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;
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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
84 features 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
100 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
101 column selection doesn't always ignore hidden columns
103 </ul> <em>Installer</em>
106 <!-- JAL-3611 -->Space character in Jalview install path on
107 Windows prevents install4j launching getdown
109 </ul> <em>Development</em>
112 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
113 version numbers in doc/building.md
119 <td width="60" align="center" nowrap><strong><a
120 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
121 <em>25/09/2020</em></strong></td>
122 <td align="left" valign="top">
126 <td align="left" valign="top">
129 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
130 "Encountered problems opening
131 https://www.jalview.org/examples/exampleFile_2_7.jvp"
137 <td width="60" align="center" nowrap><strong><a
138 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
139 <em>17/09/2020</em></strong></td>
140 <td align="left" valign="top">
143 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
144 residue in cursor mode
147 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
148 HTSJDK from 2.12 to 2.23
151 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
152 optimisations and improvements suggested by Bob Hanson and
153 improved compatibility with JalviewJS
156 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
157 alignments from Pfam and Rfam
160 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
161 import (no longer based on .gz extension)
164 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
167 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
168 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
172 <!-- JAL-3667 -->Improved warning messages, debug logging
173 and fixed Retry action when Jalview encounters errors when
174 saving or making backup files.
177 <!-- JAL-3676 -->Enhanced Jalview Java Console:
179 <li>Jalview's logging level can be configured</li>
180 <li>Copy to Clipboard Buttion</li>
184 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
185 when running on Linux (Requires Java 11+)
187 </ul> <em>Launching Jalview</em>
190 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
191 through a system property
194 <!-- JAL-3477 -->Improved built-in documentation and command
195 line help for configuring Jalview's memory
199 <td align="left" valign="top">
202 <!-- JAL-3691 -->Conservation and Quality tracks are shown
203 but not calculated and no protein or DNA score models are
204 available for tree/PCA calculation when launched with
205 Turkish language locale
208 <!-- JAL-3493 -->Escape does not clear highlights on the
209 alignment (Since Jalview 2.10.3)
212 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
213 doesn't slide selected sequences, just sequence under cursor
216 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
217 sequence under the cursor
220 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
221 multiple EMBL gene products shown forĀ a single contig
224 <!-- JAL-3696 -->Errors encountered when processing variants
225 from VCF files yield "Error processing VCF: Format specifier
229 <!-- JAL-3697 -->Count of features not shown can be wrong
230 when there are both local and complementary features mapped
231 to the position under the cursor
234 <!-- JAL-3673 -->Sequence ID for reference sequence is
235 clipped when Right align Sequence IDs enabled
238 <!-- JAL-2983 -->Slider with negative range values not
239 rendered correctly in VAqua4 (Since 2.10.4)
242 <!-- JAL-3685 -->Single quotes not displayed correctly in
243 internationalised text for some messages and log output
246 <!-- JAL-3490 -->Find doesn't report matches that span
247 hidden gapped columns
250 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
251 panels, Alignment viewport and annotation renderer.
254 <!-- JAL-3561 -->Jalview ignores file format parameter
255 specifying output format when exporting an alignment via the
259 <!-- JAL-3667 -->Windows 10: For a minority of users, if
260 backups are not enabled, Jalview sometimes fails to
261 overwrite an existing file and raises a warning dialog. (in
262 2.11.0, and 2.11.1.0, the workaround is to try to save the
263 file again, and if that fails, delete the original file and
267 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
271 <!-- JAL-3741 -->References to http://www.jalview.org in
272 program and documentation
274 </ul> <em>Launching Jalview</em>
277 <!-- JAL-3718 -->Jalview application fails when launched the
278 first time for a version that has different jars to the
279 previous launched version.
281 </ul> <em>Developing Jalview</em>
284 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
285 data, causing cloverReport gradle task to fail with an
289 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
290 monitor the release channel
292 </ul> <em>New Known defects</em>
295 <!-- JAL-3748 -->CDS shown in result of submitting proteins
296 in a CDS/Protein alignment to a web service is wrong when
297 proteins share a common transcript sequence (e.g.
298 genome of RNA viruses)
301 <!-- JAL-3576 -->Co-located features exported and re-imported
302 are ordered differently when shown on alignment and in
303 tooltips. (Also affects v2.11.1.0)
306 <!-- JAL-3702 -->Drag and drop of alignment file onto
307 alignment window when in a HiDPI scaled mode in Linux only
308 works for the top left quadrant of the alignment window
311 <!-- JAL-3701 -->Stale build data in jalview standalone jar
312 builds (only affects 2.11.1.1 branch)
315 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
316 when alignment view restored from project (since Jalview 2.11.0)
319 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
320 protein products for certain ENA records are repeatedly
321 shown via Calculate->Show Cross Refs
327 <td width="60" align="center" nowrap><strong><a
328 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
329 <em>22/04/2020</em></strong></td>
330 <td align="left" valign="top">
333 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
334 'virtual' codon features shown on protein (or vice versa)
335 for display in alignments, on structure views (including
336 transfer to UCSF chimera), in feature reports and for
340 <!-- JAL-3121 -->Feature attributes from VCF files can be
341 exported and re-imported as GFF3 files
344 <!-- JAL-3376 -->Capture VCF "fixed column" values
345 POS, ID, QUAL, FILTER as Feature Attributes
348 <!-- JAL-3375 -->More robust VCF numeric data field
349 validation while parsing
352 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
356 <!-- JAL-3535 -->Feature Settings dialog title includes name
360 <!-- JAL-3538 -->Font anti-aliasing in alignment views
364 <!-- JAL-3468 -->Very long feature descriptions truncated in
368 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
369 with no feature types visible
372 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
374 </ul><em>Jalview Installer</em>
377 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
378 in console (may be null when Jalview launched as executable jar or via conda)
381 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
384 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
387 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
389 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
390 </ul> <em>Release processes</em>
393 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
396 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
398 </ul> <em>Build System</em>
401 <!-- JAL-3510 -->Clover updated to 4.4.1
404 <!-- JAL-3513 -->Test code included in Clover coverage
408 <em>Groovy Scripts</em>
411 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
412 to stdout containing the consensus sequence for each
413 alignment in a Jalview session
416 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
417 genomic sequence_variant annotation from CDS as
418 missense_variant or synonymous_variant on protein products.
422 <td align="left" valign="top">
425 <!-- JAL-3581 -->Hidden sequence markers still visible when
426 'Show hidden markers' option is not ticked
429 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
430 PNG output when 'Automatically set ID width' is set in
431 jalview preferences or properties file
434 <!-- JAL-3571 -->Feature Editor dialog can be opened when
435 'Show Sequence Features' option is not ticked
438 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
439 buttons in Feature Settings dialog are clicked when no
443 <!-- JAL-3412 -->ID margins for CDS and Protein views not
444 equal when split frame is first opened
447 <!-- JAL-3296 -->Sequence position numbers in status bar not
448 correct after editing a sequence's start position
451 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
452 with annotation and exceptions thrown when only a few
453 columns shown in wrapped mode
456 <!-- JAL-3386 -->Sequence IDs missing in headless export of
457 wrapped alignment figure with annotations
460 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
461 ID fails with ClassCastException
464 <!-- JAL-3389 -->Chimera session not restored from Jalview
468 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
469 feature settings dialog also selects columns
472 <!-- JAL-3473 -->SpinnerNumberModel causes
473 IllegalArgumentException in some circumstances
476 <!-- JAL-3534 -->Multiple feature settings dialogs can be
480 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
481 alignment window is closed
484 <!-- JAL-3406 -->Credits missing some authors in Jalview
485 help documentation for 2.11.0 release
488 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
489 includes Pfam ID as sequence's accession rather than its
492 </ul> <em>Java 11 Compatibility issues</em>
495 <!-- JAL-2987 -->OSX - Can't view some search results in
496 PDB/Uniprot search panel
498 </ul> <em>Installer</em>
501 <!-- JAL-3447 -->Jalview should not create file associations
502 for 3D structure files (.pdb, .mmcif. .cif)
504 </ul> <em>Repository and Source Release</em>
507 <!-- JAL-3474 -->removed obsolete .cvsignore files from
511 <!-- JAL-3541 -->Clover report generation running out of
514 </ul> <em>New Known Issues</em>
517 <!-- JAL-3523 -->OSX - Current working directory not
518 preserved when Jalview.app launched with parameters from
522 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
523 clipped in headless figure export when Right Align option
527 <!-- JAL-3542 -->Jalview Installation type always reports
528 'Source' in console output
531 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
532 bamboo server but run fine locally.
538 <td width="60" align="center" nowrap>
539 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
540 <em>04/07/2019</em></strong>
542 <td align="left" valign="top">
545 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
546 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
547 source project) rather than InstallAnywhere
550 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
551 settings, receive over the air updates and launch specific
552 versions via (<a href="https://github.com/threerings/getdown">Three
556 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
557 formats supported by Jalview (including .jvp project files)
560 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
561 arguments and switch between different getdown channels
564 <!-- JAL-3141 -->Backup files created when saving Jalview project
569 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
570 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
572 <!-- JAL-2620 -->Alternative genetic code tables for
573 'Translate as cDNA'</li>
575 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
576 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
579 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
580 implementation that allows updates) used for Sequence Feature collections</li>
582 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
583 features can be filtered and shaded according to any
584 associated attributes (e.g. variant attributes from VCF
585 file, or key-value pairs imported from column 9 of GFF
589 <!-- JAL-2879 -->Feature Attributes and shading schemes
590 stored and restored from Jalview Projects
593 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
594 recognise variant features
597 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
598 sequences (also coloured red by default)
601 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
605 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
606 algorithm (Z-sort/transparency and filter aware)
609 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
615 <!-- JAL-3205 -->Symmetric score matrices for faster
616 tree and PCA calculations
618 <li><strong>Principal Components Analysis Viewer</strong>
621 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
622 and Viewer state saved in Jalview Project
624 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
627 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
631 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
636 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
638 <li><strong>Speed and Efficiency</strong>
641 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
642 multiple groups when working with large alignments
645 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
649 <li><strong>User Interface</strong>
652 <!-- JAL-2933 -->Finder panel remembers last position in each
656 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
657 what is shown)<br />Only visible regions of alignment are shown by
658 default (can be changed in user preferences)
661 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
662 to the Overwrite Dialog
665 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
669 <!-- JAL-1244 -->Status bar shows bounds when dragging a
670 selection region, and gap count when inserting or deleting gaps
673 <!-- JAL-3132 -->Status bar updates over sequence and annotation
677 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
681 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
685 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
688 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
692 <!-- JAL-3181 -->Consistent ordering of links in sequence id
696 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
698 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
702 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
703 <li><strong>Java 11 Support (not yet on general release)</strong>
706 <!-- -->OSX GUI integrations for App menu's 'About' entry and
711 <em>Deprecations</em>
713 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
714 capabilities removed from the Jalview Desktop
716 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
717 unmarshalling has been replaced by JAXB for Jalview projects
718 and XML based data retrieval clients</li>
719 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
720 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
721 </ul> <em>Documentation</em>
723 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
724 not supported in EPS figure export
726 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
727 </ul> <em>Development and Release Processes</em>
730 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
733 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
735 <!-- JAL-3225 -->Eclipse project configuration managed with
739 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
740 Bamboo continuous integration for unattended Test Suite
744 <!-- JAL-2864 -->Memory test suite to detect leaks in common
748 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
752 <!-- JAL-3248 -->Developer documentation migrated to
753 markdown (with HTML rendering)
756 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
759 <!-- JAL-3289 -->New URLs for publishing development
764 <td align="left" valign="top">
767 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
770 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
771 superposition in Jmol fail on Windows
774 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
775 structures for sequences with lots of PDB structures
778 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
782 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
783 project involving multiple views
786 <!-- JAL-3164 -->Overview for complementary view in a linked
787 CDS/Protein alignment is not updated when Hide Columns by
788 Annotation dialog hides columns
791 <!-- JAL-3158 -->Selection highlighting in the complement of a
792 CDS/Protein alignment stops working after making a selection in
793 one view, then making another selection in the other view
796 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
800 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
801 Settings and Jalview Preferences panels
804 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
805 overview with large alignments
808 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
809 region if columns were selected by dragging right-to-left and the
810 mouse moved to the left of the first column
813 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
814 hidden column marker via scale popup menu
817 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
818 doesn't tell users the invalid URL
821 <!-- JAL-2816 -->Tooltips displayed for features filtered by
825 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
826 show cross references or Fetch Database References are shown in
830 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
831 peptide sequence (computed variant shown as p.Res.null)
834 <!-- JAL-2060 -->'Graduated colour' option not offered for
835 manually created features (where feature score is Float.NaN)
838 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
839 when columns are hidden
842 <!-- JAL-3082 -->Regular expression error for '(' in Select
843 Columns by Annotation description
846 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
847 out of Scale or Annotation Panel
850 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
854 <!-- JAL-3074 -->Left/right drag in annotation can scroll
858 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
862 <!-- JAL-3002 -->Column display is out by one after Page Down,
863 Page Up in wrapped mode
866 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
869 <!-- JAL-2932 -->Finder searches in minimised alignments
872 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
873 on opening an alignment
876 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
880 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
881 different groups in the alignment are selected
884 <!-- JAL-2717 -->Internationalised colour scheme names not shown
888 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
892 <!-- JAL-3125 -->Value input for graduated feature colour
893 threshold gets 'unrounded'
896 <!-- JAL-2982 -->PCA image export doesn't respect background
900 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
903 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
906 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
910 <!-- JAL-2964 -->Associate Tree with All Views not restored from
914 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
915 shown in complementary view
918 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
919 without normalisation
922 <!-- JAL-3021 -->Sequence Details report should open positioned at top
926 <!-- JAL-914 -->Help page can be opened twice
929 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
931 </ul> <em>Editing</em>
934 <!-- JAL-2822 -->Start and End should be updated when sequence
935 data at beginning or end of alignment added/removed via 'Edit'
939 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
940 relocate sequence features correctly when start of sequence is
941 removed (Known defect since 2.10)
944 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
945 dialog corrupts dataset sequence
948 <!-- JAL-868 -->Structure colours not updated when associated tree
949 repartitions the alignment view (Regression in 2.10.5)
951 </ul> <em>Datamodel</em>
954 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
955 sequence's End is greater than its length
957 </ul> <em>Bugs fixed for Java 11 Support (not yet on
958 general release)</em>
961 <!-- JAL-3288 -->Menus work properly in split-screen
963 </ul> <em>New Known Defects</em>
966 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
969 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
970 regions of protein alignment.
973 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
974 is restored from a Jalview 2.11 project
977 <!-- JAL-3213 -->Alignment panel height can be too small after
981 <!-- JAL-3240 -->Display is incorrect after removing gapped
982 columns within hidden columns
985 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
986 window after dragging left to select columns to left of visible
990 <!-- JAL-2876 -->Features coloured according to their description
991 string and thresholded by score in earlier versions of Jalview are
992 not shown as thresholded features in 2.11. To workaround please
993 create a Score filter instead.
996 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
998 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1001 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1002 alignments with multiple views can close views unexpectedly
1005 <em>Java 11 Specific defects</em>
1008 <!-- JAL-3235 -->Jalview Properties file is not sorted
1009 alphabetically when saved
1015 <td width="60" nowrap>
1016 <div align="center">
1017 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1020 <td><div align="left">
1024 <!-- JAL-3101 -->Default memory for Jalview webstart and
1025 InstallAnywhere increased to 1G.
1028 <!-- JAL-247 -->Hidden sequence markers and representative
1029 sequence bolding included when exporting alignment as EPS,
1030 SVG, PNG or HTML. <em>Display is configured via the
1031 Format menu, or for command-line use via a Jalview
1032 properties file.</em>
1035 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1036 API and sequence data now imported as JSON.
1039 <!-- JAL-3065 -->Change in recommended way of starting
1040 Jalview via a Java command line: add jars in lib directory
1041 to CLASSPATH, rather than via the deprecated java.ext.dirs
1045 <em>Development</em>
1048 <!-- JAL-3047 -->Support added to execute test suite
1049 instrumented with <a href="http://openclover.org/">Open
1054 <td><div align="left">
1058 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1059 row shown in Feredoxin Structure alignment view of example
1063 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1064 annotation displayed.
1067 <!-- JAL-3107 -->Group conservation/consensus not shown
1068 for newly created group when 'Apply to all groups'
1072 <!-- JAL-3087 -->Corrupted display when switching to
1073 wrapped mode when sequence panel's vertical scrollbar is
1077 <!-- JAL-3003 -->Alignment is black in exported EPS file
1078 when sequences are selected in exported view.</em>
1081 <!-- JAL-3059 -->Groups with different coloured borders
1082 aren't rendered with correct colour.
1085 <!-- JAL-3092 -->Jalview could hang when importing certain
1086 types of knotted RNA secondary structure.
1089 <!-- JAL-3095 -->Sequence highlight and selection in
1090 trimmed VARNA 2D structure is incorrect for sequences that
1094 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1095 annotation when columns are inserted into an alignment,
1096 and when exporting as Stockholm flatfile.
1099 <!-- JAL-3053 -->Jalview annotation rows containing upper
1100 and lower-case 'E' and 'H' do not automatically get
1101 treated as RNA secondary structure.
1104 <!-- JAL-3106 -->.jvp should be used as default extension
1105 (not .jar) when saving a Jalview project file.
1108 <!-- JAL-3105 -->Mac Users: closing a window correctly
1109 transfers focus to previous window on OSX
1112 <em>Java 10 Issues Resolved</em>
1115 <!-- JAL-2988 -->OSX - Can't save new files via the File
1116 or export menus by typing in a name into the Save dialog
1120 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1121 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1122 'look and feel' which has improved compatibility with the
1123 latest version of OSX.
1130 <td width="60" nowrap>
1131 <div align="center">
1132 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1133 <em>7/06/2018</em></strong>
1136 <td><div align="left">
1140 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1141 annotation retrieved from Uniprot
1144 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1145 onto the Jalview Desktop
1149 <td><div align="left">
1153 <!-- JAL-3017 -->Cannot import features with multiple
1154 variant elements (blocks import of some Uniprot records)
1157 <!-- JAL-2997 -->Clustal files with sequence positions in
1158 right-hand column parsed correctly
1161 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1162 not alignment area in exported graphic
1165 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1166 window has input focus
1169 <!-- JAL-2992 -->Annotation panel set too high when
1170 annotation added to view (Windows)
1173 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1174 network connectivity is poor
1177 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1178 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1179 the currently open URL and links from a page viewed in
1180 Firefox or Chrome on Windows is now fully supported. If
1181 you are using Edge, only links in the page can be
1182 dragged, and with Internet Explorer, only the currently
1183 open URL in the browser can be dropped onto Jalview.</em>
1186 <em>New Known Defects</em>
1188 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1193 <td width="60" nowrap>
1194 <div align="center">
1195 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1198 <td><div align="left">
1202 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1203 for disabling automatic superposition of multiple
1204 structures and open structures in existing views
1207 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1208 ID and annotation area margins can be click-dragged to
1212 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1216 <!-- JAL-2759 -->Improved performance for large alignments
1217 and lots of hidden columns
1220 <!-- JAL-2593 -->Improved performance when rendering lots
1221 of features (particularly when transparency is disabled)
1224 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1225 exchange of Jalview features and Chimera attributes made
1231 <td><div align="left">
1234 <!-- JAL-2899 -->Structure and Overview aren't updated
1235 when Colour By Annotation threshold slider is adjusted
1238 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1239 overlapping alignment panel
1242 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1246 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1247 improved: CDS not handled correctly if transcript has no
1251 <!-- JAL-2321 -->Secondary structure and temperature
1252 factor annotation not added to sequence when local PDB
1253 file associated with it by drag'n'drop or structure
1257 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1258 dialog doesn't import PDB files dropped on an alignment
1261 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1262 scroll bar doesn't work for some CDS/Protein views
1265 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1266 Java 1.8u153 onwards and Java 1.9u4+.
1269 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1270 columns in annotation row
1273 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1274 honored in batch mode
1277 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1278 for structures added to existing Jmol view
1281 <!-- JAL-2223 -->'View Mappings' includes duplicate
1282 entries after importing project with multiple views
1285 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1286 protein sequences via SIFTS from associated PDB entries
1287 with negative residue numbers or missing residues fails
1290 <!-- JAL-2952 -->Exception when shading sequence with negative
1291 Temperature Factor values from annotated PDB files (e.g.
1292 as generated by CONSURF)
1295 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1296 tooltip doesn't include a text description of mutation
1299 <!-- JAL-2922 -->Invert displayed features very slow when
1300 structure and/or overview windows are also shown
1303 <!-- JAL-2954 -->Selecting columns from highlighted regions
1304 very slow for alignments with large numbers of sequences
1307 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1308 with 'StringIndexOutOfBounds'
1311 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1312 platforms running Java 10
1315 <!-- JAL-2960 -->Adding a structure to existing structure
1316 view appears to do nothing because the view is hidden behind the alignment view
1322 <!-- JAL-2926 -->Copy consensus sequence option in applet
1323 should copy the group consensus when popup is opened on it
1329 <!-- JAL-2913 -->Fixed ID width preference is not respected
1332 <em>New Known Defects</em>
1335 <!-- JAL-2973 --> Exceptions occasionally raised when
1336 editing a large alignment and overview is displayed
1339 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1340 repeatedly after a series of edits even when the overview
1341 is no longer reflecting updates
1344 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1345 structures for protein subsequence (if 'Trim Retrieved
1346 Sequences' enabled) or Ensembl isoforms (Workaround in
1347 2.10.4 is to fail back to N&W mapping)
1350 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1351 option gives blank output
1358 <td width="60" nowrap>
1359 <div align="center">
1360 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1363 <td><div align="left">
1364 <ul><li>Updated Certum Codesigning Certificate
1365 (Valid till 30th November 2018)</li></ul></div></td>
1366 <td><div align="left">
1367 <em>Desktop</em><ul>
1369 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1370 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1371 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1372 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1373 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1374 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1375 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1381 <td width="60" nowrap>
1382 <div align="center">
1383 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1386 <td><div align="left">
1390 <!-- JAL-2446 -->Faster and more efficient management and
1391 rendering of sequence features
1394 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1395 429 rate limit request hander
1398 <!-- JAL-2773 -->Structure views don't get updated unless
1399 their colours have changed
1402 <!-- JAL-2495 -->All linked sequences are highlighted for
1403 a structure mousover (Jmol) or selection (Chimera)
1406 <!-- JAL-2790 -->'Cancel' button in progress bar for
1407 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1410 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1411 view from Ensembl locus cross-references
1414 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1418 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1419 feature can be disabled
1422 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1423 PDB easier retrieval of sequences for lists of IDs
1426 <!-- JAL-2758 -->Short names for sequences retrieved from
1432 <li>Groovy interpreter updated to 2.4.12</li>
1433 <li>Example groovy script for generating a matrix of
1434 percent identity scores for current alignment.</li>
1436 <em>Testing and Deployment</em>
1439 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1443 <td><div align="left">
1447 <!-- JAL-2643 -->Pressing tab after updating the colour
1448 threshold text field doesn't trigger an update to the
1452 <!-- JAL-2682 -->Race condition when parsing sequence ID
1456 <!-- JAL-2608 -->Overview windows are also closed when
1457 alignment window is closed
1460 <!-- JAL-2548 -->Export of features doesn't always respect
1464 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1465 takes a long time in Cursor mode
1471 <!-- JAL-2777 -->Structures with whitespace chainCode
1472 cannot be viewed in Chimera
1475 <!-- JAL-2728 -->Protein annotation panel too high in
1479 <!-- JAL-2757 -->Can't edit the query after the server
1480 error warning icon is shown in Uniprot and PDB Free Text
1484 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1487 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1490 <!-- JAL-2739 -->Hidden column marker in last column not
1491 rendered when switching back from Wrapped to normal view
1494 <!-- JAL-2768 -->Annotation display corrupted when
1495 scrolling right in unwapped alignment view
1498 <!-- JAL-2542 -->Existing features on subsequence
1499 incorrectly relocated when full sequence retrieved from
1503 <!-- JAL-2733 -->Last reported memory still shown when
1504 Desktop->Show Memory is unticked (OSX only)
1507 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1508 features of same type and group to be selected for
1512 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1513 alignments when hidden columns are present
1516 <!-- JAL-2392 -->Jalview freezes when loading and
1517 displaying several structures
1520 <!-- JAL-2732 -->Black outlines left after resizing or
1524 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1525 within the Jalview desktop on OSX
1528 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1529 when in wrapped alignment mode
1532 <!-- JAL-2636 -->Scale mark not shown when close to right
1533 hand end of alignment
1536 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1537 each selected sequence do not have correct start/end
1541 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1542 after canceling the Alignment Window's Font dialog
1545 <!-- JAL-2036 -->Show cross-references not enabled after
1546 restoring project until a new view is created
1549 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1550 URL links appears when only default EMBL-EBI link is
1551 configured (since 2.10.2b2)
1554 <!-- JAL-2775 -->Overview redraws whole window when box
1555 position is adjusted
1558 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1559 in a multi-chain structure when viewing alignment
1560 involving more than one chain (since 2.10)
1563 <!-- JAL-2811 -->Double residue highlights in cursor mode
1564 if new selection moves alignment window
1567 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1568 arrow key in cursor mode to pass hidden column marker
1571 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1572 that produces correctly annotated transcripts and products
1575 <!-- JAL-2776 -->Toggling a feature group after first time
1576 doesn't update associated structure view
1579 <em>Applet</em><br />
1582 <!-- JAL-2687 -->Concurrent modification exception when
1583 closing alignment panel
1586 <em>BioJSON</em><br />
1589 <!-- JAL-2546 -->BioJSON export does not preserve
1590 non-positional features
1593 <em>New Known Issues</em>
1596 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1597 sequence features correctly (for many previous versions of
1601 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1602 using cursor in wrapped panel other than top
1605 <!-- JAL-2791 -->Select columns containing feature ignores
1606 graduated colour threshold
1609 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1610 always preserve numbering and sequence features
1613 <em>Known Java 9 Issues</em>
1616 <!-- JAL-2902 -->Groovy Console very slow to open and is
1617 not responsive when entering characters (Webstart, Java
1624 <td width="60" nowrap>
1625 <div align="center">
1626 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1627 <em>2/10/2017</em></strong>
1630 <td><div align="left">
1631 <em>New features in Jalview Desktop</em>
1634 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1636 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1640 <td><div align="left">
1644 <td width="60" nowrap>
1645 <div align="center">
1646 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1647 <em>7/9/2017</em></strong>
1650 <td><div align="left">
1654 <!-- JAL-2588 -->Show gaps in overview window by colouring
1655 in grey (sequences used to be coloured grey, and gaps were
1659 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1663 <!-- JAL-2587 -->Overview updates immediately on increase
1664 in size and progress bar shown as higher resolution
1665 overview is recalculated
1670 <td><div align="left">
1674 <!-- JAL-2664 -->Overview window redraws every hidden
1675 column region row by row
1678 <!-- JAL-2681 -->duplicate protein sequences shown after
1679 retrieving Ensembl crossrefs for sequences from Uniprot
1682 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1683 format setting is unticked
1686 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1687 if group has show boxes format setting unticked
1690 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1691 autoscrolling whilst dragging current selection group to
1692 include sequences and columns not currently displayed
1695 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1696 assemblies are imported via CIF file
1699 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1700 displayed when threshold or conservation colouring is also
1704 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1708 <!-- JAL-2673 -->Jalview continues to scroll after
1709 dragging a selected region off the visible region of the
1713 <!-- JAL-2724 -->Cannot apply annotation based
1714 colourscheme to all groups in a view
1717 <!-- JAL-2511 -->IDs don't line up with sequences
1718 initially after font size change using the Font chooser or
1725 <td width="60" nowrap>
1726 <div align="center">
1727 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1730 <td><div align="left">
1731 <em>Calculations</em>
1735 <!-- JAL-1933 -->Occupancy annotation row shows number of
1736 ungapped positions in each column of the alignment.
1739 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1740 a calculation dialog box
1743 <!-- JAL-2379 -->Revised implementation of PCA for speed
1744 and memory efficiency (~30x faster)
1747 <!-- JAL-2403 -->Revised implementation of sequence
1748 similarity scores as used by Tree, PCA, Shading Consensus
1749 and other calculations
1752 <!-- JAL-2416 -->Score matrices are stored as resource
1753 files within the Jalview codebase
1756 <!-- JAL-2500 -->Trees computed on Sequence Feature
1757 Similarity may have different topology due to increased
1764 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1765 model for alignments and groups
1768 <!-- JAL-384 -->Custom shading schemes created via groovy
1775 <!-- JAL-2526 -->Efficiency improvements for interacting
1776 with alignment and overview windows
1779 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1783 <!-- JAL-2388 -->Hidden columns and sequences can be
1787 <!-- JAL-2611 -->Click-drag in visible area allows fine
1788 adjustment of visible position
1792 <em>Data import/export</em>
1795 <!-- JAL-2535 -->Posterior probability annotation from
1796 Stockholm files imported as sequence associated annotation
1799 <!-- JAL-2507 -->More robust per-sequence positional
1800 annotation input/output via stockholm flatfile
1803 <!-- JAL-2533 -->Sequence names don't include file
1804 extension when importing structure files without embedded
1805 names or PDB accessions
1808 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1809 format sequence substitution matrices
1812 <em>User Interface</em>
1815 <!-- JAL-2447 --> Experimental Features Checkbox in
1816 Desktop's Tools menu to hide or show untested features in
1820 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1821 via Overview or sequence motif search operations
1824 <!-- JAL-2547 -->Amend sequence features dialog box can be
1825 opened by double clicking gaps within sequence feature
1829 <!-- JAL-1476 -->Status bar message shown when not enough
1830 aligned positions were available to create a 3D structure
1834 <em>3D Structure</em>
1837 <!-- JAL-2430 -->Hidden regions in alignment views are not
1838 coloured in linked structure views
1841 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1842 file-based command exchange
1845 <!-- JAL-2375 -->Structure chooser automatically shows
1846 Cached Structures rather than querying the PDBe if
1847 structures are already available for sequences
1850 <!-- JAL-2520 -->Structures imported via URL are cached in
1851 the Jalview project rather than downloaded again when the
1852 project is reopened.
1855 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1856 to transfer Chimera's structure attributes as Jalview
1857 features, and vice-versa (<strong>Experimental
1861 <em>Web Services</em>
1864 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1867 <!-- JAL-2335 -->Filter non-standard amino acids and
1868 nucleotides when submitting to AACon and other MSA
1872 <!-- JAL-2316, -->URLs for viewing database
1873 cross-references provided by identifiers.org and the
1874 EMBL-EBI's MIRIAM DB
1881 <!-- JAL-2344 -->FileFormatI interface for describing and
1882 identifying file formats (instead of String constants)
1885 <!-- JAL-2228 -->FeatureCounter script refactored for
1886 efficiency when counting all displayed features (not
1887 backwards compatible with 2.10.1)
1890 <em>Example files</em>
1893 <!-- JAL-2631 -->Graduated feature colour style example
1894 included in the example feature file
1897 <em>Documentation</em>
1900 <!-- JAL-2339 -->Release notes reformatted for readability
1901 with the built-in Java help viewer
1904 <!-- JAL-1644 -->Find documentation updated with 'search
1905 sequence description' option
1911 <!-- JAL-2485, -->External service integration tests for
1912 Uniprot REST Free Text Search Client
1915 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1918 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1923 <td><div align="left">
1924 <em>Calculations</em>
1927 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1928 matrix - C->R should be '-3'<br />Old matrix restored
1929 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1931 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1932 Jalview's treatment of gaps in PCA and substitution matrix
1933 based Tree calculations.<br /> <br />In earlier versions
1934 of Jalview, gaps matching gaps were penalised, and gaps
1935 matching non-gaps penalised even more. In the PCA
1936 calculation, gaps were actually treated as non-gaps - so
1937 different costs were applied, which meant Jalview's PCAs
1938 were different to those produced by SeqSpace.<br />Jalview
1939 now treats gaps in the same way as SeqSpace (ie it scores
1940 them as 0). <br /> <br />Enter the following in the
1941 Groovy console to restore pre-2.10.2 behaviour:<br />
1942 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1943 // for 2.10.1 mode <br />
1944 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1945 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1946 these settings will affect all subsequent tree and PCA
1947 calculations (not recommended)</em></li>
1949 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1950 scaling of branch lengths for trees computed using
1951 Sequence Feature Similarity.
1954 <!-- JAL-2377 -->PCA calculation could hang when
1955 generating output report when working with highly
1956 redundant alignments
1959 <!-- JAL-2544 --> Sort by features includes features to
1960 right of selected region when gaps present on right-hand
1964 <em>User Interface</em>
1967 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1968 doesn't reselect a specific sequence's associated
1969 annotation after it was used for colouring a view
1972 <!-- JAL-2419 -->Current selection lost if popup menu
1973 opened on a region of alignment without groups
1976 <!-- JAL-2374 -->Popup menu not always shown for regions
1977 of an alignment with overlapping groups
1980 <!-- JAL-2310 -->Finder double counts if both a sequence's
1981 name and description match
1984 <!-- JAL-2370 -->Hiding column selection containing two
1985 hidden regions results in incorrect hidden regions
1988 <!-- JAL-2386 -->'Apply to all groups' setting when
1989 changing colour does not apply Conservation slider value
1993 <!-- JAL-2373 -->Percentage identity and conservation menu
1994 items do not show a tick or allow shading to be disabled
1997 <!-- JAL-2385 -->Conservation shading or PID threshold
1998 lost when base colourscheme changed if slider not visible
2001 <!-- JAL-2547 -->Sequence features shown in tooltip for
2002 gaps before start of features
2005 <!-- JAL-2623 -->Graduated feature colour threshold not
2006 restored to UI when feature colour is edited
2009 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2010 a time when scrolling vertically in wrapped mode.
2013 <!-- JAL-2630 -->Structure and alignment overview update
2014 as graduate feature colour settings are modified via the
2018 <!-- JAL-2034 -->Overview window doesn't always update
2019 when a group defined on the alignment is resized
2022 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2023 wrapped view result in positional status updates
2027 <!-- JAL-2563 -->Status bar doesn't show position for
2028 ambiguous amino acid and nucleotide symbols
2031 <!-- JAL-2602 -->Copy consensus sequence failed if
2032 alignment included gapped columns
2035 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2036 widgets don't permanently disappear
2039 <!-- JAL-2503 -->Cannot select or filter quantitative
2040 annotation that are shown only as column labels (e.g.
2041 T-Coffee column reliability scores)
2044 <!-- JAL-2594 -->Exception thrown if trying to create a
2045 sequence feature on gaps only
2048 <!-- JAL-2504 -->Features created with 'New feature'
2049 button from a Find inherit previously defined feature type
2050 rather than the Find query string
2053 <!-- JAL-2423 -->incorrect title in output window when
2054 exporting tree calculated in Jalview
2057 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2058 and then revealing them reorders sequences on the
2062 <!-- JAL-964 -->Group panel in sequence feature settings
2063 doesn't update to reflect available set of groups after
2064 interactively adding or modifying features
2067 <!-- JAL-2225 -->Sequence Database chooser unusable on
2071 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2072 only excluded gaps in current sequence and ignored
2079 <!-- JAL-2421 -->Overview window visible region moves
2080 erratically when hidden rows or columns are present
2083 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2084 Structure Viewer's colour menu don't correspond to
2088 <!-- JAL-2405 -->Protein specific colours only offered in
2089 colour and group colour menu for protein alignments
2092 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2093 reflect currently selected view or group's shading
2097 <!-- JAL-2624 -->Feature colour thresholds not respected
2098 when rendered on overview and structures when opacity at
2102 <!-- JAL-2589 -->User defined gap colour not shown in
2103 overview when features overlaid on alignment
2106 <!-- JAL-2567 -->Feature settings for different views not
2107 recovered correctly from Jalview project file
2110 <!-- JAL-2256 -->Feature colours in overview when first opened
2111 (automatically via preferences) are different to the main
2115 <em>Data import/export</em>
2118 <!-- JAL-2576 -->Very large alignments take a long time to
2122 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2123 added after a sequence was imported are not written to
2127 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2128 when importing RNA secondary structure via Stockholm
2131 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2132 not shown in correct direction for simple pseudoknots
2135 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2136 with lightGray or darkGray via features file (but can
2140 <!-- JAL-2383 -->Above PID colour threshold not recovered
2141 when alignment view imported from project
2144 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2145 structure and sequences extracted from structure files
2146 imported via URL and viewed in Jmol
2149 <!-- JAL-2520 -->Structures loaded via URL are saved in
2150 Jalview Projects rather than fetched via URL again when
2151 the project is loaded and the structure viewed
2154 <em>Web Services</em>
2157 <!-- JAL-2519 -->EnsemblGenomes example failing after
2158 release of Ensembl v.88
2161 <!-- JAL-2366 -->Proxy server address and port always
2162 appear enabled in Preferences->Connections
2165 <!-- JAL-2461 -->DAS registry not found exceptions
2166 removed from console output
2169 <!-- JAL-2582 -->Cannot retrieve protein products from
2170 Ensembl by Peptide ID
2173 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2174 created from SIFTs, and spurious 'Couldn't open structure
2175 in Chimera' errors raised after April 2017 update (problem
2176 due to 'null' string rather than empty string used for
2177 residues with no corresponding PDB mapping).
2180 <em>Application UI</em>
2183 <!-- JAL-2361 -->User Defined Colours not added to Colour
2187 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2188 case' residues (button in colourscheme editor debugged and
2189 new documentation and tooltips added)
2192 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2193 doesn't restore group-specific text colour thresholds
2196 <!-- JAL-2243 -->Feature settings panel does not update as
2197 new features are added to alignment
2200 <!-- JAL-2532 -->Cancel in feature settings reverts
2201 changes to feature colours via the Amend features dialog
2204 <!-- JAL-2506 -->Null pointer exception when attempting to
2205 edit graduated feature colour via amend features dialog
2209 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2210 selection menu changes colours of alignment views
2213 <!-- JAL-2426 -->Spurious exceptions in console raised
2214 from alignment calculation workers after alignment has
2218 <!-- JAL-1608 -->Typo in selection popup menu - Create
2219 groups now 'Create Group'
2222 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2223 Create/Undefine group doesn't always work
2226 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2227 shown again after pressing 'Cancel'
2230 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2231 adjusts start position in wrap mode
2234 <!-- JAL-2563 -->Status bar doesn't show positions for
2235 ambiguous amino acids
2238 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2239 CDS/Protein view after CDS sequences added for aligned
2243 <!-- JAL-2592 -->User defined colourschemes called 'User
2244 Defined' don't appear in Colours menu
2250 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2251 score models doesn't always result in an updated PCA plot
2254 <!-- JAL-2442 -->Features not rendered as transparent on
2255 overview or linked structure view
2258 <!-- JAL-2372 -->Colour group by conservation doesn't
2262 <!-- JAL-2517 -->Hitting Cancel after applying
2263 user-defined colourscheme doesn't restore original
2270 <!-- JAL-2314 -->Unit test failure:
2271 jalview.ws.jabaws.RNAStructExportImport setup fails
2274 <!-- JAL-2307 -->Unit test failure:
2275 jalview.ws.sifts.SiftsClientTest due to compatibility
2276 problems with deep array comparison equality asserts in
2277 successive versions of TestNG
2280 <!-- JAL-2479 -->Relocated StructureChooserTest and
2281 ParameterUtilsTest Unit tests to Network suite
2284 <em>New Known Issues</em>
2287 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2288 phase after a sequence motif find operation
2291 <!-- JAL-2550 -->Importing annotation file with rows
2292 containing just upper and lower case letters are
2293 interpreted as WUSS RNA secondary structure symbols
2296 <!-- JAL-2590 -->Cannot load and display Newick trees
2297 reliably from eggnog Ortholog database
2300 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2301 containing features of type Highlight' when 'B' is pressed
2302 to mark columns containing highlighted regions.
2305 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2306 doesn't always add secondary structure annotation.
2311 <td width="60" nowrap>
2312 <div align="center">
2313 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2316 <td><div align="left">
2320 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2321 for all consensus calculations
2324 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2327 <li>Updated Jalview's Certum code signing certificate
2330 <em>Application</em>
2333 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2334 set of database cross-references, sorted alphabetically
2337 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2338 from database cross references. Users with custom links
2339 will receive a <a href="webServices/urllinks.html#warning">warning
2340 dialog</a> asking them to update their preferences.
2343 <!-- JAL-2287-->Cancel button and escape listener on
2344 dialog warning user about disconnecting Jalview from a
2348 <!-- JAL-2320-->Jalview's Chimera control window closes if
2349 the Chimera it is connected to is shut down
2352 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2353 columns menu item to mark columns containing highlighted
2354 regions (e.g. from structure selections or results of a
2358 <!-- JAL-2284-->Command line option for batch-generation
2359 of HTML pages rendering alignment data with the BioJS
2369 <!-- JAL-2286 -->Columns with more than one modal residue
2370 are not coloured or thresholded according to percent
2371 identity (first observed in Jalview 2.8.2)
2374 <!-- JAL-2301 -->Threonine incorrectly reported as not
2378 <!-- JAL-2318 -->Updates to documentation pages (above PID
2379 threshold, amino acid properties)
2382 <!-- JAL-2292 -->Lower case residues in sequences are not
2383 reported as mapped to residues in a structure file in the
2387 <!--JAL-2324 -->Identical features with non-numeric scores
2388 could be added multiple times to a sequence
2391 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2392 bond features shown as two highlighted residues rather
2393 than a range in linked structure views, and treated
2394 correctly when selecting and computing trees from features
2397 <!-- JAL-2281-->Custom URL links for database
2398 cross-references are matched to database name regardless
2403 <em>Application</em>
2406 <!-- JAL-2282-->Custom URL links for specific database
2407 names without regular expressions also offer links from
2411 <!-- JAL-2315-->Removing a single configured link in the
2412 URL links pane in Connections preferences doesn't actually
2413 update Jalview configuration
2416 <!-- JAL-2272-->CTRL-Click on a selected region to open
2417 the alignment area popup menu doesn't work on El-Capitan
2420 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2421 files with similarly named sequences if dropped onto the
2425 <!-- JAL-2312 -->Additional mappings are shown for PDB
2426 entries where more chains exist in the PDB accession than
2427 are reported in the SIFTS file
2430 <!-- JAL-2317-->Certain structures do not get mapped to
2431 the structure view when displayed with Chimera
2434 <!-- JAL-2317-->No chains shown in the Chimera view
2435 panel's View->Show Chains submenu
2438 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2439 work for wrapped alignment views
2442 <!--JAL-2197 -->Rename UI components for running JPred
2443 predictions from 'JNet' to 'JPred'
2446 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2447 corrupted when annotation panel vertical scroll is not at
2448 first annotation row
2451 <!--JAL-2332 -->Attempting to view structure for Hen
2452 lysozyme results in a PDB Client error dialog box
2455 <!-- JAL-2319 -->Structure View's mapping report switched
2456 ranges for PDB and sequence for SIFTS
2459 SIFTS 'Not_Observed' residues mapped to non-existant
2463 <!-- <em>New Known Issues</em>
2470 <td width="60" nowrap>
2471 <div align="center">
2472 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2473 <em>25/10/2016</em></strong>
2476 <td><em>Application</em>
2478 <li>3D Structure chooser opens with 'Cached structures'
2479 view if structures already loaded</li>
2480 <li>Progress bar reports models as they are loaded to
2481 structure views</li>
2487 <li>Colour by conservation always enabled and no tick
2488 shown in menu when BLOSUM or PID shading applied</li>
2489 <li>FER1_ARATH and FER2_ARATH labels were switched in
2490 example sequences/projects/trees</li>
2492 <em>Application</em>
2494 <li>Jalview projects with views of local PDB structure
2495 files saved on Windows cannot be opened on OSX</li>
2496 <li>Multiple structure views can be opened and superposed
2497 without timeout for structures with multiple models or
2498 multiple sequences in alignment</li>
2499 <li>Cannot import or associated local PDB files without a
2500 PDB ID HEADER line</li>
2501 <li>RMSD is not output in Jmol console when superposition
2503 <li>Drag and drop of URL from Browser fails for Linux and
2504 OSX versions earlier than El Capitan</li>
2505 <li>ENA client ignores invalid content from ENA server</li>
2506 <li>Exceptions are not raised in console when ENA client
2507 attempts to fetch non-existent IDs via Fetch DB Refs UI
2509 <li>Exceptions are not raised in console when a new view
2510 is created on the alignment</li>
2511 <li>OSX right-click fixed for group selections: CMD-click
2512 to insert/remove gaps in groups and CTRL-click to open group
2515 <em>Build and deployment</em>
2517 <li>URL link checker now copes with multi-line anchor
2520 <em>New Known Issues</em>
2522 <li>Drag and drop from URL links in browsers do not work
2529 <td width="60" nowrap>
2530 <div align="center">
2531 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2534 <td><em>General</em>
2537 <!-- JAL-2124 -->Updated Spanish translations.
2540 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2541 for importing structure data to Jalview. Enables mmCIF and
2545 <!-- JAL-192 --->Alignment ruler shows positions relative to
2549 <!-- JAL-2202 -->Position/residue shown in status bar when
2550 mousing over sequence associated annotation
2553 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2557 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2558 '()', canonical '[]' and invalid '{}' base pair populations
2562 <!-- JAL-2092 -->Feature settings popup menu options for
2563 showing or hiding columns containing a feature
2566 <!-- JAL-1557 -->Edit selected group by double clicking on
2567 group and sequence associated annotation labels
2570 <!-- JAL-2236 -->Sequence name added to annotation label in
2571 select/hide columns by annotation and colour by annotation
2575 </ul> <em>Application</em>
2578 <!-- JAL-2050-->Automatically hide introns when opening a
2579 gene/transcript view
2582 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2586 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2587 structure mappings with the EMBL-EBI PDBe SIFTS database
2590 <!-- JAL-2079 -->Updated download sites used for Rfam and
2591 Pfam sources to xfam.org
2594 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2597 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2598 over sequences in Jalview
2601 <!-- JAL-2027-->Support for reverse-complement coding
2602 regions in ENA and EMBL
2605 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2606 for record retrieval via ENA rest API
2609 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2613 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2614 groovy script execution
2617 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2618 alignment window's Calculate menu
2621 <!-- JAL-1812 -->Allow groovy scripts that call
2622 Jalview.getAlignFrames() to run in headless mode
2625 <!-- JAL-2068 -->Support for creating new alignment
2626 calculation workers from groovy scripts
2629 <!-- JAL-1369 --->Store/restore reference sequence in
2633 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2634 associations are now saved/restored from project
2637 <!-- JAL-1993 -->Database selection dialog always shown
2638 before sequence fetcher is opened
2641 <!-- JAL-2183 -->Double click on an entry in Jalview's
2642 database chooser opens a sequence fetcher
2645 <!-- JAL-1563 -->Free-text search client for UniProt using
2646 the UniProt REST API
2649 <!-- JAL-2168 -->-nonews command line parameter to prevent
2650 the news reader opening
2653 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2654 querying stored in preferences
2657 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2661 <!-- JAL-1977-->Tooltips shown on database chooser
2664 <!-- JAL-391 -->Reverse complement function in calculate
2665 menu for nucleotide sequences
2668 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2669 and feature counts preserves alignment ordering (and
2670 debugged for complex feature sets).
2673 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2674 viewing structures with Jalview 2.10
2677 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2678 genome, transcript CCDS and gene ids via the Ensembl and
2679 Ensembl Genomes REST API
2682 <!-- JAL-2049 -->Protein sequence variant annotation
2683 computed for 'sequence_variant' annotation on CDS regions
2687 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2691 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2692 Ref Fetcher fails to match, or otherwise updates sequence
2693 data from external database records.
2696 <!-- JAL-2154 -->Revised Jalview Project format for
2697 efficient recovery of sequence coding and alignment
2698 annotation relationships.
2700 </ul> <!-- <em>Applet</em>
2711 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2715 <!-- JAL-2018-->Export features in Jalview format (again)
2716 includes graduated colourschemes
2719 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2720 working with big alignments and lots of hidden columns
2723 <!-- JAL-2053-->Hidden column markers not always rendered
2724 at right of alignment window
2727 <!-- JAL-2067 -->Tidied up links in help file table of
2731 <!-- JAL-2072 -->Feature based tree calculation not shown
2735 <!-- JAL-2075 -->Hidden columns ignored during feature
2736 based tree calculation
2739 <!-- JAL-2065 -->Alignment view stops updating when show
2740 unconserved enabled for group on alignment
2743 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2747 <!-- JAL-2146 -->Alignment column in status incorrectly
2748 shown as "Sequence position" when mousing over
2752 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2753 hidden columns present
2756 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2757 user created annotation added to alignment
2760 <!-- JAL-1841 -->RNA Structure consensus only computed for
2761 '()' base pair annotation
2764 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2765 in zero scores for all base pairs in RNA Structure
2769 <!-- JAL-2174-->Extend selection with columns containing
2773 <!-- JAL-2275 -->Pfam format writer puts extra space at
2774 beginning of sequence
2777 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2781 <!-- JAL-2238 -->Cannot create groups on an alignment from
2782 from a tree when t-coffee scores are shown
2785 <!-- JAL-1836,1967 -->Cannot import and view PDB
2786 structures with chains containing negative resnums (4q4h)
2789 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2793 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2794 to Clustal, PIR and PileUp output
2797 <!-- JAL-2008 -->Reordering sequence features that are
2798 not visible causes alignment window to repaint
2801 <!-- JAL-2006 -->Threshold sliders don't work in
2802 graduated colour and colour by annotation row for e-value
2803 scores associated with features and annotation rows
2806 <!-- JAL-1797 -->amino acid physicochemical conservation
2807 calculation should be case independent
2810 <!-- JAL-2173 -->Remove annotation also updates hidden
2814 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2815 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2816 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2819 <!-- JAL-2065 -->Null pointer exceptions and redraw
2820 problems when reference sequence defined and 'show
2821 non-conserved' enabled
2824 <!-- JAL-1306 -->Quality and Conservation are now shown on
2825 load even when Consensus calculation is disabled
2828 <!-- JAL-1932 -->Remove right on penultimate column of
2829 alignment does nothing
2832 <em>Application</em>
2835 <!-- JAL-1552-->URLs and links can't be imported by
2836 drag'n'drop on OSX when launched via webstart (note - not
2837 yet fixed for El Capitan)
2840 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2841 output when running on non-gb/us i18n platforms
2844 <!-- JAL-1944 -->Error thrown when exporting a view with
2845 hidden sequences as flat-file alignment
2848 <!-- JAL-2030-->InstallAnywhere distribution fails when
2852 <!-- JAL-2080-->Jalview very slow to launch via webstart
2853 (also hotfix for 2.9.0b2)
2856 <!-- JAL-2085 -->Cannot save project when view has a
2857 reference sequence defined
2860 <!-- JAL-1011 -->Columns are suddenly selected in other
2861 alignments and views when revealing hidden columns
2864 <!-- JAL-1989 -->Hide columns not mirrored in complement
2865 view in a cDNA/Protein splitframe
2868 <!-- JAL-1369 -->Cannot save/restore representative
2869 sequence from project when only one sequence is
2873 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2874 in Structure Chooser
2877 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2878 structure consensus didn't refresh annotation panel
2881 <!-- JAL-1962 -->View mapping in structure view shows
2882 mappings between sequence and all chains in a PDB file
2885 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2886 dialogs format columns correctly, don't display array
2887 data, sort columns according to type
2890 <!-- JAL-1975 -->Export complete shown after destination
2891 file chooser is cancelled during an image export
2894 <!-- JAL-2025 -->Error when querying PDB Service with
2895 sequence name containing special characters
2898 <!-- JAL-2024 -->Manual PDB structure querying should be
2902 <!-- JAL-2104 -->Large tooltips with broken HTML
2903 formatting don't wrap
2906 <!-- JAL-1128 -->Figures exported from wrapped view are
2907 truncated so L looks like I in consensus annotation
2910 <!-- JAL-2003 -->Export features should only export the
2911 currently displayed features for the current selection or
2915 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2916 after fetching cross-references, and restoring from
2920 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2921 followed in the structure viewer
2924 <!-- JAL-2163 -->Titles for individual alignments in
2925 splitframe not restored from project
2928 <!-- JAL-2145 -->missing autocalculated annotation at
2929 trailing end of protein alignment in transcript/product
2930 splitview when pad-gaps not enabled by default
2933 <!-- JAL-1797 -->amino acid physicochemical conservation
2937 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2938 article has been read (reopened issue due to
2939 internationalisation problems)
2942 <!-- JAL-1960 -->Only offer PDB structures in structure
2943 viewer based on sequence name, PDB and UniProt
2948 <!-- JAL-1976 -->No progress bar shown during export of
2952 <!-- JAL-2213 -->Structures not always superimposed after
2953 multiple structures are shown for one or more sequences.
2956 <!-- JAL-1370 -->Reference sequence characters should not
2957 be replaced with '.' when 'Show unconserved' format option
2961 <!-- JAL-1823 -->Cannot specify chain code when entering
2962 specific PDB id for sequence
2965 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2966 'Export hidden sequences' is enabled, but 'export hidden
2967 columns' is disabled.
2970 <!--JAL-2026-->Best Quality option in structure chooser
2971 selects lowest rather than highest resolution structures
2975 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2976 to sequence mapping in 'View Mappings' report
2979 <!-- JAL-2284 -->Unable to read old Jalview projects that
2980 contain non-XML data added after Jalvew wrote project.
2983 <!-- JAL-2118 -->Newly created annotation row reorders
2984 after clicking on it to create new annotation for a
2988 <!-- JAL-1980 -->Null Pointer Exception raised when
2989 pressing Add on an orphaned cut'n'paste window.
2991 <!-- may exclude, this is an external service stability issue JAL-1941
2992 -- > RNA 3D structure not added via DSSR service</li> -->
2997 <!-- JAL-2151 -->Incorrect columns are selected when
2998 hidden columns present before start of sequence
3001 <!-- JAL-1986 -->Missing dependencies on applet pages
3005 <!-- JAL-1947 -->Overview pixel size changes when
3006 sequences are hidden in applet
3009 <!-- JAL-1996 -->Updated instructions for applet
3010 deployment on examples pages.
3017 <td width="60" nowrap>
3018 <div align="center">
3019 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3020 <em>16/10/2015</em></strong>
3023 <td><em>General</em>
3025 <li>Time stamps for signed Jalview application and applet
3030 <em>Application</em>
3032 <li>Duplicate group consensus and conservation rows
3033 shown when tree is partitioned</li>
3034 <li>Erratic behaviour when tree partitions made with
3035 multiple cDNA/Protein split views</li>
3041 <td width="60" nowrap>
3042 <div align="center">
3043 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3044 <em>8/10/2015</em></strong>
3047 <td><em>General</em>
3049 <li>Updated Spanish translations of localized text for
3051 </ul> <em>Application</em>
3053 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3054 <li>Signed OSX InstallAnywhere installer<br></li>
3055 <li>Support for per-sequence based annotations in BioJSON</li>
3056 </ul> <em>Applet</em>
3058 <li>Split frame example added to applet examples page</li>
3059 </ul> <em>Build and Deployment</em>
3062 <!-- JAL-1888 -->New ant target for running Jalview's test
3070 <li>Mapping of cDNA to protein in split frames
3071 incorrect when sequence start > 1</li>
3072 <li>Broken images in filter column by annotation dialog
3074 <li>Feature colours not parsed from features file</li>
3075 <li>Exceptions and incomplete link URLs recovered when
3076 loading a features file containing HTML tags in feature
3080 <em>Application</em>
3082 <li>Annotations corrupted after BioJS export and
3084 <li>Incorrect sequence limits after Fetch DB References
3085 with 'trim retrieved sequences'</li>
3086 <li>Incorrect warning about deleting all data when
3087 deleting selected columns</li>
3088 <li>Patch to build system for shipping properly signed
3089 JNLP templates for webstart launch</li>
3090 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3091 unreleased structures for download or viewing</li>
3092 <li>Tab/space/return keystroke operation of EMBL-PDBe
3093 fetcher/viewer dialogs works correctly</li>
3094 <li>Disabled 'minimise' button on Jalview windows
3095 running on OSX to workaround redraw hang bug</li>
3096 <li>Split cDNA/Protein view position and geometry not
3097 recovered from jalview project</li>
3098 <li>Initial enabled/disabled state of annotation menu
3099 sorter 'show autocalculated first/last' corresponds to
3101 <li>Restoring of Clustal, RNA Helices and T-Coffee
3102 color schemes from BioJSON</li>
3106 <li>Reorder sequences mirrored in cDNA/Protein split
3108 <li>Applet with Jmol examples not loading correctly</li>
3114 <td><div align="center">
3115 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3117 <td><em>General</em>
3119 <li>Linked visualisation and analysis of DNA and Protein
3122 <li>Translated cDNA alignments shown as split protein
3123 and DNA alignment views</li>
3124 <li>Codon consensus annotation for linked protein and
3125 cDNA alignment views</li>
3126 <li>Link cDNA or Protein product sequences by loading
3127 them onto Protein or cDNA alignments</li>
3128 <li>Reconstruct linked cDNA alignment from aligned
3129 protein sequences</li>
3132 <li>Jmol integration updated to Jmol v14.2.14</li>
3133 <li>Import and export of Jalview alignment views as <a
3134 href="features/bioJsonFormat.html">BioJSON</a></li>
3135 <li>New alignment annotation file statements for
3136 reference sequences and marking hidden columns</li>
3137 <li>Reference sequence based alignment shading to
3138 highlight variation</li>
3139 <li>Select or hide columns according to alignment
3141 <li>Find option for locating sequences by description</li>
3142 <li>Conserved physicochemical properties shown in amino
3143 acid conservation row</li>
3144 <li>Alignments can be sorted by number of RNA helices</li>
3145 </ul> <em>Application</em>
3147 <li>New cDNA/Protein analysis capabilities
3149 <li>Get Cross-References should open a Split Frame
3150 view with cDNA/Protein</li>
3151 <li>Detect when nucleotide sequences and protein
3152 sequences are placed in the same alignment</li>
3153 <li>Split cDNA/Protein views are saved in Jalview
3158 <li>Use REST API to talk to Chimera</li>
3159 <li>Selected regions in Chimera are highlighted in linked
3160 Jalview windows</li>
3162 <li>VARNA RNA viewer updated to v3.93</li>
3163 <li>VARNA views are saved in Jalview Projects</li>
3164 <li>Pseudoknots displayed as Jalview RNA annotation can
3165 be shown in VARNA</li>
3167 <li>Make groups for selection uses marked columns as well
3168 as the active selected region</li>
3170 <li>Calculate UPGMA and NJ trees using sequence feature
3172 <li>New Export options
3174 <li>New Export Settings dialog to control hidden
3175 region export in flat file generation</li>
3177 <li>Export alignment views for display with the <a
3178 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3180 <li>Export scrollable SVG in HTML page</li>
3181 <li>Optional embedding of BioJSON data when exporting
3182 alignment figures to HTML</li>
3184 <li>3D structure retrieval and display
3186 <li>Free text and structured queries with the PDBe
3188 <li>PDBe Search API based discovery and selection of
3189 PDB structures for a sequence set</li>
3193 <li>JPred4 employed for protein secondary structure
3195 <li>Hide Insertions menu option to hide unaligned columns
3196 for one or a group of sequences</li>
3197 <li>Automatically hide insertions in alignments imported
3198 from the JPred4 web server</li>
3199 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3200 system on OSX<br />LGPL libraries courtesy of <a
3201 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3203 <li>changed 'View nucleotide structure' submenu to 'View
3204 VARNA 2D Structure'</li>
3205 <li>change "View protein structure" menu option to "3D
3208 </ul> <em>Applet</em>
3210 <li>New layout for applet example pages</li>
3211 <li>New parameters to enable SplitFrame view
3212 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3213 <li>New example demonstrating linked viewing of cDNA and
3214 Protein alignments</li>
3215 </ul> <em>Development and deployment</em>
3217 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3218 <li>Include installation type and git revision in build
3219 properties and console log output</li>
3220 <li>Jalview Github organisation, and new github site for
3221 storing BioJsMSA Templates</li>
3222 <li>Jalview's unit tests now managed with TestNG</li>
3225 <!-- <em>General</em>
3227 </ul> --> <!-- issues resolved --> <em>Application</em>
3229 <li>Escape should close any open find dialogs</li>
3230 <li>Typo in select-by-features status report</li>
3231 <li>Consensus RNA secondary secondary structure
3232 predictions are not highlighted in amber</li>
3233 <li>Missing gap character in v2.7 example file means
3234 alignment appears unaligned when pad-gaps is not enabled</li>
3235 <li>First switch to RNA Helices colouring doesn't colour
3236 associated structure views</li>
3237 <li>ID width preference option is greyed out when auto
3238 width checkbox not enabled</li>
3239 <li>Stopped a warning dialog from being shown when
3240 creating user defined colours</li>
3241 <li>'View Mapping' in structure viewer shows sequence
3242 mappings for just that viewer's sequences</li>
3243 <li>Workaround for superposing PDB files containing
3244 multiple models in Chimera</li>
3245 <li>Report sequence position in status bar when hovering
3246 over Jmol structure</li>
3247 <li>Cannot output gaps as '.' symbols with Selection ->
3248 output to text box</li>
3249 <li>Flat file exports of alignments with hidden columns
3250 have incorrect sequence start/end</li>
3251 <li>'Aligning' a second chain to a Chimera structure from
3253 <li>Colour schemes applied to structure viewers don't
3254 work for nucleotide</li>
3255 <li>Loading/cut'n'pasting an empty or invalid file leads
3256 to a grey/invisible alignment window</li>
3257 <li>Exported Jpred annotation from a sequence region
3258 imports to different position</li>
3259 <li>Space at beginning of sequence feature tooltips shown
3260 on some platforms</li>
3261 <li>Chimera viewer 'View | Show Chain' menu is not
3263 <li>'New View' fails with a Null Pointer Exception in
3264 console if Chimera has been opened</li>
3265 <li>Mouseover to Chimera not working</li>
3266 <li>Miscellaneous ENA XML feature qualifiers not
3268 <li>NPE in annotation renderer after 'Extract Scores'</li>
3269 <li>If two structures in one Chimera window, mouseover of
3270 either sequence shows on first structure</li>
3271 <li>'Show annotations' options should not make
3272 non-positional annotations visible</li>
3273 <li>Subsequence secondary structure annotation not shown
3274 in right place after 'view flanking regions'</li>
3275 <li>File Save As type unset when current file format is
3277 <li>Save as '.jar' option removed for saving Jalview
3279 <li>Colour by Sequence colouring in Chimera more
3281 <li>Cannot 'add reference annotation' for a sequence in
3282 several views on same alignment</li>
3283 <li>Cannot show linked products for EMBL / ENA records</li>
3284 <li>Jalview's tooltip wraps long texts containing no
3286 </ul> <em>Applet</em>
3288 <li>Jmol to JalviewLite mouseover/link not working</li>
3289 <li>JalviewLite can't import sequences with ID
3290 descriptions containing angle brackets</li>
3291 </ul> <em>General</em>
3293 <li>Cannot export and reimport RNA secondary structure
3294 via jalview annotation file</li>
3295 <li>Random helix colour palette for colour by annotation
3296 with RNA secondary structure</li>
3297 <li>Mouseover to cDNA from STOP residue in protein
3298 translation doesn't work.</li>
3299 <li>hints when using the select by annotation dialog box</li>
3300 <li>Jmol alignment incorrect if PDB file has alternate CA
3302 <li>FontChooser message dialog appears to hang after
3303 choosing 1pt font</li>
3304 <li>Peptide secondary structure incorrectly imported from
3305 annotation file when annotation display text includes 'e' or
3307 <li>Cannot set colour of new feature type whilst creating
3309 <li>cDNA translation alignment should not be sequence
3310 order dependent</li>
3311 <li>'Show unconserved' doesn't work for lower case
3313 <li>Nucleotide ambiguity codes involving R not recognised</li>
3314 </ul> <em>Deployment and Documentation</em>
3316 <li>Applet example pages appear different to the rest of
3317 www.jalview.org</li>
3318 </ul> <em>Application Known issues</em>
3320 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3321 <li>Misleading message appears after trying to delete
3323 <li>Jalview icon not shown in dock after InstallAnywhere
3324 version launches</li>
3325 <li>Fetching EMBL reference for an RNA sequence results
3326 fails with a sequence mismatch</li>
3327 <li>Corrupted or unreadable alignment display when
3328 scrolling alignment to right</li>
3329 <li>ArrayIndexOutOfBoundsException thrown when remove
3330 empty columns called on alignment with ragged gapped ends</li>
3331 <li>auto calculated alignment annotation rows do not get
3332 placed above or below non-autocalculated rows</li>
3333 <li>Jalview dekstop becomes sluggish at full screen in
3334 ultra-high resolution</li>
3335 <li>Cannot disable consensus calculation independently of
3336 quality and conservation</li>
3337 <li>Mouseover highlighting between cDNA and protein can
3338 become sluggish with more than one splitframe shown</li>
3339 </ul> <em>Applet Known Issues</em>
3341 <li>Core PDB parsing code requires Jmol</li>
3342 <li>Sequence canvas panel goes white when alignment
3343 window is being resized</li>
3349 <td><div align="center">
3350 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3352 <td><em>General</em>
3354 <li>Updated Java code signing certificate donated by
3356 <li>Features and annotation preserved when performing
3357 pairwise alignment</li>
3358 <li>RNA pseudoknot annotation can be
3359 imported/exported/displayed</li>
3360 <li>'colour by annotation' can colour by RNA and
3361 protein secondary structure</li>
3362 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3363 post-hoc with 2.9 release</em>)
3366 </ul> <em>Application</em>
3368 <li>Extract and display secondary structure for sequences
3369 with 3D structures</li>
3370 <li>Support for parsing RNAML</li>
3371 <li>Annotations menu for layout
3373 <li>sort sequence annotation rows by alignment</li>
3374 <li>place sequence annotation above/below alignment
3377 <li>Output in Stockholm format</li>
3378 <li>Internationalisation: improved Spanish (es)
3380 <li>Structure viewer preferences tab</li>
3381 <li>Disorder and Secondary Structure annotation tracks
3382 shared between alignments</li>
3383 <li>UCSF Chimera launch and linked highlighting from
3385 <li>Show/hide all sequence associated annotation rows for
3386 all or current selection</li>
3387 <li>disorder and secondary structure predictions
3388 available as dataset annotation</li>
3389 <li>Per-sequence rna helices colouring</li>
3392 <li>Sequence database accessions imported when fetching
3393 alignments from Rfam</li>
3394 <li>update VARNA version to 3.91</li>
3396 <li>New groovy scripts for exporting aligned positions,
3397 conservation values, and calculating sum of pairs scores.</li>
3398 <li>Command line argument to set default JABAWS server</li>
3399 <li>include installation type in build properties and
3400 console log output</li>
3401 <li>Updated Jalview project format to preserve dataset
3405 <!-- issues resolved --> <em>Application</em>
3407 <li>Distinguish alignment and sequence associated RNA
3408 structure in structure->view->VARNA</li>
3409 <li>Raise dialog box if user deletes all sequences in an
3411 <li>Pressing F1 results in documentation opening twice</li>
3412 <li>Sequence feature tooltip is wrapped</li>
3413 <li>Double click on sequence associated annotation
3414 selects only first column</li>
3415 <li>Redundancy removal doesn't result in unlinked
3416 leaves shown in tree</li>
3417 <li>Undos after several redundancy removals don't undo
3419 <li>Hide sequence doesn't hide associated annotation</li>
3420 <li>User defined colours dialog box too big to fit on
3421 screen and buttons not visible</li>
3422 <li>author list isn't updated if already written to
3423 Jalview properties</li>
3424 <li>Popup menu won't open after retrieving sequence
3426 <li>File open window for associate PDB doesn't open</li>
3427 <li>Left-then-right click on a sequence id opens a
3428 browser search window</li>
3429 <li>Cannot open sequence feature shading/sort popup menu
3430 in feature settings dialog</li>
3431 <li>better tooltip placement for some areas of Jalview
3433 <li>Allow addition of JABAWS Server which doesn't
3434 pass validation</li>
3435 <li>Web services parameters dialog box is too large to
3437 <li>Muscle nucleotide alignment preset obscured by
3439 <li>JABAWS preset submenus don't contain newly
3440 defined user preset</li>
3441 <li>MSA web services warns user if they were launched
3442 with invalid input</li>
3443 <li>Jalview cannot contact DAS Registy when running on
3446 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3447 'Superpose with' submenu not shown when new view
3451 </ul> <!-- <em>Applet</em>
3453 </ul> <em>General</em>
3455 </ul>--> <em>Deployment and Documentation</em>
3457 <li>2G and 1G options in launchApp have no effect on
3458 memory allocation</li>
3459 <li>launchApp service doesn't automatically open
3460 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3462 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3463 InstallAnywhere reports cannot find valid JVM when Java
3464 1.7_055 is available
3466 </ul> <em>Application Known issues</em>
3469 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3470 corrupted or unreadable alignment display when scrolling
3474 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3475 retrieval fails but progress bar continues for DAS retrieval
3476 with large number of ID
3479 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3480 flatfile output of visible region has incorrect sequence
3484 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3485 rna structure consensus doesn't update when secondary
3486 structure tracks are rearranged
3489 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3490 invalid rna structure positional highlighting does not
3491 highlight position of invalid base pairs
3494 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3495 out of memory errors are not raised when saving Jalview
3496 project from alignment window file menu
3499 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3500 Switching to RNA Helices colouring doesn't propagate to
3504 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3505 colour by RNA Helices not enabled when user created
3506 annotation added to alignment
3509 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3510 Jalview icon not shown on dock in Mountain Lion/Webstart
3512 </ul> <em>Applet Known Issues</em>
3515 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3516 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3519 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3520 Jalview and Jmol example not compatible with IE9
3523 <li>Sort by annotation score doesn't reverse order
3529 <td><div align="center">
3530 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3533 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3536 <li>Internationalisation of user interface (usually
3537 called i18n support) and translation for Spanish locale</li>
3538 <li>Define/Undefine group on current selection with
3539 Ctrl-G/Shift Ctrl-G</li>
3540 <li>Improved group creation/removal options in
3541 alignment/sequence Popup menu</li>
3542 <li>Sensible precision for symbol distribution
3543 percentages shown in logo tooltip.</li>
3544 <li>Annotation panel height set according to amount of
3545 annotation when alignment first opened</li>
3546 </ul> <em>Application</em>
3548 <li>Interactive consensus RNA secondary structure
3549 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3550 <li>Select columns containing particular features from
3551 Feature Settings dialog</li>
3552 <li>View all 'representative' PDB structures for selected
3554 <li>Update Jalview project format:
3556 <li>New file extension for Jalview projects '.jvp'</li>
3557 <li>Preserve sequence and annotation dataset (to
3558 store secondary structure annotation,etc)</li>
3559 <li>Per group and alignment annotation and RNA helix
3563 <li>New similarity measures for PCA and Tree calculation
3565 <li>Experimental support for retrieval and viewing of
3566 flanking regions for an alignment</li>
3570 <!-- issues resolved --> <em>Application</em>
3572 <li>logo keeps spinning and status remains at queued or
3573 running after job is cancelled</li>
3574 <li>cannot export features from alignments imported from
3575 Jalview/VAMSAS projects</li>
3576 <li>Buggy slider for web service parameters that take
3578 <li>Newly created RNA secondary structure line doesn't
3579 have 'display all symbols' flag set</li>
3580 <li>T-COFFEE alignment score shading scheme and other
3581 annotation shading not saved in Jalview project</li>
3582 <li>Local file cannot be loaded in freshly downloaded
3584 <li>Jalview icon not shown on dock in Mountain
3586 <li>Load file from desktop file browser fails</li>
3587 <li>Occasional NPE thrown when calculating large trees</li>
3588 <li>Cannot reorder or slide sequences after dragging an
3589 alignment onto desktop</li>
3590 <li>Colour by annotation dialog throws NPE after using
3591 'extract scores' function</li>
3592 <li>Loading/cut'n'pasting an empty file leads to a grey
3593 alignment window</li>
3594 <li>Disorder thresholds rendered incorrectly after
3595 performing IUPred disorder prediction</li>
3596 <li>Multiple group annotated consensus rows shown when
3597 changing 'normalise logo' display setting</li>
3598 <li>Find shows blank dialog after 'finished searching' if
3599 nothing matches query</li>
3600 <li>Null Pointer Exceptions raised when sorting by
3601 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3603 <li>Errors in Jmol console when structures in alignment
3604 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3606 <li>Not all working JABAWS services are shown in
3608 <li>JAVAWS version of Jalview fails to launch with
3609 'invalid literal/length code'</li>
3610 <li>Annotation/RNA Helix colourschemes cannot be applied
3611 to alignment with groups (actually fixed in 2.8.0b1)</li>
3612 <li>RNA Helices and T-Coffee Scores available as default
3615 </ul> <em>Applet</em>
3617 <li>Remove group option is shown even when selection is
3619 <li>Apply to all groups ticked but colourscheme changes
3620 don't affect groups</li>
3621 <li>Documented RNA Helices and T-Coffee Scores as valid
3622 colourscheme name</li>
3623 <li>Annotation labels drawn on sequence IDs when
3624 Annotation panel is not displayed</li>
3625 <li>Increased font size for dropdown menus on OSX and
3626 embedded windows</li>
3627 </ul> <em>Other</em>
3629 <li>Consensus sequence for alignments/groups with a
3630 single sequence were not calculated</li>
3631 <li>annotation files that contain only groups imported as
3632 annotation and junk sequences</li>
3633 <li>Fasta files with sequences containing '*' incorrectly
3634 recognised as PFAM or BLC</li>
3635 <li>conservation/PID slider apply all groups option
3636 doesn't affect background (2.8.0b1)
3638 <li>redundancy highlighting is erratic at 0% and 100%</li>
3639 <li>Remove gapped columns fails for sequences with ragged
3641 <li>AMSA annotation row with leading spaces is not
3642 registered correctly on import</li>
3643 <li>Jalview crashes when selecting PCA analysis for
3644 certain alignments</li>
3645 <li>Opening the colour by annotation dialog for an
3646 existing annotation based 'use original colours'
3647 colourscheme loses original colours setting</li>
3652 <td><div align="center">
3653 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3654 <em>30/1/2014</em></strong>
3658 <li>Trusted certificates for JalviewLite applet and
3659 Jalview Desktop application<br />Certificate was donated by
3660 <a href="https://www.certum.eu">Certum</a> to the Jalview
3661 open source project).
3663 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3664 <li>Output in Stockholm format</li>
3665 <li>Allow import of data from gzipped files</li>
3666 <li>Export/import group and sequence associated line
3667 graph thresholds</li>
3668 <li>Nucleotide substitution matrix that supports RNA and
3669 ambiguity codes</li>
3670 <li>Allow disorder predictions to be made on the current
3671 selection (or visible selection) in the same way that JPred
3673 <li>Groovy scripting for headless Jalview operation</li>
3674 </ul> <em>Other improvements</em>
3676 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3677 <li>COMBINE statement uses current SEQUENCE_REF and
3678 GROUP_REF scope to group annotation rows</li>
3679 <li>Support '' style escaping of quotes in Newick
3681 <li>Group options for JABAWS service by command line name</li>
3682 <li>Empty tooltip shown for JABA service options with a
3683 link but no description</li>
3684 <li>Select primary source when selecting authority in
3685 database fetcher GUI</li>
3686 <li>Add .mfa to FASTA file extensions recognised by
3688 <li>Annotation label tooltip text wrap</li>
3693 <li>Slow scrolling when lots of annotation rows are
3695 <li>Lots of NPE (and slowness) after creating RNA
3696 secondary structure annotation line</li>
3697 <li>Sequence database accessions not imported when
3698 fetching alignments from Rfam</li>
3699 <li>Incorrect SHMR submission for sequences with
3701 <li>View all structures does not always superpose
3703 <li>Option widgets in service parameters not updated to
3704 reflect user or preset settings</li>
3705 <li>Null pointer exceptions for some services without
3706 presets or adjustable parameters</li>
3707 <li>Discover PDB IDs entry in structure menu doesn't
3708 discover PDB xRefs</li>
3709 <li>Exception encountered while trying to retrieve
3710 features with DAS</li>
3711 <li>Lowest value in annotation row isn't coloured
3712 when colour by annotation (per sequence) is coloured</li>
3713 <li>Keyboard mode P jumps to start of gapped region when
3714 residue follows a gap</li>
3715 <li>Jalview appears to hang importing an alignment with
3716 Wrap as default or after enabling Wrap</li>
3717 <li>'Right click to add annotations' message
3718 shown in wrap mode when no annotations present</li>
3719 <li>Disorder predictions fail with NPE if no automatic
3720 annotation already exists on alignment</li>
3721 <li>oninit javascript function should be called after
3722 initialisation completes</li>
3723 <li>Remove redundancy after disorder prediction corrupts
3724 alignment window display</li>
3725 <li>Example annotation file in documentation is invalid</li>
3726 <li>Grouped line graph annotation rows are not exported
3727 to annotation file</li>
3728 <li>Multi-harmony analysis cannot be run when only two
3730 <li>Cannot create multiple groups of line graphs with
3731 several 'combine' statements in annotation file</li>
3732 <li>Pressing return several times causes Number Format
3733 exceptions in keyboard mode</li>
3734 <li>Multi-harmony (SHMMR) method doesn't submit
3735 correct partitions for input data</li>
3736 <li>Translation from DNA to Amino Acids fails</li>
3737 <li>Jalview fail to load newick tree with quoted label</li>
3738 <li>--headless flag isn't understood</li>
3739 <li>ClassCastException when generating EPS in headless
3741 <li>Adjusting sequence-associated shading threshold only
3742 changes one row's threshold</li>
3743 <li>Preferences and Feature settings panel panel
3744 doesn't open</li>
3745 <li>hide consensus histogram also hides conservation and
3746 quality histograms</li>
3751 <td><div align="center">
3752 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3754 <td><em>Application</em>
3756 <li>Support for JABAWS 2.0 Services (AACon alignment
3757 conservation, protein disorder and Clustal Omega)</li>
3758 <li>JABAWS server status indicator in Web Services
3760 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3761 in Jalview alignment window</li>
3762 <li>Updated Jalview build and deploy framework for OSX
3763 mountain lion, windows 7, and 8</li>
3764 <li>Nucleotide substitution matrix for PCA that supports
3765 RNA and ambiguity codes</li>
3767 <li>Improved sequence database retrieval GUI</li>
3768 <li>Support fetching and database reference look up
3769 against multiple DAS sources (Fetch all from in 'fetch db
3771 <li>Jalview project improvements
3773 <li>Store and retrieve the 'belowAlignment'
3774 flag for annotation</li>
3775 <li>calcId attribute to group annotation rows on the
3777 <li>Store AACon calculation settings for a view in
3778 Jalview project</li>
3782 <li>horizontal scrolling gesture support</li>
3783 <li>Visual progress indicator when PCA calculation is
3785 <li>Simpler JABA web services menus</li>
3786 <li>visual indication that web service results are still
3787 being retrieved from server</li>
3788 <li>Serialise the dialogs that are shown when Jalview
3789 starts up for first time</li>
3790 <li>Jalview user agent string for interacting with HTTP
3792 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3794 <li>Examples directory and Groovy library included in
3795 InstallAnywhere distribution</li>
3796 </ul> <em>Applet</em>
3798 <li>RNA alignment and secondary structure annotation
3799 visualization applet example</li>
3800 </ul> <em>General</em>
3802 <li>Normalise option for consensus sequence logo</li>
3803 <li>Reset button in PCA window to return dimensions to
3805 <li>Allow seqspace or Jalview variant of alignment PCA
3807 <li>PCA with either nucleic acid and protein substitution
3809 <li>Allow windows containing HTML reports to be exported
3811 <li>Interactive display and editing of RNA secondary
3812 structure contacts</li>
3813 <li>RNA Helix Alignment Colouring</li>
3814 <li>RNA base pair logo consensus</li>
3815 <li>Parse sequence associated secondary structure
3816 information in Stockholm files</li>
3817 <li>HTML Export database accessions and annotation
3818 information presented in tooltip for sequences</li>
3819 <li>Import secondary structure from LOCARNA clustalw
3820 style RNA alignment files</li>
3821 <li>import and visualise T-COFFEE quality scores for an
3823 <li>'colour by annotation' per sequence option to
3824 shade each sequence according to its associated alignment
3826 <li>New Jalview Logo</li>
3827 </ul> <em>Documentation and Development</em>
3829 <li>documentation for score matrices used in Jalview</li>
3830 <li>New Website!</li>
3832 <td><em>Application</em>
3834 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3835 wsdbfetch REST service</li>
3836 <li>Stop windows being moved outside desktop on OSX</li>
3837 <li>Filetype associations not installed for webstart
3839 <li>Jalview does not always retrieve progress of a JABAWS
3840 job execution in full once it is complete</li>
3841 <li>revise SHMR RSBS definition to ensure alignment is
3842 uploaded via ali_file parameter</li>
3843 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3844 <li>View all structures superposed fails with exception</li>
3845 <li>Jnet job queues forever if a very short sequence is
3846 submitted for prediction</li>
3847 <li>Cut and paste menu not opened when mouse clicked on
3849 <li>Putting fractional value into integer text box in
3850 alignment parameter dialog causes Jalview to hang</li>
3851 <li>Structure view highlighting doesn't work on
3853 <li>View all structures fails with exception shown in
3855 <li>Characters in filename associated with PDBEntry not
3856 escaped in a platform independent way</li>
3857 <li>Jalview desktop fails to launch with exception when
3859 <li>Tree calculation reports 'you must have 2 or more
3860 sequences selected' when selection is empty</li>
3861 <li>Jalview desktop fails to launch with jar signature
3862 failure when java web start temporary file caching is
3864 <li>DAS Sequence retrieval with range qualification
3865 results in sequence xref which includes range qualification</li>
3866 <li>Errors during processing of command line arguments
3867 cause progress bar (JAL-898) to be removed</li>
3868 <li>Replace comma for semi-colon option not disabled for
3869 DAS sources in sequence fetcher</li>
3870 <li>Cannot close news reader when JABAWS server warning
3871 dialog is shown</li>
3872 <li>Option widgets not updated to reflect user settings</li>
3873 <li>Edited sequence not submitted to web service</li>
3874 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3875 <li>InstallAnywhere installer doesn't unpack and run
3876 on OSX Mountain Lion</li>
3877 <li>Annotation panel not given a scroll bar when
3878 sequences with alignment annotation are pasted into the
3880 <li>Sequence associated annotation rows not associated
3881 when loaded from Jalview project</li>
3882 <li>Browser launch fails with NPE on java 1.7</li>
3883 <li>JABAWS alignment marked as finished when job was
3884 cancelled or job failed due to invalid input</li>
3885 <li>NPE with v2.7 example when clicking on Tree
3886 associated with all views</li>
3887 <li>Exceptions when copy/paste sequences with grouped
3888 annotation rows to new window</li>
3889 </ul> <em>Applet</em>
3891 <li>Sequence features are momentarily displayed before
3892 they are hidden using hidefeaturegroups applet parameter</li>
3893 <li>loading features via javascript API automatically
3894 enables feature display</li>
3895 <li>scrollToColumnIn javascript API method doesn't
3897 </ul> <em>General</em>
3899 <li>Redundancy removal fails for rna alignment</li>
3900 <li>PCA calculation fails when sequence has been selected
3901 and then deselected</li>
3902 <li>PCA window shows grey box when first opened on OSX</li>
3903 <li>Letters coloured pink in sequence logo when alignment
3904 coloured with clustalx</li>
3905 <li>Choosing fonts without letter symbols defined causes
3906 exceptions and redraw errors</li>
3907 <li>Initial PCA plot view is not same as manually
3908 reconfigured view</li>
3909 <li>Grouped annotation graph label has incorrect line
3911 <li>Grouped annotation graph label display is corrupted
3912 for lots of labels</li>
3917 <div align="center">
3918 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3921 <td><em>Application</em>
3923 <li>Jalview Desktop News Reader</li>
3924 <li>Tweaked default layout of web services menu</li>
3925 <li>View/alignment association menu to enable user to
3926 easily specify which alignment a multi-structure view takes
3927 its colours/correspondences from</li>
3928 <li>Allow properties file location to be specified as URL</li>
3929 <li>Extend Jalview project to preserve associations
3930 between many alignment views and a single Jmol display</li>
3931 <li>Store annotation row height in Jalview project file</li>
3932 <li>Annotation row column label formatting attributes
3933 stored in project file</li>
3934 <li>Annotation row order for auto-calculated annotation
3935 rows preserved in Jalview project file</li>
3936 <li>Visual progress indication when Jalview state is
3937 saved using Desktop window menu</li>
3938 <li>Visual indication that command line arguments are
3939 still being processed</li>
3940 <li>Groovy script execution from URL</li>
3941 <li>Colour by annotation default min and max colours in
3943 <li>Automatically associate PDB files dragged onto an
3944 alignment with sequences that have high similarity and
3946 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3947 <li>'view structures' option to open many
3948 structures in same window</li>
3949 <li>Sort associated views menu option for tree panel</li>
3950 <li>Group all JABA and non-JABA services for a particular
3951 analysis function in its own submenu</li>
3952 </ul> <em>Applet</em>
3954 <li>Userdefined and autogenerated annotation rows for
3956 <li>Adjustment of alignment annotation pane height</li>
3957 <li>Annotation scrollbar for annotation panel</li>
3958 <li>Drag to reorder annotation rows in annotation panel</li>
3959 <li>'automaticScrolling' parameter</li>
3960 <li>Allow sequences with partial ID string matches to be
3961 annotated from GFF/Jalview features files</li>
3962 <li>Sequence logo annotation row in applet</li>
3963 <li>Absolute paths relative to host server in applet
3964 parameters are treated as such</li>
3965 <li>New in the JalviewLite javascript API:
3967 <li>JalviewLite.js javascript library</li>
3968 <li>Javascript callbacks for
3970 <li>Applet initialisation</li>
3971 <li>Sequence/alignment mouse-overs and selections</li>
3974 <li>scrollTo row and column alignment scrolling
3976 <li>Select sequence/alignment regions from javascript</li>
3977 <li>javascript structure viewer harness to pass
3978 messages between Jmol and Jalview when running as
3979 distinct applets</li>
3980 <li>sortBy method</li>
3981 <li>Set of applet and application examples shipped
3982 with documentation</li>
3983 <li>New example to demonstrate JalviewLite and Jmol
3984 javascript message exchange</li>
3986 </ul> <em>General</em>
3988 <li>Enable Jmol displays to be associated with multiple
3989 multiple alignments</li>
3990 <li>Option to automatically sort alignment with new tree</li>
3991 <li>User configurable link to enable redirects to a
3992 www.Jalview.org mirror</li>
3993 <li>Jmol colours option for Jmol displays</li>
3994 <li>Configurable newline string when writing alignment
3995 and other flat files</li>
3996 <li>Allow alignment annotation description lines to
3997 contain html tags</li>
3998 </ul> <em>Documentation and Development</em>
4000 <li>Add groovy test harness for bulk load testing to
4002 <li>Groovy script to load and align a set of sequences
4003 using a web service before displaying the result in the
4004 Jalview desktop</li>
4005 <li>Restructured javascript and applet api documentation</li>
4006 <li>Ant target to publish example html files with applet
4008 <li>Netbeans project for building Jalview from source</li>
4009 <li>ant task to create online javadoc for Jalview source</li>
4011 <td><em>Application</em>
4013 <li>User defined colourscheme throws exception when
4014 current built in colourscheme is saved as new scheme</li>
4015 <li>AlignFrame->Save in application pops up save
4016 dialog for valid filename/format</li>
4017 <li>Cannot view associated structure for UniProt sequence</li>
4018 <li>PDB file association breaks for UniProt sequence
4020 <li>Associate PDB from file dialog does not tell you
4021 which sequence is to be associated with the file</li>
4022 <li>Find All raises null pointer exception when query
4023 only matches sequence IDs</li>
4024 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4025 <li>Jalview project with Jmol views created with Jalview
4026 2.4 cannot be loaded</li>
4027 <li>Filetype associations not installed for webstart
4029 <li>Two or more chains in a single PDB file associated
4030 with sequences in different alignments do not get coloured
4031 by their associated sequence</li>
4032 <li>Visibility status of autocalculated annotation row
4033 not preserved when project is loaded</li>
4034 <li>Annotation row height and visibility attributes not
4035 stored in Jalview project</li>
4036 <li>Tree bootstraps are not preserved when saved as a
4037 Jalview project</li>
4038 <li>Envision2 workflow tooltips are corrupted</li>
4039 <li>Enabling show group conservation also enables colour
4040 by conservation</li>
4041 <li>Duplicate group associated conservation or consensus
4042 created on new view</li>
4043 <li>Annotation scrollbar not displayed after 'show
4044 all hidden annotation rows' option selected</li>
4045 <li>Alignment quality not updated after alignment
4046 annotation row is hidden then shown</li>
4047 <li>Preserve colouring of structures coloured by
4048 sequences in pre Jalview 2.7 projects</li>
4049 <li>Web service job parameter dialog is not laid out
4051 <li>Web services menu not refreshed after 'reset
4052 services' button is pressed in preferences</li>
4053 <li>Annotation off by one in Jalview v2_3 example project</li>
4054 <li>Structures imported from file and saved in project
4055 get name like jalview_pdb1234.txt when reloaded</li>
4056 <li>Jalview does not always retrieve progress of a JABAWS
4057 job execution in full once it is complete</li>
4058 </ul> <em>Applet</em>
4060 <li>Alignment height set incorrectly when lots of
4061 annotation rows are displayed</li>
4062 <li>Relative URLs in feature HTML text not resolved to
4064 <li>View follows highlighting does not work for positions
4066 <li><= shown as = in tooltip</li>
4067 <li>Export features raises exception when no features
4069 <li>Separator string used for serialising lists of IDs
4070 for javascript api is modified when separator string
4071 provided as parameter</li>
4072 <li>Null pointer exception when selecting tree leaves for
4073 alignment with no existing selection</li>
4074 <li>Relative URLs for datasources assumed to be relative
4075 to applet's codebase</li>
4076 <li>Status bar not updated after finished searching and
4077 search wraps around to first result</li>
4078 <li>StructureSelectionManager instance shared between
4079 several Jalview applets causes race conditions and memory
4081 <li>Hover tooltip and mouseover of position on structure
4082 not sent from Jmol in applet</li>
4083 <li>Certain sequences of javascript method calls to
4084 applet API fatally hang browser</li>
4085 </ul> <em>General</em>
4087 <li>View follows structure mouseover scrolls beyond
4088 position with wrapped view and hidden regions</li>
4089 <li>Find sequence position moves to wrong residue
4090 with/without hidden columns</li>
4091 <li>Sequence length given in alignment properties window
4093 <li>InvalidNumberFormat exceptions thrown when trying to
4094 import PDB like structure files</li>
4095 <li>Positional search results are only highlighted
4096 between user-supplied sequence start/end bounds</li>
4097 <li>End attribute of sequence is not validated</li>
4098 <li>Find dialog only finds first sequence containing a
4099 given sequence position</li>
4100 <li>Sequence numbering not preserved in MSF alignment
4102 <li>Jalview PDB file reader does not extract sequence
4103 from nucleotide chains correctly</li>
4104 <li>Structure colours not updated when tree partition
4105 changed in alignment</li>
4106 <li>Sequence associated secondary structure not correctly
4107 parsed in interleaved stockholm</li>
4108 <li>Colour by annotation dialog does not restore current
4110 <li>Hiding (nearly) all sequences doesn't work
4112 <li>Sequences containing lowercase letters are not
4113 properly associated with their pdb files</li>
4114 </ul> <em>Documentation and Development</em>
4116 <li>schemas/JalviewWsParamSet.xsd corrupted by
4117 ApplyCopyright tool</li>
4122 <div align="center">
4123 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4126 <td><em>Application</em>
4128 <li>New warning dialog when the Jalview Desktop cannot
4129 contact web services</li>
4130 <li>JABA service parameters for a preset are shown in
4131 service job window</li>
4132 <li>JABA Service menu entries reworded</li>
4136 <li>Modeller PIR IO broken - cannot correctly import a
4137 pir file emitted by Jalview</li>
4138 <li>Existing feature settings transferred to new
4139 alignment view created from cut'n'paste</li>
4140 <li>Improved test for mixed amino/nucleotide chains when
4141 parsing PDB files</li>
4142 <li>Consensus and conservation annotation rows
4143 occasionally become blank for all new windows</li>
4144 <li>Exception raised when right clicking above sequences
4145 in wrapped view mode</li>
4146 </ul> <em>Application</em>
4148 <li>multiple multiply aligned structure views cause cpu
4149 usage to hit 100% and computer to hang</li>
4150 <li>Web Service parameter layout breaks for long user
4151 parameter names</li>
4152 <li>Jaba service discovery hangs desktop if Jaba server
4159 <div align="center">
4160 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4163 <td><em>Application</em>
4165 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4166 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4169 <li>Web Services preference tab</li>
4170 <li>Analysis parameters dialog box and user defined
4172 <li>Improved speed and layout of Envision2 service menu</li>
4173 <li>Superpose structures using associated sequence
4175 <li>Export coordinates and projection as CSV from PCA
4177 </ul> <em>Applet</em>
4179 <li>enable javascript: execution by the applet via the
4180 link out mechanism</li>
4181 </ul> <em>Other</em>
4183 <li>Updated the Jmol Jalview interface to work with Jmol
4185 <li>The Jalview Desktop and JalviewLite applet now
4186 require Java 1.5</li>
4187 <li>Allow Jalview feature colour specification for GFF
4188 sequence annotation files</li>
4189 <li>New 'colour by label' keword in Jalview feature file
4190 type colour specification</li>
4191 <li>New Jalview Desktop Groovy API method that allows a
4192 script to check if it being run in an interactive session or
4193 in a batch operation from the Jalview command line</li>
4197 <li>clustalx colourscheme colours Ds preferentially when
4198 both D+E are present in over 50% of the column</li>
4199 </ul> <em>Application</em>
4201 <li>typo in AlignmentFrame->View->Hide->all but
4202 selected Regions menu item</li>
4203 <li>sequence fetcher replaces ',' for ';' when the ',' is
4204 part of a valid accession ID</li>
4205 <li>fatal OOM if object retrieved by sequence fetcher
4206 runs out of memory</li>
4207 <li>unhandled Out of Memory Error when viewing pca
4208 analysis results</li>
4209 <li>InstallAnywhere builds fail to launch on OS X java
4210 10.5 update 4 (due to apple Java 1.6 update)</li>
4211 <li>Installanywhere Jalview silently fails to launch</li>
4212 </ul> <em>Applet</em>
4214 <li>Jalview.getFeatureGroups() raises an
4215 ArrayIndexOutOfBoundsException if no feature groups are
4222 <div align="center">
4223 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4229 <li>Alignment prettyprinter doesn't cope with long
4231 <li>clustalx colourscheme colours Ds preferentially when
4232 both D+E are present in over 50% of the column</li>
4233 <li>nucleic acid structures retrieved from PDB do not
4234 import correctly</li>
4235 <li>More columns get selected than were clicked on when a
4236 number of columns are hidden</li>
4237 <li>annotation label popup menu not providing correct
4238 add/hide/show options when rows are hidden or none are
4240 <li>Stockholm format shown in list of readable formats,
4241 and parser copes better with alignments from RFAM.</li>
4242 <li>CSV output of consensus only includes the percentage
4243 of all symbols if sequence logo display is enabled</li>
4245 </ul> <em>Applet</em>
4247 <li>annotation panel disappears when annotation is
4249 </ul> <em>Application</em>
4251 <li>Alignment view not redrawn properly when new
4252 alignment opened where annotation panel is visible but no
4253 annotations are present on alignment</li>
4254 <li>pasted region containing hidden columns is
4255 incorrectly displayed in new alignment window</li>
4256 <li>Jalview slow to complete operations when stdout is
4257 flooded (fix is to close the Jalview console)</li>
4258 <li>typo in AlignmentFrame->View->Hide->all but
4259 selected Rregions menu item.</li>
4260 <li>inconsistent group submenu and Format submenu entry
4261 'Un' or 'Non'conserved</li>
4262 <li>Sequence feature settings are being shared by
4263 multiple distinct alignments</li>
4264 <li>group annotation not recreated when tree partition is
4266 <li>double click on group annotation to select sequences
4267 does not propagate to associated trees</li>
4268 <li>Mac OSX specific issues:
4270 <li>exception raised when mouse clicked on desktop
4271 window background</li>
4272 <li>Desktop menu placed on menu bar and application
4273 name set correctly</li>
4274 <li>sequence feature settings not wide enough for the
4275 save feature colourscheme button</li>
4284 <div align="center">
4285 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4288 <td><em>New Capabilities</em>
4290 <li>URL links generated from description line for
4291 regular-expression based URL links (applet and application)
4293 <li>Non-positional feature URL links are shown in link
4295 <li>Linked viewing of nucleic acid sequences and
4297 <li>Automatic Scrolling option in View menu to display
4298 the currently highlighted region of an alignment.</li>
4299 <li>Order an alignment by sequence length, or using the
4300 average score or total feature count for each sequence.</li>
4301 <li>Shading features by score or associated description</li>
4302 <li>Subdivide alignment and groups based on identity of
4303 selected subsequence (Make Groups from Selection).</li>
4304 <li>New hide/show options including Shift+Control+H to
4305 hide everything but the currently selected region.</li>
4306 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4307 </ul> <em>Application</em>
4309 <li>Fetch DB References capabilities and UI expanded to
4310 support retrieval from DAS sequence sources</li>
4311 <li>Local DAS Sequence sources can be added via the
4312 command line or via the Add local source dialog box.</li>
4313 <li>DAS Dbref and DbxRef feature types are parsed as
4314 database references and protein_name is parsed as
4315 description line (BioSapiens terms).</li>
4316 <li>Enable or disable non-positional feature and database
4317 references in sequence ID tooltip from View menu in
4319 <!-- <li>New hidden columns and rows and representatives capabilities
4320 in annotations file (in progress - not yet fully implemented)</li> -->
4321 <li>Group-associated consensus, sequence logos and
4322 conservation plots</li>
4323 <li>Symbol distributions for each column can be exported
4324 and visualized as sequence logos</li>
4325 <li>Optionally scale multi-character column labels to fit
4326 within each column of annotation row<!-- todo for applet -->
4328 <li>Optional automatic sort of associated alignment view
4329 when a new tree is opened.</li>
4330 <li>Jalview Java Console</li>
4331 <li>Better placement of desktop window when moving
4332 between different screens.</li>
4333 <li>New preference items for sequence ID tooltip and
4334 consensus annotation</li>
4335 <li>Client to submit sequences and IDs to Envision2
4337 <li><em>Vamsas Capabilities</em>
4339 <li>Improved VAMSAS synchronization (Jalview archive
4340 used to preserve views, structures, and tree display
4342 <li>Import of vamsas documents from disk or URL via
4344 <li>Sharing of selected regions between views and
4345 with other VAMSAS applications (Experimental feature!)</li>
4346 <li>Updated API to VAMSAS version 0.2</li>
4348 </ul> <em>Applet</em>
4350 <li>Middle button resizes annotation row height</li>
4353 <li>sortByTree (true/false) - automatically sort the
4354 associated alignment view by the tree when a new tree is
4356 <li>showTreeBootstraps (true/false) - show or hide
4357 branch bootstraps (default is to show them if available)</li>
4358 <li>showTreeDistances (true/false) - show or hide
4359 branch lengths (default is to show them if available)</li>
4360 <li>showUnlinkedTreeNodes (true/false) - indicate if
4361 unassociated nodes should be highlighted in the tree
4363 <li>heightScale and widthScale (1.0 or more) -
4364 increase the height or width of a cell in the alignment
4365 grid relative to the current font size.</li>
4368 <li>Non-positional features displayed in sequence ID
4370 </ul> <em>Other</em>
4372 <li>Features format: graduated colour definitions and
4373 specification of feature scores</li>
4374 <li>Alignment Annotations format: new keywords for group
4375 associated annotation (GROUP_REF) and annotation row display
4376 properties (ROW_PROPERTIES)</li>
4377 <li>XML formats extended to support graduated feature
4378 colourschemes, group associated annotation, and profile
4379 visualization settings.</li></td>
4382 <li>Source field in GFF files parsed as feature source
4383 rather than description</li>
4384 <li>Non-positional features are now included in sequence
4385 feature and gff files (controlled via non-positional feature
4386 visibility in tooltip).</li>
4387 <li>URL links generated for all feature links (bugfix)</li>
4388 <li>Added URL embedding instructions to features file
4390 <li>Codons containing ambiguous nucleotides translated as
4391 'X' in peptide product</li>
4392 <li>Match case switch in find dialog box works for both
4393 sequence ID and sequence string and query strings do not
4394 have to be in upper case to match case-insensitively.</li>
4395 <li>AMSA files only contain first column of
4396 multi-character column annotation labels</li>
4397 <li>Jalview Annotation File generation/parsing consistent
4398 with documentation (e.g. Stockholm annotation can be
4399 exported and re-imported)</li>
4400 <li>PDB files without embedded PDB IDs given a friendly
4402 <li>Find incrementally searches ID string matches as well
4403 as subsequence matches, and correctly reports total number
4407 <li>Better handling of exceptions during sequence
4409 <li>Dasobert generated non-positional feature URL
4410 link text excludes the start_end suffix</li>
4411 <li>DAS feature and source retrieval buttons disabled
4412 when fetch or registry operations in progress.</li>
4413 <li>PDB files retrieved from URLs are cached properly</li>
4414 <li>Sequence description lines properly shared via
4416 <li>Sequence fetcher fetches multiple records for all
4418 <li>Ensured that command line das feature retrieval
4419 completes before alignment figures are generated.</li>
4420 <li>Reduced time taken when opening file browser for
4422 <li>isAligned check prior to calculating tree, PCA or
4423 submitting an MSA to JNet now excludes hidden sequences.</li>
4424 <li>User defined group colours properly recovered
4425 from Jalview projects.</li>
4434 <div align="center">
4435 <strong>2.4.0.b2</strong><br> 28/10/2009
4440 <li>Experimental support for google analytics usage
4442 <li>Jalview privacy settings (user preferences and docs).</li>
4447 <li>Race condition in applet preventing startup in
4449 <li>Exception when feature created from selection beyond
4450 length of sequence.</li>
4451 <li>Allow synthetic PDB files to be imported gracefully</li>
4452 <li>Sequence associated annotation rows associate with
4453 all sequences with a given id</li>
4454 <li>Find function matches case-insensitively for sequence
4455 ID string searches</li>
4456 <li>Non-standard characters do not cause pairwise
4457 alignment to fail with exception</li>
4458 </ul> <em>Application Issues</em>
4460 <li>Sequences are now validated against EMBL database</li>
4461 <li>Sequence fetcher fetches multiple records for all
4463 </ul> <em>InstallAnywhere Issues</em>
4465 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4466 issue with installAnywhere mechanism)</li>
4467 <li>Command line launching of JARs from InstallAnywhere
4468 version (java class versioning error fixed)</li>
4475 <div align="center">
4476 <strong>2.4</strong><br> 27/8/2008
4479 <td><em>User Interface</em>
4481 <li>Linked highlighting of codon and amino acid from
4482 translation and protein products</li>
4483 <li>Linked highlighting of structure associated with
4484 residue mapping to codon position</li>
4485 <li>Sequence Fetcher provides example accession numbers
4486 and 'clear' button</li>
4487 <li>MemoryMonitor added as an option under Desktop's
4489 <li>Extract score function to parse whitespace separated
4490 numeric data in description line</li>
4491 <li>Column labels in alignment annotation can be centred.</li>
4492 <li>Tooltip for sequence associated annotation give name
4494 </ul> <em>Web Services and URL fetching</em>
4496 <li>JPred3 web service</li>
4497 <li>Prototype sequence search client (no public services
4499 <li>Fetch either seed alignment or full alignment from
4501 <li>URL Links created for matching database cross
4502 references as well as sequence ID</li>
4503 <li>URL Links can be created using regular-expressions</li>
4504 </ul> <em>Sequence Database Connectivity</em>
4506 <li>Retrieval of cross-referenced sequences from other
4508 <li>Generalised database reference retrieval and
4509 validation to all fetchable databases</li>
4510 <li>Fetch sequences from DAS sources supporting the
4511 sequence command</li>
4512 </ul> <em>Import and Export</em>
4513 <li>export annotation rows as CSV for spreadsheet import</li>
4514 <li>Jalview projects record alignment dataset associations,
4515 EMBL products, and cDNA sequence mappings</li>
4516 <li>Sequence Group colour can be specified in Annotation
4518 <li>Ad-hoc colouring of group in Annotation File using RGB
4519 triplet as name of colourscheme</li>
4520 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4522 <li>treenode binding for VAMSAS tree exchange</li>
4523 <li>local editing and update of sequences in VAMSAS
4524 alignments (experimental)</li>
4525 <li>Create new or select existing session to join</li>
4526 <li>load and save of vamsas documents</li>
4527 </ul> <em>Application command line</em>
4529 <li>-tree parameter to open trees (introduced for passing
4531 <li>-fetchfrom command line argument to specify nicknames
4532 of DAS servers to query for alignment features</li>
4533 <li>-dasserver command line argument to add new servers
4534 that are also automatically queried for features</li>
4535 <li>-groovy command line argument executes a given groovy
4536 script after all input data has been loaded and parsed</li>
4537 </ul> <em>Applet-Application data exchange</em>
4539 <li>Trees passed as applet parameters can be passed to
4540 application (when using "View in full
4541 application")</li>
4542 </ul> <em>Applet Parameters</em>
4544 <li>feature group display control parameter</li>
4545 <li>debug parameter</li>
4546 <li>showbutton parameter</li>
4547 </ul> <em>Applet API methods</em>
4549 <li>newView public method</li>
4550 <li>Window (current view) specific get/set public methods</li>
4551 <li>Feature display control methods</li>
4552 <li>get list of currently selected sequences</li>
4553 </ul> <em>New Jalview distribution features</em>
4555 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4556 <li>RELEASE file gives build properties for the latest
4557 Jalview release.</li>
4558 <li>Java 1.1 Applet build made easier and donotobfuscate
4559 property controls execution of obfuscator</li>
4560 <li>Build target for generating source distribution</li>
4561 <li>Debug flag for javacc</li>
4562 <li>.jalview_properties file is documented (slightly) in
4563 jalview.bin.Cache</li>
4564 <li>Continuous Build Integration for stable and
4565 development version of Application, Applet and source
4570 <li>selected region output includes visible annotations
4571 (for certain formats)</li>
4572 <li>edit label/displaychar contains existing label/char
4574 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4575 <li>shorter peptide product names from EMBL records</li>
4576 <li>Newick string generator makes compact representations</li>
4577 <li>bootstrap values parsed correctly for tree files with
4579 <li>pathological filechooser bug avoided by not allowing
4580 filenames containing a ':'</li>
4581 <li>Fixed exception when parsing GFF files containing
4582 global sequence features</li>
4583 <li>Alignment datasets are finalized only when number of
4584 references from alignment sequences goes to zero</li>
4585 <li>Close of tree branch colour box without colour
4586 selection causes cascading exceptions</li>
4587 <li>occasional negative imgwidth exceptions</li>
4588 <li>better reporting of non-fatal warnings to user when
4589 file parsing fails.</li>
4590 <li>Save works when Jalview project is default format</li>
4591 <li>Save as dialog opened if current alignment format is
4592 not a valid output format</li>
4593 <li>UniProt canonical names introduced for both das and
4595 <li>Histidine should be midblue (not pink!) in Zappo</li>
4596 <li>error messages passed up and output when data read
4598 <li>edit undo recovers previous dataset sequence when
4599 sequence is edited</li>
4600 <li>allow PDB files without pdb ID HEADER lines (like
4601 those generated by MODELLER) to be read in properly</li>
4602 <li>allow reading of JPred concise files as a normal
4604 <li>Stockholm annotation parsing and alignment properties
4605 import fixed for PFAM records</li>
4606 <li>Structure view windows have correct name in Desktop
4608 <li>annotation consisting of sequence associated scores
4609 can be read and written correctly to annotation file</li>
4610 <li>Aligned cDNA translation to aligned peptide works
4612 <li>Fixed display of hidden sequence markers and
4613 non-italic font for representatives in Applet</li>
4614 <li>Applet Menus are always embedded in applet window on
4616 <li>Newly shown features appear at top of stack (in
4618 <li>Annotations added via parameter not drawn properly
4619 due to null pointer exceptions</li>
4620 <li>Secondary structure lines are drawn starting from
4621 first column of alignment</li>
4622 <li>UniProt XML import updated for new schema release in
4624 <li>Sequence feature to sequence ID match for Features
4625 file is case-insensitive</li>
4626 <li>Sequence features read from Features file appended to
4627 all sequences with matching IDs</li>
4628 <li>PDB structure coloured correctly for associated views
4629 containing a sub-sequence</li>
4630 <li>PDB files can be retrieved by applet from Jar files</li>
4631 <li>feature and annotation file applet parameters
4632 referring to different directories are retrieved correctly</li>
4633 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4634 <li>Fixed application hang whilst waiting for
4635 splash-screen version check to complete</li>
4636 <li>Applet properly URLencodes input parameter values
4637 when passing them to the launchApp service</li>
4638 <li>display name and local features preserved in results
4639 retrieved from web service</li>
4640 <li>Visual delay indication for sequence retrieval and
4641 sequence fetcher initialisation</li>
4642 <li>updated Application to use DAS 1.53e version of
4643 dasobert DAS client</li>
4644 <li>Re-instated Full AMSA support and .amsa file
4646 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4654 <div align="center">
4655 <strong>2.3</strong><br> 9/5/07
4660 <li>Jmol 11.0.2 integration</li>
4661 <li>PDB views stored in Jalview XML files</li>
4662 <li>Slide sequences</li>
4663 <li>Edit sequence in place</li>
4664 <li>EMBL CDS features</li>
4665 <li>DAS Feature mapping</li>
4666 <li>Feature ordering</li>
4667 <li>Alignment Properties</li>
4668 <li>Annotation Scores</li>
4669 <li>Sort by scores</li>
4670 <li>Feature/annotation editing in applet</li>
4675 <li>Headless state operation in 2.2.1</li>
4676 <li>Incorrect and unstable DNA pairwise alignment</li>
4677 <li>Cut and paste of sequences with annotation</li>
4678 <li>Feature group display state in XML</li>
4679 <li>Feature ordering in XML</li>
4680 <li>blc file iteration selection using filename # suffix</li>
4681 <li>Stockholm alignment properties</li>
4682 <li>Stockhom alignment secondary structure annotation</li>
4683 <li>2.2.1 applet had no feature transparency</li>
4684 <li>Number pad keys can be used in cursor mode</li>
4685 <li>Structure Viewer mirror image resolved</li>
4692 <div align="center">
4693 <strong>2.2.1</strong><br> 12/2/07
4698 <li>Non standard characters can be read and displayed
4699 <li>Annotations/Features can be imported/exported to the
4701 <li>Applet allows editing of sequence/annotation/group
4702 name & description
4703 <li>Preference setting to display sequence name in
4705 <li>Annotation file format extended to allow
4706 Sequence_groups to be defined
4707 <li>Default opening of alignment overview panel can be
4708 specified in preferences
4709 <li>PDB residue numbering annotation added to associated
4715 <li>Applet crash under certain Linux OS with Java 1.6
4717 <li>Annotation file export / import bugs fixed
4718 <li>PNG / EPS image output bugs fixed
4724 <div align="center">
4725 <strong>2.2</strong><br> 27/11/06
4730 <li>Multiple views on alignment
4731 <li>Sequence feature editing
4732 <li>"Reload" alignment
4733 <li>"Save" to current filename
4734 <li>Background dependent text colour
4735 <li>Right align sequence ids
4736 <li>User-defined lower case residue colours
4739 <li>Menu item accelerator keys
4740 <li>Control-V pastes to current alignment
4741 <li>Cancel button for DAS Feature Fetching
4742 <li>PCA and PDB Viewers zoom via mouse roller
4743 <li>User-defined sub-tree colours and sub-tree selection
4745 <li>'New Window' button on the 'Output to Text box'
4750 <li>New memory efficient Undo/Redo System
4751 <li>Optimised symbol lookups and conservation/consensus
4753 <li>Region Conservation/Consensus recalculated after
4755 <li>Fixed Remove Empty Columns Bug (empty columns at end
4757 <li>Slowed DAS Feature Fetching for increased robustness.
4759 <li>Made angle brackets in ASCII feature descriptions
4761 <li>Re-instated Zoom function for PCA
4762 <li>Sequence descriptions conserved in web service
4764 <li>UniProt ID discoverer uses any word separated by
4766 <li>WsDbFetch query/result association resolved
4767 <li>Tree leaf to sequence mapping improved
4768 <li>Smooth fonts switch moved to FontChooser dialog box.
4775 <div align="center">
4776 <strong>2.1.1</strong><br> 12/9/06
4781 <li>Copy consensus sequence to clipboard</li>
4786 <li>Image output - rightmost residues are rendered if
4787 sequence id panel has been resized</li>
4788 <li>Image output - all offscreen group boundaries are
4790 <li>Annotation files with sequence references - all
4791 elements in file are relative to sequence position</li>
4792 <li>Mac Applet users can use Alt key for group editing</li>
4798 <div align="center">
4799 <strong>2.1</strong><br> 22/8/06
4804 <li>MAFFT Multiple Alignment in default Web Service list</li>
4805 <li>DAS Feature fetching</li>
4806 <li>Hide sequences and columns</li>
4807 <li>Export Annotations and Features</li>
4808 <li>GFF file reading / writing</li>
4809 <li>Associate structures with sequences from local PDB
4811 <li>Add sequences to exisiting alignment</li>
4812 <li>Recently opened files / URL lists</li>
4813 <li>Applet can launch the full application</li>
4814 <li>Applet has transparency for features (Java 1.2
4816 <li>Applet has user defined colours parameter</li>
4817 <li>Applet can load sequences from parameter
4818 "sequence<em>x</em>"
4824 <li>Redundancy Panel reinstalled in the Applet</li>
4825 <li>Monospaced font - EPS / rescaling bug fixed</li>
4826 <li>Annotation files with sequence references bug fixed</li>
4832 <div align="center">
4833 <strong>2.08.1</strong><br> 2/5/06
4838 <li>Change case of selected region from Popup menu</li>
4839 <li>Choose to match case when searching</li>
4840 <li>Middle mouse button and mouse movement can compress /
4841 expand the visible width and height of the alignment</li>
4846 <li>Annotation Panel displays complete JNet results</li>
4852 <div align="center">
4853 <strong>2.08b</strong><br> 18/4/06
4859 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4860 <li>Righthand label on wrapped alignments shows correct
4867 <div align="center">
4868 <strong>2.08</strong><br> 10/4/06
4873 <li>Editing can be locked to the selection area</li>
4874 <li>Keyboard editing</li>
4875 <li>Create sequence features from searches</li>
4876 <li>Precalculated annotations can be loaded onto
4878 <li>Features file allows grouping of features</li>
4879 <li>Annotation Colouring scheme added</li>
4880 <li>Smooth fonts off by default - Faster rendering</li>
4881 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4886 <li>Drag & Drop fixed on Linux</li>
4887 <li>Jalview Archive file faster to load/save, sequence
4888 descriptions saved.</li>
4894 <div align="center">
4895 <strong>2.07</strong><br> 12/12/05
4900 <li>PDB Structure Viewer enhanced</li>
4901 <li>Sequence Feature retrieval and display enhanced</li>
4902 <li>Choose to output sequence start-end after sequence
4903 name for file output</li>
4904 <li>Sequence Fetcher WSDBFetch@EBI</li>
4905 <li>Applet can read feature files, PDB files and can be
4906 used for HTML form input</li>
4911 <li>HTML output writes groups and features</li>
4912 <li>Group editing is Control and mouse click</li>
4913 <li>File IO bugs</li>
4919 <div align="center">
4920 <strong>2.06</strong><br> 28/9/05
4925 <li>View annotations in wrapped mode</li>
4926 <li>More options for PCA viewer</li>
4931 <li>GUI bugs resolved</li>
4932 <li>Runs with -nodisplay from command line</li>
4938 <div align="center">
4939 <strong>2.05b</strong><br> 15/9/05
4944 <li>Choose EPS export as lineart or text</li>
4945 <li>Jar files are executable</li>
4946 <li>Can read in Uracil - maps to unknown residue</li>
4951 <li>Known OutOfMemory errors give warning message</li>
4952 <li>Overview window calculated more efficiently</li>
4953 <li>Several GUI bugs resolved</li>
4959 <div align="center">
4960 <strong>2.05</strong><br> 30/8/05
4965 <li>Edit and annotate in "Wrapped" view</li>
4970 <li>Several GUI bugs resolved</li>
4976 <div align="center">
4977 <strong>2.04</strong><br> 24/8/05
4982 <li>Hold down mouse wheel & scroll to change font
4988 <li>Improved JPred client reliability</li>
4989 <li>Improved loading of Jalview files</li>
4995 <div align="center">
4996 <strong>2.03</strong><br> 18/8/05
5001 <li>Set Proxy server name and port in preferences</li>
5002 <li>Multiple URL links from sequence ids</li>
5003 <li>User Defined Colours can have a scheme name and added
5005 <li>Choose to ignore gaps in consensus calculation</li>
5006 <li>Unix users can set default web browser</li>
5007 <li>Runs without GUI for batch processing</li>
5008 <li>Dynamically generated Web Service Menus</li>
5013 <li>InstallAnywhere download for Sparc Solaris</li>
5019 <div align="center">
5020 <strong>2.02</strong><br> 18/7/05
5026 <li>Copy & Paste order of sequences maintains
5027 alignment order.</li>
5033 <div align="center">
5034 <strong>2.01</strong><br> 12/7/05
5039 <li>Use delete key for deleting selection.</li>
5040 <li>Use Mouse wheel to scroll sequences.</li>
5041 <li>Help file updated to describe how to add alignment
5043 <li>Version and build date written to build properties
5045 <li>InstallAnywhere installation will check for updates
5046 at launch of Jalview.</li>
5051 <li>Delete gaps bug fixed.</li>
5052 <li>FileChooser sorts columns.</li>
5053 <li>Can remove groups one by one.</li>
5054 <li>Filechooser icons installed.</li>
5055 <li>Finder ignores return character when searching.
5056 Return key will initiate a search.<br>
5063 <div align="center">
5064 <strong>2.0</strong><br> 20/6/05
5069 <li>New codebase</li>