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>
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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>29/09/2021</em></strong></td>
63 <td align="left" valign="top">
69 <li>Updated building instructions</li>
74 <!-- JAL-3840 -->Occupancy calculation is incorrect for
75 alignment columns with over -1+2^32 gaps (breaking filtering
79 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
80 scale factors being set with buggy window-managers (linux
84 <!-- JAL-3915 -->Removed RNAview checkbox and logic from Structure Preferences
86 </ul> <em>Development</em>
88 <li>Fixed non-fatal gradle errors during build</li>
93 <td width="60" align="center" nowrap><strong><a
94 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
95 <em>09/03/2021</em></strong></td>
96 <td align="left" valign="top"><em>Improved control of
97 Jalview's use of network services via jalview_properties</em>
100 <!-- JAL-3814 -->New .jalview_properties token controlling
101 launch of the news browser (like -nonews argument)
104 <!-- JAL-3813 -->New .jalview_properties token controlling
105 download of linkout URLs from
106 www.jalview.org/services/identifiers
109 <!-- JAL-3812 -->New .jalview_properties token controlling
110 download of BIOJSHTML templates
113 <!-- JAL-3811 -->New 'Discover Web Services' option to
114 trigger a one off JABAWS discovery if autodiscovery was
118 <td align="left" valign="top">
121 <!-- JAL-3818 -->Intermittent deadlock opening structure in
124 </ul> <em>New Known defects</em>
127 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
128 always restored from project (since 2.10.3)
131 <!-- JAL-3806 -->Selections from tree built from CDS aren't
132 propagated to Protein alignment (since 2.11.1.3)
138 <td width="60" align="center" nowrap><strong><a
139 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
140 <em>29/10/2020</em></strong></td>
141 <td align="left" valign="top">
146 <td align="left" valign="top">
149 <!-- JAL-3765 -->Find doesn't always highlight all matching
150 positions in a sequence (bug introduced in 2.11.1.2)
153 <!-- JAL-3760 -->Alignments containing one or more protein
154 sequences can be classed as nucleotide
157 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
158 sequences after alignment of protein products (known defect
159 first reported for 2.11.1.0)
162 <!-- JAL-3725 -->No tooltip or popup menu for genomic
163 features outwith CDS shown overlaid on protein
166 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
167 correctly mapped by Jalview (e.g. affects viral CDS with
168 ribosomal slippage, since 2.9.0)
171 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
175 <!-- JAL-3700 -->Selections in CDS sequence panel don't
176 always select corresponding protein sequences
179 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
180 column selection doesn't always ignore hidden columns
182 </ul> <em>Installer</em>
185 <!-- JAL-3611 -->Space character in Jalview install path on
186 Windows prevents install4j launching getdown
188 </ul> <em>Development</em>
191 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
192 version numbers in doc/building.md
198 <td width="60" align="center" nowrap><strong><a
199 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
200 <em>25/09/2020</em></strong></td>
201 <td align="left" valign="top">
205 <td align="left" valign="top">
208 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
209 "Encountered problems opening
210 https://www.jalview.org/examples/exampleFile_2_7.jvp"
216 <td width="60" align="center" nowrap><strong><a
217 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
218 <em>17/09/2020</em></strong></td>
219 <td align="left" valign="top">
222 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
223 residue in cursor mode
226 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
227 HTSJDK from 2.12 to 2.23
230 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
231 optimisations and improvements suggested by Bob Hanson and
232 improved compatibility with JalviewJS
235 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
236 alignments from Pfam and Rfam
239 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
240 import (no longer based on .gz extension)
243 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
246 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
247 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
251 <!-- JAL-3667 -->Improved warning messages, debug logging
252 and fixed Retry action when Jalview encounters errors when
253 saving or making backup files.
256 <!-- JAL-3676 -->Enhanced Jalview Java Console:
258 <li>Jalview's logging level can be configured</li>
259 <li>Copy to Clipboard Buttion</li>
263 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
264 when running on Linux (Requires Java 11+)
266 </ul> <em>Launching Jalview</em>
269 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
270 through a system property
273 <!-- JAL-3477 -->Improved built-in documentation and command
274 line help for configuring Jalview's memory
278 <td align="left" valign="top">
281 <!-- JAL-3691 -->Conservation and Quality tracks are shown
282 but not calculated and no protein or DNA score models are
283 available for tree/PCA calculation when launched with
284 Turkish language locale
287 <!-- JAL-3493 -->Escape does not clear highlights on the
288 alignment (Since Jalview 2.10.3)
291 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
292 doesn't slide selected sequences, just sequence under cursor
295 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
296 sequence under the cursor
299 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
300 multiple EMBL gene products shown for a single contig
303 <!-- JAL-3696 -->Errors encountered when processing variants
304 from VCF files yield "Error processing VCF: Format specifier
308 <!-- JAL-3697 -->Count of features not shown can be wrong
309 when there are both local and complementary features mapped
310 to the position under the cursor
313 <!-- JAL-3673 -->Sequence ID for reference sequence is
314 clipped when Right align Sequence IDs enabled
317 <!-- JAL-2983 -->Slider with negative range values not
318 rendered correctly in VAqua4 (Since 2.10.4)
321 <!-- JAL-3685 -->Single quotes not displayed correctly in
322 internationalised text for some messages and log output
325 <!-- JAL-3490 -->Find doesn't report matches that span
326 hidden gapped columns
329 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
330 panels, Alignment viewport and annotation renderer.
333 <!-- JAL-3561 -->Jalview ignores file format parameter
334 specifying output format when exporting an alignment via the
338 <!-- JAL-3667 -->Windows 10: For a minority of users, if
339 backups are not enabled, Jalview sometimes fails to
340 overwrite an existing file and raises a warning dialog. (in
341 2.11.0, and 2.11.1.0, the workaround is to try to save the
342 file again, and if that fails, delete the original file and
346 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
350 <!-- JAL-3741 -->References to http://www.jalview.org in
351 program and documentation
353 </ul> <em>Launching Jalview</em>
356 <!-- JAL-3718 -->Jalview application fails when launched the
357 first time for a version that has different jars to the
358 previous launched version.
360 </ul> <em>Developing Jalview</em>
363 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
364 data, causing cloverReport gradle task to fail with an
368 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
369 monitor the release channel
371 </ul> <em>New Known defects</em>
374 <!-- JAL-3748 -->CDS shown in result of submitting proteins
375 in a CDS/Protein alignment to a web service is wrong when
376 proteins share a common transcript sequence (e.g.
377 genome of RNA viruses)
380 <!-- JAL-3576 -->Co-located features exported and re-imported
381 are ordered differently when shown on alignment and in
382 tooltips. (Also affects v2.11.1.0)
385 <!-- JAL-3702 -->Drag and drop of alignment file onto
386 alignment window when in a HiDPI scaled mode in Linux only
387 works for the top left quadrant of the alignment window
390 <!-- JAL-3701 -->Stale build data in jalview standalone jar
391 builds (only affects 2.11.1.1 branch)
394 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
395 when alignment view restored from project (since Jalview 2.11.0)
398 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
399 protein products for certain ENA records are repeatedly
400 shown via Calculate->Show Cross Refs
406 <td width="60" align="center" nowrap><strong><a
407 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
408 <em>22/04/2020</em></strong></td>
409 <td align="left" valign="top">
412 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
413 'virtual' codon features shown on protein (or vice versa)
414 for display in alignments, on structure views (including
415 transfer to UCSF chimera), in feature reports and for
419 <!-- JAL-3121 -->Feature attributes from VCF files can be
420 exported and re-imported as GFF3 files
423 <!-- JAL-3376 -->Capture VCF "fixed column" values
424 POS, ID, QUAL, FILTER as Feature Attributes
427 <!-- JAL-3375 -->More robust VCF numeric data field
428 validation while parsing
431 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
435 <!-- JAL-3535 -->Feature Settings dialog title includes name
439 <!-- JAL-3538 -->Font anti-aliasing in alignment views
443 <!-- JAL-3468 -->Very long feature descriptions truncated in
447 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
448 with no feature types visible
451 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
453 </ul><em>Jalview Installer</em>
456 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
457 in console (may be null when Jalview launched as executable jar or via conda)
460 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
463 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
466 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
468 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
469 </ul> <em>Release processes</em>
472 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
475 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
477 </ul> <em>Build System</em>
480 <!-- JAL-3510 -->Clover updated to 4.4.1
483 <!-- JAL-3513 -->Test code included in Clover coverage
487 <em>Groovy Scripts</em>
490 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
491 to stdout containing the consensus sequence for each
492 alignment in a Jalview session
495 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
496 genomic sequence_variant annotation from CDS as
497 missense_variant or synonymous_variant on protein products.
501 <td align="left" valign="top">
504 <!-- JAL-3581 -->Hidden sequence markers still visible when
505 'Show hidden markers' option is not ticked
508 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
509 PNG output when 'Automatically set ID width' is set in
510 jalview preferences or properties file
513 <!-- JAL-3571 -->Feature Editor dialog can be opened when
514 'Show Sequence Features' option is not ticked
517 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
518 buttons in Feature Settings dialog are clicked when no
522 <!-- JAL-3412 -->ID margins for CDS and Protein views not
523 equal when split frame is first opened
526 <!-- JAL-3296 -->Sequence position numbers in status bar not
527 correct after editing a sequence's start position
530 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
531 with annotation and exceptions thrown when only a few
532 columns shown in wrapped mode
535 <!-- JAL-3386 -->Sequence IDs missing in headless export of
536 wrapped alignment figure with annotations
539 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
540 ID fails with ClassCastException
543 <!-- JAL-3389 -->Chimera session not restored from Jalview
547 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
548 feature settings dialog also selects columns
551 <!-- JAL-3473 -->SpinnerNumberModel causes
552 IllegalArgumentException in some circumstances
555 <!-- JAL-3534 -->Multiple feature settings dialogs can be
559 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
560 alignment window is closed
563 <!-- JAL-3406 -->Credits missing some authors in Jalview
564 help documentation for 2.11.0 release
567 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
568 includes Pfam ID as sequence's accession rather than its
571 </ul> <em>Java 11 Compatibility issues</em>
574 <!-- JAL-2987 -->OSX - Can't view some search results in
575 PDB/Uniprot search panel
577 </ul> <em>Installer</em>
580 <!-- JAL-3447 -->Jalview should not create file associations
581 for 3D structure files (.pdb, .mmcif. .cif)
583 </ul> <em>Repository and Source Release</em>
586 <!-- JAL-3474 -->removed obsolete .cvsignore files from
590 <!-- JAL-3541 -->Clover report generation running out of
593 </ul> <em>New Known Issues</em>
596 <!-- JAL-3523 -->OSX - Current working directory not
597 preserved when Jalview.app launched with parameters from
601 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
602 clipped in headless figure export when Right Align option
606 <!-- JAL-3542 -->Jalview Installation type always reports
607 'Source' in console output
610 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
611 bamboo server but run fine locally.
617 <td width="60" align="center" nowrap>
618 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
619 <em>04/07/2019</em></strong>
621 <td align="left" valign="top">
624 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
625 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
626 source project) rather than InstallAnywhere
629 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
630 settings, receive over the air updates and launch specific
631 versions via (<a href="https://github.com/threerings/getdown">Three
635 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
636 formats supported by Jalview (including .jvp project files)
639 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
640 arguments and switch between different getdown channels
643 <!-- JAL-3141 -->Backup files created when saving Jalview project
648 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
649 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
651 <!-- JAL-2620 -->Alternative genetic code tables for
652 'Translate as cDNA'</li>
654 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
655 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
658 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
659 implementation that allows updates) used for Sequence Feature collections</li>
661 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
662 features can be filtered and shaded according to any
663 associated attributes (e.g. variant attributes from VCF
664 file, or key-value pairs imported from column 9 of GFF
668 <!-- JAL-2879 -->Feature Attributes and shading schemes
669 stored and restored from Jalview Projects
672 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
673 recognise variant features
676 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
677 sequences (also coloured red by default)
680 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
684 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
685 algorithm (Z-sort/transparency and filter aware)
688 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
694 <!-- JAL-3205 -->Symmetric score matrices for faster
695 tree and PCA calculations
697 <li><strong>Principal Components Analysis Viewer</strong>
700 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
701 and Viewer state saved in Jalview Project
703 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
706 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
710 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
715 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
717 <li><strong>Speed and Efficiency</strong>
720 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
721 multiple groups when working with large alignments
724 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
728 <li><strong>User Interface</strong>
731 <!-- JAL-2933 -->Finder panel remembers last position in each
735 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
736 what is shown)<br />Only visible regions of alignment are shown by
737 default (can be changed in user preferences)
740 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
741 to the Overwrite Dialog
744 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
748 <!-- JAL-1244 -->Status bar shows bounds when dragging a
749 selection region, and gap count when inserting or deleting gaps
752 <!-- JAL-3132 -->Status bar updates over sequence and annotation
756 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
760 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
764 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
767 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
771 <!-- JAL-3181 -->Consistent ordering of links in sequence id
775 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
777 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
781 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
782 <li><strong>Java 11 Support (not yet on general release)</strong>
785 <!-- -->OSX GUI integrations for App menu's 'About' entry and
790 <em>Deprecations</em>
792 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
793 capabilities removed from the Jalview Desktop
795 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
796 unmarshalling has been replaced by JAXB for Jalview projects
797 and XML based data retrieval clients</li>
798 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
799 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
800 </ul> <em>Documentation</em>
802 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
803 not supported in EPS figure export
805 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
806 </ul> <em>Development and Release Processes</em>
809 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
812 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
814 <!-- JAL-3225 -->Eclipse project configuration managed with
818 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
819 Bamboo continuous integration for unattended Test Suite
823 <!-- JAL-2864 -->Memory test suite to detect leaks in common
827 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
831 <!-- JAL-3248 -->Developer documentation migrated to
832 markdown (with HTML rendering)
835 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
838 <!-- JAL-3289 -->New URLs for publishing development
843 <td align="left" valign="top">
846 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
849 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
850 superposition in Jmol fail on Windows
853 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
854 structures for sequences with lots of PDB structures
857 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
861 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
862 project involving multiple views
865 <!-- JAL-3164 -->Overview for complementary view in a linked
866 CDS/Protein alignment is not updated when Hide Columns by
867 Annotation dialog hides columns
870 <!-- JAL-3158 -->Selection highlighting in the complement of a
871 CDS/Protein alignment stops working after making a selection in
872 one view, then making another selection in the other view
875 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
879 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
880 Settings and Jalview Preferences panels
883 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
884 overview with large alignments
887 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
888 region if columns were selected by dragging right-to-left and the
889 mouse moved to the left of the first column
892 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
893 hidden column marker via scale popup menu
896 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
897 doesn't tell users the invalid URL
900 <!-- JAL-2816 -->Tooltips displayed for features filtered by
904 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
905 show cross references or Fetch Database References are shown in
909 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
910 peptide sequence (computed variant shown as p.Res.null)
913 <!-- JAL-2060 -->'Graduated colour' option not offered for
914 manually created features (where feature score is Float.NaN)
917 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
918 when columns are hidden
921 <!-- JAL-3082 -->Regular expression error for '(' in Select
922 Columns by Annotation description
925 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
926 out of Scale or Annotation Panel
929 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
933 <!-- JAL-3074 -->Left/right drag in annotation can scroll
937 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
941 <!-- JAL-3002 -->Column display is out by one after Page Down,
942 Page Up in wrapped mode
945 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
948 <!-- JAL-2932 -->Finder searches in minimised alignments
951 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
952 on opening an alignment
955 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
959 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
960 different groups in the alignment are selected
963 <!-- JAL-2717 -->Internationalised colour scheme names not shown
967 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
971 <!-- JAL-3125 -->Value input for graduated feature colour
972 threshold gets 'unrounded'
975 <!-- JAL-2982 -->PCA image export doesn't respect background
979 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
982 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
985 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
989 <!-- JAL-2964 -->Associate Tree with All Views not restored from
993 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
994 shown in complementary view
997 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
998 without normalisation
1001 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1005 <!-- JAL-914 -->Help page can be opened twice
1008 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1010 </ul> <em>Editing</em>
1013 <!-- JAL-2822 -->Start and End should be updated when sequence
1014 data at beginning or end of alignment added/removed via 'Edit'
1018 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1019 relocate sequence features correctly when start of sequence is
1020 removed (Known defect since 2.10)
1023 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1024 dialog corrupts dataset sequence
1027 <!-- JAL-868 -->Structure colours not updated when associated tree
1028 repartitions the alignment view (Regression in 2.10.5)
1030 </ul> <em>Datamodel</em>
1033 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1034 sequence's End is greater than its length
1036 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1037 general release)</em>
1040 <!-- JAL-3288 -->Menus work properly in split-screen
1042 </ul> <em>New Known Defects</em>
1045 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1048 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1049 regions of protein alignment.
1052 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1053 is restored from a Jalview 2.11 project
1056 <!-- JAL-3213 -->Alignment panel height can be too small after
1060 <!-- JAL-3240 -->Display is incorrect after removing gapped
1061 columns within hidden columns
1064 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1065 window after dragging left to select columns to left of visible
1069 <!-- JAL-2876 -->Features coloured according to their description
1070 string and thresholded by score in earlier versions of Jalview are
1071 not shown as thresholded features in 2.11. To workaround please
1072 create a Score filter instead.
1075 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1077 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1080 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1081 alignments with multiple views can close views unexpectedly
1084 <em>Java 11 Specific defects</em>
1087 <!-- JAL-3235 -->Jalview Properties file is not sorted
1088 alphabetically when saved
1094 <td width="60" nowrap>
1095 <div align="center">
1096 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1099 <td><div align="left">
1103 <!-- JAL-3101 -->Default memory for Jalview webstart and
1104 InstallAnywhere increased to 1G.
1107 <!-- JAL-247 -->Hidden sequence markers and representative
1108 sequence bolding included when exporting alignment as EPS,
1109 SVG, PNG or HTML. <em>Display is configured via the
1110 Format menu, or for command-line use via a Jalview
1111 properties file.</em>
1114 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1115 API and sequence data now imported as JSON.
1118 <!-- JAL-3065 -->Change in recommended way of starting
1119 Jalview via a Java command line: add jars in lib directory
1120 to CLASSPATH, rather than via the deprecated java.ext.dirs
1124 <em>Development</em>
1127 <!-- JAL-3047 -->Support added to execute test suite
1128 instrumented with <a href="http://openclover.org/">Open
1133 <td><div align="left">
1137 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1138 row shown in Feredoxin Structure alignment view of example
1142 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1143 annotation displayed.
1146 <!-- JAL-3107 -->Group conservation/consensus not shown
1147 for newly created group when 'Apply to all groups'
1151 <!-- JAL-3087 -->Corrupted display when switching to
1152 wrapped mode when sequence panel's vertical scrollbar is
1156 <!-- JAL-3003 -->Alignment is black in exported EPS file
1157 when sequences are selected in exported view.</em>
1160 <!-- JAL-3059 -->Groups with different coloured borders
1161 aren't rendered with correct colour.
1164 <!-- JAL-3092 -->Jalview could hang when importing certain
1165 types of knotted RNA secondary structure.
1168 <!-- JAL-3095 -->Sequence highlight and selection in
1169 trimmed VARNA 2D structure is incorrect for sequences that
1173 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1174 annotation when columns are inserted into an alignment,
1175 and when exporting as Stockholm flatfile.
1178 <!-- JAL-3053 -->Jalview annotation rows containing upper
1179 and lower-case 'E' and 'H' do not automatically get
1180 treated as RNA secondary structure.
1183 <!-- JAL-3106 -->.jvp should be used as default extension
1184 (not .jar) when saving a Jalview project file.
1187 <!-- JAL-3105 -->Mac Users: closing a window correctly
1188 transfers focus to previous window on OSX
1191 <em>Java 10 Issues Resolved</em>
1194 <!-- JAL-2988 -->OSX - Can't save new files via the File
1195 or export menus by typing in a name into the Save dialog
1199 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1200 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1201 'look and feel' which has improved compatibility with the
1202 latest version of OSX.
1209 <td width="60" nowrap>
1210 <div align="center">
1211 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1212 <em>7/06/2018</em></strong>
1215 <td><div align="left">
1219 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1220 annotation retrieved from Uniprot
1223 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1224 onto the Jalview Desktop
1228 <td><div align="left">
1232 <!-- JAL-3017 -->Cannot import features with multiple
1233 variant elements (blocks import of some Uniprot records)
1236 <!-- JAL-2997 -->Clustal files with sequence positions in
1237 right-hand column parsed correctly
1240 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1241 not alignment area in exported graphic
1244 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1245 window has input focus
1248 <!-- JAL-2992 -->Annotation panel set too high when
1249 annotation added to view (Windows)
1252 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1253 network connectivity is poor
1256 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1257 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1258 the currently open URL and links from a page viewed in
1259 Firefox or Chrome on Windows is now fully supported. If
1260 you are using Edge, only links in the page can be
1261 dragged, and with Internet Explorer, only the currently
1262 open URL in the browser can be dropped onto Jalview.</em>
1265 <em>New Known Defects</em>
1267 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1272 <td width="60" nowrap>
1273 <div align="center">
1274 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1277 <td><div align="left">
1281 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1282 for disabling automatic superposition of multiple
1283 structures and open structures in existing views
1286 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1287 ID and annotation area margins can be click-dragged to
1291 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1295 <!-- JAL-2759 -->Improved performance for large alignments
1296 and lots of hidden columns
1299 <!-- JAL-2593 -->Improved performance when rendering lots
1300 of features (particularly when transparency is disabled)
1303 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1304 exchange of Jalview features and Chimera attributes made
1310 <td><div align="left">
1313 <!-- JAL-2899 -->Structure and Overview aren't updated
1314 when Colour By Annotation threshold slider is adjusted
1317 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1318 overlapping alignment panel
1321 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1325 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1326 improved: CDS not handled correctly if transcript has no
1330 <!-- JAL-2321 -->Secondary structure and temperature
1331 factor annotation not added to sequence when local PDB
1332 file associated with it by drag'n'drop or structure
1336 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1337 dialog doesn't import PDB files dropped on an alignment
1340 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1341 scroll bar doesn't work for some CDS/Protein views
1344 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1345 Java 1.8u153 onwards and Java 1.9u4+.
1348 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1349 columns in annotation row
1352 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1353 honored in batch mode
1356 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1357 for structures added to existing Jmol view
1360 <!-- JAL-2223 -->'View Mappings' includes duplicate
1361 entries after importing project with multiple views
1364 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1365 protein sequences via SIFTS from associated PDB entries
1366 with negative residue numbers or missing residues fails
1369 <!-- JAL-2952 -->Exception when shading sequence with negative
1370 Temperature Factor values from annotated PDB files (e.g.
1371 as generated by CONSURF)
1374 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1375 tooltip doesn't include a text description of mutation
1378 <!-- JAL-2922 -->Invert displayed features very slow when
1379 structure and/or overview windows are also shown
1382 <!-- JAL-2954 -->Selecting columns from highlighted regions
1383 very slow for alignments with large numbers of sequences
1386 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1387 with 'StringIndexOutOfBounds'
1390 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1391 platforms running Java 10
1394 <!-- JAL-2960 -->Adding a structure to existing structure
1395 view appears to do nothing because the view is hidden behind the alignment view
1401 <!-- JAL-2926 -->Copy consensus sequence option in applet
1402 should copy the group consensus when popup is opened on it
1408 <!-- JAL-2913 -->Fixed ID width preference is not respected
1411 <em>New Known Defects</em>
1414 <!-- JAL-2973 --> Exceptions occasionally raised when
1415 editing a large alignment and overview is displayed
1418 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1419 repeatedly after a series of edits even when the overview
1420 is no longer reflecting updates
1423 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1424 structures for protein subsequence (if 'Trim Retrieved
1425 Sequences' enabled) or Ensembl isoforms (Workaround in
1426 2.10.4 is to fail back to N&W mapping)
1429 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1430 option gives blank output
1437 <td width="60" nowrap>
1438 <div align="center">
1439 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1442 <td><div align="left">
1443 <ul><li>Updated Certum Codesigning Certificate
1444 (Valid till 30th November 2018)</li></ul></div></td>
1445 <td><div align="left">
1446 <em>Desktop</em><ul>
1448 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1449 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1450 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1451 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1452 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1453 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1454 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1460 <td width="60" nowrap>
1461 <div align="center">
1462 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1465 <td><div align="left">
1469 <!-- JAL-2446 -->Faster and more efficient management and
1470 rendering of sequence features
1473 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1474 429 rate limit request hander
1477 <!-- JAL-2773 -->Structure views don't get updated unless
1478 their colours have changed
1481 <!-- JAL-2495 -->All linked sequences are highlighted for
1482 a structure mousover (Jmol) or selection (Chimera)
1485 <!-- JAL-2790 -->'Cancel' button in progress bar for
1486 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1489 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1490 view from Ensembl locus cross-references
1493 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1497 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1498 feature can be disabled
1501 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1502 PDB easier retrieval of sequences for lists of IDs
1505 <!-- JAL-2758 -->Short names for sequences retrieved from
1511 <li>Groovy interpreter updated to 2.4.12</li>
1512 <li>Example groovy script for generating a matrix of
1513 percent identity scores for current alignment.</li>
1515 <em>Testing and Deployment</em>
1518 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1522 <td><div align="left">
1526 <!-- JAL-2643 -->Pressing tab after updating the colour
1527 threshold text field doesn't trigger an update to the
1531 <!-- JAL-2682 -->Race condition when parsing sequence ID
1535 <!-- JAL-2608 -->Overview windows are also closed when
1536 alignment window is closed
1539 <!-- JAL-2548 -->Export of features doesn't always respect
1543 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1544 takes a long time in Cursor mode
1550 <!-- JAL-2777 -->Structures with whitespace chainCode
1551 cannot be viewed in Chimera
1554 <!-- JAL-2728 -->Protein annotation panel too high in
1558 <!-- JAL-2757 -->Can't edit the query after the server
1559 error warning icon is shown in Uniprot and PDB Free Text
1563 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1566 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1569 <!-- JAL-2739 -->Hidden column marker in last column not
1570 rendered when switching back from Wrapped to normal view
1573 <!-- JAL-2768 -->Annotation display corrupted when
1574 scrolling right in unwapped alignment view
1577 <!-- JAL-2542 -->Existing features on subsequence
1578 incorrectly relocated when full sequence retrieved from
1582 <!-- JAL-2733 -->Last reported memory still shown when
1583 Desktop->Show Memory is unticked (OSX only)
1586 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1587 features of same type and group to be selected for
1591 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1592 alignments when hidden columns are present
1595 <!-- JAL-2392 -->Jalview freezes when loading and
1596 displaying several structures
1599 <!-- JAL-2732 -->Black outlines left after resizing or
1603 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1604 within the Jalview desktop on OSX
1607 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1608 when in wrapped alignment mode
1611 <!-- JAL-2636 -->Scale mark not shown when close to right
1612 hand end of alignment
1615 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1616 each selected sequence do not have correct start/end
1620 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1621 after canceling the Alignment Window's Font dialog
1624 <!-- JAL-2036 -->Show cross-references not enabled after
1625 restoring project until a new view is created
1628 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1629 URL links appears when only default EMBL-EBI link is
1630 configured (since 2.10.2b2)
1633 <!-- JAL-2775 -->Overview redraws whole window when box
1634 position is adjusted
1637 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1638 in a multi-chain structure when viewing alignment
1639 involving more than one chain (since 2.10)
1642 <!-- JAL-2811 -->Double residue highlights in cursor mode
1643 if new selection moves alignment window
1646 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1647 arrow key in cursor mode to pass hidden column marker
1650 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1651 that produces correctly annotated transcripts and products
1654 <!-- JAL-2776 -->Toggling a feature group after first time
1655 doesn't update associated structure view
1658 <em>Applet</em><br />
1661 <!-- JAL-2687 -->Concurrent modification exception when
1662 closing alignment panel
1665 <em>BioJSON</em><br />
1668 <!-- JAL-2546 -->BioJSON export does not preserve
1669 non-positional features
1672 <em>New Known Issues</em>
1675 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1676 sequence features correctly (for many previous versions of
1680 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1681 using cursor in wrapped panel other than top
1684 <!-- JAL-2791 -->Select columns containing feature ignores
1685 graduated colour threshold
1688 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1689 always preserve numbering and sequence features
1692 <em>Known Java 9 Issues</em>
1695 <!-- JAL-2902 -->Groovy Console very slow to open and is
1696 not responsive when entering characters (Webstart, Java
1703 <td width="60" nowrap>
1704 <div align="center">
1705 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1706 <em>2/10/2017</em></strong>
1709 <td><div align="left">
1710 <em>New features in Jalview Desktop</em>
1713 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1715 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1719 <td><div align="left">
1723 <td width="60" nowrap>
1724 <div align="center">
1725 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1726 <em>7/9/2017</em></strong>
1729 <td><div align="left">
1733 <!-- JAL-2588 -->Show gaps in overview window by colouring
1734 in grey (sequences used to be coloured grey, and gaps were
1738 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1742 <!-- JAL-2587 -->Overview updates immediately on increase
1743 in size and progress bar shown as higher resolution
1744 overview is recalculated
1749 <td><div align="left">
1753 <!-- JAL-2664 -->Overview window redraws every hidden
1754 column region row by row
1757 <!-- JAL-2681 -->duplicate protein sequences shown after
1758 retrieving Ensembl crossrefs for sequences from Uniprot
1761 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1762 format setting is unticked
1765 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1766 if group has show boxes format setting unticked
1769 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1770 autoscrolling whilst dragging current selection group to
1771 include sequences and columns not currently displayed
1774 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1775 assemblies are imported via CIF file
1778 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1779 displayed when threshold or conservation colouring is also
1783 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1787 <!-- JAL-2673 -->Jalview continues to scroll after
1788 dragging a selected region off the visible region of the
1792 <!-- JAL-2724 -->Cannot apply annotation based
1793 colourscheme to all groups in a view
1796 <!-- JAL-2511 -->IDs don't line up with sequences
1797 initially after font size change using the Font chooser or
1804 <td width="60" nowrap>
1805 <div align="center">
1806 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1809 <td><div align="left">
1810 <em>Calculations</em>
1814 <!-- JAL-1933 -->Occupancy annotation row shows number of
1815 ungapped positions in each column of the alignment.
1818 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1819 a calculation dialog box
1822 <!-- JAL-2379 -->Revised implementation of PCA for speed
1823 and memory efficiency (~30x faster)
1826 <!-- JAL-2403 -->Revised implementation of sequence
1827 similarity scores as used by Tree, PCA, Shading Consensus
1828 and other calculations
1831 <!-- JAL-2416 -->Score matrices are stored as resource
1832 files within the Jalview codebase
1835 <!-- JAL-2500 -->Trees computed on Sequence Feature
1836 Similarity may have different topology due to increased
1843 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1844 model for alignments and groups
1847 <!-- JAL-384 -->Custom shading schemes created via groovy
1854 <!-- JAL-2526 -->Efficiency improvements for interacting
1855 with alignment and overview windows
1858 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1862 <!-- JAL-2388 -->Hidden columns and sequences can be
1866 <!-- JAL-2611 -->Click-drag in visible area allows fine
1867 adjustment of visible position
1871 <em>Data import/export</em>
1874 <!-- JAL-2535 -->Posterior probability annotation from
1875 Stockholm files imported as sequence associated annotation
1878 <!-- JAL-2507 -->More robust per-sequence positional
1879 annotation input/output via stockholm flatfile
1882 <!-- JAL-2533 -->Sequence names don't include file
1883 extension when importing structure files without embedded
1884 names or PDB accessions
1887 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1888 format sequence substitution matrices
1891 <em>User Interface</em>
1894 <!-- JAL-2447 --> Experimental Features Checkbox in
1895 Desktop's Tools menu to hide or show untested features in
1899 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1900 via Overview or sequence motif search operations
1903 <!-- JAL-2547 -->Amend sequence features dialog box can be
1904 opened by double clicking gaps within sequence feature
1908 <!-- JAL-1476 -->Status bar message shown when not enough
1909 aligned positions were available to create a 3D structure
1913 <em>3D Structure</em>
1916 <!-- JAL-2430 -->Hidden regions in alignment views are not
1917 coloured in linked structure views
1920 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1921 file-based command exchange
1924 <!-- JAL-2375 -->Structure chooser automatically shows
1925 Cached Structures rather than querying the PDBe if
1926 structures are already available for sequences
1929 <!-- JAL-2520 -->Structures imported via URL are cached in
1930 the Jalview project rather than downloaded again when the
1931 project is reopened.
1934 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1935 to transfer Chimera's structure attributes as Jalview
1936 features, and vice-versa (<strong>Experimental
1940 <em>Web Services</em>
1943 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1946 <!-- JAL-2335 -->Filter non-standard amino acids and
1947 nucleotides when submitting to AACon and other MSA
1951 <!-- JAL-2316, -->URLs for viewing database
1952 cross-references provided by identifiers.org and the
1953 EMBL-EBI's MIRIAM DB
1960 <!-- JAL-2344 -->FileFormatI interface for describing and
1961 identifying file formats (instead of String constants)
1964 <!-- JAL-2228 -->FeatureCounter script refactored for
1965 efficiency when counting all displayed features (not
1966 backwards compatible with 2.10.1)
1969 <em>Example files</em>
1972 <!-- JAL-2631 -->Graduated feature colour style example
1973 included in the example feature file
1976 <em>Documentation</em>
1979 <!-- JAL-2339 -->Release notes reformatted for readability
1980 with the built-in Java help viewer
1983 <!-- JAL-1644 -->Find documentation updated with 'search
1984 sequence description' option
1990 <!-- JAL-2485, -->External service integration tests for
1991 Uniprot REST Free Text Search Client
1994 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1997 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2002 <td><div align="left">
2003 <em>Calculations</em>
2006 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2007 matrix - C->R should be '-3'<br />Old matrix restored
2008 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2010 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2011 Jalview's treatment of gaps in PCA and substitution matrix
2012 based Tree calculations.<br /> <br />In earlier versions
2013 of Jalview, gaps matching gaps were penalised, and gaps
2014 matching non-gaps penalised even more. In the PCA
2015 calculation, gaps were actually treated as non-gaps - so
2016 different costs were applied, which meant Jalview's PCAs
2017 were different to those produced by SeqSpace.<br />Jalview
2018 now treats gaps in the same way as SeqSpace (ie it scores
2019 them as 0). <br /> <br />Enter the following in the
2020 Groovy console to restore pre-2.10.2 behaviour:<br />
2021 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2022 // for 2.10.1 mode <br />
2023 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2024 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2025 these settings will affect all subsequent tree and PCA
2026 calculations (not recommended)</em></li>
2028 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2029 scaling of branch lengths for trees computed using
2030 Sequence Feature Similarity.
2033 <!-- JAL-2377 -->PCA calculation could hang when
2034 generating output report when working with highly
2035 redundant alignments
2038 <!-- JAL-2544 --> Sort by features includes features to
2039 right of selected region when gaps present on right-hand
2043 <em>User Interface</em>
2046 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2047 doesn't reselect a specific sequence's associated
2048 annotation after it was used for colouring a view
2051 <!-- JAL-2419 -->Current selection lost if popup menu
2052 opened on a region of alignment without groups
2055 <!-- JAL-2374 -->Popup menu not always shown for regions
2056 of an alignment with overlapping groups
2059 <!-- JAL-2310 -->Finder double counts if both a sequence's
2060 name and description match
2063 <!-- JAL-2370 -->Hiding column selection containing two
2064 hidden regions results in incorrect hidden regions
2067 <!-- JAL-2386 -->'Apply to all groups' setting when
2068 changing colour does not apply Conservation slider value
2072 <!-- JAL-2373 -->Percentage identity and conservation menu
2073 items do not show a tick or allow shading to be disabled
2076 <!-- JAL-2385 -->Conservation shading or PID threshold
2077 lost when base colourscheme changed if slider not visible
2080 <!-- JAL-2547 -->Sequence features shown in tooltip for
2081 gaps before start of features
2084 <!-- JAL-2623 -->Graduated feature colour threshold not
2085 restored to UI when feature colour is edited
2088 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2089 a time when scrolling vertically in wrapped mode.
2092 <!-- JAL-2630 -->Structure and alignment overview update
2093 as graduate feature colour settings are modified via the
2097 <!-- JAL-2034 -->Overview window doesn't always update
2098 when a group defined on the alignment is resized
2101 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2102 wrapped view result in positional status updates
2106 <!-- JAL-2563 -->Status bar doesn't show position for
2107 ambiguous amino acid and nucleotide symbols
2110 <!-- JAL-2602 -->Copy consensus sequence failed if
2111 alignment included gapped columns
2114 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2115 widgets don't permanently disappear
2118 <!-- JAL-2503 -->Cannot select or filter quantitative
2119 annotation that are shown only as column labels (e.g.
2120 T-Coffee column reliability scores)
2123 <!-- JAL-2594 -->Exception thrown if trying to create a
2124 sequence feature on gaps only
2127 <!-- JAL-2504 -->Features created with 'New feature'
2128 button from a Find inherit previously defined feature type
2129 rather than the Find query string
2132 <!-- JAL-2423 -->incorrect title in output window when
2133 exporting tree calculated in Jalview
2136 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2137 and then revealing them reorders sequences on the
2141 <!-- JAL-964 -->Group panel in sequence feature settings
2142 doesn't update to reflect available set of groups after
2143 interactively adding or modifying features
2146 <!-- JAL-2225 -->Sequence Database chooser unusable on
2150 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2151 only excluded gaps in current sequence and ignored
2158 <!-- JAL-2421 -->Overview window visible region moves
2159 erratically when hidden rows or columns are present
2162 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2163 Structure Viewer's colour menu don't correspond to
2167 <!-- JAL-2405 -->Protein specific colours only offered in
2168 colour and group colour menu for protein alignments
2171 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2172 reflect currently selected view or group's shading
2176 <!-- JAL-2624 -->Feature colour thresholds not respected
2177 when rendered on overview and structures when opacity at
2181 <!-- JAL-2589 -->User defined gap colour not shown in
2182 overview when features overlaid on alignment
2185 <!-- JAL-2567 -->Feature settings for different views not
2186 recovered correctly from Jalview project file
2189 <!-- JAL-2256 -->Feature colours in overview when first opened
2190 (automatically via preferences) are different to the main
2194 <em>Data import/export</em>
2197 <!-- JAL-2576 -->Very large alignments take a long time to
2201 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2202 added after a sequence was imported are not written to
2206 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2207 when importing RNA secondary structure via Stockholm
2210 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2211 not shown in correct direction for simple pseudoknots
2214 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2215 with lightGray or darkGray via features file (but can
2219 <!-- JAL-2383 -->Above PID colour threshold not recovered
2220 when alignment view imported from project
2223 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2224 structure and sequences extracted from structure files
2225 imported via URL and viewed in Jmol
2228 <!-- JAL-2520 -->Structures loaded via URL are saved in
2229 Jalview Projects rather than fetched via URL again when
2230 the project is loaded and the structure viewed
2233 <em>Web Services</em>
2236 <!-- JAL-2519 -->EnsemblGenomes example failing after
2237 release of Ensembl v.88
2240 <!-- JAL-2366 -->Proxy server address and port always
2241 appear enabled in Preferences->Connections
2244 <!-- JAL-2461 -->DAS registry not found exceptions
2245 removed from console output
2248 <!-- JAL-2582 -->Cannot retrieve protein products from
2249 Ensembl by Peptide ID
2252 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2253 created from SIFTs, and spurious 'Couldn't open structure
2254 in Chimera' errors raised after April 2017 update (problem
2255 due to 'null' string rather than empty string used for
2256 residues with no corresponding PDB mapping).
2259 <em>Application UI</em>
2262 <!-- JAL-2361 -->User Defined Colours not added to Colour
2266 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2267 case' residues (button in colourscheme editor debugged and
2268 new documentation and tooltips added)
2271 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2272 doesn't restore group-specific text colour thresholds
2275 <!-- JAL-2243 -->Feature settings panel does not update as
2276 new features are added to alignment
2279 <!-- JAL-2532 -->Cancel in feature settings reverts
2280 changes to feature colours via the Amend features dialog
2283 <!-- JAL-2506 -->Null pointer exception when attempting to
2284 edit graduated feature colour via amend features dialog
2288 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2289 selection menu changes colours of alignment views
2292 <!-- JAL-2426 -->Spurious exceptions in console raised
2293 from alignment calculation workers after alignment has
2297 <!-- JAL-1608 -->Typo in selection popup menu - Create
2298 groups now 'Create Group'
2301 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2302 Create/Undefine group doesn't always work
2305 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2306 shown again after pressing 'Cancel'
2309 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2310 adjusts start position in wrap mode
2313 <!-- JAL-2563 -->Status bar doesn't show positions for
2314 ambiguous amino acids
2317 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2318 CDS/Protein view after CDS sequences added for aligned
2322 <!-- JAL-2592 -->User defined colourschemes called 'User
2323 Defined' don't appear in Colours menu
2329 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2330 score models doesn't always result in an updated PCA plot
2333 <!-- JAL-2442 -->Features not rendered as transparent on
2334 overview or linked structure view
2337 <!-- JAL-2372 -->Colour group by conservation doesn't
2341 <!-- JAL-2517 -->Hitting Cancel after applying
2342 user-defined colourscheme doesn't restore original
2349 <!-- JAL-2314 -->Unit test failure:
2350 jalview.ws.jabaws.RNAStructExportImport setup fails
2353 <!-- JAL-2307 -->Unit test failure:
2354 jalview.ws.sifts.SiftsClientTest due to compatibility
2355 problems with deep array comparison equality asserts in
2356 successive versions of TestNG
2359 <!-- JAL-2479 -->Relocated StructureChooserTest and
2360 ParameterUtilsTest Unit tests to Network suite
2363 <em>New Known Issues</em>
2366 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2367 phase after a sequence motif find operation
2370 <!-- JAL-2550 -->Importing annotation file with rows
2371 containing just upper and lower case letters are
2372 interpreted as WUSS RNA secondary structure symbols
2375 <!-- JAL-2590 -->Cannot load and display Newick trees
2376 reliably from eggnog Ortholog database
2379 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2380 containing features of type Highlight' when 'B' is pressed
2381 to mark columns containing highlighted regions.
2384 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2385 doesn't always add secondary structure annotation.
2390 <td width="60" nowrap>
2391 <div align="center">
2392 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2395 <td><div align="left">
2399 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2400 for all consensus calculations
2403 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2406 <li>Updated Jalview's Certum code signing certificate
2409 <em>Application</em>
2412 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2413 set of database cross-references, sorted alphabetically
2416 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2417 from database cross references. Users with custom links
2418 will receive a <a href="webServices/urllinks.html#warning">warning
2419 dialog</a> asking them to update their preferences.
2422 <!-- JAL-2287-->Cancel button and escape listener on
2423 dialog warning user about disconnecting Jalview from a
2427 <!-- JAL-2320-->Jalview's Chimera control window closes if
2428 the Chimera it is connected to is shut down
2431 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2432 columns menu item to mark columns containing highlighted
2433 regions (e.g. from structure selections or results of a
2437 <!-- JAL-2284-->Command line option for batch-generation
2438 of HTML pages rendering alignment data with the BioJS
2448 <!-- JAL-2286 -->Columns with more than one modal residue
2449 are not coloured or thresholded according to percent
2450 identity (first observed in Jalview 2.8.2)
2453 <!-- JAL-2301 -->Threonine incorrectly reported as not
2457 <!-- JAL-2318 -->Updates to documentation pages (above PID
2458 threshold, amino acid properties)
2461 <!-- JAL-2292 -->Lower case residues in sequences are not
2462 reported as mapped to residues in a structure file in the
2466 <!--JAL-2324 -->Identical features with non-numeric scores
2467 could be added multiple times to a sequence
2470 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2471 bond features shown as two highlighted residues rather
2472 than a range in linked structure views, and treated
2473 correctly when selecting and computing trees from features
2476 <!-- JAL-2281-->Custom URL links for database
2477 cross-references are matched to database name regardless
2482 <em>Application</em>
2485 <!-- JAL-2282-->Custom URL links for specific database
2486 names without regular expressions also offer links from
2490 <!-- JAL-2315-->Removing a single configured link in the
2491 URL links pane in Connections preferences doesn't actually
2492 update Jalview configuration
2495 <!-- JAL-2272-->CTRL-Click on a selected region to open
2496 the alignment area popup menu doesn't work on El-Capitan
2499 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2500 files with similarly named sequences if dropped onto the
2504 <!-- JAL-2312 -->Additional mappings are shown for PDB
2505 entries where more chains exist in the PDB accession than
2506 are reported in the SIFTS file
2509 <!-- JAL-2317-->Certain structures do not get mapped to
2510 the structure view when displayed with Chimera
2513 <!-- JAL-2317-->No chains shown in the Chimera view
2514 panel's View->Show Chains submenu
2517 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2518 work for wrapped alignment views
2521 <!--JAL-2197 -->Rename UI components for running JPred
2522 predictions from 'JNet' to 'JPred'
2525 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2526 corrupted when annotation panel vertical scroll is not at
2527 first annotation row
2530 <!--JAL-2332 -->Attempting to view structure for Hen
2531 lysozyme results in a PDB Client error dialog box
2534 <!-- JAL-2319 -->Structure View's mapping report switched
2535 ranges for PDB and sequence for SIFTS
2538 SIFTS 'Not_Observed' residues mapped to non-existant
2542 <!-- <em>New Known Issues</em>
2549 <td width="60" nowrap>
2550 <div align="center">
2551 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2552 <em>25/10/2016</em></strong>
2555 <td><em>Application</em>
2557 <li>3D Structure chooser opens with 'Cached structures'
2558 view if structures already loaded</li>
2559 <li>Progress bar reports models as they are loaded to
2560 structure views</li>
2566 <li>Colour by conservation always enabled and no tick
2567 shown in menu when BLOSUM or PID shading applied</li>
2568 <li>FER1_ARATH and FER2_ARATH labels were switched in
2569 example sequences/projects/trees</li>
2571 <em>Application</em>
2573 <li>Jalview projects with views of local PDB structure
2574 files saved on Windows cannot be opened on OSX</li>
2575 <li>Multiple structure views can be opened and superposed
2576 without timeout for structures with multiple models or
2577 multiple sequences in alignment</li>
2578 <li>Cannot import or associated local PDB files without a
2579 PDB ID HEADER line</li>
2580 <li>RMSD is not output in Jmol console when superposition
2582 <li>Drag and drop of URL from Browser fails for Linux and
2583 OSX versions earlier than El Capitan</li>
2584 <li>ENA client ignores invalid content from ENA server</li>
2585 <li>Exceptions are not raised in console when ENA client
2586 attempts to fetch non-existent IDs via Fetch DB Refs UI
2588 <li>Exceptions are not raised in console when a new view
2589 is created on the alignment</li>
2590 <li>OSX right-click fixed for group selections: CMD-click
2591 to insert/remove gaps in groups and CTRL-click to open group
2594 <em>Build and deployment</em>
2596 <li>URL link checker now copes with multi-line anchor
2599 <em>New Known Issues</em>
2601 <li>Drag and drop from URL links in browsers do not work
2608 <td width="60" nowrap>
2609 <div align="center">
2610 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2613 <td><em>General</em>
2616 <!-- JAL-2124 -->Updated Spanish translations.
2619 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2620 for importing structure data to Jalview. Enables mmCIF and
2624 <!-- JAL-192 --->Alignment ruler shows positions relative to
2628 <!-- JAL-2202 -->Position/residue shown in status bar when
2629 mousing over sequence associated annotation
2632 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2636 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2637 '()', canonical '[]' and invalid '{}' base pair populations
2641 <!-- JAL-2092 -->Feature settings popup menu options for
2642 showing or hiding columns containing a feature
2645 <!-- JAL-1557 -->Edit selected group by double clicking on
2646 group and sequence associated annotation labels
2649 <!-- JAL-2236 -->Sequence name added to annotation label in
2650 select/hide columns by annotation and colour by annotation
2654 </ul> <em>Application</em>
2657 <!-- JAL-2050-->Automatically hide introns when opening a
2658 gene/transcript view
2661 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2665 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2666 structure mappings with the EMBL-EBI PDBe SIFTS database
2669 <!-- JAL-2079 -->Updated download sites used for Rfam and
2670 Pfam sources to xfam.org
2673 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2676 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2677 over sequences in Jalview
2680 <!-- JAL-2027-->Support for reverse-complement coding
2681 regions in ENA and EMBL
2684 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2685 for record retrieval via ENA rest API
2688 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2692 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2693 groovy script execution
2696 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2697 alignment window's Calculate menu
2700 <!-- JAL-1812 -->Allow groovy scripts that call
2701 Jalview.getAlignFrames() to run in headless mode
2704 <!-- JAL-2068 -->Support for creating new alignment
2705 calculation workers from groovy scripts
2708 <!-- JAL-1369 --->Store/restore reference sequence in
2712 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2713 associations are now saved/restored from project
2716 <!-- JAL-1993 -->Database selection dialog always shown
2717 before sequence fetcher is opened
2720 <!-- JAL-2183 -->Double click on an entry in Jalview's
2721 database chooser opens a sequence fetcher
2724 <!-- JAL-1563 -->Free-text search client for UniProt using
2725 the UniProt REST API
2728 <!-- JAL-2168 -->-nonews command line parameter to prevent
2729 the news reader opening
2732 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2733 querying stored in preferences
2736 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2740 <!-- JAL-1977-->Tooltips shown on database chooser
2743 <!-- JAL-391 -->Reverse complement function in calculate
2744 menu for nucleotide sequences
2747 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2748 and feature counts preserves alignment ordering (and
2749 debugged for complex feature sets).
2752 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2753 viewing structures with Jalview 2.10
2756 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2757 genome, transcript CCDS and gene ids via the Ensembl and
2758 Ensembl Genomes REST API
2761 <!-- JAL-2049 -->Protein sequence variant annotation
2762 computed for 'sequence_variant' annotation on CDS regions
2766 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2770 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2771 Ref Fetcher fails to match, or otherwise updates sequence
2772 data from external database records.
2775 <!-- JAL-2154 -->Revised Jalview Project format for
2776 efficient recovery of sequence coding and alignment
2777 annotation relationships.
2779 </ul> <!-- <em>Applet</em>
2790 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2794 <!-- JAL-2018-->Export features in Jalview format (again)
2795 includes graduated colourschemes
2798 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2799 working with big alignments and lots of hidden columns
2802 <!-- JAL-2053-->Hidden column markers not always rendered
2803 at right of alignment window
2806 <!-- JAL-2067 -->Tidied up links in help file table of
2810 <!-- JAL-2072 -->Feature based tree calculation not shown
2814 <!-- JAL-2075 -->Hidden columns ignored during feature
2815 based tree calculation
2818 <!-- JAL-2065 -->Alignment view stops updating when show
2819 unconserved enabled for group on alignment
2822 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2826 <!-- JAL-2146 -->Alignment column in status incorrectly
2827 shown as "Sequence position" when mousing over
2831 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2832 hidden columns present
2835 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2836 user created annotation added to alignment
2839 <!-- JAL-1841 -->RNA Structure consensus only computed for
2840 '()' base pair annotation
2843 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2844 in zero scores for all base pairs in RNA Structure
2848 <!-- JAL-2174-->Extend selection with columns containing
2852 <!-- JAL-2275 -->Pfam format writer puts extra space at
2853 beginning of sequence
2856 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2860 <!-- JAL-2238 -->Cannot create groups on an alignment from
2861 from a tree when t-coffee scores are shown
2864 <!-- JAL-1836,1967 -->Cannot import and view PDB
2865 structures with chains containing negative resnums (4q4h)
2868 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2872 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2873 to Clustal, PIR and PileUp output
2876 <!-- JAL-2008 -->Reordering sequence features that are
2877 not visible causes alignment window to repaint
2880 <!-- JAL-2006 -->Threshold sliders don't work in
2881 graduated colour and colour by annotation row for e-value
2882 scores associated with features and annotation rows
2885 <!-- JAL-1797 -->amino acid physicochemical conservation
2886 calculation should be case independent
2889 <!-- JAL-2173 -->Remove annotation also updates hidden
2893 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2894 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2895 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2898 <!-- JAL-2065 -->Null pointer exceptions and redraw
2899 problems when reference sequence defined and 'show
2900 non-conserved' enabled
2903 <!-- JAL-1306 -->Quality and Conservation are now shown on
2904 load even when Consensus calculation is disabled
2907 <!-- JAL-1932 -->Remove right on penultimate column of
2908 alignment does nothing
2911 <em>Application</em>
2914 <!-- JAL-1552-->URLs and links can't be imported by
2915 drag'n'drop on OSX when launched via webstart (note - not
2916 yet fixed for El Capitan)
2919 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2920 output when running on non-gb/us i18n platforms
2923 <!-- JAL-1944 -->Error thrown when exporting a view with
2924 hidden sequences as flat-file alignment
2927 <!-- JAL-2030-->InstallAnywhere distribution fails when
2931 <!-- JAL-2080-->Jalview very slow to launch via webstart
2932 (also hotfix for 2.9.0b2)
2935 <!-- JAL-2085 -->Cannot save project when view has a
2936 reference sequence defined
2939 <!-- JAL-1011 -->Columns are suddenly selected in other
2940 alignments and views when revealing hidden columns
2943 <!-- JAL-1989 -->Hide columns not mirrored in complement
2944 view in a cDNA/Protein splitframe
2947 <!-- JAL-1369 -->Cannot save/restore representative
2948 sequence from project when only one sequence is
2952 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2953 in Structure Chooser
2956 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2957 structure consensus didn't refresh annotation panel
2960 <!-- JAL-1962 -->View mapping in structure view shows
2961 mappings between sequence and all chains in a PDB file
2964 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2965 dialogs format columns correctly, don't display array
2966 data, sort columns according to type
2969 <!-- JAL-1975 -->Export complete shown after destination
2970 file chooser is cancelled during an image export
2973 <!-- JAL-2025 -->Error when querying PDB Service with
2974 sequence name containing special characters
2977 <!-- JAL-2024 -->Manual PDB structure querying should be
2981 <!-- JAL-2104 -->Large tooltips with broken HTML
2982 formatting don't wrap
2985 <!-- JAL-1128 -->Figures exported from wrapped view are
2986 truncated so L looks like I in consensus annotation
2989 <!-- JAL-2003 -->Export features should only export the
2990 currently displayed features for the current selection or
2994 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2995 after fetching cross-references, and restoring from
2999 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3000 followed in the structure viewer
3003 <!-- JAL-2163 -->Titles for individual alignments in
3004 splitframe not restored from project
3007 <!-- JAL-2145 -->missing autocalculated annotation at
3008 trailing end of protein alignment in transcript/product
3009 splitview when pad-gaps not enabled by default
3012 <!-- JAL-1797 -->amino acid physicochemical conservation
3016 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3017 article has been read (reopened issue due to
3018 internationalisation problems)
3021 <!-- JAL-1960 -->Only offer PDB structures in structure
3022 viewer based on sequence name, PDB and UniProt
3027 <!-- JAL-1976 -->No progress bar shown during export of
3031 <!-- JAL-2213 -->Structures not always superimposed after
3032 multiple structures are shown for one or more sequences.
3035 <!-- JAL-1370 -->Reference sequence characters should not
3036 be replaced with '.' when 'Show unconserved' format option
3040 <!-- JAL-1823 -->Cannot specify chain code when entering
3041 specific PDB id for sequence
3044 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3045 'Export hidden sequences' is enabled, but 'export hidden
3046 columns' is disabled.
3049 <!--JAL-2026-->Best Quality option in structure chooser
3050 selects lowest rather than highest resolution structures
3054 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3055 to sequence mapping in 'View Mappings' report
3058 <!-- JAL-2284 -->Unable to read old Jalview projects that
3059 contain non-XML data added after Jalvew wrote project.
3062 <!-- JAL-2118 -->Newly created annotation row reorders
3063 after clicking on it to create new annotation for a
3067 <!-- JAL-1980 -->Null Pointer Exception raised when
3068 pressing Add on an orphaned cut'n'paste window.
3070 <!-- may exclude, this is an external service stability issue JAL-1941
3071 -- > RNA 3D structure not added via DSSR service</li> -->
3076 <!-- JAL-2151 -->Incorrect columns are selected when
3077 hidden columns present before start of sequence
3080 <!-- JAL-1986 -->Missing dependencies on applet pages
3084 <!-- JAL-1947 -->Overview pixel size changes when
3085 sequences are hidden in applet
3088 <!-- JAL-1996 -->Updated instructions for applet
3089 deployment on examples pages.
3096 <td width="60" nowrap>
3097 <div align="center">
3098 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3099 <em>16/10/2015</em></strong>
3102 <td><em>General</em>
3104 <li>Time stamps for signed Jalview application and applet
3109 <em>Application</em>
3111 <li>Duplicate group consensus and conservation rows
3112 shown when tree is partitioned</li>
3113 <li>Erratic behaviour when tree partitions made with
3114 multiple cDNA/Protein split views</li>
3120 <td width="60" nowrap>
3121 <div align="center">
3122 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3123 <em>8/10/2015</em></strong>
3126 <td><em>General</em>
3128 <li>Updated Spanish translations of localized text for
3130 </ul> <em>Application</em>
3132 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3133 <li>Signed OSX InstallAnywhere installer<br></li>
3134 <li>Support for per-sequence based annotations in BioJSON</li>
3135 </ul> <em>Applet</em>
3137 <li>Split frame example added to applet examples page</li>
3138 </ul> <em>Build and Deployment</em>
3141 <!-- JAL-1888 -->New ant target for running Jalview's test
3149 <li>Mapping of cDNA to protein in split frames
3150 incorrect when sequence start > 1</li>
3151 <li>Broken images in filter column by annotation dialog
3153 <li>Feature colours not parsed from features file</li>
3154 <li>Exceptions and incomplete link URLs recovered when
3155 loading a features file containing HTML tags in feature
3159 <em>Application</em>
3161 <li>Annotations corrupted after BioJS export and
3163 <li>Incorrect sequence limits after Fetch DB References
3164 with 'trim retrieved sequences'</li>
3165 <li>Incorrect warning about deleting all data when
3166 deleting selected columns</li>
3167 <li>Patch to build system for shipping properly signed
3168 JNLP templates for webstart launch</li>
3169 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3170 unreleased structures for download or viewing</li>
3171 <li>Tab/space/return keystroke operation of EMBL-PDBe
3172 fetcher/viewer dialogs works correctly</li>
3173 <li>Disabled 'minimise' button on Jalview windows
3174 running on OSX to workaround redraw hang bug</li>
3175 <li>Split cDNA/Protein view position and geometry not
3176 recovered from jalview project</li>
3177 <li>Initial enabled/disabled state of annotation menu
3178 sorter 'show autocalculated first/last' corresponds to
3180 <li>Restoring of Clustal, RNA Helices and T-Coffee
3181 color schemes from BioJSON</li>
3185 <li>Reorder sequences mirrored in cDNA/Protein split
3187 <li>Applet with Jmol examples not loading correctly</li>
3193 <td><div align="center">
3194 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3196 <td><em>General</em>
3198 <li>Linked visualisation and analysis of DNA and Protein
3201 <li>Translated cDNA alignments shown as split protein
3202 and DNA alignment views</li>
3203 <li>Codon consensus annotation for linked protein and
3204 cDNA alignment views</li>
3205 <li>Link cDNA or Protein product sequences by loading
3206 them onto Protein or cDNA alignments</li>
3207 <li>Reconstruct linked cDNA alignment from aligned
3208 protein sequences</li>
3211 <li>Jmol integration updated to Jmol v14.2.14</li>
3212 <li>Import and export of Jalview alignment views as <a
3213 href="features/bioJsonFormat.html">BioJSON</a></li>
3214 <li>New alignment annotation file statements for
3215 reference sequences and marking hidden columns</li>
3216 <li>Reference sequence based alignment shading to
3217 highlight variation</li>
3218 <li>Select or hide columns according to alignment
3220 <li>Find option for locating sequences by description</li>
3221 <li>Conserved physicochemical properties shown in amino
3222 acid conservation row</li>
3223 <li>Alignments can be sorted by number of RNA helices</li>
3224 </ul> <em>Application</em>
3226 <li>New cDNA/Protein analysis capabilities
3228 <li>Get Cross-References should open a Split Frame
3229 view with cDNA/Protein</li>
3230 <li>Detect when nucleotide sequences and protein
3231 sequences are placed in the same alignment</li>
3232 <li>Split cDNA/Protein views are saved in Jalview
3237 <li>Use REST API to talk to Chimera</li>
3238 <li>Selected regions in Chimera are highlighted in linked
3239 Jalview windows</li>
3241 <li>VARNA RNA viewer updated to v3.93</li>
3242 <li>VARNA views are saved in Jalview Projects</li>
3243 <li>Pseudoknots displayed as Jalview RNA annotation can
3244 be shown in VARNA</li>
3246 <li>Make groups for selection uses marked columns as well
3247 as the active selected region</li>
3249 <li>Calculate UPGMA and NJ trees using sequence feature
3251 <li>New Export options
3253 <li>New Export Settings dialog to control hidden
3254 region export in flat file generation</li>
3256 <li>Export alignment views for display with the <a
3257 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3259 <li>Export scrollable SVG in HTML page</li>
3260 <li>Optional embedding of BioJSON data when exporting
3261 alignment figures to HTML</li>
3263 <li>3D structure retrieval and display
3265 <li>Free text and structured queries with the PDBe
3267 <li>PDBe Search API based discovery and selection of
3268 PDB structures for a sequence set</li>
3272 <li>JPred4 employed for protein secondary structure
3274 <li>Hide Insertions menu option to hide unaligned columns
3275 for one or a group of sequences</li>
3276 <li>Automatically hide insertions in alignments imported
3277 from the JPred4 web server</li>
3278 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3279 system on OSX<br />LGPL libraries courtesy of <a
3280 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3282 <li>changed 'View nucleotide structure' submenu to 'View
3283 VARNA 2D Structure'</li>
3284 <li>change "View protein structure" menu option to "3D
3287 </ul> <em>Applet</em>
3289 <li>New layout for applet example pages</li>
3290 <li>New parameters to enable SplitFrame view
3291 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3292 <li>New example demonstrating linked viewing of cDNA and
3293 Protein alignments</li>
3294 </ul> <em>Development and deployment</em>
3296 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3297 <li>Include installation type and git revision in build
3298 properties and console log output</li>
3299 <li>Jalview Github organisation, and new github site for
3300 storing BioJsMSA Templates</li>
3301 <li>Jalview's unit tests now managed with TestNG</li>
3304 <!-- <em>General</em>
3306 </ul> --> <!-- issues resolved --> <em>Application</em>
3308 <li>Escape should close any open find dialogs</li>
3309 <li>Typo in select-by-features status report</li>
3310 <li>Consensus RNA secondary secondary structure
3311 predictions are not highlighted in amber</li>
3312 <li>Missing gap character in v2.7 example file means
3313 alignment appears unaligned when pad-gaps is not enabled</li>
3314 <li>First switch to RNA Helices colouring doesn't colour
3315 associated structure views</li>
3316 <li>ID width preference option is greyed out when auto
3317 width checkbox not enabled</li>
3318 <li>Stopped a warning dialog from being shown when
3319 creating user defined colours</li>
3320 <li>'View Mapping' in structure viewer shows sequence
3321 mappings for just that viewer's sequences</li>
3322 <li>Workaround for superposing PDB files containing
3323 multiple models in Chimera</li>
3324 <li>Report sequence position in status bar when hovering
3325 over Jmol structure</li>
3326 <li>Cannot output gaps as '.' symbols with Selection ->
3327 output to text box</li>
3328 <li>Flat file exports of alignments with hidden columns
3329 have incorrect sequence start/end</li>
3330 <li>'Aligning' a second chain to a Chimera structure from
3332 <li>Colour schemes applied to structure viewers don't
3333 work for nucleotide</li>
3334 <li>Loading/cut'n'pasting an empty or invalid file leads
3335 to a grey/invisible alignment window</li>
3336 <li>Exported Jpred annotation from a sequence region
3337 imports to different position</li>
3338 <li>Space at beginning of sequence feature tooltips shown
3339 on some platforms</li>
3340 <li>Chimera viewer 'View | Show Chain' menu is not
3342 <li>'New View' fails with a Null Pointer Exception in
3343 console if Chimera has been opened</li>
3344 <li>Mouseover to Chimera not working</li>
3345 <li>Miscellaneous ENA XML feature qualifiers not
3347 <li>NPE in annotation renderer after 'Extract Scores'</li>
3348 <li>If two structures in one Chimera window, mouseover of
3349 either sequence shows on first structure</li>
3350 <li>'Show annotations' options should not make
3351 non-positional annotations visible</li>
3352 <li>Subsequence secondary structure annotation not shown
3353 in right place after 'view flanking regions'</li>
3354 <li>File Save As type unset when current file format is
3356 <li>Save as '.jar' option removed for saving Jalview
3358 <li>Colour by Sequence colouring in Chimera more
3360 <li>Cannot 'add reference annotation' for a sequence in
3361 several views on same alignment</li>
3362 <li>Cannot show linked products for EMBL / ENA records</li>
3363 <li>Jalview's tooltip wraps long texts containing no
3365 </ul> <em>Applet</em>
3367 <li>Jmol to JalviewLite mouseover/link not working</li>
3368 <li>JalviewLite can't import sequences with ID
3369 descriptions containing angle brackets</li>
3370 </ul> <em>General</em>
3372 <li>Cannot export and reimport RNA secondary structure
3373 via jalview annotation file</li>
3374 <li>Random helix colour palette for colour by annotation
3375 with RNA secondary structure</li>
3376 <li>Mouseover to cDNA from STOP residue in protein
3377 translation doesn't work.</li>
3378 <li>hints when using the select by annotation dialog box</li>
3379 <li>Jmol alignment incorrect if PDB file has alternate CA
3381 <li>FontChooser message dialog appears to hang after
3382 choosing 1pt font</li>
3383 <li>Peptide secondary structure incorrectly imported from
3384 annotation file when annotation display text includes 'e' or
3386 <li>Cannot set colour of new feature type whilst creating
3388 <li>cDNA translation alignment should not be sequence
3389 order dependent</li>
3390 <li>'Show unconserved' doesn't work for lower case
3392 <li>Nucleotide ambiguity codes involving R not recognised</li>
3393 </ul> <em>Deployment and Documentation</em>
3395 <li>Applet example pages appear different to the rest of
3396 www.jalview.org</li>
3397 </ul> <em>Application Known issues</em>
3399 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3400 <li>Misleading message appears after trying to delete
3402 <li>Jalview icon not shown in dock after InstallAnywhere
3403 version launches</li>
3404 <li>Fetching EMBL reference for an RNA sequence results
3405 fails with a sequence mismatch</li>
3406 <li>Corrupted or unreadable alignment display when
3407 scrolling alignment to right</li>
3408 <li>ArrayIndexOutOfBoundsException thrown when remove
3409 empty columns called on alignment with ragged gapped ends</li>
3410 <li>auto calculated alignment annotation rows do not get
3411 placed above or below non-autocalculated rows</li>
3412 <li>Jalview dekstop becomes sluggish at full screen in
3413 ultra-high resolution</li>
3414 <li>Cannot disable consensus calculation independently of
3415 quality and conservation</li>
3416 <li>Mouseover highlighting between cDNA and protein can
3417 become sluggish with more than one splitframe shown</li>
3418 </ul> <em>Applet Known Issues</em>
3420 <li>Core PDB parsing code requires Jmol</li>
3421 <li>Sequence canvas panel goes white when alignment
3422 window is being resized</li>
3428 <td><div align="center">
3429 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3431 <td><em>General</em>
3433 <li>Updated Java code signing certificate donated by
3435 <li>Features and annotation preserved when performing
3436 pairwise alignment</li>
3437 <li>RNA pseudoknot annotation can be
3438 imported/exported/displayed</li>
3439 <li>'colour by annotation' can colour by RNA and
3440 protein secondary structure</li>
3441 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3442 post-hoc with 2.9 release</em>)
3445 </ul> <em>Application</em>
3447 <li>Extract and display secondary structure for sequences
3448 with 3D structures</li>
3449 <li>Support for parsing RNAML</li>
3450 <li>Annotations menu for layout
3452 <li>sort sequence annotation rows by alignment</li>
3453 <li>place sequence annotation above/below alignment
3456 <li>Output in Stockholm format</li>
3457 <li>Internationalisation: improved Spanish (es)
3459 <li>Structure viewer preferences tab</li>
3460 <li>Disorder and Secondary Structure annotation tracks
3461 shared between alignments</li>
3462 <li>UCSF Chimera launch and linked highlighting from
3464 <li>Show/hide all sequence associated annotation rows for
3465 all or current selection</li>
3466 <li>disorder and secondary structure predictions
3467 available as dataset annotation</li>
3468 <li>Per-sequence rna helices colouring</li>
3471 <li>Sequence database accessions imported when fetching
3472 alignments from Rfam</li>
3473 <li>update VARNA version to 3.91</li>
3475 <li>New groovy scripts for exporting aligned positions,
3476 conservation values, and calculating sum of pairs scores.</li>
3477 <li>Command line argument to set default JABAWS server</li>
3478 <li>include installation type in build properties and
3479 console log output</li>
3480 <li>Updated Jalview project format to preserve dataset
3484 <!-- issues resolved --> <em>Application</em>
3486 <li>Distinguish alignment and sequence associated RNA
3487 structure in structure->view->VARNA</li>
3488 <li>Raise dialog box if user deletes all sequences in an
3490 <li>Pressing F1 results in documentation opening twice</li>
3491 <li>Sequence feature tooltip is wrapped</li>
3492 <li>Double click on sequence associated annotation
3493 selects only first column</li>
3494 <li>Redundancy removal doesn't result in unlinked
3495 leaves shown in tree</li>
3496 <li>Undos after several redundancy removals don't undo
3498 <li>Hide sequence doesn't hide associated annotation</li>
3499 <li>User defined colours dialog box too big to fit on
3500 screen and buttons not visible</li>
3501 <li>author list isn't updated if already written to
3502 Jalview properties</li>
3503 <li>Popup menu won't open after retrieving sequence
3505 <li>File open window for associate PDB doesn't open</li>
3506 <li>Left-then-right click on a sequence id opens a
3507 browser search window</li>
3508 <li>Cannot open sequence feature shading/sort popup menu
3509 in feature settings dialog</li>
3510 <li>better tooltip placement for some areas of Jalview
3512 <li>Allow addition of JABAWS Server which doesn't
3513 pass validation</li>
3514 <li>Web services parameters dialog box is too large to
3516 <li>Muscle nucleotide alignment preset obscured by
3518 <li>JABAWS preset submenus don't contain newly
3519 defined user preset</li>
3520 <li>MSA web services warns user if they were launched
3521 with invalid input</li>
3522 <li>Jalview cannot contact DAS Registy when running on
3525 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3526 'Superpose with' submenu not shown when new view
3530 </ul> <!-- <em>Applet</em>
3532 </ul> <em>General</em>
3534 </ul>--> <em>Deployment and Documentation</em>
3536 <li>2G and 1G options in launchApp have no effect on
3537 memory allocation</li>
3538 <li>launchApp service doesn't automatically open
3539 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3541 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3542 InstallAnywhere reports cannot find valid JVM when Java
3543 1.7_055 is available
3545 </ul> <em>Application Known issues</em>
3548 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3549 corrupted or unreadable alignment display when scrolling
3553 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3554 retrieval fails but progress bar continues for DAS retrieval
3555 with large number of ID
3558 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3559 flatfile output of visible region has incorrect sequence
3563 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3564 rna structure consensus doesn't update when secondary
3565 structure tracks are rearranged
3568 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3569 invalid rna structure positional highlighting does not
3570 highlight position of invalid base pairs
3573 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3574 out of memory errors are not raised when saving Jalview
3575 project from alignment window file menu
3578 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3579 Switching to RNA Helices colouring doesn't propagate to
3583 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3584 colour by RNA Helices not enabled when user created
3585 annotation added to alignment
3588 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3589 Jalview icon not shown on dock in Mountain Lion/Webstart
3591 </ul> <em>Applet Known Issues</em>
3594 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3595 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3598 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3599 Jalview and Jmol example not compatible with IE9
3602 <li>Sort by annotation score doesn't reverse order
3608 <td><div align="center">
3609 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3612 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3615 <li>Internationalisation of user interface (usually
3616 called i18n support) and translation for Spanish locale</li>
3617 <li>Define/Undefine group on current selection with
3618 Ctrl-G/Shift Ctrl-G</li>
3619 <li>Improved group creation/removal options in
3620 alignment/sequence Popup menu</li>
3621 <li>Sensible precision for symbol distribution
3622 percentages shown in logo tooltip.</li>
3623 <li>Annotation panel height set according to amount of
3624 annotation when alignment first opened</li>
3625 </ul> <em>Application</em>
3627 <li>Interactive consensus RNA secondary structure
3628 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3629 <li>Select columns containing particular features from
3630 Feature Settings dialog</li>
3631 <li>View all 'representative' PDB structures for selected
3633 <li>Update Jalview project format:
3635 <li>New file extension for Jalview projects '.jvp'</li>
3636 <li>Preserve sequence and annotation dataset (to
3637 store secondary structure annotation,etc)</li>
3638 <li>Per group and alignment annotation and RNA helix
3642 <li>New similarity measures for PCA and Tree calculation
3644 <li>Experimental support for retrieval and viewing of
3645 flanking regions for an alignment</li>
3649 <!-- issues resolved --> <em>Application</em>
3651 <li>logo keeps spinning and status remains at queued or
3652 running after job is cancelled</li>
3653 <li>cannot export features from alignments imported from
3654 Jalview/VAMSAS projects</li>
3655 <li>Buggy slider for web service parameters that take
3657 <li>Newly created RNA secondary structure line doesn't
3658 have 'display all symbols' flag set</li>
3659 <li>T-COFFEE alignment score shading scheme and other
3660 annotation shading not saved in Jalview project</li>
3661 <li>Local file cannot be loaded in freshly downloaded
3663 <li>Jalview icon not shown on dock in Mountain
3665 <li>Load file from desktop file browser fails</li>
3666 <li>Occasional NPE thrown when calculating large trees</li>
3667 <li>Cannot reorder or slide sequences after dragging an
3668 alignment onto desktop</li>
3669 <li>Colour by annotation dialog throws NPE after using
3670 'extract scores' function</li>
3671 <li>Loading/cut'n'pasting an empty file leads to a grey
3672 alignment window</li>
3673 <li>Disorder thresholds rendered incorrectly after
3674 performing IUPred disorder prediction</li>
3675 <li>Multiple group annotated consensus rows shown when
3676 changing 'normalise logo' display setting</li>
3677 <li>Find shows blank dialog after 'finished searching' if
3678 nothing matches query</li>
3679 <li>Null Pointer Exceptions raised when sorting by
3680 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3682 <li>Errors in Jmol console when structures in alignment
3683 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3685 <li>Not all working JABAWS services are shown in
3687 <li>JAVAWS version of Jalview fails to launch with
3688 'invalid literal/length code'</li>
3689 <li>Annotation/RNA Helix colourschemes cannot be applied
3690 to alignment with groups (actually fixed in 2.8.0b1)</li>
3691 <li>RNA Helices and T-Coffee Scores available as default
3694 </ul> <em>Applet</em>
3696 <li>Remove group option is shown even when selection is
3698 <li>Apply to all groups ticked but colourscheme changes
3699 don't affect groups</li>
3700 <li>Documented RNA Helices and T-Coffee Scores as valid
3701 colourscheme name</li>
3702 <li>Annotation labels drawn on sequence IDs when
3703 Annotation panel is not displayed</li>
3704 <li>Increased font size for dropdown menus on OSX and
3705 embedded windows</li>
3706 </ul> <em>Other</em>
3708 <li>Consensus sequence for alignments/groups with a
3709 single sequence were not calculated</li>
3710 <li>annotation files that contain only groups imported as
3711 annotation and junk sequences</li>
3712 <li>Fasta files with sequences containing '*' incorrectly
3713 recognised as PFAM or BLC</li>
3714 <li>conservation/PID slider apply all groups option
3715 doesn't affect background (2.8.0b1)
3717 <li>redundancy highlighting is erratic at 0% and 100%</li>
3718 <li>Remove gapped columns fails for sequences with ragged
3720 <li>AMSA annotation row with leading spaces is not
3721 registered correctly on import</li>
3722 <li>Jalview crashes when selecting PCA analysis for
3723 certain alignments</li>
3724 <li>Opening the colour by annotation dialog for an
3725 existing annotation based 'use original colours'
3726 colourscheme loses original colours setting</li>
3731 <td><div align="center">
3732 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3733 <em>30/1/2014</em></strong>
3737 <li>Trusted certificates for JalviewLite applet and
3738 Jalview Desktop application<br />Certificate was donated by
3739 <a href="https://www.certum.eu">Certum</a> to the Jalview
3740 open source project).
3742 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3743 <li>Output in Stockholm format</li>
3744 <li>Allow import of data from gzipped files</li>
3745 <li>Export/import group and sequence associated line
3746 graph thresholds</li>
3747 <li>Nucleotide substitution matrix that supports RNA and
3748 ambiguity codes</li>
3749 <li>Allow disorder predictions to be made on the current
3750 selection (or visible selection) in the same way that JPred
3752 <li>Groovy scripting for headless Jalview operation</li>
3753 </ul> <em>Other improvements</em>
3755 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3756 <li>COMBINE statement uses current SEQUENCE_REF and
3757 GROUP_REF scope to group annotation rows</li>
3758 <li>Support '' style escaping of quotes in Newick
3760 <li>Group options for JABAWS service by command line name</li>
3761 <li>Empty tooltip shown for JABA service options with a
3762 link but no description</li>
3763 <li>Select primary source when selecting authority in
3764 database fetcher GUI</li>
3765 <li>Add .mfa to FASTA file extensions recognised by
3767 <li>Annotation label tooltip text wrap</li>
3772 <li>Slow scrolling when lots of annotation rows are
3774 <li>Lots of NPE (and slowness) after creating RNA
3775 secondary structure annotation line</li>
3776 <li>Sequence database accessions not imported when
3777 fetching alignments from Rfam</li>
3778 <li>Incorrect SHMR submission for sequences with
3780 <li>View all structures does not always superpose
3782 <li>Option widgets in service parameters not updated to
3783 reflect user or preset settings</li>
3784 <li>Null pointer exceptions for some services without
3785 presets or adjustable parameters</li>
3786 <li>Discover PDB IDs entry in structure menu doesn't
3787 discover PDB xRefs</li>
3788 <li>Exception encountered while trying to retrieve
3789 features with DAS</li>
3790 <li>Lowest value in annotation row isn't coloured
3791 when colour by annotation (per sequence) is coloured</li>
3792 <li>Keyboard mode P jumps to start of gapped region when
3793 residue follows a gap</li>
3794 <li>Jalview appears to hang importing an alignment with
3795 Wrap as default or after enabling Wrap</li>
3796 <li>'Right click to add annotations' message
3797 shown in wrap mode when no annotations present</li>
3798 <li>Disorder predictions fail with NPE if no automatic
3799 annotation already exists on alignment</li>
3800 <li>oninit javascript function should be called after
3801 initialisation completes</li>
3802 <li>Remove redundancy after disorder prediction corrupts
3803 alignment window display</li>
3804 <li>Example annotation file in documentation is invalid</li>
3805 <li>Grouped line graph annotation rows are not exported
3806 to annotation file</li>
3807 <li>Multi-harmony analysis cannot be run when only two
3809 <li>Cannot create multiple groups of line graphs with
3810 several 'combine' statements in annotation file</li>
3811 <li>Pressing return several times causes Number Format
3812 exceptions in keyboard mode</li>
3813 <li>Multi-harmony (SHMMR) method doesn't submit
3814 correct partitions for input data</li>
3815 <li>Translation from DNA to Amino Acids fails</li>
3816 <li>Jalview fail to load newick tree with quoted label</li>
3817 <li>--headless flag isn't understood</li>
3818 <li>ClassCastException when generating EPS in headless
3820 <li>Adjusting sequence-associated shading threshold only
3821 changes one row's threshold</li>
3822 <li>Preferences and Feature settings panel panel
3823 doesn't open</li>
3824 <li>hide consensus histogram also hides conservation and
3825 quality histograms</li>
3830 <td><div align="center">
3831 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3833 <td><em>Application</em>
3835 <li>Support for JABAWS 2.0 Services (AACon alignment
3836 conservation, protein disorder and Clustal Omega)</li>
3837 <li>JABAWS server status indicator in Web Services
3839 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3840 in Jalview alignment window</li>
3841 <li>Updated Jalview build and deploy framework for OSX
3842 mountain lion, windows 7, and 8</li>
3843 <li>Nucleotide substitution matrix for PCA that supports
3844 RNA and ambiguity codes</li>
3846 <li>Improved sequence database retrieval GUI</li>
3847 <li>Support fetching and database reference look up
3848 against multiple DAS sources (Fetch all from in 'fetch db
3850 <li>Jalview project improvements
3852 <li>Store and retrieve the 'belowAlignment'
3853 flag for annotation</li>
3854 <li>calcId attribute to group annotation rows on the
3856 <li>Store AACon calculation settings for a view in
3857 Jalview project</li>
3861 <li>horizontal scrolling gesture support</li>
3862 <li>Visual progress indicator when PCA calculation is
3864 <li>Simpler JABA web services menus</li>
3865 <li>visual indication that web service results are still
3866 being retrieved from server</li>
3867 <li>Serialise the dialogs that are shown when Jalview
3868 starts up for first time</li>
3869 <li>Jalview user agent string for interacting with HTTP
3871 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3873 <li>Examples directory and Groovy library included in
3874 InstallAnywhere distribution</li>
3875 </ul> <em>Applet</em>
3877 <li>RNA alignment and secondary structure annotation
3878 visualization applet example</li>
3879 </ul> <em>General</em>
3881 <li>Normalise option for consensus sequence logo</li>
3882 <li>Reset button in PCA window to return dimensions to
3884 <li>Allow seqspace or Jalview variant of alignment PCA
3886 <li>PCA with either nucleic acid and protein substitution
3888 <li>Allow windows containing HTML reports to be exported
3890 <li>Interactive display and editing of RNA secondary
3891 structure contacts</li>
3892 <li>RNA Helix Alignment Colouring</li>
3893 <li>RNA base pair logo consensus</li>
3894 <li>Parse sequence associated secondary structure
3895 information in Stockholm files</li>
3896 <li>HTML Export database accessions and annotation
3897 information presented in tooltip for sequences</li>
3898 <li>Import secondary structure from LOCARNA clustalw
3899 style RNA alignment files</li>
3900 <li>import and visualise T-COFFEE quality scores for an
3902 <li>'colour by annotation' per sequence option to
3903 shade each sequence according to its associated alignment
3905 <li>New Jalview Logo</li>
3906 </ul> <em>Documentation and Development</em>
3908 <li>documentation for score matrices used in Jalview</li>
3909 <li>New Website!</li>
3911 <td><em>Application</em>
3913 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3914 wsdbfetch REST service</li>
3915 <li>Stop windows being moved outside desktop on OSX</li>
3916 <li>Filetype associations not installed for webstart
3918 <li>Jalview does not always retrieve progress of a JABAWS
3919 job execution in full once it is complete</li>
3920 <li>revise SHMR RSBS definition to ensure alignment is
3921 uploaded via ali_file parameter</li>
3922 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3923 <li>View all structures superposed fails with exception</li>
3924 <li>Jnet job queues forever if a very short sequence is
3925 submitted for prediction</li>
3926 <li>Cut and paste menu not opened when mouse clicked on
3928 <li>Putting fractional value into integer text box in
3929 alignment parameter dialog causes Jalview to hang</li>
3930 <li>Structure view highlighting doesn't work on
3932 <li>View all structures fails with exception shown in
3934 <li>Characters in filename associated with PDBEntry not
3935 escaped in a platform independent way</li>
3936 <li>Jalview desktop fails to launch with exception when
3938 <li>Tree calculation reports 'you must have 2 or more
3939 sequences selected' when selection is empty</li>
3940 <li>Jalview desktop fails to launch with jar signature
3941 failure when java web start temporary file caching is
3943 <li>DAS Sequence retrieval with range qualification
3944 results in sequence xref which includes range qualification</li>
3945 <li>Errors during processing of command line arguments
3946 cause progress bar (JAL-898) to be removed</li>
3947 <li>Replace comma for semi-colon option not disabled for
3948 DAS sources in sequence fetcher</li>
3949 <li>Cannot close news reader when JABAWS server warning
3950 dialog is shown</li>
3951 <li>Option widgets not updated to reflect user settings</li>
3952 <li>Edited sequence not submitted to web service</li>
3953 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3954 <li>InstallAnywhere installer doesn't unpack and run
3955 on OSX Mountain Lion</li>
3956 <li>Annotation panel not given a scroll bar when
3957 sequences with alignment annotation are pasted into the
3959 <li>Sequence associated annotation rows not associated
3960 when loaded from Jalview project</li>
3961 <li>Browser launch fails with NPE on java 1.7</li>
3962 <li>JABAWS alignment marked as finished when job was
3963 cancelled or job failed due to invalid input</li>
3964 <li>NPE with v2.7 example when clicking on Tree
3965 associated with all views</li>
3966 <li>Exceptions when copy/paste sequences with grouped
3967 annotation rows to new window</li>
3968 </ul> <em>Applet</em>
3970 <li>Sequence features are momentarily displayed before
3971 they are hidden using hidefeaturegroups applet parameter</li>
3972 <li>loading features via javascript API automatically
3973 enables feature display</li>
3974 <li>scrollToColumnIn javascript API method doesn't
3976 </ul> <em>General</em>
3978 <li>Redundancy removal fails for rna alignment</li>
3979 <li>PCA calculation fails when sequence has been selected
3980 and then deselected</li>
3981 <li>PCA window shows grey box when first opened on OSX</li>
3982 <li>Letters coloured pink in sequence logo when alignment
3983 coloured with clustalx</li>
3984 <li>Choosing fonts without letter symbols defined causes
3985 exceptions and redraw errors</li>
3986 <li>Initial PCA plot view is not same as manually
3987 reconfigured view</li>
3988 <li>Grouped annotation graph label has incorrect line
3990 <li>Grouped annotation graph label display is corrupted
3991 for lots of labels</li>
3996 <div align="center">
3997 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4000 <td><em>Application</em>
4002 <li>Jalview Desktop News Reader</li>
4003 <li>Tweaked default layout of web services menu</li>
4004 <li>View/alignment association menu to enable user to
4005 easily specify which alignment a multi-structure view takes
4006 its colours/correspondences from</li>
4007 <li>Allow properties file location to be specified as URL</li>
4008 <li>Extend Jalview project to preserve associations
4009 between many alignment views and a single Jmol display</li>
4010 <li>Store annotation row height in Jalview project file</li>
4011 <li>Annotation row column label formatting attributes
4012 stored in project file</li>
4013 <li>Annotation row order for auto-calculated annotation
4014 rows preserved in Jalview project file</li>
4015 <li>Visual progress indication when Jalview state is
4016 saved using Desktop window menu</li>
4017 <li>Visual indication that command line arguments are
4018 still being processed</li>
4019 <li>Groovy script execution from URL</li>
4020 <li>Colour by annotation default min and max colours in
4022 <li>Automatically associate PDB files dragged onto an
4023 alignment with sequences that have high similarity and
4025 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4026 <li>'view structures' option to open many
4027 structures in same window</li>
4028 <li>Sort associated views menu option for tree panel</li>
4029 <li>Group all JABA and non-JABA services for a particular
4030 analysis function in its own submenu</li>
4031 </ul> <em>Applet</em>
4033 <li>Userdefined and autogenerated annotation rows for
4035 <li>Adjustment of alignment annotation pane height</li>
4036 <li>Annotation scrollbar for annotation panel</li>
4037 <li>Drag to reorder annotation rows in annotation panel</li>
4038 <li>'automaticScrolling' parameter</li>
4039 <li>Allow sequences with partial ID string matches to be
4040 annotated from GFF/Jalview features files</li>
4041 <li>Sequence logo annotation row in applet</li>
4042 <li>Absolute paths relative to host server in applet
4043 parameters are treated as such</li>
4044 <li>New in the JalviewLite javascript API:
4046 <li>JalviewLite.js javascript library</li>
4047 <li>Javascript callbacks for
4049 <li>Applet initialisation</li>
4050 <li>Sequence/alignment mouse-overs and selections</li>
4053 <li>scrollTo row and column alignment scrolling
4055 <li>Select sequence/alignment regions from javascript</li>
4056 <li>javascript structure viewer harness to pass
4057 messages between Jmol and Jalview when running as
4058 distinct applets</li>
4059 <li>sortBy method</li>
4060 <li>Set of applet and application examples shipped
4061 with documentation</li>
4062 <li>New example to demonstrate JalviewLite and Jmol
4063 javascript message exchange</li>
4065 </ul> <em>General</em>
4067 <li>Enable Jmol displays to be associated with multiple
4068 multiple alignments</li>
4069 <li>Option to automatically sort alignment with new tree</li>
4070 <li>User configurable link to enable redirects to a
4071 www.Jalview.org mirror</li>
4072 <li>Jmol colours option for Jmol displays</li>
4073 <li>Configurable newline string when writing alignment
4074 and other flat files</li>
4075 <li>Allow alignment annotation description lines to
4076 contain html tags</li>
4077 </ul> <em>Documentation and Development</em>
4079 <li>Add groovy test harness for bulk load testing to
4081 <li>Groovy script to load and align a set of sequences
4082 using a web service before displaying the result in the
4083 Jalview desktop</li>
4084 <li>Restructured javascript and applet api documentation</li>
4085 <li>Ant target to publish example html files with applet
4087 <li>Netbeans project for building Jalview from source</li>
4088 <li>ant task to create online javadoc for Jalview source</li>
4090 <td><em>Application</em>
4092 <li>User defined colourscheme throws exception when
4093 current built in colourscheme is saved as new scheme</li>
4094 <li>AlignFrame->Save in application pops up save
4095 dialog for valid filename/format</li>
4096 <li>Cannot view associated structure for UniProt sequence</li>
4097 <li>PDB file association breaks for UniProt sequence
4099 <li>Associate PDB from file dialog does not tell you
4100 which sequence is to be associated with the file</li>
4101 <li>Find All raises null pointer exception when query
4102 only matches sequence IDs</li>
4103 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4104 <li>Jalview project with Jmol views created with Jalview
4105 2.4 cannot be loaded</li>
4106 <li>Filetype associations not installed for webstart
4108 <li>Two or more chains in a single PDB file associated
4109 with sequences in different alignments do not get coloured
4110 by their associated sequence</li>
4111 <li>Visibility status of autocalculated annotation row
4112 not preserved when project is loaded</li>
4113 <li>Annotation row height and visibility attributes not
4114 stored in Jalview project</li>
4115 <li>Tree bootstraps are not preserved when saved as a
4116 Jalview project</li>
4117 <li>Envision2 workflow tooltips are corrupted</li>
4118 <li>Enabling show group conservation also enables colour
4119 by conservation</li>
4120 <li>Duplicate group associated conservation or consensus
4121 created on new view</li>
4122 <li>Annotation scrollbar not displayed after 'show
4123 all hidden annotation rows' option selected</li>
4124 <li>Alignment quality not updated after alignment
4125 annotation row is hidden then shown</li>
4126 <li>Preserve colouring of structures coloured by
4127 sequences in pre Jalview 2.7 projects</li>
4128 <li>Web service job parameter dialog is not laid out
4130 <li>Web services menu not refreshed after 'reset
4131 services' button is pressed in preferences</li>
4132 <li>Annotation off by one in Jalview v2_3 example project</li>
4133 <li>Structures imported from file and saved in project
4134 get name like jalview_pdb1234.txt when reloaded</li>
4135 <li>Jalview does not always retrieve progress of a JABAWS
4136 job execution in full once it is complete</li>
4137 </ul> <em>Applet</em>
4139 <li>Alignment height set incorrectly when lots of
4140 annotation rows are displayed</li>
4141 <li>Relative URLs in feature HTML text not resolved to
4143 <li>View follows highlighting does not work for positions
4145 <li><= shown as = in tooltip</li>
4146 <li>Export features raises exception when no features
4148 <li>Separator string used for serialising lists of IDs
4149 for javascript api is modified when separator string
4150 provided as parameter</li>
4151 <li>Null pointer exception when selecting tree leaves for
4152 alignment with no existing selection</li>
4153 <li>Relative URLs for datasources assumed to be relative
4154 to applet's codebase</li>
4155 <li>Status bar not updated after finished searching and
4156 search wraps around to first result</li>
4157 <li>StructureSelectionManager instance shared between
4158 several Jalview applets causes race conditions and memory
4160 <li>Hover tooltip and mouseover of position on structure
4161 not sent from Jmol in applet</li>
4162 <li>Certain sequences of javascript method calls to
4163 applet API fatally hang browser</li>
4164 </ul> <em>General</em>
4166 <li>View follows structure mouseover scrolls beyond
4167 position with wrapped view and hidden regions</li>
4168 <li>Find sequence position moves to wrong residue
4169 with/without hidden columns</li>
4170 <li>Sequence length given in alignment properties window
4172 <li>InvalidNumberFormat exceptions thrown when trying to
4173 import PDB like structure files</li>
4174 <li>Positional search results are only highlighted
4175 between user-supplied sequence start/end bounds</li>
4176 <li>End attribute of sequence is not validated</li>
4177 <li>Find dialog only finds first sequence containing a
4178 given sequence position</li>
4179 <li>Sequence numbering not preserved in MSF alignment
4181 <li>Jalview PDB file reader does not extract sequence
4182 from nucleotide chains correctly</li>
4183 <li>Structure colours not updated when tree partition
4184 changed in alignment</li>
4185 <li>Sequence associated secondary structure not correctly
4186 parsed in interleaved stockholm</li>
4187 <li>Colour by annotation dialog does not restore current
4189 <li>Hiding (nearly) all sequences doesn't work
4191 <li>Sequences containing lowercase letters are not
4192 properly associated with their pdb files</li>
4193 </ul> <em>Documentation and Development</em>
4195 <li>schemas/JalviewWsParamSet.xsd corrupted by
4196 ApplyCopyright tool</li>
4201 <div align="center">
4202 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4205 <td><em>Application</em>
4207 <li>New warning dialog when the Jalview Desktop cannot
4208 contact web services</li>
4209 <li>JABA service parameters for a preset are shown in
4210 service job window</li>
4211 <li>JABA Service menu entries reworded</li>
4215 <li>Modeller PIR IO broken - cannot correctly import a
4216 pir file emitted by Jalview</li>
4217 <li>Existing feature settings transferred to new
4218 alignment view created from cut'n'paste</li>
4219 <li>Improved test for mixed amino/nucleotide chains when
4220 parsing PDB files</li>
4221 <li>Consensus and conservation annotation rows
4222 occasionally become blank for all new windows</li>
4223 <li>Exception raised when right clicking above sequences
4224 in wrapped view mode</li>
4225 </ul> <em>Application</em>
4227 <li>multiple multiply aligned structure views cause cpu
4228 usage to hit 100% and computer to hang</li>
4229 <li>Web Service parameter layout breaks for long user
4230 parameter names</li>
4231 <li>Jaba service discovery hangs desktop if Jaba server
4238 <div align="center">
4239 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4242 <td><em>Application</em>
4244 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4245 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4248 <li>Web Services preference tab</li>
4249 <li>Analysis parameters dialog box and user defined
4251 <li>Improved speed and layout of Envision2 service menu</li>
4252 <li>Superpose structures using associated sequence
4254 <li>Export coordinates and projection as CSV from PCA
4256 </ul> <em>Applet</em>
4258 <li>enable javascript: execution by the applet via the
4259 link out mechanism</li>
4260 </ul> <em>Other</em>
4262 <li>Updated the Jmol Jalview interface to work with Jmol
4264 <li>The Jalview Desktop and JalviewLite applet now
4265 require Java 1.5</li>
4266 <li>Allow Jalview feature colour specification for GFF
4267 sequence annotation files</li>
4268 <li>New 'colour by label' keword in Jalview feature file
4269 type colour specification</li>
4270 <li>New Jalview Desktop Groovy API method that allows a
4271 script to check if it being run in an interactive session or
4272 in a batch operation from the Jalview command line</li>
4276 <li>clustalx colourscheme colours Ds preferentially when
4277 both D+E are present in over 50% of the column</li>
4278 </ul> <em>Application</em>
4280 <li>typo in AlignmentFrame->View->Hide->all but
4281 selected Regions menu item</li>
4282 <li>sequence fetcher replaces ',' for ';' when the ',' is
4283 part of a valid accession ID</li>
4284 <li>fatal OOM if object retrieved by sequence fetcher
4285 runs out of memory</li>
4286 <li>unhandled Out of Memory Error when viewing pca
4287 analysis results</li>
4288 <li>InstallAnywhere builds fail to launch on OS X java
4289 10.5 update 4 (due to apple Java 1.6 update)</li>
4290 <li>Installanywhere Jalview silently fails to launch</li>
4291 </ul> <em>Applet</em>
4293 <li>Jalview.getFeatureGroups() raises an
4294 ArrayIndexOutOfBoundsException if no feature groups are
4301 <div align="center">
4302 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4308 <li>Alignment prettyprinter doesn't cope with long
4310 <li>clustalx colourscheme colours Ds preferentially when
4311 both D+E are present in over 50% of the column</li>
4312 <li>nucleic acid structures retrieved from PDB do not
4313 import correctly</li>
4314 <li>More columns get selected than were clicked on when a
4315 number of columns are hidden</li>
4316 <li>annotation label popup menu not providing correct
4317 add/hide/show options when rows are hidden or none are
4319 <li>Stockholm format shown in list of readable formats,
4320 and parser copes better with alignments from RFAM.</li>
4321 <li>CSV output of consensus only includes the percentage
4322 of all symbols if sequence logo display is enabled</li>
4324 </ul> <em>Applet</em>
4326 <li>annotation panel disappears when annotation is
4328 </ul> <em>Application</em>
4330 <li>Alignment view not redrawn properly when new
4331 alignment opened where annotation panel is visible but no
4332 annotations are present on alignment</li>
4333 <li>pasted region containing hidden columns is
4334 incorrectly displayed in new alignment window</li>
4335 <li>Jalview slow to complete operations when stdout is
4336 flooded (fix is to close the Jalview console)</li>
4337 <li>typo in AlignmentFrame->View->Hide->all but
4338 selected Rregions menu item.</li>
4339 <li>inconsistent group submenu and Format submenu entry
4340 'Un' or 'Non'conserved</li>
4341 <li>Sequence feature settings are being shared by
4342 multiple distinct alignments</li>
4343 <li>group annotation not recreated when tree partition is
4345 <li>double click on group annotation to select sequences
4346 does not propagate to associated trees</li>
4347 <li>Mac OSX specific issues:
4349 <li>exception raised when mouse clicked on desktop
4350 window background</li>
4351 <li>Desktop menu placed on menu bar and application
4352 name set correctly</li>
4353 <li>sequence feature settings not wide enough for the
4354 save feature colourscheme button</li>
4363 <div align="center">
4364 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4367 <td><em>New Capabilities</em>
4369 <li>URL links generated from description line for
4370 regular-expression based URL links (applet and application)
4372 <li>Non-positional feature URL links are shown in link
4374 <li>Linked viewing of nucleic acid sequences and
4376 <li>Automatic Scrolling option in View menu to display
4377 the currently highlighted region of an alignment.</li>
4378 <li>Order an alignment by sequence length, or using the
4379 average score or total feature count for each sequence.</li>
4380 <li>Shading features by score or associated description</li>
4381 <li>Subdivide alignment and groups based on identity of
4382 selected subsequence (Make Groups from Selection).</li>
4383 <li>New hide/show options including Shift+Control+H to
4384 hide everything but the currently selected region.</li>
4385 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4386 </ul> <em>Application</em>
4388 <li>Fetch DB References capabilities and UI expanded to
4389 support retrieval from DAS sequence sources</li>
4390 <li>Local DAS Sequence sources can be added via the
4391 command line or via the Add local source dialog box.</li>
4392 <li>DAS Dbref and DbxRef feature types are parsed as
4393 database references and protein_name is parsed as
4394 description line (BioSapiens terms).</li>
4395 <li>Enable or disable non-positional feature and database
4396 references in sequence ID tooltip from View menu in
4398 <!-- <li>New hidden columns and rows and representatives capabilities
4399 in annotations file (in progress - not yet fully implemented)</li> -->
4400 <li>Group-associated consensus, sequence logos and
4401 conservation plots</li>
4402 <li>Symbol distributions for each column can be exported
4403 and visualized as sequence logos</li>
4404 <li>Optionally scale multi-character column labels to fit
4405 within each column of annotation row<!-- todo for applet -->
4407 <li>Optional automatic sort of associated alignment view
4408 when a new tree is opened.</li>
4409 <li>Jalview Java Console</li>
4410 <li>Better placement of desktop window when moving
4411 between different screens.</li>
4412 <li>New preference items for sequence ID tooltip and
4413 consensus annotation</li>
4414 <li>Client to submit sequences and IDs to Envision2
4416 <li><em>Vamsas Capabilities</em>
4418 <li>Improved VAMSAS synchronization (Jalview archive
4419 used to preserve views, structures, and tree display
4421 <li>Import of vamsas documents from disk or URL via
4423 <li>Sharing of selected regions between views and
4424 with other VAMSAS applications (Experimental feature!)</li>
4425 <li>Updated API to VAMSAS version 0.2</li>
4427 </ul> <em>Applet</em>
4429 <li>Middle button resizes annotation row height</li>
4432 <li>sortByTree (true/false) - automatically sort the
4433 associated alignment view by the tree when a new tree is
4435 <li>showTreeBootstraps (true/false) - show or hide
4436 branch bootstraps (default is to show them if available)</li>
4437 <li>showTreeDistances (true/false) - show or hide
4438 branch lengths (default is to show them if available)</li>
4439 <li>showUnlinkedTreeNodes (true/false) - indicate if
4440 unassociated nodes should be highlighted in the tree
4442 <li>heightScale and widthScale (1.0 or more) -
4443 increase the height or width of a cell in the alignment
4444 grid relative to the current font size.</li>
4447 <li>Non-positional features displayed in sequence ID
4449 </ul> <em>Other</em>
4451 <li>Features format: graduated colour definitions and
4452 specification of feature scores</li>
4453 <li>Alignment Annotations format: new keywords for group
4454 associated annotation (GROUP_REF) and annotation row display
4455 properties (ROW_PROPERTIES)</li>
4456 <li>XML formats extended to support graduated feature
4457 colourschemes, group associated annotation, and profile
4458 visualization settings.</li></td>
4461 <li>Source field in GFF files parsed as feature source
4462 rather than description</li>
4463 <li>Non-positional features are now included in sequence
4464 feature and gff files (controlled via non-positional feature
4465 visibility in tooltip).</li>
4466 <li>URL links generated for all feature links (bugfix)</li>
4467 <li>Added URL embedding instructions to features file
4469 <li>Codons containing ambiguous nucleotides translated as
4470 'X' in peptide product</li>
4471 <li>Match case switch in find dialog box works for both
4472 sequence ID and sequence string and query strings do not
4473 have to be in upper case to match case-insensitively.</li>
4474 <li>AMSA files only contain first column of
4475 multi-character column annotation labels</li>
4476 <li>Jalview Annotation File generation/parsing consistent
4477 with documentation (e.g. Stockholm annotation can be
4478 exported and re-imported)</li>
4479 <li>PDB files without embedded PDB IDs given a friendly
4481 <li>Find incrementally searches ID string matches as well
4482 as subsequence matches, and correctly reports total number
4486 <li>Better handling of exceptions during sequence
4488 <li>Dasobert generated non-positional feature URL
4489 link text excludes the start_end suffix</li>
4490 <li>DAS feature and source retrieval buttons disabled
4491 when fetch or registry operations in progress.</li>
4492 <li>PDB files retrieved from URLs are cached properly</li>
4493 <li>Sequence description lines properly shared via
4495 <li>Sequence fetcher fetches multiple records for all
4497 <li>Ensured that command line das feature retrieval
4498 completes before alignment figures are generated.</li>
4499 <li>Reduced time taken when opening file browser for
4501 <li>isAligned check prior to calculating tree, PCA or
4502 submitting an MSA to JNet now excludes hidden sequences.</li>
4503 <li>User defined group colours properly recovered
4504 from Jalview projects.</li>
4513 <div align="center">
4514 <strong>2.4.0.b2</strong><br> 28/10/2009
4519 <li>Experimental support for google analytics usage
4521 <li>Jalview privacy settings (user preferences and docs).</li>
4526 <li>Race condition in applet preventing startup in
4528 <li>Exception when feature created from selection beyond
4529 length of sequence.</li>
4530 <li>Allow synthetic PDB files to be imported gracefully</li>
4531 <li>Sequence associated annotation rows associate with
4532 all sequences with a given id</li>
4533 <li>Find function matches case-insensitively for sequence
4534 ID string searches</li>
4535 <li>Non-standard characters do not cause pairwise
4536 alignment to fail with exception</li>
4537 </ul> <em>Application Issues</em>
4539 <li>Sequences are now validated against EMBL database</li>
4540 <li>Sequence fetcher fetches multiple records for all
4542 </ul> <em>InstallAnywhere Issues</em>
4544 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4545 issue with installAnywhere mechanism)</li>
4546 <li>Command line launching of JARs from InstallAnywhere
4547 version (java class versioning error fixed)</li>
4554 <div align="center">
4555 <strong>2.4</strong><br> 27/8/2008
4558 <td><em>User Interface</em>
4560 <li>Linked highlighting of codon and amino acid from
4561 translation and protein products</li>
4562 <li>Linked highlighting of structure associated with
4563 residue mapping to codon position</li>
4564 <li>Sequence Fetcher provides example accession numbers
4565 and 'clear' button</li>
4566 <li>MemoryMonitor added as an option under Desktop's
4568 <li>Extract score function to parse whitespace separated
4569 numeric data in description line</li>
4570 <li>Column labels in alignment annotation can be centred.</li>
4571 <li>Tooltip for sequence associated annotation give name
4573 </ul> <em>Web Services and URL fetching</em>
4575 <li>JPred3 web service</li>
4576 <li>Prototype sequence search client (no public services
4578 <li>Fetch either seed alignment or full alignment from
4580 <li>URL Links created for matching database cross
4581 references as well as sequence ID</li>
4582 <li>URL Links can be created using regular-expressions</li>
4583 </ul> <em>Sequence Database Connectivity</em>
4585 <li>Retrieval of cross-referenced sequences from other
4587 <li>Generalised database reference retrieval and
4588 validation to all fetchable databases</li>
4589 <li>Fetch sequences from DAS sources supporting the
4590 sequence command</li>
4591 </ul> <em>Import and Export</em>
4592 <li>export annotation rows as CSV for spreadsheet import</li>
4593 <li>Jalview projects record alignment dataset associations,
4594 EMBL products, and cDNA sequence mappings</li>
4595 <li>Sequence Group colour can be specified in Annotation
4597 <li>Ad-hoc colouring of group in Annotation File using RGB
4598 triplet as name of colourscheme</li>
4599 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4601 <li>treenode binding for VAMSAS tree exchange</li>
4602 <li>local editing and update of sequences in VAMSAS
4603 alignments (experimental)</li>
4604 <li>Create new or select existing session to join</li>
4605 <li>load and save of vamsas documents</li>
4606 </ul> <em>Application command line</em>
4608 <li>-tree parameter to open trees (introduced for passing
4610 <li>-fetchfrom command line argument to specify nicknames
4611 of DAS servers to query for alignment features</li>
4612 <li>-dasserver command line argument to add new servers
4613 that are also automatically queried for features</li>
4614 <li>-groovy command line argument executes a given groovy
4615 script after all input data has been loaded and parsed</li>
4616 </ul> <em>Applet-Application data exchange</em>
4618 <li>Trees passed as applet parameters can be passed to
4619 application (when using "View in full
4620 application")</li>
4621 </ul> <em>Applet Parameters</em>
4623 <li>feature group display control parameter</li>
4624 <li>debug parameter</li>
4625 <li>showbutton parameter</li>
4626 </ul> <em>Applet API methods</em>
4628 <li>newView public method</li>
4629 <li>Window (current view) specific get/set public methods</li>
4630 <li>Feature display control methods</li>
4631 <li>get list of currently selected sequences</li>
4632 </ul> <em>New Jalview distribution features</em>
4634 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4635 <li>RELEASE file gives build properties for the latest
4636 Jalview release.</li>
4637 <li>Java 1.1 Applet build made easier and donotobfuscate
4638 property controls execution of obfuscator</li>
4639 <li>Build target for generating source distribution</li>
4640 <li>Debug flag for javacc</li>
4641 <li>.jalview_properties file is documented (slightly) in
4642 jalview.bin.Cache</li>
4643 <li>Continuous Build Integration for stable and
4644 development version of Application, Applet and source
4649 <li>selected region output includes visible annotations
4650 (for certain formats)</li>
4651 <li>edit label/displaychar contains existing label/char
4653 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4654 <li>shorter peptide product names from EMBL records</li>
4655 <li>Newick string generator makes compact representations</li>
4656 <li>bootstrap values parsed correctly for tree files with
4658 <li>pathological filechooser bug avoided by not allowing
4659 filenames containing a ':'</li>
4660 <li>Fixed exception when parsing GFF files containing
4661 global sequence features</li>
4662 <li>Alignment datasets are finalized only when number of
4663 references from alignment sequences goes to zero</li>
4664 <li>Close of tree branch colour box without colour
4665 selection causes cascading exceptions</li>
4666 <li>occasional negative imgwidth exceptions</li>
4667 <li>better reporting of non-fatal warnings to user when
4668 file parsing fails.</li>
4669 <li>Save works when Jalview project is default format</li>
4670 <li>Save as dialog opened if current alignment format is
4671 not a valid output format</li>
4672 <li>UniProt canonical names introduced for both das and
4674 <li>Histidine should be midblue (not pink!) in Zappo</li>
4675 <li>error messages passed up and output when data read
4677 <li>edit undo recovers previous dataset sequence when
4678 sequence is edited</li>
4679 <li>allow PDB files without pdb ID HEADER lines (like
4680 those generated by MODELLER) to be read in properly</li>
4681 <li>allow reading of JPred concise files as a normal
4683 <li>Stockholm annotation parsing and alignment properties
4684 import fixed for PFAM records</li>
4685 <li>Structure view windows have correct name in Desktop
4687 <li>annotation consisting of sequence associated scores
4688 can be read and written correctly to annotation file</li>
4689 <li>Aligned cDNA translation to aligned peptide works
4691 <li>Fixed display of hidden sequence markers and
4692 non-italic font for representatives in Applet</li>
4693 <li>Applet Menus are always embedded in applet window on
4695 <li>Newly shown features appear at top of stack (in
4697 <li>Annotations added via parameter not drawn properly
4698 due to null pointer exceptions</li>
4699 <li>Secondary structure lines are drawn starting from
4700 first column of alignment</li>
4701 <li>UniProt XML import updated for new schema release in
4703 <li>Sequence feature to sequence ID match for Features
4704 file is case-insensitive</li>
4705 <li>Sequence features read from Features file appended to
4706 all sequences with matching IDs</li>
4707 <li>PDB structure coloured correctly for associated views
4708 containing a sub-sequence</li>
4709 <li>PDB files can be retrieved by applet from Jar files</li>
4710 <li>feature and annotation file applet parameters
4711 referring to different directories are retrieved correctly</li>
4712 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4713 <li>Fixed application hang whilst waiting for
4714 splash-screen version check to complete</li>
4715 <li>Applet properly URLencodes input parameter values
4716 when passing them to the launchApp service</li>
4717 <li>display name and local features preserved in results
4718 retrieved from web service</li>
4719 <li>Visual delay indication for sequence retrieval and
4720 sequence fetcher initialisation</li>
4721 <li>updated Application to use DAS 1.53e version of
4722 dasobert DAS client</li>
4723 <li>Re-instated Full AMSA support and .amsa file
4725 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4733 <div align="center">
4734 <strong>2.3</strong><br> 9/5/07
4739 <li>Jmol 11.0.2 integration</li>
4740 <li>PDB views stored in Jalview XML files</li>
4741 <li>Slide sequences</li>
4742 <li>Edit sequence in place</li>
4743 <li>EMBL CDS features</li>
4744 <li>DAS Feature mapping</li>
4745 <li>Feature ordering</li>
4746 <li>Alignment Properties</li>
4747 <li>Annotation Scores</li>
4748 <li>Sort by scores</li>
4749 <li>Feature/annotation editing in applet</li>
4754 <li>Headless state operation in 2.2.1</li>
4755 <li>Incorrect and unstable DNA pairwise alignment</li>
4756 <li>Cut and paste of sequences with annotation</li>
4757 <li>Feature group display state in XML</li>
4758 <li>Feature ordering in XML</li>
4759 <li>blc file iteration selection using filename # suffix</li>
4760 <li>Stockholm alignment properties</li>
4761 <li>Stockhom alignment secondary structure annotation</li>
4762 <li>2.2.1 applet had no feature transparency</li>
4763 <li>Number pad keys can be used in cursor mode</li>
4764 <li>Structure Viewer mirror image resolved</li>
4771 <div align="center">
4772 <strong>2.2.1</strong><br> 12/2/07
4777 <li>Non standard characters can be read and displayed
4778 <li>Annotations/Features can be imported/exported to the
4780 <li>Applet allows editing of sequence/annotation/group
4781 name & description
4782 <li>Preference setting to display sequence name in
4784 <li>Annotation file format extended to allow
4785 Sequence_groups to be defined
4786 <li>Default opening of alignment overview panel can be
4787 specified in preferences
4788 <li>PDB residue numbering annotation added to associated
4794 <li>Applet crash under certain Linux OS with Java 1.6
4796 <li>Annotation file export / import bugs fixed
4797 <li>PNG / EPS image output bugs fixed
4803 <div align="center">
4804 <strong>2.2</strong><br> 27/11/06
4809 <li>Multiple views on alignment
4810 <li>Sequence feature editing
4811 <li>"Reload" alignment
4812 <li>"Save" to current filename
4813 <li>Background dependent text colour
4814 <li>Right align sequence ids
4815 <li>User-defined lower case residue colours
4818 <li>Menu item accelerator keys
4819 <li>Control-V pastes to current alignment
4820 <li>Cancel button for DAS Feature Fetching
4821 <li>PCA and PDB Viewers zoom via mouse roller
4822 <li>User-defined sub-tree colours and sub-tree selection
4824 <li>'New Window' button on the 'Output to Text box'
4829 <li>New memory efficient Undo/Redo System
4830 <li>Optimised symbol lookups and conservation/consensus
4832 <li>Region Conservation/Consensus recalculated after
4834 <li>Fixed Remove Empty Columns Bug (empty columns at end
4836 <li>Slowed DAS Feature Fetching for increased robustness.
4838 <li>Made angle brackets in ASCII feature descriptions
4840 <li>Re-instated Zoom function for PCA
4841 <li>Sequence descriptions conserved in web service
4843 <li>UniProt ID discoverer uses any word separated by
4845 <li>WsDbFetch query/result association resolved
4846 <li>Tree leaf to sequence mapping improved
4847 <li>Smooth fonts switch moved to FontChooser dialog box.
4854 <div align="center">
4855 <strong>2.1.1</strong><br> 12/9/06
4860 <li>Copy consensus sequence to clipboard</li>
4865 <li>Image output - rightmost residues are rendered if
4866 sequence id panel has been resized</li>
4867 <li>Image output - all offscreen group boundaries are
4869 <li>Annotation files with sequence references - all
4870 elements in file are relative to sequence position</li>
4871 <li>Mac Applet users can use Alt key for group editing</li>
4877 <div align="center">
4878 <strong>2.1</strong><br> 22/8/06
4883 <li>MAFFT Multiple Alignment in default Web Service list</li>
4884 <li>DAS Feature fetching</li>
4885 <li>Hide sequences and columns</li>
4886 <li>Export Annotations and Features</li>
4887 <li>GFF file reading / writing</li>
4888 <li>Associate structures with sequences from local PDB
4890 <li>Add sequences to exisiting alignment</li>
4891 <li>Recently opened files / URL lists</li>
4892 <li>Applet can launch the full application</li>
4893 <li>Applet has transparency for features (Java 1.2
4895 <li>Applet has user defined colours parameter</li>
4896 <li>Applet can load sequences from parameter
4897 "sequence<em>x</em>"
4903 <li>Redundancy Panel reinstalled in the Applet</li>
4904 <li>Monospaced font - EPS / rescaling bug fixed</li>
4905 <li>Annotation files with sequence references bug fixed</li>
4911 <div align="center">
4912 <strong>2.08.1</strong><br> 2/5/06
4917 <li>Change case of selected region from Popup menu</li>
4918 <li>Choose to match case when searching</li>
4919 <li>Middle mouse button and mouse movement can compress /
4920 expand the visible width and height of the alignment</li>
4925 <li>Annotation Panel displays complete JNet results</li>
4931 <div align="center">
4932 <strong>2.08b</strong><br> 18/4/06
4938 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4939 <li>Righthand label on wrapped alignments shows correct
4946 <div align="center">
4947 <strong>2.08</strong><br> 10/4/06
4952 <li>Editing can be locked to the selection area</li>
4953 <li>Keyboard editing</li>
4954 <li>Create sequence features from searches</li>
4955 <li>Precalculated annotations can be loaded onto
4957 <li>Features file allows grouping of features</li>
4958 <li>Annotation Colouring scheme added</li>
4959 <li>Smooth fonts off by default - Faster rendering</li>
4960 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4965 <li>Drag & Drop fixed on Linux</li>
4966 <li>Jalview Archive file faster to load/save, sequence
4967 descriptions saved.</li>
4973 <div align="center">
4974 <strong>2.07</strong><br> 12/12/05
4979 <li>PDB Structure Viewer enhanced</li>
4980 <li>Sequence Feature retrieval and display enhanced</li>
4981 <li>Choose to output sequence start-end after sequence
4982 name for file output</li>
4983 <li>Sequence Fetcher WSDBFetch@EBI</li>
4984 <li>Applet can read feature files, PDB files and can be
4985 used for HTML form input</li>
4990 <li>HTML output writes groups and features</li>
4991 <li>Group editing is Control and mouse click</li>
4992 <li>File IO bugs</li>
4998 <div align="center">
4999 <strong>2.06</strong><br> 28/9/05
5004 <li>View annotations in wrapped mode</li>
5005 <li>More options for PCA viewer</li>
5010 <li>GUI bugs resolved</li>
5011 <li>Runs with -nodisplay from command line</li>
5017 <div align="center">
5018 <strong>2.05b</strong><br> 15/9/05
5023 <li>Choose EPS export as lineart or text</li>
5024 <li>Jar files are executable</li>
5025 <li>Can read in Uracil - maps to unknown residue</li>
5030 <li>Known OutOfMemory errors give warning message</li>
5031 <li>Overview window calculated more efficiently</li>
5032 <li>Several GUI bugs resolved</li>
5038 <div align="center">
5039 <strong>2.05</strong><br> 30/8/05
5044 <li>Edit and annotate in "Wrapped" view</li>
5049 <li>Several GUI bugs resolved</li>
5055 <div align="center">
5056 <strong>2.04</strong><br> 24/8/05
5061 <li>Hold down mouse wheel & scroll to change font
5067 <li>Improved JPred client reliability</li>
5068 <li>Improved loading of Jalview files</li>
5074 <div align="center">
5075 <strong>2.03</strong><br> 18/8/05
5080 <li>Set Proxy server name and port in preferences</li>
5081 <li>Multiple URL links from sequence ids</li>
5082 <li>User Defined Colours can have a scheme name and added
5084 <li>Choose to ignore gaps in consensus calculation</li>
5085 <li>Unix users can set default web browser</li>
5086 <li>Runs without GUI for batch processing</li>
5087 <li>Dynamically generated Web Service Menus</li>
5092 <li>InstallAnywhere download for Sparc Solaris</li>
5098 <div align="center">
5099 <strong>2.02</strong><br> 18/7/05
5105 <li>Copy & Paste order of sequences maintains
5106 alignment order.</li>
5112 <div align="center">
5113 <strong>2.01</strong><br> 12/7/05
5118 <li>Use delete key for deleting selection.</li>
5119 <li>Use Mouse wheel to scroll sequences.</li>
5120 <li>Help file updated to describe how to add alignment
5122 <li>Version and build date written to build properties
5124 <li>InstallAnywhere installation will check for updates
5125 at launch of Jalview.</li>
5130 <li>Delete gaps bug fixed.</li>
5131 <li>FileChooser sorts columns.</li>
5132 <li>Can remove groups one by one.</li>
5133 <li>Filechooser icons installed.</li>
5134 <li>Finder ignores return character when searching.
5135 Return key will initiate a search.<br>
5142 <div align="center">
5143 <strong>2.0</strong><br> 20/6/05
5148 <li>New codebase</li>