3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
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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>
58 <td width="60" align="center" nowrap><strong><a
59 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
60 <em>26/02/2021</em></strong></td>
61 <td align="left" valign="top"><em>Improved control of
62 Jalview's use of network services via jalview_properties</em>
65 <!-- JAL-3814 -->New .jalview_properties token controlling
66 launch of the news browser (like -nonews argument)
69 <!-- JAL-3813 -->New .jalview_properties token controlling
70 download of linkout URLs from
71 www.jalview.org/services/identifiers
74 <!-- JAL-3812 -->New .jalview_properties token controlling
75 download of BIOJSHTML templates
78 <!-- JAL-3811 -->New 'Discover Web Services' option to trigger
79 a one off JABAWS discovery if autodiscovery was disabled
82 <td align="left" valign="top">
84 <li><!-- JAL-3818 -->Intermittent deadlock opening structure in Jmol</li>
85 <li><!-- JAL-3806 -->Selections from tree built from CDS aren't propagated to Protein alignment</li>
90 <td width="60" align="center" nowrap><strong><a
91 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
92 <em>29/10/2020</em></strong></td>
93 <td align="left" valign="top">
98 <td align="left" valign="top">
101 <!-- JAL-3765 -->Find doesn't always highlight all matching
102 positions in a sequence (bug introduced in 2.11.1.2)
105 <!-- JAL-3760 -->Alignments containing one or more protein
106 sequences can be classed as nucleotide
109 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
110 sequences after alignment of protein products (known defect
111 first reported for 2.11.1.0)
114 <!-- JAL-3725 -->No tooltip or popup menu for genomic
115 features outwith CDS shown overlaid on protein
118 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
119 correctly mapped by Jalview (e.g. affects viral CDS with
120 ribosomal slippage, since 2.9.0)
123 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
127 <!-- JAL-3700 -->Selections in CDS sequence panel don't
128 always select corresponding protein sequences
131 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
132 column selection doesn't always ignore hidden columns
134 </ul> <em>Installer</em>
137 <!-- JAL-3611 -->Space character in Jalview install path on
138 Windows prevents install4j launching getdown
140 </ul> <em>Development</em>
143 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
144 version numbers in doc/building.md
150 <td width="60" align="center" nowrap><strong><a
151 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
152 <em>25/09/2020</em></strong></td>
153 <td align="left" valign="top">
157 <td align="left" valign="top">
160 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
161 "Encountered problems opening
162 https://www.jalview.org/examples/exampleFile_2_7.jvp"
168 <td width="60" align="center" nowrap><strong><a
169 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
170 <em>17/09/2020</em></strong></td>
171 <td align="left" valign="top">
174 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
175 residue in cursor mode
178 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
179 HTSJDK from 2.12 to 2.23
182 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
183 optimisations and improvements suggested by Bob Hanson and
184 improved compatibility with JalviewJS
187 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
188 alignments from Pfam and Rfam
191 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
192 import (no longer based on .gz extension)
195 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
198 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
199 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
203 <!-- JAL-3667 -->Improved warning messages, debug logging
204 and fixed Retry action when Jalview encounters errors when
205 saving or making backup files.
208 <!-- JAL-3676 -->Enhanced Jalview Java Console:
210 <li>Jalview's logging level can be configured</li>
211 <li>Copy to Clipboard Buttion</li>
215 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
216 when running on Linux (Requires Java 11+)
218 </ul> <em>Launching Jalview</em>
221 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
222 through a system property
225 <!-- JAL-3477 -->Improved built-in documentation and command
226 line help for configuring Jalview's memory
230 <td align="left" valign="top">
233 <!-- JAL-3691 -->Conservation and Quality tracks are shown
234 but not calculated and no protein or DNA score models are
235 available for tree/PCA calculation when launched with
236 Turkish language locale
239 <!-- JAL-3493 -->Escape does not clear highlights on the
240 alignment (Since Jalview 2.10.3)
243 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
244 doesn't slide selected sequences, just sequence under cursor
247 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
248 sequence under the cursor
251 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
252 multiple EMBL gene products shown for a single contig
255 <!-- JAL-3696 -->Errors encountered when processing variants
256 from VCF files yield "Error processing VCF: Format specifier
260 <!-- JAL-3697 -->Count of features not shown can be wrong
261 when there are both local and complementary features mapped
262 to the position under the cursor
265 <!-- JAL-3673 -->Sequence ID for reference sequence is
266 clipped when Right align Sequence IDs enabled
269 <!-- JAL-2983 -->Slider with negative range values not
270 rendered correctly in VAqua4 (Since 2.10.4)
273 <!-- JAL-3685 -->Single quotes not displayed correctly in
274 internationalised text for some messages and log output
277 <!-- JAL-3490 -->Find doesn't report matches that span
278 hidden gapped columns
281 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
282 panels, Alignment viewport and annotation renderer.
285 <!-- JAL-3561 -->Jalview ignores file format parameter
286 specifying output format when exporting an alignment via the
290 <!-- JAL-3667 -->Windows 10: For a minority of users, if
291 backups are not enabled, Jalview sometimes fails to
292 overwrite an existing file and raises a warning dialog. (in
293 2.11.0, and 2.11.1.0, the workaround is to try to save the
294 file again, and if that fails, delete the original file and
298 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
302 <!-- JAL-3741 -->References to http://www.jalview.org in
303 program and documentation
305 </ul> <em>Launching Jalview</em>
308 <!-- JAL-3718 -->Jalview application fails when launched the
309 first time for a version that has different jars to the
310 previous launched version.
312 </ul> <em>Developing Jalview</em>
315 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
316 data, causing cloverReport gradle task to fail with an
320 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
321 monitor the release channel
323 </ul> <em>New Known defects</em>
326 <!-- JAL-3748 -->CDS shown in result of submitting proteins
327 in a CDS/Protein alignment to a web service is wrong when
328 proteins share a common transcript sequence (e.g.
329 genome of RNA viruses)
332 <!-- JAL-3576 -->Co-located features exported and re-imported
333 are ordered differently when shown on alignment and in
334 tooltips. (Also affects v2.11.1.0)
337 <!-- JAL-3702 -->Drag and drop of alignment file onto
338 alignment window when in a HiDPI scaled mode in Linux only
339 works for the top left quadrant of the alignment window
342 <!-- JAL-3701 -->Stale build data in jalview standalone jar
343 builds (only affects 2.11.1.1 branch)
346 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
347 when alignment view restored from project (since Jalview 2.11.0)
350 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
351 protein products for certain ENA records are repeatedly
352 shown via Calculate->Show Cross Refs
358 <td width="60" align="center" nowrap><strong><a
359 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
360 <em>22/04/2020</em></strong></td>
361 <td align="left" valign="top">
364 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
365 'virtual' codon features shown on protein (or vice versa)
366 for display in alignments, on structure views (including
367 transfer to UCSF chimera), in feature reports and for
371 <!-- JAL-3121 -->Feature attributes from VCF files can be
372 exported and re-imported as GFF3 files
375 <!-- JAL-3376 -->Capture VCF "fixed column" values
376 POS, ID, QUAL, FILTER as Feature Attributes
379 <!-- JAL-3375 -->More robust VCF numeric data field
380 validation while parsing
383 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
387 <!-- JAL-3535 -->Feature Settings dialog title includes name
391 <!-- JAL-3538 -->Font anti-aliasing in alignment views
395 <!-- JAL-3468 -->Very long feature descriptions truncated in
399 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
400 with no feature types visible
403 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
405 </ul><em>Jalview Installer</em>
408 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
409 in console (may be null when Jalview launched as executable jar or via conda)
412 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
415 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
418 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
420 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
421 </ul> <em>Release processes</em>
424 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
427 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
429 </ul> <em>Build System</em>
432 <!-- JAL-3510 -->Clover updated to 4.4.1
435 <!-- JAL-3513 -->Test code included in Clover coverage
439 <em>Groovy Scripts</em>
442 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
443 to stdout containing the consensus sequence for each
444 alignment in a Jalview session
447 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
448 genomic sequence_variant annotation from CDS as
449 missense_variant or synonymous_variant on protein products.
453 <td align="left" valign="top">
456 <!-- JAL-3581 -->Hidden sequence markers still visible when
457 'Show hidden markers' option is not ticked
460 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
461 PNG output when 'Automatically set ID width' is set in
462 jalview preferences or properties file
465 <!-- JAL-3571 -->Feature Editor dialog can be opened when
466 'Show Sequence Features' option is not ticked
469 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
470 buttons in Feature Settings dialog are clicked when no
474 <!-- JAL-3412 -->ID margins for CDS and Protein views not
475 equal when split frame is first opened
478 <!-- JAL-3296 -->Sequence position numbers in status bar not
479 correct after editing a sequence's start position
482 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
483 with annotation and exceptions thrown when only a few
484 columns shown in wrapped mode
487 <!-- JAL-3386 -->Sequence IDs missing in headless export of
488 wrapped alignment figure with annotations
491 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
492 ID fails with ClassCastException
495 <!-- JAL-3389 -->Chimera session not restored from Jalview
499 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
500 feature settings dialog also selects columns
503 <!-- JAL-3473 -->SpinnerNumberModel causes
504 IllegalArgumentException in some circumstances
507 <!-- JAL-3534 -->Multiple feature settings dialogs can be
511 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
512 alignment window is closed
515 <!-- JAL-3406 -->Credits missing some authors in Jalview
516 help documentation for 2.11.0 release
519 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
520 includes Pfam ID as sequence's accession rather than its
523 </ul> <em>Java 11 Compatibility issues</em>
526 <!-- JAL-2987 -->OSX - Can't view some search results in
527 PDB/Uniprot search panel
529 </ul> <em>Installer</em>
532 <!-- JAL-3447 -->Jalview should not create file associations
533 for 3D structure files (.pdb, .mmcif. .cif)
535 </ul> <em>Repository and Source Release</em>
538 <!-- JAL-3474 -->removed obsolete .cvsignore files from
542 <!-- JAL-3541 -->Clover report generation running out of
545 </ul> <em>New Known Issues</em>
548 <!-- JAL-3523 -->OSX - Current working directory not
549 preserved when Jalview.app launched with parameters from
553 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
554 clipped in headless figure export when Right Align option
558 <!-- JAL-3542 -->Jalview Installation type always reports
559 'Source' in console output
562 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
563 bamboo server but run fine locally.
569 <td width="60" align="center" nowrap>
570 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
571 <em>04/07/2019</em></strong>
573 <td align="left" valign="top">
576 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
577 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
578 source project) rather than InstallAnywhere
581 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
582 settings, receive over the air updates and launch specific
583 versions via (<a href="https://github.com/threerings/getdown">Three
587 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
588 formats supported by Jalview (including .jvp project files)
591 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
592 arguments and switch between different getdown channels
595 <!-- JAL-3141 -->Backup files created when saving Jalview project
600 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
601 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
603 <!-- JAL-2620 -->Alternative genetic code tables for
604 'Translate as cDNA'</li>
606 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
607 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
610 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
611 implementation that allows updates) used for Sequence Feature collections</li>
613 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
614 features can be filtered and shaded according to any
615 associated attributes (e.g. variant attributes from VCF
616 file, or key-value pairs imported from column 9 of GFF
620 <!-- JAL-2879 -->Feature Attributes and shading schemes
621 stored and restored from Jalview Projects
624 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
625 recognise variant features
628 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
629 sequences (also coloured red by default)
632 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
636 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
637 algorithm (Z-sort/transparency and filter aware)
640 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
646 <!-- JAL-3205 -->Symmetric score matrices for faster
647 tree and PCA calculations
649 <li><strong>Principal Components Analysis Viewer</strong>
652 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
653 and Viewer state saved in Jalview Project
655 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
658 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
662 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
667 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
669 <li><strong>Speed and Efficiency</strong>
672 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
673 multiple groups when working with large alignments
676 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
680 <li><strong>User Interface</strong>
683 <!-- JAL-2933 -->Finder panel remembers last position in each
687 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
688 what is shown)<br />Only visible regions of alignment are shown by
689 default (can be changed in user preferences)
692 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
693 to the Overwrite Dialog
696 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
700 <!-- JAL-1244 -->Status bar shows bounds when dragging a
701 selection region, and gap count when inserting or deleting gaps
704 <!-- JAL-3132 -->Status bar updates over sequence and annotation
708 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
712 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
716 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
719 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
723 <!-- JAL-3181 -->Consistent ordering of links in sequence id
727 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
729 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
733 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
734 <li><strong>Java 11 Support (not yet on general release)</strong>
737 <!-- -->OSX GUI integrations for App menu's 'About' entry and
742 <em>Deprecations</em>
744 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
745 capabilities removed from the Jalview Desktop
747 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
748 unmarshalling has been replaced by JAXB for Jalview projects
749 and XML based data retrieval clients</li>
750 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
751 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
752 </ul> <em>Documentation</em>
754 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
755 not supported in EPS figure export
757 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
758 </ul> <em>Development and Release Processes</em>
761 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
764 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
766 <!-- JAL-3225 -->Eclipse project configuration managed with
770 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
771 Bamboo continuous integration for unattended Test Suite
775 <!-- JAL-2864 -->Memory test suite to detect leaks in common
779 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
783 <!-- JAL-3248 -->Developer documentation migrated to
784 markdown (with HTML rendering)
787 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
790 <!-- JAL-3289 -->New URLs for publishing development
795 <td align="left" valign="top">
798 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
801 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
802 superposition in Jmol fail on Windows
805 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
806 structures for sequences with lots of PDB structures
809 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
813 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
814 project involving multiple views
817 <!-- JAL-3164 -->Overview for complementary view in a linked
818 CDS/Protein alignment is not updated when Hide Columns by
819 Annotation dialog hides columns
822 <!-- JAL-3158 -->Selection highlighting in the complement of a
823 CDS/Protein alignment stops working after making a selection in
824 one view, then making another selection in the other view
827 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
831 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
832 Settings and Jalview Preferences panels
835 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
836 overview with large alignments
839 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
840 region if columns were selected by dragging right-to-left and the
841 mouse moved to the left of the first column
844 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
845 hidden column marker via scale popup menu
848 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
849 doesn't tell users the invalid URL
852 <!-- JAL-2816 -->Tooltips displayed for features filtered by
856 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
857 show cross references or Fetch Database References are shown in
861 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
862 peptide sequence (computed variant shown as p.Res.null)
865 <!-- JAL-2060 -->'Graduated colour' option not offered for
866 manually created features (where feature score is Float.NaN)
869 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
870 when columns are hidden
873 <!-- JAL-3082 -->Regular expression error for '(' in Select
874 Columns by Annotation description
877 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
878 out of Scale or Annotation Panel
881 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
885 <!-- JAL-3074 -->Left/right drag in annotation can scroll
889 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
893 <!-- JAL-3002 -->Column display is out by one after Page Down,
894 Page Up in wrapped mode
897 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
900 <!-- JAL-2932 -->Finder searches in minimised alignments
903 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
904 on opening an alignment
907 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
911 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
912 different groups in the alignment are selected
915 <!-- JAL-2717 -->Internationalised colour scheme names not shown
919 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
923 <!-- JAL-3125 -->Value input for graduated feature colour
924 threshold gets 'unrounded'
927 <!-- JAL-2982 -->PCA image export doesn't respect background
931 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
934 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
937 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
941 <!-- JAL-2964 -->Associate Tree with All Views not restored from
945 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
946 shown in complementary view
949 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
950 without normalisation
953 <!-- JAL-3021 -->Sequence Details report should open positioned at top
957 <!-- JAL-914 -->Help page can be opened twice
960 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
962 </ul> <em>Editing</em>
965 <!-- JAL-2822 -->Start and End should be updated when sequence
966 data at beginning or end of alignment added/removed via 'Edit'
970 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
971 relocate sequence features correctly when start of sequence is
972 removed (Known defect since 2.10)
975 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
976 dialog corrupts dataset sequence
979 <!-- JAL-868 -->Structure colours not updated when associated tree
980 repartitions the alignment view (Regression in 2.10.5)
982 </ul> <em>Datamodel</em>
985 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
986 sequence's End is greater than its length
988 </ul> <em>Bugs fixed for Java 11 Support (not yet on
989 general release)</em>
992 <!-- JAL-3288 -->Menus work properly in split-screen
994 </ul> <em>New Known Defects</em>
997 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1000 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1001 regions of protein alignment.
1004 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1005 is restored from a Jalview 2.11 project
1008 <!-- JAL-3213 -->Alignment panel height can be too small after
1012 <!-- JAL-3240 -->Display is incorrect after removing gapped
1013 columns within hidden columns
1016 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1017 window after dragging left to select columns to left of visible
1021 <!-- JAL-2876 -->Features coloured according to their description
1022 string and thresholded by score in earlier versions of Jalview are
1023 not shown as thresholded features in 2.11. To workaround please
1024 create a Score filter instead.
1027 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1029 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1032 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1033 alignments with multiple views can close views unexpectedly
1036 <em>Java 11 Specific defects</em>
1039 <!-- JAL-3235 -->Jalview Properties file is not sorted
1040 alphabetically when saved
1046 <td width="60" nowrap>
1047 <div align="center">
1048 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1051 <td><div align="left">
1055 <!-- JAL-3101 -->Default memory for Jalview webstart and
1056 InstallAnywhere increased to 1G.
1059 <!-- JAL-247 -->Hidden sequence markers and representative
1060 sequence bolding included when exporting alignment as EPS,
1061 SVG, PNG or HTML. <em>Display is configured via the
1062 Format menu, or for command-line use via a Jalview
1063 properties file.</em>
1066 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1067 API and sequence data now imported as JSON.
1070 <!-- JAL-3065 -->Change in recommended way of starting
1071 Jalview via a Java command line: add jars in lib directory
1072 to CLASSPATH, rather than via the deprecated java.ext.dirs
1076 <em>Development</em>
1079 <!-- JAL-3047 -->Support added to execute test suite
1080 instrumented with <a href="http://openclover.org/">Open
1085 <td><div align="left">
1089 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1090 row shown in Feredoxin Structure alignment view of example
1094 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1095 annotation displayed.
1098 <!-- JAL-3107 -->Group conservation/consensus not shown
1099 for newly created group when 'Apply to all groups'
1103 <!-- JAL-3087 -->Corrupted display when switching to
1104 wrapped mode when sequence panel's vertical scrollbar is
1108 <!-- JAL-3003 -->Alignment is black in exported EPS file
1109 when sequences are selected in exported view.</em>
1112 <!-- JAL-3059 -->Groups with different coloured borders
1113 aren't rendered with correct colour.
1116 <!-- JAL-3092 -->Jalview could hang when importing certain
1117 types of knotted RNA secondary structure.
1120 <!-- JAL-3095 -->Sequence highlight and selection in
1121 trimmed VARNA 2D structure is incorrect for sequences that
1125 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1126 annotation when columns are inserted into an alignment,
1127 and when exporting as Stockholm flatfile.
1130 <!-- JAL-3053 -->Jalview annotation rows containing upper
1131 and lower-case 'E' and 'H' do not automatically get
1132 treated as RNA secondary structure.
1135 <!-- JAL-3106 -->.jvp should be used as default extension
1136 (not .jar) when saving a Jalview project file.
1139 <!-- JAL-3105 -->Mac Users: closing a window correctly
1140 transfers focus to previous window on OSX
1143 <em>Java 10 Issues Resolved</em>
1146 <!-- JAL-2988 -->OSX - Can't save new files via the File
1147 or export menus by typing in a name into the Save dialog
1151 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1152 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1153 'look and feel' which has improved compatibility with the
1154 latest version of OSX.
1161 <td width="60" nowrap>
1162 <div align="center">
1163 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1164 <em>7/06/2018</em></strong>
1167 <td><div align="left">
1171 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1172 annotation retrieved from Uniprot
1175 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1176 onto the Jalview Desktop
1180 <td><div align="left">
1184 <!-- JAL-3017 -->Cannot import features with multiple
1185 variant elements (blocks import of some Uniprot records)
1188 <!-- JAL-2997 -->Clustal files with sequence positions in
1189 right-hand column parsed correctly
1192 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1193 not alignment area in exported graphic
1196 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1197 window has input focus
1200 <!-- JAL-2992 -->Annotation panel set too high when
1201 annotation added to view (Windows)
1204 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1205 network connectivity is poor
1208 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1209 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1210 the currently open URL and links from a page viewed in
1211 Firefox or Chrome on Windows is now fully supported. If
1212 you are using Edge, only links in the page can be
1213 dragged, and with Internet Explorer, only the currently
1214 open URL in the browser can be dropped onto Jalview.</em>
1217 <em>New Known Defects</em>
1219 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1224 <td width="60" nowrap>
1225 <div align="center">
1226 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1229 <td><div align="left">
1233 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1234 for disabling automatic superposition of multiple
1235 structures and open structures in existing views
1238 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1239 ID and annotation area margins can be click-dragged to
1243 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1247 <!-- JAL-2759 -->Improved performance for large alignments
1248 and lots of hidden columns
1251 <!-- JAL-2593 -->Improved performance when rendering lots
1252 of features (particularly when transparency is disabled)
1255 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1256 exchange of Jalview features and Chimera attributes made
1262 <td><div align="left">
1265 <!-- JAL-2899 -->Structure and Overview aren't updated
1266 when Colour By Annotation threshold slider is adjusted
1269 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1270 overlapping alignment panel
1273 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1277 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1278 improved: CDS not handled correctly if transcript has no
1282 <!-- JAL-2321 -->Secondary structure and temperature
1283 factor annotation not added to sequence when local PDB
1284 file associated with it by drag'n'drop or structure
1288 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1289 dialog doesn't import PDB files dropped on an alignment
1292 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1293 scroll bar doesn't work for some CDS/Protein views
1296 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1297 Java 1.8u153 onwards and Java 1.9u4+.
1300 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1301 columns in annotation row
1304 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1305 honored in batch mode
1308 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1309 for structures added to existing Jmol view
1312 <!-- JAL-2223 -->'View Mappings' includes duplicate
1313 entries after importing project with multiple views
1316 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1317 protein sequences via SIFTS from associated PDB entries
1318 with negative residue numbers or missing residues fails
1321 <!-- JAL-2952 -->Exception when shading sequence with negative
1322 Temperature Factor values from annotated PDB files (e.g.
1323 as generated by CONSURF)
1326 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1327 tooltip doesn't include a text description of mutation
1330 <!-- JAL-2922 -->Invert displayed features very slow when
1331 structure and/or overview windows are also shown
1334 <!-- JAL-2954 -->Selecting columns from highlighted regions
1335 very slow for alignments with large numbers of sequences
1338 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1339 with 'StringIndexOutOfBounds'
1342 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1343 platforms running Java 10
1346 <!-- JAL-2960 -->Adding a structure to existing structure
1347 view appears to do nothing because the view is hidden behind the alignment view
1353 <!-- JAL-2926 -->Copy consensus sequence option in applet
1354 should copy the group consensus when popup is opened on it
1360 <!-- JAL-2913 -->Fixed ID width preference is not respected
1363 <em>New Known Defects</em>
1366 <!-- JAL-2973 --> Exceptions occasionally raised when
1367 editing a large alignment and overview is displayed
1370 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1371 repeatedly after a series of edits even when the overview
1372 is no longer reflecting updates
1375 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1376 structures for protein subsequence (if 'Trim Retrieved
1377 Sequences' enabled) or Ensembl isoforms (Workaround in
1378 2.10.4 is to fail back to N&W mapping)
1381 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1382 option gives blank output
1389 <td width="60" nowrap>
1390 <div align="center">
1391 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1394 <td><div align="left">
1395 <ul><li>Updated Certum Codesigning Certificate
1396 (Valid till 30th November 2018)</li></ul></div></td>
1397 <td><div align="left">
1398 <em>Desktop</em><ul>
1400 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1401 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1402 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1403 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1404 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1405 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1406 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1412 <td width="60" nowrap>
1413 <div align="center">
1414 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1417 <td><div align="left">
1421 <!-- JAL-2446 -->Faster and more efficient management and
1422 rendering of sequence features
1425 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1426 429 rate limit request hander
1429 <!-- JAL-2773 -->Structure views don't get updated unless
1430 their colours have changed
1433 <!-- JAL-2495 -->All linked sequences are highlighted for
1434 a structure mousover (Jmol) or selection (Chimera)
1437 <!-- JAL-2790 -->'Cancel' button in progress bar for
1438 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1441 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1442 view from Ensembl locus cross-references
1445 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1449 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1450 feature can be disabled
1453 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1454 PDB easier retrieval of sequences for lists of IDs
1457 <!-- JAL-2758 -->Short names for sequences retrieved from
1463 <li>Groovy interpreter updated to 2.4.12</li>
1464 <li>Example groovy script for generating a matrix of
1465 percent identity scores for current alignment.</li>
1467 <em>Testing and Deployment</em>
1470 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1474 <td><div align="left">
1478 <!-- JAL-2643 -->Pressing tab after updating the colour
1479 threshold text field doesn't trigger an update to the
1483 <!-- JAL-2682 -->Race condition when parsing sequence ID
1487 <!-- JAL-2608 -->Overview windows are also closed when
1488 alignment window is closed
1491 <!-- JAL-2548 -->Export of features doesn't always respect
1495 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1496 takes a long time in Cursor mode
1502 <!-- JAL-2777 -->Structures with whitespace chainCode
1503 cannot be viewed in Chimera
1506 <!-- JAL-2728 -->Protein annotation panel too high in
1510 <!-- JAL-2757 -->Can't edit the query after the server
1511 error warning icon is shown in Uniprot and PDB Free Text
1515 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1518 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1521 <!-- JAL-2739 -->Hidden column marker in last column not
1522 rendered when switching back from Wrapped to normal view
1525 <!-- JAL-2768 -->Annotation display corrupted when
1526 scrolling right in unwapped alignment view
1529 <!-- JAL-2542 -->Existing features on subsequence
1530 incorrectly relocated when full sequence retrieved from
1534 <!-- JAL-2733 -->Last reported memory still shown when
1535 Desktop->Show Memory is unticked (OSX only)
1538 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1539 features of same type and group to be selected for
1543 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1544 alignments when hidden columns are present
1547 <!-- JAL-2392 -->Jalview freezes when loading and
1548 displaying several structures
1551 <!-- JAL-2732 -->Black outlines left after resizing or
1555 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1556 within the Jalview desktop on OSX
1559 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1560 when in wrapped alignment mode
1563 <!-- JAL-2636 -->Scale mark not shown when close to right
1564 hand end of alignment
1567 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1568 each selected sequence do not have correct start/end
1572 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1573 after canceling the Alignment Window's Font dialog
1576 <!-- JAL-2036 -->Show cross-references not enabled after
1577 restoring project until a new view is created
1580 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1581 URL links appears when only default EMBL-EBI link is
1582 configured (since 2.10.2b2)
1585 <!-- JAL-2775 -->Overview redraws whole window when box
1586 position is adjusted
1589 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1590 in a multi-chain structure when viewing alignment
1591 involving more than one chain (since 2.10)
1594 <!-- JAL-2811 -->Double residue highlights in cursor mode
1595 if new selection moves alignment window
1598 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1599 arrow key in cursor mode to pass hidden column marker
1602 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1603 that produces correctly annotated transcripts and products
1606 <!-- JAL-2776 -->Toggling a feature group after first time
1607 doesn't update associated structure view
1610 <em>Applet</em><br />
1613 <!-- JAL-2687 -->Concurrent modification exception when
1614 closing alignment panel
1617 <em>BioJSON</em><br />
1620 <!-- JAL-2546 -->BioJSON export does not preserve
1621 non-positional features
1624 <em>New Known Issues</em>
1627 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1628 sequence features correctly (for many previous versions of
1632 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1633 using cursor in wrapped panel other than top
1636 <!-- JAL-2791 -->Select columns containing feature ignores
1637 graduated colour threshold
1640 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1641 always preserve numbering and sequence features
1644 <em>Known Java 9 Issues</em>
1647 <!-- JAL-2902 -->Groovy Console very slow to open and is
1648 not responsive when entering characters (Webstart, Java
1655 <td width="60" nowrap>
1656 <div align="center">
1657 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1658 <em>2/10/2017</em></strong>
1661 <td><div align="left">
1662 <em>New features in Jalview Desktop</em>
1665 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1667 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1671 <td><div align="left">
1675 <td width="60" nowrap>
1676 <div align="center">
1677 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1678 <em>7/9/2017</em></strong>
1681 <td><div align="left">
1685 <!-- JAL-2588 -->Show gaps in overview window by colouring
1686 in grey (sequences used to be coloured grey, and gaps were
1690 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1694 <!-- JAL-2587 -->Overview updates immediately on increase
1695 in size and progress bar shown as higher resolution
1696 overview is recalculated
1701 <td><div align="left">
1705 <!-- JAL-2664 -->Overview window redraws every hidden
1706 column region row by row
1709 <!-- JAL-2681 -->duplicate protein sequences shown after
1710 retrieving Ensembl crossrefs for sequences from Uniprot
1713 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1714 format setting is unticked
1717 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1718 if group has show boxes format setting unticked
1721 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1722 autoscrolling whilst dragging current selection group to
1723 include sequences and columns not currently displayed
1726 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1727 assemblies are imported via CIF file
1730 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1731 displayed when threshold or conservation colouring is also
1735 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1739 <!-- JAL-2673 -->Jalview continues to scroll after
1740 dragging a selected region off the visible region of the
1744 <!-- JAL-2724 -->Cannot apply annotation based
1745 colourscheme to all groups in a view
1748 <!-- JAL-2511 -->IDs don't line up with sequences
1749 initially after font size change using the Font chooser or
1756 <td width="60" nowrap>
1757 <div align="center">
1758 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1761 <td><div align="left">
1762 <em>Calculations</em>
1766 <!-- JAL-1933 -->Occupancy annotation row shows number of
1767 ungapped positions in each column of the alignment.
1770 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1771 a calculation dialog box
1774 <!-- JAL-2379 -->Revised implementation of PCA for speed
1775 and memory efficiency (~30x faster)
1778 <!-- JAL-2403 -->Revised implementation of sequence
1779 similarity scores as used by Tree, PCA, Shading Consensus
1780 and other calculations
1783 <!-- JAL-2416 -->Score matrices are stored as resource
1784 files within the Jalview codebase
1787 <!-- JAL-2500 -->Trees computed on Sequence Feature
1788 Similarity may have different topology due to increased
1795 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1796 model for alignments and groups
1799 <!-- JAL-384 -->Custom shading schemes created via groovy
1806 <!-- JAL-2526 -->Efficiency improvements for interacting
1807 with alignment and overview windows
1810 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1814 <!-- JAL-2388 -->Hidden columns and sequences can be
1818 <!-- JAL-2611 -->Click-drag in visible area allows fine
1819 adjustment of visible position
1823 <em>Data import/export</em>
1826 <!-- JAL-2535 -->Posterior probability annotation from
1827 Stockholm files imported as sequence associated annotation
1830 <!-- JAL-2507 -->More robust per-sequence positional
1831 annotation input/output via stockholm flatfile
1834 <!-- JAL-2533 -->Sequence names don't include file
1835 extension when importing structure files without embedded
1836 names or PDB accessions
1839 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1840 format sequence substitution matrices
1843 <em>User Interface</em>
1846 <!-- JAL-2447 --> Experimental Features Checkbox in
1847 Desktop's Tools menu to hide or show untested features in
1851 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1852 via Overview or sequence motif search operations
1855 <!-- JAL-2547 -->Amend sequence features dialog box can be
1856 opened by double clicking gaps within sequence feature
1860 <!-- JAL-1476 -->Status bar message shown when not enough
1861 aligned positions were available to create a 3D structure
1865 <em>3D Structure</em>
1868 <!-- JAL-2430 -->Hidden regions in alignment views are not
1869 coloured in linked structure views
1872 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1873 file-based command exchange
1876 <!-- JAL-2375 -->Structure chooser automatically shows
1877 Cached Structures rather than querying the PDBe if
1878 structures are already available for sequences
1881 <!-- JAL-2520 -->Structures imported via URL are cached in
1882 the Jalview project rather than downloaded again when the
1883 project is reopened.
1886 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1887 to transfer Chimera's structure attributes as Jalview
1888 features, and vice-versa (<strong>Experimental
1892 <em>Web Services</em>
1895 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1898 <!-- JAL-2335 -->Filter non-standard amino acids and
1899 nucleotides when submitting to AACon and other MSA
1903 <!-- JAL-2316, -->URLs for viewing database
1904 cross-references provided by identifiers.org and the
1905 EMBL-EBI's MIRIAM DB
1912 <!-- JAL-2344 -->FileFormatI interface for describing and
1913 identifying file formats (instead of String constants)
1916 <!-- JAL-2228 -->FeatureCounter script refactored for
1917 efficiency when counting all displayed features (not
1918 backwards compatible with 2.10.1)
1921 <em>Example files</em>
1924 <!-- JAL-2631 -->Graduated feature colour style example
1925 included in the example feature file
1928 <em>Documentation</em>
1931 <!-- JAL-2339 -->Release notes reformatted for readability
1932 with the built-in Java help viewer
1935 <!-- JAL-1644 -->Find documentation updated with 'search
1936 sequence description' option
1942 <!-- JAL-2485, -->External service integration tests for
1943 Uniprot REST Free Text Search Client
1946 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1949 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1954 <td><div align="left">
1955 <em>Calculations</em>
1958 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1959 matrix - C->R should be '-3'<br />Old matrix restored
1960 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1962 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1963 Jalview's treatment of gaps in PCA and substitution matrix
1964 based Tree calculations.<br /> <br />In earlier versions
1965 of Jalview, gaps matching gaps were penalised, and gaps
1966 matching non-gaps penalised even more. In the PCA
1967 calculation, gaps were actually treated as non-gaps - so
1968 different costs were applied, which meant Jalview's PCAs
1969 were different to those produced by SeqSpace.<br />Jalview
1970 now treats gaps in the same way as SeqSpace (ie it scores
1971 them as 0). <br /> <br />Enter the following in the
1972 Groovy console to restore pre-2.10.2 behaviour:<br />
1973 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1974 // for 2.10.1 mode <br />
1975 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1976 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1977 these settings will affect all subsequent tree and PCA
1978 calculations (not recommended)</em></li>
1980 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1981 scaling of branch lengths for trees computed using
1982 Sequence Feature Similarity.
1985 <!-- JAL-2377 -->PCA calculation could hang when
1986 generating output report when working with highly
1987 redundant alignments
1990 <!-- JAL-2544 --> Sort by features includes features to
1991 right of selected region when gaps present on right-hand
1995 <em>User Interface</em>
1998 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1999 doesn't reselect a specific sequence's associated
2000 annotation after it was used for colouring a view
2003 <!-- JAL-2419 -->Current selection lost if popup menu
2004 opened on a region of alignment without groups
2007 <!-- JAL-2374 -->Popup menu not always shown for regions
2008 of an alignment with overlapping groups
2011 <!-- JAL-2310 -->Finder double counts if both a sequence's
2012 name and description match
2015 <!-- JAL-2370 -->Hiding column selection containing two
2016 hidden regions results in incorrect hidden regions
2019 <!-- JAL-2386 -->'Apply to all groups' setting when
2020 changing colour does not apply Conservation slider value
2024 <!-- JAL-2373 -->Percentage identity and conservation menu
2025 items do not show a tick or allow shading to be disabled
2028 <!-- JAL-2385 -->Conservation shading or PID threshold
2029 lost when base colourscheme changed if slider not visible
2032 <!-- JAL-2547 -->Sequence features shown in tooltip for
2033 gaps before start of features
2036 <!-- JAL-2623 -->Graduated feature colour threshold not
2037 restored to UI when feature colour is edited
2040 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2041 a time when scrolling vertically in wrapped mode.
2044 <!-- JAL-2630 -->Structure and alignment overview update
2045 as graduate feature colour settings are modified via the
2049 <!-- JAL-2034 -->Overview window doesn't always update
2050 when a group defined on the alignment is resized
2053 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2054 wrapped view result in positional status updates
2058 <!-- JAL-2563 -->Status bar doesn't show position for
2059 ambiguous amino acid and nucleotide symbols
2062 <!-- JAL-2602 -->Copy consensus sequence failed if
2063 alignment included gapped columns
2066 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2067 widgets don't permanently disappear
2070 <!-- JAL-2503 -->Cannot select or filter quantitative
2071 annotation that are shown only as column labels (e.g.
2072 T-Coffee column reliability scores)
2075 <!-- JAL-2594 -->Exception thrown if trying to create a
2076 sequence feature on gaps only
2079 <!-- JAL-2504 -->Features created with 'New feature'
2080 button from a Find inherit previously defined feature type
2081 rather than the Find query string
2084 <!-- JAL-2423 -->incorrect title in output window when
2085 exporting tree calculated in Jalview
2088 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2089 and then revealing them reorders sequences on the
2093 <!-- JAL-964 -->Group panel in sequence feature settings
2094 doesn't update to reflect available set of groups after
2095 interactively adding or modifying features
2098 <!-- JAL-2225 -->Sequence Database chooser unusable on
2102 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2103 only excluded gaps in current sequence and ignored
2110 <!-- JAL-2421 -->Overview window visible region moves
2111 erratically when hidden rows or columns are present
2114 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2115 Structure Viewer's colour menu don't correspond to
2119 <!-- JAL-2405 -->Protein specific colours only offered in
2120 colour and group colour menu for protein alignments
2123 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2124 reflect currently selected view or group's shading
2128 <!-- JAL-2624 -->Feature colour thresholds not respected
2129 when rendered on overview and structures when opacity at
2133 <!-- JAL-2589 -->User defined gap colour not shown in
2134 overview when features overlaid on alignment
2137 <!-- JAL-2567 -->Feature settings for different views not
2138 recovered correctly from Jalview project file
2141 <!-- JAL-2256 -->Feature colours in overview when first opened
2142 (automatically via preferences) are different to the main
2146 <em>Data import/export</em>
2149 <!-- JAL-2576 -->Very large alignments take a long time to
2153 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2154 added after a sequence was imported are not written to
2158 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2159 when importing RNA secondary structure via Stockholm
2162 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2163 not shown in correct direction for simple pseudoknots
2166 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2167 with lightGray or darkGray via features file (but can
2171 <!-- JAL-2383 -->Above PID colour threshold not recovered
2172 when alignment view imported from project
2175 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2176 structure and sequences extracted from structure files
2177 imported via URL and viewed in Jmol
2180 <!-- JAL-2520 -->Structures loaded via URL are saved in
2181 Jalview Projects rather than fetched via URL again when
2182 the project is loaded and the structure viewed
2185 <em>Web Services</em>
2188 <!-- JAL-2519 -->EnsemblGenomes example failing after
2189 release of Ensembl v.88
2192 <!-- JAL-2366 -->Proxy server address and port always
2193 appear enabled in Preferences->Connections
2196 <!-- JAL-2461 -->DAS registry not found exceptions
2197 removed from console output
2200 <!-- JAL-2582 -->Cannot retrieve protein products from
2201 Ensembl by Peptide ID
2204 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2205 created from SIFTs, and spurious 'Couldn't open structure
2206 in Chimera' errors raised after April 2017 update (problem
2207 due to 'null' string rather than empty string used for
2208 residues with no corresponding PDB mapping).
2211 <em>Application UI</em>
2214 <!-- JAL-2361 -->User Defined Colours not added to Colour
2218 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2219 case' residues (button in colourscheme editor debugged and
2220 new documentation and tooltips added)
2223 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2224 doesn't restore group-specific text colour thresholds
2227 <!-- JAL-2243 -->Feature settings panel does not update as
2228 new features are added to alignment
2231 <!-- JAL-2532 -->Cancel in feature settings reverts
2232 changes to feature colours via the Amend features dialog
2235 <!-- JAL-2506 -->Null pointer exception when attempting to
2236 edit graduated feature colour via amend features dialog
2240 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2241 selection menu changes colours of alignment views
2244 <!-- JAL-2426 -->Spurious exceptions in console raised
2245 from alignment calculation workers after alignment has
2249 <!-- JAL-1608 -->Typo in selection popup menu - Create
2250 groups now 'Create Group'
2253 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2254 Create/Undefine group doesn't always work
2257 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2258 shown again after pressing 'Cancel'
2261 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2262 adjusts start position in wrap mode
2265 <!-- JAL-2563 -->Status bar doesn't show positions for
2266 ambiguous amino acids
2269 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2270 CDS/Protein view after CDS sequences added for aligned
2274 <!-- JAL-2592 -->User defined colourschemes called 'User
2275 Defined' don't appear in Colours menu
2281 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2282 score models doesn't always result in an updated PCA plot
2285 <!-- JAL-2442 -->Features not rendered as transparent on
2286 overview or linked structure view
2289 <!-- JAL-2372 -->Colour group by conservation doesn't
2293 <!-- JAL-2517 -->Hitting Cancel after applying
2294 user-defined colourscheme doesn't restore original
2301 <!-- JAL-2314 -->Unit test failure:
2302 jalview.ws.jabaws.RNAStructExportImport setup fails
2305 <!-- JAL-2307 -->Unit test failure:
2306 jalview.ws.sifts.SiftsClientTest due to compatibility
2307 problems with deep array comparison equality asserts in
2308 successive versions of TestNG
2311 <!-- JAL-2479 -->Relocated StructureChooserTest and
2312 ParameterUtilsTest Unit tests to Network suite
2315 <em>New Known Issues</em>
2318 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2319 phase after a sequence motif find operation
2322 <!-- JAL-2550 -->Importing annotation file with rows
2323 containing just upper and lower case letters are
2324 interpreted as WUSS RNA secondary structure symbols
2327 <!-- JAL-2590 -->Cannot load and display Newick trees
2328 reliably from eggnog Ortholog database
2331 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2332 containing features of type Highlight' when 'B' is pressed
2333 to mark columns containing highlighted regions.
2336 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2337 doesn't always add secondary structure annotation.
2342 <td width="60" nowrap>
2343 <div align="center">
2344 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2347 <td><div align="left">
2351 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2352 for all consensus calculations
2355 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2358 <li>Updated Jalview's Certum code signing certificate
2361 <em>Application</em>
2364 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2365 set of database cross-references, sorted alphabetically
2368 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2369 from database cross references. Users with custom links
2370 will receive a <a href="webServices/urllinks.html#warning">warning
2371 dialog</a> asking them to update their preferences.
2374 <!-- JAL-2287-->Cancel button and escape listener on
2375 dialog warning user about disconnecting Jalview from a
2379 <!-- JAL-2320-->Jalview's Chimera control window closes if
2380 the Chimera it is connected to is shut down
2383 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2384 columns menu item to mark columns containing highlighted
2385 regions (e.g. from structure selections or results of a
2389 <!-- JAL-2284-->Command line option for batch-generation
2390 of HTML pages rendering alignment data with the BioJS
2400 <!-- JAL-2286 -->Columns with more than one modal residue
2401 are not coloured or thresholded according to percent
2402 identity (first observed in Jalview 2.8.2)
2405 <!-- JAL-2301 -->Threonine incorrectly reported as not
2409 <!-- JAL-2318 -->Updates to documentation pages (above PID
2410 threshold, amino acid properties)
2413 <!-- JAL-2292 -->Lower case residues in sequences are not
2414 reported as mapped to residues in a structure file in the
2418 <!--JAL-2324 -->Identical features with non-numeric scores
2419 could be added multiple times to a sequence
2422 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2423 bond features shown as two highlighted residues rather
2424 than a range in linked structure views, and treated
2425 correctly when selecting and computing trees from features
2428 <!-- JAL-2281-->Custom URL links for database
2429 cross-references are matched to database name regardless
2434 <em>Application</em>
2437 <!-- JAL-2282-->Custom URL links for specific database
2438 names without regular expressions also offer links from
2442 <!-- JAL-2315-->Removing a single configured link in the
2443 URL links pane in Connections preferences doesn't actually
2444 update Jalview configuration
2447 <!-- JAL-2272-->CTRL-Click on a selected region to open
2448 the alignment area popup menu doesn't work on El-Capitan
2451 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2452 files with similarly named sequences if dropped onto the
2456 <!-- JAL-2312 -->Additional mappings are shown for PDB
2457 entries where more chains exist in the PDB accession than
2458 are reported in the SIFTS file
2461 <!-- JAL-2317-->Certain structures do not get mapped to
2462 the structure view when displayed with Chimera
2465 <!-- JAL-2317-->No chains shown in the Chimera view
2466 panel's View->Show Chains submenu
2469 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2470 work for wrapped alignment views
2473 <!--JAL-2197 -->Rename UI components for running JPred
2474 predictions from 'JNet' to 'JPred'
2477 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2478 corrupted when annotation panel vertical scroll is not at
2479 first annotation row
2482 <!--JAL-2332 -->Attempting to view structure for Hen
2483 lysozyme results in a PDB Client error dialog box
2486 <!-- JAL-2319 -->Structure View's mapping report switched
2487 ranges for PDB and sequence for SIFTS
2490 SIFTS 'Not_Observed' residues mapped to non-existant
2494 <!-- <em>New Known Issues</em>
2501 <td width="60" nowrap>
2502 <div align="center">
2503 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2504 <em>25/10/2016</em></strong>
2507 <td><em>Application</em>
2509 <li>3D Structure chooser opens with 'Cached structures'
2510 view if structures already loaded</li>
2511 <li>Progress bar reports models as they are loaded to
2512 structure views</li>
2518 <li>Colour by conservation always enabled and no tick
2519 shown in menu when BLOSUM or PID shading applied</li>
2520 <li>FER1_ARATH and FER2_ARATH labels were switched in
2521 example sequences/projects/trees</li>
2523 <em>Application</em>
2525 <li>Jalview projects with views of local PDB structure
2526 files saved on Windows cannot be opened on OSX</li>
2527 <li>Multiple structure views can be opened and superposed
2528 without timeout for structures with multiple models or
2529 multiple sequences in alignment</li>
2530 <li>Cannot import or associated local PDB files without a
2531 PDB ID HEADER line</li>
2532 <li>RMSD is not output in Jmol console when superposition
2534 <li>Drag and drop of URL from Browser fails for Linux and
2535 OSX versions earlier than El Capitan</li>
2536 <li>ENA client ignores invalid content from ENA server</li>
2537 <li>Exceptions are not raised in console when ENA client
2538 attempts to fetch non-existent IDs via Fetch DB Refs UI
2540 <li>Exceptions are not raised in console when a new view
2541 is created on the alignment</li>
2542 <li>OSX right-click fixed for group selections: CMD-click
2543 to insert/remove gaps in groups and CTRL-click to open group
2546 <em>Build and deployment</em>
2548 <li>URL link checker now copes with multi-line anchor
2551 <em>New Known Issues</em>
2553 <li>Drag and drop from URL links in browsers do not work
2560 <td width="60" nowrap>
2561 <div align="center">
2562 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2565 <td><em>General</em>
2568 <!-- JAL-2124 -->Updated Spanish translations.
2571 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2572 for importing structure data to Jalview. Enables mmCIF and
2576 <!-- JAL-192 --->Alignment ruler shows positions relative to
2580 <!-- JAL-2202 -->Position/residue shown in status bar when
2581 mousing over sequence associated annotation
2584 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2588 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2589 '()', canonical '[]' and invalid '{}' base pair populations
2593 <!-- JAL-2092 -->Feature settings popup menu options for
2594 showing or hiding columns containing a feature
2597 <!-- JAL-1557 -->Edit selected group by double clicking on
2598 group and sequence associated annotation labels
2601 <!-- JAL-2236 -->Sequence name added to annotation label in
2602 select/hide columns by annotation and colour by annotation
2606 </ul> <em>Application</em>
2609 <!-- JAL-2050-->Automatically hide introns when opening a
2610 gene/transcript view
2613 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2617 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2618 structure mappings with the EMBL-EBI PDBe SIFTS database
2621 <!-- JAL-2079 -->Updated download sites used for Rfam and
2622 Pfam sources to xfam.org
2625 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2628 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2629 over sequences in Jalview
2632 <!-- JAL-2027-->Support for reverse-complement coding
2633 regions in ENA and EMBL
2636 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2637 for record retrieval via ENA rest API
2640 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2644 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2645 groovy script execution
2648 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2649 alignment window's Calculate menu
2652 <!-- JAL-1812 -->Allow groovy scripts that call
2653 Jalview.getAlignFrames() to run in headless mode
2656 <!-- JAL-2068 -->Support for creating new alignment
2657 calculation workers from groovy scripts
2660 <!-- JAL-1369 --->Store/restore reference sequence in
2664 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2665 associations are now saved/restored from project
2668 <!-- JAL-1993 -->Database selection dialog always shown
2669 before sequence fetcher is opened
2672 <!-- JAL-2183 -->Double click on an entry in Jalview's
2673 database chooser opens a sequence fetcher
2676 <!-- JAL-1563 -->Free-text search client for UniProt using
2677 the UniProt REST API
2680 <!-- JAL-2168 -->-nonews command line parameter to prevent
2681 the news reader opening
2684 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2685 querying stored in preferences
2688 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2692 <!-- JAL-1977-->Tooltips shown on database chooser
2695 <!-- JAL-391 -->Reverse complement function in calculate
2696 menu for nucleotide sequences
2699 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2700 and feature counts preserves alignment ordering (and
2701 debugged for complex feature sets).
2704 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2705 viewing structures with Jalview 2.10
2708 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2709 genome, transcript CCDS and gene ids via the Ensembl and
2710 Ensembl Genomes REST API
2713 <!-- JAL-2049 -->Protein sequence variant annotation
2714 computed for 'sequence_variant' annotation on CDS regions
2718 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2722 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2723 Ref Fetcher fails to match, or otherwise updates sequence
2724 data from external database records.
2727 <!-- JAL-2154 -->Revised Jalview Project format for
2728 efficient recovery of sequence coding and alignment
2729 annotation relationships.
2731 </ul> <!-- <em>Applet</em>
2742 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2746 <!-- JAL-2018-->Export features in Jalview format (again)
2747 includes graduated colourschemes
2750 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2751 working with big alignments and lots of hidden columns
2754 <!-- JAL-2053-->Hidden column markers not always rendered
2755 at right of alignment window
2758 <!-- JAL-2067 -->Tidied up links in help file table of
2762 <!-- JAL-2072 -->Feature based tree calculation not shown
2766 <!-- JAL-2075 -->Hidden columns ignored during feature
2767 based tree calculation
2770 <!-- JAL-2065 -->Alignment view stops updating when show
2771 unconserved enabled for group on alignment
2774 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2778 <!-- JAL-2146 -->Alignment column in status incorrectly
2779 shown as "Sequence position" when mousing over
2783 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2784 hidden columns present
2787 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2788 user created annotation added to alignment
2791 <!-- JAL-1841 -->RNA Structure consensus only computed for
2792 '()' base pair annotation
2795 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2796 in zero scores for all base pairs in RNA Structure
2800 <!-- JAL-2174-->Extend selection with columns containing
2804 <!-- JAL-2275 -->Pfam format writer puts extra space at
2805 beginning of sequence
2808 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2812 <!-- JAL-2238 -->Cannot create groups on an alignment from
2813 from a tree when t-coffee scores are shown
2816 <!-- JAL-1836,1967 -->Cannot import and view PDB
2817 structures with chains containing negative resnums (4q4h)
2820 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2824 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2825 to Clustal, PIR and PileUp output
2828 <!-- JAL-2008 -->Reordering sequence features that are
2829 not visible causes alignment window to repaint
2832 <!-- JAL-2006 -->Threshold sliders don't work in
2833 graduated colour and colour by annotation row for e-value
2834 scores associated with features and annotation rows
2837 <!-- JAL-1797 -->amino acid physicochemical conservation
2838 calculation should be case independent
2841 <!-- JAL-2173 -->Remove annotation also updates hidden
2845 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2846 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2847 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2850 <!-- JAL-2065 -->Null pointer exceptions and redraw
2851 problems when reference sequence defined and 'show
2852 non-conserved' enabled
2855 <!-- JAL-1306 -->Quality and Conservation are now shown on
2856 load even when Consensus calculation is disabled
2859 <!-- JAL-1932 -->Remove right on penultimate column of
2860 alignment does nothing
2863 <em>Application</em>
2866 <!-- JAL-1552-->URLs and links can't be imported by
2867 drag'n'drop on OSX when launched via webstart (note - not
2868 yet fixed for El Capitan)
2871 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2872 output when running on non-gb/us i18n platforms
2875 <!-- JAL-1944 -->Error thrown when exporting a view with
2876 hidden sequences as flat-file alignment
2879 <!-- JAL-2030-->InstallAnywhere distribution fails when
2883 <!-- JAL-2080-->Jalview very slow to launch via webstart
2884 (also hotfix for 2.9.0b2)
2887 <!-- JAL-2085 -->Cannot save project when view has a
2888 reference sequence defined
2891 <!-- JAL-1011 -->Columns are suddenly selected in other
2892 alignments and views when revealing hidden columns
2895 <!-- JAL-1989 -->Hide columns not mirrored in complement
2896 view in a cDNA/Protein splitframe
2899 <!-- JAL-1369 -->Cannot save/restore representative
2900 sequence from project when only one sequence is
2904 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2905 in Structure Chooser
2908 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2909 structure consensus didn't refresh annotation panel
2912 <!-- JAL-1962 -->View mapping in structure view shows
2913 mappings between sequence and all chains in a PDB file
2916 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2917 dialogs format columns correctly, don't display array
2918 data, sort columns according to type
2921 <!-- JAL-1975 -->Export complete shown after destination
2922 file chooser is cancelled during an image export
2925 <!-- JAL-2025 -->Error when querying PDB Service with
2926 sequence name containing special characters
2929 <!-- JAL-2024 -->Manual PDB structure querying should be
2933 <!-- JAL-2104 -->Large tooltips with broken HTML
2934 formatting don't wrap
2937 <!-- JAL-1128 -->Figures exported from wrapped view are
2938 truncated so L looks like I in consensus annotation
2941 <!-- JAL-2003 -->Export features should only export the
2942 currently displayed features for the current selection or
2946 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2947 after fetching cross-references, and restoring from
2951 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2952 followed in the structure viewer
2955 <!-- JAL-2163 -->Titles for individual alignments in
2956 splitframe not restored from project
2959 <!-- JAL-2145 -->missing autocalculated annotation at
2960 trailing end of protein alignment in transcript/product
2961 splitview when pad-gaps not enabled by default
2964 <!-- JAL-1797 -->amino acid physicochemical conservation
2968 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2969 article has been read (reopened issue due to
2970 internationalisation problems)
2973 <!-- JAL-1960 -->Only offer PDB structures in structure
2974 viewer based on sequence name, PDB and UniProt
2979 <!-- JAL-1976 -->No progress bar shown during export of
2983 <!-- JAL-2213 -->Structures not always superimposed after
2984 multiple structures are shown for one or more sequences.
2987 <!-- JAL-1370 -->Reference sequence characters should not
2988 be replaced with '.' when 'Show unconserved' format option
2992 <!-- JAL-1823 -->Cannot specify chain code when entering
2993 specific PDB id for sequence
2996 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2997 'Export hidden sequences' is enabled, but 'export hidden
2998 columns' is disabled.
3001 <!--JAL-2026-->Best Quality option in structure chooser
3002 selects lowest rather than highest resolution structures
3006 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3007 to sequence mapping in 'View Mappings' report
3010 <!-- JAL-2284 -->Unable to read old Jalview projects that
3011 contain non-XML data added after Jalvew wrote project.
3014 <!-- JAL-2118 -->Newly created annotation row reorders
3015 after clicking on it to create new annotation for a
3019 <!-- JAL-1980 -->Null Pointer Exception raised when
3020 pressing Add on an orphaned cut'n'paste window.
3022 <!-- may exclude, this is an external service stability issue JAL-1941
3023 -- > RNA 3D structure not added via DSSR service</li> -->
3028 <!-- JAL-2151 -->Incorrect columns are selected when
3029 hidden columns present before start of sequence
3032 <!-- JAL-1986 -->Missing dependencies on applet pages
3036 <!-- JAL-1947 -->Overview pixel size changes when
3037 sequences are hidden in applet
3040 <!-- JAL-1996 -->Updated instructions for applet
3041 deployment on examples pages.
3048 <td width="60" nowrap>
3049 <div align="center">
3050 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3051 <em>16/10/2015</em></strong>
3054 <td><em>General</em>
3056 <li>Time stamps for signed Jalview application and applet
3061 <em>Application</em>
3063 <li>Duplicate group consensus and conservation rows
3064 shown when tree is partitioned</li>
3065 <li>Erratic behaviour when tree partitions made with
3066 multiple cDNA/Protein split views</li>
3072 <td width="60" nowrap>
3073 <div align="center">
3074 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3075 <em>8/10/2015</em></strong>
3078 <td><em>General</em>
3080 <li>Updated Spanish translations of localized text for
3082 </ul> <em>Application</em>
3084 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3085 <li>Signed OSX InstallAnywhere installer<br></li>
3086 <li>Support for per-sequence based annotations in BioJSON</li>
3087 </ul> <em>Applet</em>
3089 <li>Split frame example added to applet examples page</li>
3090 </ul> <em>Build and Deployment</em>
3093 <!-- JAL-1888 -->New ant target for running Jalview's test
3101 <li>Mapping of cDNA to protein in split frames
3102 incorrect when sequence start > 1</li>
3103 <li>Broken images in filter column by annotation dialog
3105 <li>Feature colours not parsed from features file</li>
3106 <li>Exceptions and incomplete link URLs recovered when
3107 loading a features file containing HTML tags in feature
3111 <em>Application</em>
3113 <li>Annotations corrupted after BioJS export and
3115 <li>Incorrect sequence limits after Fetch DB References
3116 with 'trim retrieved sequences'</li>
3117 <li>Incorrect warning about deleting all data when
3118 deleting selected columns</li>
3119 <li>Patch to build system for shipping properly signed
3120 JNLP templates for webstart launch</li>
3121 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3122 unreleased structures for download or viewing</li>
3123 <li>Tab/space/return keystroke operation of EMBL-PDBe
3124 fetcher/viewer dialogs works correctly</li>
3125 <li>Disabled 'minimise' button on Jalview windows
3126 running on OSX to workaround redraw hang bug</li>
3127 <li>Split cDNA/Protein view position and geometry not
3128 recovered from jalview project</li>
3129 <li>Initial enabled/disabled state of annotation menu
3130 sorter 'show autocalculated first/last' corresponds to
3132 <li>Restoring of Clustal, RNA Helices and T-Coffee
3133 color schemes from BioJSON</li>
3137 <li>Reorder sequences mirrored in cDNA/Protein split
3139 <li>Applet with Jmol examples not loading correctly</li>
3145 <td><div align="center">
3146 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3148 <td><em>General</em>
3150 <li>Linked visualisation and analysis of DNA and Protein
3153 <li>Translated cDNA alignments shown as split protein
3154 and DNA alignment views</li>
3155 <li>Codon consensus annotation for linked protein and
3156 cDNA alignment views</li>
3157 <li>Link cDNA or Protein product sequences by loading
3158 them onto Protein or cDNA alignments</li>
3159 <li>Reconstruct linked cDNA alignment from aligned
3160 protein sequences</li>
3163 <li>Jmol integration updated to Jmol v14.2.14</li>
3164 <li>Import and export of Jalview alignment views as <a
3165 href="features/bioJsonFormat.html">BioJSON</a></li>
3166 <li>New alignment annotation file statements for
3167 reference sequences and marking hidden columns</li>
3168 <li>Reference sequence based alignment shading to
3169 highlight variation</li>
3170 <li>Select or hide columns according to alignment
3172 <li>Find option for locating sequences by description</li>
3173 <li>Conserved physicochemical properties shown in amino
3174 acid conservation row</li>
3175 <li>Alignments can be sorted by number of RNA helices</li>
3176 </ul> <em>Application</em>
3178 <li>New cDNA/Protein analysis capabilities
3180 <li>Get Cross-References should open a Split Frame
3181 view with cDNA/Protein</li>
3182 <li>Detect when nucleotide sequences and protein
3183 sequences are placed in the same alignment</li>
3184 <li>Split cDNA/Protein views are saved in Jalview
3189 <li>Use REST API to talk to Chimera</li>
3190 <li>Selected regions in Chimera are highlighted in linked
3191 Jalview windows</li>
3193 <li>VARNA RNA viewer updated to v3.93</li>
3194 <li>VARNA views are saved in Jalview Projects</li>
3195 <li>Pseudoknots displayed as Jalview RNA annotation can
3196 be shown in VARNA</li>
3198 <li>Make groups for selection uses marked columns as well
3199 as the active selected region</li>
3201 <li>Calculate UPGMA and NJ trees using sequence feature
3203 <li>New Export options
3205 <li>New Export Settings dialog to control hidden
3206 region export in flat file generation</li>
3208 <li>Export alignment views for display with the <a
3209 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3211 <li>Export scrollable SVG in HTML page</li>
3212 <li>Optional embedding of BioJSON data when exporting
3213 alignment figures to HTML</li>
3215 <li>3D structure retrieval and display
3217 <li>Free text and structured queries with the PDBe
3219 <li>PDBe Search API based discovery and selection of
3220 PDB structures for a sequence set</li>
3224 <li>JPred4 employed for protein secondary structure
3226 <li>Hide Insertions menu option to hide unaligned columns
3227 for one or a group of sequences</li>
3228 <li>Automatically hide insertions in alignments imported
3229 from the JPred4 web server</li>
3230 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3231 system on OSX<br />LGPL libraries courtesy of <a
3232 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3234 <li>changed 'View nucleotide structure' submenu to 'View
3235 VARNA 2D Structure'</li>
3236 <li>change "View protein structure" menu option to "3D
3239 </ul> <em>Applet</em>
3241 <li>New layout for applet example pages</li>
3242 <li>New parameters to enable SplitFrame view
3243 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3244 <li>New example demonstrating linked viewing of cDNA and
3245 Protein alignments</li>
3246 </ul> <em>Development and deployment</em>
3248 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3249 <li>Include installation type and git revision in build
3250 properties and console log output</li>
3251 <li>Jalview Github organisation, and new github site for
3252 storing BioJsMSA Templates</li>
3253 <li>Jalview's unit tests now managed with TestNG</li>
3256 <!-- <em>General</em>
3258 </ul> --> <!-- issues resolved --> <em>Application</em>
3260 <li>Escape should close any open find dialogs</li>
3261 <li>Typo in select-by-features status report</li>
3262 <li>Consensus RNA secondary secondary structure
3263 predictions are not highlighted in amber</li>
3264 <li>Missing gap character in v2.7 example file means
3265 alignment appears unaligned when pad-gaps is not enabled</li>
3266 <li>First switch to RNA Helices colouring doesn't colour
3267 associated structure views</li>
3268 <li>ID width preference option is greyed out when auto
3269 width checkbox not enabled</li>
3270 <li>Stopped a warning dialog from being shown when
3271 creating user defined colours</li>
3272 <li>'View Mapping' in structure viewer shows sequence
3273 mappings for just that viewer's sequences</li>
3274 <li>Workaround for superposing PDB files containing
3275 multiple models in Chimera</li>
3276 <li>Report sequence position in status bar when hovering
3277 over Jmol structure</li>
3278 <li>Cannot output gaps as '.' symbols with Selection ->
3279 output to text box</li>
3280 <li>Flat file exports of alignments with hidden columns
3281 have incorrect sequence start/end</li>
3282 <li>'Aligning' a second chain to a Chimera structure from
3284 <li>Colour schemes applied to structure viewers don't
3285 work for nucleotide</li>
3286 <li>Loading/cut'n'pasting an empty or invalid file leads
3287 to a grey/invisible alignment window</li>
3288 <li>Exported Jpred annotation from a sequence region
3289 imports to different position</li>
3290 <li>Space at beginning of sequence feature tooltips shown
3291 on some platforms</li>
3292 <li>Chimera viewer 'View | Show Chain' menu is not
3294 <li>'New View' fails with a Null Pointer Exception in
3295 console if Chimera has been opened</li>
3296 <li>Mouseover to Chimera not working</li>
3297 <li>Miscellaneous ENA XML feature qualifiers not
3299 <li>NPE in annotation renderer after 'Extract Scores'</li>
3300 <li>If two structures in one Chimera window, mouseover of
3301 either sequence shows on first structure</li>
3302 <li>'Show annotations' options should not make
3303 non-positional annotations visible</li>
3304 <li>Subsequence secondary structure annotation not shown
3305 in right place after 'view flanking regions'</li>
3306 <li>File Save As type unset when current file format is
3308 <li>Save as '.jar' option removed for saving Jalview
3310 <li>Colour by Sequence colouring in Chimera more
3312 <li>Cannot 'add reference annotation' for a sequence in
3313 several views on same alignment</li>
3314 <li>Cannot show linked products for EMBL / ENA records</li>
3315 <li>Jalview's tooltip wraps long texts containing no
3317 </ul> <em>Applet</em>
3319 <li>Jmol to JalviewLite mouseover/link not working</li>
3320 <li>JalviewLite can't import sequences with ID
3321 descriptions containing angle brackets</li>
3322 </ul> <em>General</em>
3324 <li>Cannot export and reimport RNA secondary structure
3325 via jalview annotation file</li>
3326 <li>Random helix colour palette for colour by annotation
3327 with RNA secondary structure</li>
3328 <li>Mouseover to cDNA from STOP residue in protein
3329 translation doesn't work.</li>
3330 <li>hints when using the select by annotation dialog box</li>
3331 <li>Jmol alignment incorrect if PDB file has alternate CA
3333 <li>FontChooser message dialog appears to hang after
3334 choosing 1pt font</li>
3335 <li>Peptide secondary structure incorrectly imported from
3336 annotation file when annotation display text includes 'e' or
3338 <li>Cannot set colour of new feature type whilst creating
3340 <li>cDNA translation alignment should not be sequence
3341 order dependent</li>
3342 <li>'Show unconserved' doesn't work for lower case
3344 <li>Nucleotide ambiguity codes involving R not recognised</li>
3345 </ul> <em>Deployment and Documentation</em>
3347 <li>Applet example pages appear different to the rest of
3348 www.jalview.org</li>
3349 </ul> <em>Application Known issues</em>
3351 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3352 <li>Misleading message appears after trying to delete
3354 <li>Jalview icon not shown in dock after InstallAnywhere
3355 version launches</li>
3356 <li>Fetching EMBL reference for an RNA sequence results
3357 fails with a sequence mismatch</li>
3358 <li>Corrupted or unreadable alignment display when
3359 scrolling alignment to right</li>
3360 <li>ArrayIndexOutOfBoundsException thrown when remove
3361 empty columns called on alignment with ragged gapped ends</li>
3362 <li>auto calculated alignment annotation rows do not get
3363 placed above or below non-autocalculated rows</li>
3364 <li>Jalview dekstop becomes sluggish at full screen in
3365 ultra-high resolution</li>
3366 <li>Cannot disable consensus calculation independently of
3367 quality and conservation</li>
3368 <li>Mouseover highlighting between cDNA and protein can
3369 become sluggish with more than one splitframe shown</li>
3370 </ul> <em>Applet Known Issues</em>
3372 <li>Core PDB parsing code requires Jmol</li>
3373 <li>Sequence canvas panel goes white when alignment
3374 window is being resized</li>
3380 <td><div align="center">
3381 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3383 <td><em>General</em>
3385 <li>Updated Java code signing certificate donated by
3387 <li>Features and annotation preserved when performing
3388 pairwise alignment</li>
3389 <li>RNA pseudoknot annotation can be
3390 imported/exported/displayed</li>
3391 <li>'colour by annotation' can colour by RNA and
3392 protein secondary structure</li>
3393 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3394 post-hoc with 2.9 release</em>)
3397 </ul> <em>Application</em>
3399 <li>Extract and display secondary structure for sequences
3400 with 3D structures</li>
3401 <li>Support for parsing RNAML</li>
3402 <li>Annotations menu for layout
3404 <li>sort sequence annotation rows by alignment</li>
3405 <li>place sequence annotation above/below alignment
3408 <li>Output in Stockholm format</li>
3409 <li>Internationalisation: improved Spanish (es)
3411 <li>Structure viewer preferences tab</li>
3412 <li>Disorder and Secondary Structure annotation tracks
3413 shared between alignments</li>
3414 <li>UCSF Chimera launch and linked highlighting from
3416 <li>Show/hide all sequence associated annotation rows for
3417 all or current selection</li>
3418 <li>disorder and secondary structure predictions
3419 available as dataset annotation</li>
3420 <li>Per-sequence rna helices colouring</li>
3423 <li>Sequence database accessions imported when fetching
3424 alignments from Rfam</li>
3425 <li>update VARNA version to 3.91</li>
3427 <li>New groovy scripts for exporting aligned positions,
3428 conservation values, and calculating sum of pairs scores.</li>
3429 <li>Command line argument to set default JABAWS server</li>
3430 <li>include installation type in build properties and
3431 console log output</li>
3432 <li>Updated Jalview project format to preserve dataset
3436 <!-- issues resolved --> <em>Application</em>
3438 <li>Distinguish alignment and sequence associated RNA
3439 structure in structure->view->VARNA</li>
3440 <li>Raise dialog box if user deletes all sequences in an
3442 <li>Pressing F1 results in documentation opening twice</li>
3443 <li>Sequence feature tooltip is wrapped</li>
3444 <li>Double click on sequence associated annotation
3445 selects only first column</li>
3446 <li>Redundancy removal doesn't result in unlinked
3447 leaves shown in tree</li>
3448 <li>Undos after several redundancy removals don't undo
3450 <li>Hide sequence doesn't hide associated annotation</li>
3451 <li>User defined colours dialog box too big to fit on
3452 screen and buttons not visible</li>
3453 <li>author list isn't updated if already written to
3454 Jalview properties</li>
3455 <li>Popup menu won't open after retrieving sequence
3457 <li>File open window for associate PDB doesn't open</li>
3458 <li>Left-then-right click on a sequence id opens a
3459 browser search window</li>
3460 <li>Cannot open sequence feature shading/sort popup menu
3461 in feature settings dialog</li>
3462 <li>better tooltip placement for some areas of Jalview
3464 <li>Allow addition of JABAWS Server which doesn't
3465 pass validation</li>
3466 <li>Web services parameters dialog box is too large to
3468 <li>Muscle nucleotide alignment preset obscured by
3470 <li>JABAWS preset submenus don't contain newly
3471 defined user preset</li>
3472 <li>MSA web services warns user if they were launched
3473 with invalid input</li>
3474 <li>Jalview cannot contact DAS Registy when running on
3477 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3478 'Superpose with' submenu not shown when new view
3482 </ul> <!-- <em>Applet</em>
3484 </ul> <em>General</em>
3486 </ul>--> <em>Deployment and Documentation</em>
3488 <li>2G and 1G options in launchApp have no effect on
3489 memory allocation</li>
3490 <li>launchApp service doesn't automatically open
3491 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3493 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3494 InstallAnywhere reports cannot find valid JVM when Java
3495 1.7_055 is available
3497 </ul> <em>Application Known issues</em>
3500 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3501 corrupted or unreadable alignment display when scrolling
3505 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3506 retrieval fails but progress bar continues for DAS retrieval
3507 with large number of ID
3510 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3511 flatfile output of visible region has incorrect sequence
3515 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3516 rna structure consensus doesn't update when secondary
3517 structure tracks are rearranged
3520 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3521 invalid rna structure positional highlighting does not
3522 highlight position of invalid base pairs
3525 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3526 out of memory errors are not raised when saving Jalview
3527 project from alignment window file menu
3530 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3531 Switching to RNA Helices colouring doesn't propagate to
3535 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3536 colour by RNA Helices not enabled when user created
3537 annotation added to alignment
3540 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3541 Jalview icon not shown on dock in Mountain Lion/Webstart
3543 </ul> <em>Applet Known Issues</em>
3546 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3547 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3550 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3551 Jalview and Jmol example not compatible with IE9
3554 <li>Sort by annotation score doesn't reverse order
3560 <td><div align="center">
3561 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3564 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3567 <li>Internationalisation of user interface (usually
3568 called i18n support) and translation for Spanish locale</li>
3569 <li>Define/Undefine group on current selection with
3570 Ctrl-G/Shift Ctrl-G</li>
3571 <li>Improved group creation/removal options in
3572 alignment/sequence Popup menu</li>
3573 <li>Sensible precision for symbol distribution
3574 percentages shown in logo tooltip.</li>
3575 <li>Annotation panel height set according to amount of
3576 annotation when alignment first opened</li>
3577 </ul> <em>Application</em>
3579 <li>Interactive consensus RNA secondary structure
3580 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3581 <li>Select columns containing particular features from
3582 Feature Settings dialog</li>
3583 <li>View all 'representative' PDB structures for selected
3585 <li>Update Jalview project format:
3587 <li>New file extension for Jalview projects '.jvp'</li>
3588 <li>Preserve sequence and annotation dataset (to
3589 store secondary structure annotation,etc)</li>
3590 <li>Per group and alignment annotation and RNA helix
3594 <li>New similarity measures for PCA and Tree calculation
3596 <li>Experimental support for retrieval and viewing of
3597 flanking regions for an alignment</li>
3601 <!-- issues resolved --> <em>Application</em>
3603 <li>logo keeps spinning and status remains at queued or
3604 running after job is cancelled</li>
3605 <li>cannot export features from alignments imported from
3606 Jalview/VAMSAS projects</li>
3607 <li>Buggy slider for web service parameters that take
3609 <li>Newly created RNA secondary structure line doesn't
3610 have 'display all symbols' flag set</li>
3611 <li>T-COFFEE alignment score shading scheme and other
3612 annotation shading not saved in Jalview project</li>
3613 <li>Local file cannot be loaded in freshly downloaded
3615 <li>Jalview icon not shown on dock in Mountain
3617 <li>Load file from desktop file browser fails</li>
3618 <li>Occasional NPE thrown when calculating large trees</li>
3619 <li>Cannot reorder or slide sequences after dragging an
3620 alignment onto desktop</li>
3621 <li>Colour by annotation dialog throws NPE after using
3622 'extract scores' function</li>
3623 <li>Loading/cut'n'pasting an empty file leads to a grey
3624 alignment window</li>
3625 <li>Disorder thresholds rendered incorrectly after
3626 performing IUPred disorder prediction</li>
3627 <li>Multiple group annotated consensus rows shown when
3628 changing 'normalise logo' display setting</li>
3629 <li>Find shows blank dialog after 'finished searching' if
3630 nothing matches query</li>
3631 <li>Null Pointer Exceptions raised when sorting by
3632 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3634 <li>Errors in Jmol console when structures in alignment
3635 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3637 <li>Not all working JABAWS services are shown in
3639 <li>JAVAWS version of Jalview fails to launch with
3640 'invalid literal/length code'</li>
3641 <li>Annotation/RNA Helix colourschemes cannot be applied
3642 to alignment with groups (actually fixed in 2.8.0b1)</li>
3643 <li>RNA Helices and T-Coffee Scores available as default
3646 </ul> <em>Applet</em>
3648 <li>Remove group option is shown even when selection is
3650 <li>Apply to all groups ticked but colourscheme changes
3651 don't affect groups</li>
3652 <li>Documented RNA Helices and T-Coffee Scores as valid
3653 colourscheme name</li>
3654 <li>Annotation labels drawn on sequence IDs when
3655 Annotation panel is not displayed</li>
3656 <li>Increased font size for dropdown menus on OSX and
3657 embedded windows</li>
3658 </ul> <em>Other</em>
3660 <li>Consensus sequence for alignments/groups with a
3661 single sequence were not calculated</li>
3662 <li>annotation files that contain only groups imported as
3663 annotation and junk sequences</li>
3664 <li>Fasta files with sequences containing '*' incorrectly
3665 recognised as PFAM or BLC</li>
3666 <li>conservation/PID slider apply all groups option
3667 doesn't affect background (2.8.0b1)
3669 <li>redundancy highlighting is erratic at 0% and 100%</li>
3670 <li>Remove gapped columns fails for sequences with ragged
3672 <li>AMSA annotation row with leading spaces is not
3673 registered correctly on import</li>
3674 <li>Jalview crashes when selecting PCA analysis for
3675 certain alignments</li>
3676 <li>Opening the colour by annotation dialog for an
3677 existing annotation based 'use original colours'
3678 colourscheme loses original colours setting</li>
3683 <td><div align="center">
3684 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3685 <em>30/1/2014</em></strong>
3689 <li>Trusted certificates for JalviewLite applet and
3690 Jalview Desktop application<br />Certificate was donated by
3691 <a href="https://www.certum.eu">Certum</a> to the Jalview
3692 open source project).
3694 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3695 <li>Output in Stockholm format</li>
3696 <li>Allow import of data from gzipped files</li>
3697 <li>Export/import group and sequence associated line
3698 graph thresholds</li>
3699 <li>Nucleotide substitution matrix that supports RNA and
3700 ambiguity codes</li>
3701 <li>Allow disorder predictions to be made on the current
3702 selection (or visible selection) in the same way that JPred
3704 <li>Groovy scripting for headless Jalview operation</li>
3705 </ul> <em>Other improvements</em>
3707 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3708 <li>COMBINE statement uses current SEQUENCE_REF and
3709 GROUP_REF scope to group annotation rows</li>
3710 <li>Support '' style escaping of quotes in Newick
3712 <li>Group options for JABAWS service by command line name</li>
3713 <li>Empty tooltip shown for JABA service options with a
3714 link but no description</li>
3715 <li>Select primary source when selecting authority in
3716 database fetcher GUI</li>
3717 <li>Add .mfa to FASTA file extensions recognised by
3719 <li>Annotation label tooltip text wrap</li>
3724 <li>Slow scrolling when lots of annotation rows are
3726 <li>Lots of NPE (and slowness) after creating RNA
3727 secondary structure annotation line</li>
3728 <li>Sequence database accessions not imported when
3729 fetching alignments from Rfam</li>
3730 <li>Incorrect SHMR submission for sequences with
3732 <li>View all structures does not always superpose
3734 <li>Option widgets in service parameters not updated to
3735 reflect user or preset settings</li>
3736 <li>Null pointer exceptions for some services without
3737 presets or adjustable parameters</li>
3738 <li>Discover PDB IDs entry in structure menu doesn't
3739 discover PDB xRefs</li>
3740 <li>Exception encountered while trying to retrieve
3741 features with DAS</li>
3742 <li>Lowest value in annotation row isn't coloured
3743 when colour by annotation (per sequence) is coloured</li>
3744 <li>Keyboard mode P jumps to start of gapped region when
3745 residue follows a gap</li>
3746 <li>Jalview appears to hang importing an alignment with
3747 Wrap as default or after enabling Wrap</li>
3748 <li>'Right click to add annotations' message
3749 shown in wrap mode when no annotations present</li>
3750 <li>Disorder predictions fail with NPE if no automatic
3751 annotation already exists on alignment</li>
3752 <li>oninit javascript function should be called after
3753 initialisation completes</li>
3754 <li>Remove redundancy after disorder prediction corrupts
3755 alignment window display</li>
3756 <li>Example annotation file in documentation is invalid</li>
3757 <li>Grouped line graph annotation rows are not exported
3758 to annotation file</li>
3759 <li>Multi-harmony analysis cannot be run when only two
3761 <li>Cannot create multiple groups of line graphs with
3762 several 'combine' statements in annotation file</li>
3763 <li>Pressing return several times causes Number Format
3764 exceptions in keyboard mode</li>
3765 <li>Multi-harmony (SHMMR) method doesn't submit
3766 correct partitions for input data</li>
3767 <li>Translation from DNA to Amino Acids fails</li>
3768 <li>Jalview fail to load newick tree with quoted label</li>
3769 <li>--headless flag isn't understood</li>
3770 <li>ClassCastException when generating EPS in headless
3772 <li>Adjusting sequence-associated shading threshold only
3773 changes one row's threshold</li>
3774 <li>Preferences and Feature settings panel panel
3775 doesn't open</li>
3776 <li>hide consensus histogram also hides conservation and
3777 quality histograms</li>
3782 <td><div align="center">
3783 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3785 <td><em>Application</em>
3787 <li>Support for JABAWS 2.0 Services (AACon alignment
3788 conservation, protein disorder and Clustal Omega)</li>
3789 <li>JABAWS server status indicator in Web Services
3791 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3792 in Jalview alignment window</li>
3793 <li>Updated Jalview build and deploy framework for OSX
3794 mountain lion, windows 7, and 8</li>
3795 <li>Nucleotide substitution matrix for PCA that supports
3796 RNA and ambiguity codes</li>
3798 <li>Improved sequence database retrieval GUI</li>
3799 <li>Support fetching and database reference look up
3800 against multiple DAS sources (Fetch all from in 'fetch db
3802 <li>Jalview project improvements
3804 <li>Store and retrieve the 'belowAlignment'
3805 flag for annotation</li>
3806 <li>calcId attribute to group annotation rows on the
3808 <li>Store AACon calculation settings for a view in
3809 Jalview project</li>
3813 <li>horizontal scrolling gesture support</li>
3814 <li>Visual progress indicator when PCA calculation is
3816 <li>Simpler JABA web services menus</li>
3817 <li>visual indication that web service results are still
3818 being retrieved from server</li>
3819 <li>Serialise the dialogs that are shown when Jalview
3820 starts up for first time</li>
3821 <li>Jalview user agent string for interacting with HTTP
3823 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3825 <li>Examples directory and Groovy library included in
3826 InstallAnywhere distribution</li>
3827 </ul> <em>Applet</em>
3829 <li>RNA alignment and secondary structure annotation
3830 visualization applet example</li>
3831 </ul> <em>General</em>
3833 <li>Normalise option for consensus sequence logo</li>
3834 <li>Reset button in PCA window to return dimensions to
3836 <li>Allow seqspace or Jalview variant of alignment PCA
3838 <li>PCA with either nucleic acid and protein substitution
3840 <li>Allow windows containing HTML reports to be exported
3842 <li>Interactive display and editing of RNA secondary
3843 structure contacts</li>
3844 <li>RNA Helix Alignment Colouring</li>
3845 <li>RNA base pair logo consensus</li>
3846 <li>Parse sequence associated secondary structure
3847 information in Stockholm files</li>
3848 <li>HTML Export database accessions and annotation
3849 information presented in tooltip for sequences</li>
3850 <li>Import secondary structure from LOCARNA clustalw
3851 style RNA alignment files</li>
3852 <li>import and visualise T-COFFEE quality scores for an
3854 <li>'colour by annotation' per sequence option to
3855 shade each sequence according to its associated alignment
3857 <li>New Jalview Logo</li>
3858 </ul> <em>Documentation and Development</em>
3860 <li>documentation for score matrices used in Jalview</li>
3861 <li>New Website!</li>
3863 <td><em>Application</em>
3865 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3866 wsdbfetch REST service</li>
3867 <li>Stop windows being moved outside desktop on OSX</li>
3868 <li>Filetype associations not installed for webstart
3870 <li>Jalview does not always retrieve progress of a JABAWS
3871 job execution in full once it is complete</li>
3872 <li>revise SHMR RSBS definition to ensure alignment is
3873 uploaded via ali_file parameter</li>
3874 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3875 <li>View all structures superposed fails with exception</li>
3876 <li>Jnet job queues forever if a very short sequence is
3877 submitted for prediction</li>
3878 <li>Cut and paste menu not opened when mouse clicked on
3880 <li>Putting fractional value into integer text box in
3881 alignment parameter dialog causes Jalview to hang</li>
3882 <li>Structure view highlighting doesn't work on
3884 <li>View all structures fails with exception shown in
3886 <li>Characters in filename associated with PDBEntry not
3887 escaped in a platform independent way</li>
3888 <li>Jalview desktop fails to launch with exception when
3890 <li>Tree calculation reports 'you must have 2 or more
3891 sequences selected' when selection is empty</li>
3892 <li>Jalview desktop fails to launch with jar signature
3893 failure when java web start temporary file caching is
3895 <li>DAS Sequence retrieval with range qualification
3896 results in sequence xref which includes range qualification</li>
3897 <li>Errors during processing of command line arguments
3898 cause progress bar (JAL-898) to be removed</li>
3899 <li>Replace comma for semi-colon option not disabled for
3900 DAS sources in sequence fetcher</li>
3901 <li>Cannot close news reader when JABAWS server warning
3902 dialog is shown</li>
3903 <li>Option widgets not updated to reflect user settings</li>
3904 <li>Edited sequence not submitted to web service</li>
3905 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3906 <li>InstallAnywhere installer doesn't unpack and run
3907 on OSX Mountain Lion</li>
3908 <li>Annotation panel not given a scroll bar when
3909 sequences with alignment annotation are pasted into the
3911 <li>Sequence associated annotation rows not associated
3912 when loaded from Jalview project</li>
3913 <li>Browser launch fails with NPE on java 1.7</li>
3914 <li>JABAWS alignment marked as finished when job was
3915 cancelled or job failed due to invalid input</li>
3916 <li>NPE with v2.7 example when clicking on Tree
3917 associated with all views</li>
3918 <li>Exceptions when copy/paste sequences with grouped
3919 annotation rows to new window</li>
3920 </ul> <em>Applet</em>
3922 <li>Sequence features are momentarily displayed before
3923 they are hidden using hidefeaturegroups applet parameter</li>
3924 <li>loading features via javascript API automatically
3925 enables feature display</li>
3926 <li>scrollToColumnIn javascript API method doesn't
3928 </ul> <em>General</em>
3930 <li>Redundancy removal fails for rna alignment</li>
3931 <li>PCA calculation fails when sequence has been selected
3932 and then deselected</li>
3933 <li>PCA window shows grey box when first opened on OSX</li>
3934 <li>Letters coloured pink in sequence logo when alignment
3935 coloured with clustalx</li>
3936 <li>Choosing fonts without letter symbols defined causes
3937 exceptions and redraw errors</li>
3938 <li>Initial PCA plot view is not same as manually
3939 reconfigured view</li>
3940 <li>Grouped annotation graph label has incorrect line
3942 <li>Grouped annotation graph label display is corrupted
3943 for lots of labels</li>
3948 <div align="center">
3949 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3952 <td><em>Application</em>
3954 <li>Jalview Desktop News Reader</li>
3955 <li>Tweaked default layout of web services menu</li>
3956 <li>View/alignment association menu to enable user to
3957 easily specify which alignment a multi-structure view takes
3958 its colours/correspondences from</li>
3959 <li>Allow properties file location to be specified as URL</li>
3960 <li>Extend Jalview project to preserve associations
3961 between many alignment views and a single Jmol display</li>
3962 <li>Store annotation row height in Jalview project file</li>
3963 <li>Annotation row column label formatting attributes
3964 stored in project file</li>
3965 <li>Annotation row order for auto-calculated annotation
3966 rows preserved in Jalview project file</li>
3967 <li>Visual progress indication when Jalview state is
3968 saved using Desktop window menu</li>
3969 <li>Visual indication that command line arguments are
3970 still being processed</li>
3971 <li>Groovy script execution from URL</li>
3972 <li>Colour by annotation default min and max colours in
3974 <li>Automatically associate PDB files dragged onto an
3975 alignment with sequences that have high similarity and
3977 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3978 <li>'view structures' option to open many
3979 structures in same window</li>
3980 <li>Sort associated views menu option for tree panel</li>
3981 <li>Group all JABA and non-JABA services for a particular
3982 analysis function in its own submenu</li>
3983 </ul> <em>Applet</em>
3985 <li>Userdefined and autogenerated annotation rows for
3987 <li>Adjustment of alignment annotation pane height</li>
3988 <li>Annotation scrollbar for annotation panel</li>
3989 <li>Drag to reorder annotation rows in annotation panel</li>
3990 <li>'automaticScrolling' parameter</li>
3991 <li>Allow sequences with partial ID string matches to be
3992 annotated from GFF/Jalview features files</li>
3993 <li>Sequence logo annotation row in applet</li>
3994 <li>Absolute paths relative to host server in applet
3995 parameters are treated as such</li>
3996 <li>New in the JalviewLite javascript API:
3998 <li>JalviewLite.js javascript library</li>
3999 <li>Javascript callbacks for
4001 <li>Applet initialisation</li>
4002 <li>Sequence/alignment mouse-overs and selections</li>
4005 <li>scrollTo row and column alignment scrolling
4007 <li>Select sequence/alignment regions from javascript</li>
4008 <li>javascript structure viewer harness to pass
4009 messages between Jmol and Jalview when running as
4010 distinct applets</li>
4011 <li>sortBy method</li>
4012 <li>Set of applet and application examples shipped
4013 with documentation</li>
4014 <li>New example to demonstrate JalviewLite and Jmol
4015 javascript message exchange</li>
4017 </ul> <em>General</em>
4019 <li>Enable Jmol displays to be associated with multiple
4020 multiple alignments</li>
4021 <li>Option to automatically sort alignment with new tree</li>
4022 <li>User configurable link to enable redirects to a
4023 www.Jalview.org mirror</li>
4024 <li>Jmol colours option for Jmol displays</li>
4025 <li>Configurable newline string when writing alignment
4026 and other flat files</li>
4027 <li>Allow alignment annotation description lines to
4028 contain html tags</li>
4029 </ul> <em>Documentation and Development</em>
4031 <li>Add groovy test harness for bulk load testing to
4033 <li>Groovy script to load and align a set of sequences
4034 using a web service before displaying the result in the
4035 Jalview desktop</li>
4036 <li>Restructured javascript and applet api documentation</li>
4037 <li>Ant target to publish example html files with applet
4039 <li>Netbeans project for building Jalview from source</li>
4040 <li>ant task to create online javadoc for Jalview source</li>
4042 <td><em>Application</em>
4044 <li>User defined colourscheme throws exception when
4045 current built in colourscheme is saved as new scheme</li>
4046 <li>AlignFrame->Save in application pops up save
4047 dialog for valid filename/format</li>
4048 <li>Cannot view associated structure for UniProt sequence</li>
4049 <li>PDB file association breaks for UniProt sequence
4051 <li>Associate PDB from file dialog does not tell you
4052 which sequence is to be associated with the file</li>
4053 <li>Find All raises null pointer exception when query
4054 only matches sequence IDs</li>
4055 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4056 <li>Jalview project with Jmol views created with Jalview
4057 2.4 cannot be loaded</li>
4058 <li>Filetype associations not installed for webstart
4060 <li>Two or more chains in a single PDB file associated
4061 with sequences in different alignments do not get coloured
4062 by their associated sequence</li>
4063 <li>Visibility status of autocalculated annotation row
4064 not preserved when project is loaded</li>
4065 <li>Annotation row height and visibility attributes not
4066 stored in Jalview project</li>
4067 <li>Tree bootstraps are not preserved when saved as a
4068 Jalview project</li>
4069 <li>Envision2 workflow tooltips are corrupted</li>
4070 <li>Enabling show group conservation also enables colour
4071 by conservation</li>
4072 <li>Duplicate group associated conservation or consensus
4073 created on new view</li>
4074 <li>Annotation scrollbar not displayed after 'show
4075 all hidden annotation rows' option selected</li>
4076 <li>Alignment quality not updated after alignment
4077 annotation row is hidden then shown</li>
4078 <li>Preserve colouring of structures coloured by
4079 sequences in pre Jalview 2.7 projects</li>
4080 <li>Web service job parameter dialog is not laid out
4082 <li>Web services menu not refreshed after 'reset
4083 services' button is pressed in preferences</li>
4084 <li>Annotation off by one in Jalview v2_3 example project</li>
4085 <li>Structures imported from file and saved in project
4086 get name like jalview_pdb1234.txt when reloaded</li>
4087 <li>Jalview does not always retrieve progress of a JABAWS
4088 job execution in full once it is complete</li>
4089 </ul> <em>Applet</em>
4091 <li>Alignment height set incorrectly when lots of
4092 annotation rows are displayed</li>
4093 <li>Relative URLs in feature HTML text not resolved to
4095 <li>View follows highlighting does not work for positions
4097 <li><= shown as = in tooltip</li>
4098 <li>Export features raises exception when no features
4100 <li>Separator string used for serialising lists of IDs
4101 for javascript api is modified when separator string
4102 provided as parameter</li>
4103 <li>Null pointer exception when selecting tree leaves for
4104 alignment with no existing selection</li>
4105 <li>Relative URLs for datasources assumed to be relative
4106 to applet's codebase</li>
4107 <li>Status bar not updated after finished searching and
4108 search wraps around to first result</li>
4109 <li>StructureSelectionManager instance shared between
4110 several Jalview applets causes race conditions and memory
4112 <li>Hover tooltip and mouseover of position on structure
4113 not sent from Jmol in applet</li>
4114 <li>Certain sequences of javascript method calls to
4115 applet API fatally hang browser</li>
4116 </ul> <em>General</em>
4118 <li>View follows structure mouseover scrolls beyond
4119 position with wrapped view and hidden regions</li>
4120 <li>Find sequence position moves to wrong residue
4121 with/without hidden columns</li>
4122 <li>Sequence length given in alignment properties window
4124 <li>InvalidNumberFormat exceptions thrown when trying to
4125 import PDB like structure files</li>
4126 <li>Positional search results are only highlighted
4127 between user-supplied sequence start/end bounds</li>
4128 <li>End attribute of sequence is not validated</li>
4129 <li>Find dialog only finds first sequence containing a
4130 given sequence position</li>
4131 <li>Sequence numbering not preserved in MSF alignment
4133 <li>Jalview PDB file reader does not extract sequence
4134 from nucleotide chains correctly</li>
4135 <li>Structure colours not updated when tree partition
4136 changed in alignment</li>
4137 <li>Sequence associated secondary structure not correctly
4138 parsed in interleaved stockholm</li>
4139 <li>Colour by annotation dialog does not restore current
4141 <li>Hiding (nearly) all sequences doesn't work
4143 <li>Sequences containing lowercase letters are not
4144 properly associated with their pdb files</li>
4145 </ul> <em>Documentation and Development</em>
4147 <li>schemas/JalviewWsParamSet.xsd corrupted by
4148 ApplyCopyright tool</li>
4153 <div align="center">
4154 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4157 <td><em>Application</em>
4159 <li>New warning dialog when the Jalview Desktop cannot
4160 contact web services</li>
4161 <li>JABA service parameters for a preset are shown in
4162 service job window</li>
4163 <li>JABA Service menu entries reworded</li>
4167 <li>Modeller PIR IO broken - cannot correctly import a
4168 pir file emitted by Jalview</li>
4169 <li>Existing feature settings transferred to new
4170 alignment view created from cut'n'paste</li>
4171 <li>Improved test for mixed amino/nucleotide chains when
4172 parsing PDB files</li>
4173 <li>Consensus and conservation annotation rows
4174 occasionally become blank for all new windows</li>
4175 <li>Exception raised when right clicking above sequences
4176 in wrapped view mode</li>
4177 </ul> <em>Application</em>
4179 <li>multiple multiply aligned structure views cause cpu
4180 usage to hit 100% and computer to hang</li>
4181 <li>Web Service parameter layout breaks for long user
4182 parameter names</li>
4183 <li>Jaba service discovery hangs desktop if Jaba server
4190 <div align="center">
4191 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4194 <td><em>Application</em>
4196 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4197 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4200 <li>Web Services preference tab</li>
4201 <li>Analysis parameters dialog box and user defined
4203 <li>Improved speed and layout of Envision2 service menu</li>
4204 <li>Superpose structures using associated sequence
4206 <li>Export coordinates and projection as CSV from PCA
4208 </ul> <em>Applet</em>
4210 <li>enable javascript: execution by the applet via the
4211 link out mechanism</li>
4212 </ul> <em>Other</em>
4214 <li>Updated the Jmol Jalview interface to work with Jmol
4216 <li>The Jalview Desktop and JalviewLite applet now
4217 require Java 1.5</li>
4218 <li>Allow Jalview feature colour specification for GFF
4219 sequence annotation files</li>
4220 <li>New 'colour by label' keword in Jalview feature file
4221 type colour specification</li>
4222 <li>New Jalview Desktop Groovy API method that allows a
4223 script to check if it being run in an interactive session or
4224 in a batch operation from the Jalview command line</li>
4228 <li>clustalx colourscheme colours Ds preferentially when
4229 both D+E are present in over 50% of the column</li>
4230 </ul> <em>Application</em>
4232 <li>typo in AlignmentFrame->View->Hide->all but
4233 selected Regions menu item</li>
4234 <li>sequence fetcher replaces ',' for ';' when the ',' is
4235 part of a valid accession ID</li>
4236 <li>fatal OOM if object retrieved by sequence fetcher
4237 runs out of memory</li>
4238 <li>unhandled Out of Memory Error when viewing pca
4239 analysis results</li>
4240 <li>InstallAnywhere builds fail to launch on OS X java
4241 10.5 update 4 (due to apple Java 1.6 update)</li>
4242 <li>Installanywhere Jalview silently fails to launch</li>
4243 </ul> <em>Applet</em>
4245 <li>Jalview.getFeatureGroups() raises an
4246 ArrayIndexOutOfBoundsException if no feature groups are
4253 <div align="center">
4254 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4260 <li>Alignment prettyprinter doesn't cope with long
4262 <li>clustalx colourscheme colours Ds preferentially when
4263 both D+E are present in over 50% of the column</li>
4264 <li>nucleic acid structures retrieved from PDB do not
4265 import correctly</li>
4266 <li>More columns get selected than were clicked on when a
4267 number of columns are hidden</li>
4268 <li>annotation label popup menu not providing correct
4269 add/hide/show options when rows are hidden or none are
4271 <li>Stockholm format shown in list of readable formats,
4272 and parser copes better with alignments from RFAM.</li>
4273 <li>CSV output of consensus only includes the percentage
4274 of all symbols if sequence logo display is enabled</li>
4276 </ul> <em>Applet</em>
4278 <li>annotation panel disappears when annotation is
4280 </ul> <em>Application</em>
4282 <li>Alignment view not redrawn properly when new
4283 alignment opened where annotation panel is visible but no
4284 annotations are present on alignment</li>
4285 <li>pasted region containing hidden columns is
4286 incorrectly displayed in new alignment window</li>
4287 <li>Jalview slow to complete operations when stdout is
4288 flooded (fix is to close the Jalview console)</li>
4289 <li>typo in AlignmentFrame->View->Hide->all but
4290 selected Rregions menu item.</li>
4291 <li>inconsistent group submenu and Format submenu entry
4292 'Un' or 'Non'conserved</li>
4293 <li>Sequence feature settings are being shared by
4294 multiple distinct alignments</li>
4295 <li>group annotation not recreated when tree partition is
4297 <li>double click on group annotation to select sequences
4298 does not propagate to associated trees</li>
4299 <li>Mac OSX specific issues:
4301 <li>exception raised when mouse clicked on desktop
4302 window background</li>
4303 <li>Desktop menu placed on menu bar and application
4304 name set correctly</li>
4305 <li>sequence feature settings not wide enough for the
4306 save feature colourscheme button</li>
4315 <div align="center">
4316 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4319 <td><em>New Capabilities</em>
4321 <li>URL links generated from description line for
4322 regular-expression based URL links (applet and application)
4324 <li>Non-positional feature URL links are shown in link
4326 <li>Linked viewing of nucleic acid sequences and
4328 <li>Automatic Scrolling option in View menu to display
4329 the currently highlighted region of an alignment.</li>
4330 <li>Order an alignment by sequence length, or using the
4331 average score or total feature count for each sequence.</li>
4332 <li>Shading features by score or associated description</li>
4333 <li>Subdivide alignment and groups based on identity of
4334 selected subsequence (Make Groups from Selection).</li>
4335 <li>New hide/show options including Shift+Control+H to
4336 hide everything but the currently selected region.</li>
4337 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4338 </ul> <em>Application</em>
4340 <li>Fetch DB References capabilities and UI expanded to
4341 support retrieval from DAS sequence sources</li>
4342 <li>Local DAS Sequence sources can be added via the
4343 command line or via the Add local source dialog box.</li>
4344 <li>DAS Dbref and DbxRef feature types are parsed as
4345 database references and protein_name is parsed as
4346 description line (BioSapiens terms).</li>
4347 <li>Enable or disable non-positional feature and database
4348 references in sequence ID tooltip from View menu in
4350 <!-- <li>New hidden columns and rows and representatives capabilities
4351 in annotations file (in progress - not yet fully implemented)</li> -->
4352 <li>Group-associated consensus, sequence logos and
4353 conservation plots</li>
4354 <li>Symbol distributions for each column can be exported
4355 and visualized as sequence logos</li>
4356 <li>Optionally scale multi-character column labels to fit
4357 within each column of annotation row<!-- todo for applet -->
4359 <li>Optional automatic sort of associated alignment view
4360 when a new tree is opened.</li>
4361 <li>Jalview Java Console</li>
4362 <li>Better placement of desktop window when moving
4363 between different screens.</li>
4364 <li>New preference items for sequence ID tooltip and
4365 consensus annotation</li>
4366 <li>Client to submit sequences and IDs to Envision2
4368 <li><em>Vamsas Capabilities</em>
4370 <li>Improved VAMSAS synchronization (Jalview archive
4371 used to preserve views, structures, and tree display
4373 <li>Import of vamsas documents from disk or URL via
4375 <li>Sharing of selected regions between views and
4376 with other VAMSAS applications (Experimental feature!)</li>
4377 <li>Updated API to VAMSAS version 0.2</li>
4379 </ul> <em>Applet</em>
4381 <li>Middle button resizes annotation row height</li>
4384 <li>sortByTree (true/false) - automatically sort the
4385 associated alignment view by the tree when a new tree is
4387 <li>showTreeBootstraps (true/false) - show or hide
4388 branch bootstraps (default is to show them if available)</li>
4389 <li>showTreeDistances (true/false) - show or hide
4390 branch lengths (default is to show them if available)</li>
4391 <li>showUnlinkedTreeNodes (true/false) - indicate if
4392 unassociated nodes should be highlighted in the tree
4394 <li>heightScale and widthScale (1.0 or more) -
4395 increase the height or width of a cell in the alignment
4396 grid relative to the current font size.</li>
4399 <li>Non-positional features displayed in sequence ID
4401 </ul> <em>Other</em>
4403 <li>Features format: graduated colour definitions and
4404 specification of feature scores</li>
4405 <li>Alignment Annotations format: new keywords for group
4406 associated annotation (GROUP_REF) and annotation row display
4407 properties (ROW_PROPERTIES)</li>
4408 <li>XML formats extended to support graduated feature
4409 colourschemes, group associated annotation, and profile
4410 visualization settings.</li></td>
4413 <li>Source field in GFF files parsed as feature source
4414 rather than description</li>
4415 <li>Non-positional features are now included in sequence
4416 feature and gff files (controlled via non-positional feature
4417 visibility in tooltip).</li>
4418 <li>URL links generated for all feature links (bugfix)</li>
4419 <li>Added URL embedding instructions to features file
4421 <li>Codons containing ambiguous nucleotides translated as
4422 'X' in peptide product</li>
4423 <li>Match case switch in find dialog box works for both
4424 sequence ID and sequence string and query strings do not
4425 have to be in upper case to match case-insensitively.</li>
4426 <li>AMSA files only contain first column of
4427 multi-character column annotation labels</li>
4428 <li>Jalview Annotation File generation/parsing consistent
4429 with documentation (e.g. Stockholm annotation can be
4430 exported and re-imported)</li>
4431 <li>PDB files without embedded PDB IDs given a friendly
4433 <li>Find incrementally searches ID string matches as well
4434 as subsequence matches, and correctly reports total number
4438 <li>Better handling of exceptions during sequence
4440 <li>Dasobert generated non-positional feature URL
4441 link text excludes the start_end suffix</li>
4442 <li>DAS feature and source retrieval buttons disabled
4443 when fetch or registry operations in progress.</li>
4444 <li>PDB files retrieved from URLs are cached properly</li>
4445 <li>Sequence description lines properly shared via
4447 <li>Sequence fetcher fetches multiple records for all
4449 <li>Ensured that command line das feature retrieval
4450 completes before alignment figures are generated.</li>
4451 <li>Reduced time taken when opening file browser for
4453 <li>isAligned check prior to calculating tree, PCA or
4454 submitting an MSA to JNet now excludes hidden sequences.</li>
4455 <li>User defined group colours properly recovered
4456 from Jalview projects.</li>
4465 <div align="center">
4466 <strong>2.4.0.b2</strong><br> 28/10/2009
4471 <li>Experimental support for google analytics usage
4473 <li>Jalview privacy settings (user preferences and docs).</li>
4478 <li>Race condition in applet preventing startup in
4480 <li>Exception when feature created from selection beyond
4481 length of sequence.</li>
4482 <li>Allow synthetic PDB files to be imported gracefully</li>
4483 <li>Sequence associated annotation rows associate with
4484 all sequences with a given id</li>
4485 <li>Find function matches case-insensitively for sequence
4486 ID string searches</li>
4487 <li>Non-standard characters do not cause pairwise
4488 alignment to fail with exception</li>
4489 </ul> <em>Application Issues</em>
4491 <li>Sequences are now validated against EMBL database</li>
4492 <li>Sequence fetcher fetches multiple records for all
4494 </ul> <em>InstallAnywhere Issues</em>
4496 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4497 issue with installAnywhere mechanism)</li>
4498 <li>Command line launching of JARs from InstallAnywhere
4499 version (java class versioning error fixed)</li>
4506 <div align="center">
4507 <strong>2.4</strong><br> 27/8/2008
4510 <td><em>User Interface</em>
4512 <li>Linked highlighting of codon and amino acid from
4513 translation and protein products</li>
4514 <li>Linked highlighting of structure associated with
4515 residue mapping to codon position</li>
4516 <li>Sequence Fetcher provides example accession numbers
4517 and 'clear' button</li>
4518 <li>MemoryMonitor added as an option under Desktop's
4520 <li>Extract score function to parse whitespace separated
4521 numeric data in description line</li>
4522 <li>Column labels in alignment annotation can be centred.</li>
4523 <li>Tooltip for sequence associated annotation give name
4525 </ul> <em>Web Services and URL fetching</em>
4527 <li>JPred3 web service</li>
4528 <li>Prototype sequence search client (no public services
4530 <li>Fetch either seed alignment or full alignment from
4532 <li>URL Links created for matching database cross
4533 references as well as sequence ID</li>
4534 <li>URL Links can be created using regular-expressions</li>
4535 </ul> <em>Sequence Database Connectivity</em>
4537 <li>Retrieval of cross-referenced sequences from other
4539 <li>Generalised database reference retrieval and
4540 validation to all fetchable databases</li>
4541 <li>Fetch sequences from DAS sources supporting the
4542 sequence command</li>
4543 </ul> <em>Import and Export</em>
4544 <li>export annotation rows as CSV for spreadsheet import</li>
4545 <li>Jalview projects record alignment dataset associations,
4546 EMBL products, and cDNA sequence mappings</li>
4547 <li>Sequence Group colour can be specified in Annotation
4549 <li>Ad-hoc colouring of group in Annotation File using RGB
4550 triplet as name of colourscheme</li>
4551 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4553 <li>treenode binding for VAMSAS tree exchange</li>
4554 <li>local editing and update of sequences in VAMSAS
4555 alignments (experimental)</li>
4556 <li>Create new or select existing session to join</li>
4557 <li>load and save of vamsas documents</li>
4558 </ul> <em>Application command line</em>
4560 <li>-tree parameter to open trees (introduced for passing
4562 <li>-fetchfrom command line argument to specify nicknames
4563 of DAS servers to query for alignment features</li>
4564 <li>-dasserver command line argument to add new servers
4565 that are also automatically queried for features</li>
4566 <li>-groovy command line argument executes a given groovy
4567 script after all input data has been loaded and parsed</li>
4568 </ul> <em>Applet-Application data exchange</em>
4570 <li>Trees passed as applet parameters can be passed to
4571 application (when using "View in full
4572 application")</li>
4573 </ul> <em>Applet Parameters</em>
4575 <li>feature group display control parameter</li>
4576 <li>debug parameter</li>
4577 <li>showbutton parameter</li>
4578 </ul> <em>Applet API methods</em>
4580 <li>newView public method</li>
4581 <li>Window (current view) specific get/set public methods</li>
4582 <li>Feature display control methods</li>
4583 <li>get list of currently selected sequences</li>
4584 </ul> <em>New Jalview distribution features</em>
4586 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4587 <li>RELEASE file gives build properties for the latest
4588 Jalview release.</li>
4589 <li>Java 1.1 Applet build made easier and donotobfuscate
4590 property controls execution of obfuscator</li>
4591 <li>Build target for generating source distribution</li>
4592 <li>Debug flag for javacc</li>
4593 <li>.jalview_properties file is documented (slightly) in
4594 jalview.bin.Cache</li>
4595 <li>Continuous Build Integration for stable and
4596 development version of Application, Applet and source
4601 <li>selected region output includes visible annotations
4602 (for certain formats)</li>
4603 <li>edit label/displaychar contains existing label/char
4605 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4606 <li>shorter peptide product names from EMBL records</li>
4607 <li>Newick string generator makes compact representations</li>
4608 <li>bootstrap values parsed correctly for tree files with
4610 <li>pathological filechooser bug avoided by not allowing
4611 filenames containing a ':'</li>
4612 <li>Fixed exception when parsing GFF files containing
4613 global sequence features</li>
4614 <li>Alignment datasets are finalized only when number of
4615 references from alignment sequences goes to zero</li>
4616 <li>Close of tree branch colour box without colour
4617 selection causes cascading exceptions</li>
4618 <li>occasional negative imgwidth exceptions</li>
4619 <li>better reporting of non-fatal warnings to user when
4620 file parsing fails.</li>
4621 <li>Save works when Jalview project is default format</li>
4622 <li>Save as dialog opened if current alignment format is
4623 not a valid output format</li>
4624 <li>UniProt canonical names introduced for both das and
4626 <li>Histidine should be midblue (not pink!) in Zappo</li>
4627 <li>error messages passed up and output when data read
4629 <li>edit undo recovers previous dataset sequence when
4630 sequence is edited</li>
4631 <li>allow PDB files without pdb ID HEADER lines (like
4632 those generated by MODELLER) to be read in properly</li>
4633 <li>allow reading of JPred concise files as a normal
4635 <li>Stockholm annotation parsing and alignment properties
4636 import fixed for PFAM records</li>
4637 <li>Structure view windows have correct name in Desktop
4639 <li>annotation consisting of sequence associated scores
4640 can be read and written correctly to annotation file</li>
4641 <li>Aligned cDNA translation to aligned peptide works
4643 <li>Fixed display of hidden sequence markers and
4644 non-italic font for representatives in Applet</li>
4645 <li>Applet Menus are always embedded in applet window on
4647 <li>Newly shown features appear at top of stack (in
4649 <li>Annotations added via parameter not drawn properly
4650 due to null pointer exceptions</li>
4651 <li>Secondary structure lines are drawn starting from
4652 first column of alignment</li>
4653 <li>UniProt XML import updated for new schema release in
4655 <li>Sequence feature to sequence ID match for Features
4656 file is case-insensitive</li>
4657 <li>Sequence features read from Features file appended to
4658 all sequences with matching IDs</li>
4659 <li>PDB structure coloured correctly for associated views
4660 containing a sub-sequence</li>
4661 <li>PDB files can be retrieved by applet from Jar files</li>
4662 <li>feature and annotation file applet parameters
4663 referring to different directories are retrieved correctly</li>
4664 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4665 <li>Fixed application hang whilst waiting for
4666 splash-screen version check to complete</li>
4667 <li>Applet properly URLencodes input parameter values
4668 when passing them to the launchApp service</li>
4669 <li>display name and local features preserved in results
4670 retrieved from web service</li>
4671 <li>Visual delay indication for sequence retrieval and
4672 sequence fetcher initialisation</li>
4673 <li>updated Application to use DAS 1.53e version of
4674 dasobert DAS client</li>
4675 <li>Re-instated Full AMSA support and .amsa file
4677 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4685 <div align="center">
4686 <strong>2.3</strong><br> 9/5/07
4691 <li>Jmol 11.0.2 integration</li>
4692 <li>PDB views stored in Jalview XML files</li>
4693 <li>Slide sequences</li>
4694 <li>Edit sequence in place</li>
4695 <li>EMBL CDS features</li>
4696 <li>DAS Feature mapping</li>
4697 <li>Feature ordering</li>
4698 <li>Alignment Properties</li>
4699 <li>Annotation Scores</li>
4700 <li>Sort by scores</li>
4701 <li>Feature/annotation editing in applet</li>
4706 <li>Headless state operation in 2.2.1</li>
4707 <li>Incorrect and unstable DNA pairwise alignment</li>
4708 <li>Cut and paste of sequences with annotation</li>
4709 <li>Feature group display state in XML</li>
4710 <li>Feature ordering in XML</li>
4711 <li>blc file iteration selection using filename # suffix</li>
4712 <li>Stockholm alignment properties</li>
4713 <li>Stockhom alignment secondary structure annotation</li>
4714 <li>2.2.1 applet had no feature transparency</li>
4715 <li>Number pad keys can be used in cursor mode</li>
4716 <li>Structure Viewer mirror image resolved</li>
4723 <div align="center">
4724 <strong>2.2.1</strong><br> 12/2/07
4729 <li>Non standard characters can be read and displayed
4730 <li>Annotations/Features can be imported/exported to the
4732 <li>Applet allows editing of sequence/annotation/group
4733 name & description
4734 <li>Preference setting to display sequence name in
4736 <li>Annotation file format extended to allow
4737 Sequence_groups to be defined
4738 <li>Default opening of alignment overview panel can be
4739 specified in preferences
4740 <li>PDB residue numbering annotation added to associated
4746 <li>Applet crash under certain Linux OS with Java 1.6
4748 <li>Annotation file export / import bugs fixed
4749 <li>PNG / EPS image output bugs fixed
4755 <div align="center">
4756 <strong>2.2</strong><br> 27/11/06
4761 <li>Multiple views on alignment
4762 <li>Sequence feature editing
4763 <li>"Reload" alignment
4764 <li>"Save" to current filename
4765 <li>Background dependent text colour
4766 <li>Right align sequence ids
4767 <li>User-defined lower case residue colours
4770 <li>Menu item accelerator keys
4771 <li>Control-V pastes to current alignment
4772 <li>Cancel button for DAS Feature Fetching
4773 <li>PCA and PDB Viewers zoom via mouse roller
4774 <li>User-defined sub-tree colours and sub-tree selection
4776 <li>'New Window' button on the 'Output to Text box'
4781 <li>New memory efficient Undo/Redo System
4782 <li>Optimised symbol lookups and conservation/consensus
4784 <li>Region Conservation/Consensus recalculated after
4786 <li>Fixed Remove Empty Columns Bug (empty columns at end
4788 <li>Slowed DAS Feature Fetching for increased robustness.
4790 <li>Made angle brackets in ASCII feature descriptions
4792 <li>Re-instated Zoom function for PCA
4793 <li>Sequence descriptions conserved in web service
4795 <li>UniProt ID discoverer uses any word separated by
4797 <li>WsDbFetch query/result association resolved
4798 <li>Tree leaf to sequence mapping improved
4799 <li>Smooth fonts switch moved to FontChooser dialog box.
4806 <div align="center">
4807 <strong>2.1.1</strong><br> 12/9/06
4812 <li>Copy consensus sequence to clipboard</li>
4817 <li>Image output - rightmost residues are rendered if
4818 sequence id panel has been resized</li>
4819 <li>Image output - all offscreen group boundaries are
4821 <li>Annotation files with sequence references - all
4822 elements in file are relative to sequence position</li>
4823 <li>Mac Applet users can use Alt key for group editing</li>
4829 <div align="center">
4830 <strong>2.1</strong><br> 22/8/06
4835 <li>MAFFT Multiple Alignment in default Web Service list</li>
4836 <li>DAS Feature fetching</li>
4837 <li>Hide sequences and columns</li>
4838 <li>Export Annotations and Features</li>
4839 <li>GFF file reading / writing</li>
4840 <li>Associate structures with sequences from local PDB
4842 <li>Add sequences to exisiting alignment</li>
4843 <li>Recently opened files / URL lists</li>
4844 <li>Applet can launch the full application</li>
4845 <li>Applet has transparency for features (Java 1.2
4847 <li>Applet has user defined colours parameter</li>
4848 <li>Applet can load sequences from parameter
4849 "sequence<em>x</em>"
4855 <li>Redundancy Panel reinstalled in the Applet</li>
4856 <li>Monospaced font - EPS / rescaling bug fixed</li>
4857 <li>Annotation files with sequence references bug fixed</li>
4863 <div align="center">
4864 <strong>2.08.1</strong><br> 2/5/06
4869 <li>Change case of selected region from Popup menu</li>
4870 <li>Choose to match case when searching</li>
4871 <li>Middle mouse button and mouse movement can compress /
4872 expand the visible width and height of the alignment</li>
4877 <li>Annotation Panel displays complete JNet results</li>
4883 <div align="center">
4884 <strong>2.08b</strong><br> 18/4/06
4890 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4891 <li>Righthand label on wrapped alignments shows correct
4898 <div align="center">
4899 <strong>2.08</strong><br> 10/4/06
4904 <li>Editing can be locked to the selection area</li>
4905 <li>Keyboard editing</li>
4906 <li>Create sequence features from searches</li>
4907 <li>Precalculated annotations can be loaded onto
4909 <li>Features file allows grouping of features</li>
4910 <li>Annotation Colouring scheme added</li>
4911 <li>Smooth fonts off by default - Faster rendering</li>
4912 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4917 <li>Drag & Drop fixed on Linux</li>
4918 <li>Jalview Archive file faster to load/save, sequence
4919 descriptions saved.</li>
4925 <div align="center">
4926 <strong>2.07</strong><br> 12/12/05
4931 <li>PDB Structure Viewer enhanced</li>
4932 <li>Sequence Feature retrieval and display enhanced</li>
4933 <li>Choose to output sequence start-end after sequence
4934 name for file output</li>
4935 <li>Sequence Fetcher WSDBFetch@EBI</li>
4936 <li>Applet can read feature files, PDB files and can be
4937 used for HTML form input</li>
4942 <li>HTML output writes groups and features</li>
4943 <li>Group editing is Control and mouse click</li>
4944 <li>File IO bugs</li>
4950 <div align="center">
4951 <strong>2.06</strong><br> 28/9/05
4956 <li>View annotations in wrapped mode</li>
4957 <li>More options for PCA viewer</li>
4962 <li>GUI bugs resolved</li>
4963 <li>Runs with -nodisplay from command line</li>
4969 <div align="center">
4970 <strong>2.05b</strong><br> 15/9/05
4975 <li>Choose EPS export as lineart or text</li>
4976 <li>Jar files are executable</li>
4977 <li>Can read in Uracil - maps to unknown residue</li>
4982 <li>Known OutOfMemory errors give warning message</li>
4983 <li>Overview window calculated more efficiently</li>
4984 <li>Several GUI bugs resolved</li>
4990 <div align="center">
4991 <strong>2.05</strong><br> 30/8/05
4996 <li>Edit and annotate in "Wrapped" view</li>
5001 <li>Several GUI bugs resolved</li>
5007 <div align="center">
5008 <strong>2.04</strong><br> 24/8/05
5013 <li>Hold down mouse wheel & scroll to change font
5019 <li>Improved JPred client reliability</li>
5020 <li>Improved loading of Jalview files</li>
5026 <div align="center">
5027 <strong>2.03</strong><br> 18/8/05
5032 <li>Set Proxy server name and port in preferences</li>
5033 <li>Multiple URL links from sequence ids</li>
5034 <li>User Defined Colours can have a scheme name and added
5036 <li>Choose to ignore gaps in consensus calculation</li>
5037 <li>Unix users can set default web browser</li>
5038 <li>Runs without GUI for batch processing</li>
5039 <li>Dynamically generated Web Service Menus</li>
5044 <li>InstallAnywhere download for Sparc Solaris</li>
5050 <div align="center">
5051 <strong>2.02</strong><br> 18/7/05
5057 <li>Copy & Paste order of sequences maintains
5058 alignment order.</li>
5064 <div align="center">
5065 <strong>2.01</strong><br> 12/7/05
5070 <li>Use delete key for deleting selection.</li>
5071 <li>Use Mouse wheel to scroll sequences.</li>
5072 <li>Help file updated to describe how to add alignment
5074 <li>Version and build date written to build properties
5076 <li>InstallAnywhere installation will check for updates
5077 at launch of Jalview.</li>
5082 <li>Delete gaps bug fixed.</li>
5083 <li>FileChooser sorts columns.</li>
5084 <li>Can remove groups one by one.</li>
5085 <li>Filechooser icons installed.</li>
5086 <li>Finder ignores return character when searching.
5087 Return key will initiate a search.<br>
5094 <div align="center">
5095 <strong>2.0</strong><br> 20/6/05
5100 <li>New codebase</li>