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>3/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
67 structures with ChimeraX and Pymol in addition to Jmol and
71 <!-- JAL-3829 -->Discover 3D structure data for sequences
72 with Uniprot references via 3D-Beacons
75 <!-- JAL-3391 -->Rank and select available structures for
76 Uniprot sequences according to number of residues in
77 structure mapped to positions involved in the alignment
80 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
81 memory settings at launch
84 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
85 menu for selecting which database to fetch from in sequence
89 <!-- JAL-2226 -->Structure annotation rows for all mapped
90 chains in 3D structures are included in the 'Reference
91 Annotation' for a sequence
94 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
97 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
98 molecules imported from ENA records are shown as RNA
100 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
103 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
107 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
111 <!-- JAL-3530 -->-nowebservicediscovery command line
112 argument to prevent automatic discovery of analysis
113 webservices on launch
116 <!-- JAL-3618 -->Allow 'App' directories to be opened when
117 locating Chimera, ChimeraX or Pymol binaries via filechooser
118 opened by double clicking the Structure Preferences' path
122 <em>Jalview Native App</em>
125 <!-- JAL- -->New Jalview Develop app - making it even easier
126 to get at Jalview's development builds
129 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
130 and Jalview Develop applications.
133 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
134 Console and other window widgets in taskbar and dock rather
135 than anonymous 'Java' icons
137 </ul> <em>JalviewJS</em>
140 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
144 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
153 <!-- JAL-3163 -->Missing message bundle keys are only
154 reported once per key (avoids excessive log output in js
158 <!-- JAL-3168 -->Feature type is included in the title of
159 the Feature Settings' Colour Chooser dialog
162 </ul> <em>Development</em>
165 <!-- -->First integrated JalviewJS and Jalview release
167 <li>Updated building instructions</li>
169 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
170 process, added support for system package provided eclipse
173 <li>Install4j 9.0.x used for installer packaging</li>
174 <li>Notarized MacOS installer for compatibility with Big
175 Sur and Monterey</li>
177 <!-- JAL-3805 -->Uninstaller application for old
178 (InstallAnywhere based) Jalview installations removed from
182 <!-- JAL-3930 -->Improved use of installers for unattended
183 installation with a customizedId of "JALVIEW" in install4j's
193 <!-- JAL-3674 -->Slow structure commands can block Jalview
197 <!-- JAL-3904 -->Structure window's viewer-specific menu
198 disappears when only one structure is shown (and many
199 sequences:one chain mappings are present)
202 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
203 the first SEQUENCE_GROUP defined
208 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
209 propagated between Linked CDS - Protein alignments and their
210 trees (known defect from 2.11.1.3)
213 <!-- JAL-3761 -->Not all codon positions highlighted for
214 overlapping exon splice sites (e.g due to RNA slippage)
217 <!-- JAL-3794 -->X was not being recognised as the unknown
218 base in DNA sequences
221 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
222 Structure Preferences
225 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
228 <!-- JAL-3162 -->Can edit a feature so that start > end
231 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
232 modified graduated colour
235 <!-- JAL-3788 -->New View with automatic 'Show Overview'
236 preference enabled results in Null Pointer Exceptions when
237 clustal colouring is enabled
240 <!-- JAL-3275 -->Can open multiple Preferences panels
243 <!-- JAL-3949 -->Standard out logging broken: messages only
244 routing to stderr and appear as a raw template
246 </ul> <em>JalviewJS</em>
249 <!-- JAL-3202 -->Consensus profile may include zero (rounded
250 down) percentage values causing a divide by zero
265 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
266 via Info.args when there are arguments on the URL
269 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
272 <!-- JAL-3603 -->Annotation file fails to load from URL in
275 </ul> <em>Development</em>
279 <li>Fixed non-fatal gradle errors during build</li>
281 <!-- JAL-3745 -->Updated build.gradle for use with
291 <td width="60" align="center" nowrap><strong><a
292 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
293 <em>18/01/2022</em></strong></td>
295 <td align="left" valign="top">
298 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
299 updated by Jalview or other applications (Windows, other non
302 </ul> <em>Security</em>
305 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
311 <td width="60" align="center" nowrap><strong><a
312 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
313 <em>6/01/2022</em></strong></td>
315 <td align="left" valign="top"><em>Security</em>
318 <!-- JAL-3934 -->Version bump library dependency: Log4j
325 <td width="60" align="center" nowrap><strong><a
326 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
327 <em>20/12/2021</em></strong></td>
329 <td align="left" valign="top"><em>Security</em>
332 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
334 </ul> <em>Development</em>
336 <li>Updated building instructions</li>
341 <!-- JAL-3840 -->Occupancy calculation is incorrect for
342 alignment columns with over -1+2^32 gaps (breaking filtering
346 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
347 scale factors being set with buggy window-managers (linux
350 </ul> <em>Development</em>
352 <li>Fixed non-fatal gradle errors during build</li>
357 <td width="60" align="center" nowrap><strong><a
358 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
359 <em>09/03/2021</em></strong></td>
360 <td align="left" valign="top"><em>Improved control of
361 Jalview's use of network services via jalview_properties</em>
364 <!-- JAL-3814 -->New .jalview_properties token controlling
365 launch of the news browser (like -nonews argument)
368 <!-- JAL-3813 -->New .jalview_properties token controlling
369 download of linkout URLs from
370 www.jalview.org/services/identifiers
373 <!-- JAL-3812 -->New .jalview_properties token controlling
374 download of BIOJSHTML templates
377 <!-- JAL-3811 -->New 'Discover Web Services' option to
378 trigger a one off JABAWS discovery if autodiscovery was
382 <td align="left" valign="top">
385 <!-- JAL-3818 -->Intermittent deadlock opening structure in
388 </ul> <em>New Known defects</em>
391 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
392 always restored from project (since 2.10.3)
395 <!-- JAL-3806 -->Selections from tree built from CDS aren't
396 propagated to Protein alignment (since 2.11.1.3)
402 <td width="60" align="center" nowrap><strong><a
403 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
404 <em>29/10/2020</em></strong></td>
405 <td align="left" valign="top">
410 <td align="left" valign="top">
413 <!-- JAL-3765 -->Find doesn't always highlight all matching
414 positions in a sequence (bug introduced in 2.11.1.2)
417 <!-- JAL-3760 -->Alignments containing one or more protein
418 sequences can be classed as nucleotide
421 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
422 sequences after alignment of protein products (known defect
423 first reported for 2.11.1.0)
426 <!-- JAL-3725 -->No tooltip or popup menu for genomic
427 features outwith CDS shown overlaid on protein
430 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
431 correctly mapped by Jalview (e.g. affects viral CDS with
432 ribosomal slippage, since 2.9.0)
435 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
439 <!-- JAL-3700 -->Selections in CDS sequence panel don't
440 always select corresponding protein sequences
443 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
444 column selection doesn't always ignore hidden columns
446 </ul> <em>Installer</em>
449 <!-- JAL-3611 -->Space character in Jalview install path on
450 Windows prevents install4j launching getdown
452 </ul> <em>Development</em>
455 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
456 version numbers in doc/building.md
462 <td width="60" align="center" nowrap><strong><a
463 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
464 <em>25/09/2020</em></strong></td>
465 <td align="left" valign="top">
469 <td align="left" valign="top">
472 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
473 "Encountered problems opening
474 https://www.jalview.org/examples/exampleFile_2_7.jvp"
480 <td width="60" align="center" nowrap><strong><a
481 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
482 <em>17/09/2020</em></strong></td>
483 <td align="left" valign="top">
486 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
487 residue in cursor mode
490 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
491 HTSJDK from 2.12 to 2.23
494 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
495 optimisations and improvements suggested by Bob Hanson and
496 improved compatibility with JalviewJS
499 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
500 alignments from Pfam and Rfam
503 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
504 import (no longer based on .gz extension)
507 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
510 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
511 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
515 <!-- JAL-3667 -->Improved warning messages, debug logging
516 and fixed Retry action when Jalview encounters errors when
517 saving or making backup files.
520 <!-- JAL-3676 -->Enhanced Jalview Java Console:
522 <li>Jalview's logging level can be configured</li>
523 <li>Copy to Clipboard Buttion</li>
527 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
528 when running on Linux (Requires Java 11+)
530 </ul> <em>Launching Jalview</em>
533 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
534 through a system property
537 <!-- JAL-3477 -->Improved built-in documentation and command
538 line help for configuring Jalview's memory
542 <td align="left" valign="top">
545 <!-- JAL-3691 -->Conservation and Quality tracks are shown
546 but not calculated and no protein or DNA score models are
547 available for tree/PCA calculation when launched with
548 Turkish language locale
551 <!-- JAL-3493 -->Escape does not clear highlights on the
552 alignment (Since Jalview 2.10.3)
555 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
556 doesn't slide selected sequences, just sequence under cursor
559 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
560 sequence under the cursor
563 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
564 multiple EMBL gene products shown for a single contig
567 <!-- JAL-3696 -->Errors encountered when processing variants
568 from VCF files yield "Error processing VCF: Format specifier
572 <!-- JAL-3697 -->Count of features not shown can be wrong
573 when there are both local and complementary features mapped
574 to the position under the cursor
577 <!-- JAL-3673 -->Sequence ID for reference sequence is
578 clipped when Right align Sequence IDs enabled
581 <!-- JAL-2983 -->Slider with negative range values not
582 rendered correctly in VAqua4 (Since 2.10.4)
585 <!-- JAL-3685 -->Single quotes not displayed correctly in
586 internationalised text for some messages and log output
589 <!-- JAL-3490 -->Find doesn't report matches that span
590 hidden gapped columns
593 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
594 panels, Alignment viewport and annotation renderer.
597 <!-- JAL-3561 -->Jalview ignores file format parameter
598 specifying output format when exporting an alignment via the
602 <!-- JAL-3667 -->Windows 10: For a minority of users, if
603 backups are not enabled, Jalview sometimes fails to
604 overwrite an existing file and raises a warning dialog. (in
605 2.11.0, and 2.11.1.0, the workaround is to try to save the
606 file again, and if that fails, delete the original file and
610 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
614 <!-- JAL-3741 -->References to http://www.jalview.org in
615 program and documentation
617 </ul> <em>Launching Jalview</em>
620 <!-- JAL-3718 -->Jalview application fails when launched the
621 first time for a version that has different jars to the
622 previous launched version.
624 </ul> <em>Developing Jalview</em>
627 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
628 data, causing cloverReport gradle task to fail with an
632 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
633 monitor the release channel
635 </ul> <em>New Known defects</em>
638 <!-- JAL-3748 -->CDS shown in result of submitting proteins
639 in a CDS/Protein alignment to a web service is wrong when
640 proteins share a common transcript sequence (e.g. genome of
644 <!-- JAL-3576 -->Co-located features exported and
645 re-imported are ordered differently when shown on alignment
646 and in tooltips. (Also affects v2.11.1.0)
649 <!-- JAL-3702 -->Drag and drop of alignment file onto
650 alignment window when in a HiDPI scaled mode in Linux only
651 works for the top left quadrant of the alignment window
654 <!-- JAL-3701 -->Stale build data in jalview standalone jar
655 builds (only affects 2.11.1.1 branch)
658 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
659 when alignment view restored from project (since Jalview
663 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
664 protein products for certain ENA records are repeatedly
665 shown via Calculate->Show Cross Refs
671 <td width="60" align="center" nowrap><strong><a
672 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
673 <em>22/04/2020</em></strong></td>
674 <td align="left" valign="top">
677 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
678 'virtual' codon features shown on protein (or vice versa)
679 for display in alignments, on structure views (including
680 transfer to UCSF chimera), in feature reports and for
684 <!-- JAL-3121 -->Feature attributes from VCF files can be
685 exported and re-imported as GFF3 files
688 <!-- JAL-3376 -->Capture VCF "fixed column" values
689 POS, ID, QUAL, FILTER as Feature Attributes
692 <!-- JAL-3375 -->More robust VCF numeric data field
693 validation while parsing
696 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
700 <!-- JAL-3535 -->Feature Settings dialog title includes name
704 <!-- JAL-3538 -->Font anti-aliasing in alignment views
708 <!-- JAL-3468 -->Very long feature descriptions truncated in
712 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
713 with no feature types visible
716 <!-- JAL-3574 -->Improved support for filtering feature
717 attributes with large integer values
720 <em>Jalview Installer</em>
723 <!-- JAL-3449 -->Versions for install4j and getdown and
724 installer template version reported in console (may be null
725 when Jalview launched as executable jar or via conda)
728 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
729 higher quality background images
732 <!-- JAL-3394 -->New installer/application launcher
733 generated with install4j 8.0.4
736 <!-- JAL-3420 -->Jalview File Associations shown for Unix
740 <!-- JAL-3477 -->Improved defaults for maximum memory
741 setting when running on large memory machines
743 </ul> <em>Release processes</em>
746 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
749 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
750 access to test-release channel builds
752 </ul> <em>Build System</em>
755 <!-- JAL-3510 -->Clover updated to 4.4.1
758 <!-- JAL-3513 -->Test code included in Clover coverage
761 </ul> <em>Groovy Scripts</em>
764 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
765 to stdout containing the consensus sequence for each
766 alignment in a Jalview session
769 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
770 genomic sequence_variant annotation from CDS as
771 missense_variant or synonymous_variant on protein products.
775 <td align="left" valign="top">
778 <!-- JAL-3581 -->Hidden sequence markers still visible when
779 'Show hidden markers' option is not ticked
782 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
783 PNG output when 'Automatically set ID width' is set in
784 jalview preferences or properties file
787 <!-- JAL-3571 -->Feature Editor dialog can be opened when
788 'Show Sequence Features' option is not ticked
791 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
792 buttons in Feature Settings dialog are clicked when no
796 <!-- JAL-3412 -->ID margins for CDS and Protein views not
797 equal when split frame is first opened
800 <!-- JAL-3296 -->Sequence position numbers in status bar not
801 correct after editing a sequence's start position
804 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
805 with annotation and exceptions thrown when only a few
806 columns shown in wrapped mode
809 <!-- JAL-3386 -->Sequence IDs missing in headless export of
810 wrapped alignment figure with annotations
813 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
814 ID fails with ClassCastException
817 <!-- JAL-3389 -->Chimera session not restored from Jalview
821 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
822 feature settings dialog also selects columns
825 <!-- JAL-3473 -->SpinnerNumberModel causes
826 IllegalArgumentException in some circumstances
829 <!-- JAL-3534 -->Multiple feature settings dialogs can be
833 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
834 alignment window is closed
837 <!-- JAL-3406 -->Credits missing some authors in Jalview
838 help documentation for 2.11.0 release
841 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
842 includes Pfam ID as sequence's accession rather than its
845 </ul> <em>Java 11 Compatibility issues</em>
848 <!-- JAL-2987 -->OSX - Can't view some search results in
849 PDB/Uniprot search panel
851 </ul> <em>Installer</em>
854 <!-- JAL-3447 -->Jalview should not create file associations
855 for 3D structure files (.pdb, .mmcif. .cif)
857 </ul> <em>Repository and Source Release</em>
860 <!-- JAL-3474 -->removed obsolete .cvsignore files from
864 <!-- JAL-3541 -->Clover report generation running out of
867 </ul> <em>New Known Issues</em>
870 <!-- JAL-3523 -->OSX - Current working directory not
871 preserved when Jalview.app launched with parameters from
875 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
876 clipped in headless figure export when Right Align option
880 <!-- JAL-3542 -->Jalview Installation type always reports
881 'Source' in console output
884 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
885 on jalview's bamboo server but run fine locally.
891 <td width="60" align="center" nowrap><strong><a
892 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
893 <td align="left" valign="top">
896 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
897 Application and Installers built with <a
898 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
899 (licensed to the Jalview open source project) rather than
903 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
904 memory settings, receive over the air updates and launch
905 specific versions via (<a
906 href="https://github.com/threerings/getdown">Three
910 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
911 for formats supported by Jalview (including .jvp project
915 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
916 line arguments and switch between different getdown channels
919 <!-- JAL-3141 -->Backup files created when saving Jalview
920 project or alignment files
924 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
928 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
929 updated to version 2.12.0
932 <!-- JAL-2620 -->Alternative genetic code tables for
936 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
938 <li><strong>Enhanced visualisation and analysis
939 of Sequence Features</strong>
942 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
943 implementation that allows updates) used for Sequence
947 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
948 features can be filtered and shaded according to any
949 associated attributes (e.g. variant attributes from VCF
950 file, or key-value pairs imported from column 9 of GFF
954 <!-- JAL-2879 -->Feature Attributes and shading schemes
955 stored and restored from Jalview Projects
958 <!-- JAL-3334 -->Use full Sequence Ontology (via
959 BioJava) to recognise variant features
962 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
963 on peptide sequences (also coloured red by default)
966 <!-- JAL-2792 -->Popup window to show full report for a
967 selected sequence feature's details
970 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
971 sequence feature render algorithm (Z-sort/transparency
975 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
980 <!-- JAL-3205 -->Symmetric score matrices for faster tree
983 <li><strong>Principal Components Analysis Viewer</strong>
986 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
987 results and Viewer state saved in Jalview Project
990 <!-- JAL-2962 -->'Change parameters' option removed from
991 viewer's drop-down menus
994 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
995 PCA image incrementally
998 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1002 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1004 <li><strong>Speed and Efficiency</strong>
1007 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1008 selections and multiple groups when working with large
1012 <!-- JAL-3200 -->Speedier import of annotation rows when
1013 parsing Stockholm files
1016 <li><strong>User Interface</strong>
1019 <!-- JAL-2933 -->Finder panel remembers last position in
1023 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1024 (What you see is what is shown)<br />Only visible
1025 regions of alignment are shown by default (can be
1026 changed in user preferences)
1029 <!-- JAL-3169 -->File Chooser stays open after
1030 responding Cancel to the Overwrite Dialog
1033 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1034 when all sequences are hidden
1037 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1038 selection region, and gap count when inserting or
1042 <!-- JAL-3132 -->Status bar updates over sequence and
1046 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1047 shown when in wrapped mode
1050 <!-- JAL-3073 -->Can select columns by dragging
1051 left/right in a graph or histogram annotation
1054 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1058 <!-- JAL-2621 -->Cursor changes over draggable box in
1062 <!-- JAL-3181 -->Consistent ordering of links in
1063 sequence id popup menu
1066 <!-- JAL-3080 -->Red line indicating tree-cut position
1067 not shown if no subgroups are created
1070 <!-- JAL-3042 -->Removed ability to configure length of
1071 search history by right-clicking search box
1077 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1080 <li><strong>Java 11 Support (not yet on general
1084 <!-- -->OSX GUI integrations for App menu's 'About'
1085 entry and trapping CMD-Q
1088 </ul> <em>Deprecations</em>
1091 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1092 capabilities removed from the Jalview Desktop
1095 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1096 and unmarshalling has been replaced by JAXB for Jalview
1097 projects and XML based data retrieval clients
1100 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1104 <!-- -->Jalview Desktop no longer distributed via Java Web
1107 </ul> <em>Documentation</em>
1110 <!-- JAL-3003 -->Added remarks about transparent rendering
1111 effects not supported in EPS figure export
1114 <!-- JAL-2903 -->Typos in documentation for Preferences
1117 </ul> <em>Development and Release Processes</em>
1120 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1124 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1125 keys in Message bundles
1128 <!-- JAL-3225 -->Eclipse project configuration managed with
1132 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1133 continuous integration for unattended Test Suite execution
1136 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1140 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1144 <!-- JAL-3248 -->Developer documentation migrated to
1145 markdown (with HTML rendering)
1148 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1151 <!-- JAL-3289 -->New URLs for publishing development
1156 <td align="left" valign="top">
1159 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1162 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1163 superposition in Jmol fail on Windows
1166 <!-- JAL-3286 -->Blank error dialog is displayed when
1167 discovering structures for sequences with lots of PDB
1171 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1172 with monospaced font
1175 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1176 Jalview project involving multiple views
1179 <!-- JAL-3164 -->Overview for complementary view in a linked
1180 CDS/Protein alignment is not updated when Hide Columns by
1181 Annotation dialog hides columns
1184 <!-- JAL-3158 -->Selection highlighting in the complement of
1185 a CDS/Protein alignment stops working after making a
1186 selection in one view, then making another selection in the
1190 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1194 <!-- JAL-3154 -->Table Columns could be re-ordered in
1195 Feature Settings and Jalview Preferences panels
1198 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1199 redrawing the overview with large alignments
1202 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1203 region if columns were selected by dragging right-to-left
1204 and the mouse moved to the left of the first column
1207 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1208 a hidden column marker via scale popup menu
1211 <!-- JAL-2846 -->Error message for trying to load in invalid
1212 URLs doesn't tell users the invalid URL
1215 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1219 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1220 during show cross references or Fetch Database References
1221 are shown in red in original view
1224 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1225 correctly on peptide sequence (computed variant shown as
1229 <!-- JAL-2060 -->'Graduated colour' option not offered for
1230 manually created features (where feature score is Float.NaN)
1233 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1234 printed when columns are hidden
1237 <!-- JAL-3082 -->Regular expression error for '(' in Select
1238 Columns by Annotation description
1241 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1242 dragging out of Scale or Annotation Panel
1245 <!-- JAL-3075 -->Column selection incorrect after scrolling
1249 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1253 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1257 <!-- JAL-3002 -->Column display is out by one after Page
1258 Down, Page Up in wrapped mode
1261 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1264 <!-- JAL-2932 -->Finder searches in minimised alignments
1267 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1268 selected on opening an alignment
1271 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1275 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1276 when different groups in the alignment are selected
1279 <!-- JAL-2717 -->Internationalised colour scheme names not
1280 shown correctly in menu
1283 <!-- JAL-3206 -->Colour by Annotation can go black at
1284 min/max threshold limit
1287 <!-- JAL-3125 -->Value input for graduated feature colour
1288 threshold gets 'unrounded'
1291 <!-- JAL-2982 -->PCA image export doesn't respect background
1295 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1299 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1302 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1303 alignment, not Tree font
1306 <!-- JAL-2964 -->Associate Tree with All Views not restored
1310 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1311 Overview shown in complementary view
1314 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1315 shown without normalisation
1318 <!-- JAL-3021 -->Sequence Details report should open
1319 positioned at top of report
1322 <!-- JAL-914 -->Help page can be opened twice
1325 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1328 </ul> <em>Editing</em>
1331 <!-- JAL-2822 -->Start and End should be updated when
1332 sequence data at beginning or end of alignment added/removed
1336 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1337 doesn't relocate sequence features correctly when start of
1338 sequence is removed (Known defect since 2.10)
1341 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1342 Sequence dialog corrupts dataset sequence
1345 <!-- JAL-868 -->Structure colours not updated when
1346 associated tree repartitions the alignment view (Regression
1349 </ul> <em>Datamodel</em>
1352 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1353 sequence's End is greater than its length
1355 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1359 <!-- JAL-3288 -->Menus work properly in split-screen
1361 </ul> <em>New Known Defects</em>
1364 <!-- JAL-3340 -->Select columns containing feature by double
1365 clicking ignores bounds of an existing selected region
1368 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1369 gapped regions of protein alignment.
1372 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1373 PCA View is restored from a Jalview 2.11 project
1376 <!-- JAL-3213 -->Alignment panel height can be too small
1380 <!-- JAL-3240 -->Display is incorrect after removing gapped
1381 columns within hidden columns
1384 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1385 re-enters window after dragging left to select columns to
1386 left of visible region
1389 <!-- JAL-2876 -->Features coloured according to their
1390 description string and thresholded by score in earlier
1391 versions of Jalview are not shown as thresholded features in
1392 2.11. To workaround please create a Score filter instead.
1395 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1396 reset group visibility
1399 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1400 linked CDS/Protein view
1403 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1404 alignments with multiple views can close views unexpectedly
1406 </ul> <em>Java 11 Specific defects</em>
1409 <!-- JAL-3235 -->Jalview Properties file is not sorted
1410 alphabetically when saved
1416 <td width="60" nowrap>
1417 <div align="center">
1418 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1421 <td><div align="left">
1425 <!-- JAL-3101 -->Default memory for Jalview webstart and
1426 InstallAnywhere increased to 1G.
1429 <!-- JAL-247 -->Hidden sequence markers and representative
1430 sequence bolding included when exporting alignment as EPS,
1431 SVG, PNG or HTML. <em>Display is configured via the
1432 Format menu, or for command-line use via a Jalview
1433 properties file.</em>
1436 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1437 API and sequence data now imported as JSON.
1440 <!-- JAL-3065 -->Change in recommended way of starting
1441 Jalview via a Java command line: add jars in lib directory
1442 to CLASSPATH, rather than via the deprecated java.ext.dirs
1446 <em>Development</em>
1449 <!-- JAL-3047 -->Support added to execute test suite
1450 instrumented with <a href="http://openclover.org/">Open
1455 <td><div align="left">
1459 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1460 row shown in Feredoxin Structure alignment view of example
1464 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1465 annotation displayed.
1468 <!-- JAL-3107 -->Group conservation/consensus not shown
1469 for newly created group when 'Apply to all groups'
1473 <!-- JAL-3087 -->Corrupted display when switching to
1474 wrapped mode when sequence panel's vertical scrollbar is
1478 <!-- JAL-3003 -->Alignment is black in exported EPS file
1479 when sequences are selected in exported view.</em>
1482 <!-- JAL-3059 -->Groups with different coloured borders
1483 aren't rendered with correct colour.
1486 <!-- JAL-3092 -->Jalview could hang when importing certain
1487 types of knotted RNA secondary structure.
1490 <!-- JAL-3095 -->Sequence highlight and selection in
1491 trimmed VARNA 2D structure is incorrect for sequences that
1495 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1496 annotation when columns are inserted into an alignment,
1497 and when exporting as Stockholm flatfile.
1500 <!-- JAL-3053 -->Jalview annotation rows containing upper
1501 and lower-case 'E' and 'H' do not automatically get
1502 treated as RNA secondary structure.
1505 <!-- JAL-3106 -->.jvp should be used as default extension
1506 (not .jar) when saving a Jalview project file.
1509 <!-- JAL-3105 -->Mac Users: closing a window correctly
1510 transfers focus to previous window on OSX
1513 <em>Java 10 Issues Resolved</em>
1516 <!-- JAL-2988 -->OSX - Can't save new files via the File
1517 or export menus by typing in a name into the Save dialog
1521 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1522 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1523 'look and feel' which has improved compatibility with the
1524 latest version of OSX.
1530 <td width="60" nowrap>
1531 <div align="center">
1532 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1533 <em>7/06/2018</em></strong>
1536 <td><div align="left">
1540 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1541 annotation retrieved from Uniprot
1544 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1545 onto the Jalview Desktop
1549 <td><div align="left">
1553 <!-- JAL-3017 -->Cannot import features with multiple
1554 variant elements (blocks import of some Uniprot records)
1557 <!-- JAL-2997 -->Clustal files with sequence positions in
1558 right-hand column parsed correctly
1561 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1562 not alignment area in exported graphic
1565 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1566 window has input focus
1569 <!-- JAL-2992 -->Annotation panel set too high when
1570 annotation added to view (Windows)
1573 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1574 network connectivity is poor
1577 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1578 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1579 the currently open URL and links from a page viewed in
1580 Firefox or Chrome on Windows is now fully supported. If
1581 you are using Edge, only links in the page can be
1582 dragged, and with Internet Explorer, only the currently
1583 open URL in the browser can be dropped onto Jalview.</em>
1586 <em>New Known Defects</em>
1589 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1596 <td width="60" nowrap>
1597 <div align="center">
1598 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1601 <td><div align="left">
1605 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1606 for disabling automatic superposition of multiple
1607 structures and open structures in existing views
1610 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1611 ID and annotation area margins can be click-dragged to
1615 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1619 <!-- JAL-2759 -->Improved performance for large alignments
1620 and lots of hidden columns
1623 <!-- JAL-2593 -->Improved performance when rendering lots
1624 of features (particularly when transparency is disabled)
1627 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1628 for exchange of Jalview features and Chimera attributes
1629 made generally available
1633 <td><div align="left">
1636 <!-- JAL-2899 -->Structure and Overview aren't updated
1637 when Colour By Annotation threshold slider is adjusted
1640 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1641 overlapping alignment panel
1644 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1648 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1649 improved: CDS not handled correctly if transcript has no
1653 <!-- JAL-2321 -->Secondary structure and temperature
1654 factor annotation not added to sequence when local PDB
1655 file associated with it by drag'n'drop or structure
1659 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1660 dialog doesn't import PDB files dropped on an alignment
1663 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1664 scroll bar doesn't work for some CDS/Protein views
1667 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1668 Java 1.8u153 onwards and Java 1.9u4+.
1671 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1672 columns in annotation row
1675 <!-- JAL-2913 -->Preferences panel's ID Width control is
1676 not honored in batch mode
1679 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1680 for structures added to existing Jmol view
1683 <!-- JAL-2223 -->'View Mappings' includes duplicate
1684 entries after importing project with multiple views
1687 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1688 protein sequences via SIFTS from associated PDB entries
1689 with negative residue numbers or missing residues fails
1692 <!-- JAL-2952 -->Exception when shading sequence with
1693 negative Temperature Factor values from annotated PDB
1694 files (e.g. as generated by CONSURF)
1697 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1698 tooltip doesn't include a text description of mutation
1701 <!-- JAL-2922 -->Invert displayed features very slow when
1702 structure and/or overview windows are also shown
1705 <!-- JAL-2954 -->Selecting columns from highlighted
1706 regions very slow for alignments with large numbers of
1710 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1711 with 'StringIndexOutOfBounds'
1714 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1715 Feel for OSX platforms running Java 10
1718 <!-- JAL-2960 -->Adding a structure to existing structure
1719 view appears to do nothing because the view is hidden
1720 behind the alignment view
1726 <!-- JAL-2926 -->Copy consensus sequence option in applet
1727 should copy the group consensus when popup is opened on it
1733 <!-- JAL-2913 -->Fixed ID width preference is not
1737 <em>New Known Defects</em>
1740 <!-- JAL-2973 --> Exceptions occasionally raised when
1741 editing a large alignment and overview is displayed
1744 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1745 repeatedly after a series of edits even when the overview
1746 is no longer reflecting updates
1749 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1750 structures for protein subsequence (if 'Trim Retrieved
1751 Sequences' enabled) or Ensembl isoforms (Workaround in
1752 2.10.4 is to fail back to N&W mapping)
1755 <!-- JAL-2990 -->Export Annotations from File Menu with
1756 CSV option gives blank output
1762 <td width="60" nowrap>
1763 <div align="center">
1764 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1765 <em>24/1/2018</em></strong>
1768 <td><div align="left">
1770 <li>Updated Certum Codesigning Certificate (Valid till
1771 30th November 2018)</li>
1774 <td><div align="left">
1779 <!-- JAL-2859-->Only one structure is loaded when
1780 several sequences and structures are selected for
1784 <!-- JAL-2851-->Alignment doesn't appear to scroll
1785 vertically via trackpad and scrollwheel
1788 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1789 in cursor mode when cursor lies in hidden region at
1793 <!-- JAL-2827-->Helix annotation has 'notches' when
1794 scrolled into view if columns are hidden
1797 <!-- JAL-2740-->Annotation column filter can be slow to
1798 reset (ie after hitting cancel) for large numbers of
1802 <!-- JAL-2849-->User preference for disabling inclusion
1803 of sequence limits when exporting as flat file has no
1807 <!-- JAL-2679-->Reproducible cross-reference
1808 relationships when retrieving sequences from
1815 <td width="60" nowrap>
1816 <div align="center">
1817 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1820 <td><div align="left">
1824 <!-- JAL-2446 -->Faster and more efficient management and
1825 rendering of sequence features
1828 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1829 429 rate limit request hander
1832 <!-- JAL-2773 -->Structure views don't get updated unless
1833 their colours have changed
1836 <!-- JAL-2495 -->All linked sequences are highlighted for
1837 a structure mousover (Jmol) or selection (Chimera)
1840 <!-- JAL-2790 -->'Cancel' button in progress bar for
1841 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1844 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1845 view from Ensembl locus cross-references
1848 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1852 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1853 feature can be disabled
1856 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1857 PDB easier retrieval of sequences for lists of IDs
1860 <!-- JAL-2758 -->Short names for sequences retrieved from
1866 <li>Groovy interpreter updated to 2.4.12</li>
1867 <li>Example groovy script for generating a matrix of
1868 percent identity scores for current alignment.</li>
1870 <em>Testing and Deployment</em>
1873 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1877 <td><div align="left">
1881 <!-- JAL-2643 -->Pressing tab after updating the colour
1882 threshold text field doesn't trigger an update to the
1886 <!-- JAL-2682 -->Race condition when parsing sequence ID
1890 <!-- JAL-2608 -->Overview windows are also closed when
1891 alignment window is closed
1894 <!-- JAL-2548 -->Export of features doesn't always respect
1898 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1899 takes a long time in Cursor mode
1905 <!-- JAL-2777 -->Structures with whitespace chainCode
1906 cannot be viewed in Chimera
1909 <!-- JAL-2728 -->Protein annotation panel too high in
1913 <!-- JAL-2757 -->Can't edit the query after the server
1914 error warning icon is shown in Uniprot and PDB Free Text
1918 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1921 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1924 <!-- JAL-2739 -->Hidden column marker in last column not
1925 rendered when switching back from Wrapped to normal view
1928 <!-- JAL-2768 -->Annotation display corrupted when
1929 scrolling right in unwapped alignment view
1932 <!-- JAL-2542 -->Existing features on subsequence
1933 incorrectly relocated when full sequence retrieved from
1937 <!-- JAL-2733 -->Last reported memory still shown when
1938 Desktop->Show Memory is unticked (OSX only)
1941 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1942 features of same type and group to be selected for
1946 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1947 alignments when hidden columns are present
1950 <!-- JAL-2392 -->Jalview freezes when loading and
1951 displaying several structures
1954 <!-- JAL-2732 -->Black outlines left after resizing or
1958 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1959 within the Jalview desktop on OSX
1962 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1963 when in wrapped alignment mode
1966 <!-- JAL-2636 -->Scale mark not shown when close to right
1967 hand end of alignment
1970 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1971 each selected sequence do not have correct start/end
1975 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1976 after canceling the Alignment Window's Font dialog
1979 <!-- JAL-2036 -->Show cross-references not enabled after
1980 restoring project until a new view is created
1983 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1984 URL links appears when only default EMBL-EBI link is
1985 configured (since 2.10.2b2)
1988 <!-- JAL-2775 -->Overview redraws whole window when box
1989 position is adjusted
1992 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1993 in a multi-chain structure when viewing alignment
1994 involving more than one chain (since 2.10)
1997 <!-- JAL-2811 -->Double residue highlights in cursor mode
1998 if new selection moves alignment window
2001 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2002 arrow key in cursor mode to pass hidden column marker
2005 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2006 that produces correctly annotated transcripts and products
2009 <!-- JAL-2776 -->Toggling a feature group after first time
2010 doesn't update associated structure view
2013 <em>Applet</em><br />
2016 <!-- JAL-2687 -->Concurrent modification exception when
2017 closing alignment panel
2020 <em>BioJSON</em><br />
2023 <!-- JAL-2546 -->BioJSON export does not preserve
2024 non-positional features
2027 <em>New Known Issues</em>
2030 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2031 sequence features correctly (for many previous versions of
2035 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2036 using cursor in wrapped panel other than top
2039 <!-- JAL-2791 -->Select columns containing feature ignores
2040 graduated colour threshold
2043 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2044 always preserve numbering and sequence features
2047 <em>Known Java 9 Issues</em>
2050 <!-- JAL-2902 -->Groovy Console very slow to open and is
2051 not responsive when entering characters (Webstart, Java
2058 <td width="60" nowrap>
2059 <div align="center">
2060 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2061 <em>2/10/2017</em></strong>
2064 <td><div align="left">
2065 <em>New features in Jalview Desktop</em>
2068 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2072 <!-- JAL-2745 -->HTTPS used for all connections to
2077 <td><div align="left"></div></td>
2080 <td width="60" nowrap>
2081 <div align="center">
2082 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2083 <em>7/9/2017</em></strong>
2086 <td><div align="left">
2090 <!-- JAL-2588 -->Show gaps in overview window by colouring
2091 in grey (sequences used to be coloured grey, and gaps were
2095 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2099 <!-- JAL-2587 -->Overview updates immediately on increase
2100 in size and progress bar shown as higher resolution
2101 overview is recalculated
2106 <td><div align="left">
2110 <!-- JAL-2664 -->Overview window redraws every hidden
2111 column region row by row
2114 <!-- JAL-2681 -->duplicate protein sequences shown after
2115 retrieving Ensembl crossrefs for sequences from Uniprot
2118 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2119 format setting is unticked
2122 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2123 if group has show boxes format setting unticked
2126 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2127 autoscrolling whilst dragging current selection group to
2128 include sequences and columns not currently displayed
2131 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2132 assemblies are imported via CIF file
2135 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2136 displayed when threshold or conservation colouring is also
2140 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2144 <!-- JAL-2673 -->Jalview continues to scroll after
2145 dragging a selected region off the visible region of the
2149 <!-- JAL-2724 -->Cannot apply annotation based
2150 colourscheme to all groups in a view
2153 <!-- JAL-2511 -->IDs don't line up with sequences
2154 initially after font size change using the Font chooser or
2161 <td width="60" nowrap>
2162 <div align="center">
2163 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2166 <td><div align="left">
2167 <em>Calculations</em>
2171 <!-- JAL-1933 -->Occupancy annotation row shows number of
2172 ungapped positions in each column of the alignment.
2175 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2176 a calculation dialog box
2179 <!-- JAL-2379 -->Revised implementation of PCA for speed
2180 and memory efficiency (~30x faster)
2183 <!-- JAL-2403 -->Revised implementation of sequence
2184 similarity scores as used by Tree, PCA, Shading Consensus
2185 and other calculations
2188 <!-- JAL-2416 -->Score matrices are stored as resource
2189 files within the Jalview codebase
2192 <!-- JAL-2500 -->Trees computed on Sequence Feature
2193 Similarity may have different topology due to increased
2200 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2201 model for alignments and groups
2204 <!-- JAL-384 -->Custom shading schemes created via groovy
2211 <!-- JAL-2526 -->Efficiency improvements for interacting
2212 with alignment and overview windows
2215 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2219 <!-- JAL-2388 -->Hidden columns and sequences can be
2223 <!-- JAL-2611 -->Click-drag in visible area allows fine
2224 adjustment of visible position
2228 <em>Data import/export</em>
2231 <!-- JAL-2535 -->Posterior probability annotation from
2232 Stockholm files imported as sequence associated annotation
2235 <!-- JAL-2507 -->More robust per-sequence positional
2236 annotation input/output via stockholm flatfile
2239 <!-- JAL-2533 -->Sequence names don't include file
2240 extension when importing structure files without embedded
2241 names or PDB accessions
2244 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2245 format sequence substitution matrices
2248 <em>User Interface</em>
2251 <!-- JAL-2447 --> Experimental Features Checkbox in
2252 Desktop's Tools menu to hide or show untested features in
2256 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2257 via Overview or sequence motif search operations
2260 <!-- JAL-2547 -->Amend sequence features dialog box can be
2261 opened by double clicking gaps within sequence feature
2265 <!-- JAL-1476 -->Status bar message shown when not enough
2266 aligned positions were available to create a 3D structure
2270 <em>3D Structure</em>
2273 <!-- JAL-2430 -->Hidden regions in alignment views are not
2274 coloured in linked structure views
2277 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2278 file-based command exchange
2281 <!-- JAL-2375 -->Structure chooser automatically shows
2282 Cached Structures rather than querying the PDBe if
2283 structures are already available for sequences
2286 <!-- JAL-2520 -->Structures imported via URL are cached in
2287 the Jalview project rather than downloaded again when the
2288 project is reopened.
2291 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2292 to transfer Chimera's structure attributes as Jalview
2293 features, and vice-versa (<strong>Experimental
2297 <em>Web Services</em>
2300 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2303 <!-- JAL-2335 -->Filter non-standard amino acids and
2304 nucleotides when submitting to AACon and other MSA
2308 <!-- JAL-2316, -->URLs for viewing database
2309 cross-references provided by identifiers.org and the
2310 EMBL-EBI's MIRIAM DB
2317 <!-- JAL-2344 -->FileFormatI interface for describing and
2318 identifying file formats (instead of String constants)
2321 <!-- JAL-2228 -->FeatureCounter script refactored for
2322 efficiency when counting all displayed features (not
2323 backwards compatible with 2.10.1)
2326 <em>Example files</em>
2329 <!-- JAL-2631 -->Graduated feature colour style example
2330 included in the example feature file
2333 <em>Documentation</em>
2336 <!-- JAL-2339 -->Release notes reformatted for readability
2337 with the built-in Java help viewer
2340 <!-- JAL-1644 -->Find documentation updated with 'search
2341 sequence description' option
2347 <!-- JAL-2485, -->External service integration tests for
2348 Uniprot REST Free Text Search Client
2351 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2354 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2359 <td><div align="left">
2360 <em>Calculations</em>
2363 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2364 matrix - C->R should be '-3'<br />Old matrix restored
2365 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2367 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2368 Jalview's treatment of gaps in PCA and substitution matrix
2369 based Tree calculations.<br /> <br />In earlier versions
2370 of Jalview, gaps matching gaps were penalised, and gaps
2371 matching non-gaps penalised even more. In the PCA
2372 calculation, gaps were actually treated as non-gaps - so
2373 different costs were applied, which meant Jalview's PCAs
2374 were different to those produced by SeqSpace.<br />Jalview
2375 now treats gaps in the same way as SeqSpace (ie it scores
2376 them as 0). <br /> <br />Enter the following in the
2377 Groovy console to restore pre-2.10.2 behaviour:<br />
2378 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2379 // for 2.10.1 mode <br />
2380 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2381 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2382 these settings will affect all subsequent tree and PCA
2383 calculations (not recommended)</em></li>
2385 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2386 scaling of branch lengths for trees computed using
2387 Sequence Feature Similarity.
2390 <!-- JAL-2377 -->PCA calculation could hang when
2391 generating output report when working with highly
2392 redundant alignments
2395 <!-- JAL-2544 --> Sort by features includes features to
2396 right of selected region when gaps present on right-hand
2400 <em>User Interface</em>
2403 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2404 doesn't reselect a specific sequence's associated
2405 annotation after it was used for colouring a view
2408 <!-- JAL-2419 -->Current selection lost if popup menu
2409 opened on a region of alignment without groups
2412 <!-- JAL-2374 -->Popup menu not always shown for regions
2413 of an alignment with overlapping groups
2416 <!-- JAL-2310 -->Finder double counts if both a sequence's
2417 name and description match
2420 <!-- JAL-2370 -->Hiding column selection containing two
2421 hidden regions results in incorrect hidden regions
2424 <!-- JAL-2386 -->'Apply to all groups' setting when
2425 changing colour does not apply Conservation slider value
2429 <!-- JAL-2373 -->Percentage identity and conservation menu
2430 items do not show a tick or allow shading to be disabled
2433 <!-- JAL-2385 -->Conservation shading or PID threshold
2434 lost when base colourscheme changed if slider not visible
2437 <!-- JAL-2547 -->Sequence features shown in tooltip for
2438 gaps before start of features
2441 <!-- JAL-2623 -->Graduated feature colour threshold not
2442 restored to UI when feature colour is edited
2445 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2446 a time when scrolling vertically in wrapped mode.
2449 <!-- JAL-2630 -->Structure and alignment overview update
2450 as graduate feature colour settings are modified via the
2454 <!-- JAL-2034 -->Overview window doesn't always update
2455 when a group defined on the alignment is resized
2458 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2459 wrapped view result in positional status updates
2463 <!-- JAL-2563 -->Status bar doesn't show position for
2464 ambiguous amino acid and nucleotide symbols
2467 <!-- JAL-2602 -->Copy consensus sequence failed if
2468 alignment included gapped columns
2471 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2472 widgets don't permanently disappear
2475 <!-- JAL-2503 -->Cannot select or filter quantitative
2476 annotation that are shown only as column labels (e.g.
2477 T-Coffee column reliability scores)
2480 <!-- JAL-2594 -->Exception thrown if trying to create a
2481 sequence feature on gaps only
2484 <!-- JAL-2504 -->Features created with 'New feature'
2485 button from a Find inherit previously defined feature type
2486 rather than the Find query string
2489 <!-- JAL-2423 -->incorrect title in output window when
2490 exporting tree calculated in Jalview
2493 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2494 and then revealing them reorders sequences on the
2498 <!-- JAL-964 -->Group panel in sequence feature settings
2499 doesn't update to reflect available set of groups after
2500 interactively adding or modifying features
2503 <!-- JAL-2225 -->Sequence Database chooser unusable on
2507 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2508 only excluded gaps in current sequence and ignored
2515 <!-- JAL-2421 -->Overview window visible region moves
2516 erratically when hidden rows or columns are present
2519 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2520 Structure Viewer's colour menu don't correspond to
2524 <!-- JAL-2405 -->Protein specific colours only offered in
2525 colour and group colour menu for protein alignments
2528 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2529 reflect currently selected view or group's shading
2533 <!-- JAL-2624 -->Feature colour thresholds not respected
2534 when rendered on overview and structures when opacity at
2538 <!-- JAL-2589 -->User defined gap colour not shown in
2539 overview when features overlaid on alignment
2542 <!-- JAL-2567 -->Feature settings for different views not
2543 recovered correctly from Jalview project file
2546 <!-- JAL-2256 -->Feature colours in overview when first
2547 opened (automatically via preferences) are different to
2548 the main alignment panel
2551 <em>Data import/export</em>
2554 <!-- JAL-2576 -->Very large alignments take a long time to
2558 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2559 added after a sequence was imported are not written to
2563 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2564 when importing RNA secondary structure via Stockholm
2567 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2568 not shown in correct direction for simple pseudoknots
2571 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2572 with lightGray or darkGray via features file (but can
2576 <!-- JAL-2383 -->Above PID colour threshold not recovered
2577 when alignment view imported from project
2580 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2581 structure and sequences extracted from structure files
2582 imported via URL and viewed in Jmol
2585 <!-- JAL-2520 -->Structures loaded via URL are saved in
2586 Jalview Projects rather than fetched via URL again when
2587 the project is loaded and the structure viewed
2590 <em>Web Services</em>
2593 <!-- JAL-2519 -->EnsemblGenomes example failing after
2594 release of Ensembl v.88
2597 <!-- JAL-2366 -->Proxy server address and port always
2598 appear enabled in Preferences->Connections
2601 <!-- JAL-2461 -->DAS registry not found exceptions
2602 removed from console output
2605 <!-- JAL-2582 -->Cannot retrieve protein products from
2606 Ensembl by Peptide ID
2609 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2610 created from SIFTs, and spurious 'Couldn't open structure
2611 in Chimera' errors raised after April 2017 update (problem
2612 due to 'null' string rather than empty string used for
2613 residues with no corresponding PDB mapping).
2616 <em>Application UI</em>
2619 <!-- JAL-2361 -->User Defined Colours not added to Colour
2623 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2624 case' residues (button in colourscheme editor debugged and
2625 new documentation and tooltips added)
2628 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2629 doesn't restore group-specific text colour thresholds
2632 <!-- JAL-2243 -->Feature settings panel does not update as
2633 new features are added to alignment
2636 <!-- JAL-2532 -->Cancel in feature settings reverts
2637 changes to feature colours via the Amend features dialog
2640 <!-- JAL-2506 -->Null pointer exception when attempting to
2641 edit graduated feature colour via amend features dialog
2645 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2646 selection menu changes colours of alignment views
2649 <!-- JAL-2426 -->Spurious exceptions in console raised
2650 from alignment calculation workers after alignment has
2654 <!-- JAL-1608 -->Typo in selection popup menu - Create
2655 groups now 'Create Group'
2658 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2659 Create/Undefine group doesn't always work
2662 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2663 shown again after pressing 'Cancel'
2666 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2667 adjusts start position in wrap mode
2670 <!-- JAL-2563 -->Status bar doesn't show positions for
2671 ambiguous amino acids
2674 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2675 CDS/Protein view after CDS sequences added for aligned
2679 <!-- JAL-2592 -->User defined colourschemes called 'User
2680 Defined' don't appear in Colours menu
2686 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2687 score models doesn't always result in an updated PCA plot
2690 <!-- JAL-2442 -->Features not rendered as transparent on
2691 overview or linked structure view
2694 <!-- JAL-2372 -->Colour group by conservation doesn't
2698 <!-- JAL-2517 -->Hitting Cancel after applying
2699 user-defined colourscheme doesn't restore original
2706 <!-- JAL-2314 -->Unit test failure:
2707 jalview.ws.jabaws.RNAStructExportImport setup fails
2710 <!-- JAL-2307 -->Unit test failure:
2711 jalview.ws.sifts.SiftsClientTest due to compatibility
2712 problems with deep array comparison equality asserts in
2713 successive versions of TestNG
2716 <!-- JAL-2479 -->Relocated StructureChooserTest and
2717 ParameterUtilsTest Unit tests to Network suite
2720 <em>New Known Issues</em>
2723 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2724 phase after a sequence motif find operation
2727 <!-- JAL-2550 -->Importing annotation file with rows
2728 containing just upper and lower case letters are
2729 interpreted as WUSS RNA secondary structure symbols
2732 <!-- JAL-2590 -->Cannot load and display Newick trees
2733 reliably from eggnog Ortholog database
2736 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2737 containing features of type Highlight' when 'B' is pressed
2738 to mark columns containing highlighted regions.
2741 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2742 doesn't always add secondary structure annotation.
2747 <td width="60" nowrap>
2748 <div align="center">
2749 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2752 <td><div align="left">
2756 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2757 for all consensus calculations
2760 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2763 <li>Updated Jalview's Certum code signing certificate
2766 <em>Application</em>
2769 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2770 set of database cross-references, sorted alphabetically
2773 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2774 from database cross references. Users with custom links
2775 will receive a <a href="webServices/urllinks.html#warning">warning
2776 dialog</a> asking them to update their preferences.
2779 <!-- JAL-2287-->Cancel button and escape listener on
2780 dialog warning user about disconnecting Jalview from a
2784 <!-- JAL-2320-->Jalview's Chimera control window closes if
2785 the Chimera it is connected to is shut down
2788 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2789 columns menu item to mark columns containing highlighted
2790 regions (e.g. from structure selections or results of a
2794 <!-- JAL-2284-->Command line option for batch-generation
2795 of HTML pages rendering alignment data with the BioJS
2805 <!-- JAL-2286 -->Columns with more than one modal residue
2806 are not coloured or thresholded according to percent
2807 identity (first observed in Jalview 2.8.2)
2810 <!-- JAL-2301 -->Threonine incorrectly reported as not
2814 <!-- JAL-2318 -->Updates to documentation pages (above PID
2815 threshold, amino acid properties)
2818 <!-- JAL-2292 -->Lower case residues in sequences are not
2819 reported as mapped to residues in a structure file in the
2823 <!--JAL-2324 -->Identical features with non-numeric scores
2824 could be added multiple times to a sequence
2827 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2828 bond features shown as two highlighted residues rather
2829 than a range in linked structure views, and treated
2830 correctly when selecting and computing trees from features
2833 <!-- JAL-2281-->Custom URL links for database
2834 cross-references are matched to database name regardless
2839 <em>Application</em>
2842 <!-- JAL-2282-->Custom URL links for specific database
2843 names without regular expressions also offer links from
2847 <!-- JAL-2315-->Removing a single configured link in the
2848 URL links pane in Connections preferences doesn't actually
2849 update Jalview configuration
2852 <!-- JAL-2272-->CTRL-Click on a selected region to open
2853 the alignment area popup menu doesn't work on El-Capitan
2856 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2857 files with similarly named sequences if dropped onto the
2861 <!-- JAL-2312 -->Additional mappings are shown for PDB
2862 entries where more chains exist in the PDB accession than
2863 are reported in the SIFTS file
2866 <!-- JAL-2317-->Certain structures do not get mapped to
2867 the structure view when displayed with Chimera
2870 <!-- JAL-2317-->No chains shown in the Chimera view
2871 panel's View->Show Chains submenu
2874 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2875 work for wrapped alignment views
2878 <!--JAL-2197 -->Rename UI components for running JPred
2879 predictions from 'JNet' to 'JPred'
2882 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2883 corrupted when annotation panel vertical scroll is not at
2884 first annotation row
2887 <!--JAL-2332 -->Attempting to view structure for Hen
2888 lysozyme results in a PDB Client error dialog box
2891 <!-- JAL-2319 -->Structure View's mapping report switched
2892 ranges for PDB and sequence for SIFTS
2895 SIFTS 'Not_Observed' residues mapped to non-existant
2899 <!-- <em>New Known Issues</em>
2906 <td width="60" nowrap>
2907 <div align="center">
2908 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2909 <em>25/10/2016</em></strong>
2912 <td><em>Application</em>
2914 <li>3D Structure chooser opens with 'Cached structures'
2915 view if structures already loaded</li>
2916 <li>Progress bar reports models as they are loaded to
2917 structure views</li>
2923 <li>Colour by conservation always enabled and no tick
2924 shown in menu when BLOSUM or PID shading applied</li>
2925 <li>FER1_ARATH and FER2_ARATH labels were switched in
2926 example sequences/projects/trees</li>
2928 <em>Application</em>
2930 <li>Jalview projects with views of local PDB structure
2931 files saved on Windows cannot be opened on OSX</li>
2932 <li>Multiple structure views can be opened and superposed
2933 without timeout for structures with multiple models or
2934 multiple sequences in alignment</li>
2935 <li>Cannot import or associated local PDB files without a
2936 PDB ID HEADER line</li>
2937 <li>RMSD is not output in Jmol console when superposition
2939 <li>Drag and drop of URL from Browser fails for Linux and
2940 OSX versions earlier than El Capitan</li>
2941 <li>ENA client ignores invalid content from ENA server</li>
2942 <li>Exceptions are not raised in console when ENA client
2943 attempts to fetch non-existent IDs via Fetch DB Refs UI
2945 <li>Exceptions are not raised in console when a new view
2946 is created on the alignment</li>
2947 <li>OSX right-click fixed for group selections: CMD-click
2948 to insert/remove gaps in groups and CTRL-click to open group
2951 <em>Build and deployment</em>
2953 <li>URL link checker now copes with multi-line anchor
2956 <em>New Known Issues</em>
2958 <li>Drag and drop from URL links in browsers do not work
2965 <td width="60" nowrap>
2966 <div align="center">
2967 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2970 <td><em>General</em>
2973 <!-- JAL-2124 -->Updated Spanish translations.
2976 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2977 for importing structure data to Jalview. Enables mmCIF and
2981 <!-- JAL-192 --->Alignment ruler shows positions relative to
2985 <!-- JAL-2202 -->Position/residue shown in status bar when
2986 mousing over sequence associated annotation
2989 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2993 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2994 '()', canonical '[]' and invalid '{}' base pair populations
2998 <!-- JAL-2092 -->Feature settings popup menu options for
2999 showing or hiding columns containing a feature
3002 <!-- JAL-1557 -->Edit selected group by double clicking on
3003 group and sequence associated annotation labels
3006 <!-- JAL-2236 -->Sequence name added to annotation label in
3007 select/hide columns by annotation and colour by annotation
3011 </ul> <em>Application</em>
3014 <!-- JAL-2050-->Automatically hide introns when opening a
3015 gene/transcript view
3018 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3022 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3023 structure mappings with the EMBL-EBI PDBe SIFTS database
3026 <!-- JAL-2079 -->Updated download sites used for Rfam and
3027 Pfam sources to xfam.org
3030 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3033 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3034 over sequences in Jalview
3037 <!-- JAL-2027-->Support for reverse-complement coding
3038 regions in ENA and EMBL
3041 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3042 for record retrieval via ENA rest API
3045 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3049 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3050 groovy script execution
3053 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3054 alignment window's Calculate menu
3057 <!-- JAL-1812 -->Allow groovy scripts that call
3058 Jalview.getAlignFrames() to run in headless mode
3061 <!-- JAL-2068 -->Support for creating new alignment
3062 calculation workers from groovy scripts
3065 <!-- JAL-1369 --->Store/restore reference sequence in
3069 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3070 associations are now saved/restored from project
3073 <!-- JAL-1993 -->Database selection dialog always shown
3074 before sequence fetcher is opened
3077 <!-- JAL-2183 -->Double click on an entry in Jalview's
3078 database chooser opens a sequence fetcher
3081 <!-- JAL-1563 -->Free-text search client for UniProt using
3082 the UniProt REST API
3085 <!-- JAL-2168 -->-nonews command line parameter to prevent
3086 the news reader opening
3089 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3090 querying stored in preferences
3093 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3097 <!-- JAL-1977-->Tooltips shown on database chooser
3100 <!-- JAL-391 -->Reverse complement function in calculate
3101 menu for nucleotide sequences
3104 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3105 and feature counts preserves alignment ordering (and
3106 debugged for complex feature sets).
3109 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3110 viewing structures with Jalview 2.10
3113 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3114 genome, transcript CCDS and gene ids via the Ensembl and
3115 Ensembl Genomes REST API
3118 <!-- JAL-2049 -->Protein sequence variant annotation
3119 computed for 'sequence_variant' annotation on CDS regions
3123 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3127 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3128 Ref Fetcher fails to match, or otherwise updates sequence
3129 data from external database records.
3132 <!-- JAL-2154 -->Revised Jalview Project format for
3133 efficient recovery of sequence coding and alignment
3134 annotation relationships.
3136 </ul> <!-- <em>Applet</em>
3147 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3151 <!-- JAL-2018-->Export features in Jalview format (again)
3152 includes graduated colourschemes
3155 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3156 working with big alignments and lots of hidden columns
3159 <!-- JAL-2053-->Hidden column markers not always rendered
3160 at right of alignment window
3163 <!-- JAL-2067 -->Tidied up links in help file table of
3167 <!-- JAL-2072 -->Feature based tree calculation not shown
3171 <!-- JAL-2075 -->Hidden columns ignored during feature
3172 based tree calculation
3175 <!-- JAL-2065 -->Alignment view stops updating when show
3176 unconserved enabled for group on alignment
3179 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3183 <!-- JAL-2146 -->Alignment column in status incorrectly
3184 shown as "Sequence position" when mousing over
3188 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3189 hidden columns present
3192 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3193 user created annotation added to alignment
3196 <!-- JAL-1841 -->RNA Structure consensus only computed for
3197 '()' base pair annotation
3200 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3201 in zero scores for all base pairs in RNA Structure
3205 <!-- JAL-2174-->Extend selection with columns containing
3209 <!-- JAL-2275 -->Pfam format writer puts extra space at
3210 beginning of sequence
3213 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3217 <!-- JAL-2238 -->Cannot create groups on an alignment from
3218 from a tree when t-coffee scores are shown
3221 <!-- JAL-1836,1967 -->Cannot import and view PDB
3222 structures with chains containing negative resnums (4q4h)
3225 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3229 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3230 to Clustal, PIR and PileUp output
3233 <!-- JAL-2008 -->Reordering sequence features that are
3234 not visible causes alignment window to repaint
3237 <!-- JAL-2006 -->Threshold sliders don't work in
3238 graduated colour and colour by annotation row for e-value
3239 scores associated with features and annotation rows
3242 <!-- JAL-1797 -->amino acid physicochemical conservation
3243 calculation should be case independent
3246 <!-- JAL-2173 -->Remove annotation also updates hidden
3250 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3251 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3252 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3255 <!-- JAL-2065 -->Null pointer exceptions and redraw
3256 problems when reference sequence defined and 'show
3257 non-conserved' enabled
3260 <!-- JAL-1306 -->Quality and Conservation are now shown on
3261 load even when Consensus calculation is disabled
3264 <!-- JAL-1932 -->Remove right on penultimate column of
3265 alignment does nothing
3268 <em>Application</em>
3271 <!-- JAL-1552-->URLs and links can't be imported by
3272 drag'n'drop on OSX when launched via webstart (note - not
3273 yet fixed for El Capitan)
3276 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3277 output when running on non-gb/us i18n platforms
3280 <!-- JAL-1944 -->Error thrown when exporting a view with
3281 hidden sequences as flat-file alignment
3284 <!-- JAL-2030-->InstallAnywhere distribution fails when
3288 <!-- JAL-2080-->Jalview very slow to launch via webstart
3289 (also hotfix for 2.9.0b2)
3292 <!-- JAL-2085 -->Cannot save project when view has a
3293 reference sequence defined
3296 <!-- JAL-1011 -->Columns are suddenly selected in other
3297 alignments and views when revealing hidden columns
3300 <!-- JAL-1989 -->Hide columns not mirrored in complement
3301 view in a cDNA/Protein splitframe
3304 <!-- JAL-1369 -->Cannot save/restore representative
3305 sequence from project when only one sequence is
3309 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3310 in Structure Chooser
3313 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3314 structure consensus didn't refresh annotation panel
3317 <!-- JAL-1962 -->View mapping in structure view shows
3318 mappings between sequence and all chains in a PDB file
3321 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3322 dialogs format columns correctly, don't display array
3323 data, sort columns according to type
3326 <!-- JAL-1975 -->Export complete shown after destination
3327 file chooser is cancelled during an image export
3330 <!-- JAL-2025 -->Error when querying PDB Service with
3331 sequence name containing special characters
3334 <!-- JAL-2024 -->Manual PDB structure querying should be
3338 <!-- JAL-2104 -->Large tooltips with broken HTML
3339 formatting don't wrap
3342 <!-- JAL-1128 -->Figures exported from wrapped view are
3343 truncated so L looks like I in consensus annotation
3346 <!-- JAL-2003 -->Export features should only export the
3347 currently displayed features for the current selection or
3351 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3352 after fetching cross-references, and restoring from
3356 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3357 followed in the structure viewer
3360 <!-- JAL-2163 -->Titles for individual alignments in
3361 splitframe not restored from project
3364 <!-- JAL-2145 -->missing autocalculated annotation at
3365 trailing end of protein alignment in transcript/product
3366 splitview when pad-gaps not enabled by default
3369 <!-- JAL-1797 -->amino acid physicochemical conservation
3373 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3374 article has been read (reopened issue due to
3375 internationalisation problems)
3378 <!-- JAL-1960 -->Only offer PDB structures in structure
3379 viewer based on sequence name, PDB and UniProt
3384 <!-- JAL-1976 -->No progress bar shown during export of
3388 <!-- JAL-2213 -->Structures not always superimposed after
3389 multiple structures are shown for one or more sequences.
3392 <!-- JAL-1370 -->Reference sequence characters should not
3393 be replaced with '.' when 'Show unconserved' format option
3397 <!-- JAL-1823 -->Cannot specify chain code when entering
3398 specific PDB id for sequence
3401 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3402 'Export hidden sequences' is enabled, but 'export hidden
3403 columns' is disabled.
3406 <!--JAL-2026-->Best Quality option in structure chooser
3407 selects lowest rather than highest resolution structures
3411 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3412 to sequence mapping in 'View Mappings' report
3415 <!-- JAL-2284 -->Unable to read old Jalview projects that
3416 contain non-XML data added after Jalvew wrote project.
3419 <!-- JAL-2118 -->Newly created annotation row reorders
3420 after clicking on it to create new annotation for a
3424 <!-- JAL-1980 -->Null Pointer Exception raised when
3425 pressing Add on an orphaned cut'n'paste window.
3427 <!-- may exclude, this is an external service stability issue JAL-1941
3428 -- > RNA 3D structure not added via DSSR service</li> -->
3433 <!-- JAL-2151 -->Incorrect columns are selected when
3434 hidden columns present before start of sequence
3437 <!-- JAL-1986 -->Missing dependencies on applet pages
3441 <!-- JAL-1947 -->Overview pixel size changes when
3442 sequences are hidden in applet
3445 <!-- JAL-1996 -->Updated instructions for applet
3446 deployment on examples pages.
3453 <td width="60" nowrap>
3454 <div align="center">
3455 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3456 <em>16/10/2015</em></strong>
3459 <td><em>General</em>
3461 <li>Time stamps for signed Jalview application and applet
3466 <em>Application</em>
3468 <li>Duplicate group consensus and conservation rows
3469 shown when tree is partitioned</li>
3470 <li>Erratic behaviour when tree partitions made with
3471 multiple cDNA/Protein split views</li>
3477 <td width="60" nowrap>
3478 <div align="center">
3479 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3480 <em>8/10/2015</em></strong>
3483 <td><em>General</em>
3485 <li>Updated Spanish translations of localized text for
3487 </ul> <em>Application</em>
3489 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3490 <li>Signed OSX InstallAnywhere installer<br></li>
3491 <li>Support for per-sequence based annotations in BioJSON</li>
3492 </ul> <em>Applet</em>
3494 <li>Split frame example added to applet examples page</li>
3495 </ul> <em>Build and Deployment</em>
3498 <!-- JAL-1888 -->New ant target for running Jalview's test
3506 <li>Mapping of cDNA to protein in split frames
3507 incorrect when sequence start > 1</li>
3508 <li>Broken images in filter column by annotation dialog
3510 <li>Feature colours not parsed from features file</li>
3511 <li>Exceptions and incomplete link URLs recovered when
3512 loading a features file containing HTML tags in feature
3516 <em>Application</em>
3518 <li>Annotations corrupted after BioJS export and
3520 <li>Incorrect sequence limits after Fetch DB References
3521 with 'trim retrieved sequences'</li>
3522 <li>Incorrect warning about deleting all data when
3523 deleting selected columns</li>
3524 <li>Patch to build system for shipping properly signed
3525 JNLP templates for webstart launch</li>
3526 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3527 unreleased structures for download or viewing</li>
3528 <li>Tab/space/return keystroke operation of EMBL-PDBe
3529 fetcher/viewer dialogs works correctly</li>
3530 <li>Disabled 'minimise' button on Jalview windows
3531 running on OSX to workaround redraw hang bug</li>
3532 <li>Split cDNA/Protein view position and geometry not
3533 recovered from jalview project</li>
3534 <li>Initial enabled/disabled state of annotation menu
3535 sorter 'show autocalculated first/last' corresponds to
3537 <li>Restoring of Clustal, RNA Helices and T-Coffee
3538 color schemes from BioJSON</li>
3542 <li>Reorder sequences mirrored in cDNA/Protein split
3544 <li>Applet with Jmol examples not loading correctly</li>
3550 <td><div align="center">
3551 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3553 <td><em>General</em>
3555 <li>Linked visualisation and analysis of DNA and Protein
3558 <li>Translated cDNA alignments shown as split protein
3559 and DNA alignment views</li>
3560 <li>Codon consensus annotation for linked protein and
3561 cDNA alignment views</li>
3562 <li>Link cDNA or Protein product sequences by loading
3563 them onto Protein or cDNA alignments</li>
3564 <li>Reconstruct linked cDNA alignment from aligned
3565 protein sequences</li>
3568 <li>Jmol integration updated to Jmol v14.2.14</li>
3569 <li>Import and export of Jalview alignment views as <a
3570 href="features/bioJsonFormat.html">BioJSON</a></li>
3571 <li>New alignment annotation file statements for
3572 reference sequences and marking hidden columns</li>
3573 <li>Reference sequence based alignment shading to
3574 highlight variation</li>
3575 <li>Select or hide columns according to alignment
3577 <li>Find option for locating sequences by description</li>
3578 <li>Conserved physicochemical properties shown in amino
3579 acid conservation row</li>
3580 <li>Alignments can be sorted by number of RNA helices</li>
3581 </ul> <em>Application</em>
3583 <li>New cDNA/Protein analysis capabilities
3585 <li>Get Cross-References should open a Split Frame
3586 view with cDNA/Protein</li>
3587 <li>Detect when nucleotide sequences and protein
3588 sequences are placed in the same alignment</li>
3589 <li>Split cDNA/Protein views are saved in Jalview
3594 <li>Use REST API to talk to Chimera</li>
3595 <li>Selected regions in Chimera are highlighted in linked
3596 Jalview windows</li>
3598 <li>VARNA RNA viewer updated to v3.93</li>
3599 <li>VARNA views are saved in Jalview Projects</li>
3600 <li>Pseudoknots displayed as Jalview RNA annotation can
3601 be shown in VARNA</li>
3603 <li>Make groups for selection uses marked columns as well
3604 as the active selected region</li>
3606 <li>Calculate UPGMA and NJ trees using sequence feature
3608 <li>New Export options
3610 <li>New Export Settings dialog to control hidden
3611 region export in flat file generation</li>
3613 <li>Export alignment views for display with the <a
3614 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3616 <li>Export scrollable SVG in HTML page</li>
3617 <li>Optional embedding of BioJSON data when exporting
3618 alignment figures to HTML</li>
3620 <li>3D structure retrieval and display
3622 <li>Free text and structured queries with the PDBe
3624 <li>PDBe Search API based discovery and selection of
3625 PDB structures for a sequence set</li>
3629 <li>JPred4 employed for protein secondary structure
3631 <li>Hide Insertions menu option to hide unaligned columns
3632 for one or a group of sequences</li>
3633 <li>Automatically hide insertions in alignments imported
3634 from the JPred4 web server</li>
3635 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3636 system on OSX<br />LGPL libraries courtesy of <a
3637 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3639 <li>changed 'View nucleotide structure' submenu to 'View
3640 VARNA 2D Structure'</li>
3641 <li>change "View protein structure" menu option to "3D
3644 </ul> <em>Applet</em>
3646 <li>New layout for applet example pages</li>
3647 <li>New parameters to enable SplitFrame view
3648 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3649 <li>New example demonstrating linked viewing of cDNA and
3650 Protein alignments</li>
3651 </ul> <em>Development and deployment</em>
3653 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3654 <li>Include installation type and git revision in build
3655 properties and console log output</li>
3656 <li>Jalview Github organisation, and new github site for
3657 storing BioJsMSA Templates</li>
3658 <li>Jalview's unit tests now managed with TestNG</li>
3661 <!-- <em>General</em>
3663 </ul> --> <!-- issues resolved --> <em>Application</em>
3665 <li>Escape should close any open find dialogs</li>
3666 <li>Typo in select-by-features status report</li>
3667 <li>Consensus RNA secondary secondary structure
3668 predictions are not highlighted in amber</li>
3669 <li>Missing gap character in v2.7 example file means
3670 alignment appears unaligned when pad-gaps is not enabled</li>
3671 <li>First switch to RNA Helices colouring doesn't colour
3672 associated structure views</li>
3673 <li>ID width preference option is greyed out when auto
3674 width checkbox not enabled</li>
3675 <li>Stopped a warning dialog from being shown when
3676 creating user defined colours</li>
3677 <li>'View Mapping' in structure viewer shows sequence
3678 mappings for just that viewer's sequences</li>
3679 <li>Workaround for superposing PDB files containing
3680 multiple models in Chimera</li>
3681 <li>Report sequence position in status bar when hovering
3682 over Jmol structure</li>
3683 <li>Cannot output gaps as '.' symbols with Selection ->
3684 output to text box</li>
3685 <li>Flat file exports of alignments with hidden columns
3686 have incorrect sequence start/end</li>
3687 <li>'Aligning' a second chain to a Chimera structure from
3689 <li>Colour schemes applied to structure viewers don't
3690 work for nucleotide</li>
3691 <li>Loading/cut'n'pasting an empty or invalid file leads
3692 to a grey/invisible alignment window</li>
3693 <li>Exported Jpred annotation from a sequence region
3694 imports to different position</li>
3695 <li>Space at beginning of sequence feature tooltips shown
3696 on some platforms</li>
3697 <li>Chimera viewer 'View | Show Chain' menu is not
3699 <li>'New View' fails with a Null Pointer Exception in
3700 console if Chimera has been opened</li>
3701 <li>Mouseover to Chimera not working</li>
3702 <li>Miscellaneous ENA XML feature qualifiers not
3704 <li>NPE in annotation renderer after 'Extract Scores'</li>
3705 <li>If two structures in one Chimera window, mouseover of
3706 either sequence shows on first structure</li>
3707 <li>'Show annotations' options should not make
3708 non-positional annotations visible</li>
3709 <li>Subsequence secondary structure annotation not shown
3710 in right place after 'view flanking regions'</li>
3711 <li>File Save As type unset when current file format is
3713 <li>Save as '.jar' option removed for saving Jalview
3715 <li>Colour by Sequence colouring in Chimera more
3717 <li>Cannot 'add reference annotation' for a sequence in
3718 several views on same alignment</li>
3719 <li>Cannot show linked products for EMBL / ENA records</li>
3720 <li>Jalview's tooltip wraps long texts containing no
3722 </ul> <em>Applet</em>
3724 <li>Jmol to JalviewLite mouseover/link not working</li>
3725 <li>JalviewLite can't import sequences with ID
3726 descriptions containing angle brackets</li>
3727 </ul> <em>General</em>
3729 <li>Cannot export and reimport RNA secondary structure
3730 via jalview annotation file</li>
3731 <li>Random helix colour palette for colour by annotation
3732 with RNA secondary structure</li>
3733 <li>Mouseover to cDNA from STOP residue in protein
3734 translation doesn't work.</li>
3735 <li>hints when using the select by annotation dialog box</li>
3736 <li>Jmol alignment incorrect if PDB file has alternate CA
3738 <li>FontChooser message dialog appears to hang after
3739 choosing 1pt font</li>
3740 <li>Peptide secondary structure incorrectly imported from
3741 annotation file when annotation display text includes 'e' or
3743 <li>Cannot set colour of new feature type whilst creating
3745 <li>cDNA translation alignment should not be sequence
3746 order dependent</li>
3747 <li>'Show unconserved' doesn't work for lower case
3749 <li>Nucleotide ambiguity codes involving R not recognised</li>
3750 </ul> <em>Deployment and Documentation</em>
3752 <li>Applet example pages appear different to the rest of
3753 www.jalview.org</li>
3754 </ul> <em>Application Known issues</em>
3756 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3757 <li>Misleading message appears after trying to delete
3759 <li>Jalview icon not shown in dock after InstallAnywhere
3760 version launches</li>
3761 <li>Fetching EMBL reference for an RNA sequence results
3762 fails with a sequence mismatch</li>
3763 <li>Corrupted or unreadable alignment display when
3764 scrolling alignment to right</li>
3765 <li>ArrayIndexOutOfBoundsException thrown when remove
3766 empty columns called on alignment with ragged gapped ends</li>
3767 <li>auto calculated alignment annotation rows do not get
3768 placed above or below non-autocalculated rows</li>
3769 <li>Jalview dekstop becomes sluggish at full screen in
3770 ultra-high resolution</li>
3771 <li>Cannot disable consensus calculation independently of
3772 quality and conservation</li>
3773 <li>Mouseover highlighting between cDNA and protein can
3774 become sluggish with more than one splitframe shown</li>
3775 </ul> <em>Applet Known Issues</em>
3777 <li>Core PDB parsing code requires Jmol</li>
3778 <li>Sequence canvas panel goes white when alignment
3779 window is being resized</li>
3785 <td><div align="center">
3786 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3788 <td><em>General</em>
3790 <li>Updated Java code signing certificate donated by
3792 <li>Features and annotation preserved when performing
3793 pairwise alignment</li>
3794 <li>RNA pseudoknot annotation can be
3795 imported/exported/displayed</li>
3796 <li>'colour by annotation' can colour by RNA and
3797 protein secondary structure</li>
3798 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3799 post-hoc with 2.9 release</em>)
3802 </ul> <em>Application</em>
3804 <li>Extract and display secondary structure for sequences
3805 with 3D structures</li>
3806 <li>Support for parsing RNAML</li>
3807 <li>Annotations menu for layout
3809 <li>sort sequence annotation rows by alignment</li>
3810 <li>place sequence annotation above/below alignment
3813 <li>Output in Stockholm format</li>
3814 <li>Internationalisation: improved Spanish (es)
3816 <li>Structure viewer preferences tab</li>
3817 <li>Disorder and Secondary Structure annotation tracks
3818 shared between alignments</li>
3819 <li>UCSF Chimera launch and linked highlighting from
3821 <li>Show/hide all sequence associated annotation rows for
3822 all or current selection</li>
3823 <li>disorder and secondary structure predictions
3824 available as dataset annotation</li>
3825 <li>Per-sequence rna helices colouring</li>
3828 <li>Sequence database accessions imported when fetching
3829 alignments from Rfam</li>
3830 <li>update VARNA version to 3.91</li>
3832 <li>New groovy scripts for exporting aligned positions,
3833 conservation values, and calculating sum of pairs scores.</li>
3834 <li>Command line argument to set default JABAWS server</li>
3835 <li>include installation type in build properties and
3836 console log output</li>
3837 <li>Updated Jalview project format to preserve dataset
3841 <!-- issues resolved --> <em>Application</em>
3843 <li>Distinguish alignment and sequence associated RNA
3844 structure in structure->view->VARNA</li>
3845 <li>Raise dialog box if user deletes all sequences in an
3847 <li>Pressing F1 results in documentation opening twice</li>
3848 <li>Sequence feature tooltip is wrapped</li>
3849 <li>Double click on sequence associated annotation
3850 selects only first column</li>
3851 <li>Redundancy removal doesn't result in unlinked
3852 leaves shown in tree</li>
3853 <li>Undos after several redundancy removals don't undo
3855 <li>Hide sequence doesn't hide associated annotation</li>
3856 <li>User defined colours dialog box too big to fit on
3857 screen and buttons not visible</li>
3858 <li>author list isn't updated if already written to
3859 Jalview properties</li>
3860 <li>Popup menu won't open after retrieving sequence
3862 <li>File open window for associate PDB doesn't open</li>
3863 <li>Left-then-right click on a sequence id opens a
3864 browser search window</li>
3865 <li>Cannot open sequence feature shading/sort popup menu
3866 in feature settings dialog</li>
3867 <li>better tooltip placement for some areas of Jalview
3869 <li>Allow addition of JABAWS Server which doesn't
3870 pass validation</li>
3871 <li>Web services parameters dialog box is too large to
3873 <li>Muscle nucleotide alignment preset obscured by
3875 <li>JABAWS preset submenus don't contain newly
3876 defined user preset</li>
3877 <li>MSA web services warns user if they were launched
3878 with invalid input</li>
3879 <li>Jalview cannot contact DAS Registy when running on
3882 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3883 'Superpose with' submenu not shown when new view
3887 </ul> <!-- <em>Applet</em>
3889 </ul> <em>General</em>
3891 </ul>--> <em>Deployment and Documentation</em>
3893 <li>2G and 1G options in launchApp have no effect on
3894 memory allocation</li>
3895 <li>launchApp service doesn't automatically open
3896 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3898 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3899 InstallAnywhere reports cannot find valid JVM when Java
3900 1.7_055 is available
3902 </ul> <em>Application Known issues</em>
3905 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3906 corrupted or unreadable alignment display when scrolling
3910 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3911 retrieval fails but progress bar continues for DAS retrieval
3912 with large number of ID
3915 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3916 flatfile output of visible region has incorrect sequence
3920 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3921 rna structure consensus doesn't update when secondary
3922 structure tracks are rearranged
3925 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3926 invalid rna structure positional highlighting does not
3927 highlight position of invalid base pairs
3930 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3931 out of memory errors are not raised when saving Jalview
3932 project from alignment window file menu
3935 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3936 Switching to RNA Helices colouring doesn't propagate to
3940 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3941 colour by RNA Helices not enabled when user created
3942 annotation added to alignment
3945 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3946 Jalview icon not shown on dock in Mountain Lion/Webstart
3948 </ul> <em>Applet Known Issues</em>
3951 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3952 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3955 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3956 Jalview and Jmol example not compatible with IE9
3959 <li>Sort by annotation score doesn't reverse order
3965 <td><div align="center">
3966 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3969 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3972 <li>Internationalisation of user interface (usually
3973 called i18n support) and translation for Spanish locale</li>
3974 <li>Define/Undefine group on current selection with
3975 Ctrl-G/Shift Ctrl-G</li>
3976 <li>Improved group creation/removal options in
3977 alignment/sequence Popup menu</li>
3978 <li>Sensible precision for symbol distribution
3979 percentages shown in logo tooltip.</li>
3980 <li>Annotation panel height set according to amount of
3981 annotation when alignment first opened</li>
3982 </ul> <em>Application</em>
3984 <li>Interactive consensus RNA secondary structure
3985 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3986 <li>Select columns containing particular features from
3987 Feature Settings dialog</li>
3988 <li>View all 'representative' PDB structures for selected
3990 <li>Update Jalview project format:
3992 <li>New file extension for Jalview projects '.jvp'</li>
3993 <li>Preserve sequence and annotation dataset (to
3994 store secondary structure annotation,etc)</li>
3995 <li>Per group and alignment annotation and RNA helix
3999 <li>New similarity measures for PCA and Tree calculation
4001 <li>Experimental support for retrieval and viewing of
4002 flanking regions for an alignment</li>
4006 <!-- issues resolved --> <em>Application</em>
4008 <li>logo keeps spinning and status remains at queued or
4009 running after job is cancelled</li>
4010 <li>cannot export features from alignments imported from
4011 Jalview/VAMSAS projects</li>
4012 <li>Buggy slider for web service parameters that take
4014 <li>Newly created RNA secondary structure line doesn't
4015 have 'display all symbols' flag set</li>
4016 <li>T-COFFEE alignment score shading scheme and other
4017 annotation shading not saved in Jalview project</li>
4018 <li>Local file cannot be loaded in freshly downloaded
4020 <li>Jalview icon not shown on dock in Mountain
4022 <li>Load file from desktop file browser fails</li>
4023 <li>Occasional NPE thrown when calculating large trees</li>
4024 <li>Cannot reorder or slide sequences after dragging an
4025 alignment onto desktop</li>
4026 <li>Colour by annotation dialog throws NPE after using
4027 'extract scores' function</li>
4028 <li>Loading/cut'n'pasting an empty file leads to a grey
4029 alignment window</li>
4030 <li>Disorder thresholds rendered incorrectly after
4031 performing IUPred disorder prediction</li>
4032 <li>Multiple group annotated consensus rows shown when
4033 changing 'normalise logo' display setting</li>
4034 <li>Find shows blank dialog after 'finished searching' if
4035 nothing matches query</li>
4036 <li>Null Pointer Exceptions raised when sorting by
4037 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4039 <li>Errors in Jmol console when structures in alignment
4040 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4042 <li>Not all working JABAWS services are shown in
4044 <li>JAVAWS version of Jalview fails to launch with
4045 'invalid literal/length code'</li>
4046 <li>Annotation/RNA Helix colourschemes cannot be applied
4047 to alignment with groups (actually fixed in 2.8.0b1)</li>
4048 <li>RNA Helices and T-Coffee Scores available as default
4051 </ul> <em>Applet</em>
4053 <li>Remove group option is shown even when selection is
4055 <li>Apply to all groups ticked but colourscheme changes
4056 don't affect groups</li>
4057 <li>Documented RNA Helices and T-Coffee Scores as valid
4058 colourscheme name</li>
4059 <li>Annotation labels drawn on sequence IDs when
4060 Annotation panel is not displayed</li>
4061 <li>Increased font size for dropdown menus on OSX and
4062 embedded windows</li>
4063 </ul> <em>Other</em>
4065 <li>Consensus sequence for alignments/groups with a
4066 single sequence were not calculated</li>
4067 <li>annotation files that contain only groups imported as
4068 annotation and junk sequences</li>
4069 <li>Fasta files with sequences containing '*' incorrectly
4070 recognised as PFAM or BLC</li>
4071 <li>conservation/PID slider apply all groups option
4072 doesn't affect background (2.8.0b1)
4074 <li>redundancy highlighting is erratic at 0% and 100%</li>
4075 <li>Remove gapped columns fails for sequences with ragged
4077 <li>AMSA annotation row with leading spaces is not
4078 registered correctly on import</li>
4079 <li>Jalview crashes when selecting PCA analysis for
4080 certain alignments</li>
4081 <li>Opening the colour by annotation dialog for an
4082 existing annotation based 'use original colours'
4083 colourscheme loses original colours setting</li>
4088 <td><div align="center">
4089 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4090 <em>30/1/2014</em></strong>
4094 <li>Trusted certificates for JalviewLite applet and
4095 Jalview Desktop application<br />Certificate was donated by
4096 <a href="https://www.certum.eu">Certum</a> to the Jalview
4097 open source project).
4099 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4100 <li>Output in Stockholm format</li>
4101 <li>Allow import of data from gzipped files</li>
4102 <li>Export/import group and sequence associated line
4103 graph thresholds</li>
4104 <li>Nucleotide substitution matrix that supports RNA and
4105 ambiguity codes</li>
4106 <li>Allow disorder predictions to be made on the current
4107 selection (or visible selection) in the same way that JPred
4109 <li>Groovy scripting for headless Jalview operation</li>
4110 </ul> <em>Other improvements</em>
4112 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4113 <li>COMBINE statement uses current SEQUENCE_REF and
4114 GROUP_REF scope to group annotation rows</li>
4115 <li>Support '' style escaping of quotes in Newick
4117 <li>Group options for JABAWS service by command line name</li>
4118 <li>Empty tooltip shown for JABA service options with a
4119 link but no description</li>
4120 <li>Select primary source when selecting authority in
4121 database fetcher GUI</li>
4122 <li>Add .mfa to FASTA file extensions recognised by
4124 <li>Annotation label tooltip text wrap</li>
4129 <li>Slow scrolling when lots of annotation rows are
4131 <li>Lots of NPE (and slowness) after creating RNA
4132 secondary structure annotation line</li>
4133 <li>Sequence database accessions not imported when
4134 fetching alignments from Rfam</li>
4135 <li>Incorrect SHMR submission for sequences with
4137 <li>View all structures does not always superpose
4139 <li>Option widgets in service parameters not updated to
4140 reflect user or preset settings</li>
4141 <li>Null pointer exceptions for some services without
4142 presets or adjustable parameters</li>
4143 <li>Discover PDB IDs entry in structure menu doesn't
4144 discover PDB xRefs</li>
4145 <li>Exception encountered while trying to retrieve
4146 features with DAS</li>
4147 <li>Lowest value in annotation row isn't coloured
4148 when colour by annotation (per sequence) is coloured</li>
4149 <li>Keyboard mode P jumps to start of gapped region when
4150 residue follows a gap</li>
4151 <li>Jalview appears to hang importing an alignment with
4152 Wrap as default or after enabling Wrap</li>
4153 <li>'Right click to add annotations' message
4154 shown in wrap mode when no annotations present</li>
4155 <li>Disorder predictions fail with NPE if no automatic
4156 annotation already exists on alignment</li>
4157 <li>oninit javascript function should be called after
4158 initialisation completes</li>
4159 <li>Remove redundancy after disorder prediction corrupts
4160 alignment window display</li>
4161 <li>Example annotation file in documentation is invalid</li>
4162 <li>Grouped line graph annotation rows are not exported
4163 to annotation file</li>
4164 <li>Multi-harmony analysis cannot be run when only two
4166 <li>Cannot create multiple groups of line graphs with
4167 several 'combine' statements in annotation file</li>
4168 <li>Pressing return several times causes Number Format
4169 exceptions in keyboard mode</li>
4170 <li>Multi-harmony (SHMMR) method doesn't submit
4171 correct partitions for input data</li>
4172 <li>Translation from DNA to Amino Acids fails</li>
4173 <li>Jalview fail to load newick tree with quoted label</li>
4174 <li>--headless flag isn't understood</li>
4175 <li>ClassCastException when generating EPS in headless
4177 <li>Adjusting sequence-associated shading threshold only
4178 changes one row's threshold</li>
4179 <li>Preferences and Feature settings panel panel
4180 doesn't open</li>
4181 <li>hide consensus histogram also hides conservation and
4182 quality histograms</li>
4187 <td><div align="center">
4188 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4190 <td><em>Application</em>
4192 <li>Support for JABAWS 2.0 Services (AACon alignment
4193 conservation, protein disorder and Clustal Omega)</li>
4194 <li>JABAWS server status indicator in Web Services
4196 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4197 in Jalview alignment window</li>
4198 <li>Updated Jalview build and deploy framework for OSX
4199 mountain lion, windows 7, and 8</li>
4200 <li>Nucleotide substitution matrix for PCA that supports
4201 RNA and ambiguity codes</li>
4203 <li>Improved sequence database retrieval GUI</li>
4204 <li>Support fetching and database reference look up
4205 against multiple DAS sources (Fetch all from in 'fetch db
4207 <li>Jalview project improvements
4209 <li>Store and retrieve the 'belowAlignment'
4210 flag for annotation</li>
4211 <li>calcId attribute to group annotation rows on the
4213 <li>Store AACon calculation settings for a view in
4214 Jalview project</li>
4218 <li>horizontal scrolling gesture support</li>
4219 <li>Visual progress indicator when PCA calculation is
4221 <li>Simpler JABA web services menus</li>
4222 <li>visual indication that web service results are still
4223 being retrieved from server</li>
4224 <li>Serialise the dialogs that are shown when Jalview
4225 starts up for first time</li>
4226 <li>Jalview user agent string for interacting with HTTP
4228 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4230 <li>Examples directory and Groovy library included in
4231 InstallAnywhere distribution</li>
4232 </ul> <em>Applet</em>
4234 <li>RNA alignment and secondary structure annotation
4235 visualization applet example</li>
4236 </ul> <em>General</em>
4238 <li>Normalise option for consensus sequence logo</li>
4239 <li>Reset button in PCA window to return dimensions to
4241 <li>Allow seqspace or Jalview variant of alignment PCA
4243 <li>PCA with either nucleic acid and protein substitution
4245 <li>Allow windows containing HTML reports to be exported
4247 <li>Interactive display and editing of RNA secondary
4248 structure contacts</li>
4249 <li>RNA Helix Alignment Colouring</li>
4250 <li>RNA base pair logo consensus</li>
4251 <li>Parse sequence associated secondary structure
4252 information in Stockholm files</li>
4253 <li>HTML Export database accessions and annotation
4254 information presented in tooltip for sequences</li>
4255 <li>Import secondary structure from LOCARNA clustalw
4256 style RNA alignment files</li>
4257 <li>import and visualise T-COFFEE quality scores for an
4259 <li>'colour by annotation' per sequence option to
4260 shade each sequence according to its associated alignment
4262 <li>New Jalview Logo</li>
4263 </ul> <em>Documentation and Development</em>
4265 <li>documentation for score matrices used in Jalview</li>
4266 <li>New Website!</li>
4268 <td><em>Application</em>
4270 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4271 wsdbfetch REST service</li>
4272 <li>Stop windows being moved outside desktop on OSX</li>
4273 <li>Filetype associations not installed for webstart
4275 <li>Jalview does not always retrieve progress of a JABAWS
4276 job execution in full once it is complete</li>
4277 <li>revise SHMR RSBS definition to ensure alignment is
4278 uploaded via ali_file parameter</li>
4279 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4280 <li>View all structures superposed fails with exception</li>
4281 <li>Jnet job queues forever if a very short sequence is
4282 submitted for prediction</li>
4283 <li>Cut and paste menu not opened when mouse clicked on
4285 <li>Putting fractional value into integer text box in
4286 alignment parameter dialog causes Jalview to hang</li>
4287 <li>Structure view highlighting doesn't work on
4289 <li>View all structures fails with exception shown in
4291 <li>Characters in filename associated with PDBEntry not
4292 escaped in a platform independent way</li>
4293 <li>Jalview desktop fails to launch with exception when
4295 <li>Tree calculation reports 'you must have 2 or more
4296 sequences selected' when selection is empty</li>
4297 <li>Jalview desktop fails to launch with jar signature
4298 failure when java web start temporary file caching is
4300 <li>DAS Sequence retrieval with range qualification
4301 results in sequence xref which includes range qualification</li>
4302 <li>Errors during processing of command line arguments
4303 cause progress bar (JAL-898) to be removed</li>
4304 <li>Replace comma for semi-colon option not disabled for
4305 DAS sources in sequence fetcher</li>
4306 <li>Cannot close news reader when JABAWS server warning
4307 dialog is shown</li>
4308 <li>Option widgets not updated to reflect user settings</li>
4309 <li>Edited sequence not submitted to web service</li>
4310 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4311 <li>InstallAnywhere installer doesn't unpack and run
4312 on OSX Mountain Lion</li>
4313 <li>Annotation panel not given a scroll bar when
4314 sequences with alignment annotation are pasted into the
4316 <li>Sequence associated annotation rows not associated
4317 when loaded from Jalview project</li>
4318 <li>Browser launch fails with NPE on java 1.7</li>
4319 <li>JABAWS alignment marked as finished when job was
4320 cancelled or job failed due to invalid input</li>
4321 <li>NPE with v2.7 example when clicking on Tree
4322 associated with all views</li>
4323 <li>Exceptions when copy/paste sequences with grouped
4324 annotation rows to new window</li>
4325 </ul> <em>Applet</em>
4327 <li>Sequence features are momentarily displayed before
4328 they are hidden using hidefeaturegroups applet parameter</li>
4329 <li>loading features via javascript API automatically
4330 enables feature display</li>
4331 <li>scrollToColumnIn javascript API method doesn't
4333 </ul> <em>General</em>
4335 <li>Redundancy removal fails for rna alignment</li>
4336 <li>PCA calculation fails when sequence has been selected
4337 and then deselected</li>
4338 <li>PCA window shows grey box when first opened on OSX</li>
4339 <li>Letters coloured pink in sequence logo when alignment
4340 coloured with clustalx</li>
4341 <li>Choosing fonts without letter symbols defined causes
4342 exceptions and redraw errors</li>
4343 <li>Initial PCA plot view is not same as manually
4344 reconfigured view</li>
4345 <li>Grouped annotation graph label has incorrect line
4347 <li>Grouped annotation graph label display is corrupted
4348 for lots of labels</li>
4353 <div align="center">
4354 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4357 <td><em>Application</em>
4359 <li>Jalview Desktop News Reader</li>
4360 <li>Tweaked default layout of web services menu</li>
4361 <li>View/alignment association menu to enable user to
4362 easily specify which alignment a multi-structure view takes
4363 its colours/correspondences from</li>
4364 <li>Allow properties file location to be specified as URL</li>
4365 <li>Extend Jalview project to preserve associations
4366 between many alignment views and a single Jmol display</li>
4367 <li>Store annotation row height in Jalview project file</li>
4368 <li>Annotation row column label formatting attributes
4369 stored in project file</li>
4370 <li>Annotation row order for auto-calculated annotation
4371 rows preserved in Jalview project file</li>
4372 <li>Visual progress indication when Jalview state is
4373 saved using Desktop window menu</li>
4374 <li>Visual indication that command line arguments are
4375 still being processed</li>
4376 <li>Groovy script execution from URL</li>
4377 <li>Colour by annotation default min and max colours in
4379 <li>Automatically associate PDB files dragged onto an
4380 alignment with sequences that have high similarity and
4382 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4383 <li>'view structures' option to open many
4384 structures in same window</li>
4385 <li>Sort associated views menu option for tree panel</li>
4386 <li>Group all JABA and non-JABA services for a particular
4387 analysis function in its own submenu</li>
4388 </ul> <em>Applet</em>
4390 <li>Userdefined and autogenerated annotation rows for
4392 <li>Adjustment of alignment annotation pane height</li>
4393 <li>Annotation scrollbar for annotation panel</li>
4394 <li>Drag to reorder annotation rows in annotation panel</li>
4395 <li>'automaticScrolling' parameter</li>
4396 <li>Allow sequences with partial ID string matches to be
4397 annotated from GFF/Jalview features files</li>
4398 <li>Sequence logo annotation row in applet</li>
4399 <li>Absolute paths relative to host server in applet
4400 parameters are treated as such</li>
4401 <li>New in the JalviewLite javascript API:
4403 <li>JalviewLite.js javascript library</li>
4404 <li>Javascript callbacks for
4406 <li>Applet initialisation</li>
4407 <li>Sequence/alignment mouse-overs and selections</li>
4410 <li>scrollTo row and column alignment scrolling
4412 <li>Select sequence/alignment regions from javascript</li>
4413 <li>javascript structure viewer harness to pass
4414 messages between Jmol and Jalview when running as
4415 distinct applets</li>
4416 <li>sortBy method</li>
4417 <li>Set of applet and application examples shipped
4418 with documentation</li>
4419 <li>New example to demonstrate JalviewLite and Jmol
4420 javascript message exchange</li>
4422 </ul> <em>General</em>
4424 <li>Enable Jmol displays to be associated with multiple
4425 multiple alignments</li>
4426 <li>Option to automatically sort alignment with new tree</li>
4427 <li>User configurable link to enable redirects to a
4428 www.Jalview.org mirror</li>
4429 <li>Jmol colours option for Jmol displays</li>
4430 <li>Configurable newline string when writing alignment
4431 and other flat files</li>
4432 <li>Allow alignment annotation description lines to
4433 contain html tags</li>
4434 </ul> <em>Documentation and Development</em>
4436 <li>Add groovy test harness for bulk load testing to
4438 <li>Groovy script to load and align a set of sequences
4439 using a web service before displaying the result in the
4440 Jalview desktop</li>
4441 <li>Restructured javascript and applet api documentation</li>
4442 <li>Ant target to publish example html files with applet
4444 <li>Netbeans project for building Jalview from source</li>
4445 <li>ant task to create online javadoc for Jalview source</li>
4447 <td><em>Application</em>
4449 <li>User defined colourscheme throws exception when
4450 current built in colourscheme is saved as new scheme</li>
4451 <li>AlignFrame->Save in application pops up save
4452 dialog for valid filename/format</li>
4453 <li>Cannot view associated structure for UniProt sequence</li>
4454 <li>PDB file association breaks for UniProt sequence
4456 <li>Associate PDB from file dialog does not tell you
4457 which sequence is to be associated with the file</li>
4458 <li>Find All raises null pointer exception when query
4459 only matches sequence IDs</li>
4460 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4461 <li>Jalview project with Jmol views created with Jalview
4462 2.4 cannot be loaded</li>
4463 <li>Filetype associations not installed for webstart
4465 <li>Two or more chains in a single PDB file associated
4466 with sequences in different alignments do not get coloured
4467 by their associated sequence</li>
4468 <li>Visibility status of autocalculated annotation row
4469 not preserved when project is loaded</li>
4470 <li>Annotation row height and visibility attributes not
4471 stored in Jalview project</li>
4472 <li>Tree bootstraps are not preserved when saved as a
4473 Jalview project</li>
4474 <li>Envision2 workflow tooltips are corrupted</li>
4475 <li>Enabling show group conservation also enables colour
4476 by conservation</li>
4477 <li>Duplicate group associated conservation or consensus
4478 created on new view</li>
4479 <li>Annotation scrollbar not displayed after 'show
4480 all hidden annotation rows' option selected</li>
4481 <li>Alignment quality not updated after alignment
4482 annotation row is hidden then shown</li>
4483 <li>Preserve colouring of structures coloured by
4484 sequences in pre Jalview 2.7 projects</li>
4485 <li>Web service job parameter dialog is not laid out
4487 <li>Web services menu not refreshed after 'reset
4488 services' button is pressed in preferences</li>
4489 <li>Annotation off by one in Jalview v2_3 example project</li>
4490 <li>Structures imported from file and saved in project
4491 get name like jalview_pdb1234.txt when reloaded</li>
4492 <li>Jalview does not always retrieve progress of a JABAWS
4493 job execution in full once it is complete</li>
4494 </ul> <em>Applet</em>
4496 <li>Alignment height set incorrectly when lots of
4497 annotation rows are displayed</li>
4498 <li>Relative URLs in feature HTML text not resolved to
4500 <li>View follows highlighting does not work for positions
4502 <li><= shown as = in tooltip</li>
4503 <li>Export features raises exception when no features
4505 <li>Separator string used for serialising lists of IDs
4506 for javascript api is modified when separator string
4507 provided as parameter</li>
4508 <li>Null pointer exception when selecting tree leaves for
4509 alignment with no existing selection</li>
4510 <li>Relative URLs for datasources assumed to be relative
4511 to applet's codebase</li>
4512 <li>Status bar not updated after finished searching and
4513 search wraps around to first result</li>
4514 <li>StructureSelectionManager instance shared between
4515 several Jalview applets causes race conditions and memory
4517 <li>Hover tooltip and mouseover of position on structure
4518 not sent from Jmol in applet</li>
4519 <li>Certain sequences of javascript method calls to
4520 applet API fatally hang browser</li>
4521 </ul> <em>General</em>
4523 <li>View follows structure mouseover scrolls beyond
4524 position with wrapped view and hidden regions</li>
4525 <li>Find sequence position moves to wrong residue
4526 with/without hidden columns</li>
4527 <li>Sequence length given in alignment properties window
4529 <li>InvalidNumberFormat exceptions thrown when trying to
4530 import PDB like structure files</li>
4531 <li>Positional search results are only highlighted
4532 between user-supplied sequence start/end bounds</li>
4533 <li>End attribute of sequence is not validated</li>
4534 <li>Find dialog only finds first sequence containing a
4535 given sequence position</li>
4536 <li>Sequence numbering not preserved in MSF alignment
4538 <li>Jalview PDB file reader does not extract sequence
4539 from nucleotide chains correctly</li>
4540 <li>Structure colours not updated when tree partition
4541 changed in alignment</li>
4542 <li>Sequence associated secondary structure not correctly
4543 parsed in interleaved stockholm</li>
4544 <li>Colour by annotation dialog does not restore current
4546 <li>Hiding (nearly) all sequences doesn't work
4548 <li>Sequences containing lowercase letters are not
4549 properly associated with their pdb files</li>
4550 </ul> <em>Documentation and Development</em>
4552 <li>schemas/JalviewWsParamSet.xsd corrupted by
4553 ApplyCopyright tool</li>
4558 <div align="center">
4559 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4562 <td><em>Application</em>
4564 <li>New warning dialog when the Jalview Desktop cannot
4565 contact web services</li>
4566 <li>JABA service parameters for a preset are shown in
4567 service job window</li>
4568 <li>JABA Service menu entries reworded</li>
4572 <li>Modeller PIR IO broken - cannot correctly import a
4573 pir file emitted by Jalview</li>
4574 <li>Existing feature settings transferred to new
4575 alignment view created from cut'n'paste</li>
4576 <li>Improved test for mixed amino/nucleotide chains when
4577 parsing PDB files</li>
4578 <li>Consensus and conservation annotation rows
4579 occasionally become blank for all new windows</li>
4580 <li>Exception raised when right clicking above sequences
4581 in wrapped view mode</li>
4582 </ul> <em>Application</em>
4584 <li>multiple multiply aligned structure views cause cpu
4585 usage to hit 100% and computer to hang</li>
4586 <li>Web Service parameter layout breaks for long user
4587 parameter names</li>
4588 <li>Jaba service discovery hangs desktop if Jaba server
4595 <div align="center">
4596 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4599 <td><em>Application</em>
4601 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4602 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4605 <li>Web Services preference tab</li>
4606 <li>Analysis parameters dialog box and user defined
4608 <li>Improved speed and layout of Envision2 service menu</li>
4609 <li>Superpose structures using associated sequence
4611 <li>Export coordinates and projection as CSV from PCA
4613 </ul> <em>Applet</em>
4615 <li>enable javascript: execution by the applet via the
4616 link out mechanism</li>
4617 </ul> <em>Other</em>
4619 <li>Updated the Jmol Jalview interface to work with Jmol
4621 <li>The Jalview Desktop and JalviewLite applet now
4622 require Java 1.5</li>
4623 <li>Allow Jalview feature colour specification for GFF
4624 sequence annotation files</li>
4625 <li>New 'colour by label' keword in Jalview feature file
4626 type colour specification</li>
4627 <li>New Jalview Desktop Groovy API method that allows a
4628 script to check if it being run in an interactive session or
4629 in a batch operation from the Jalview command line</li>
4633 <li>clustalx colourscheme colours Ds preferentially when
4634 both D+E are present in over 50% of the column</li>
4635 </ul> <em>Application</em>
4637 <li>typo in AlignmentFrame->View->Hide->all but
4638 selected Regions menu item</li>
4639 <li>sequence fetcher replaces ',' for ';' when the ',' is
4640 part of a valid accession ID</li>
4641 <li>fatal OOM if object retrieved by sequence fetcher
4642 runs out of memory</li>
4643 <li>unhandled Out of Memory Error when viewing pca
4644 analysis results</li>
4645 <li>InstallAnywhere builds fail to launch on OS X java
4646 10.5 update 4 (due to apple Java 1.6 update)</li>
4647 <li>Installanywhere Jalview silently fails to launch</li>
4648 </ul> <em>Applet</em>
4650 <li>Jalview.getFeatureGroups() raises an
4651 ArrayIndexOutOfBoundsException if no feature groups are
4658 <div align="center">
4659 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4665 <li>Alignment prettyprinter doesn't cope with long
4667 <li>clustalx colourscheme colours Ds preferentially when
4668 both D+E are present in over 50% of the column</li>
4669 <li>nucleic acid structures retrieved from PDB do not
4670 import correctly</li>
4671 <li>More columns get selected than were clicked on when a
4672 number of columns are hidden</li>
4673 <li>annotation label popup menu not providing correct
4674 add/hide/show options when rows are hidden or none are
4676 <li>Stockholm format shown in list of readable formats,
4677 and parser copes better with alignments from RFAM.</li>
4678 <li>CSV output of consensus only includes the percentage
4679 of all symbols if sequence logo display is enabled</li>
4681 </ul> <em>Applet</em>
4683 <li>annotation panel disappears when annotation is
4685 </ul> <em>Application</em>
4687 <li>Alignment view not redrawn properly when new
4688 alignment opened where annotation panel is visible but no
4689 annotations are present on alignment</li>
4690 <li>pasted region containing hidden columns is
4691 incorrectly displayed in new alignment window</li>
4692 <li>Jalview slow to complete operations when stdout is
4693 flooded (fix is to close the Jalview console)</li>
4694 <li>typo in AlignmentFrame->View->Hide->all but
4695 selected Rregions menu item.</li>
4696 <li>inconsistent group submenu and Format submenu entry
4697 'Un' or 'Non'conserved</li>
4698 <li>Sequence feature settings are being shared by
4699 multiple distinct alignments</li>
4700 <li>group annotation not recreated when tree partition is
4702 <li>double click on group annotation to select sequences
4703 does not propagate to associated trees</li>
4704 <li>Mac OSX specific issues:
4706 <li>exception raised when mouse clicked on desktop
4707 window background</li>
4708 <li>Desktop menu placed on menu bar and application
4709 name set correctly</li>
4710 <li>sequence feature settings not wide enough for the
4711 save feature colourscheme button</li>
4720 <div align="center">
4721 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4724 <td><em>New Capabilities</em>
4726 <li>URL links generated from description line for
4727 regular-expression based URL links (applet and application)
4730 <li>Non-positional feature URL links are shown in link
4732 <li>Linked viewing of nucleic acid sequences and
4734 <li>Automatic Scrolling option in View menu to display
4735 the currently highlighted region of an alignment.</li>
4736 <li>Order an alignment by sequence length, or using the
4737 average score or total feature count for each sequence.</li>
4738 <li>Shading features by score or associated description</li>
4739 <li>Subdivide alignment and groups based on identity of
4740 selected subsequence (Make Groups from Selection).</li>
4741 <li>New hide/show options including Shift+Control+H to
4742 hide everything but the currently selected region.</li>
4743 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4744 </ul> <em>Application</em>
4746 <li>Fetch DB References capabilities and UI expanded to
4747 support retrieval from DAS sequence sources</li>
4748 <li>Local DAS Sequence sources can be added via the
4749 command line or via the Add local source dialog box.</li>
4750 <li>DAS Dbref and DbxRef feature types are parsed as
4751 database references and protein_name is parsed as
4752 description line (BioSapiens terms).</li>
4753 <li>Enable or disable non-positional feature and database
4754 references in sequence ID tooltip from View menu in
4756 <!-- <li>New hidden columns and rows and representatives capabilities
4757 in annotations file (in progress - not yet fully implemented)</li> -->
4758 <li>Group-associated consensus, sequence logos and
4759 conservation plots</li>
4760 <li>Symbol distributions for each column can be exported
4761 and visualized as sequence logos</li>
4762 <li>Optionally scale multi-character column labels to fit
4763 within each column of annotation row<!-- todo for applet -->
4765 <li>Optional automatic sort of associated alignment view
4766 when a new tree is opened.</li>
4767 <li>Jalview Java Console</li>
4768 <li>Better placement of desktop window when moving
4769 between different screens.</li>
4770 <li>New preference items for sequence ID tooltip and
4771 consensus annotation</li>
4772 <li>Client to submit sequences and IDs to Envision2
4774 <li><em>Vamsas Capabilities</em>
4776 <li>Improved VAMSAS synchronization (Jalview archive
4777 used to preserve views, structures, and tree display
4779 <li>Import of vamsas documents from disk or URL via
4781 <li>Sharing of selected regions between views and
4782 with other VAMSAS applications (Experimental feature!)</li>
4783 <li>Updated API to VAMSAS version 0.2</li>
4785 </ul> <em>Applet</em>
4787 <li>Middle button resizes annotation row height</li>
4790 <li>sortByTree (true/false) - automatically sort the
4791 associated alignment view by the tree when a new tree is
4793 <li>showTreeBootstraps (true/false) - show or hide
4794 branch bootstraps (default is to show them if available)</li>
4795 <li>showTreeDistances (true/false) - show or hide
4796 branch lengths (default is to show them if available)</li>
4797 <li>showUnlinkedTreeNodes (true/false) - indicate if
4798 unassociated nodes should be highlighted in the tree
4800 <li>heightScale and widthScale (1.0 or more) -
4801 increase the height or width of a cell in the alignment
4802 grid relative to the current font size.</li>
4805 <li>Non-positional features displayed in sequence ID
4807 </ul> <em>Other</em>
4809 <li>Features format: graduated colour definitions and
4810 specification of feature scores</li>
4811 <li>Alignment Annotations format: new keywords for group
4812 associated annotation (GROUP_REF) and annotation row display
4813 properties (ROW_PROPERTIES)</li>
4814 <li>XML formats extended to support graduated feature
4815 colourschemes, group associated annotation, and profile
4816 visualization settings.</li></td>
4819 <li>Source field in GFF files parsed as feature source
4820 rather than description</li>
4821 <li>Non-positional features are now included in sequence
4822 feature and gff files (controlled via non-positional feature
4823 visibility in tooltip).</li>
4824 <li>URL links generated for all feature links (bugfix)</li>
4825 <li>Added URL embedding instructions to features file
4827 <li>Codons containing ambiguous nucleotides translated as
4828 'X' in peptide product</li>
4829 <li>Match case switch in find dialog box works for both
4830 sequence ID and sequence string and query strings do not
4831 have to be in upper case to match case-insensitively.</li>
4832 <li>AMSA files only contain first column of
4833 multi-character column annotation labels</li>
4834 <li>Jalview Annotation File generation/parsing consistent
4835 with documentation (e.g. Stockholm annotation can be
4836 exported and re-imported)</li>
4837 <li>PDB files without embedded PDB IDs given a friendly
4839 <li>Find incrementally searches ID string matches as well
4840 as subsequence matches, and correctly reports total number
4844 <li>Better handling of exceptions during sequence
4846 <li>Dasobert generated non-positional feature URL
4847 link text excludes the start_end suffix</li>
4848 <li>DAS feature and source retrieval buttons disabled
4849 when fetch or registry operations in progress.</li>
4850 <li>PDB files retrieved from URLs are cached properly</li>
4851 <li>Sequence description lines properly shared via
4853 <li>Sequence fetcher fetches multiple records for all
4855 <li>Ensured that command line das feature retrieval
4856 completes before alignment figures are generated.</li>
4857 <li>Reduced time taken when opening file browser for
4859 <li>isAligned check prior to calculating tree, PCA or
4860 submitting an MSA to JNet now excludes hidden sequences.</li>
4861 <li>User defined group colours properly recovered
4862 from Jalview projects.</li>
4871 <div align="center">
4872 <strong>2.4.0.b2</strong><br> 28/10/2009
4877 <li>Experimental support for google analytics usage
4879 <li>Jalview privacy settings (user preferences and docs).</li>
4884 <li>Race condition in applet preventing startup in
4886 <li>Exception when feature created from selection beyond
4887 length of sequence.</li>
4888 <li>Allow synthetic PDB files to be imported gracefully</li>
4889 <li>Sequence associated annotation rows associate with
4890 all sequences with a given id</li>
4891 <li>Find function matches case-insensitively for sequence
4892 ID string searches</li>
4893 <li>Non-standard characters do not cause pairwise
4894 alignment to fail with exception</li>
4895 </ul> <em>Application Issues</em>
4897 <li>Sequences are now validated against EMBL database</li>
4898 <li>Sequence fetcher fetches multiple records for all
4900 </ul> <em>InstallAnywhere Issues</em>
4902 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4903 issue with installAnywhere mechanism)</li>
4904 <li>Command line launching of JARs from InstallAnywhere
4905 version (java class versioning error fixed)</li>
4912 <div align="center">
4913 <strong>2.4</strong><br> 27/8/2008
4916 <td><em>User Interface</em>
4918 <li>Linked highlighting of codon and amino acid from
4919 translation and protein products</li>
4920 <li>Linked highlighting of structure associated with
4921 residue mapping to codon position</li>
4922 <li>Sequence Fetcher provides example accession numbers
4923 and 'clear' button</li>
4924 <li>MemoryMonitor added as an option under Desktop's
4926 <li>Extract score function to parse whitespace separated
4927 numeric data in description line</li>
4928 <li>Column labels in alignment annotation can be centred.</li>
4929 <li>Tooltip for sequence associated annotation give name
4931 </ul> <em>Web Services and URL fetching</em>
4933 <li>JPred3 web service</li>
4934 <li>Prototype sequence search client (no public services
4936 <li>Fetch either seed alignment or full alignment from
4938 <li>URL Links created for matching database cross
4939 references as well as sequence ID</li>
4940 <li>URL Links can be created using regular-expressions</li>
4941 </ul> <em>Sequence Database Connectivity</em>
4943 <li>Retrieval of cross-referenced sequences from other
4945 <li>Generalised database reference retrieval and
4946 validation to all fetchable databases</li>
4947 <li>Fetch sequences from DAS sources supporting the
4948 sequence command</li>
4949 </ul> <em>Import and Export</em>
4950 <li>export annotation rows as CSV for spreadsheet import</li>
4951 <li>Jalview projects record alignment dataset associations,
4952 EMBL products, and cDNA sequence mappings</li>
4953 <li>Sequence Group colour can be specified in Annotation
4955 <li>Ad-hoc colouring of group in Annotation File using RGB
4956 triplet as name of colourscheme</li>
4957 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4959 <li>treenode binding for VAMSAS tree exchange</li>
4960 <li>local editing and update of sequences in VAMSAS
4961 alignments (experimental)</li>
4962 <li>Create new or select existing session to join</li>
4963 <li>load and save of vamsas documents</li>
4964 </ul> <em>Application command line</em>
4966 <li>-tree parameter to open trees (introduced for passing
4968 <li>-fetchfrom command line argument to specify nicknames
4969 of DAS servers to query for alignment features</li>
4970 <li>-dasserver command line argument to add new servers
4971 that are also automatically queried for features</li>
4972 <li>-groovy command line argument executes a given groovy
4973 script after all input data has been loaded and parsed</li>
4974 </ul> <em>Applet-Application data exchange</em>
4976 <li>Trees passed as applet parameters can be passed to
4977 application (when using "View in full
4978 application")</li>
4979 </ul> <em>Applet Parameters</em>
4981 <li>feature group display control parameter</li>
4982 <li>debug parameter</li>
4983 <li>showbutton parameter</li>
4984 </ul> <em>Applet API methods</em>
4986 <li>newView public method</li>
4987 <li>Window (current view) specific get/set public methods</li>
4988 <li>Feature display control methods</li>
4989 <li>get list of currently selected sequences</li>
4990 </ul> <em>New Jalview distribution features</em>
4992 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4993 <li>RELEASE file gives build properties for the latest
4994 Jalview release.</li>
4995 <li>Java 1.1 Applet build made easier and donotobfuscate
4996 property controls execution of obfuscator</li>
4997 <li>Build target for generating source distribution</li>
4998 <li>Debug flag for javacc</li>
4999 <li>.jalview_properties file is documented (slightly) in
5000 jalview.bin.Cache</li>
5001 <li>Continuous Build Integration for stable and
5002 development version of Application, Applet and source
5007 <li>selected region output includes visible annotations
5008 (for certain formats)</li>
5009 <li>edit label/displaychar contains existing label/char
5011 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5012 <li>shorter peptide product names from EMBL records</li>
5013 <li>Newick string generator makes compact representations</li>
5014 <li>bootstrap values parsed correctly for tree files with
5016 <li>pathological filechooser bug avoided by not allowing
5017 filenames containing a ':'</li>
5018 <li>Fixed exception when parsing GFF files containing
5019 global sequence features</li>
5020 <li>Alignment datasets are finalized only when number of
5021 references from alignment sequences goes to zero</li>
5022 <li>Close of tree branch colour box without colour
5023 selection causes cascading exceptions</li>
5024 <li>occasional negative imgwidth exceptions</li>
5025 <li>better reporting of non-fatal warnings to user when
5026 file parsing fails.</li>
5027 <li>Save works when Jalview project is default format</li>
5028 <li>Save as dialog opened if current alignment format is
5029 not a valid output format</li>
5030 <li>UniProt canonical names introduced for both das and
5032 <li>Histidine should be midblue (not pink!) in Zappo</li>
5033 <li>error messages passed up and output when data read
5035 <li>edit undo recovers previous dataset sequence when
5036 sequence is edited</li>
5037 <li>allow PDB files without pdb ID HEADER lines (like
5038 those generated by MODELLER) to be read in properly</li>
5039 <li>allow reading of JPred concise files as a normal
5041 <li>Stockholm annotation parsing and alignment properties
5042 import fixed for PFAM records</li>
5043 <li>Structure view windows have correct name in Desktop
5045 <li>annotation consisting of sequence associated scores
5046 can be read and written correctly to annotation file</li>
5047 <li>Aligned cDNA translation to aligned peptide works
5049 <li>Fixed display of hidden sequence markers and
5050 non-italic font for representatives in Applet</li>
5051 <li>Applet Menus are always embedded in applet window on
5053 <li>Newly shown features appear at top of stack (in
5055 <li>Annotations added via parameter not drawn properly
5056 due to null pointer exceptions</li>
5057 <li>Secondary structure lines are drawn starting from
5058 first column of alignment</li>
5059 <li>UniProt XML import updated for new schema release in
5061 <li>Sequence feature to sequence ID match for Features
5062 file is case-insensitive</li>
5063 <li>Sequence features read from Features file appended to
5064 all sequences with matching IDs</li>
5065 <li>PDB structure coloured correctly for associated views
5066 containing a sub-sequence</li>
5067 <li>PDB files can be retrieved by applet from Jar files</li>
5068 <li>feature and annotation file applet parameters
5069 referring to different directories are retrieved correctly</li>
5070 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5071 <li>Fixed application hang whilst waiting for
5072 splash-screen version check to complete</li>
5073 <li>Applet properly URLencodes input parameter values
5074 when passing them to the launchApp service</li>
5075 <li>display name and local features preserved in results
5076 retrieved from web service</li>
5077 <li>Visual delay indication for sequence retrieval and
5078 sequence fetcher initialisation</li>
5079 <li>updated Application to use DAS 1.53e version of
5080 dasobert DAS client</li>
5081 <li>Re-instated Full AMSA support and .amsa file
5083 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5091 <div align="center">
5092 <strong>2.3</strong><br> 9/5/07
5097 <li>Jmol 11.0.2 integration</li>
5098 <li>PDB views stored in Jalview XML files</li>
5099 <li>Slide sequences</li>
5100 <li>Edit sequence in place</li>
5101 <li>EMBL CDS features</li>
5102 <li>DAS Feature mapping</li>
5103 <li>Feature ordering</li>
5104 <li>Alignment Properties</li>
5105 <li>Annotation Scores</li>
5106 <li>Sort by scores</li>
5107 <li>Feature/annotation editing in applet</li>
5112 <li>Headless state operation in 2.2.1</li>
5113 <li>Incorrect and unstable DNA pairwise alignment</li>
5114 <li>Cut and paste of sequences with annotation</li>
5115 <li>Feature group display state in XML</li>
5116 <li>Feature ordering in XML</li>
5117 <li>blc file iteration selection using filename # suffix</li>
5118 <li>Stockholm alignment properties</li>
5119 <li>Stockhom alignment secondary structure annotation</li>
5120 <li>2.2.1 applet had no feature transparency</li>
5121 <li>Number pad keys can be used in cursor mode</li>
5122 <li>Structure Viewer mirror image resolved</li>
5129 <div align="center">
5130 <strong>2.2.1</strong><br> 12/2/07
5135 <li>Non standard characters can be read and displayed
5136 <li>Annotations/Features can be imported/exported to the
5138 <li>Applet allows editing of sequence/annotation/group
5139 name & description
5140 <li>Preference setting to display sequence name in
5142 <li>Annotation file format extended to allow
5143 Sequence_groups to be defined
5144 <li>Default opening of alignment overview panel can be
5145 specified in preferences
5146 <li>PDB residue numbering annotation added to associated
5152 <li>Applet crash under certain Linux OS with Java 1.6
5154 <li>Annotation file export / import bugs fixed
5155 <li>PNG / EPS image output bugs fixed
5161 <div align="center">
5162 <strong>2.2</strong><br> 27/11/06
5167 <li>Multiple views on alignment
5168 <li>Sequence feature editing
5169 <li>"Reload" alignment
5170 <li>"Save" to current filename
5171 <li>Background dependent text colour
5172 <li>Right align sequence ids
5173 <li>User-defined lower case residue colours
5176 <li>Menu item accelerator keys
5177 <li>Control-V pastes to current alignment
5178 <li>Cancel button for DAS Feature Fetching
5179 <li>PCA and PDB Viewers zoom via mouse roller
5180 <li>User-defined sub-tree colours and sub-tree selection
5183 <li>'New Window' button on the 'Output to Text box'
5188 <li>New memory efficient Undo/Redo System
5189 <li>Optimised symbol lookups and conservation/consensus
5191 <li>Region Conservation/Consensus recalculated after
5193 <li>Fixed Remove Empty Columns Bug (empty columns at end
5195 <li>Slowed DAS Feature Fetching for increased robustness.
5198 <li>Made angle brackets in ASCII feature descriptions
5200 <li>Re-instated Zoom function for PCA
5201 <li>Sequence descriptions conserved in web service
5203 <li>UniProt ID discoverer uses any word separated by
5205 <li>WsDbFetch query/result association resolved
5206 <li>Tree leaf to sequence mapping improved
5207 <li>Smooth fonts switch moved to FontChooser dialog box.
5215 <div align="center">
5216 <strong>2.1.1</strong><br> 12/9/06
5221 <li>Copy consensus sequence to clipboard</li>
5226 <li>Image output - rightmost residues are rendered if
5227 sequence id panel has been resized</li>
5228 <li>Image output - all offscreen group boundaries are
5230 <li>Annotation files with sequence references - all
5231 elements in file are relative to sequence position</li>
5232 <li>Mac Applet users can use Alt key for group editing</li>
5238 <div align="center">
5239 <strong>2.1</strong><br> 22/8/06
5244 <li>MAFFT Multiple Alignment in default Web Service list</li>
5245 <li>DAS Feature fetching</li>
5246 <li>Hide sequences and columns</li>
5247 <li>Export Annotations and Features</li>
5248 <li>GFF file reading / writing</li>
5249 <li>Associate structures with sequences from local PDB
5251 <li>Add sequences to exisiting alignment</li>
5252 <li>Recently opened files / URL lists</li>
5253 <li>Applet can launch the full application</li>
5254 <li>Applet has transparency for features (Java 1.2
5256 <li>Applet has user defined colours parameter</li>
5257 <li>Applet can load sequences from parameter
5258 "sequence<em>x</em>"
5264 <li>Redundancy Panel reinstalled in the Applet</li>
5265 <li>Monospaced font - EPS / rescaling bug fixed</li>
5266 <li>Annotation files with sequence references bug fixed</li>
5272 <div align="center">
5273 <strong>2.08.1</strong><br> 2/5/06
5278 <li>Change case of selected region from Popup menu</li>
5279 <li>Choose to match case when searching</li>
5280 <li>Middle mouse button and mouse movement can compress /
5281 expand the visible width and height of the alignment</li>
5286 <li>Annotation Panel displays complete JNet results</li>
5292 <div align="center">
5293 <strong>2.08b</strong><br> 18/4/06
5299 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5300 <li>Righthand label on wrapped alignments shows correct
5307 <div align="center">
5308 <strong>2.08</strong><br> 10/4/06
5313 <li>Editing can be locked to the selection area</li>
5314 <li>Keyboard editing</li>
5315 <li>Create sequence features from searches</li>
5316 <li>Precalculated annotations can be loaded onto
5318 <li>Features file allows grouping of features</li>
5319 <li>Annotation Colouring scheme added</li>
5320 <li>Smooth fonts off by default - Faster rendering</li>
5321 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5326 <li>Drag & Drop fixed on Linux</li>
5327 <li>Jalview Archive file faster to load/save, sequence
5328 descriptions saved.</li>
5334 <div align="center">
5335 <strong>2.07</strong><br> 12/12/05
5340 <li>PDB Structure Viewer enhanced</li>
5341 <li>Sequence Feature retrieval and display enhanced</li>
5342 <li>Choose to output sequence start-end after sequence
5343 name for file output</li>
5344 <li>Sequence Fetcher WSDBFetch@EBI</li>
5345 <li>Applet can read feature files, PDB files and can be
5346 used for HTML form input</li>
5351 <li>HTML output writes groups and features</li>
5352 <li>Group editing is Control and mouse click</li>
5353 <li>File IO bugs</li>
5359 <div align="center">
5360 <strong>2.06</strong><br> 28/9/05
5365 <li>View annotations in wrapped mode</li>
5366 <li>More options for PCA viewer</li>
5371 <li>GUI bugs resolved</li>
5372 <li>Runs with -nodisplay from command line</li>
5378 <div align="center">
5379 <strong>2.05b</strong><br> 15/9/05
5384 <li>Choose EPS export as lineart or text</li>
5385 <li>Jar files are executable</li>
5386 <li>Can read in Uracil - maps to unknown residue</li>
5391 <li>Known OutOfMemory errors give warning message</li>
5392 <li>Overview window calculated more efficiently</li>
5393 <li>Several GUI bugs resolved</li>
5399 <div align="center">
5400 <strong>2.05</strong><br> 30/8/05
5405 <li>Edit and annotate in "Wrapped" view</li>
5410 <li>Several GUI bugs resolved</li>
5416 <div align="center">
5417 <strong>2.04</strong><br> 24/8/05
5422 <li>Hold down mouse wheel & scroll to change font
5428 <li>Improved JPred client reliability</li>
5429 <li>Improved loading of Jalview files</li>
5435 <div align="center">
5436 <strong>2.03</strong><br> 18/8/05
5441 <li>Set Proxy server name and port in preferences</li>
5442 <li>Multiple URL links from sequence ids</li>
5443 <li>User Defined Colours can have a scheme name and added
5445 <li>Choose to ignore gaps in consensus calculation</li>
5446 <li>Unix users can set default web browser</li>
5447 <li>Runs without GUI for batch processing</li>
5448 <li>Dynamically generated Web Service Menus</li>
5453 <li>InstallAnywhere download for Sparc Solaris</li>
5459 <div align="center">
5460 <strong>2.02</strong><br> 18/7/05
5466 <li>Copy & Paste order of sequences maintains
5467 alignment order.</li>
5473 <div align="center">
5474 <strong>2.01</strong><br> 12/7/05
5479 <li>Use delete key for deleting selection.</li>
5480 <li>Use Mouse wheel to scroll sequences.</li>
5481 <li>Help file updated to describe how to add alignment
5483 <li>Version and build date written to build properties
5485 <li>InstallAnywhere installation will check for updates
5486 at launch of Jalview.</li>
5491 <li>Delete gaps bug fixed.</li>
5492 <li>FileChooser sorts columns.</li>
5493 <li>Can remove groups one by one.</li>
5494 <li>Filechooser icons installed.</li>
5495 <li>Finder ignores return character when searching.
5496 Return key will initiate a search.<br>
5503 <div align="center">
5504 <strong>2.0</strong><br> 20/6/05
5509 <li>New codebase</li>