed (Known defect since 2.10)
940 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
941 dialog corrupts dataset sequence
944 <!-- JAL-868 -->Structure colours not updated when associated tree
945 repartitions the alignment view (Regression in 2.10.5)
947 </ul> <em>Datamodel</em>
950 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
951 sequence's End is greater than its length
953 </ul> <em>Bugs fixed for Java 11 Support (not yet on
954 general release)</em>
957 <!-- JAL-3288 -->Menus work properly in split-screen
959 </ul> <em>New Known Defects</em>
962 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
965 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
966 regions of protein alignment.
969 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
970 is restored from a Jalview 2.11 project
973 <!-- JAL-3213 -->Alignment panel height can be too small after
977 <!-- JAL-3240 -->Display is incorrect after removing gapped
978 columns within hidden columns
981 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
982 window after dragging left to select columns to left of visible
986 <!-- JAL-2876 -->Features coloured according to their description
987 string and thresholded by score in earlier versions of Jalview are
988 not shown as thresholded features in 2.11. To workaround please
989 create a Score filter instead.
992 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
994 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
997 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
998 alignments with multiple views can close views unexpectedly
1001 <em>Java 11 Specific defects</em>
1004 <!-- JAL-3235 -->Jalview Properties file is not sorted
1005 alphabetically when saved
1011 <td width="60" nowrap>
1012 <div align="center">
1013 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1016 <td><div align="left">
1020 <!-- JAL-3101 -->Default memory for Jalview webstart and
1021 InstallAnywhere increased to 1G.
1024 <!-- JAL-247 -->Hidden sequence markers and representative
1025 sequence bolding included when exporting alignment as EPS,
1026 SVG, PNG or HTML. <em>Display is configured via the
1027 Format menu, or for command-line use via a Jalview
1028 properties file.</em>
1031 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1032 API and sequence data now imported as JSON.
1035 <!-- JAL-3065 -->Change in recommended way of starting
1036 Jalview via a Java command line: add jars in lib directory
1037 to CLASSPATH, rather than via the deprecated java.ext.dirs
1041 <em>Development</em>
1044 <!-- JAL-3047 -->Support added to execute test suite
1045 instrumented with <a href="http://openclover.org/">Open
1050 <td><div align="left">
1054 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1055 row shown in Feredoxin Structure alignment view of example
1059 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1060 annotation displayed.
1063 <!-- JAL-3107 -->Group conservation/consensus not shown
1064 for newly created group when 'Apply to all groups'
1068 <!-- JAL-3087 -->Corrupted display when switching to
1069 wrapped mode when sequence panel's vertical scrollbar is
1073 <!-- JAL-3003 -->Alignment is black in exported EPS file
1074 when sequences are selected in exported view.</em>
1077 <!-- JAL-3059 -->Groups with different coloured borders
1078 aren't rendered with correct colour.
1081 <!-- JAL-3092 -->Jalview could hang when importing certain
1082 types of knotted RNA secondary structure.
1085 <!-- JAL-3095 -->Sequence highlight and selection in
1086 trimmed VARNA 2D structure is incorrect for sequences that
1090 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1091 annotation when columns are inserted into an alignment,
1092 and when exporting as Stockholm flatfile.
1095 <!-- JAL-3053 -->Jalview annotation rows containing upper
1096 and lower-case 'E' and 'H' do not automatically get
1097 treated as RNA secondary structure.
1100 <!-- JAL-3106 -->.jvp should be used as default extension
1101 (not .jar) when saving a Jalview project file.
1104 <!-- JAL-3105 -->Mac Users: closing a window correctly
1105 transfers focus to previous window on OSX
1108 <em>Java 10 Issues Resolved</em>
1111 <!-- JAL-2988 -->OSX - Can't save new files via the File
1112 or export menus by typing in a name into the Save dialog
1116 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1117 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1118 'look and feel' which has improved compatibility with the
1119 latest version of OSX.
1126 <td width="60" nowrap>
1127 <div align="center">
1128 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1129 <em>7/06/2018</em></strong>
1132 <td><div align="left">
1136 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1137 annotation retrieved from Uniprot
1140 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1141 onto the Jalview Desktop
1145 <td><div align="left">
1149 <!-- JAL-3017 -->Cannot import features with multiple
1150 variant elements (blocks import of some Uniprot records)
1153 <!-- JAL-2997 -->Clustal files with sequence positions in
1154 right-hand column parsed correctly
1157 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1158 not alignment area in exported graphic
1161 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1162 window has input focus
1165 <!-- JAL-2992 -->Annotation panel set too high when
1166 annotation added to view (Windows)
1169 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1170 network connectivity is poor
1173 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1174 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1175 the currently open URL and links from a page viewed in
1176 Firefox or Chrome on Windows is now fully supported. If
1177 you are using Edge, only links in the page can be
1178 dragged, and with Internet Explorer, only the currently
1179 open URL in the browser can be dropped onto Jalview.</em>
1182 <em>New Known Defects</em>
1184 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1189 <td width="60" nowrap>
1190 <div align="center">
1191 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1194 <td><div align="left">
1198 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1199 for disabling automatic superposition of multiple
1200 structures and open structures in existing views
1203 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1204 ID and annotation area margins can be click-dragged to
1208 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1212 <!-- JAL-2759 -->Improved performance for large alignments
1213 and lots of hidden columns
1216 <!-- JAL-2593 -->Improved performance when rendering lots
1217 of features (particularly when transparency is disabled)
1220 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1221 exchange of Jalview features and Chimera attributes made
1227 <td><div align="left">
1230 <!-- JAL-2899 -->Structure and Overview aren't updated
1231 when Colour By Annotation threshold slider is adjusted
1234 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1235 overlapping alignment panel
1238 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1242 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1243 improved: CDS not handled correctly if transcript has no
1247 <!-- JAL-2321 -->Secondary structure and temperature
1248 factor annotation not added to sequence when local PDB
1249 file associated with it by drag'n'drop or structure
1253 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1254 dialog doesn't import PDB files dropped on an alignment
1257 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1258 scroll bar doesn't work for some CDS/Protein views
1261 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1262 Java 1.8u153 onwards and Java 1.9u4+.
1265 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1266 columns in annotation row
1269 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1270 honored in batch mode
1273 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1274 for structures added to existing Jmol view
1277 <!-- JAL-2223 -->'View Mappings' includes duplicate
1278 entries after importing project with multiple views
1281 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1282 protein sequences via SIFTS from associated PDB entries
1283 with negative residue numbers or missing residues fails
1286 <!-- JAL-2952 -->Exception when shading sequence with negative
1287 Temperature Factor values from annotated PDB files (e.g.
1288 as generated by CONSURF)
1291 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1292 tooltip doesn't include a text description of mutation
1295 <!-- JAL-2922 -->Invert displayed features very slow when
1296 structure and/or overview windows are also shown
1299 <!-- JAL-2954 -->Selecting columns from highlighted regions
1300 very slow for alignments with large numbers of sequences
1303 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1304 with 'StringIndexOutOfBounds'
1307 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1308 platforms running Java 10
1311 <!-- JAL-2960 -->Adding a structure to existing structure
1312 view appears to do nothing because the view is hidden behind the alignment view
1318 <!-- JAL-2926 -->Copy consensus sequence option in applet
1319 should copy the group consensus when popup is opened on it
1325 <!-- JAL-2913 -->Fixed ID width preference is not respected
1328 <em>New Known Defects</em>
1331 <!-- JAL-2973 --> Exceptions occasionally raised when
1332 editing a large alignment and overview is displayed
1335 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1336 repeatedly after a series of edits even when the overview
1337 is no longer reflecting updates
1340 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1341 structures for protein subsequence (if 'Trim Retrieved
1342 Sequences' enabled) or Ensembl isoforms (Workaround in
1343 2.10.4 is to fail back to N&W mapping)
1346 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1347 option gives blank output
1354 <td width="60" nowrap>
1355 <div align="center">
1356 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1359 <td><div align="left">
1360 <ul><li>Updated Certum Codesigning Certificate
1361 (Valid till 30th November 2018)</li></ul></div></td>
1362 <td><div align="left">
1363 <em>Desktop</em><ul>
1365 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1366 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1367 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1368 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1369 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1370 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1371 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1377 <td width="60" nowrap>
1378 <div align="center">
1379 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1382 <td><div align="left">
1386 <!-- JAL-2446 -->Faster and more efficient management and
1387 rendering of sequence features
1390 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1391 429 rate limit request hander
1394 <!-- JAL-2773 -->Structure views don't get updated unless
1395 their colours have changed
1398 <!-- JAL-2495 -->All linked sequences are highlighted for
1399 a structure mousover (Jmol) or selection (Chimera)
1402 <!-- JAL-2790 -->'Cancel' button in progress bar for
1403 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1406 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1407 view from Ensembl locus cross-references
1410 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1414 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1415 feature can be disabled
1418 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1419 PDB easier retrieval of sequences for lists of IDs
1422 <!-- JAL-2758 -->Short names for sequences retrieved from
1428 <li>Groovy interpreter updated to 2.4.12</li>
1429 <li>Example groovy script for generating a matrix of
1430 percent identity scores for current alignment.</li>
1432 <em>Testing and Deployment</em>
1435 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1439 <td><div align="left">
1443 <!-- JAL-2643 -->Pressing tab after updating the colour
1444 threshold text field doesn't trigger an update to the
1448 <!-- JAL-2682 -->Race condition when parsing sequence ID
1452 <!-- JAL-2608 -->Overview windows are also closed when
1453 alignment window is closed
1456 <!-- JAL-2548 -->Export of features doesn't always respect
1460 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1461 takes a long time in Cursor mode
1467 <!-- JAL-2777 -->Structures with whitespace chainCode
1468 cannot be viewed in Chimera
1471 <!-- JAL-2728 -->Protein annotation panel too high in
1475 <!-- JAL-2757 -->Can't edit the query after the server
1476 error warning icon is shown in Uniprot and PDB Free Text
1480 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1483 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1486 <!-- JAL-2739 -->Hidden column marker in last column not
1487 rendered when switching back from Wrapped to normal view
1490 <!-- JAL-2768 -->Annotation display corrupted when
1491 scrolling right in unwapped alignment view
1494 <!-- JAL-2542 -->Existing features on subsequence
1495 incorrectly relocated when full sequence retrieved from
1499 <!-- JAL-2733 -->Last reported memory still shown when
1500 Desktop->Show Memory is unticked (OSX only)
1503 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1504 features of same type and group to be selected for
1508 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1509 alignments when hidden columns are present
1512 <!-- JAL-2392 -->Jalview freezes when loading and
1513 displaying several structures
1516 <!-- JAL-2732 -->Black outlines left after resizing or
1520 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1521 within the Jalview desktop on OSX
1524 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1525 when in wrapped alignment mode
1528 <!-- JAL-2636 -->Scale mark not shown when close to right
1529 hand end of alignment
1532 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1533 each selected sequence do not have correct start/end
1537 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1538 after canceling the Alignment Window's Font dialog
1541 <!-- JAL-2036 -->Show cross-references not enabled after
1542 restoring project until a new view is created
1545 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1546 URL links appears when only default EMBL-EBI link is
1547 configured (since 2.10.2b2)
1550 <!-- JAL-2775 -->Overview redraws whole window when box
1551 position is adjusted
1554 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1555 in a multi-chain structure when viewing alignment
1556 involving more than one chain (since 2.10)
1559 <!-- JAL-2811 -->Double residue highlights in cursor mode
1560 if new selection moves alignment window
1563 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1564 arrow key in cursor mode to pass hidden column marker
1567 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1568 that produces correctly annotated transcripts and products
1571 <!-- JAL-2776 -->Toggling a feature group after first time
1572 doesn't update associated structure view
1575 <em>Applet</em><br />
1578 <!-- JAL-2687 -->Concurrent modification exception when
1579 closing alignment panel
1582 <em>BioJSON</em><br />
1585 <!-- JAL-2546 -->BioJSON export does not preserve
1586 non-positional features
1589 <em>New Known Issues</em>
1592 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1593 sequence features correctly (for many previous versions of
1597 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1598 using cursor in wrapped panel other than top
1601 <!-- JAL-2791 -->Select columns containing feature ignores
1602 graduated colour threshold
1605 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1606 always preserve numbering and sequence features
1609 <em>Known Java 9 Issues</em>
1612 <!-- JAL-2902 -->Groovy Console very slow to open and is
1613 not responsive when entering characters (Webstart, Java
1620 <td width="60" nowrap>
1621 <div align="center">
1622 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1623 <em>2/10/2017</em></strong>
1626 <td><div align="left">
1627 <em>New features in Jalview Desktop</em>
1630 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1632 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1636 <td><div align="left">
1640 <td width="60" nowrap>
1641 <div align="center">
1642 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1643 <em>7/9/2017</em></strong>
1646 <td><div align="left">
1650 <!-- JAL-2588 -->Show gaps in overview window by colouring
1651 in grey (sequences used to be coloured grey, and gaps were
1655 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1659 <!-- JAL-2587 -->Overview updates immediately on increase
1660 in size and progress bar shown as higher resolution
1661 overview is recalculated
1666 <td><div align="left">
1670 <!-- JAL-2664 -->Overview window redraws every hidden
1671 column region row by row
1674 <!-- JAL-2681 -->duplicate protein sequences shown after
1675 retrieving Ensembl crossrefs for sequences from Uniprot
1678 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1679 format setting is unticked
1682 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1683 if group has show boxes format setting unticked
1686 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1687 autoscrolling whilst dragging current selection group to
1688 include sequences and columns not currently displayed
1691 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1692 assemblies are imported via CIF file
1695 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1696 displayed when threshold or conservation colouring is also
1700 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1704 <!-- JAL-2673 -->Jalview continues to scroll after
1705 dragging a selected region off the visible region of the
1709 <!-- JAL-2724 -->Cannot apply annotation based
1710 colourscheme to all groups in a view
1713 <!-- JAL-2511 -->IDs don't line up with sequences
1714 initially after font size change using the Font chooser or
1721 <td width="60" nowrap>
1722 <div align="center">
1723 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1726 <td><div align="left">
1727 <em>Calculations</em>
1731 <!-- JAL-1933 -->Occupancy annotation row shows number of
1732 ungapped positions in each column of the alignment.
1735 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1736 a calculation dialog box
1739 <!-- JAL-2379 -->Revised implementation of PCA for speed
1740 and memory efficiency (~30x faster)
1743 <!-- JAL-2403 -->Revised implementation of sequence
1744 similarity scores as used by Tree, PCA, Shading Consensus
1745 and other calculations
1748 <!-- JAL-2416 -->Score matrices are stored as resource
1749 files within the Jalview codebase
1752 <!-- JAL-2500 -->Trees computed on Sequence Feature
1753 Similarity may have different topology due to increased
1760 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1761 model for alignments and groups
1764 <!-- JAL-384 -->Custom shading schemes created via groovy
1771 <!-- JAL-2526 -->Efficiency improvements for interacting
1772 with alignment and overview windows
1775 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1779 <!-- JAL-2388 -->Hidden columns and sequences can be
1783 <!-- JAL-2611 -->Click-drag in visible area allows fine
1784 adjustment of visible position
1788 <em>Data import/export</em>
1791 <!-- JAL-2535 -->Posterior probability annotation from
1792 Stockholm files imported as sequence associated annotation
1795 <!-- JAL-2507 -->More robust per-sequence positional
1796 annotation input/output via stockholm flatfile
1799 <!-- JAL-2533 -->Sequence names don't include file
1800 extension when importing structure files without embedded
1801 names or PDB accessions
1804 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1805 format sequence substitution matrices
1808 <em>User Interface</em>
1811 <!-- JAL-2447 --> Experimental Features Checkbox in
1812 Desktop's Tools menu to hide or show untested features in
1816 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1817 via Overview or sequence motif search operations
1820 <!-- JAL-2547 -->Amend sequence features dialog box can be
1821 opened by double clicking gaps within sequence feature
1825 <!-- JAL-1476 -->Status bar message shown when not enough
1826 aligned positions were available to create a 3D structure
1830 <em>3D Structure</em>
1833 <!-- JAL-2430 -->Hidden regions in alignment views are not
1834 coloured in linked structure views
1837 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1838 file-based command exchange
1841 <!-- JAL-2375 -->Structure chooser automatically shows
1842 Cached Structures rather than querying the PDBe if
1843 structures are already available for sequences
1846 <!-- JAL-2520 -->Structures imported via URL are cached in
1847 the Jalview project rather than downloaded again when the
1848 project is reopened.
1851 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1852 to transfer Chimera's structure attributes as Jalview
1853 features, and vice-versa (<strong>Experimental
1857 <em>Web Services</em>
1860 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1863 <!-- JAL-2335 -->Filter non-standard amino acids and
1864 nucleotides when submitting to AACon and other MSA
1868 <!-- JAL-2316, -->URLs for viewing database
1869 cross-references provided by identifiers.org and the
1870 EMBL-EBI's MIRIAM DB
1877 <!-- JAL-2344 -->FileFormatI interface for describing and
1878 identifying file formats (instead of String constants)
1881 <!-- JAL-2228 -->FeatureCounter script refactored for
1882 efficiency when counting all displayed features (not
1883 backwards compatible with 2.10.1)
1886 <em>Example files</em>
1889 <!-- JAL-2631 -->Graduated feature colour style example
1890 included in the example feature file
1893 <em>Documentation</em>
1896 <!-- JAL-2339 -->Release notes reformatted for readability
1897 with the built-in Java help viewer
1900 <!-- JAL-1644 -->Find documentation updated with 'search
1901 sequence description' option
1907 <!-- JAL-2485, -->External service integration tests for
1908 Uniprot REST Free Text Search Client
1911 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1914 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1919 <td><div align="left">
1920 <em>Calculations</em>
1923 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1924 matrix - C->R should be '-3'<br />Old matrix restored
1925 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1927 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1928 Jalview's treatment of gaps in PCA and substitution matrix
1929 based Tree calculations.<br /> <br />In earlier versions
1930 of Jalview, gaps matching gaps were penalised, and gaps
1931 matching non-gaps penalised even more. In the PCA
1932 calculation, gaps were actually treated as non-gaps - so
1933 different costs were applied, which meant Jalview's PCAs
1934 were different to those produced by SeqSpace.<br />Jalview
1935 now treats gaps in the same way as SeqSpace (ie it scores
1936 them as 0). <br /> <br />Enter the following in the
1937 Groovy console to restore pre-2.10.2 behaviour:<br />
1938 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1939 // for 2.10.1 mode <br />
1940 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1941 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1942 these settings will affect all subsequent tree and PCA
1943 calculations (not recommended)</em></li>
1945 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1946 scaling of branch lengths for trees computed using
1947 Sequence Feature Similarity.
1950 <!-- JAL-2377 -->PCA calculation could hang when
1951 generating output report when working with highly
1952 redundant alignments
1955 <!-- JAL-2544 --> Sort by features includes features to
1956 right of selected region when gaps present on right-hand
1960 <em>User Interface</em>
1963 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1964 doesn't reselect a specific sequence's associated
1965 annotation after it was used for colouring a view
1968 <!-- JAL-2419 -->Current selection lost if popup menu
1969 opened on a region of alignment without groups
1972 <!-- JAL-2374 -->Popup menu not always shown for regions
1973 of an alignment with overlapping groups
1976 <!-- JAL-2310 -->Finder double counts if both a sequence's
1977 name and description match
1980 <!-- JAL-2370 -->Hiding column selection containing two
1981 hidden regions results in incorrect hidden regions
1984 <!-- JAL-2386 -->'Apply to all groups' setting when
1985 changing colour does not apply Conservation slider value
1989 <!-- JAL-2373 -->Percentage identity and conservation menu
1990 items do not show a tick or allow shading to be disabled
1993 <!-- JAL-2385 -->Conservation shading or PID threshold
1994 lost when base colourscheme changed if slider not visible
1997 <!-- JAL-2547 -->Sequence features shown in tooltip for
1998 gaps before start of features
2001 <!-- JAL-2623 -->Graduated feature colour threshold not
2002 restored to UI when feature colour is edited
2005 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2006 a time when scrolling vertically in wrapped mode.
2009 <!-- JAL-2630 -->Structure and alignment overview update
2010 as graduate feature colour settings are modified via the
2014 <!-- JAL-2034 -->Overview window doesn't always update
2015 when a group defined on the alignment is resized
2018 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2019 wrapped view result in positional status updates
2023 <!-- JAL-2563 -->Status bar doesn't show position for
2024 ambiguous amino acid and nucleotide symbols
2027 <!-- JAL-2602 -->Copy consensus sequence failed if
2028 alignment included gapped columns
2031 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2032 widgets don't permanently disappear
2035 <!-- JAL-2503 -->Cannot select or filter quantitative
2036 annotation that are shown only as column labels (e.g.
2037 T-Coffee column reliability scores)
2040 <!-- JAL-2594 -->Exception thrown if trying to create a
2041 sequence feature on gaps only
2044 <!-- JAL-2504 -->Features created with 'New feature'
2045 button from a Find inherit previously defined feature type
2046 rather than the Find query string
2049 <!-- JAL-2423 -->incorrect title in output window when
2050 exporting tree calculated in Jalview
2053 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2054 and then revealing them reorders sequences on the
2058 <!-- JAL-964 -->Group panel in sequence feature settings
2059 doesn't update to reflect available set of groups after
2060 interactively adding or modifying features
2063 <!-- JAL-2225 -->Sequence Database chooser unusable on
2067 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2068 only excluded gaps in current sequence and ignored
2075 <!-- JAL-2421 -->Overview window visible region moves
2076 erratically when hidden rows or columns are present
2079 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2080 Structure Viewer's colour menu don't correspond to
2084 <!-- JAL-2405 -->Protein specific colours only offered in
2085 colour and group colour menu for protein alignments
2088 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2089 reflect currently selected view or group's shading
2093 <!-- JAL-2624 -->Feature colour thresholds not respected
2094 when rendered on overview and structures when opacity at
2098 <!-- JAL-2589 -->User defined gap colour not shown in
2099 overview when features overlaid on alignment
2102 <!-- JAL-2567 -->Feature settings for different views not
2103 recovered correctly from Jalview project file
2106 <!-- JAL-2256 -->Feature colours in overview when first opened
2107 (automatically via preferences) are different to the main
2111 <em>Data import/export</em>
2114 <!-- JAL-2576 -->Very large alignments take a long time to
2118 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2119 added after a sequence was imported are not written to
2123 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2124 when importing RNA secondary structure via Stockholm
2127 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2128 not shown in correct direction for simple pseudoknots
2131 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2132 with lightGray or darkGray via features file (but can
2136 <!-- JAL-2383 -->Above PID colour threshold not recovered
2137 when alignment view imported from project
2140 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2141 structure and sequences extracted from structure files
2142 imported via URL and viewed in Jmol
2145 <!-- JAL-2520 -->Structures loaded via URL are saved in
2146 Jalview Projects rather than fetched via URL again when
2147 the project is loaded and the structure viewed
2150 <em>Web Services</em>
2153 <!-- JAL-2519 -->EnsemblGenomes example failing after
2154 release of Ensembl v.88
2157 <!-- JAL-2366 -->Proxy server address and port always
2158 appear enabled in Preferences->Connections
2161 <!-- JAL-2461 -->DAS registry not found exceptions
2162 removed from console output
2165 <!-- JAL-2582 -->Cannot retrieve protein products from
2166 Ensembl by Peptide ID
2169 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2170 created from SIFTs, and spurious 'Couldn't open structure
2171 in Chimera' errors raised after April 2017 update (problem
2172 due to 'null' string rather than empty string used for
2173 residues with no corresponding PDB mapping).
2176 <em>Application UI</em>
2179 <!-- JAL-2361 -->User Defined Colours not added to Colour
2183 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2184 case' residues (button in colourscheme editor debugged and
2185 new documentation and tooltips added)
2188 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2189 doesn't restore group-specific text colour thresholds
2192 <!-- JAL-2243 -->Feature settings panel does not update as
2193 new features are added to alignment
2196 <!-- JAL-2532 -->Cancel in feature settings reverts
2197 changes to feature colours via the Amend features dialog
2200 <!-- JAL-2506 -->Null pointer exception when attempting to
2201 edit graduated feature colour via amend features dialog
2205 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2206 selection menu changes colours of alignment views
2209 <!-- JAL-2426 -->Spurious exceptions in console raised
2210 from alignment calculation workers after alignment has
2214 <!-- JAL-1608 -->Typo in selection popup menu - Create
2215 groups now 'Create Group'
2218 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2219 Create/Undefine group doesn't always work
2222 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2223 shown again after pressing 'Cancel'
2226 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2227 adjusts start position in wrap mode
2230 <!-- JAL-2563 -->Status bar doesn't show positions for
2231 ambiguous amino acids
2234 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2235 CDS/Protein view after CDS sequences added for aligned
2239 <!-- JAL-2592 -->User defined colourschemes called 'User
2240 Defined' don't appear in Colours menu
2246 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2247 score models doesn't always result in an updated PCA plot
2250 <!-- JAL-2442 -->Features not rendered as transparent on
2251 overview or linked structure view
2254 <!-- JAL-2372 -->Colour group by conservation doesn't
2258 <!-- JAL-2517 -->Hitting Cancel after applying
2259 user-defined colourscheme doesn't restore original
2266 <!-- JAL-2314 -->Unit test failure:
2267 jalview.ws.jabaws.RNAStructExportImport setup fails
2270 <!-- JAL-2307 -->Unit test failure:
2271 jalview.ws.sifts.SiftsClientTest due to compatibility
2272 problems with deep array comparison equality asserts in
2273 successive versions of TestNG
2276 <!-- JAL-2479 -->Relocated StructureChooserTest and
2277 ParameterUtilsTest Unit tests to Network suite
2280 <em>New Known Issues</em>
2283 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2284 phase after a sequence motif find operation
2287 <!-- JAL-2550 -->Importing annotation file with rows
2288 containing just upper and lower case letters are
2289 interpreted as WUSS RNA secondary structure symbols
2292 <!-- JAL-2590 -->Cannot load and display Newick trees
2293 reliably from eggnog Ortholog database
2296 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2297 containing features of type Highlight' when 'B' is pressed
2298 to mark columns containing highlighted regions.
2301 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2302 doesn't always add secondary structure annotation.
2307 <td width="60" nowrap>
2308 <div align="center">
2309 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2312 <td><div align="left">
2316 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2317 for all consensus calculations
2320 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2323 <li>Updated Jalview's Certum code signing certificate
2326 <em>Application</em>
2329 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2330 set of database cross-references, sorted alphabetically
2333 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2334 from database cross references. Users with custom links
2335 will receive a <a href="webServices/urllinks.html#warning">warning
2336 dialog</a> asking them to update their preferences.
2339 <!-- JAL-2287-->Cancel button and escape listener on
2340 dialog warning user about disconnecting Jalview from a
2344 <!-- JAL-2320-->Jalview's Chimera control window closes if
2345 the Chimera it is connected to is shut down
2348 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2349 columns menu item to mark columns containing highlighted
2350 regions (e.g. from structure selections or results of a
2354 <!-- JAL-2284-->Command line option for batch-generation
2355 of HTML pages rendering alignment data with the BioJS
2365 <!-- JAL-2286 -->Columns with more than one modal residue
2366 are not coloured or thresholded according to percent
2367 identity (first observed in Jalview 2.8.2)
2370 <!-- JAL-2301 -->Threonine incorrectly reported as not
2374 <!-- JAL-2318 -->Updates to documentation pages (above PID
2375 threshold, amino acid properties)
2378 <!-- JAL-2292 -->Lower case residues in sequences are not
2379 reported as mapped to residues in a structure file in the
2383 <!--JAL-2324 -->Identical features with non-numeric scores
2384 could be added multiple times to a sequence
2387 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2388 bond features shown as two highlighted residues rather
2389 than a range in linked structure views, and treated
2390 correctly when selecting and computing trees from features
2393 <!-- JAL-2281-->Custom URL links for database
2394 cross-references are matched to database name regardless
2399 <em>Application</em>
2402 <!-- JAL-2282-->Custom URL links for specific database
2403 names without regular expressions also offer links from
2407 <!-- JAL-2315-->Removing a single configured link in the
2408 URL links pane in Connections preferences doesn't actually
2409 update Jalview configuration
2412 <!-- JAL-2272-->CTRL-Click on a selected region to open
2413 the alignment area popup menu doesn't work on El-Capitan
2416 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2417 files with similarly named sequences if dropped onto the
2421 <!-- JAL-2312 -->Additional mappings are shown for PDB
2422 entries where more chains exist in the PDB accession than
2423 are reported in the SIFTS file
2426 <!-- JAL-2317-->Certain structures do not get mapped to
2427 the structure view when displayed with Chimera
2430 <!-- JAL-2317-->No chains shown in the Chimera view
2431 panel's View->Show Chains submenu
2434 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2435 work for wrapped alignment views
2438 <!--JAL-2197 -->Rename UI components for running JPred
2439 predictions from 'JNet' to 'JPred'
2442 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2443 corrupted when annotation panel vertical scroll is not at
2444 first annotation row
2447 <!--JAL-2332 -->Attempting to view structure for Hen
2448 lysozyme results in a PDB Client error dialog box
2451 <!-- JAL-2319 -->Structure View's mapping report switched
2452 ranges for PDB and sequence for SIFTS
2455 SIFTS 'Not_Observed' residues mapped to non-existant
2459 <!-- <em>New Known Issues</em>
2466 <td width="60" nowrap>
2467 <div align="center">
2468 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2469 <em>25/10/2016</em></strong>
2472 <td><em>Application</em>
2474 <li>3D Structure chooser opens with 'Cached structures'
2475 view if structures already loaded</li>
2476 <li>Progress bar reports models as they are loaded to
2477 structure views</li>
2483 <li>Colour by conservation always enabled and no tick
2484 shown in menu when BLOSUM or PID shading applied</li>
2485 <li>FER1_ARATH and FER2_ARATH labels were switched in
2486 example sequences/projects/trees</li>
2488 <em>Application</em>
2490 <li>Jalview projects with views of local PDB structure
2491 files saved on Windows cannot be opened on OSX</li>
2492 <li>Multiple structure views can be opened and superposed
2493 without timeout for structures with multiple models or
2494 multiple sequences in alignment</li>
2495 <li>Cannot import or associated local PDB files without a
2496 PDB ID HEADER line</li>
2497 <li>RMSD is not output in Jmol console when superposition
2499 <li>Drag and drop of URL from Browser fails for Linux and
2500 OSX versions earlier than El Capitan</li>
2501 <li>ENA client ignores invalid content from ENA server</li>
2502 <li>Exceptions are not raised in console when ENA client
2503 attempts to fetch non-existent IDs via Fetch DB Refs UI
2505 <li>Exceptions are not raised in console when a new view
2506 is created on the alignment</li>
2507 <li>OSX right-click fixed for group selections: CMD-click
2508 to insert/remove gaps in groups and CTRL-click to open group
2511 <em>Build and deployment</em>
2513 <li>URL link checker now copes with multi-line anchor
2516 <em>New Known Issues</em>
2518 <li>Drag and drop from URL links in browsers do not work
2525 <td width="60" nowrap>
2526 <div align="center">
2527 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2530 <td><em>General</em>
2533 <!-- JAL-2124 -->Updated Spanish translations.
2536 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2537 for importing structure data to Jalview. Enables mmCIF and
2541 <!-- JAL-192 --->Alignment ruler shows positions relative to
2545 <!-- JAL-2202 -->Position/residue shown in status bar when
2546 mousing over sequence associated annotation
2549 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2553 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2554 '()', canonical '[]' and invalid '{}' base pair populations
2558 <!-- JAL-2092 -->Feature settings popup menu options for
2559 showing or hiding columns containing a feature
2562 <!-- JAL-1557 -->Edit selected group by double clicking on
2563 group and sequence associated annotation labels
2566 <!-- JAL-2236 -->Sequence name added to annotation label in
2567 select/hide columns by annotation and colour by annotation
2571 </ul> <em>Application</em>
2574 <!-- JAL-2050-->Automatically hide introns when opening a
2575 gene/transcript view
2578 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2582 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2583 structure mappings with the EMBL-EBI PDBe SIFTS database
2586 <!-- JAL-2079 -->Updated download sites used for Rfam and
2587 Pfam sources to xfam.org
2590 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2593 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2594 over sequences in Jalview
2597 <!-- JAL-2027-->Support for reverse-complement coding
2598 regions in ENA and EMBL
2601 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2602 for record retrieval via ENA rest API
2605 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2609 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2610 groovy script execution
2613 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2614 alignment window's Calculate menu
2617 <!-- JAL-1812 -->Allow groovy scripts that call
2618 Jalview.getAlignFrames() to run in headless mode
2621 <!-- JAL-2068 -->Support for creating new alignment
2622 calculation workers from groovy scripts
2625 <!-- JAL-1369 --->Store/restore reference sequence in
2629 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2630 associations are now saved/restored from project
2633 <!-- JAL-1993 -->Database selection dialog always shown
2634 before sequence fetcher is opened
2637 <!-- JAL-2183 -->Double click on an entry in Jalview's
2638 database chooser opens a sequence fetcher
2641 <!-- JAL-1563 -->Free-text search client for UniProt using
2642 the UniProt REST API
2645 <!-- JAL-2168 -->-nonews command line parameter to prevent
2646 the news reader opening
2649 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2650 querying stored in preferences
2653 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2657 <!-- JAL-1977-->Tooltips shown on database chooser
2660 <!-- JAL-391 -->Reverse complement function in calculate
2661 menu for nucleotide sequences
2664 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2665 and feature counts preserves alignment ordering (and
2666 debugged for complex feature sets).
2669 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2670 viewing structures with Jalview 2.10
2673 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2674 genome, transcript CCDS and gene ids via the Ensembl and
2675 Ensembl Genomes REST API
2678 <!-- JAL-2049 -->Protein sequence variant annotation
2679 computed for 'sequence_variant' annotation on CDS regions
2683 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2687 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2688 Ref Fetcher fails to match, or otherwise updates sequence
2689 data from external database records.
2692 <!-- JAL-2154 -->Revised Jalview Project format for
2693 efficient recovery of sequence coding and alignment
2694 annotation relationships.
2696 </ul> <!-- <em>Applet</em>
2707 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2711 <!-- JAL-2018-->Export features in Jalview format (again)
2712 includes graduated colourschemes
2715 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2716 working with big alignments and lots of hidden columns
2719 <!-- JAL-2053-->Hidden column markers not always rendered
2720 at right of alignment window
2723 <!-- JAL-2067 -->Tidied up links in help file table of
2727 <!-- JAL-2072 -->Feature based tree calculation not shown
2731 <!-- JAL-2075 -->Hidden columns ignored during feature
2732 based tree calculation
2735 <!-- JAL-2065 -->Alignment view stops updating when show
2736 unconserved enabled for group on alignment
2739 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2743 <!-- JAL-2146 -->Alignment column in status incorrectly
2744 shown as "Sequence position" when mousing over
2748 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2749 hidden columns present
2752 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2753 user created annotation added to alignment
2756 <!-- JAL-1841 -->RNA Structure consensus only computed for
2757 '()' base pair annotation
2760 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2761 in zero scores for all base pairs in RNA Structure
2765 <!-- JAL-2174-->Extend selection with columns containing
2769 <!-- JAL-2275 -->Pfam format writer puts extra space at
2770 beginning of sequence
2773 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2777 <!-- JAL-2238 -->Cannot create groups on an alignment from
2778 from a tree when t-coffee scores are shown
2781 <!-- JAL-1836,1967 -->Cannot import and view PDB
2782 structures with chains containing negative resnums (4q4h)
2785 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2789 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2790 to Clustal, PIR and PileUp output
2793 <!-- JAL-2008 -->Reordering sequence features that are
2794 not visible causes alignment window to repaint
2797 <!-- JAL-2006 -->Threshold sliders don't work in
2798 graduated colour and colour by annotation row for e-value
2799 scores associated with features and annotation rows
2802 <!-- JAL-1797 -->amino acid physicochemical conservation
2803 calculation should be case independent
2806 <!-- JAL-2173 -->Remove annotation also updates hidden
2810 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2811 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2812 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2815 <!-- JAL-2065 -->Null pointer exceptions and redraw
2816 problems when reference sequence defined and 'show
2817 non-conserved' enabled
2820 <!-- JAL-1306 -->Quality and Conservation are now shown on
2821 load even when Consensus calculation is disabled
2824 <!-- JAL-1932 -->Remove right on penultimate column of
2825 alignment does nothing
2828 <em>Application</em>
2831 <!-- JAL-1552-->URLs and links can't be imported by
2832 drag'n'drop on OSX when launched via webstart (note - not
2833 yet fixed for El Capitan)
2836 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2837 output when running on non-gb/us i18n platforms
2840 <!-- JAL-1944 -->Error thrown when exporting a view with
2841 hidden sequences as flat-file alignment
2844 <!-- JAL-2030-->InstallAnywhere distribution fails when
2848 <!-- JAL-2080-->Jalview very slow to launch via webstart
2849 (also hotfix for 2.9.0b2)
2852 <!-- JAL-2085 -->Cannot save project when view has a
2853 reference sequence defined
2856 <!-- JAL-1011 -->Columns are suddenly selected in other
2857 alignments and views when revealing hidden columns
2860 <!-- JAL-1989 -->Hide columns not mirrored in complement
2861 view in a cDNA/Protein splitframe
2864 <!-- JAL-1369 -->Cannot save/restore representative
2865 sequence from project when only one sequence is
2869 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2870 in Structure Chooser
2873 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2874 structure consensus didn't refresh annotation panel
2877 <!-- JAL-1962 -->View mapping in structure view shows
2878 mappings between sequence and all chains in a PDB file
2881 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2882 dialogs format columns correctly, don't display array
2883 data, sort columns according to type
2886 <!-- JAL-1975 -->Export complete shown after destination
2887 file chooser is cancelled during an image export
2890 <!-- JAL-2025 -->Error when querying PDB Service with
2891 sequence name containing special characters
2894 <!-- JAL-2024 -->Manual PDB structure querying should be
2898 <!-- JAL-2104 -->Large tooltips with broken HTML
2899 formatting don't wrap
2902 <!-- JAL-1128 -->Figures exported from wrapped view are
2903 truncated so L looks like I in consensus annotation
2906 <!-- JAL-2003 -->Export features should only export the
2907 currently displayed features for the current selection or
2911 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2912 after fetching cross-references, and restoring from
2916 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2917 followed in the structure viewer
2920 <!-- JAL-2163 -->Titles for individual alignments in
2921 splitframe not restored from project
2924 <!-- JAL-2145 -->missing autocalculated annotation at
2925 trailing end of protein alignment in transcript/product
2926 splitview when pad-gaps not enabled by default
2929 <!-- JAL-1797 -->amino acid physicochemical conservation
2933 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2934 article has been read (reopened issue due to
2935 internationalisation problems)
2938 <!-- JAL-1960 -->Only offer PDB structures in structure
2939 viewer based on sequence name, PDB and UniProt
2944 <!-- JAL-1976 -->No progress bar shown during export of
2948 <!-- JAL-2213 -->Structures not always superimposed after
2949 multiple structures are shown for one or more sequences.
2952 <!-- JAL-1370 -->Reference sequence characters should not
2953 be replaced with '.' when 'Show unconserved' format option
2957 <!-- JAL-1823 -->Cannot specify chain code when entering
2958 specific PDB id for sequence
2961 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2962 'Export hidden sequences' is enabled, but 'export hidden
2963 columns' is disabled.
2966 <!--JAL-2026-->Best Quality option in structure chooser
2967 selects lowest rather than highest resolution structures
2971 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2972 to sequence mapping in 'View Mappings' report
2975 <!-- JAL-2284 -->Unable to read old Jalview projects that
2976 contain non-XML data added after Jalvew wrote project.
2979 <!-- JAL-2118 -->Newly created annotation row reorders
2980 after clicking on it to create new annotation for a
2984 <!-- JAL-1980 -->Null Pointer Exception raised when
2985 pressing Add on an orphaned cut'n'paste window.
2987 <!-- may exclude, this is an external service stability issue JAL-1941
2988 -- > RNA 3D structure not added via DSSR service</li> -->
2993 <!-- JAL-2151 -->Incorrect columns are selected when
2994 hidden columns present before start of sequence
2997 <!-- JAL-1986 -->Missing dependencies on applet pages
3001 <!-- JAL-1947 -->Overview pixel size changes when
3002 sequences are hidden in applet
3005 <!-- JAL-1996 -->Updated instructions for applet
3006 deployment on examples pages.
3013 <td width="60" nowrap>
3014 <div align="center">
3015 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3016 <em>16/10/2015</em></strong>
3019 <td><em>General</em>
3021 <li>Time stamps for signed Jalview application and applet
3026 <em>Application</em>
3028 <li>Duplicate group consensus and conservation rows
3029 shown when tree is partitioned</li>
3030 <li>Erratic behaviour when tree partitions made with
3031 multiple cDNA/Protein split views</li>
3037 <td width="60" nowrap>
3038 <div align="center">
3039 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3040 <em>8/10/2015</em></strong>
3043 <td><em>General</em>
3045 <li>Updated Spanish translations of localized text for
3047 </ul> <em>Application</em>
3049 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3050 <li>Signed OSX InstallAnywhere installer<br></li>
3051 <li>Support for per-sequence based annotations in BioJSON</li>
3052 </ul> <em>Applet</em>
3054 <li>Split frame example added to applet examples page</li>
3055 </ul> <em>Build and Deployment</em>
3058 <!-- JAL-1888 -->New ant target for running Jalview's test
3066 <li>Mapping of cDNA to protein in split frames
3067 incorrect when sequence start > 1</li>
3068 <li>Broken images in filter column by annotation dialog
3070 <li>Feature colours not parsed from features file</li>
3071 <li>Exceptions and incomplete link URLs recovered when
3072 loading a features file containing HTML tags in feature
3076 <em>Application</em>
3078 <li>Annotations corrupted after BioJS export and
3080 <li>Incorrect sequence limits after Fetch DB References
3081 with 'trim retrieved sequences'</li>
3082 <li>Incorrect warning about deleting all data when
3083 deleting selected columns</li>
3084 <li>Patch to build system for shipping properly signed
3085 JNLP templates for webstart launch</li>
3086 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3087 unreleased structures for download or viewing</li>
3088 <li>Tab/space/return keystroke operation of EMBL-PDBe
3089 fetcher/viewer dialogs works correctly</li>
3090 <li>Disabled 'minimise' button on Jalview windows
3091 running on OSX to workaround redraw hang bug</li>
3092 <li>Split cDNA/Protein view position and geometry not
3093 recovered from jalview project</li>
3094 <li>Initial enabled/disabled state of annotation menu
3095 sorter 'show autocalculated first/last' corresponds to
3097 <li>Restoring of Clustal, RNA Helices and T-Coffee
3098 color schemes from BioJSON</li>
3102 <li>Reorder sequences mirrored in cDNA/Protein split
3104 <li>Applet with Jmol examples not loading correctly</li>
3110 <td><div align="center">
3111 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3113 <td><em>General</em>
3115 <li>Linked visualisation and analysis of DNA and Protein
3118 <li>Translated cDNA alignments shown as split protein
3119 and DNA alignment views</li>
3120 <li>Codon consensus annotation for linked protein and
3121 cDNA alignment views</li>
3122 <li>Link cDNA or Protein product sequences by loading
3123 them onto Protein or cDNA alignments</li>
3124 <li>Reconstruct linked cDNA alignment from aligned
3125 protein sequences</li>
3128 <li>Jmol integration updated to Jmol v14.2.14</li>
3129 <li>Import and export of Jalview alignment views as <a
3130 href="features/bioJsonFormat.html">BioJSON</a></li>
3131 <li>New alignment annotation file statements for
3132 reference sequences and marking hidden columns</li>
3133 <li>Reference sequence based alignment shading to
3134 highlight variation</li>
3135 <li>Select or hide columns according to alignment
3137 <li>Find option for locating sequences by description</li>
3138 <li>Conserved physicochemical properties shown in amino
3139 acid conservation row</li>
3140 <li>Alignments can be sorted by number of RNA helices</li>
3141 </ul> <em>Application</em>
3143 <li>New cDNA/Protein analysis capabilities
3145 <li>Get Cross-References should open a Split Frame
3146 view with cDNA/Protein</li>
3147 <li>Detect when nucleotide sequences and protein
3148 sequences are placed in the same alignment</li>
3149 <li>Split cDNA/Protein views are saved in Jalview
3154 <li>Use REST API to talk to Chimera</li>
3155 <li>Selected regions in Chimera are highlighted in linked
3156 Jalview windows</li>
3158 <li>VARNA RNA viewer updated to v3.93</li>
3159 <li>VARNA views are saved in Jalview Projects</li>
3160 <li>Pseudoknots displayed as Jalview RNA annotation can
3161 be shown in VARNA</li>
3163 <li>Make groups for selection uses marked columns as well
3164 as the active selected region</li>
3166 <li>Calculate UPGMA and NJ trees using sequence feature
3168 <li>New Export options
3170 <li>New Export Settings dialog to control hidden
3171 region export in flat file generation</li>
3173 <li>Export alignment views for display with the <a
3174 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3176 <li>Export scrollable SVG in HTML page</li>
3177 <li>Optional embedding of BioJSON data when exporting
3178 alignment figures to HTML</li>
3180 <li>3D structure retrieval and display
3182 <li>Free text and structured queries with the PDBe
3184 <li>PDBe Search API based discovery and selection of
3185 PDB structures for a sequence set</li>
3189 <li>JPred4 employed for protein secondary structure
3191 <li>Hide Insertions menu option to hide unaligned columns
3192 for one or a group of sequences</li>
3193 <li>Automatically hide insertions in alignments imported
3194 from the JPred4 web server</li>
3195 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3196 system on OSX<br />LGPL libraries courtesy of <a
3197 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3199 <li>changed 'View nucleotide structure' submenu to 'View
3200 VARNA 2D Structure'</li>
3201 <li>change "View protein structure" menu option to "3D
3204 </ul> <em>Applet</em>
3206 <li>New layout for applet example pages</li>
3207 <li>New parameters to enable SplitFrame view
3208 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3209 <li>New example demonstrating linked viewing of cDNA and
3210 Protein alignments</li>
3211 </ul> <em>Development and deployment</em>
3213 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3214 <li>Include installation type and git revision in build
3215 properties and console log output</li>
3216 <li>Jalview Github organisation, and new github site for
3217 storing BioJsMSA Templates</li>
3218 <li>Jalview's unit tests now managed with TestNG</li>
3221 <!-- <em>General</em>
3223 </ul> --> <!-- issues resolved --> <em>Application</em>
3225 <li>Escape should close any open find dialogs</li>
3226 <li>Typo in select-by-features status report</li>
3227 <li>Consensus RNA secondary secondary structure
3228 predictions are not highlighted in amber</li>
3229 <li>Missing gap character in v2.7 example file means
3230 alignment appears unaligned when pad-gaps is not enabled</li>
3231 <li>First switch to RNA Helices colouring doesn't colour
3232 associated structure views</li>
3233 <li>ID width preference option is greyed out when auto
3234 width checkbox not enabled</li>
3235 <li>Stopped a warning dialog from being shown when
3236 creating user defined colours</li>
3237 <li>'View Mapping' in structure viewer shows sequence
3238 mappings for just that viewer's sequences</li>
3239 <li>Workaround for superposing PDB files containing
3240 multiple models in Chimera</li>
3241 <li>Report sequence position in status bar when hovering
3242 over Jmol structure</li>
3243 <li>Cannot output gaps as '.' symbols with Selection ->
3244 output to text box</li>
3245 <li>Flat file exports of alignments with hidden columns
3246 have incorrect sequence start/end</li>
3247 <li>'Aligning' a second chain to a Chimera structure from
3249 <li>Colour schemes applied to structure viewers don't
3250 work for nucleotide</li>
3251 <li>Loading/cut'n'pasting an empty or invalid file leads
3252 to a grey/invisible alignment window</li>
3253 <li>Exported Jpred annotation from a sequence region
3254 imports to different position</li>
3255 <li>Space at beginning of sequence feature tooltips shown
3256 on some platforms</li>
3257 <li>Chimera viewer 'View | Show Chain' menu is not
3259 <li>'New View' fails with a Null Pointer Exception in
3260 console if Chimera has been opened</li>
3261 <li>Mouseover to Chimera not working</li>
3262 <li>Miscellaneous ENA XML feature qualifiers not
3264 <li>NPE in annotation renderer after 'Extract Scores'</li>
3265 <li>If two structures in one Chimera window, mouseover of
3266 either sequence shows on first structure</li>
3267 <li>'Show annotations' options should not make
3268 non-positional annotations visible</li>
3269 <li>Subsequence secondary structure annotation not shown
3270 in right place after 'view flanking regions'</li>
3271 <li>File Save As type unset when current file format is
3273 <li>Save as '.jar' option removed for saving Jalview
3275 <li>Colour by Sequence colouring in Chimera more
3277 <li>Cannot 'add reference annotation' for a sequence in
3278 several views on same alignment</li>
3279 <li>Cannot show linked products for EMBL / ENA records</li>
3280 <li>Jalview's tooltip wraps long texts containing no
3282 </ul> <em>Applet</em>
3284 <li>Jmol to JalviewLite mouseover/link not working</li>
3285 <li>JalviewLite can't import sequences with ID
3286 descriptions containing angle brackets</li>
3287 </ul> <em>General</em>
3289 <li>Cannot export and reimport RNA secondary structure
3290 via jalview annotation file</li>
3291 <li>Random helix colour palette for colour by annotation
3292 with RNA secondary structure</li>
3293 <li>Mouseover to cDNA from STOP residue in protein
3294 translation doesn't work.</li>
3295 <li>hints when using the select by annotation dialog box</li>
3296 <li>Jmol alignment incorrect if PDB file has alternate CA
3298 <li>FontChooser message dialog appears to hang after
3299 choosing 1pt font</li>
3300 <li>Peptide secondary structure incorrectly imported from
3301 annotation file when annotation display text includes 'e' or
3303 <li>Cannot set colour of new feature type whilst creating
3305 <li>cDNA translation alignment should not be sequence
3306 order dependent</li>
3307 <li>'Show unconserved' doesn't work for lower case
3309 <li>Nucleotide ambiguity codes involving R not recognised</li>
3310 </ul> <em>Deployment and Documentation</em>
3312 <li>Applet example pages appear different to the rest of
3313 www.jalview.org</li>
3314 </ul> <em>Application Known issues</em>
3316 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3317 <li>Misleading message appears after trying to delete
3319 <li>Jalview icon not shown in dock after InstallAnywhere
3320 version launches</li>
3321 <li>Fetching EMBL reference for an RNA sequence results
3322 fails with a sequence mismatch</li>
3323 <li>Corrupted or unreadable alignment display when
3324 scrolling alignment to right</li>
3325 <li>ArrayIndexOutOfBoundsException thrown when remove
3326 empty columns called on alignment with ragged gapped ends</li>
3327 <li>auto calculated alignment annotation rows do not get
3328 placed above or below non-autocalculated rows</li>
3329 <li>Jalview dekstop becomes sluggish at full screen in
3330 ultra-high resolution</li>
3331 <li>Cannot disable consensus calculation independently of
3332 quality and conservation</li>
3333 <li>Mouseover highlighting between cDNA and protein can
3334 become sluggish with more than one splitframe shown</li>
3335 </ul> <em>Applet Known Issues</em>
3337 <li>Core PDB parsing code requires Jmol</li>
3338 <li>Sequence canvas panel goes white when alignment
3339 window is being resized</li>
3345 <td><div align="center">
3346 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3348 <td><em>General</em>
3350 <li>Updated Java code signing certificate donated by
3352 <li>Features and annotation preserved when performing
3353 pairwise alignment</li>
3354 <li>RNA pseudoknot annotation can be
3355 imported/exported/displayed</li>
3356 <li>'colour by annotation' can colour by RNA and
3357 protein secondary structure</li>
3358 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3359 post-hoc with 2.9 release</em>)
3362 </ul> <em>Application</em>
3364 <li>Extract and display secondary structure for sequences
3365 with 3D structures</li>
3366 <li>Support for parsing RNAML</li>
3367 <li>Annotations menu for layout
3369 <li>sort sequence annotation rows by alignment</li>
3370 <li>place sequence annotation above/below alignment
3373 <li>Output in Stockholm format</li>
3374 <li>Internationalisation: improved Spanish (es)
3376 <li>Structure viewer preferences tab</li>
3377 <li>Disorder and Secondary Structure annotation tracks
3378 shared between alignments</li>
3379 <li>UCSF Chimera launch and linked highlighting from
3381 <li>Show/hide all sequence associated annotation rows for
3382 all or current selection</li>
3383 <li>disorder and secondary structure predictions
3384 available as dataset annotation</li>
3385 <li>Per-sequence rna helices colouring</li>
3388 <li>Sequence database accessions imported when fetching
3389 alignments from Rfam</li>
3390 <li>update VARNA version to 3.91</li>
3392 <li>New groovy scripts for exporting aligned positions,
3393 conservation values, and calculating sum of pairs scores.</li>
3394 <li>Command line argument to set default JABAWS server</li>
3395 <li>include installation type in build properties and
3396 console log output</li>
3397 <li>Updated Jalview project format to preserve dataset
3401 <!-- issues resolved --> <em>Application</em>
3403 <li>Distinguish alignment and sequence associated RNA
3404 structure in structure->view->VARNA</li>
3405 <li>Raise dialog box if user deletes all sequences in an
3407 <li>Pressing F1 results in documentation opening twice</li>
3408 <li>Sequence feature tooltip is wrapped</li>
3409 <li>Double click on sequence associated annotation
3410 selects only first column</li>
3411 <li>Redundancy removal doesn't result in unlinked
3412 leaves shown in tree</li>
3413 <li>Undos after several redundancy removals don't undo
3415 <li>Hide sequence doesn't hide associated annotation</li>
3416 <li>User defined colours dialog box too big to fit on
3417 screen and buttons not visible</li>
3418 <li>author list isn't updated if already written to
3419 Jalview properties</li>
3420 <li>Popup menu won't open after retrieving sequence
3422 <li>File open window for associate PDB doesn't open</li>
3423 <li>Left-then-right click on a sequence id opens a
3424 browser search window</li>
3425 <li>Cannot open sequence feature shading/sort popup menu
3426 in feature settings dialog</li>
3427 <li>better tooltip placement for some areas of Jalview
3429 <li>Allow addition of JABAWS Server which doesn't
3430 pass validation</li>
3431 <li>Web services parameters dialog box is too large to
3433 <li>Muscle nucleotide alignment preset obscured by
3435 <li>JABAWS preset submenus don't contain newly
3436 defined user preset</li>
3437 <li>MSA web services warns user if they were launched
3438 with invalid input</li>
3439 <li>Jalview cannot contact DAS Registy when running on
3442 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3443 'Superpose with' submenu not shown when new view
3447 </ul> <!-- <em>Applet</em>
3449 </ul> <em>General</em>
3451 </ul>--> <em>Deployment and Documentation</em>
3453 <li>2G and 1G options in launchApp have no effect on
3454 memory allocation</li>
3455 <li>launchApp service doesn't automatically open
3456 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3458 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3459 InstallAnywhere reports cannot find valid JVM when Java
3460 1.7_055 is available
3462 </ul> <em>Application Known issues</em>
3465 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3466 corrupted or unreadable alignment display when scrolling
3470 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3471 retrieval fails but progress bar continues for DAS retrieval
3472 with large number of ID
3475 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3476 flatfile output of visible region has incorrect sequence
3480 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3481 rna structure consensus doesn't update when secondary
3482 structure tracks are rearranged
3485 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3486 invalid rna structure positional highlighting does not
3487 highlight position of invalid base pairs
3490 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3491 out of memory errors are not raised when saving Jalview
3492 project from alignment window file menu
3495 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3496 Switching to RNA Helices colouring doesn't propagate to
3500 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3501 colour by RNA Helices not enabled when user created
3502 annotation added to alignment
3505 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3506 Jalview icon not shown on dock in Mountain Lion/Webstart
3508 </ul> <em>Applet Known Issues</em>
3511 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3512 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3515 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3516 Jalview and Jmol example not compatible with IE9
3519 <li>Sort by annotation score doesn't reverse order
3525 <td><div align="center">
3526 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3529 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3532 <li>Internationalisation of user interface (usually
3533 called i18n support) and translation for Spanish locale</li>
3534 <li>Define/Undefine group on current selection with
3535 Ctrl-G/Shift Ctrl-G</li>
3536 <li>Improved group creation/removal options in
3537 alignment/sequence Popup menu</li>
3538 <li>Sensible precision for symbol distribution
3539 percentages shown in logo tooltip.</li>
3540 <li>Annotation panel height set according to amount of
3541 annotation when alignment first opened</li>
3542 </ul> <em>Application</em>
3544 <li>Interactive consensus RNA secondary structure
3545 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3546 <li>Select columns containing particular features from
3547 Feature Settings dialog</li>
3548 <li>View all 'representative' PDB structures for selected
3550 <li>Update Jalview project format:
3552 <li>New file extension for Jalview projects '.jvp'</li>
3553 <li>Preserve sequence and annotation dataset (to
3554 store secondary structure annotation,etc)</li>
3555 <li>Per group and alignment annotation and RNA helix
3559 <li>New similarity measures for PCA and Tree calculation
3561 <li>Experimental support for retrieval and viewing of
3562 flanking regions for an alignment</li>
3566 <!-- issues resolved --> <em>Application</em>
3568 <li>logo keeps spinning and status remains at queued or
3569 running after job is cancelled</li>
3570 <li>cannot export features from alignments imported from
3571 Jalview/VAMSAS projects</li>
3572 <li>Buggy slider for web service parameters that take
3574 <li>Newly created RNA secondary structure line doesn't
3575 have 'display all symbols' flag set</li>
3576 <li>T-COFFEE alignment score shading scheme and other
3577 annotation shading not saved in Jalview project</li>
3578 <li>Local file cannot be loaded in freshly downloaded
3580 <li>Jalview icon not shown on dock in Mountain
3582 <li>Load file from desktop file browser fails</li>
3583 <li>Occasional NPE thrown when calculating large trees</li>
3584 <li>Cannot reorder or slide sequences after dragging an
3585 alignment onto desktop</li>
3586 <li>Colour by annotation dialog throws NPE after using
3587 'extract scores' function</li>
3588 <li>Loading/cut'n'pasting an empty file leads to a grey
3589 alignment window</li>
3590 <li>Disorder thresholds rendered incorrectly after
3591 performing IUPred disorder prediction</li>
3592 <li>Multiple group annotated consensus rows shown when
3593 changing 'normalise logo' display setting</li>
3594 <li>Find shows blank dialog after 'finished searching' if
3595 nothing matches query</li>
3596 <li>Null Pointer Exceptions raised when sorting by
3597 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3599 <li>Errors in Jmol console when structures in alignment
3600 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3602 <li>Not all working JABAWS services are shown in
3604 <li>JAVAWS version of Jalview fails to launch with
3605 'invalid literal/length code'</li>
3606 <li>Annotation/RNA Helix colourschemes cannot be applied
3607 to alignment with groups (actually fixed in 2.8.0b1)</li>
3608 <li>RNA Helices and T-Coffee Scores available as default
3611 </ul> <em>Applet</em>
3613 <li>Remove group option is shown even when selection is
3615 <li>Apply to all groups ticked but colourscheme changes
3616 don't affect groups</li>
3617 <li>Documented RNA Helices and T-Coffee Scores as valid
3618 colourscheme name</li>
3619 <li>Annotation labels drawn on sequence IDs when
3620 Annotation panel is not displayed</li>
3621 <li>Increased font size for dropdown menus on OSX and
3622 embedded windows</li>
3623 </ul> <em>Other</em>
3625 <li>Consensus sequence for alignments/groups with a
3626 single sequence were not calculated</li>
3627 <li>annotation files that contain only groups imported as
3628 annotation and junk sequences</li>
3629 <li>Fasta files with sequences containing '*' incorrectly
3630 recognised as PFAM or BLC</li>
3631 <li>conservation/PID slider apply all groups option
3632 doesn't affect background (2.8.0b1)
3634 <li>redundancy highlighting is erratic at 0% and 100%</li>
3635 <li>Remove gapped columns fails for sequences with ragged
3637 <li>AMSA annotation row with leading spaces is not
3638 registered correctly on import</li>
3639 <li>Jalview crashes when selecting PCA analysis for
3640 certain alignments</li>
3641 <li>Opening the colour by annotation dialog for an
3642 existing annotation based 'use original colours'
3643 colourscheme loses original colours setting</li>
3648 <td><div align="center">
3649 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3650 <em>30/1/2014</em></strong>
3654 <li>Trusted certificates for JalviewLite applet and
3655 Jalview Desktop application<br />Certificate was donated by
3656 <a href="https://www.certum.eu">Certum</a> to the Jalview
3657 open source project).
3659 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3660 <li>Output in Stockholm format</li>
3661 <li>Allow import of data from gzipped files</li>
3662 <li>Export/import group and sequence associated line
3663 graph thresholds</li>
3664 <li>Nucleotide substitution matrix that supports RNA and
3665 ambiguity codes</li>
3666 <li>Allow disorder predictions to be made on the current
3667 selection (or visible selection) in the same way that JPred
3669 <li>Groovy scripting for headless Jalview operation</li>
3670 </ul> <em>Other improvements</em>
3672 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3673 <li>COMBINE statement uses current SEQUENCE_REF and
3674 GROUP_REF scope to group annotation rows</li>
3675 <li>Support '' style escaping of quotes in Newick
3677 <li>Group options for JABAWS service by command line name</li>
3678 <li>Empty tooltip shown for JABA service options with a
3679 link but no description</li>
3680 <li>Select primary source when selecting authority in
3681 database fetcher GUI</li>
3682 <li>Add .mfa to FASTA file extensions recognised by
3684 <li>Annotation label tooltip text wrap</li>
3689 <li>Slow scrolling when lots of annotation rows are
3691 <li>Lots of NPE (and slowness) after creating RNA
3692 secondary structure annotation line</li>
3693 <li>Sequence database accessions not imported when
3694 fetching alignments from Rfam</li>
3695 <li>Incorrect SHMR submission for sequences with
3697 <li>View all structures does not always superpose
3699 <li>Option widgets in service parameters not updated to
3700 reflect user or preset settings</li>
3701 <li>Null pointer exceptions for some services without
3702 presets or adjustable parameters</li>
3703 <li>Discover PDB IDs entry in structure menu doesn't
3704 discover PDB xRefs</li>
3705 <li>Exception encountered while trying to retrieve
3706 features with DAS</li>
3707 <li>Lowest value in annotation row isn't coloured
3708 when colour by annotation (per sequence) is coloured</li>
3709 <li>Keyboard mode P jumps to start of gapped region when
3710 residue follows a gap</li>
3711 <li>Jalview appears to hang importing an alignment with
3712 Wrap as default or after enabling Wrap</li>
3713 <li>'Right click to add annotations' message
3714 shown in wrap mode when no annotations present</li>
3715 <li>Disorder predictions fail with NPE if no automatic
3716 annotation already exists on alignment</li>
3717 <li>oninit javascript function should be called after
3718 initialisation completes</li>
3719 <li>Remove redundancy after disorder prediction corrupts
3720 alignment window display</li>
3721 <li>Example annotation file in documentation is invalid</li>
3722 <li>Grouped line graph annotation rows are not exported
3723 to annotation file</li>
3724 <li>Multi-harmony analysis cannot be run when only two
3726 <li>Cannot create multiple groups of line graphs with
3727 several 'combine' statements in annotation file</li>
3728 <li>Pressing return several times causes Number Format
3729 exceptions in keyboard mode</li>
3730 <li>Multi-harmony (SHMMR) method doesn't submit
3731 correct partitions for input data</li>
3732 <li>Translation from DNA to Amino Acids fails</li>
3733 <li>Jalview fail to load newick tree with quoted label</li>
3734 <li>--headless flag isn't understood</li>
3735 <li>ClassCastException when generating EPS in headless
3737 <li>Adjusting sequence-associated shading threshold only
3738 changes one row's threshold</li>
3739 <li>Preferences and Feature settings panel panel
3740 doesn't open</li>
3741 <li>hide consensus histogram also hides conservation and
3742 quality histograms</li>
3747 <td><div align="center">
3748 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3750 <td><em>Application</em>
3752 <li>Support for JABAWS 2.0 Services (AACon alignment
3753 conservation, protein disorder and Clustal Omega)</li>
3754 <li>JABAWS server status indicator in Web Services
3756 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3757 in Jalview alignment window</li>
3758 <li>Updated Jalview build and deploy framework for OSX
3759 mountain lion, windows 7, and 8</li>
3760 <li>Nucleotide substitution matrix for PCA that supports
3761 RNA and ambiguity codes</li>
3763 <li>Improved sequence database retrieval GUI</li>
3764 <li>Support fetching and database reference look up
3765 against multiple DAS sources (Fetch all from in 'fetch db
3767 <li>Jalview project improvements
3769 <li>Store and retrieve the 'belowAlignment'
3770 flag for annotation</li>
3771 <li>calcId attribute to group annotation rows on the
3773 <li>Store AACon calculation settings for a view in
3774 Jalview project</li>
3778 <li>horizontal scrolling gesture support</li>
3779 <li>Visual progress indicator when PCA calculation is
3781 <li>Simpler JABA web services menus</li>
3782 <li>visual indication that web service results are still
3783 being retrieved from server</li>
3784 <li>Serialise the dialogs that are shown when Jalview
3785 starts up for first time</li>
3786 <li>Jalview user agent string for interacting with HTTP
3788 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3790 <li>Examples directory and Groovy library included in
3791 InstallAnywhere distribution</li>
3792 </ul> <em>Applet</em>
3794 <li>RNA alignment and secondary structure annotation
3795 visualization applet example</li>
3796 </ul> <em>General</em>
3798 <li>Normalise option for consensus sequence logo</li>
3799 <li>Reset button in PCA window to return dimensions to
3801 <li>Allow seqspace or Jalview variant of alignment PCA
3803 <li>PCA with either nucleic acid and protein substitution
3805 <li>Allow windows containing HTML reports to be exported
3807 <li>Interactive display and editing of RNA secondary
3808 structure contacts</li>
3809 <li>RNA Helix Alignment Colouring</li>
3810 <li>RNA base pair logo consensus</li>
3811 <li>Parse sequence associated secondary structure
3812 information in Stockholm files</li>
3813 <li>HTML Export database accessions and annotation
3814 information presented in tooltip for sequences</li>
3815 <li>Import secondary structure from LOCARNA clustalw
3816 style RNA alignment files</li>
3817 <li>import and visualise T-COFFEE quality scores for an
3819 <li>'colour by annotation' per sequence option to
3820 shade each sequence according to its associated alignment
3822 <li>New Jalview Logo</li>
3823 </ul> <em>Documentation and Development</em>
3825 <li>documentation for score matrices used in Jalview</li>
3826 <li>New Website!</li>
3828 <td><em>Application</em>
3830 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3831 wsdbfetch REST service</li>
3832 <li>Stop windows being moved outside desktop on OSX</li>
3833 <li>Filetype associations not installed for webstart
3835 <li>Jalview does not always retrieve progress of a JABAWS
3836 job execution in full once it is complete</li>
3837 <li>revise SHMR RSBS definition to ensure alignment is
3838 uploaded via ali_file parameter</li>
3839 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3840 <li>View all structures superposed fails with exception</li>
3841 <li>Jnet job queues forever if a very short sequence is
3842 submitted for prediction</li>
3843 <li>Cut and paste menu not opened when mouse clicked on
3845 <li>Putting fractional value into integer text box in
3846 alignment parameter dialog causes Jalview to hang</li>
3847 <li>Structure view highlighting doesn't work on
3849 <li>View all structures fails with exception shown in
3851 <li>Characters in filename associated with PDBEntry not
3852 escaped in a platform independent way</li>
3853 <li>Jalview desktop fails to launch with exception when
3855 <li>Tree calculation reports 'you must have 2 or more
3856 sequences selected' when selection is empty</li>
3857 <li>Jalview desktop fails to launch with jar signature
3858 failure when java web start temporary file caching is
3860 <li>DAS Sequence retrieval with range qualification
3861 results in sequence xref which includes range qualification</li>
3862 <li>Errors during processing of command line arguments
3863 cause progress bar (JAL-898) to be removed</li>
3864 <li>Replace comma for semi-colon option not disabled for
3865 DAS sources in sequence fetcher</li>
3866 <li>Cannot close news reader when JABAWS server warning
3867 dialog is shown</li>
3868 <li>Option widgets not updated to reflect user settings</li>
3869 <li>Edited sequence not submitted to web service</li>
3870 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3871 <li>InstallAnywhere installer doesn't unpack and run
3872 on OSX Mountain Lion</li>
3873 <li>Annotation panel not given a scroll bar when
3874 sequences with alignment annotation are pasted into the
3876 <li>Sequence associated annotation rows not associated
3877 when loaded from Jalview project</li>
3878 <li>Browser launch fails with NPE on java 1.7</li>
3879 <li>JABAWS alignment marked as finished when job was
3880 cancelled or job failed due to invalid input</li>
3881 <li>NPE with v2.7 example when clicking on Tree
3882 associated with all views</li>
3883 <li>Exceptions when copy/paste sequences with grouped
3884 annotation rows to new window</li>
3885 </ul> <em>Applet</em>
3887 <li>Sequence features are momentarily displayed before
3888 they are hidden using hidefeaturegroups applet parameter</li>
3889 <li>loading features via javascript API automatically
3890 enables feature display</li>
3891 <li>scrollToColumnIn javascript API method doesn't
3893 </ul> <em>General</em>
3895 <li>Redundancy removal fails for rna alignment</li>
3896 <li>PCA calculation fails when sequence has been selected
3897 and then deselected</li>
3898 <li>PCA window shows grey box when first opened on OSX</li>
3899 <li>Letters coloured pink in sequence logo when alignment
3900 coloured with clustalx</li>
3901 <li>Choosing fonts without letter symbols defined causes
3902 exceptions and redraw errors</li>
3903 <li>Initial PCA plot view is not same as manually
3904 reconfigured view</li>
3905 <li>Grouped annotation graph label has incorrect line
3907 <li>Grouped annotation graph label display is corrupted
3908 for lots of labels</li>
3913 <div align="center">
3914 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3917 <td><em>Application</em>
3919 <li>Jalview Desktop News Reader</li>
3920 <li>Tweaked default layout of web services menu</li>
3921 <li>View/alignment association menu to enable user to
3922 easily specify which alignment a multi-structure view takes
3923 its colours/correspondences from</li>
3924 <li>Allow properties file location to be specified as URL</li>
3925 <li>Extend Jalview project to preserve associations
3926 between many alignment views and a single Jmol display</li>
3927 <li>Store annotation row height in Jalview project file</li>
3928 <li>Annotation row column label formatting attributes
3929 stored in project file</li>
3930 <li>Annotation row order for auto-calculated annotation
3931 rows preserved in Jalview project file</li>
3932 <li>Visual progress indication when Jalview state is
3933 saved using Desktop window menu</li>
3934 <li>Visual indication that command line arguments are
3935 still being processed</li>
3936 <li>Groovy script execution from URL</li>
3937 <li>Colour by annotation default min and max colours in
3939 <li>Automatically associate PDB files dragged onto an
3940 alignment with sequences that have high similarity and
3942 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3943 <li>'view structures' option to open many
3944 structures in same window</li>
3945 <li>Sort associated views menu option for tree panel</li>
3946 <li>Group all JABA and non-JABA services for a particular
3947 analysis function in its own submenu</li>
3948 </ul> <em>Applet</em>
3950 <li>Userdefined and autogenerated annotation rows for
3952 <li>Adjustment of alignment annotation pane height</li>
3953 <li>Annotation scrollbar for annotation panel</li>
3954 <li>Drag to reorder annotation rows in annotation panel</li>
3955 <li>'automaticScrolling' parameter</li>
3956 <li>Allow sequences with partial ID string matches to be
3957 annotated from GFF/Jalview features files</li>
3958 <li>Sequence logo annotation row in applet</li>
3959 <li>Absolute paths relative to host server in applet
3960 parameters are treated as such</li>
3961 <li>New in the JalviewLite javascript API:
3963 <li>JalviewLite.js javascript library</li>
3964 <li>Javascript callbacks for
3966 <li>Applet initialisation</li>
3967 <li>Sequence/alignment mouse-overs and selections</li>
3970 <li>scrollTo row and column alignment scrolling
3972 <li>Select sequence/alignment regions from javascript</li>
3973 <li>javascript structure viewer harness to pass
3974 messages between Jmol and Jalview when running as
3975 distinct applets</li>
3976 <li>sortBy method</li>
3977 <li>Set of applet and application examples shipped
3978 with documentation</li>
3979 <li>New example to demonstrate JalviewLite and Jmol
3980 javascript message exchange</li>
3982 </ul> <em>General</em>
3984 <li>Enable Jmol displays to be associated with multiple
3985 multiple alignments</li>
3986 <li>Option to automatically sort alignment with new tree</li>
3987 <li>User configurable link to enable redirects to a
3988 www.Jalview.org mirror</li>
3989 <li>Jmol colours option for Jmol displays</li>
3990 <li>Configurable newline string when writing alignment
3991 and other flat files</li>
3992 <li>Allow alignment annotation description lines to
3993 contain html tags</li>
3994 </ul> <em>Documentation and Development</em>
3996 <li>Add groovy test harness for bulk load testing to
3998 <li>Groovy script to load and align a set of sequences
3999 using a web service before displaying the result in the
4000 Jalview desktop</li>
4001 <li>Restructured javascript and applet api documentation</li>
4002 <li>Ant target to publish example html files with applet
4004 <li>Netbeans project for building Jalview from source</li>
4005 <li>ant task to create online javadoc for Jalview source</li>
4007 <td><em>Application</em>
4009 <li>User defined colourscheme throws exception when
4010 current built in colourscheme is saved as new scheme</li>
4011 <li>AlignFrame->Save in application pops up save
4012 dialog for valid filename/format</li>
4013 <li>Cannot view associated structure for UniProt sequence</li>
4014 <li>PDB file association breaks for UniProt sequence
4016 <li>Associate PDB from file dialog does not tell you
4017 which sequence is to be associated with the file</li>
4018 <li>Find All raises null pointer exception when query
4019 only matches sequence IDs</li>
4020 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4021 <li>Jalview project with Jmol views created with Jalview
4022 2.4 cannot be loaded</li>
4023 <li>Filetype associations not installed for webstart
4025 <li>Two or more chains in a single PDB file associated
4026 with sequences in different alignments do not get coloured
4027 by their associated sequence</li>
4028 <li>Visibility status of autocalculated annotation row
4029 not preserved when project is loaded</li>
4030 <li>Annotation row height and visibility attributes not
4031 stored in Jalview project</li>
4032 <li>Tree bootstraps are not preserved when saved as a
4033 Jalview project</li>
4034 <li>Envision2 workflow tooltips are corrupted</li>
4035 <li>Enabling show group conservation also enables colour
4036 by conservation</li>
4037 <li>Duplicate group associated conservation or consensus
4038 created on new view</li>
4039 <li>Annotation scrollbar not displayed after 'show
4040 all hidden annotation rows' option selected</li>
4041 <li>Alignment quality not updated after alignment
4042 annotation row is hidden then shown</li>
4043 <li>Preserve colouring of structures coloured by
4044 sequences in pre Jalview 2.7 projects</li>
4045 <li>Web service job parameter dialog is not laid out
4047 <li>Web services menu not refreshed after 'reset
4048 services' button is pressed in preferences</li>
4049 <li>Annotation off by one in Jalview v2_3 example project</li>
4050 <li>Structures imported from file and saved in project
4051 get name like jalview_pdb1234.txt when reloaded</li>
4052 <li>Jalview does not always retrieve progress of a JABAWS
4053 job execution in full once it is complete</li>
4054 </ul> <em>Applet</em>
4056 <li>Alignment height set incorrectly when lots of
4057 annotation rows are displayed</li>
4058 <li>Relative URLs in feature HTML text not resolved to
4060 <li>View follows highlighting does not work for positions
4062 <li><= shown as = in tooltip</li>
4063 <li>Export features raises exception when no features
4065 <li>Separator string used for serialising lists of IDs
4066 for javascript api is modified when separator string
4067 provided as parameter</li>
4068 <li>Null pointer exception when selecting tree leaves for
4069 alignment with no existing selection</li>
4070 <li>Relative URLs for datasources assumed to be relative
4071 to applet's codebase</li>
4072 <li>Status bar not updated after finished searching and
4073 search wraps around to first result</li>
4074 <li>StructureSelectionManager instance shared between
4075 several Jalview applets causes race conditions and memory
4077 <li>Hover tooltip and mouseover of position on structure
4078 not sent from Jmol in applet</li>
4079 <li>Certain sequences of javascript method calls to
4080 applet API fatally hang browser</li>
4081 </ul> <em>General</em>
4083 <li>View follows structure mouseover scrolls beyond
4084 position with wrapped view and hidden regions</li>
4085 <li>Find sequence position moves to wrong residue
4086 with/without hidden columns</li>
4087 <li>Sequence length given in alignment properties window
4089 <li>InvalidNumberFormat exceptions thrown when trying to
4090 import PDB like structure files</li>
4091 <li>Positional search results are only highlighted
4092 between user-supplied sequence start/end bounds</li>
4093 <li>End attribute of sequence is not validated</li>
4094 <li>Find dialog only finds first sequence containing a
4095 given sequence position</li>
4096 <li>Sequence numbering not preserved in MSF alignment
4098 <li>Jalview PDB file reader does not extract sequence
4099 from nucleotide chains correctly</li>
4100 <li>Structure colours not updated when tree partition
4101 changed in alignment</li>
4102 <li>Sequence associated secondary structure not correctly
4103 parsed in interleaved stockholm</li>
4104 <li>Colour by annotation dialog does not restore current
4106 <li>Hiding (nearly) all sequences doesn't work
4108 <li>Sequences containing lowercase letters are not
4109 properly associated with their pdb files</li>
4110 </ul> <em>Documentation and Development</em>
4112 <li>schemas/JalviewWsParamSet.xsd corrupted by
4113 ApplyCopyright tool</li>
4118 <div align="center">
4119 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4122 <td><em>Application</em>
4124 <li>New warning dialog when the Jalview Desktop cannot
4125 contact web services</li>
4126 <li>JABA service parameters for a preset are shown in
4127 service job window</li>
4128 <li>JABA Service menu entries reworded</li>
4132 <li>Modeller PIR IO broken - cannot correctly import a
4133 pir file emitted by Jalview</li>
4134 <li>Existing feature settings transferred to new
4135 alignment view created from cut'n'paste</li>
4136 <li>Improved test for mixed amino/nucleotide chains when
4137 parsing PDB files</li>
4138 <li>Consensus and conservation annotation rows
4139 occasionally become blank for all new windows</li>
4140 <li>Exception raised when right clicking above sequences
4141 in wrapped view mode</li>
4142 </ul> <em>Application</em>
4144 <li>multiple multiply aligned structure views cause cpu
4145 usage to hit 100% and computer to hang</li>
4146 <li>Web Service parameter layout breaks for long user
4147 parameter names</li>
4148 <li>Jaba service discovery hangs desktop if Jaba server
4155 <div align="center">
4156 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4159 <td><em>Application</em>
4161 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4162 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4165 <li>Web Services preference tab</li>
4166 <li>Analysis parameters dialog box and user defined
4168 <li>Improved speed and layout of Envision2 service menu</li>
4169 <li>Superpose structures using associated sequence
4171 <li>Export coordinates and projection as CSV from PCA
4173 </ul> <em>Applet</em>
4175 <li>enable javascript: execution by the applet via the
4176 link out mechanism</li>
4177 </ul> <em>Other</em>
4179 <li>Updated the Jmol Jalview interface to work with Jmol
4181 <li>The Jalview Desktop and JalviewLite applet now
4182 require Java 1.5</li>
4183 <li>Allow Jalview feature colour specification for GFF
4184 sequence annotation files</li>
4185 <li>New 'colour by label' keword in Jalview feature file
4186 type colour specification</li>
4187 <li>New Jalview Desktop Groovy API method that allows a
4188 script to check if it being run in an interactive session or
4189 in a batch operation from the Jalview command line</li>
4193 <li>clustalx colourscheme colours Ds preferentially when
4194 both D+E are present in over 50% of the column</li>
4195 </ul> <em>Application</em>
4197 <li>typo in AlignmentFrame->View->Hide->all but
4198 selected Regions menu item</li>
4199 <li>sequence fetcher replaces ',' for ';' when the ',' is
4200 part of a valid accession ID</li>
4201 <li>fatal OOM if object retrieved by sequence fetcher
4202 runs out of memory</li>
4203 <li>unhandled Out of Memory Error when viewing pca
4204 analysis results</li>
4205 <li>InstallAnywhere builds fail to launch on OS X java
4206 10.5 update 4 (due to apple Java 1.6 update)</li>
4207 <li>Installanywhere Jalview silently fails to launch</li>
4208 </ul> <em>Applet</em>
4210 <li>Jalview.getFeatureGroups() raises an
4211 ArrayIndexOutOfBoundsException if no feature groups are
4218 <div align="center">
4219 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4225 <li>Alignment prettyprinter doesn't cope with long
4227 <li>clustalx colourscheme colours Ds preferentially when
4228 both D+E are present in over 50% of the column</li>
4229 <li>nucleic acid structures retrieved from PDB do not
4230 import correctly</li>
4231 <li>More columns get selected than were clicked on when a
4232 number of columns are hidden</li>
4233 <li>annotation label popup menu not providing correct
4234 add/hide/show options when rows are hidden or none are
4236 <li>Stockholm format shown in list of readable formats,
4237 and parser copes better with alignments from RFAM.</li>
4238 <li>CSV output of consensus only includes the percentage
4239 of all symbols if sequence logo display is enabled</li>
4241 </ul> <em>Applet</em>
4243 <li>annotation panel disappears when annotation is
4245 </ul> <em>Application</em>
4247 <li>Alignment view not redrawn properly when new
4248 alignment opened where annotation panel is visible but no
4249 annotations are present on alignment</li>
4250 <li>pasted region containing hidden columns is
4251 incorrectly displayed in new alignment window</li>
4252 <li>Jalview slow to complete operations when stdout is
4253 flooded (fix is to close the Jalview console)</li>
4254 <li>typo in AlignmentFrame->View->Hide->all but
4255 selected Rregions menu item.</li>
4256 <li>inconsistent group submenu and Format submenu entry
4257 'Un' or 'Non'conserved</li>
4258 <li>Sequence feature settings are being shared by
4259 multiple distinct alignments</li>
4260 <li>group annotation not recreated when tree partition is
4262 <li>double click on group annotation to select sequences
4263 does not propagate to associated trees</li>
4264 <li>Mac OSX specific issues:
4266 <li>exception raised when mouse clicked on desktop
4267 window background</li>
4268 <li>Desktop menu placed on menu bar and application
4269 name set correctly</li>
4270 <li>sequence feature settings not wide enough for the
4271 save feature colourscheme button</li>
4280 <div align="center">
4281 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4284 <td><em>New Capabilities</em>
4286 <li>URL links generated from description line for
4287 regular-expression based URL links (applet and application)
4289 <li>Non-positional feature URL links are shown in link
4291 <li>Linked viewing of nucleic acid sequences and
4293 <li>Automatic Scrolling option in View menu to display
4294 the currently highlighted region of an alignment.</li>
4295 <li>Order an alignment by sequence length, or using the
4296 average score or total feature count for each sequence.</li>
4297 <li>Shading features by score or associated description</li>
4298 <li>Subdivide alignment and groups based on identity of
4299 selected subsequence (Make Groups from Selection).</li>
4300 <li>New hide/show options including Shift+Control+H to
4301 hide everything but the currently selected region.</li>
4302 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4303 </ul> <em>Application</em>
4305 <li>Fetch DB References capabilities and UI expanded to
4306 support retrieval from DAS sequence sources</li>
4307 <li>Local DAS Sequence sources can be added via the
4308 command line or via the Add local source dialog box.</li>
4309 <li>DAS Dbref and DbxRef feature types are parsed as
4310 database references and protein_name is parsed as
4311 description line (BioSapiens terms).</li>
4312 <li>Enable or disable non-positional feature and database
4313 references in sequence ID tooltip from View menu in
4315 <!-- <li>New hidden columns and rows and representatives capabilities
4316 in annotations file (in progress - not yet fully implemented)</li> -->
4317 <li>Group-associated consensus, sequence logos and
4318 conservation plots</li>
4319 <li>Symbol distributions for each column can be exported
4320 and visualized as sequence logos</li>
4321 <li>Optionally scale multi-character column labels to fit
4322 within each column of annotation row<!-- todo for applet -->
4324 <li>Optional automatic sort of associated alignment view
4325 when a new tree is opened.</li>
4326 <li>Jalview Java Console</li>
4327 <li>Better placement of desktop window when moving
4328 between different screens.</li>
4329 <li>New preference items for sequence ID tooltip and
4330 consensus annotation</li>
4331 <li>Client to submit sequences and IDs to Envision2
4333 <li><em>Vamsas Capabilities</em>
4335 <li>Improved VAMSAS synchronization (Jalview archive
4336 used to preserve views, structures, and tree display
4338 <li>Import of vamsas documents from disk or URL via
4340 <li>Sharing of selected regions between views and
4341 with other VAMSAS applications (Experimental feature!)</li>
4342 <li>Updated API to VAMSAS version 0.2</li>
4344 </ul> <em>Applet</em>
4346 <li>Middle button resizes annotation row height</li>
4349 <li>sortByTree (true/false) - automatically sort the
4350 associated alignment view by the tree when a new tree is
4352 <li>showTreeBootstraps (true/false) - show or hide
4353 branch bootstraps (default is to show them if available)</li>
4354 <li>showTreeDistances (true/false) - show or hide
4355 branch lengths (default is to show them if available)</li>
4356 <li>showUnlinkedTreeNodes (true/false) - indicate if
4357 unassociated nodes should be highlighted in the tree
4359 <li>heightScale and widthScale (1.0 or more) -
4360 increase the height or width of a cell in the alignment
4361 grid relative to the current font size.</li>
4364 <li>Non-positional features displayed in sequence ID
4366 </ul> <em>Other</em>
4368 <li>Features format: graduated colour definitions and
4369 specification of feature scores</li>
4370 <li>Alignment Annotations format: new keywords for group
4371 associated annotation (GROUP_REF) and annotation row display
4372 properties (ROW_PROPERTIES)</li>
4373 <li>XML formats extended to support graduated feature
4374 colourschemes, group associated annotation, and profile
4375 visualization settings.</li></td>
4378 <li>Source field in GFF files parsed as feature source
4379 rather than description</li>
4380 <li>Non-positional features are now included in sequence
4381 feature and gff files (controlled via non-positional feature
4382 visibility in tooltip).</li>
4383 <li>URL links generated for all feature links (bugfix)</li>
4384 <li>Added URL embedding instructions to features file
4386 <li>Codons containing ambiguous nucleotides translated as
4387 'X' in peptide product</li>
4388 <li>Match case switch in find dialog box works for both
4389 sequence ID and sequence string and query strings do not
4390 have to be in upper case to match case-insensitively.</li>
4391 <li>AMSA files only contain first column of
4392 multi-character column annotation labels</li>
4393 <li>Jalview Annotation File generation/parsing consistent
4394 with documentation (e.g. Stockholm annotation can be
4395 exported and re-imported)</li>
4396 <li>PDB files without embedded PDB IDs given a friendly
4398 <li>Find incrementally searches ID string matches as well
4399 as subsequence matches, and correctly reports total number
4403 <li>Better handling of exceptions during sequence
4405 <li>Dasobert generated non-positional feature URL
4406 link text excludes the start_end suffix</li>
4407 <li>DAS feature and source retrieval buttons disabled
4408 when fetch or registry operations in progress.</li>
4409 <li>PDB files retrieved from URLs are cached properly</li>
4410 <li>Sequence description lines properly shared via
4412 <li>Sequence fetcher fetches multiple records for all
4414 <li>Ensured that command line das feature retrieval
4415 completes before alignment figures are generated.</li>
4416 <li>Reduced time taken when opening file browser for
4418 <li>isAligned check prior to calculating tree, PCA or
4419 submitting an MSA to JNet now excludes hidden sequences.</li>
4420 <li>User defined group colours properly recovered
4421 from Jalview projects.</li>
4430 <div align="center">
4431 <strong>2.4.0.b2</strong><br> 28/10/2009
4436 <li>Experimental support for google analytics usage
4438 <li>Jalview privacy settings (user preferences and docs).</li>
4443 <li>Race condition in applet preventing startup in
4445 <li>Exception when feature created from selection beyond
4446 length of sequence.</li>
4447 <li>Allow synthetic PDB files to be imported gracefully</li>
4448 <li>Sequence associated annotation rows associate with
4449 all sequences with a given id</li>
4450 <li>Find function matches case-insensitively for sequence
4451 ID string searches</li>
4452 <li>Non-standard characters do not cause pairwise
4453 alignment to fail with exception</li>
4454 </ul> <em>Application Issues</em>
4456 <li>Sequences are now validated against EMBL database</li>
4457 <li>Sequence fetcher fetches multiple records for all
4459 </ul> <em>InstallAnywhere Issues</em>
4461 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4462 issue with installAnywhere mechanism)</li>
4463 <li>Command line launching of JARs from InstallAnywhere
4464 version (java class versioning error fixed)</li>
4471 <div align="center">
4472 <strong>2.4</strong><br> 27/8/2008
4475 <td><em>User Interface</em>
4477 <li>Linked highlighting of codon and amino acid from
4478 translation and protein products</li>
4479 <li>Linked highlighting of structure associated with
4480 residue mapping to codon position</li>
4481 <li>Sequence Fetcher provides example accession numbers
4482 and 'clear' button</li>
4483 <li>MemoryMonitor added as an option under Desktop's
4485 <li>Extract score function to parse whitespace separated
4486 numeric data in description line</li>
4487 <li>Column labels in alignment annotation can be centred.</li>
4488 <li>Tooltip for sequence associated annotation give name
4490 </ul> <em>Web Services and URL fetching</em>
4492 <li>JPred3 web service</li>
4493 <li>Prototype sequence search client (no public services
4495 <li>Fetch either seed alignment or full alignment from
4497 <li>URL Links created for matching database cross
4498 references as well as sequence ID</li>
4499 <li>URL Links can be created using regular-expressions</li>
4500 </ul> <em>Sequence Database Connectivity</em>
4502 <li>Retrieval of cross-referenced sequences from other
4504 <li>Generalised database reference retrieval and
4505 validation to all fetchable databases</li>
4506 <li>Fetch sequences from DAS sources supporting the
4507 sequence command</li>
4508 </ul> <em>Import and Export</em>
4509 <li>export annotation rows as CSV for spreadsheet import</li>
4510 <li>Jalview projects record alignment dataset associations,
4511 EMBL products, and cDNA sequence mappings</li>
4512 <li>Sequence Group colour can be specified in Annotation
4514 <li>Ad-hoc colouring of group in Annotation File using RGB
4515 triplet as name of colourscheme</li>
4516 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4518 <li>treenode binding for VAMSAS tree exchange</li>
4519 <li>local editing and update of sequences in VAMSAS
4520 alignments (experimental)</li>
4521 <li>Create new or select existing session to join</li>
4522 <li>load and save of vamsas documents</li>
4523 </ul> <em>Application command line</em>
4525 <li>-tree parameter to open trees (introduced for passing
4527 <li>-fetchfrom command line argument to specify nicknames
4528 of DAS servers to query for alignment features</li>
4529 <li>-dasserver command line argument to add new servers
4530 that are also automatically queried for features</li>
4531 <li>-groovy command line argument executes a given groovy
4532 script after all input data has been loaded and parsed</li>
4533 </ul> <em>Applet-Application data exchange</em>
4535 <li>Trees passed as applet parameters can be passed to
4536 application (when using "View in full
4537 application")</li>
4538 </ul> <em>Applet Parameters</em>
4540 <li>feature group display control parameter</li>
4541 <li>debug parameter</li>
4542 <li>showbutton parameter</li>
4543 </ul> <em>Applet API methods</em>
4545 <li>newView public method</li>
4546 <li>Window (current view) specific get/set public methods</li>
4547 <li>Feature display control methods</li>
4548 <li>get list of currently selected sequences</li>
4549 </ul> <em>New Jalview distribution features</em>
4551 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4552 <li>RELEASE file gives build properties for the latest
4553 Jalview release.</li>
4554 <li>Java 1.1 Applet build made easier and donotobfuscate
4555 property controls execution of obfuscator</li>
4556 <li>Build target for generating source distribution</li>
4557 <li>Debug flag for javacc</li>
4558 <li>.jalview_properties file is documented (slightly) in
4559 jalview.bin.Cache</li>
4560 <li>Continuous Build Integration for stable and
4561 development version of Application, Applet and source
4566 <li>selected region output includes visible annotations
4567 (for certain formats)</li>
4568 <li>edit label/displaychar contains existing label/char
4570 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4571 <li>shorter peptide product names from EMBL records</li>
4572 <li>Newick string generator makes compact representations</li>
4573 <li>bootstrap values parsed correctly for tree files with
4575 <li>pathological filechooser bug avoided by not allowing
4576 filenames containing a ':'</li>
4577 <li>Fixed exception when parsing GFF files containing
4578 global sequence features</li>
4579 <li>Alignment datasets are finalized only when number of
4580 references from alignment sequences goes to zero</li>
4581 <li>Close of tree branch colour box without colour
4582 selection causes cascading exceptions</li>
4583 <li>occasional negative imgwidth exceptions</li>
4584 <li>better reporting of non-fatal warnings to user when
4585 file parsing fails.</li>
4586 <li>Save works when Jalview project is default format</li>
4587 <li>Save as dialog opened if current alignment format is
4588 not a valid output format</li>
4589 <li>UniProt canonical names introduced for both das and
4591 <li>Histidine should be midblue (not pink!) in Zappo</li>
4592 <li>error messages passed up and output when data read
4594 <li>edit undo recovers previous dataset sequence when
4595 sequence is edited</li>
4596 <li>allow PDB files without pdb ID HEADER lines (like
4597 those generated by MODELLER) to be read in properly</li>
4598 <li>allow reading of JPred concise files as a normal
4600 <li>Stockholm annotation parsing and alignment properties
4601 import fixed for PFAM records</li>
4602 <li>Structure view windows have correct name in Desktop
4604 <li>annotation consisting of sequence associated scores
4605 can be read and written correctly to annotation file</li>
4606 <li>Aligned cDNA translation to aligned peptide works
4608 <li>Fixed display of hidden sequence markers and
4609 non-italic font for representatives in Applet</li>
4610 <li>Applet Menus are always embedded in applet window on
4612 <li>Newly shown features appear at top of stack (in
4614 <li>Annotations added via parameter not drawn properly
4615 due to null pointer exceptions</li>
4616 <li>Secondary structure lines are drawn starting from
4617 first column of alignment</li>
4618 <li>UniProt XML import updated for new schema release in
4620 <li>Sequence feature to sequence ID match for Features
4621 file is case-insensitive</li>
4622 <li>Sequence features read from Features file appended to
4623 all sequences with matching IDs</li>
4624 <li>PDB structure coloured correctly for associated views
4625 containing a sub-sequence</li>
4626 <li>PDB files can be retrieved by applet from Jar files</li>
4627 <li>feature and annotation file applet parameters
4628 referring to different directories are retrieved correctly</li>
4629 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4630 <li>Fixed application hang whilst waiting for
4631 splash-screen version check to complete</li>
4632 <li>Applet properly URLencodes input parameter values
4633 when passing them to the launchApp service</li>
4634 <li>display name and local features preserved in results
4635 retrieved from web service</li>
4636 <li>Visual delay indication for sequence retrieval and
4637 sequence fetcher initialisation</li>
4638 <li>updated Application to use DAS 1.53e version of
4639 dasobert DAS client</li>
4640 <li>Re-instated Full AMSA support and .amsa file
4642 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4650 <div align="center">
4651 <strong>2.3</strong><br> 9/5/07
4656 <li>Jmol 11.0.2 integration</li>
4657 <li>PDB views stored in Jalview XML files</li>
4658 <li>Slide sequences</li>
4659 <li>Edit sequence in place</li>
4660 <li>EMBL CDS features</li>
4661 <li>DAS Feature mapping</li>
4662 <li>Feature ordering</li>
4663 <li>Alignment Properties</li>
4664 <li>Annotation Scores</li>
4665 <li>Sort by scores</li>
4666 <li>Feature/annotation editing in applet</li>
4671 <li>Headless state operation in 2.2.1</li>
4672 <li>Incorrect and unstable DNA pairwise alignment</li>
4673 <li>Cut and paste of sequences with annotation</li>
4674 <li>Feature group display state in XML</li>
4675 <li>Feature ordering in XML</li>
4676 <li>blc file iteration selection using filename # suffix</li>
4677 <li>Stockholm alignment properties</li>
4678 <li>Stockhom alignment secondary structure annotation</li>
4679 <li>2.2.1 applet had no feature transparency</li>
4680 <li>Number pad keys can be used in cursor mode</li>
4681 <li>Structure Viewer mirror image resolved</li>
4688 <div align="center">
4689 <strong>2.2.1</strong><br> 12/2/07
4694 <li>Non standard characters can be read and displayed
4695 <li>Annotations/Features can be imported/exported to the
4697 <li>Applet allows editing of sequence/annotation/group
4698 name & description
4699 <li>Preference setting to display sequence name in
4701 <li>Annotation file format extended to allow
4702 Sequence_groups to be defined
4703 <li>Default opening of alignment overview panel can be
4704 specified in preferences
4705 <li>PDB residue numbering annotation added to associated
4711 <li>Applet crash under certain Linux OS with Java 1.6
4713 <li>Annotation file export / import bugs fixed
4714 <li>PNG / EPS image output bugs fixed
4720 <div align="center">
4721 <strong>2.2</strong><br> 27/11/06
4726 <li>Multiple views on alignment
4727 <li>Sequence feature editing
4728 <li>"Reload" alignment
4729 <li>"Save" to current filename
4730 <li>Background dependent text colour
4731 <li>Right align sequence ids
4732 <li>User-defined lower case residue colours
4735 <li>Menu item accelerator keys
4736 <li>Control-V pastes to current alignment
4737 <li>Cancel button for DAS Feature Fetching
4738 <li>PCA and PDB Viewers zoom via mouse roller
4739 <li>User-defined sub-tree colours and sub-tree selection
4741 <li>'New Window' button on the 'Output to Text box'
4746 <li>New memory efficient Undo/Redo System
4747 <li>Optimised symbol lookups and conservation/consensus
4749 <li>Region Conservation/Consensus recalculated after
4751 <li>Fixed Remove Empty Columns Bug (empty columns at end
4753 <li>Slowed DAS Feature Fetching for increased robustness.
4755 <li>Made angle brackets in ASCII feature descriptions
4757 <li>Re-instated Zoom function for PCA
4758 <li>Sequence descriptions conserved in web service
4760 <li>UniProt ID discoverer uses any word separated by
4762 <li>WsDbFetch query/result association resolved
4763 <li>Tree leaf to sequence mapping improved
4764 <li>Smooth fonts switch moved to FontChooser dialog box.
4771 <div align="center">
4772 <strong>2.1.1</strong><br> 12/9/06
4777 <li>Copy consensus sequence to clipboard</li>
4782 <li>Image output - rightmost residues are rendered if
4783 sequence id panel has been resized</li>
4784 <li>Image output - all offscreen group boundaries are
4786 <li>Annotation files with sequence references - all
4787 elements in file are relative to sequence position</li>
4788 <li>Mac Applet users can use Alt key for group editing</li>
4794 <div align="center">
4795 <strong>2.1</strong><br> 22/8/06
4800 <li>MAFFT Multiple Alignment in default Web Service list</li>
4801 <li>DAS Feature fetching</li>
4802 <li>Hide sequences and columns</li>
4803 <li>Export Annotations and Features</li>
4804 <li>GFF file reading / writing</li>
4805 <li>Associate structures with sequences from local PDB
4807 <li>Add sequences to exisiting alignment</li>
4808 <li>Recently opened files / URL lists</li>
4809 <li>Applet can launch the full application</li>
4810 <li>Applet has transparency for features (Java 1.2
4812 <li>Applet has user defined colours parameter</li>
4813 <li>Applet can load sequences from parameter
4814 "sequence<em>x</em>"
4820 <li>Redundancy Panel reinstalled in the Applet</li>
4821 <li>Monospaced font - EPS / rescaling bug fixed</li>
4822 <li>Annotation files with sequence references bug fixed</li>
4828 <div align="center">
4829 <strong>2.08.1</strong><br> 2/5/06
4834 <li>Change case of selected region from Popup menu</li>
4835 <li>Choose to match case when searching</li>
4836 <li>Middle mouse button and mouse movement can compress /
4837 expand the visible width and height of the alignment</li>
4842 <li>Annotation Panel displays complete JNet results</li>
4848 <div align="center">
4849 <strong>2.08b</strong><br> 18/4/06
4855 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4856 <li>Righthand label on wrapped alignments shows correct
4863 <div align="center">
4864 <strong>2.08</strong><br> 10/4/06
4869 <li>Editing can be locked to the selection area</li>
4870 <li>Keyboard editing</li>
4871 <li>Create sequence features from searches</li>
4872 <li>Precalculated annotations can be loaded onto
4874 <li>Features file allows grouping of features</li>
4875 <li>Annotation Colouring scheme added</li>
4876 <li>Smooth fonts off by default - Faster rendering</li>
4877 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4882 <li>Drag & Drop fixed on Linux</li>
4883 <li>Jalview Archive file faster to load/save, sequence
4884 descriptions saved.</li>
4890 <div align="center">
4891 <strong>2.07</strong><br> 12/12/05
4896 <li>PDB Structure Viewer enhanced</li>
4897 <li>Sequence Feature retrieval and display enhanced</li>
4898 <li>Choose to output sequence start-end after sequence
4899 name for file output</li>
4900 <li>Sequence Fetcher WSDBFetch@EBI</li>
4901 <li>Applet can read feature files, PDB files and can be
4902 used for HTML form input</li>
4907 <li>HTML output writes groups and features</li>
4908 <li>Group editing is Control and mouse click</li>
4909 <li>File IO bugs</li>
4915 <div align="center">
4916 <strong>2.06</strong><br> 28/9/05
4921 <li>View annotations in wrapped mode</li>
4922 <li>More options for PCA viewer</li>
4927 <li>GUI bugs resolved</li>
4928 <li>Runs with -nodisplay from command line</li>
4934 <div align="center">
4935 <strong>2.05b</strong><br> 15/9/05
4940 <li>Choose EPS export as lineart or text</li>
4941 <li>Jar files are executable</li>
4942 <li>Can read in Uracil - maps to unknown residue</li>
4947 <li>Known OutOfMemory errors give warning message</li>
4948 <li>Overview window calculated more efficiently</li>
4949 <li>Several GUI bugs resolved</li>
4955 <div align="center">
4956 <strong>2.05</strong><br> 30/8/05
4961 <li>Edit and annotate in "Wrapped" view</li>
4966 <li>Several GUI bugs resolved</li>
4972 <div align="center">
4973 <strong>2.04</strong><br> 24/8/05
4978 <li>Hold down mouse wheel & scroll to change font
4984 <li>Improved JPred client reliability</li>
4985 <li>Improved loading of Jalview files</li>
4991 <div align="center">
4992 <strong>2.03</strong><br> 18/8/05
4997 <li>Set Proxy server name and port in preferences</li>
4998 <li>Multiple URL links from sequence ids</li>
4999 <li>User Defined Colours can have a scheme name and added
5001 <li>Choose to ignore gaps in consensus calculation</li>
5002 <li>Unix users can set default web browser</li>
5003 <li>Runs without GUI for batch processing</li>
5004 <li>Dynamically generated Web Service Menus</li>
5009 <li>InstallAnywhere download for Sparc Solaris</li>
5015 <div align="center">
5016 <strong>2.02</strong><br> 18/7/05
5022 <li>Copy & Paste order of sequences maintains
5023 alignment order.</li>
5029 <div align="center">
5030 <strong>2.01</strong><br> 12/7/05
5035 <li>Use delete key for deleting selection.</li>
5036 <li>Use Mouse wheel to scroll sequences.</li>
5037 <li>Help file updated to describe how to add alignment
5039 <li>Version and build date written to build properties
5041 <li>InstallAnywhere installation will check for updates
5042 at launch of Jalview.</li>
5047 <li>Delete gaps bug fixed.</li>
5048 <li>FileChooser sorts columns.</li>
5049 <li>Can remove groups one by one.</li>
5050 <li>Filechooser icons installed.</li>
5051 <li>Finder ignores return character when searching.
5052 Return key will initiate a search.<br>
5059 <div align="center">
5060 <strong>2.0</strong><br> 20/6/05
5065 <li>New codebase</li>