4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>01/02/2022</em></strong></td>
63 <td align="left" valign="top">
68 </ul> <!-- <em>Development</em>
70 <li>Updated building instructions</li>
77 TO DOCUMENT: JAL-3700,JAL-3751,JAL-3763
80 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
83 </ul> <em>Development</em>
85 <li>Fixed non-fatal gradle errors during build</li>
90 <td width="60" align="center" nowrap><strong><a
91 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
92 <em>18/01/2022</em></strong></td>
94 <td align="left" valign="top">
97 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
98 updated by Jalview or other applications (Windows, other non
101 </ul> <em>Security</em>
104 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
110 <td width="60" align="center" nowrap><strong><a
111 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
112 <em>6/01/2022</em></strong></td>
114 <td align="left" valign="top"><em>Security</em>
117 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
124 <td width="60" align="center" nowrap><strong><a
125 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
126 <em>20/12/2021</em></strong></td>
128 <td align="left" valign="top"><em>Security</em>
131 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
133 </ul> <em>Development</em>
135 <li>Updated building instructions</li>
140 <!-- JAL-3840 -->Occupancy calculation is incorrect for
141 alignment columns with over -1+2^32 gaps (breaking filtering
145 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
146 scale factors being set with buggy window-managers (linux
149 </ul> <em>Development</em>
151 <li>Fixed non-fatal gradle errors during build</li>
156 <td width="60" align="center" nowrap><strong><a
157 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
158 <em>09/03/2021</em></strong></td>
159 <td align="left" valign="top"><em>Improved control of
160 Jalview's use of network services via jalview_properties</em>
163 <!-- JAL-3814 -->New .jalview_properties token controlling
164 launch of the news browser (like -nonews argument)
167 <!-- JAL-3813 -->New .jalview_properties token controlling
168 download of linkout URLs from
169 www.jalview.org/services/identifiers
172 <!-- JAL-3812 -->New .jalview_properties token controlling
173 download of BIOJSHTML templates
176 <!-- JAL-3811 -->New 'Discover Web Services' option to
177 trigger a one off JABAWS discovery if autodiscovery was
181 <td align="left" valign="top">
184 <!-- JAL-3818 -->Intermittent deadlock opening structure in
187 </ul> <em>New Known defects</em>
190 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
191 always restored from project (since 2.10.3)
194 <!-- JAL-3806 -->Selections from tree built from CDS aren't
195 propagated to Protein alignment (since 2.11.1.3)
201 <td width="60" align="center" nowrap><strong><a
202 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
203 <em>29/10/2020</em></strong></td>
204 <td align="left" valign="top">
209 <td align="left" valign="top">
212 <!-- JAL-3765 -->Find doesn't always highlight all matching
213 positions in a sequence (bug introduced in 2.11.1.2)
216 <!-- JAL-3760 -->Alignments containing one or more protein
217 sequences can be classed as nucleotide
220 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
221 sequences after alignment of protein products (known defect
222 first reported for 2.11.1.0)
225 <!-- JAL-3725 -->No tooltip or popup menu for genomic
226 features outwith CDS shown overlaid on protein
229 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
230 correctly mapped by Jalview (e.g. affects viral CDS with
231 ribosomal slippage, since 2.9.0)
234 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
238 <!-- JAL-3700 -->Selections in CDS sequence panel don't
239 always select corresponding protein sequences
242 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
243 column selection doesn't always ignore hidden columns
245 </ul> <em>Installer</em>
248 <!-- JAL-3611 -->Space character in Jalview install path on
249 Windows prevents install4j launching getdown
251 </ul> <em>Development</em>
254 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
255 version numbers in doc/building.md
261 <td width="60" align="center" nowrap><strong><a
262 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
263 <em>25/09/2020</em></strong></td>
264 <td align="left" valign="top">
268 <td align="left" valign="top">
271 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
272 "Encountered problems opening
273 https://www.jalview.org/examples/exampleFile_2_7.jvp"
279 <td width="60" align="center" nowrap><strong><a
280 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
281 <em>17/09/2020</em></strong></td>
282 <td align="left" valign="top">
285 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
286 residue in cursor mode
289 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
290 HTSJDK from 2.12 to 2.23
293 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
294 optimisations and improvements suggested by Bob Hanson and
295 improved compatibility with JalviewJS
298 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
299 alignments from Pfam and Rfam
302 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
303 import (no longer based on .gz extension)
306 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
309 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
310 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
314 <!-- JAL-3667 -->Improved warning messages, debug logging
315 and fixed Retry action when Jalview encounters errors when
316 saving or making backup files.
319 <!-- JAL-3676 -->Enhanced Jalview Java Console:
321 <li>Jalview's logging level can be configured</li>
322 <li>Copy to Clipboard Buttion</li>
326 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
327 when running on Linux (Requires Java 11+)
329 </ul> <em>Launching Jalview</em>
332 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
333 through a system property
336 <!-- JAL-3477 -->Improved built-in documentation and command
337 line help for configuring Jalview's memory
341 <td align="left" valign="top">
344 <!-- JAL-3691 -->Conservation and Quality tracks are shown
345 but not calculated and no protein or DNA score models are
346 available for tree/PCA calculation when launched with
347 Turkish language locale
350 <!-- JAL-3493 -->Escape does not clear highlights on the
351 alignment (Since Jalview 2.10.3)
354 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
355 doesn't slide selected sequences, just sequence under cursor
358 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
359 sequence under the cursor
362 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
363 multiple EMBL gene products shown for a single contig
366 <!-- JAL-3696 -->Errors encountered when processing variants
367 from VCF files yield "Error processing VCF: Format specifier
371 <!-- JAL-3697 -->Count of features not shown can be wrong
372 when there are both local and complementary features mapped
373 to the position under the cursor
376 <!-- JAL-3673 -->Sequence ID for reference sequence is
377 clipped when Right align Sequence IDs enabled
380 <!-- JAL-2983 -->Slider with negative range values not
381 rendered correctly in VAqua4 (Since 2.10.4)
384 <!-- JAL-3685 -->Single quotes not displayed correctly in
385 internationalised text for some messages and log output
388 <!-- JAL-3490 -->Find doesn't report matches that span
389 hidden gapped columns
392 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
393 panels, Alignment viewport and annotation renderer.
396 <!-- JAL-3561 -->Jalview ignores file format parameter
397 specifying output format when exporting an alignment via the
401 <!-- JAL-3667 -->Windows 10: For a minority of users, if
402 backups are not enabled, Jalview sometimes fails to
403 overwrite an existing file and raises a warning dialog. (in
404 2.11.0, and 2.11.1.0, the workaround is to try to save the
405 file again, and if that fails, delete the original file and
409 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
413 <!-- JAL-3741 -->References to http://www.jalview.org in
414 program and documentation
416 </ul> <em>Launching Jalview</em>
419 <!-- JAL-3718 -->Jalview application fails when launched the
420 first time for a version that has different jars to the
421 previous launched version.
423 </ul> <em>Developing Jalview</em>
426 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
427 data, causing cloverReport gradle task to fail with an
431 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
432 monitor the release channel
434 </ul> <em>New Known defects</em>
437 <!-- JAL-3748 -->CDS shown in result of submitting proteins
438 in a CDS/Protein alignment to a web service is wrong when
439 proteins share a common transcript sequence (e.g.
440 genome of RNA viruses)
443 <!-- JAL-3576 -->Co-located features exported and re-imported
444 are ordered differently when shown on alignment and in
445 tooltips. (Also affects v2.11.1.0)
448 <!-- JAL-3702 -->Drag and drop of alignment file onto
449 alignment window when in a HiDPI scaled mode in Linux only
450 works for the top left quadrant of the alignment window
453 <!-- JAL-3701 -->Stale build data in jalview standalone jar
454 builds (only affects 2.11.1.1 branch)
457 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
458 when alignment view restored from project (since Jalview 2.11.0)
461 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
462 protein products for certain ENA records are repeatedly
463 shown via Calculate->Show Cross Refs
469 <td width="60" align="center" nowrap><strong><a
470 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
471 <em>22/04/2020</em></strong></td>
472 <td align="left" valign="top">
475 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
476 'virtual' codon features shown on protein (or vice versa)
477 for display in alignments, on structure views (including
478 transfer to UCSF chimera), in feature reports and for
482 <!-- JAL-3121 -->Feature attributes from VCF files can be
483 exported and re-imported as GFF3 files
486 <!-- JAL-3376 -->Capture VCF "fixed column" values
487 POS, ID, QUAL, FILTER as Feature Attributes
490 <!-- JAL-3375 -->More robust VCF numeric data field
491 validation while parsing
494 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
498 <!-- JAL-3535 -->Feature Settings dialog title includes name
502 <!-- JAL-3538 -->Font anti-aliasing in alignment views
506 <!-- JAL-3468 -->Very long feature descriptions truncated in
510 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
511 with no feature types visible
514 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
516 </ul><em>Jalview Installer</em>
519 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
520 in console (may be null when Jalview launched as executable jar or via conda)
523 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
526 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
529 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
531 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
532 </ul> <em>Release processes</em>
535 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
538 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
540 </ul> <em>Build System</em>
543 <!-- JAL-3510 -->Clover updated to 4.4.1
546 <!-- JAL-3513 -->Test code included in Clover coverage
550 <em>Groovy Scripts</em>
553 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
554 to stdout containing the consensus sequence for each
555 alignment in a Jalview session
558 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
559 genomic sequence_variant annotation from CDS as
560 missense_variant or synonymous_variant on protein products.
564 <td align="left" valign="top">
567 <!-- JAL-3581 -->Hidden sequence markers still visible when
568 'Show hidden markers' option is not ticked
571 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
572 PNG output when 'Automatically set ID width' is set in
573 jalview preferences or properties file
576 <!-- JAL-3571 -->Feature Editor dialog can be opened when
577 'Show Sequence Features' option is not ticked
580 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
581 buttons in Feature Settings dialog are clicked when no
585 <!-- JAL-3412 -->ID margins for CDS and Protein views not
586 equal when split frame is first opened
589 <!-- JAL-3296 -->Sequence position numbers in status bar not
590 correct after editing a sequence's start position
593 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
594 with annotation and exceptions thrown when only a few
595 columns shown in wrapped mode
598 <!-- JAL-3386 -->Sequence IDs missing in headless export of
599 wrapped alignment figure with annotations
602 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
603 ID fails with ClassCastException
606 <!-- JAL-3389 -->Chimera session not restored from Jalview
610 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
611 feature settings dialog also selects columns
614 <!-- JAL-3473 -->SpinnerNumberModel causes
615 IllegalArgumentException in some circumstances
618 <!-- JAL-3534 -->Multiple feature settings dialogs can be
622 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
623 alignment window is closed
626 <!-- JAL-3406 -->Credits missing some authors in Jalview
627 help documentation for 2.11.0 release
630 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
631 includes Pfam ID as sequence's accession rather than its
634 </ul> <em>Java 11 Compatibility issues</em>
637 <!-- JAL-2987 -->OSX - Can't view some search results in
638 PDB/Uniprot search panel
640 </ul> <em>Installer</em>
643 <!-- JAL-3447 -->Jalview should not create file associations
644 for 3D structure files (.pdb, .mmcif. .cif)
646 </ul> <em>Repository and Source Release</em>
649 <!-- JAL-3474 -->removed obsolete .cvsignore files from
653 <!-- JAL-3541 -->Clover report generation running out of
656 </ul> <em>New Known Issues</em>
659 <!-- JAL-3523 -->OSX - Current working directory not
660 preserved when Jalview.app launched with parameters from
664 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
665 clipped in headless figure export when Right Align option
669 <!-- JAL-3542 -->Jalview Installation type always reports
670 'Source' in console output
673 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
674 bamboo server but run fine locally.
680 <td width="60" align="center" nowrap>
681 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
682 <em>04/07/2019</em></strong>
684 <td align="left" valign="top">
687 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
688 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
689 source project) rather than InstallAnywhere
692 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
693 settings, receive over the air updates and launch specific
694 versions via (<a href="https://github.com/threerings/getdown">Three
698 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
699 formats supported by Jalview (including .jvp project files)
702 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
703 arguments and switch between different getdown channels
706 <!-- JAL-3141 -->Backup files created when saving Jalview project
711 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
712 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
714 <!-- JAL-2620 -->Alternative genetic code tables for
715 'Translate as cDNA'</li>
717 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
718 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
721 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
722 implementation that allows updates) used for Sequence Feature collections</li>
724 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
725 features can be filtered and shaded according to any
726 associated attributes (e.g. variant attributes from VCF
727 file, or key-value pairs imported from column 9 of GFF
731 <!-- JAL-2879 -->Feature Attributes and shading schemes
732 stored and restored from Jalview Projects
735 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
736 recognise variant features
739 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
740 sequences (also coloured red by default)
743 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
747 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
748 algorithm (Z-sort/transparency and filter aware)
751 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
757 <!-- JAL-3205 -->Symmetric score matrices for faster
758 tree and PCA calculations
760 <li><strong>Principal Components Analysis Viewer</strong>
763 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
764 and Viewer state saved in Jalview Project
766 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
769 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
773 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
778 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
780 <li><strong>Speed and Efficiency</strong>
783 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
784 multiple groups when working with large alignments
787 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
791 <li><strong>User Interface</strong>
794 <!-- JAL-2933 -->Finder panel remembers last position in each
798 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
799 what is shown)<br />Only visible regions of alignment are shown by
800 default (can be changed in user preferences)
803 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
804 to the Overwrite Dialog
807 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
811 <!-- JAL-1244 -->Status bar shows bounds when dragging a
812 selection region, and gap count when inserting or deleting gaps
815 <!-- JAL-3132 -->Status bar updates over sequence and annotation
819 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
823 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
827 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
830 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
834 <!-- JAL-3181 -->Consistent ordering of links in sequence id
838 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
840 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
844 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
845 <li><strong>Java 11 Support (not yet on general release)</strong>
848 <!-- -->OSX GUI integrations for App menu's 'About' entry and
853 <em>Deprecations</em>
855 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
856 capabilities removed from the Jalview Desktop
858 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
859 unmarshalling has been replaced by JAXB for Jalview projects
860 and XML based data retrieval clients</li>
861 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
862 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
863 </ul> <em>Documentation</em>
865 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
866 not supported in EPS figure export
868 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
869 </ul> <em>Development and Release Processes</em>
872 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
875 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
877 <!-- JAL-3225 -->Eclipse project configuration managed with
881 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
882 Bamboo continuous integration for unattended Test Suite
886 <!-- JAL-2864 -->Memory test suite to detect leaks in common
890 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
894 <!-- JAL-3248 -->Developer documentation migrated to
895 markdown (with HTML rendering)
898 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
901 <!-- JAL-3289 -->New URLs for publishing development
906 <td align="left" valign="top">
909 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
912 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
913 superposition in Jmol fail on Windows
916 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
917 structures for sequences with lots of PDB structures
920 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
924 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
925 project involving multiple views
928 <!-- JAL-3164 -->Overview for complementary view in a linked
929 CDS/Protein alignment is not updated when Hide Columns by
930 Annotation dialog hides columns
933 <!-- JAL-3158 -->Selection highlighting in the complement of a
934 CDS/Protein alignment stops working after making a selection in
935 one view, then making another selection in the other view
938 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
942 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
943 Settings and Jalview Preferences panels
946 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
947 overview with large alignments
950 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
951 region if columns were selected by dragging right-to-left and the
952 mouse moved to the left of the first column
955 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
956 hidden column marker via scale popup menu
959 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
960 doesn't tell users the invalid URL
963 <!-- JAL-2816 -->Tooltips displayed for features filtered by
967 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
968 show cross references or Fetch Database References are shown in
972 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
973 peptide sequence (computed variant shown as p.Res.null)
976 <!-- JAL-2060 -->'Graduated colour' option not offered for
977 manually created features (where feature score is Float.NaN)
980 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
981 when columns are hidden
984 <!-- JAL-3082 -->Regular expression error for '(' in Select
985 Columns by Annotation description
988 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
989 out of Scale or Annotation Panel
992 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
996 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1000 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
1004 <!-- JAL-3002 -->Column display is out by one after Page Down,
1005 Page Up in wrapped mode
1008 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1011 <!-- JAL-2932 -->Finder searches in minimised alignments
1014 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
1015 on opening an alignment
1018 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
1022 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
1023 different groups in the alignment are selected
1026 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1030 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1034 <!-- JAL-3125 -->Value input for graduated feature colour
1035 threshold gets 'unrounded'
1038 <!-- JAL-2982 -->PCA image export doesn't respect background
1042 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1045 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1048 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1052 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1056 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1057 shown in complementary view
1060 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1061 without normalisation
1064 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1068 <!-- JAL-914 -->Help page can be opened twice
1071 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1073 </ul> <em>Editing</em>
1076 <!-- JAL-2822 -->Start and End should be updated when sequence
1077 data at beginning or end of alignment added/removed via 'Edit'
1081 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1082 relocate sequence features correctly when start of sequence is
1083 removed (Known defect since 2.10)
1086 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1087 dialog corrupts dataset sequence
1090 <!-- JAL-868 -->Structure colours not updated when associated tree
1091 repartitions the alignment view (Regression in 2.10.5)
1093 </ul> <em>Datamodel</em>
1096 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1097 sequence's End is greater than its length
1099 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1100 general release)</em>
1103 <!-- JAL-3288 -->Menus work properly in split-screen
1105 </ul> <em>New Known Defects</em>
1108 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1111 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1112 regions of protein alignment.
1115 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1116 is restored from a Jalview 2.11 project
1119 <!-- JAL-3213 -->Alignment panel height can be too small after
1123 <!-- JAL-3240 -->Display is incorrect after removing gapped
1124 columns within hidden columns
1127 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1128 window after dragging left to select columns to left of visible
1132 <!-- JAL-2876 -->Features coloured according to their description
1133 string and thresholded by score in earlier versions of Jalview are
1134 not shown as thresholded features in 2.11. To workaround please
1135 create a Score filter instead.
1138 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1140 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1143 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1144 alignments with multiple views can close views unexpectedly
1147 <em>Java 11 Specific defects</em>
1150 <!-- JAL-3235 -->Jalview Properties file is not sorted
1151 alphabetically when saved
1157 <td width="60" nowrap>
1158 <div align="center">
1159 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1162 <td><div align="left">
1166 <!-- JAL-3101 -->Default memory for Jalview webstart and
1167 InstallAnywhere increased to 1G.
1170 <!-- JAL-247 -->Hidden sequence markers and representative
1171 sequence bolding included when exporting alignment as EPS,
1172 SVG, PNG or HTML. <em>Display is configured via the
1173 Format menu, or for command-line use via a Jalview
1174 properties file.</em>
1177 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1178 API and sequence data now imported as JSON.
1181 <!-- JAL-3065 -->Change in recommended way of starting
1182 Jalview via a Java command line: add jars in lib directory
1183 to CLASSPATH, rather than via the deprecated java.ext.dirs
1187 <em>Development</em>
1190 <!-- JAL-3047 -->Support added to execute test suite
1191 instrumented with <a href="http://openclover.org/">Open
1196 <td><div align="left">
1200 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1201 row shown in Feredoxin Structure alignment view of example
1205 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1206 annotation displayed.
1209 <!-- JAL-3107 -->Group conservation/consensus not shown
1210 for newly created group when 'Apply to all groups'
1214 <!-- JAL-3087 -->Corrupted display when switching to
1215 wrapped mode when sequence panel's vertical scrollbar is
1219 <!-- JAL-3003 -->Alignment is black in exported EPS file
1220 when sequences are selected in exported view.</em>
1223 <!-- JAL-3059 -->Groups with different coloured borders
1224 aren't rendered with correct colour.
1227 <!-- JAL-3092 -->Jalview could hang when importing certain
1228 types of knotted RNA secondary structure.
1231 <!-- JAL-3095 -->Sequence highlight and selection in
1232 trimmed VARNA 2D structure is incorrect for sequences that
1236 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1237 annotation when columns are inserted into an alignment,
1238 and when exporting as Stockholm flatfile.
1241 <!-- JAL-3053 -->Jalview annotation rows containing upper
1242 and lower-case 'E' and 'H' do not automatically get
1243 treated as RNA secondary structure.
1246 <!-- JAL-3106 -->.jvp should be used as default extension
1247 (not .jar) when saving a Jalview project file.
1250 <!-- JAL-3105 -->Mac Users: closing a window correctly
1251 transfers focus to previous window on OSX
1254 <em>Java 10 Issues Resolved</em>
1257 <!-- JAL-2988 -->OSX - Can't save new files via the File
1258 or export menus by typing in a name into the Save dialog
1262 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1263 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1264 'look and feel' which has improved compatibility with the
1265 latest version of OSX.
1272 <td width="60" nowrap>
1273 <div align="center">
1274 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1275 <em>7/06/2018</em></strong>
1278 <td><div align="left">
1282 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1283 annotation retrieved from Uniprot
1286 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1287 onto the Jalview Desktop
1291 <td><div align="left">
1295 <!-- JAL-3017 -->Cannot import features with multiple
1296 variant elements (blocks import of some Uniprot records)
1299 <!-- JAL-2997 -->Clustal files with sequence positions in
1300 right-hand column parsed correctly
1303 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1304 not alignment area in exported graphic
1307 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1308 window has input focus
1311 <!-- JAL-2992 -->Annotation panel set too high when
1312 annotation added to view (Windows)
1315 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1316 network connectivity is poor
1319 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1320 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1321 the currently open URL and links from a page viewed in
1322 Firefox or Chrome on Windows is now fully supported. If
1323 you are using Edge, only links in the page can be
1324 dragged, and with Internet Explorer, only the currently
1325 open URL in the browser can be dropped onto Jalview.</em>
1328 <em>New Known Defects</em>
1330 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1335 <td width="60" nowrap>
1336 <div align="center">
1337 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1340 <td><div align="left">
1344 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1345 for disabling automatic superposition of multiple
1346 structures and open structures in existing views
1349 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1350 ID and annotation area margins can be click-dragged to
1354 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1358 <!-- JAL-2759 -->Improved performance for large alignments
1359 and lots of hidden columns
1362 <!-- JAL-2593 -->Improved performance when rendering lots
1363 of features (particularly when transparency is disabled)
1366 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1367 exchange of Jalview features and Chimera attributes made
1373 <td><div align="left">
1376 <!-- JAL-2899 -->Structure and Overview aren't updated
1377 when Colour By Annotation threshold slider is adjusted
1380 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1381 overlapping alignment panel
1384 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1388 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1389 improved: CDS not handled correctly if transcript has no
1393 <!-- JAL-2321 -->Secondary structure and temperature
1394 factor annotation not added to sequence when local PDB
1395 file associated with it by drag'n'drop or structure
1399 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1400 dialog doesn't import PDB files dropped on an alignment
1403 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1404 scroll bar doesn't work for some CDS/Protein views
1407 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1408 Java 1.8u153 onwards and Java 1.9u4+.
1411 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1412 columns in annotation row
1415 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1416 honored in batch mode
1419 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1420 for structures added to existing Jmol view
1423 <!-- JAL-2223 -->'View Mappings' includes duplicate
1424 entries after importing project with multiple views
1427 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1428 protein sequences via SIFTS from associated PDB entries
1429 with negative residue numbers or missing residues fails
1432 <!-- JAL-2952 -->Exception when shading sequence with negative
1433 Temperature Factor values from annotated PDB files (e.g.
1434 as generated by CONSURF)
1437 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1438 tooltip doesn't include a text description of mutation
1441 <!-- JAL-2922 -->Invert displayed features very slow when
1442 structure and/or overview windows are also shown
1445 <!-- JAL-2954 -->Selecting columns from highlighted regions
1446 very slow for alignments with large numbers of sequences
1449 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1450 with 'StringIndexOutOfBounds'
1453 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1454 platforms running Java 10
1457 <!-- JAL-2960 -->Adding a structure to existing structure
1458 view appears to do nothing because the view is hidden behind the alignment view
1464 <!-- JAL-2926 -->Copy consensus sequence option in applet
1465 should copy the group consensus when popup is opened on it
1471 <!-- JAL-2913 -->Fixed ID width preference is not respected
1474 <em>New Known Defects</em>
1477 <!-- JAL-2973 --> Exceptions occasionally raised when
1478 editing a large alignment and overview is displayed
1481 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1482 repeatedly after a series of edits even when the overview
1483 is no longer reflecting updates
1486 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1487 structures for protein subsequence (if 'Trim Retrieved
1488 Sequences' enabled) or Ensembl isoforms (Workaround in
1489 2.10.4 is to fail back to N&W mapping)
1492 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1493 option gives blank output
1500 <td width="60" nowrap>
1501 <div align="center">
1502 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1505 <td><div align="left">
1506 <ul><li>Updated Certum Codesigning Certificate
1507 (Valid till 30th November 2018)</li></ul></div></td>
1508 <td><div align="left">
1509 <em>Desktop</em><ul>
1511 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1512 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1513 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1514 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1515 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1516 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1517 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1523 <td width="60" nowrap>
1524 <div align="center">
1525 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1528 <td><div align="left">
1532 <!-- JAL-2446 -->Faster and more efficient management and
1533 rendering of sequence features
1536 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1537 429 rate limit request hander
1540 <!-- JAL-2773 -->Structure views don't get updated unless
1541 their colours have changed
1544 <!-- JAL-2495 -->All linked sequences are highlighted for
1545 a structure mousover (Jmol) or selection (Chimera)
1548 <!-- JAL-2790 -->'Cancel' button in progress bar for
1549 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1552 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1553 view from Ensembl locus cross-references
1556 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1560 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1561 feature can be disabled
1564 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1565 PDB easier retrieval of sequences for lists of IDs
1568 <!-- JAL-2758 -->Short names for sequences retrieved from
1574 <li>Groovy interpreter updated to 2.4.12</li>
1575 <li>Example groovy script for generating a matrix of
1576 percent identity scores for current alignment.</li>
1578 <em>Testing and Deployment</em>
1581 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1585 <td><div align="left">
1589 <!-- JAL-2643 -->Pressing tab after updating the colour
1590 threshold text field doesn't trigger an update to the
1594 <!-- JAL-2682 -->Race condition when parsing sequence ID
1598 <!-- JAL-2608 -->Overview windows are also closed when
1599 alignment window is closed
1602 <!-- JAL-2548 -->Export of features doesn't always respect
1606 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1607 takes a long time in Cursor mode
1613 <!-- JAL-2777 -->Structures with whitespace chainCode
1614 cannot be viewed in Chimera
1617 <!-- JAL-2728 -->Protein annotation panel too high in
1621 <!-- JAL-2757 -->Can't edit the query after the server
1622 error warning icon is shown in Uniprot and PDB Free Text
1626 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1629 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1632 <!-- JAL-2739 -->Hidden column marker in last column not
1633 rendered when switching back from Wrapped to normal view
1636 <!-- JAL-2768 -->Annotation display corrupted when
1637 scrolling right in unwapped alignment view
1640 <!-- JAL-2542 -->Existing features on subsequence
1641 incorrectly relocated when full sequence retrieved from
1645 <!-- JAL-2733 -->Last reported memory still shown when
1646 Desktop->Show Memory is unticked (OSX only)
1649 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1650 features of same type and group to be selected for
1654 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1655 alignments when hidden columns are present
1658 <!-- JAL-2392 -->Jalview freezes when loading and
1659 displaying several structures
1662 <!-- JAL-2732 -->Black outlines left after resizing or
1666 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1667 within the Jalview desktop on OSX
1670 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1671 when in wrapped alignment mode
1674 <!-- JAL-2636 -->Scale mark not shown when close to right
1675 hand end of alignment
1678 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1679 each selected sequence do not have correct start/end
1683 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1684 after canceling the Alignment Window's Font dialog
1687 <!-- JAL-2036 -->Show cross-references not enabled after
1688 restoring project until a new view is created
1691 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1692 URL links appears when only default EMBL-EBI link is
1693 configured (since 2.10.2b2)
1696 <!-- JAL-2775 -->Overview redraws whole window when box
1697 position is adjusted
1700 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1701 in a multi-chain structure when viewing alignment
1702 involving more than one chain (since 2.10)
1705 <!-- JAL-2811 -->Double residue highlights in cursor mode
1706 if new selection moves alignment window
1709 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1710 arrow key in cursor mode to pass hidden column marker
1713 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1714 that produces correctly annotated transcripts and products
1717 <!-- JAL-2776 -->Toggling a feature group after first time
1718 doesn't update associated structure view
1721 <em>Applet</em><br />
1724 <!-- JAL-2687 -->Concurrent modification exception when
1725 closing alignment panel
1728 <em>BioJSON</em><br />
1731 <!-- JAL-2546 -->BioJSON export does not preserve
1732 non-positional features
1735 <em>New Known Issues</em>
1738 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1739 sequence features correctly (for many previous versions of
1743 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1744 using cursor in wrapped panel other than top
1747 <!-- JAL-2791 -->Select columns containing feature ignores
1748 graduated colour threshold
1751 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1752 always preserve numbering and sequence features
1755 <em>Known Java 9 Issues</em>
1758 <!-- JAL-2902 -->Groovy Console very slow to open and is
1759 not responsive when entering characters (Webstart, Java
1766 <td width="60" nowrap>
1767 <div align="center">
1768 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1769 <em>2/10/2017</em></strong>
1772 <td><div align="left">
1773 <em>New features in Jalview Desktop</em>
1776 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1778 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1782 <td><div align="left">
1786 <td width="60" nowrap>
1787 <div align="center">
1788 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1789 <em>7/9/2017</em></strong>
1792 <td><div align="left">
1796 <!-- JAL-2588 -->Show gaps in overview window by colouring
1797 in grey (sequences used to be coloured grey, and gaps were
1801 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1805 <!-- JAL-2587 -->Overview updates immediately on increase
1806 in size and progress bar shown as higher resolution
1807 overview is recalculated
1812 <td><div align="left">
1816 <!-- JAL-2664 -->Overview window redraws every hidden
1817 column region row by row
1820 <!-- JAL-2681 -->duplicate protein sequences shown after
1821 retrieving Ensembl crossrefs for sequences from Uniprot
1824 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1825 format setting is unticked
1828 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1829 if group has show boxes format setting unticked
1832 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1833 autoscrolling whilst dragging current selection group to
1834 include sequences and columns not currently displayed
1837 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1838 assemblies are imported via CIF file
1841 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1842 displayed when threshold or conservation colouring is also
1846 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1850 <!-- JAL-2673 -->Jalview continues to scroll after
1851 dragging a selected region off the visible region of the
1855 <!-- JAL-2724 -->Cannot apply annotation based
1856 colourscheme to all groups in a view
1859 <!-- JAL-2511 -->IDs don't line up with sequences
1860 initially after font size change using the Font chooser or
1867 <td width="60" nowrap>
1868 <div align="center">
1869 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1872 <td><div align="left">
1873 <em>Calculations</em>
1877 <!-- JAL-1933 -->Occupancy annotation row shows number of
1878 ungapped positions in each column of the alignment.
1881 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1882 a calculation dialog box
1885 <!-- JAL-2379 -->Revised implementation of PCA for speed
1886 and memory efficiency (~30x faster)
1889 <!-- JAL-2403 -->Revised implementation of sequence
1890 similarity scores as used by Tree, PCA, Shading Consensus
1891 and other calculations
1894 <!-- JAL-2416 -->Score matrices are stored as resource
1895 files within the Jalview codebase
1898 <!-- JAL-2500 -->Trees computed on Sequence Feature
1899 Similarity may have different topology due to increased
1906 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1907 model for alignments and groups
1910 <!-- JAL-384 -->Custom shading schemes created via groovy
1917 <!-- JAL-2526 -->Efficiency improvements for interacting
1918 with alignment and overview windows
1921 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1925 <!-- JAL-2388 -->Hidden columns and sequences can be
1929 <!-- JAL-2611 -->Click-drag in visible area allows fine
1930 adjustment of visible position
1934 <em>Data import/export</em>
1937 <!-- JAL-2535 -->Posterior probability annotation from
1938 Stockholm files imported as sequence associated annotation
1941 <!-- JAL-2507 -->More robust per-sequence positional
1942 annotation input/output via stockholm flatfile
1945 <!-- JAL-2533 -->Sequence names don't include file
1946 extension when importing structure files without embedded
1947 names or PDB accessions
1950 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1951 format sequence substitution matrices
1954 <em>User Interface</em>
1957 <!-- JAL-2447 --> Experimental Features Checkbox in
1958 Desktop's Tools menu to hide or show untested features in
1962 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1963 via Overview or sequence motif search operations
1966 <!-- JAL-2547 -->Amend sequence features dialog box can be
1967 opened by double clicking gaps within sequence feature
1971 <!-- JAL-1476 -->Status bar message shown when not enough
1972 aligned positions were available to create a 3D structure
1976 <em>3D Structure</em>
1979 <!-- JAL-2430 -->Hidden regions in alignment views are not
1980 coloured in linked structure views
1983 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1984 file-based command exchange
1987 <!-- JAL-2375 -->Structure chooser automatically shows
1988 Cached Structures rather than querying the PDBe if
1989 structures are already available for sequences
1992 <!-- JAL-2520 -->Structures imported via URL are cached in
1993 the Jalview project rather than downloaded again when the
1994 project is reopened.
1997 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1998 to transfer Chimera's structure attributes as Jalview
1999 features, and vice-versa (<strong>Experimental
2003 <em>Web Services</em>
2006 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2009 <!-- JAL-2335 -->Filter non-standard amino acids and
2010 nucleotides when submitting to AACon and other MSA
2014 <!-- JAL-2316, -->URLs for viewing database
2015 cross-references provided by identifiers.org and the
2016 EMBL-EBI's MIRIAM DB
2023 <!-- JAL-2344 -->FileFormatI interface for describing and
2024 identifying file formats (instead of String constants)
2027 <!-- JAL-2228 -->FeatureCounter script refactored for
2028 efficiency when counting all displayed features (not
2029 backwards compatible with 2.10.1)
2032 <em>Example files</em>
2035 <!-- JAL-2631 -->Graduated feature colour style example
2036 included in the example feature file
2039 <em>Documentation</em>
2042 <!-- JAL-2339 -->Release notes reformatted for readability
2043 with the built-in Java help viewer
2046 <!-- JAL-1644 -->Find documentation updated with 'search
2047 sequence description' option
2053 <!-- JAL-2485, -->External service integration tests for
2054 Uniprot REST Free Text Search Client
2057 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2060 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2065 <td><div align="left">
2066 <em>Calculations</em>
2069 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2070 matrix - C->R should be '-3'<br />Old matrix restored
2071 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2073 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2074 Jalview's treatment of gaps in PCA and substitution matrix
2075 based Tree calculations.<br /> <br />In earlier versions
2076 of Jalview, gaps matching gaps were penalised, and gaps
2077 matching non-gaps penalised even more. In the PCA
2078 calculation, gaps were actually treated as non-gaps - so
2079 different costs were applied, which meant Jalview's PCAs
2080 were different to those produced by SeqSpace.<br />Jalview
2081 now treats gaps in the same way as SeqSpace (ie it scores
2082 them as 0). <br /> <br />Enter the following in the
2083 Groovy console to restore pre-2.10.2 behaviour:<br />
2084 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2085 // for 2.10.1 mode <br />
2086 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2087 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2088 these settings will affect all subsequent tree and PCA
2089 calculations (not recommended)</em></li>
2091 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2092 scaling of branch lengths for trees computed using
2093 Sequence Feature Similarity.
2096 <!-- JAL-2377 -->PCA calculation could hang when
2097 generating output report when working with highly
2098 redundant alignments
2101 <!-- JAL-2544 --> Sort by features includes features to
2102 right of selected region when gaps present on right-hand
2106 <em>User Interface</em>
2109 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2110 doesn't reselect a specific sequence's associated
2111 annotation after it was used for colouring a view
2114 <!-- JAL-2419 -->Current selection lost if popup menu
2115 opened on a region of alignment without groups
2118 <!-- JAL-2374 -->Popup menu not always shown for regions
2119 of an alignment with overlapping groups
2122 <!-- JAL-2310 -->Finder double counts if both a sequence's
2123 name and description match
2126 <!-- JAL-2370 -->Hiding column selection containing two
2127 hidden regions results in incorrect hidden regions
2130 <!-- JAL-2386 -->'Apply to all groups' setting when
2131 changing colour does not apply Conservation slider value
2135 <!-- JAL-2373 -->Percentage identity and conservation menu
2136 items do not show a tick or allow shading to be disabled
2139 <!-- JAL-2385 -->Conservation shading or PID threshold
2140 lost when base colourscheme changed if slider not visible
2143 <!-- JAL-2547 -->Sequence features shown in tooltip for
2144 gaps before start of features
2147 <!-- JAL-2623 -->Graduated feature colour threshold not
2148 restored to UI when feature colour is edited
2151 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2152 a time when scrolling vertically in wrapped mode.
2155 <!-- JAL-2630 -->Structure and alignment overview update
2156 as graduate feature colour settings are modified via the
2160 <!-- JAL-2034 -->Overview window doesn't always update
2161 when a group defined on the alignment is resized
2164 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2165 wrapped view result in positional status updates
2169 <!-- JAL-2563 -->Status bar doesn't show position for
2170 ambiguous amino acid and nucleotide symbols
2173 <!-- JAL-2602 -->Copy consensus sequence failed if
2174 alignment included gapped columns
2177 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2178 widgets don't permanently disappear
2181 <!-- JAL-2503 -->Cannot select or filter quantitative
2182 annotation that are shown only as column labels (e.g.
2183 T-Coffee column reliability scores)
2186 <!-- JAL-2594 -->Exception thrown if trying to create a
2187 sequence feature on gaps only
2190 <!-- JAL-2504 -->Features created with 'New feature'
2191 button from a Find inherit previously defined feature type
2192 rather than the Find query string
2195 <!-- JAL-2423 -->incorrect title in output window when
2196 exporting tree calculated in Jalview
2199 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2200 and then revealing them reorders sequences on the
2204 <!-- JAL-964 -->Group panel in sequence feature settings
2205 doesn't update to reflect available set of groups after
2206 interactively adding or modifying features
2209 <!-- JAL-2225 -->Sequence Database chooser unusable on
2213 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2214 only excluded gaps in current sequence and ignored
2221 <!-- JAL-2421 -->Overview window visible region moves
2222 erratically when hidden rows or columns are present
2225 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2226 Structure Viewer's colour menu don't correspond to
2230 <!-- JAL-2405 -->Protein specific colours only offered in
2231 colour and group colour menu for protein alignments
2234 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2235 reflect currently selected view or group's shading
2239 <!-- JAL-2624 -->Feature colour thresholds not respected
2240 when rendered on overview and structures when opacity at
2244 <!-- JAL-2589 -->User defined gap colour not shown in
2245 overview when features overlaid on alignment
2248 <!-- JAL-2567 -->Feature settings for different views not
2249 recovered correctly from Jalview project file
2252 <!-- JAL-2256 -->Feature colours in overview when first opened
2253 (automatically via preferences) are different to the main
2257 <em>Data import/export</em>
2260 <!-- JAL-2576 -->Very large alignments take a long time to
2264 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2265 added after a sequence was imported are not written to
2269 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2270 when importing RNA secondary structure via Stockholm
2273 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2274 not shown in correct direction for simple pseudoknots
2277 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2278 with lightGray or darkGray via features file (but can
2282 <!-- JAL-2383 -->Above PID colour threshold not recovered
2283 when alignment view imported from project
2286 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2287 structure and sequences extracted from structure files
2288 imported via URL and viewed in Jmol
2291 <!-- JAL-2520 -->Structures loaded via URL are saved in
2292 Jalview Projects rather than fetched via URL again when
2293 the project is loaded and the structure viewed
2296 <em>Web Services</em>
2299 <!-- JAL-2519 -->EnsemblGenomes example failing after
2300 release of Ensembl v.88
2303 <!-- JAL-2366 -->Proxy server address and port always
2304 appear enabled in Preferences->Connections
2307 <!-- JAL-2461 -->DAS registry not found exceptions
2308 removed from console output
2311 <!-- JAL-2582 -->Cannot retrieve protein products from
2312 Ensembl by Peptide ID
2315 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2316 created from SIFTs, and spurious 'Couldn't open structure
2317 in Chimera' errors raised after April 2017 update (problem
2318 due to 'null' string rather than empty string used for
2319 residues with no corresponding PDB mapping).
2322 <em>Application UI</em>
2325 <!-- JAL-2361 -->User Defined Colours not added to Colour
2329 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2330 case' residues (button in colourscheme editor debugged and
2331 new documentation and tooltips added)
2334 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2335 doesn't restore group-specific text colour thresholds
2338 <!-- JAL-2243 -->Feature settings panel does not update as
2339 new features are added to alignment
2342 <!-- JAL-2532 -->Cancel in feature settings reverts
2343 changes to feature colours via the Amend features dialog
2346 <!-- JAL-2506 -->Null pointer exception when attempting to
2347 edit graduated feature colour via amend features dialog
2351 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2352 selection menu changes colours of alignment views
2355 <!-- JAL-2426 -->Spurious exceptions in console raised
2356 from alignment calculation workers after alignment has
2360 <!-- JAL-1608 -->Typo in selection popup menu - Create
2361 groups now 'Create Group'
2364 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2365 Create/Undefine group doesn't always work
2368 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2369 shown again after pressing 'Cancel'
2372 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2373 adjusts start position in wrap mode
2376 <!-- JAL-2563 -->Status bar doesn't show positions for
2377 ambiguous amino acids
2380 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2381 CDS/Protein view after CDS sequences added for aligned
2385 <!-- JAL-2592 -->User defined colourschemes called 'User
2386 Defined' don't appear in Colours menu
2392 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2393 score models doesn't always result in an updated PCA plot
2396 <!-- JAL-2442 -->Features not rendered as transparent on
2397 overview or linked structure view
2400 <!-- JAL-2372 -->Colour group by conservation doesn't
2404 <!-- JAL-2517 -->Hitting Cancel after applying
2405 user-defined colourscheme doesn't restore original
2412 <!-- JAL-2314 -->Unit test failure:
2413 jalview.ws.jabaws.RNAStructExportImport setup fails
2416 <!-- JAL-2307 -->Unit test failure:
2417 jalview.ws.sifts.SiftsClientTest due to compatibility
2418 problems with deep array comparison equality asserts in
2419 successive versions of TestNG
2422 <!-- JAL-2479 -->Relocated StructureChooserTest and
2423 ParameterUtilsTest Unit tests to Network suite
2426 <em>New Known Issues</em>
2429 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2430 phase after a sequence motif find operation
2433 <!-- JAL-2550 -->Importing annotation file with rows
2434 containing just upper and lower case letters are
2435 interpreted as WUSS RNA secondary structure symbols
2438 <!-- JAL-2590 -->Cannot load and display Newick trees
2439 reliably from eggnog Ortholog database
2442 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2443 containing features of type Highlight' when 'B' is pressed
2444 to mark columns containing highlighted regions.
2447 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2448 doesn't always add secondary structure annotation.
2453 <td width="60" nowrap>
2454 <div align="center">
2455 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2458 <td><div align="left">
2462 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2463 for all consensus calculations
2466 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2469 <li>Updated Jalview's Certum code signing certificate
2472 <em>Application</em>
2475 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2476 set of database cross-references, sorted alphabetically
2479 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2480 from database cross references. Users with custom links
2481 will receive a <a href="webServices/urllinks.html#warning">warning
2482 dialog</a> asking them to update their preferences.
2485 <!-- JAL-2287-->Cancel button and escape listener on
2486 dialog warning user about disconnecting Jalview from a
2490 <!-- JAL-2320-->Jalview's Chimera control window closes if
2491 the Chimera it is connected to is shut down
2494 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2495 columns menu item to mark columns containing highlighted
2496 regions (e.g. from structure selections or results of a
2500 <!-- JAL-2284-->Command line option for batch-generation
2501 of HTML pages rendering alignment data with the BioJS
2511 <!-- JAL-2286 -->Columns with more than one modal residue
2512 are not coloured or thresholded according to percent
2513 identity (first observed in Jalview 2.8.2)
2516 <!-- JAL-2301 -->Threonine incorrectly reported as not
2520 <!-- JAL-2318 -->Updates to documentation pages (above PID
2521 threshold, amino acid properties)
2524 <!-- JAL-2292 -->Lower case residues in sequences are not
2525 reported as mapped to residues in a structure file in the
2529 <!--JAL-2324 -->Identical features with non-numeric scores
2530 could be added multiple times to a sequence
2533 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2534 bond features shown as two highlighted residues rather
2535 than a range in linked structure views, and treated
2536 correctly when selecting and computing trees from features
2539 <!-- JAL-2281-->Custom URL links for database
2540 cross-references are matched to database name regardless
2545 <em>Application</em>
2548 <!-- JAL-2282-->Custom URL links for specific database
2549 names without regular expressions also offer links from
2553 <!-- JAL-2315-->Removing a single configured link in the
2554 URL links pane in Connections preferences doesn't actually
2555 update Jalview configuration
2558 <!-- JAL-2272-->CTRL-Click on a selected region to open
2559 the alignment area popup menu doesn't work on El-Capitan
2562 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2563 files with similarly named sequences if dropped onto the
2567 <!-- JAL-2312 -->Additional mappings are shown for PDB
2568 entries where more chains exist in the PDB accession than
2569 are reported in the SIFTS file
2572 <!-- JAL-2317-->Certain structures do not get mapped to
2573 the structure view when displayed with Chimera
2576 <!-- JAL-2317-->No chains shown in the Chimera view
2577 panel's View->Show Chains submenu
2580 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2581 work for wrapped alignment views
2584 <!--JAL-2197 -->Rename UI components for running JPred
2585 predictions from 'JNet' to 'JPred'
2588 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2589 corrupted when annotation panel vertical scroll is not at
2590 first annotation row
2593 <!--JAL-2332 -->Attempting to view structure for Hen
2594 lysozyme results in a PDB Client error dialog box
2597 <!-- JAL-2319 -->Structure View's mapping report switched
2598 ranges for PDB and sequence for SIFTS
2601 SIFTS 'Not_Observed' residues mapped to non-existant
2605 <!-- <em>New Known Issues</em>
2612 <td width="60" nowrap>
2613 <div align="center">
2614 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2615 <em>25/10/2016</em></strong>
2618 <td><em>Application</em>
2620 <li>3D Structure chooser opens with 'Cached structures'
2621 view if structures already loaded</li>
2622 <li>Progress bar reports models as they are loaded to
2623 structure views</li>
2629 <li>Colour by conservation always enabled and no tick
2630 shown in menu when BLOSUM or PID shading applied</li>
2631 <li>FER1_ARATH and FER2_ARATH labels were switched in
2632 example sequences/projects/trees</li>
2634 <em>Application</em>
2636 <li>Jalview projects with views of local PDB structure
2637 files saved on Windows cannot be opened on OSX</li>
2638 <li>Multiple structure views can be opened and superposed
2639 without timeout for structures with multiple models or
2640 multiple sequences in alignment</li>
2641 <li>Cannot import or associated local PDB files without a
2642 PDB ID HEADER line</li>
2643 <li>RMSD is not output in Jmol console when superposition
2645 <li>Drag and drop of URL from Browser fails for Linux and
2646 OSX versions earlier than El Capitan</li>
2647 <li>ENA client ignores invalid content from ENA server</li>
2648 <li>Exceptions are not raised in console when ENA client
2649 attempts to fetch non-existent IDs via Fetch DB Refs UI
2651 <li>Exceptions are not raised in console when a new view
2652 is created on the alignment</li>
2653 <li>OSX right-click fixed for group selections: CMD-click
2654 to insert/remove gaps in groups and CTRL-click to open group
2657 <em>Build and deployment</em>
2659 <li>URL link checker now copes with multi-line anchor
2662 <em>New Known Issues</em>
2664 <li>Drag and drop from URL links in browsers do not work
2671 <td width="60" nowrap>
2672 <div align="center">
2673 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2676 <td><em>General</em>
2679 <!-- JAL-2124 -->Updated Spanish translations.
2682 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2683 for importing structure data to Jalview. Enables mmCIF and
2687 <!-- JAL-192 --->Alignment ruler shows positions relative to
2691 <!-- JAL-2202 -->Position/residue shown in status bar when
2692 mousing over sequence associated annotation
2695 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2699 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2700 '()', canonical '[]' and invalid '{}' base pair populations
2704 <!-- JAL-2092 -->Feature settings popup menu options for
2705 showing or hiding columns containing a feature
2708 <!-- JAL-1557 -->Edit selected group by double clicking on
2709 group and sequence associated annotation labels
2712 <!-- JAL-2236 -->Sequence name added to annotation label in
2713 select/hide columns by annotation and colour by annotation
2717 </ul> <em>Application</em>
2720 <!-- JAL-2050-->Automatically hide introns when opening a
2721 gene/transcript view
2724 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2728 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2729 structure mappings with the EMBL-EBI PDBe SIFTS database
2732 <!-- JAL-2079 -->Updated download sites used for Rfam and
2733 Pfam sources to xfam.org
2736 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2739 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2740 over sequences in Jalview
2743 <!-- JAL-2027-->Support for reverse-complement coding
2744 regions in ENA and EMBL
2747 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2748 for record retrieval via ENA rest API
2751 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2755 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2756 groovy script execution
2759 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2760 alignment window's Calculate menu
2763 <!-- JAL-1812 -->Allow groovy scripts that call
2764 Jalview.getAlignFrames() to run in headless mode
2767 <!-- JAL-2068 -->Support for creating new alignment
2768 calculation workers from groovy scripts
2771 <!-- JAL-1369 --->Store/restore reference sequence in
2775 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2776 associations are now saved/restored from project
2779 <!-- JAL-1993 -->Database selection dialog always shown
2780 before sequence fetcher is opened
2783 <!-- JAL-2183 -->Double click on an entry in Jalview's
2784 database chooser opens a sequence fetcher
2787 <!-- JAL-1563 -->Free-text search client for UniProt using
2788 the UniProt REST API
2791 <!-- JAL-2168 -->-nonews command line parameter to prevent
2792 the news reader opening
2795 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2796 querying stored in preferences
2799 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2803 <!-- JAL-1977-->Tooltips shown on database chooser
2806 <!-- JAL-391 -->Reverse complement function in calculate
2807 menu for nucleotide sequences
2810 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2811 and feature counts preserves alignment ordering (and
2812 debugged for complex feature sets).
2815 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2816 viewing structures with Jalview 2.10
2819 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2820 genome, transcript CCDS and gene ids via the Ensembl and
2821 Ensembl Genomes REST API
2824 <!-- JAL-2049 -->Protein sequence variant annotation
2825 computed for 'sequence_variant' annotation on CDS regions
2829 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2833 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2834 Ref Fetcher fails to match, or otherwise updates sequence
2835 data from external database records.
2838 <!-- JAL-2154 -->Revised Jalview Project format for
2839 efficient recovery of sequence coding and alignment
2840 annotation relationships.
2842 </ul> <!-- <em>Applet</em>
2853 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2857 <!-- JAL-2018-->Export features in Jalview format (again)
2858 includes graduated colourschemes
2861 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2862 working with big alignments and lots of hidden columns
2865 <!-- JAL-2053-->Hidden column markers not always rendered
2866 at right of alignment window
2869 <!-- JAL-2067 -->Tidied up links in help file table of
2873 <!-- JAL-2072 -->Feature based tree calculation not shown
2877 <!-- JAL-2075 -->Hidden columns ignored during feature
2878 based tree calculation
2881 <!-- JAL-2065 -->Alignment view stops updating when show
2882 unconserved enabled for group on alignment
2885 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2889 <!-- JAL-2146 -->Alignment column in status incorrectly
2890 shown as "Sequence position" when mousing over
2894 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2895 hidden columns present
2898 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2899 user created annotation added to alignment
2902 <!-- JAL-1841 -->RNA Structure consensus only computed for
2903 '()' base pair annotation
2906 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2907 in zero scores for all base pairs in RNA Structure
2911 <!-- JAL-2174-->Extend selection with columns containing
2915 <!-- JAL-2275 -->Pfam format writer puts extra space at
2916 beginning of sequence
2919 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2923 <!-- JAL-2238 -->Cannot create groups on an alignment from
2924 from a tree when t-coffee scores are shown
2927 <!-- JAL-1836,1967 -->Cannot import and view PDB
2928 structures with chains containing negative resnums (4q4h)
2931 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2935 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2936 to Clustal, PIR and PileUp output
2939 <!-- JAL-2008 -->Reordering sequence features that are
2940 not visible causes alignment window to repaint
2943 <!-- JAL-2006 -->Threshold sliders don't work in
2944 graduated colour and colour by annotation row for e-value
2945 scores associated with features and annotation rows
2948 <!-- JAL-1797 -->amino acid physicochemical conservation
2949 calculation should be case independent
2952 <!-- JAL-2173 -->Remove annotation also updates hidden
2956 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2957 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2958 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2961 <!-- JAL-2065 -->Null pointer exceptions and redraw
2962 problems when reference sequence defined and 'show
2963 non-conserved' enabled
2966 <!-- JAL-1306 -->Quality and Conservation are now shown on
2967 load even when Consensus calculation is disabled
2970 <!-- JAL-1932 -->Remove right on penultimate column of
2971 alignment does nothing
2974 <em>Application</em>
2977 <!-- JAL-1552-->URLs and links can't be imported by
2978 drag'n'drop on OSX when launched via webstart (note - not
2979 yet fixed for El Capitan)
2982 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2983 output when running on non-gb/us i18n platforms
2986 <!-- JAL-1944 -->Error thrown when exporting a view with
2987 hidden sequences as flat-file alignment
2990 <!-- JAL-2030-->InstallAnywhere distribution fails when
2994 <!-- JAL-2080-->Jalview very slow to launch via webstart
2995 (also hotfix for 2.9.0b2)
2998 <!-- JAL-2085 -->Cannot save project when view has a
2999 reference sequence defined
3002 <!-- JAL-1011 -->Columns are suddenly selected in other
3003 alignments and views when revealing hidden columns
3006 <!-- JAL-1989 -->Hide columns not mirrored in complement
3007 view in a cDNA/Protein splitframe
3010 <!-- JAL-1369 -->Cannot save/restore representative
3011 sequence from project when only one sequence is
3015 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3016 in Structure Chooser
3019 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3020 structure consensus didn't refresh annotation panel
3023 <!-- JAL-1962 -->View mapping in structure view shows
3024 mappings between sequence and all chains in a PDB file
3027 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3028 dialogs format columns correctly, don't display array
3029 data, sort columns according to type
3032 <!-- JAL-1975 -->Export complete shown after destination
3033 file chooser is cancelled during an image export
3036 <!-- JAL-2025 -->Error when querying PDB Service with
3037 sequence name containing special characters
3040 <!-- JAL-2024 -->Manual PDB structure querying should be
3044 <!-- JAL-2104 -->Large tooltips with broken HTML
3045 formatting don't wrap
3048 <!-- JAL-1128 -->Figures exported from wrapped view are
3049 truncated so L looks like I in consensus annotation
3052 <!-- JAL-2003 -->Export features should only export the
3053 currently displayed features for the current selection or
3057 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3058 after fetching cross-references, and restoring from
3062 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3063 followed in the structure viewer
3066 <!-- JAL-2163 -->Titles for individual alignments in
3067 splitframe not restored from project
3070 <!-- JAL-2145 -->missing autocalculated annotation at
3071 trailing end of protein alignment in transcript/product
3072 splitview when pad-gaps not enabled by default
3075 <!-- JAL-1797 -->amino acid physicochemical conservation
3079 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3080 article has been read (reopened issue due to
3081 internationalisation problems)
3084 <!-- JAL-1960 -->Only offer PDB structures in structure
3085 viewer based on sequence name, PDB and UniProt
3090 <!-- JAL-1976 -->No progress bar shown during export of
3094 <!-- JAL-2213 -->Structures not always superimposed after
3095 multiple structures are shown for one or more sequences.
3098 <!-- JAL-1370 -->Reference sequence characters should not
3099 be replaced with '.' when 'Show unconserved' format option
3103 <!-- JAL-1823 -->Cannot specify chain code when entering
3104 specific PDB id for sequence
3107 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3108 'Export hidden sequences' is enabled, but 'export hidden
3109 columns' is disabled.
3112 <!--JAL-2026-->Best Quality option in structure chooser
3113 selects lowest rather than highest resolution structures
3117 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3118 to sequence mapping in 'View Mappings' report
3121 <!-- JAL-2284 -->Unable to read old Jalview projects that
3122 contain non-XML data added after Jalvew wrote project.
3125 <!-- JAL-2118 -->Newly created annotation row reorders
3126 after clicking on it to create new annotation for a
3130 <!-- JAL-1980 -->Null Pointer Exception raised when
3131 pressing Add on an orphaned cut'n'paste window.
3133 <!-- may exclude, this is an external service stability issue JAL-1941
3134 -- > RNA 3D structure not added via DSSR service</li> -->
3139 <!-- JAL-2151 -->Incorrect columns are selected when
3140 hidden columns present before start of sequence
3143 <!-- JAL-1986 -->Missing dependencies on applet pages
3147 <!-- JAL-1947 -->Overview pixel size changes when
3148 sequences are hidden in applet
3151 <!-- JAL-1996 -->Updated instructions for applet
3152 deployment on examples pages.
3159 <td width="60" nowrap>
3160 <div align="center">
3161 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3162 <em>16/10/2015</em></strong>
3165 <td><em>General</em>
3167 <li>Time stamps for signed Jalview application and applet
3172 <em>Application</em>
3174 <li>Duplicate group consensus and conservation rows
3175 shown when tree is partitioned</li>
3176 <li>Erratic behaviour when tree partitions made with
3177 multiple cDNA/Protein split views</li>
3183 <td width="60" nowrap>
3184 <div align="center">
3185 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3186 <em>8/10/2015</em></strong>
3189 <td><em>General</em>
3191 <li>Updated Spanish translations of localized text for
3193 </ul> <em>Application</em>
3195 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3196 <li>Signed OSX InstallAnywhere installer<br></li>
3197 <li>Support for per-sequence based annotations in BioJSON</li>
3198 </ul> <em>Applet</em>
3200 <li>Split frame example added to applet examples page</li>
3201 </ul> <em>Build and Deployment</em>
3204 <!-- JAL-1888 -->New ant target for running Jalview's test
3212 <li>Mapping of cDNA to protein in split frames
3213 incorrect when sequence start > 1</li>
3214 <li>Broken images in filter column by annotation dialog
3216 <li>Feature colours not parsed from features file</li>
3217 <li>Exceptions and incomplete link URLs recovered when
3218 loading a features file containing HTML tags in feature
3222 <em>Application</em>
3224 <li>Annotations corrupted after BioJS export and
3226 <li>Incorrect sequence limits after Fetch DB References
3227 with 'trim retrieved sequences'</li>
3228 <li>Incorrect warning about deleting all data when
3229 deleting selected columns</li>
3230 <li>Patch to build system for shipping properly signed
3231 JNLP templates for webstart launch</li>
3232 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3233 unreleased structures for download or viewing</li>
3234 <li>Tab/space/return keystroke operation of EMBL-PDBe
3235 fetcher/viewer dialogs works correctly</li>
3236 <li>Disabled 'minimise' button on Jalview windows
3237 running on OSX to workaround redraw hang bug</li>
3238 <li>Split cDNA/Protein view position and geometry not
3239 recovered from jalview project</li>
3240 <li>Initial enabled/disabled state of annotation menu
3241 sorter 'show autocalculated first/last' corresponds to
3243 <li>Restoring of Clustal, RNA Helices and T-Coffee
3244 color schemes from BioJSON</li>
3248 <li>Reorder sequences mirrored in cDNA/Protein split
3250 <li>Applet with Jmol examples not loading correctly</li>
3256 <td><div align="center">
3257 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3259 <td><em>General</em>
3261 <li>Linked visualisation and analysis of DNA and Protein
3264 <li>Translated cDNA alignments shown as split protein
3265 and DNA alignment views</li>
3266 <li>Codon consensus annotation for linked protein and
3267 cDNA alignment views</li>
3268 <li>Link cDNA or Protein product sequences by loading
3269 them onto Protein or cDNA alignments</li>
3270 <li>Reconstruct linked cDNA alignment from aligned
3271 protein sequences</li>
3274 <li>Jmol integration updated to Jmol v14.2.14</li>
3275 <li>Import and export of Jalview alignment views as <a
3276 href="features/bioJsonFormat.html">BioJSON</a></li>
3277 <li>New alignment annotation file statements for
3278 reference sequences and marking hidden columns</li>
3279 <li>Reference sequence based alignment shading to
3280 highlight variation</li>
3281 <li>Select or hide columns according to alignment
3283 <li>Find option for locating sequences by description</li>
3284 <li>Conserved physicochemical properties shown in amino
3285 acid conservation row</li>
3286 <li>Alignments can be sorted by number of RNA helices</li>
3287 </ul> <em>Application</em>
3289 <li>New cDNA/Protein analysis capabilities
3291 <li>Get Cross-References should open a Split Frame
3292 view with cDNA/Protein</li>
3293 <li>Detect when nucleotide sequences and protein
3294 sequences are placed in the same alignment</li>
3295 <li>Split cDNA/Protein views are saved in Jalview
3300 <li>Use REST API to talk to Chimera</li>
3301 <li>Selected regions in Chimera are highlighted in linked
3302 Jalview windows</li>
3304 <li>VARNA RNA viewer updated to v3.93</li>
3305 <li>VARNA views are saved in Jalview Projects</li>
3306 <li>Pseudoknots displayed as Jalview RNA annotation can
3307 be shown in VARNA</li>
3309 <li>Make groups for selection uses marked columns as well
3310 as the active selected region</li>
3312 <li>Calculate UPGMA and NJ trees using sequence feature
3314 <li>New Export options
3316 <li>New Export Settings dialog to control hidden
3317 region export in flat file generation</li>
3319 <li>Export alignment views for display with the <a
3320 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3322 <li>Export scrollable SVG in HTML page</li>
3323 <li>Optional embedding of BioJSON data when exporting
3324 alignment figures to HTML</li>
3326 <li>3D structure retrieval and display
3328 <li>Free text and structured queries with the PDBe
3330 <li>PDBe Search API based discovery and selection of
3331 PDB structures for a sequence set</li>
3335 <li>JPred4 employed for protein secondary structure
3337 <li>Hide Insertions menu option to hide unaligned columns
3338 for one or a group of sequences</li>
3339 <li>Automatically hide insertions in alignments imported
3340 from the JPred4 web server</li>
3341 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3342 system on OSX<br />LGPL libraries courtesy of <a
3343 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3345 <li>changed 'View nucleotide structure' submenu to 'View
3346 VARNA 2D Structure'</li>
3347 <li>change "View protein structure" menu option to "3D
3350 </ul> <em>Applet</em>
3352 <li>New layout for applet example pages</li>
3353 <li>New parameters to enable SplitFrame view
3354 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3355 <li>New example demonstrating linked viewing of cDNA and
3356 Protein alignments</li>
3357 </ul> <em>Development and deployment</em>
3359 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3360 <li>Include installation type and git revision in build
3361 properties and console log output</li>
3362 <li>Jalview Github organisation, and new github site for
3363 storing BioJsMSA Templates</li>
3364 <li>Jalview's unit tests now managed with TestNG</li>
3367 <!-- <em>General</em>
3369 </ul> --> <!-- issues resolved --> <em>Application</em>
3371 <li>Escape should close any open find dialogs</li>
3372 <li>Typo in select-by-features status report</li>
3373 <li>Consensus RNA secondary secondary structure
3374 predictions are not highlighted in amber</li>
3375 <li>Missing gap character in v2.7 example file means
3376 alignment appears unaligned when pad-gaps is not enabled</li>
3377 <li>First switch to RNA Helices colouring doesn't colour
3378 associated structure views</li>
3379 <li>ID width preference option is greyed out when auto
3380 width checkbox not enabled</li>
3381 <li>Stopped a warning dialog from being shown when
3382 creating user defined colours</li>
3383 <li>'View Mapping' in structure viewer shows sequence
3384 mappings for just that viewer's sequences</li>
3385 <li>Workaround for superposing PDB files containing
3386 multiple models in Chimera</li>
3387 <li>Report sequence position in status bar when hovering
3388 over Jmol structure</li>
3389 <li>Cannot output gaps as '.' symbols with Selection ->
3390 output to text box</li>
3391 <li>Flat file exports of alignments with hidden columns
3392 have incorrect sequence start/end</li>
3393 <li>'Aligning' a second chain to a Chimera structure from
3395 <li>Colour schemes applied to structure viewers don't
3396 work for nucleotide</li>
3397 <li>Loading/cut'n'pasting an empty or invalid file leads
3398 to a grey/invisible alignment window</li>
3399 <li>Exported Jpred annotation from a sequence region
3400 imports to different position</li>
3401 <li>Space at beginning of sequence feature tooltips shown
3402 on some platforms</li>
3403 <li>Chimera viewer 'View | Show Chain' menu is not
3405 <li>'New View' fails with a Null Pointer Exception in
3406 console if Chimera has been opened</li>
3407 <li>Mouseover to Chimera not working</li>
3408 <li>Miscellaneous ENA XML feature qualifiers not
3410 <li>NPE in annotation renderer after 'Extract Scores'</li>
3411 <li>If two structures in one Chimera window, mouseover of
3412 either sequence shows on first structure</li>
3413 <li>'Show annotations' options should not make
3414 non-positional annotations visible</li>
3415 <li>Subsequence secondary structure annotation not shown
3416 in right place after 'view flanking regions'</li>
3417 <li>File Save As type unset when current file format is
3419 <li>Save as '.jar' option removed for saving Jalview
3421 <li>Colour by Sequence colouring in Chimera more
3423 <li>Cannot 'add reference annotation' for a sequence in
3424 several views on same alignment</li>
3425 <li>Cannot show linked products for EMBL / ENA records</li>
3426 <li>Jalview's tooltip wraps long texts containing no
3428 </ul> <em>Applet</em>
3430 <li>Jmol to JalviewLite mouseover/link not working</li>
3431 <li>JalviewLite can't import sequences with ID
3432 descriptions containing angle brackets</li>
3433 </ul> <em>General</em>
3435 <li>Cannot export and reimport RNA secondary structure
3436 via jalview annotation file</li>
3437 <li>Random helix colour palette for colour by annotation
3438 with RNA secondary structure</li>
3439 <li>Mouseover to cDNA from STOP residue in protein
3440 translation doesn't work.</li>
3441 <li>hints when using the select by annotation dialog box</li>
3442 <li>Jmol alignment incorrect if PDB file has alternate CA
3444 <li>FontChooser message dialog appears to hang after
3445 choosing 1pt font</li>
3446 <li>Peptide secondary structure incorrectly imported from
3447 annotation file when annotation display text includes 'e' or
3449 <li>Cannot set colour of new feature type whilst creating
3451 <li>cDNA translation alignment should not be sequence
3452 order dependent</li>
3453 <li>'Show unconserved' doesn't work for lower case
3455 <li>Nucleotide ambiguity codes involving R not recognised</li>
3456 </ul> <em>Deployment and Documentation</em>
3458 <li>Applet example pages appear different to the rest of
3459 www.jalview.org</li>
3460 </ul> <em>Application Known issues</em>
3462 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3463 <li>Misleading message appears after trying to delete
3465 <li>Jalview icon not shown in dock after InstallAnywhere
3466 version launches</li>
3467 <li>Fetching EMBL reference for an RNA sequence results
3468 fails with a sequence mismatch</li>
3469 <li>Corrupted or unreadable alignment display when
3470 scrolling alignment to right</li>
3471 <li>ArrayIndexOutOfBoundsException thrown when remove
3472 empty columns called on alignment with ragged gapped ends</li>
3473 <li>auto calculated alignment annotation rows do not get
3474 placed above or below non-autocalculated rows</li>
3475 <li>Jalview dekstop becomes sluggish at full screen in
3476 ultra-high resolution</li>
3477 <li>Cannot disable consensus calculation independently of
3478 quality and conservation</li>
3479 <li>Mouseover highlighting between cDNA and protein can
3480 become sluggish with more than one splitframe shown</li>
3481 </ul> <em>Applet Known Issues</em>
3483 <li>Core PDB parsing code requires Jmol</li>
3484 <li>Sequence canvas panel goes white when alignment
3485 window is being resized</li>
3491 <td><div align="center">
3492 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3494 <td><em>General</em>
3496 <li>Updated Java code signing certificate donated by
3498 <li>Features and annotation preserved when performing
3499 pairwise alignment</li>
3500 <li>RNA pseudoknot annotation can be
3501 imported/exported/displayed</li>
3502 <li>'colour by annotation' can colour by RNA and
3503 protein secondary structure</li>
3504 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3505 post-hoc with 2.9 release</em>)
3508 </ul> <em>Application</em>
3510 <li>Extract and display secondary structure for sequences
3511 with 3D structures</li>
3512 <li>Support for parsing RNAML</li>
3513 <li>Annotations menu for layout
3515 <li>sort sequence annotation rows by alignment</li>
3516 <li>place sequence annotation above/below alignment
3519 <li>Output in Stockholm format</li>
3520 <li>Internationalisation: improved Spanish (es)
3522 <li>Structure viewer preferences tab</li>
3523 <li>Disorder and Secondary Structure annotation tracks
3524 shared between alignments</li>
3525 <li>UCSF Chimera launch and linked highlighting from
3527 <li>Show/hide all sequence associated annotation rows for
3528 all or current selection</li>
3529 <li>disorder and secondary structure predictions
3530 available as dataset annotation</li>
3531 <li>Per-sequence rna helices colouring</li>
3534 <li>Sequence database accessions imported when fetching
3535 alignments from Rfam</li>
3536 <li>update VARNA version to 3.91</li>
3538 <li>New groovy scripts for exporting aligned positions,
3539 conservation values, and calculating sum of pairs scores.</li>
3540 <li>Command line argument to set default JABAWS server</li>
3541 <li>include installation type in build properties and
3542 console log output</li>
3543 <li>Updated Jalview project format to preserve dataset
3547 <!-- issues resolved --> <em>Application</em>
3549 <li>Distinguish alignment and sequence associated RNA
3550 structure in structure->view->VARNA</li>
3551 <li>Raise dialog box if user deletes all sequences in an
3553 <li>Pressing F1 results in documentation opening twice</li>
3554 <li>Sequence feature tooltip is wrapped</li>
3555 <li>Double click on sequence associated annotation
3556 selects only first column</li>
3557 <li>Redundancy removal doesn't result in unlinked
3558 leaves shown in tree</li>
3559 <li>Undos after several redundancy removals don't undo
3561 <li>Hide sequence doesn't hide associated annotation</li>
3562 <li>User defined colours dialog box too big to fit on
3563 screen and buttons not visible</li>
3564 <li>author list isn't updated if already written to
3565 Jalview properties</li>
3566 <li>Popup menu won't open after retrieving sequence
3568 <li>File open window for associate PDB doesn't open</li>
3569 <li>Left-then-right click on a sequence id opens a
3570 browser search window</li>
3571 <li>Cannot open sequence feature shading/sort popup menu
3572 in feature settings dialog</li>
3573 <li>better tooltip placement for some areas of Jalview
3575 <li>Allow addition of JABAWS Server which doesn't
3576 pass validation</li>
3577 <li>Web services parameters dialog box is too large to
3579 <li>Muscle nucleotide alignment preset obscured by
3581 <li>JABAWS preset submenus don't contain newly
3582 defined user preset</li>
3583 <li>MSA web services warns user if they were launched
3584 with invalid input</li>
3585 <li>Jalview cannot contact DAS Registy when running on
3588 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3589 'Superpose with' submenu not shown when new view
3593 </ul> <!-- <em>Applet</em>
3595 </ul> <em>General</em>
3597 </ul>--> <em>Deployment and Documentation</em>
3599 <li>2G and 1G options in launchApp have no effect on
3600 memory allocation</li>
3601 <li>launchApp service doesn't automatically open
3602 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3604 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3605 InstallAnywhere reports cannot find valid JVM when Java
3606 1.7_055 is available
3608 </ul> <em>Application Known issues</em>
3611 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3612 corrupted or unreadable alignment display when scrolling
3616 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3617 retrieval fails but progress bar continues for DAS retrieval
3618 with large number of ID
3621 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3622 flatfile output of visible region has incorrect sequence
3626 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3627 rna structure consensus doesn't update when secondary
3628 structure tracks are rearranged
3631 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3632 invalid rna structure positional highlighting does not
3633 highlight position of invalid base pairs
3636 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3637 out of memory errors are not raised when saving Jalview
3638 project from alignment window file menu
3641 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3642 Switching to RNA Helices colouring doesn't propagate to
3646 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3647 colour by RNA Helices not enabled when user created
3648 annotation added to alignment
3651 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3652 Jalview icon not shown on dock in Mountain Lion/Webstart
3654 </ul> <em>Applet Known Issues</em>
3657 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3658 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3661 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3662 Jalview and Jmol example not compatible with IE9
3665 <li>Sort by annotation score doesn't reverse order
3671 <td><div align="center">
3672 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3675 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3678 <li>Internationalisation of user interface (usually
3679 called i18n support) and translation for Spanish locale</li>
3680 <li>Define/Undefine group on current selection with
3681 Ctrl-G/Shift Ctrl-G</li>
3682 <li>Improved group creation/removal options in
3683 alignment/sequence Popup menu</li>
3684 <li>Sensible precision for symbol distribution
3685 percentages shown in logo tooltip.</li>
3686 <li>Annotation panel height set according to amount of
3687 annotation when alignment first opened</li>
3688 </ul> <em>Application</em>
3690 <li>Interactive consensus RNA secondary structure
3691 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3692 <li>Select columns containing particular features from
3693 Feature Settings dialog</li>
3694 <li>View all 'representative' PDB structures for selected
3696 <li>Update Jalview project format:
3698 <li>New file extension for Jalview projects '.jvp'</li>
3699 <li>Preserve sequence and annotation dataset (to
3700 store secondary structure annotation,etc)</li>
3701 <li>Per group and alignment annotation and RNA helix
3705 <li>New similarity measures for PCA and Tree calculation
3707 <li>Experimental support for retrieval and viewing of
3708 flanking regions for an alignment</li>
3712 <!-- issues resolved --> <em>Application</em>
3714 <li>logo keeps spinning and status remains at queued or
3715 running after job is cancelled</li>
3716 <li>cannot export features from alignments imported from
3717 Jalview/VAMSAS projects</li>
3718 <li>Buggy slider for web service parameters that take
3720 <li>Newly created RNA secondary structure line doesn't
3721 have 'display all symbols' flag set</li>
3722 <li>T-COFFEE alignment score shading scheme and other
3723 annotation shading not saved in Jalview project</li>
3724 <li>Local file cannot be loaded in freshly downloaded
3726 <li>Jalview icon not shown on dock in Mountain
3728 <li>Load file from desktop file browser fails</li>
3729 <li>Occasional NPE thrown when calculating large trees</li>
3730 <li>Cannot reorder or slide sequences after dragging an
3731 alignment onto desktop</li>
3732 <li>Colour by annotation dialog throws NPE after using
3733 'extract scores' function</li>
3734 <li>Loading/cut'n'pasting an empty file leads to a grey
3735 alignment window</li>
3736 <li>Disorder thresholds rendered incorrectly after
3737 performing IUPred disorder prediction</li>
3738 <li>Multiple group annotated consensus rows shown when
3739 changing 'normalise logo' display setting</li>
3740 <li>Find shows blank dialog after 'finished searching' if
3741 nothing matches query</li>
3742 <li>Null Pointer Exceptions raised when sorting by
3743 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3745 <li>Errors in Jmol console when structures in alignment
3746 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3748 <li>Not all working JABAWS services are shown in
3750 <li>JAVAWS version of Jalview fails to launch with
3751 'invalid literal/length code'</li>
3752 <li>Annotation/RNA Helix colourschemes cannot be applied
3753 to alignment with groups (actually fixed in 2.8.0b1)</li>
3754 <li>RNA Helices and T-Coffee Scores available as default
3757 </ul> <em>Applet</em>
3759 <li>Remove group option is shown even when selection is
3761 <li>Apply to all groups ticked but colourscheme changes
3762 don't affect groups</li>
3763 <li>Documented RNA Helices and T-Coffee Scores as valid
3764 colourscheme name</li>
3765 <li>Annotation labels drawn on sequence IDs when
3766 Annotation panel is not displayed</li>
3767 <li>Increased font size for dropdown menus on OSX and
3768 embedded windows</li>
3769 </ul> <em>Other</em>
3771 <li>Consensus sequence for alignments/groups with a
3772 single sequence were not calculated</li>
3773 <li>annotation files that contain only groups imported as
3774 annotation and junk sequences</li>
3775 <li>Fasta files with sequences containing '*' incorrectly
3776 recognised as PFAM or BLC</li>
3777 <li>conservation/PID slider apply all groups option
3778 doesn't affect background (2.8.0b1)
3780 <li>redundancy highlighting is erratic at 0% and 100%</li>
3781 <li>Remove gapped columns fails for sequences with ragged
3783 <li>AMSA annotation row with leading spaces is not
3784 registered correctly on import</li>
3785 <li>Jalview crashes when selecting PCA analysis for
3786 certain alignments</li>
3787 <li>Opening the colour by annotation dialog for an
3788 existing annotation based 'use original colours'
3789 colourscheme loses original colours setting</li>
3794 <td><div align="center">
3795 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3796 <em>30/1/2014</em></strong>
3800 <li>Trusted certificates for JalviewLite applet and
3801 Jalview Desktop application<br />Certificate was donated by
3802 <a href="https://www.certum.eu">Certum</a> to the Jalview
3803 open source project).
3805 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3806 <li>Output in Stockholm format</li>
3807 <li>Allow import of data from gzipped files</li>
3808 <li>Export/import group and sequence associated line
3809 graph thresholds</li>
3810 <li>Nucleotide substitution matrix that supports RNA and
3811 ambiguity codes</li>
3812 <li>Allow disorder predictions to be made on the current
3813 selection (or visible selection) in the same way that JPred
3815 <li>Groovy scripting for headless Jalview operation</li>
3816 </ul> <em>Other improvements</em>
3818 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3819 <li>COMBINE statement uses current SEQUENCE_REF and
3820 GROUP_REF scope to group annotation rows</li>
3821 <li>Support '' style escaping of quotes in Newick
3823 <li>Group options for JABAWS service by command line name</li>
3824 <li>Empty tooltip shown for JABA service options with a
3825 link but no description</li>
3826 <li>Select primary source when selecting authority in
3827 database fetcher GUI</li>
3828 <li>Add .mfa to FASTA file extensions recognised by
3830 <li>Annotation label tooltip text wrap</li>
3835 <li>Slow scrolling when lots of annotation rows are
3837 <li>Lots of NPE (and slowness) after creating RNA
3838 secondary structure annotation line</li>
3839 <li>Sequence database accessions not imported when
3840 fetching alignments from Rfam</li>
3841 <li>Incorrect SHMR submission for sequences with
3843 <li>View all structures does not always superpose
3845 <li>Option widgets in service parameters not updated to
3846 reflect user or preset settings</li>
3847 <li>Null pointer exceptions for some services without
3848 presets or adjustable parameters</li>
3849 <li>Discover PDB IDs entry in structure menu doesn't
3850 discover PDB xRefs</li>
3851 <li>Exception encountered while trying to retrieve
3852 features with DAS</li>
3853 <li>Lowest value in annotation row isn't coloured
3854 when colour by annotation (per sequence) is coloured</li>
3855 <li>Keyboard mode P jumps to start of gapped region when
3856 residue follows a gap</li>
3857 <li>Jalview appears to hang importing an alignment with
3858 Wrap as default or after enabling Wrap</li>
3859 <li>'Right click to add annotations' message
3860 shown in wrap mode when no annotations present</li>
3861 <li>Disorder predictions fail with NPE if no automatic
3862 annotation already exists on alignment</li>
3863 <li>oninit javascript function should be called after
3864 initialisation completes</li>
3865 <li>Remove redundancy after disorder prediction corrupts
3866 alignment window display</li>
3867 <li>Example annotation file in documentation is invalid</li>
3868 <li>Grouped line graph annotation rows are not exported
3869 to annotation file</li>
3870 <li>Multi-harmony analysis cannot be run when only two
3872 <li>Cannot create multiple groups of line graphs with
3873 several 'combine' statements in annotation file</li>
3874 <li>Pressing return several times causes Number Format
3875 exceptions in keyboard mode</li>
3876 <li>Multi-harmony (SHMMR) method doesn't submit
3877 correct partitions for input data</li>
3878 <li>Translation from DNA to Amino Acids fails</li>
3879 <li>Jalview fail to load newick tree with quoted label</li>
3880 <li>--headless flag isn't understood</li>
3881 <li>ClassCastException when generating EPS in headless
3883 <li>Adjusting sequence-associated shading threshold only
3884 changes one row's threshold</li>
3885 <li>Preferences and Feature settings panel panel
3886 doesn't open</li>
3887 <li>hide consensus histogram also hides conservation and
3888 quality histograms</li>
3893 <td><div align="center">
3894 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3896 <td><em>Application</em>
3898 <li>Support for JABAWS 2.0 Services (AACon alignment
3899 conservation, protein disorder and Clustal Omega)</li>
3900 <li>JABAWS server status indicator in Web Services
3902 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3903 in Jalview alignment window</li>
3904 <li>Updated Jalview build and deploy framework for OSX
3905 mountain lion, windows 7, and 8</li>
3906 <li>Nucleotide substitution matrix for PCA that supports
3907 RNA and ambiguity codes</li>
3909 <li>Improved sequence database retrieval GUI</li>
3910 <li>Support fetching and database reference look up
3911 against multiple DAS sources (Fetch all from in 'fetch db
3913 <li>Jalview project improvements
3915 <li>Store and retrieve the 'belowAlignment'
3916 flag for annotation</li>
3917 <li>calcId attribute to group annotation rows on the
3919 <li>Store AACon calculation settings for a view in
3920 Jalview project</li>
3924 <li>horizontal scrolling gesture support</li>
3925 <li>Visual progress indicator when PCA calculation is
3927 <li>Simpler JABA web services menus</li>
3928 <li>visual indication that web service results are still
3929 being retrieved from server</li>
3930 <li>Serialise the dialogs that are shown when Jalview
3931 starts up for first time</li>
3932 <li>Jalview user agent string for interacting with HTTP
3934 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3936 <li>Examples directory and Groovy library included in
3937 InstallAnywhere distribution</li>
3938 </ul> <em>Applet</em>
3940 <li>RNA alignment and secondary structure annotation
3941 visualization applet example</li>
3942 </ul> <em>General</em>
3944 <li>Normalise option for consensus sequence logo</li>
3945 <li>Reset button in PCA window to return dimensions to
3947 <li>Allow seqspace or Jalview variant of alignment PCA
3949 <li>PCA with either nucleic acid and protein substitution
3951 <li>Allow windows containing HTML reports to be exported
3953 <li>Interactive display and editing of RNA secondary
3954 structure contacts</li>
3955 <li>RNA Helix Alignment Colouring</li>
3956 <li>RNA base pair logo consensus</li>
3957 <li>Parse sequence associated secondary structure
3958 information in Stockholm files</li>
3959 <li>HTML Export database accessions and annotation
3960 information presented in tooltip for sequences</li>
3961 <li>Import secondary structure from LOCARNA clustalw
3962 style RNA alignment files</li>
3963 <li>import and visualise T-COFFEE quality scores for an
3965 <li>'colour by annotation' per sequence option to
3966 shade each sequence according to its associated alignment
3968 <li>New Jalview Logo</li>
3969 </ul> <em>Documentation and Development</em>
3971 <li>documentation for score matrices used in Jalview</li>
3972 <li>New Website!</li>
3974 <td><em>Application</em>
3976 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3977 wsdbfetch REST service</li>
3978 <li>Stop windows being moved outside desktop on OSX</li>
3979 <li>Filetype associations not installed for webstart
3981 <li>Jalview does not always retrieve progress of a JABAWS
3982 job execution in full once it is complete</li>
3983 <li>revise SHMR RSBS definition to ensure alignment is
3984 uploaded via ali_file parameter</li>
3985 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3986 <li>View all structures superposed fails with exception</li>
3987 <li>Jnet job queues forever if a very short sequence is
3988 submitted for prediction</li>
3989 <li>Cut and paste menu not opened when mouse clicked on
3991 <li>Putting fractional value into integer text box in
3992 alignment parameter dialog causes Jalview to hang</li>
3993 <li>Structure view highlighting doesn't work on
3995 <li>View all structures fails with exception shown in
3997 <li>Characters in filename associated with PDBEntry not
3998 escaped in a platform independent way</li>
3999 <li>Jalview desktop fails to launch with exception when
4001 <li>Tree calculation reports 'you must have 2 or more
4002 sequences selected' when selection is empty</li>
4003 <li>Jalview desktop fails to launch with jar signature
4004 failure when java web start temporary file caching is
4006 <li>DAS Sequence retrieval with range qualification
4007 results in sequence xref which includes range qualification</li>
4008 <li>Errors during processing of command line arguments
4009 cause progress bar (JAL-898) to be removed</li>
4010 <li>Replace comma for semi-colon option not disabled for
4011 DAS sources in sequence fetcher</li>
4012 <li>Cannot close news reader when JABAWS server warning
4013 dialog is shown</li>
4014 <li>Option widgets not updated to reflect user settings</li>
4015 <li>Edited sequence not submitted to web service</li>
4016 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4017 <li>InstallAnywhere installer doesn't unpack and run
4018 on OSX Mountain Lion</li>
4019 <li>Annotation panel not given a scroll bar when
4020 sequences with alignment annotation are pasted into the
4022 <li>Sequence associated annotation rows not associated
4023 when loaded from Jalview project</li>
4024 <li>Browser launch fails with NPE on java 1.7</li>
4025 <li>JABAWS alignment marked as finished when job was
4026 cancelled or job failed due to invalid input</li>
4027 <li>NPE with v2.7 example when clicking on Tree
4028 associated with all views</li>
4029 <li>Exceptions when copy/paste sequences with grouped
4030 annotation rows to new window</li>
4031 </ul> <em>Applet</em>
4033 <li>Sequence features are momentarily displayed before
4034 they are hidden using hidefeaturegroups applet parameter</li>
4035 <li>loading features via javascript API automatically
4036 enables feature display</li>
4037 <li>scrollToColumnIn javascript API method doesn't
4039 </ul> <em>General</em>
4041 <li>Redundancy removal fails for rna alignment</li>
4042 <li>PCA calculation fails when sequence has been selected
4043 and then deselected</li>
4044 <li>PCA window shows grey box when first opened on OSX</li>
4045 <li>Letters coloured pink in sequence logo when alignment
4046 coloured with clustalx</li>
4047 <li>Choosing fonts without letter symbols defined causes
4048 exceptions and redraw errors</li>
4049 <li>Initial PCA plot view is not same as manually
4050 reconfigured view</li>
4051 <li>Grouped annotation graph label has incorrect line
4053 <li>Grouped annotation graph label display is corrupted
4054 for lots of labels</li>
4059 <div align="center">
4060 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4063 <td><em>Application</em>
4065 <li>Jalview Desktop News Reader</li>
4066 <li>Tweaked default layout of web services menu</li>
4067 <li>View/alignment association menu to enable user to
4068 easily specify which alignment a multi-structure view takes
4069 its colours/correspondences from</li>
4070 <li>Allow properties file location to be specified as URL</li>
4071 <li>Extend Jalview project to preserve associations
4072 between many alignment views and a single Jmol display</li>
4073 <li>Store annotation row height in Jalview project file</li>
4074 <li>Annotation row column label formatting attributes
4075 stored in project file</li>
4076 <li>Annotation row order for auto-calculated annotation
4077 rows preserved in Jalview project file</li>
4078 <li>Visual progress indication when Jalview state is
4079 saved using Desktop window menu</li>
4080 <li>Visual indication that command line arguments are
4081 still being processed</li>
4082 <li>Groovy script execution from URL</li>
4083 <li>Colour by annotation default min and max colours in
4085 <li>Automatically associate PDB files dragged onto an
4086 alignment with sequences that have high similarity and
4088 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4089 <li>'view structures' option to open many
4090 structures in same window</li>
4091 <li>Sort associated views menu option for tree panel</li>
4092 <li>Group all JABA and non-JABA services for a particular
4093 analysis function in its own submenu</li>
4094 </ul> <em>Applet</em>
4096 <li>Userdefined and autogenerated annotation rows for
4098 <li>Adjustment of alignment annotation pane height</li>
4099 <li>Annotation scrollbar for annotation panel</li>
4100 <li>Drag to reorder annotation rows in annotation panel</li>
4101 <li>'automaticScrolling' parameter</li>
4102 <li>Allow sequences with partial ID string matches to be
4103 annotated from GFF/Jalview features files</li>
4104 <li>Sequence logo annotation row in applet</li>
4105 <li>Absolute paths relative to host server in applet
4106 parameters are treated as such</li>
4107 <li>New in the JalviewLite javascript API:
4109 <li>JalviewLite.js javascript library</li>
4110 <li>Javascript callbacks for
4112 <li>Applet initialisation</li>
4113 <li>Sequence/alignment mouse-overs and selections</li>
4116 <li>scrollTo row and column alignment scrolling
4118 <li>Select sequence/alignment regions from javascript</li>
4119 <li>javascript structure viewer harness to pass
4120 messages between Jmol and Jalview when running as
4121 distinct applets</li>
4122 <li>sortBy method</li>
4123 <li>Set of applet and application examples shipped
4124 with documentation</li>
4125 <li>New example to demonstrate JalviewLite and Jmol
4126 javascript message exchange</li>
4128 </ul> <em>General</em>
4130 <li>Enable Jmol displays to be associated with multiple
4131 multiple alignments</li>
4132 <li>Option to automatically sort alignment with new tree</li>
4133 <li>User configurable link to enable redirects to a
4134 www.Jalview.org mirror</li>
4135 <li>Jmol colours option for Jmol displays</li>
4136 <li>Configurable newline string when writing alignment
4137 and other flat files</li>
4138 <li>Allow alignment annotation description lines to
4139 contain html tags</li>
4140 </ul> <em>Documentation and Development</em>
4142 <li>Add groovy test harness for bulk load testing to
4144 <li>Groovy script to load and align a set of sequences
4145 using a web service before displaying the result in the
4146 Jalview desktop</li>
4147 <li>Restructured javascript and applet api documentation</li>
4148 <li>Ant target to publish example html files with applet
4150 <li>Netbeans project for building Jalview from source</li>
4151 <li>ant task to create online javadoc for Jalview source</li>
4153 <td><em>Application</em>
4155 <li>User defined colourscheme throws exception when
4156 current built in colourscheme is saved as new scheme</li>
4157 <li>AlignFrame->Save in application pops up save
4158 dialog for valid filename/format</li>
4159 <li>Cannot view associated structure for UniProt sequence</li>
4160 <li>PDB file association breaks for UniProt sequence
4162 <li>Associate PDB from file dialog does not tell you
4163 which sequence is to be associated with the file</li>
4164 <li>Find All raises null pointer exception when query
4165 only matches sequence IDs</li>
4166 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4167 <li>Jalview project with Jmol views created with Jalview
4168 2.4 cannot be loaded</li>
4169 <li>Filetype associations not installed for webstart
4171 <li>Two or more chains in a single PDB file associated
4172 with sequences in different alignments do not get coloured
4173 by their associated sequence</li>
4174 <li>Visibility status of autocalculated annotation row
4175 not preserved when project is loaded</li>
4176 <li>Annotation row height and visibility attributes not
4177 stored in Jalview project</li>
4178 <li>Tree bootstraps are not preserved when saved as a
4179 Jalview project</li>
4180 <li>Envision2 workflow tooltips are corrupted</li>
4181 <li>Enabling show group conservation also enables colour
4182 by conservation</li>
4183 <li>Duplicate group associated conservation or consensus
4184 created on new view</li>
4185 <li>Annotation scrollbar not displayed after 'show
4186 all hidden annotation rows' option selected</li>
4187 <li>Alignment quality not updated after alignment
4188 annotation row is hidden then shown</li>
4189 <li>Preserve colouring of structures coloured by
4190 sequences in pre Jalview 2.7 projects</li>
4191 <li>Web service job parameter dialog is not laid out
4193 <li>Web services menu not refreshed after 'reset
4194 services' button is pressed in preferences</li>
4195 <li>Annotation off by one in Jalview v2_3 example project</li>
4196 <li>Structures imported from file and saved in project
4197 get name like jalview_pdb1234.txt when reloaded</li>
4198 <li>Jalview does not always retrieve progress of a JABAWS
4199 job execution in full once it is complete</li>
4200 </ul> <em>Applet</em>
4202 <li>Alignment height set incorrectly when lots of
4203 annotation rows are displayed</li>
4204 <li>Relative URLs in feature HTML text not resolved to
4206 <li>View follows highlighting does not work for positions
4208 <li><= shown as = in tooltip</li>
4209 <li>Export features raises exception when no features
4211 <li>Separator string used for serialising lists of IDs
4212 for javascript api is modified when separator string
4213 provided as parameter</li>
4214 <li>Null pointer exception when selecting tree leaves for
4215 alignment with no existing selection</li>
4216 <li>Relative URLs for datasources assumed to be relative
4217 to applet's codebase</li>
4218 <li>Status bar not updated after finished searching and
4219 search wraps around to first result</li>
4220 <li>StructureSelectionManager instance shared between
4221 several Jalview applets causes race conditions and memory
4223 <li>Hover tooltip and mouseover of position on structure
4224 not sent from Jmol in applet</li>
4225 <li>Certain sequences of javascript method calls to
4226 applet API fatally hang browser</li>
4227 </ul> <em>General</em>
4229 <li>View follows structure mouseover scrolls beyond
4230 position with wrapped view and hidden regions</li>
4231 <li>Find sequence position moves to wrong residue
4232 with/without hidden columns</li>
4233 <li>Sequence length given in alignment properties window
4235 <li>InvalidNumberFormat exceptions thrown when trying to
4236 import PDB like structure files</li>
4237 <li>Positional search results are only highlighted
4238 between user-supplied sequence start/end bounds</li>
4239 <li>End attribute of sequence is not validated</li>
4240 <li>Find dialog only finds first sequence containing a
4241 given sequence position</li>
4242 <li>Sequence numbering not preserved in MSF alignment
4244 <li>Jalview PDB file reader does not extract sequence
4245 from nucleotide chains correctly</li>
4246 <li>Structure colours not updated when tree partition
4247 changed in alignment</li>
4248 <li>Sequence associated secondary structure not correctly
4249 parsed in interleaved stockholm</li>
4250 <li>Colour by annotation dialog does not restore current
4252 <li>Hiding (nearly) all sequences doesn't work
4254 <li>Sequences containing lowercase letters are not
4255 properly associated with their pdb files</li>
4256 </ul> <em>Documentation and Development</em>
4258 <li>schemas/JalviewWsParamSet.xsd corrupted by
4259 ApplyCopyright tool</li>
4264 <div align="center">
4265 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4268 <td><em>Application</em>
4270 <li>New warning dialog when the Jalview Desktop cannot
4271 contact web services</li>
4272 <li>JABA service parameters for a preset are shown in
4273 service job window</li>
4274 <li>JABA Service menu entries reworded</li>
4278 <li>Modeller PIR IO broken - cannot correctly import a
4279 pir file emitted by Jalview</li>
4280 <li>Existing feature settings transferred to new
4281 alignment view created from cut'n'paste</li>
4282 <li>Improved test for mixed amino/nucleotide chains when
4283 parsing PDB files</li>
4284 <li>Consensus and conservation annotation rows
4285 occasionally become blank for all new windows</li>
4286 <li>Exception raised when right clicking above sequences
4287 in wrapped view mode</li>
4288 </ul> <em>Application</em>
4290 <li>multiple multiply aligned structure views cause cpu
4291 usage to hit 100% and computer to hang</li>
4292 <li>Web Service parameter layout breaks for long user
4293 parameter names</li>
4294 <li>Jaba service discovery hangs desktop if Jaba server
4301 <div align="center">
4302 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4305 <td><em>Application</em>
4307 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4308 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4311 <li>Web Services preference tab</li>
4312 <li>Analysis parameters dialog box and user defined
4314 <li>Improved speed and layout of Envision2 service menu</li>
4315 <li>Superpose structures using associated sequence
4317 <li>Export coordinates and projection as CSV from PCA
4319 </ul> <em>Applet</em>
4321 <li>enable javascript: execution by the applet via the
4322 link out mechanism</li>
4323 </ul> <em>Other</em>
4325 <li>Updated the Jmol Jalview interface to work with Jmol
4327 <li>The Jalview Desktop and JalviewLite applet now
4328 require Java 1.5</li>
4329 <li>Allow Jalview feature colour specification for GFF
4330 sequence annotation files</li>
4331 <li>New 'colour by label' keword in Jalview feature file
4332 type colour specification</li>
4333 <li>New Jalview Desktop Groovy API method that allows a
4334 script to check if it being run in an interactive session or
4335 in a batch operation from the Jalview command line</li>
4339 <li>clustalx colourscheme colours Ds preferentially when
4340 both D+E are present in over 50% of the column</li>
4341 </ul> <em>Application</em>
4343 <li>typo in AlignmentFrame->View->Hide->all but
4344 selected Regions menu item</li>
4345 <li>sequence fetcher replaces ',' for ';' when the ',' is
4346 part of a valid accession ID</li>
4347 <li>fatal OOM if object retrieved by sequence fetcher
4348 runs out of memory</li>
4349 <li>unhandled Out of Memory Error when viewing pca
4350 analysis results</li>
4351 <li>InstallAnywhere builds fail to launch on OS X java
4352 10.5 update 4 (due to apple Java 1.6 update)</li>
4353 <li>Installanywhere Jalview silently fails to launch</li>
4354 </ul> <em>Applet</em>
4356 <li>Jalview.getFeatureGroups() raises an
4357 ArrayIndexOutOfBoundsException if no feature groups are
4364 <div align="center">
4365 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4371 <li>Alignment prettyprinter doesn't cope with long
4373 <li>clustalx colourscheme colours Ds preferentially when
4374 both D+E are present in over 50% of the column</li>
4375 <li>nucleic acid structures retrieved from PDB do not
4376 import correctly</li>
4377 <li>More columns get selected than were clicked on when a
4378 number of columns are hidden</li>
4379 <li>annotation label popup menu not providing correct
4380 add/hide/show options when rows are hidden or none are
4382 <li>Stockholm format shown in list of readable formats,
4383 and parser copes better with alignments from RFAM.</li>
4384 <li>CSV output of consensus only includes the percentage
4385 of all symbols if sequence logo display is enabled</li>
4387 </ul> <em>Applet</em>
4389 <li>annotation panel disappears when annotation is
4391 </ul> <em>Application</em>
4393 <li>Alignment view not redrawn properly when new
4394 alignment opened where annotation panel is visible but no
4395 annotations are present on alignment</li>
4396 <li>pasted region containing hidden columns is
4397 incorrectly displayed in new alignment window</li>
4398 <li>Jalview slow to complete operations when stdout is
4399 flooded (fix is to close the Jalview console)</li>
4400 <li>typo in AlignmentFrame->View->Hide->all but
4401 selected Rregions menu item.</li>
4402 <li>inconsistent group submenu and Format submenu entry
4403 'Un' or 'Non'conserved</li>
4404 <li>Sequence feature settings are being shared by
4405 multiple distinct alignments</li>
4406 <li>group annotation not recreated when tree partition is
4408 <li>double click on group annotation to select sequences
4409 does not propagate to associated trees</li>
4410 <li>Mac OSX specific issues:
4412 <li>exception raised when mouse clicked on desktop
4413 window background</li>
4414 <li>Desktop menu placed on menu bar and application
4415 name set correctly</li>
4416 <li>sequence feature settings not wide enough for the
4417 save feature colourscheme button</li>
4426 <div align="center">
4427 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4430 <td><em>New Capabilities</em>
4432 <li>URL links generated from description line for
4433 regular-expression based URL links (applet and application)
4435 <li>Non-positional feature URL links are shown in link
4437 <li>Linked viewing of nucleic acid sequences and
4439 <li>Automatic Scrolling option in View menu to display
4440 the currently highlighted region of an alignment.</li>
4441 <li>Order an alignment by sequence length, or using the
4442 average score or total feature count for each sequence.</li>
4443 <li>Shading features by score or associated description</li>
4444 <li>Subdivide alignment and groups based on identity of
4445 selected subsequence (Make Groups from Selection).</li>
4446 <li>New hide/show options including Shift+Control+H to
4447 hide everything but the currently selected region.</li>
4448 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4449 </ul> <em>Application</em>
4451 <li>Fetch DB References capabilities and UI expanded to
4452 support retrieval from DAS sequence sources</li>
4453 <li>Local DAS Sequence sources can be added via the
4454 command line or via the Add local source dialog box.</li>
4455 <li>DAS Dbref and DbxRef feature types are parsed as
4456 database references and protein_name is parsed as
4457 description line (BioSapiens terms).</li>
4458 <li>Enable or disable non-positional feature and database
4459 references in sequence ID tooltip from View menu in
4461 <!-- <li>New hidden columns and rows and representatives capabilities
4462 in annotations file (in progress - not yet fully implemented)</li> -->
4463 <li>Group-associated consensus, sequence logos and
4464 conservation plots</li>
4465 <li>Symbol distributions for each column can be exported
4466 and visualized as sequence logos</li>
4467 <li>Optionally scale multi-character column labels to fit
4468 within each column of annotation row<!-- todo for applet -->
4470 <li>Optional automatic sort of associated alignment view
4471 when a new tree is opened.</li>
4472 <li>Jalview Java Console</li>
4473 <li>Better placement of desktop window when moving
4474 between different screens.</li>
4475 <li>New preference items for sequence ID tooltip and
4476 consensus annotation</li>
4477 <li>Client to submit sequences and IDs to Envision2
4479 <li><em>Vamsas Capabilities</em>
4481 <li>Improved VAMSAS synchronization (Jalview archive
4482 used to preserve views, structures, and tree display
4484 <li>Import of vamsas documents from disk or URL via
4486 <li>Sharing of selected regions between views and
4487 with other VAMSAS applications (Experimental feature!)</li>
4488 <li>Updated API to VAMSAS version 0.2</li>
4490 </ul> <em>Applet</em>
4492 <li>Middle button resizes annotation row height</li>
4495 <li>sortByTree (true/false) - automatically sort the
4496 associated alignment view by the tree when a new tree is
4498 <li>showTreeBootstraps (true/false) - show or hide
4499 branch bootstraps (default is to show them if available)</li>
4500 <li>showTreeDistances (true/false) - show or hide
4501 branch lengths (default is to show them if available)</li>
4502 <li>showUnlinkedTreeNodes (true/false) - indicate if
4503 unassociated nodes should be highlighted in the tree
4505 <li>heightScale and widthScale (1.0 or more) -
4506 increase the height or width of a cell in the alignment
4507 grid relative to the current font size.</li>
4510 <li>Non-positional features displayed in sequence ID
4512 </ul> <em>Other</em>
4514 <li>Features format: graduated colour definitions and
4515 specification of feature scores</li>
4516 <li>Alignment Annotations format: new keywords for group
4517 associated annotation (GROUP_REF) and annotation row display
4518 properties (ROW_PROPERTIES)</li>
4519 <li>XML formats extended to support graduated feature
4520 colourschemes, group associated annotation, and profile
4521 visualization settings.</li></td>
4524 <li>Source field in GFF files parsed as feature source
4525 rather than description</li>
4526 <li>Non-positional features are now included in sequence
4527 feature and gff files (controlled via non-positional feature
4528 visibility in tooltip).</li>
4529 <li>URL links generated for all feature links (bugfix)</li>
4530 <li>Added URL embedding instructions to features file
4532 <li>Codons containing ambiguous nucleotides translated as
4533 'X' in peptide product</li>
4534 <li>Match case switch in find dialog box works for both
4535 sequence ID and sequence string and query strings do not
4536 have to be in upper case to match case-insensitively.</li>
4537 <li>AMSA files only contain first column of
4538 multi-character column annotation labels</li>
4539 <li>Jalview Annotation File generation/parsing consistent
4540 with documentation (e.g. Stockholm annotation can be
4541 exported and re-imported)</li>
4542 <li>PDB files without embedded PDB IDs given a friendly
4544 <li>Find incrementally searches ID string matches as well
4545 as subsequence matches, and correctly reports total number
4549 <li>Better handling of exceptions during sequence
4551 <li>Dasobert generated non-positional feature URL
4552 link text excludes the start_end suffix</li>
4553 <li>DAS feature and source retrieval buttons disabled
4554 when fetch or registry operations in progress.</li>
4555 <li>PDB files retrieved from URLs are cached properly</li>
4556 <li>Sequence description lines properly shared via
4558 <li>Sequence fetcher fetches multiple records for all
4560 <li>Ensured that command line das feature retrieval
4561 completes before alignment figures are generated.</li>
4562 <li>Reduced time taken when opening file browser for
4564 <li>isAligned check prior to calculating tree, PCA or
4565 submitting an MSA to JNet now excludes hidden sequences.</li>
4566 <li>User defined group colours properly recovered
4567 from Jalview projects.</li>
4576 <div align="center">
4577 <strong>2.4.0.b2</strong><br> 28/10/2009
4582 <li>Experimental support for google analytics usage
4584 <li>Jalview privacy settings (user preferences and docs).</li>
4589 <li>Race condition in applet preventing startup in
4591 <li>Exception when feature created from selection beyond
4592 length of sequence.</li>
4593 <li>Allow synthetic PDB files to be imported gracefully</li>
4594 <li>Sequence associated annotation rows associate with
4595 all sequences with a given id</li>
4596 <li>Find function matches case-insensitively for sequence
4597 ID string searches</li>
4598 <li>Non-standard characters do not cause pairwise
4599 alignment to fail with exception</li>
4600 </ul> <em>Application Issues</em>
4602 <li>Sequences are now validated against EMBL database</li>
4603 <li>Sequence fetcher fetches multiple records for all
4605 </ul> <em>InstallAnywhere Issues</em>
4607 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4608 issue with installAnywhere mechanism)</li>
4609 <li>Command line launching of JARs from InstallAnywhere
4610 version (java class versioning error fixed)</li>
4617 <div align="center">
4618 <strong>2.4</strong><br> 27/8/2008
4621 <td><em>User Interface</em>
4623 <li>Linked highlighting of codon and amino acid from
4624 translation and protein products</li>
4625 <li>Linked highlighting of structure associated with
4626 residue mapping to codon position</li>
4627 <li>Sequence Fetcher provides example accession numbers
4628 and 'clear' button</li>
4629 <li>MemoryMonitor added as an option under Desktop's
4631 <li>Extract score function to parse whitespace separated
4632 numeric data in description line</li>
4633 <li>Column labels in alignment annotation can be centred.</li>
4634 <li>Tooltip for sequence associated annotation give name
4636 </ul> <em>Web Services and URL fetching</em>
4638 <li>JPred3 web service</li>
4639 <li>Prototype sequence search client (no public services
4641 <li>Fetch either seed alignment or full alignment from
4643 <li>URL Links created for matching database cross
4644 references as well as sequence ID</li>
4645 <li>URL Links can be created using regular-expressions</li>
4646 </ul> <em>Sequence Database Connectivity</em>
4648 <li>Retrieval of cross-referenced sequences from other
4650 <li>Generalised database reference retrieval and
4651 validation to all fetchable databases</li>
4652 <li>Fetch sequences from DAS sources supporting the
4653 sequence command</li>
4654 </ul> <em>Import and Export</em>
4655 <li>export annotation rows as CSV for spreadsheet import</li>
4656 <li>Jalview projects record alignment dataset associations,
4657 EMBL products, and cDNA sequence mappings</li>
4658 <li>Sequence Group colour can be specified in Annotation
4660 <li>Ad-hoc colouring of group in Annotation File using RGB
4661 triplet as name of colourscheme</li>
4662 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4664 <li>treenode binding for VAMSAS tree exchange</li>
4665 <li>local editing and update of sequences in VAMSAS
4666 alignments (experimental)</li>
4667 <li>Create new or select existing session to join</li>
4668 <li>load and save of vamsas documents</li>
4669 </ul> <em>Application command line</em>
4671 <li>-tree parameter to open trees (introduced for passing
4673 <li>-fetchfrom command line argument to specify nicknames
4674 of DAS servers to query for alignment features</li>
4675 <li>-dasserver command line argument to add new servers
4676 that are also automatically queried for features</li>
4677 <li>-groovy command line argument executes a given groovy
4678 script after all input data has been loaded and parsed</li>
4679 </ul> <em>Applet-Application data exchange</em>
4681 <li>Trees passed as applet parameters can be passed to
4682 application (when using "View in full
4683 application")</li>
4684 </ul> <em>Applet Parameters</em>
4686 <li>feature group display control parameter</li>
4687 <li>debug parameter</li>
4688 <li>showbutton parameter</li>
4689 </ul> <em>Applet API methods</em>
4691 <li>newView public method</li>
4692 <li>Window (current view) specific get/set public methods</li>
4693 <li>Feature display control methods</li>
4694 <li>get list of currently selected sequences</li>
4695 </ul> <em>New Jalview distribution features</em>
4697 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4698 <li>RELEASE file gives build properties for the latest
4699 Jalview release.</li>
4700 <li>Java 1.1 Applet build made easier and donotobfuscate
4701 property controls execution of obfuscator</li>
4702 <li>Build target for generating source distribution</li>
4703 <li>Debug flag for javacc</li>
4704 <li>.jalview_properties file is documented (slightly) in
4705 jalview.bin.Cache</li>
4706 <li>Continuous Build Integration for stable and
4707 development version of Application, Applet and source
4712 <li>selected region output includes visible annotations
4713 (for certain formats)</li>
4714 <li>edit label/displaychar contains existing label/char
4716 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4717 <li>shorter peptide product names from EMBL records</li>
4718 <li>Newick string generator makes compact representations</li>
4719 <li>bootstrap values parsed correctly for tree files with
4721 <li>pathological filechooser bug avoided by not allowing
4722 filenames containing a ':'</li>
4723 <li>Fixed exception when parsing GFF files containing
4724 global sequence features</li>
4725 <li>Alignment datasets are finalized only when number of
4726 references from alignment sequences goes to zero</li>
4727 <li>Close of tree branch colour box without colour
4728 selection causes cascading exceptions</li>
4729 <li>occasional negative imgwidth exceptions</li>
4730 <li>better reporting of non-fatal warnings to user when
4731 file parsing fails.</li>
4732 <li>Save works when Jalview project is default format</li>
4733 <li>Save as dialog opened if current alignment format is
4734 not a valid output format</li>
4735 <li>UniProt canonical names introduced for both das and
4737 <li>Histidine should be midblue (not pink!) in Zappo</li>
4738 <li>error messages passed up and output when data read
4740 <li>edit undo recovers previous dataset sequence when
4741 sequence is edited</li>
4742 <li>allow PDB files without pdb ID HEADER lines (like
4743 those generated by MODELLER) to be read in properly</li>
4744 <li>allow reading of JPred concise files as a normal
4746 <li>Stockholm annotation parsing and alignment properties
4747 import fixed for PFAM records</li>
4748 <li>Structure view windows have correct name in Desktop
4750 <li>annotation consisting of sequence associated scores
4751 can be read and written correctly to annotation file</li>
4752 <li>Aligned cDNA translation to aligned peptide works
4754 <li>Fixed display of hidden sequence markers and
4755 non-italic font for representatives in Applet</li>
4756 <li>Applet Menus are always embedded in applet window on
4758 <li>Newly shown features appear at top of stack (in
4760 <li>Annotations added via parameter not drawn properly
4761 due to null pointer exceptions</li>
4762 <li>Secondary structure lines are drawn starting from
4763 first column of alignment</li>
4764 <li>UniProt XML import updated for new schema release in
4766 <li>Sequence feature to sequence ID match for Features
4767 file is case-insensitive</li>
4768 <li>Sequence features read from Features file appended to
4769 all sequences with matching IDs</li>
4770 <li>PDB structure coloured correctly for associated views
4771 containing a sub-sequence</li>
4772 <li>PDB files can be retrieved by applet from Jar files</li>
4773 <li>feature and annotation file applet parameters
4774 referring to different directories are retrieved correctly</li>
4775 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4776 <li>Fixed application hang whilst waiting for
4777 splash-screen version check to complete</li>
4778 <li>Applet properly URLencodes input parameter values
4779 when passing them to the launchApp service</li>
4780 <li>display name and local features preserved in results
4781 retrieved from web service</li>
4782 <li>Visual delay indication for sequence retrieval and
4783 sequence fetcher initialisation</li>
4784 <li>updated Application to use DAS 1.53e version of
4785 dasobert DAS client</li>
4786 <li>Re-instated Full AMSA support and .amsa file
4788 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4796 <div align="center">
4797 <strong>2.3</strong><br> 9/5/07
4802 <li>Jmol 11.0.2 integration</li>
4803 <li>PDB views stored in Jalview XML files</li>
4804 <li>Slide sequences</li>
4805 <li>Edit sequence in place</li>
4806 <li>EMBL CDS features</li>
4807 <li>DAS Feature mapping</li>
4808 <li>Feature ordering</li>
4809 <li>Alignment Properties</li>
4810 <li>Annotation Scores</li>
4811 <li>Sort by scores</li>
4812 <li>Feature/annotation editing in applet</li>
4817 <li>Headless state operation in 2.2.1</li>
4818 <li>Incorrect and unstable DNA pairwise alignment</li>
4819 <li>Cut and paste of sequences with annotation</li>
4820 <li>Feature group display state in XML</li>
4821 <li>Feature ordering in XML</li>
4822 <li>blc file iteration selection using filename # suffix</li>
4823 <li>Stockholm alignment properties</li>
4824 <li>Stockhom alignment secondary structure annotation</li>
4825 <li>2.2.1 applet had no feature transparency</li>
4826 <li>Number pad keys can be used in cursor mode</li>
4827 <li>Structure Viewer mirror image resolved</li>
4834 <div align="center">
4835 <strong>2.2.1</strong><br> 12/2/07
4840 <li>Non standard characters can be read and displayed
4841 <li>Annotations/Features can be imported/exported to the
4843 <li>Applet allows editing of sequence/annotation/group
4844 name & description
4845 <li>Preference setting to display sequence name in
4847 <li>Annotation file format extended to allow
4848 Sequence_groups to be defined
4849 <li>Default opening of alignment overview panel can be
4850 specified in preferences
4851 <li>PDB residue numbering annotation added to associated
4857 <li>Applet crash under certain Linux OS with Java 1.6
4859 <li>Annotation file export / import bugs fixed
4860 <li>PNG / EPS image output bugs fixed
4866 <div align="center">
4867 <strong>2.2</strong><br> 27/11/06
4872 <li>Multiple views on alignment
4873 <li>Sequence feature editing
4874 <li>"Reload" alignment
4875 <li>"Save" to current filename
4876 <li>Background dependent text colour
4877 <li>Right align sequence ids
4878 <li>User-defined lower case residue colours
4881 <li>Menu item accelerator keys
4882 <li>Control-V pastes to current alignment
4883 <li>Cancel button for DAS Feature Fetching
4884 <li>PCA and PDB Viewers zoom via mouse roller
4885 <li>User-defined sub-tree colours and sub-tree selection
4887 <li>'New Window' button on the 'Output to Text box'
4892 <li>New memory efficient Undo/Redo System
4893 <li>Optimised symbol lookups and conservation/consensus
4895 <li>Region Conservation/Consensus recalculated after
4897 <li>Fixed Remove Empty Columns Bug (empty columns at end
4899 <li>Slowed DAS Feature Fetching for increased robustness.
4901 <li>Made angle brackets in ASCII feature descriptions
4903 <li>Re-instated Zoom function for PCA
4904 <li>Sequence descriptions conserved in web service
4906 <li>UniProt ID discoverer uses any word separated by
4908 <li>WsDbFetch query/result association resolved
4909 <li>Tree leaf to sequence mapping improved
4910 <li>Smooth fonts switch moved to FontChooser dialog box.
4917 <div align="center">
4918 <strong>2.1.1</strong><br> 12/9/06
4923 <li>Copy consensus sequence to clipboard</li>
4928 <li>Image output - rightmost residues are rendered if
4929 sequence id panel has been resized</li>
4930 <li>Image output - all offscreen group boundaries are
4932 <li>Annotation files with sequence references - all
4933 elements in file are relative to sequence position</li>
4934 <li>Mac Applet users can use Alt key for group editing</li>
4940 <div align="center">
4941 <strong>2.1</strong><br> 22/8/06
4946 <li>MAFFT Multiple Alignment in default Web Service list</li>
4947 <li>DAS Feature fetching</li>
4948 <li>Hide sequences and columns</li>
4949 <li>Export Annotations and Features</li>
4950 <li>GFF file reading / writing</li>
4951 <li>Associate structures with sequences from local PDB
4953 <li>Add sequences to exisiting alignment</li>
4954 <li>Recently opened files / URL lists</li>
4955 <li>Applet can launch the full application</li>
4956 <li>Applet has transparency for features (Java 1.2
4958 <li>Applet has user defined colours parameter</li>
4959 <li>Applet can load sequences from parameter
4960 "sequence<em>x</em>"
4966 <li>Redundancy Panel reinstalled in the Applet</li>
4967 <li>Monospaced font - EPS / rescaling bug fixed</li>
4968 <li>Annotation files with sequence references bug fixed</li>
4974 <div align="center">
4975 <strong>2.08.1</strong><br> 2/5/06
4980 <li>Change case of selected region from Popup menu</li>
4981 <li>Choose to match case when searching</li>
4982 <li>Middle mouse button and mouse movement can compress /
4983 expand the visible width and height of the alignment</li>
4988 <li>Annotation Panel displays complete JNet results</li>
4994 <div align="center">
4995 <strong>2.08b</strong><br> 18/4/06
5001 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5002 <li>Righthand label on wrapped alignments shows correct
5009 <div align="center">
5010 <strong>2.08</strong><br> 10/4/06
5015 <li>Editing can be locked to the selection area</li>
5016 <li>Keyboard editing</li>
5017 <li>Create sequence features from searches</li>
5018 <li>Precalculated annotations can be loaded onto
5020 <li>Features file allows grouping of features</li>
5021 <li>Annotation Colouring scheme added</li>
5022 <li>Smooth fonts off by default - Faster rendering</li>
5023 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5028 <li>Drag & Drop fixed on Linux</li>
5029 <li>Jalview Archive file faster to load/save, sequence
5030 descriptions saved.</li>
5036 <div align="center">
5037 <strong>2.07</strong><br> 12/12/05
5042 <li>PDB Structure Viewer enhanced</li>
5043 <li>Sequence Feature retrieval and display enhanced</li>
5044 <li>Choose to output sequence start-end after sequence
5045 name for file output</li>
5046 <li>Sequence Fetcher WSDBFetch@EBI</li>
5047 <li>Applet can read feature files, PDB files and can be
5048 used for HTML form input</li>
5053 <li>HTML output writes groups and features</li>
5054 <li>Group editing is Control and mouse click</li>
5055 <li>File IO bugs</li>
5061 <div align="center">
5062 <strong>2.06</strong><br> 28/9/05
5067 <li>View annotations in wrapped mode</li>
5068 <li>More options for PCA viewer</li>
5073 <li>GUI bugs resolved</li>
5074 <li>Runs with -nodisplay from command line</li>
5080 <div align="center">
5081 <strong>2.05b</strong><br> 15/9/05
5086 <li>Choose EPS export as lineart or text</li>
5087 <li>Jar files are executable</li>
5088 <li>Can read in Uracil - maps to unknown residue</li>
5093 <li>Known OutOfMemory errors give warning message</li>
5094 <li>Overview window calculated more efficiently</li>
5095 <li>Several GUI bugs resolved</li>
5101 <div align="center">
5102 <strong>2.05</strong><br> 30/8/05
5107 <li>Edit and annotate in "Wrapped" view</li>
5112 <li>Several GUI bugs resolved</li>
5118 <div align="center">
5119 <strong>2.04</strong><br> 24/8/05
5124 <li>Hold down mouse wheel & scroll to change font
5130 <li>Improved JPred client reliability</li>
5131 <li>Improved loading of Jalview files</li>
5137 <div align="center">
5138 <strong>2.03</strong><br> 18/8/05
5143 <li>Set Proxy server name and port in preferences</li>
5144 <li>Multiple URL links from sequence ids</li>
5145 <li>User Defined Colours can have a scheme name and added
5147 <li>Choose to ignore gaps in consensus calculation</li>
5148 <li>Unix users can set default web browser</li>
5149 <li>Runs without GUI for batch processing</li>
5150 <li>Dynamically generated Web Service Menus</li>
5155 <li>InstallAnywhere download for Sparc Solaris</li>
5161 <div align="center">
5162 <strong>2.02</strong><br> 18/7/05
5168 <li>Copy & Paste order of sequences maintains
5169 alignment order.</li>
5175 <div align="center">
5176 <strong>2.01</strong><br> 12/7/05
5181 <li>Use delete key for deleting selection.</li>
5182 <li>Use Mouse wheel to scroll sequences.</li>
5183 <li>Help file updated to describe how to add alignment
5185 <li>Version and build date written to build properties
5187 <li>InstallAnywhere installation will check for updates
5188 at launch of Jalview.</li>
5193 <li>Delete gaps bug fixed.</li>
5194 <li>FileChooser sorts columns.</li>
5195 <li>Can remove groups one by one.</li>
5196 <li>Filechooser icons installed.</li>
5197 <li>Finder ignores return character when searching.
5198 Return key will initiate a search.<br>
5205 <div align="center">
5206 <strong>2.0</strong><br> 20/6/05
5211 <li>New codebase</li>