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.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
62 <em>20/12/2021</em></strong></td>
64 <td align="left" valign="top"><em>Security</em>
67 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
69 </ul> <em>Development</em>
71 <li>Updated building instructions</li>
76 <!-- JAL-3840 -->Occupancy calculation is incorrect for
77 alignment columns with over -1+2^32 gaps (breaking filtering
81 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
82 scale factors being set with buggy window-managers (linux
85 </ul> <em>Development</em>
87 <li>Fixed non-fatal gradle errors during build</li>
92 <td width="60" align="center" nowrap><strong><a
93 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
94 <em>09/03/2021</em></strong></td>
95 <td align="left" valign="top"><em>Improved control of
96 Jalview's use of network services via jalview_properties</em>
99 <!-- JAL-3814 -->New .jalview_properties token controlling
100 launch of the news browser (like -nonews argument)
103 <!-- JAL-3813 -->New .jalview_properties token controlling
104 download of linkout URLs from
105 www.jalview.org/services/identifiers
108 <!-- JAL-3812 -->New .jalview_properties token controlling
109 download of BIOJSHTML templates
112 <!-- JAL-3811 -->New 'Discover Web Services' option to
113 trigger a one off JABAWS discovery if autodiscovery was
117 <td align="left" valign="top">
120 <!-- JAL-3818 -->Intermittent deadlock opening structure in
123 </ul> <em>New Known defects</em>
126 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
127 always restored from project (since 2.10.3)
130 <!-- JAL-3806 -->Selections from tree built from CDS aren't
131 propagated to Protein alignment (since 2.11.1.3)
137 <td width="60" align="center" nowrap><strong><a
138 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
139 <em>29/10/2020</em></strong></td>
140 <td align="left" valign="top">
145 <td align="left" valign="top">
148 <!-- JAL-3765 -->Find doesn't always highlight all matching
149 positions in a sequence (bug introduced in 2.11.1.2)
152 <!-- JAL-3760 -->Alignments containing one or more protein
153 sequences can be classed as nucleotide
156 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
157 sequences after alignment of protein products (known defect
158 first reported for 2.11.1.0)
161 <!-- JAL-3725 -->No tooltip or popup menu for genomic
162 features outwith CDS shown overlaid on protein
165 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
166 correctly mapped by Jalview (e.g. affects viral CDS with
167 ribosomal slippage, since 2.9.0)
170 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
174 <!-- JAL-3700 -->Selections in CDS sequence panel don't
175 always select corresponding protein sequences
178 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
179 column selection doesn't always ignore hidden columns
181 </ul> <em>Installer</em>
184 <!-- JAL-3611 -->Space character in Jalview install path on
185 Windows prevents install4j launching getdown
187 </ul> <em>Development</em>
190 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
191 version numbers in doc/building.md
197 <td width="60" align="center" nowrap><strong><a
198 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
199 <em>25/09/2020</em></strong></td>
200 <td align="left" valign="top">
204 <td align="left" valign="top">
207 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
208 "Encountered problems opening
209 https://www.jalview.org/examples/exampleFile_2_7.jvp"
215 <td width="60" align="center" nowrap><strong><a
216 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
217 <em>17/09/2020</em></strong></td>
218 <td align="left" valign="top">
221 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
222 residue in cursor mode
225 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
226 HTSJDK from 2.12 to 2.23
229 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
230 optimisations and improvements suggested by Bob Hanson and
231 improved compatibility with JalviewJS
234 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
235 alignments from Pfam and Rfam
238 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
239 import (no longer based on .gz extension)
242 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
245 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
246 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
250 <!-- JAL-3667 -->Improved warning messages, debug logging
251 and fixed Retry action when Jalview encounters errors when
252 saving or making backup files.
255 <!-- JAL-3676 -->Enhanced Jalview Java Console:
257 <li>Jalview's logging level can be configured</li>
258 <li>Copy to Clipboard Buttion</li>
262 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
263 when running on Linux (Requires Java 11+)
265 </ul> <em>Launching Jalview</em>
268 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
269 through a system property
272 <!-- JAL-3477 -->Improved built-in documentation and command
273 line help for configuring Jalview's memory
277 <td align="left" valign="top">
280 <!-- JAL-3691 -->Conservation and Quality tracks are shown
281 but not calculated and no protein or DNA score models are
282 available for tree/PCA calculation when launched with
283 Turkish language locale
286 <!-- JAL-3493 -->Escape does not clear highlights on the
287 alignment (Since Jalview 2.10.3)
290 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
291 doesn't slide selected sequences, just sequence under cursor
294 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
295 sequence under the cursor
298 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
299 multiple EMBL gene products shown for a single contig
302 <!-- JAL-3696 -->Errors encountered when processing variants
303 from VCF files yield "Error processing VCF: Format specifier
307 <!-- JAL-3697 -->Count of features not shown can be wrong
308 when there are both local and complementary features mapped
309 to the position under the cursor
312 <!-- JAL-3673 -->Sequence ID for reference sequence is
313 clipped when Right align Sequence IDs enabled
316 <!-- JAL-2983 -->Slider with negative range values not
317 rendered correctly in VAqua4 (Since 2.10.4)
320 <!-- JAL-3685 -->Single quotes not displayed correctly in
321 internationalised text for some messages and log output
324 <!-- JAL-3490 -->Find doesn't report matches that span
325 hidden gapped columns
328 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
329 panels, Alignment viewport and annotation renderer.
332 <!-- JAL-3561 -->Jalview ignores file format parameter
333 specifying output format when exporting an alignment via the
337 <!-- JAL-3667 -->Windows 10: For a minority of users, if
338 backups are not enabled, Jalview sometimes fails to
339 overwrite an existing file and raises a warning dialog. (in
340 2.11.0, and 2.11.1.0, the workaround is to try to save the
341 file again, and if that fails, delete the original file and
345 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
349 <!-- JAL-3741 -->References to http://www.jalview.org in
350 program and documentation
352 </ul> <em>Launching Jalview</em>
355 <!-- JAL-3718 -->Jalview application fails when launched the
356 first time for a version that has different jars to the
357 previous launched version.
359 </ul> <em>Developing Jalview</em>
362 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
363 data, causing cloverReport gradle task to fail with an
367 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
368 monitor the release channel
370 </ul> <em>New Known defects</em>
373 <!-- JAL-3748 -->CDS shown in result of submitting proteins
374 in a CDS/Protein alignment to a web service is wrong when
375 proteins share a common transcript sequence (e.g.
376 genome of RNA viruses)
379 <!-- JAL-3576 -->Co-located features exported and re-imported
380 are ordered differently when shown on alignment and in
381 tooltips. (Also affects v2.11.1.0)
384 <!-- JAL-3702 -->Drag and drop of alignment file onto
385 alignment window when in a HiDPI scaled mode in Linux only
386 works for the top left quadrant of the alignment window
389 <!-- JAL-3701 -->Stale build data in jalview standalone jar
390 builds (only affects 2.11.1.1 branch)
393 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
394 when alignment view restored from project (since Jalview 2.11.0)
397 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
398 protein products for certain ENA records are repeatedly
399 shown via Calculate->Show Cross Refs
405 <td width="60" align="center" nowrap><strong><a
406 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
407 <em>22/04/2020</em></strong></td>
408 <td align="left" valign="top">
411 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
412 'virtual' codon features shown on protein (or vice versa)
413 for display in alignments, on structure views (including
414 transfer to UCSF chimera), in feature reports and for
418 <!-- JAL-3121 -->Feature attributes from VCF files can be
419 exported and re-imported as GFF3 files
422 <!-- JAL-3376 -->Capture VCF "fixed column" values
423 POS, ID, QUAL, FILTER as Feature Attributes
426 <!-- JAL-3375 -->More robust VCF numeric data field
427 validation while parsing
430 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
434 <!-- JAL-3535 -->Feature Settings dialog title includes name
438 <!-- JAL-3538 -->Font anti-aliasing in alignment views
442 <!-- JAL-3468 -->Very long feature descriptions truncated in
446 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
447 with no feature types visible
450 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
452 </ul><em>Jalview Installer</em>
455 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
456 in console (may be null when Jalview launched as executable jar or via conda)
459 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
462 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
465 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
467 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
468 </ul> <em>Release processes</em>
471 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
474 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
476 </ul> <em>Build System</em>
479 <!-- JAL-3510 -->Clover updated to 4.4.1
482 <!-- JAL-3513 -->Test code included in Clover coverage
486 <em>Groovy Scripts</em>
489 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
490 to stdout containing the consensus sequence for each
491 alignment in a Jalview session
494 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
495 genomic sequence_variant annotation from CDS as
496 missense_variant or synonymous_variant on protein products.
500 <td align="left" valign="top">
503 <!-- JAL-3581 -->Hidden sequence markers still visible when
504 'Show hidden markers' option is not ticked
507 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
508 PNG output when 'Automatically set ID width' is set in
509 jalview preferences or properties file
512 <!-- JAL-3571 -->Feature Editor dialog can be opened when
513 'Show Sequence Features' option is not ticked
516 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
517 buttons in Feature Settings dialog are clicked when no
521 <!-- JAL-3412 -->ID margins for CDS and Protein views not
522 equal when split frame is first opened
525 <!-- JAL-3296 -->Sequence position numbers in status bar not
526 correct after editing a sequence's start position
529 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
530 with annotation and exceptions thrown when only a few
531 columns shown in wrapped mode
534 <!-- JAL-3386 -->Sequence IDs missing in headless export of
535 wrapped alignment figure with annotations
538 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
539 ID fails with ClassCastException
542 <!-- JAL-3389 -->Chimera session not restored from Jalview
546 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
547 feature settings dialog also selects columns
550 <!-- JAL-3473 -->SpinnerNumberModel causes
551 IllegalArgumentException in some circumstances
554 <!-- JAL-3534 -->Multiple feature settings dialogs can be
558 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
559 alignment window is closed
562 <!-- JAL-3406 -->Credits missing some authors in Jalview
563 help documentation for 2.11.0 release
566 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
567 includes Pfam ID as sequence's accession rather than its
570 </ul> <em>Java 11 Compatibility issues</em>
573 <!-- JAL-2987 -->OSX - Can't view some search results in
574 PDB/Uniprot search panel
576 </ul> <em>Installer</em>
579 <!-- JAL-3447 -->Jalview should not create file associations
580 for 3D structure files (.pdb, .mmcif. .cif)
582 </ul> <em>Repository and Source Release</em>
585 <!-- JAL-3474 -->removed obsolete .cvsignore files from
589 <!-- JAL-3541 -->Clover report generation running out of
592 </ul> <em>New Known Issues</em>
595 <!-- JAL-3523 -->OSX - Current working directory not
596 preserved when Jalview.app launched with parameters from
600 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
601 clipped in headless figure export when Right Align option
605 <!-- JAL-3542 -->Jalview Installation type always reports
606 'Source' in console output
609 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
610 bamboo server but run fine locally.
616 <td width="60" align="center" nowrap>
617 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
618 <em>04/07/2019</em></strong>
620 <td align="left" valign="top">
623 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
624 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
625 source project) rather than InstallAnywhere
628 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
629 settings, receive over the air updates and launch specific
630 versions via (<a href="https://github.com/threerings/getdown">Three
634 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
635 formats supported by Jalview (including .jvp project files)
638 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
639 arguments and switch between different getdown channels
642 <!-- JAL-3141 -->Backup files created when saving Jalview project
647 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
648 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
650 <!-- JAL-2620 -->Alternative genetic code tables for
651 'Translate as cDNA'</li>
653 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
654 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
657 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
658 implementation that allows updates) used for Sequence Feature collections</li>
660 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
661 features can be filtered and shaded according to any
662 associated attributes (e.g. variant attributes from VCF
663 file, or key-value pairs imported from column 9 of GFF
667 <!-- JAL-2879 -->Feature Attributes and shading schemes
668 stored and restored from Jalview Projects
671 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
672 recognise variant features
675 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
676 sequences (also coloured red by default)
679 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
683 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
684 algorithm (Z-sort/transparency and filter aware)
687 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
693 <!-- JAL-3205 -->Symmetric score matrices for faster
694 tree and PCA calculations
696 <li><strong>Principal Components Analysis Viewer</strong>
699 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
700 and Viewer state saved in Jalview Project
702 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
705 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
709 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
714 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
716 <li><strong>Speed and Efficiency</strong>
719 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
720 multiple groups when working with large alignments
723 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
727 <li><strong>User Interface</strong>
730 <!-- JAL-2933 -->Finder panel remembers last position in each
734 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
735 what is shown)<br />Only visible regions of alignment are shown by
736 default (can be changed in user preferences)
739 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
740 to the Overwrite Dialog
743 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
747 <!-- JAL-1244 -->Status bar shows bounds when dragging a
748 selection region, and gap count when inserting or deleting gaps
751 <!-- JAL-3132 -->Status bar updates over sequence and annotation
755 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
759 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
763 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
766 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
770 <!-- JAL-3181 -->Consistent ordering of links in sequence id
774 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
776 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
780 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
781 <li><strong>Java 11 Support (not yet on general release)</strong>
784 <!-- -->OSX GUI integrations for App menu's 'About' entry and
789 <em>Deprecations</em>
791 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
792 capabilities removed from the Jalview Desktop
794 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
795 unmarshalling has been replaced by JAXB for Jalview projects
796 and XML based data retrieval clients</li>
797 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
798 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
799 </ul> <em>Documentation</em>
801 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
802 not supported in EPS figure export
804 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
805 </ul> <em>Development and Release Processes</em>
808 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
811 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
813 <!-- JAL-3225 -->Eclipse project configuration managed with
817 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
818 Bamboo continuous integration for unattended Test Suite
822 <!-- JAL-2864 -->Memory test suite to detect leaks in common
826 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
830 <!-- JAL-3248 -->Developer documentation migrated to
831 markdown (with HTML rendering)
834 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
837 <!-- JAL-3289 -->New URLs for publishing development
842 <td align="left" valign="top">
845 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
848 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
849 superposition in Jmol fail on Windows
852 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
853 structures for sequences with lots of PDB structures
856 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
860 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
861 project involving multiple views
864 <!-- JAL-3164 -->Overview for complementary view in a linked
865 CDS/Protein alignment is not updated when Hide Columns by
866 Annotation dialog hides columns
869 <!-- JAL-3158 -->Selection highlighting in the complement of a
870 CDS/Protein alignment stops working after making a selection in
871 one view, then making another selection in the other view
874 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
878 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
879 Settings and Jalview Preferences panels
882 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
883 overview with large alignments
886 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
887 region if columns were selected by dragging right-to-left and the
888 mouse moved to the left of the first column
891 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
892 hidden column marker via scale popup menu
895 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
896 doesn't tell users the invalid URL
899 <!-- JAL-2816 -->Tooltips displayed for features filtered by
903 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
904 show cross references or Fetch Database References are shown in
908 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
909 peptide sequence (computed variant shown as p.Res.null)
912 <!-- JAL-2060 -->'Graduated colour' option not offered for
913 manually created features (where feature score is Float.NaN)
916 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
917 when columns are hidden
920 <!-- JAL-3082 -->Regular expression error for '(' in Select
921 Columns by Annotation description
924 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
925 out of Scale or Annotation Panel
928 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
932 <!-- JAL-3074 -->Left/right drag in annotation can scroll
936 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
940 <!-- JAL-3002 -->Column display is out by one after Page Down,
941 Page Up in wrapped mode
944 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
947 <!-- JAL-2932 -->Finder searches in minimised alignments
950 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
951 on opening an alignment
954 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
958 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
959 different groups in the alignment are selected
962 <!-- JAL-2717 -->Internationalised colour scheme names not shown
966 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
970 <!-- JAL-3125 -->Value input for graduated feature colour
971 threshold gets 'unrounded'
974 <!-- JAL-2982 -->PCA image export doesn't respect background
978 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
981 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
984 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
988 <!-- JAL-2964 -->Associate Tree with All Views not restored from
992 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
993 shown in complementary view
996 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
997 without normalisation
1000 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1004 <!-- JAL-914 -->Help page can be opened twice
1007 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1009 </ul> <em>Editing</em>
1012 <!-- JAL-2822 -->Start and End should be updated when sequence
1013 data at beginning or end of alignment added/removed via 'Edit'
1017 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1018 relocate sequence features correctly when start of sequence is
1019 removed (Known defect since 2.10)
1022 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1023 dialog corrupts dataset sequence
1026 <!-- JAL-868 -->Structure colours not updated when associated tree
1027 repartitions the alignment view (Regression in 2.10.5)
1029 </ul> <em>Datamodel</em>
1032 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1033 sequence's End is greater than its length
1035 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1036 general release)</em>
1039 <!-- JAL-3288 -->Menus work properly in split-screen
1041 </ul> <em>New Known Defects</em>
1044 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1047 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1048 regions of protein alignment.
1051 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1052 is restored from a Jalview 2.11 project
1055 <!-- JAL-3213 -->Alignment panel height can be too small after
1059 <!-- JAL-3240 -->Display is incorrect after removing gapped
1060 columns within hidden columns
1063 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1064 window after dragging left to select columns to left of visible
1068 <!-- JAL-2876 -->Features coloured according to their description
1069 string and thresholded by score in earlier versions of Jalview are
1070 not shown as thresholded features in 2.11. To workaround please
1071 create a Score filter instead.
1074 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1076 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1079 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1080 alignments with multiple views can close views unexpectedly
1083 <em>Java 11 Specific defects</em>
1086 <!-- JAL-3235 -->Jalview Properties file is not sorted
1087 alphabetically when saved
1093 <td width="60" nowrap>
1094 <div align="center">
1095 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1098 <td><div align="left">
1102 <!-- JAL-3101 -->Default memory for Jalview webstart and
1103 InstallAnywhere increased to 1G.
1106 <!-- JAL-247 -->Hidden sequence markers and representative
1107 sequence bolding included when exporting alignment as EPS,
1108 SVG, PNG or HTML. <em>Display is configured via the
1109 Format menu, or for command-line use via a Jalview
1110 properties file.</em>
1113 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1114 API and sequence data now imported as JSON.
1117 <!-- JAL-3065 -->Change in recommended way of starting
1118 Jalview via a Java command line: add jars in lib directory
1119 to CLASSPATH, rather than via the deprecated java.ext.dirs
1123 <em>Development</em>
1126 <!-- JAL-3047 -->Support added to execute test suite
1127 instrumented with <a href="http://openclover.org/">Open
1132 <td><div align="left">
1136 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1137 row shown in Feredoxin Structure alignment view of example
1141 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1142 annotation displayed.
1145 <!-- JAL-3107 -->Group conservation/consensus not shown
1146 for newly created group when 'Apply to all groups'
1150 <!-- JAL-3087 -->Corrupted display when switching to
1151 wrapped mode when sequence panel's vertical scrollbar is
1155 <!-- JAL-3003 -->Alignment is black in exported EPS file
1156 when sequences are selected in exported view.</em>
1159 <!-- JAL-3059 -->Groups with different coloured borders
1160 aren't rendered with correct colour.
1163 <!-- JAL-3092 -->Jalview could hang when importing certain
1164 types of knotted RNA secondary structure.
1167 <!-- JAL-3095 -->Sequence highlight and selection in
1168 trimmed VARNA 2D structure is incorrect for sequences that
1172 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1173 annotation when columns are inserted into an alignment,
1174 and when exporting as Stockholm flatfile.
1177 <!-- JAL-3053 -->Jalview annotation rows containing upper
1178 and lower-case 'E' and 'H' do not automatically get
1179 treated as RNA secondary structure.
1182 <!-- JAL-3106 -->.jvp should be used as default extension
1183 (not .jar) when saving a Jalview project file.
1186 <!-- JAL-3105 -->Mac Users: closing a window correctly
1187 transfers focus to previous window on OSX
1190 <em>Java 10 Issues Resolved</em>
1193 <!-- JAL-2988 -->OSX - Can't save new files via the File
1194 or export menus by typing in a name into the Save dialog
1198 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1199 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1200 'look and feel' which has improved compatibility with the
1201 latest version of OSX.
1208 <td width="60" nowrap>
1209 <div align="center">
1210 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1211 <em>7/06/2018</em></strong>
1214 <td><div align="left">
1218 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1219 annotation retrieved from Uniprot
1222 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1223 onto the Jalview Desktop
1227 <td><div align="left">
1231 <!-- JAL-3017 -->Cannot import features with multiple
1232 variant elements (blocks import of some Uniprot records)
1235 <!-- JAL-2997 -->Clustal files with sequence positions in
1236 right-hand column parsed correctly
1239 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1240 not alignment area in exported graphic
1243 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1244 window has input focus
1247 <!-- JAL-2992 -->Annotation panel set too high when
1248 annotation added to view (Windows)
1251 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1252 network connectivity is poor
1255 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1256 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1257 the currently open URL and links from a page viewed in
1258 Firefox or Chrome on Windows is now fully supported. If
1259 you are using Edge, only links in the page can be
1260 dragged, and with Internet Explorer, only the currently
1261 open URL in the browser can be dropped onto Jalview.</em>
1264 <em>New Known Defects</em>
1266 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1271 <td width="60" nowrap>
1272 <div align="center">
1273 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1276 <td><div align="left">
1280 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1281 for disabling automatic superposition of multiple
1282 structures and open structures in existing views
1285 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1286 ID and annotation area margins can be click-dragged to
1290 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1294 <!-- JAL-2759 -->Improved performance for large alignments
1295 and lots of hidden columns
1298 <!-- JAL-2593 -->Improved performance when rendering lots
1299 of features (particularly when transparency is disabled)
1302 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1303 exchange of Jalview features and Chimera attributes made
1309 <td><div align="left">
1312 <!-- JAL-2899 -->Structure and Overview aren't updated
1313 when Colour By Annotation threshold slider is adjusted
1316 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1317 overlapping alignment panel
1320 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1324 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1325 improved: CDS not handled correctly if transcript has no
1329 <!-- JAL-2321 -->Secondary structure and temperature
1330 factor annotation not added to sequence when local PDB
1331 file associated with it by drag'n'drop or structure
1335 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1336 dialog doesn't import PDB files dropped on an alignment
1339 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1340 scroll bar doesn't work for some CDS/Protein views
1343 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1344 Java 1.8u153 onwards and Java 1.9u4+.
1347 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1348 columns in annotation row
1351 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1352 honored in batch mode
1355 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1356 for structures added to existing Jmol view
1359 <!-- JAL-2223 -->'View Mappings' includes duplicate
1360 entries after importing project with multiple views
1363 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1364 protein sequences via SIFTS from associated PDB entries
1365 with negative residue numbers or missing residues fails
1368 <!-- JAL-2952 -->Exception when shading sequence with negative
1369 Temperature Factor values from annotated PDB files (e.g.
1370 as generated by CONSURF)
1373 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1374 tooltip doesn't include a text description of mutation
1377 <!-- JAL-2922 -->Invert displayed features very slow when
1378 structure and/or overview windows are also shown
1381 <!-- JAL-2954 -->Selecting columns from highlighted regions
1382 very slow for alignments with large numbers of sequences
1385 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1386 with 'StringIndexOutOfBounds'
1389 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1390 platforms running Java 10
1393 <!-- JAL-2960 -->Adding a structure to existing structure
1394 view appears to do nothing because the view is hidden behind the alignment view
1400 <!-- JAL-2926 -->Copy consensus sequence option in applet
1401 should copy the group consensus when popup is opened on it
1407 <!-- JAL-2913 -->Fixed ID width preference is not respected
1410 <em>New Known Defects</em>
1413 <!-- JAL-2973 --> Exceptions occasionally raised when
1414 editing a large alignment and overview is displayed
1417 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1418 repeatedly after a series of edits even when the overview
1419 is no longer reflecting updates
1422 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1423 structures for protein subsequence (if 'Trim Retrieved
1424 Sequences' enabled) or Ensembl isoforms (Workaround in
1425 2.10.4 is to fail back to N&W mapping)
1428 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1429 option gives blank output
1436 <td width="60" nowrap>
1437 <div align="center">
1438 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1441 <td><div align="left">
1442 <ul><li>Updated Certum Codesigning Certificate
1443 (Valid till 30th November 2018)</li></ul></div></td>
1444 <td><div align="left">
1445 <em>Desktop</em><ul>
1447 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1448 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1449 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1450 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1451 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1452 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1453 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1459 <td width="60" nowrap>
1460 <div align="center">
1461 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1464 <td><div align="left">
1468 <!-- JAL-2446 -->Faster and more efficient management and
1469 rendering of sequence features
1472 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1473 429 rate limit request hander
1476 <!-- JAL-2773 -->Structure views don't get updated unless
1477 their colours have changed
1480 <!-- JAL-2495 -->All linked sequences are highlighted for
1481 a structure mousover (Jmol) or selection (Chimera)
1484 <!-- JAL-2790 -->'Cancel' button in progress bar for
1485 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1488 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1489 view from Ensembl locus cross-references
1492 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1496 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1497 feature can be disabled
1500 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1501 PDB easier retrieval of sequences for lists of IDs
1504 <!-- JAL-2758 -->Short names for sequences retrieved from
1510 <li>Groovy interpreter updated to 2.4.12</li>
1511 <li>Example groovy script for generating a matrix of
1512 percent identity scores for current alignment.</li>
1514 <em>Testing and Deployment</em>
1517 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1521 <td><div align="left">
1525 <!-- JAL-2643 -->Pressing tab after updating the colour
1526 threshold text field doesn't trigger an update to the
1530 <!-- JAL-2682 -->Race condition when parsing sequence ID
1534 <!-- JAL-2608 -->Overview windows are also closed when
1535 alignment window is closed
1538 <!-- JAL-2548 -->Export of features doesn't always respect
1542 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1543 takes a long time in Cursor mode
1549 <!-- JAL-2777 -->Structures with whitespace chainCode
1550 cannot be viewed in Chimera
1553 <!-- JAL-2728 -->Protein annotation panel too high in
1557 <!-- JAL-2757 -->Can't edit the query after the server
1558 error warning icon is shown in Uniprot and PDB Free Text
1562 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1565 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1568 <!-- JAL-2739 -->Hidden column marker in last column not
1569 rendered when switching back from Wrapped to normal view
1572 <!-- JAL-2768 -->Annotation display corrupted when
1573 scrolling right in unwapped alignment view
1576 <!-- JAL-2542 -->Existing features on subsequence
1577 incorrectly relocated when full sequence retrieved from
1581 <!-- JAL-2733 -->Last reported memory still shown when
1582 Desktop->Show Memory is unticked (OSX only)
1585 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1586 features of same type and group to be selected for
1590 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1591 alignments when hidden columns are present
1594 <!-- JAL-2392 -->Jalview freezes when loading and
1595 displaying several structures
1598 <!-- JAL-2732 -->Black outlines left after resizing or
1602 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1603 within the Jalview desktop on OSX
1606 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1607 when in wrapped alignment mode
1610 <!-- JAL-2636 -->Scale mark not shown when close to right
1611 hand end of alignment
1614 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1615 each selected sequence do not have correct start/end
1619 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1620 after canceling the Alignment Window's Font dialog
1623 <!-- JAL-2036 -->Show cross-references not enabled after
1624 restoring project until a new view is created
1627 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1628 URL links appears when only default EMBL-EBI link is
1629 configured (since 2.10.2b2)
1632 <!-- JAL-2775 -->Overview redraws whole window when box
1633 position is adjusted
1636 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1637 in a multi-chain structure when viewing alignment
1638 involving more than one chain (since 2.10)
1641 <!-- JAL-2811 -->Double residue highlights in cursor mode
1642 if new selection moves alignment window
1645 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1646 arrow key in cursor mode to pass hidden column marker
1649 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1650 that produces correctly annotated transcripts and products
1653 <!-- JAL-2776 -->Toggling a feature group after first time
1654 doesn't update associated structure view
1657 <em>Applet</em><br />
1660 <!-- JAL-2687 -->Concurrent modification exception when
1661 closing alignment panel
1664 <em>BioJSON</em><br />
1667 <!-- JAL-2546 -->BioJSON export does not preserve
1668 non-positional features
1671 <em>New Known Issues</em>
1674 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1675 sequence features correctly (for many previous versions of
1679 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1680 using cursor in wrapped panel other than top
1683 <!-- JAL-2791 -->Select columns containing feature ignores
1684 graduated colour threshold
1687 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1688 always preserve numbering and sequence features
1691 <em>Known Java 9 Issues</em>
1694 <!-- JAL-2902 -->Groovy Console very slow to open and is
1695 not responsive when entering characters (Webstart, Java
1702 <td width="60" nowrap>
1703 <div align="center">
1704 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1705 <em>2/10/2017</em></strong>
1708 <td><div align="left">
1709 <em>New features in Jalview Desktop</em>
1712 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1714 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1718 <td><div align="left">
1722 <td width="60" nowrap>
1723 <div align="center">
1724 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1725 <em>7/9/2017</em></strong>
1728 <td><div align="left">
1732 <!-- JAL-2588 -->Show gaps in overview window by colouring
1733 in grey (sequences used to be coloured grey, and gaps were
1737 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1741 <!-- JAL-2587 -->Overview updates immediately on increase
1742 in size and progress bar shown as higher resolution
1743 overview is recalculated
1748 <td><div align="left">
1752 <!-- JAL-2664 -->Overview window redraws every hidden
1753 column region row by row
1756 <!-- JAL-2681 -->duplicate protein sequences shown after
1757 retrieving Ensembl crossrefs for sequences from Uniprot
1760 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1761 format setting is unticked
1764 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1765 if group has show boxes format setting unticked
1768 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1769 autoscrolling whilst dragging current selection group to
1770 include sequences and columns not currently displayed
1773 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1774 assemblies are imported via CIF file
1777 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1778 displayed when threshold or conservation colouring is also
1782 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1786 <!-- JAL-2673 -->Jalview continues to scroll after
1787 dragging a selected region off the visible region of the
1791 <!-- JAL-2724 -->Cannot apply annotation based
1792 colourscheme to all groups in a view
1795 <!-- JAL-2511 -->IDs don't line up with sequences
1796 initially after font size change using the Font chooser or
1803 <td width="60" nowrap>
1804 <div align="center">
1805 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1808 <td><div align="left">
1809 <em>Calculations</em>
1813 <!-- JAL-1933 -->Occupancy annotation row shows number of
1814 ungapped positions in each column of the alignment.
1817 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1818 a calculation dialog box
1821 <!-- JAL-2379 -->Revised implementation of PCA for speed
1822 and memory efficiency (~30x faster)
1825 <!-- JAL-2403 -->Revised implementation of sequence
1826 similarity scores as used by Tree, PCA, Shading Consensus
1827 and other calculations
1830 <!-- JAL-2416 -->Score matrices are stored as resource
1831 files within the Jalview codebase
1834 <!-- JAL-2500 -->Trees computed on Sequence Feature
1835 Similarity may have different topology due to increased
1842 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1843 model for alignments and groups
1846 <!-- JAL-384 -->Custom shading schemes created via groovy
1853 <!-- JAL-2526 -->Efficiency improvements for interacting
1854 with alignment and overview windows
1857 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1861 <!-- JAL-2388 -->Hidden columns and sequences can be
1865 <!-- JAL-2611 -->Click-drag in visible area allows fine
1866 adjustment of visible position
1870 <em>Data import/export</em>
1873 <!-- JAL-2535 -->Posterior probability annotation from
1874 Stockholm files imported as sequence associated annotation
1877 <!-- JAL-2507 -->More robust per-sequence positional
1878 annotation input/output via stockholm flatfile
1881 <!-- JAL-2533 -->Sequence names don't include file
1882 extension when importing structure files without embedded
1883 names or PDB accessions
1886 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1887 format sequence substitution matrices
1890 <em>User Interface</em>
1893 <!-- JAL-2447 --> Experimental Features Checkbox in
1894 Desktop's Tools menu to hide or show untested features in
1898 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1899 via Overview or sequence motif search operations
1902 <!-- JAL-2547 -->Amend sequence features dialog box can be
1903 opened by double clicking gaps within sequence feature
1907 <!-- JAL-1476 -->Status bar message shown when not enough
1908 aligned positions were available to create a 3D structure
1912 <em>3D Structure</em>
1915 <!-- JAL-2430 -->Hidden regions in alignment views are not
1916 coloured in linked structure views
1919 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1920 file-based command exchange
1923 <!-- JAL-2375 -->Structure chooser automatically shows
1924 Cached Structures rather than querying the PDBe if
1925 structures are already available for sequences
1928 <!-- JAL-2520 -->Structures imported via URL are cached in
1929 the Jalview project rather than downloaded again when the
1930 project is reopened.
1933 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1934 to transfer Chimera's structure attributes as Jalview
1935 features, and vice-versa (<strong>Experimental
1939 <em>Web Services</em>
1942 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1945 <!-- JAL-2335 -->Filter non-standard amino acids and
1946 nucleotides when submitting to AACon and other MSA
1950 <!-- JAL-2316, -->URLs for viewing database
1951 cross-references provided by identifiers.org and the
1952 EMBL-EBI's MIRIAM DB
1959 <!-- JAL-2344 -->FileFormatI interface for describing and
1960 identifying file formats (instead of String constants)
1963 <!-- JAL-2228 -->FeatureCounter script refactored for
1964 efficiency when counting all displayed features (not
1965 backwards compatible with 2.10.1)
1968 <em>Example files</em>
1971 <!-- JAL-2631 -->Graduated feature colour style example
1972 included in the example feature file
1975 <em>Documentation</em>
1978 <!-- JAL-2339 -->Release notes reformatted for readability
1979 with the built-in Java help viewer
1982 <!-- JAL-1644 -->Find documentation updated with 'search
1983 sequence description' option
1989 <!-- JAL-2485, -->External service integration tests for
1990 Uniprot REST Free Text Search Client
1993 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1996 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2001 <td><div align="left">
2002 <em>Calculations</em>
2005 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2006 matrix - C->R should be '-3'<br />Old matrix restored
2007 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2009 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2010 Jalview's treatment of gaps in PCA and substitution matrix
2011 based Tree calculations.<br /> <br />In earlier versions
2012 of Jalview, gaps matching gaps were penalised, and gaps
2013 matching non-gaps penalised even more. In the PCA
2014 calculation, gaps were actually treated as non-gaps - so
2015 different costs were applied, which meant Jalview's PCAs
2016 were different to those produced by SeqSpace.<br />Jalview
2017 now treats gaps in the same way as SeqSpace (ie it scores
2018 them as 0). <br /> <br />Enter the following in the
2019 Groovy console to restore pre-2.10.2 behaviour:<br />
2020 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2021 // for 2.10.1 mode <br />
2022 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2023 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2024 these settings will affect all subsequent tree and PCA
2025 calculations (not recommended)</em></li>
2027 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2028 scaling of branch lengths for trees computed using
2029 Sequence Feature Similarity.
2032 <!-- JAL-2377 -->PCA calculation could hang when
2033 generating output report when working with highly
2034 redundant alignments
2037 <!-- JAL-2544 --> Sort by features includes features to
2038 right of selected region when gaps present on right-hand
2042 <em>User Interface</em>
2045 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2046 doesn't reselect a specific sequence's associated
2047 annotation after it was used for colouring a view
2050 <!-- JAL-2419 -->Current selection lost if popup menu
2051 opened on a region of alignment without groups
2054 <!-- JAL-2374 -->Popup menu not always shown for regions
2055 of an alignment with overlapping groups
2058 <!-- JAL-2310 -->Finder double counts if both a sequence's
2059 name and description match
2062 <!-- JAL-2370 -->Hiding column selection containing two
2063 hidden regions results in incorrect hidden regions
2066 <!-- JAL-2386 -->'Apply to all groups' setting when
2067 changing colour does not apply Conservation slider value
2071 <!-- JAL-2373 -->Percentage identity and conservation menu
2072 items do not show a tick or allow shading to be disabled
2075 <!-- JAL-2385 -->Conservation shading or PID threshold
2076 lost when base colourscheme changed if slider not visible
2079 <!-- JAL-2547 -->Sequence features shown in tooltip for
2080 gaps before start of features
2083 <!-- JAL-2623 -->Graduated feature colour threshold not
2084 restored to UI when feature colour is edited
2087 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2088 a time when scrolling vertically in wrapped mode.
2091 <!-- JAL-2630 -->Structure and alignment overview update
2092 as graduate feature colour settings are modified via the
2096 <!-- JAL-2034 -->Overview window doesn't always update
2097 when a group defined on the alignment is resized
2100 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2101 wrapped view result in positional status updates
2105 <!-- JAL-2563 -->Status bar doesn't show position for
2106 ambiguous amino acid and nucleotide symbols
2109 <!-- JAL-2602 -->Copy consensus sequence failed if
2110 alignment included gapped columns
2113 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2114 widgets don't permanently disappear
2117 <!-- JAL-2503 -->Cannot select or filter quantitative
2118 annotation that are shown only as column labels (e.g.
2119 T-Coffee column reliability scores)
2122 <!-- JAL-2594 -->Exception thrown if trying to create a
2123 sequence feature on gaps only
2126 <!-- JAL-2504 -->Features created with 'New feature'
2127 button from a Find inherit previously defined feature type
2128 rather than the Find query string
2131 <!-- JAL-2423 -->incorrect title in output window when
2132 exporting tree calculated in Jalview
2135 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2136 and then revealing them reorders sequences on the
2140 <!-- JAL-964 -->Group panel in sequence feature settings
2141 doesn't update to reflect available set of groups after
2142 interactively adding or modifying features
2145 <!-- JAL-2225 -->Sequence Database chooser unusable on
2149 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2150 only excluded gaps in current sequence and ignored
2157 <!-- JAL-2421 -->Overview window visible region moves
2158 erratically when hidden rows or columns are present
2161 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2162 Structure Viewer's colour menu don't correspond to
2166 <!-- JAL-2405 -->Protein specific colours only offered in
2167 colour and group colour menu for protein alignments
2170 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2171 reflect currently selected view or group's shading
2175 <!-- JAL-2624 -->Feature colour thresholds not respected
2176 when rendered on overview and structures when opacity at
2180 <!-- JAL-2589 -->User defined gap colour not shown in
2181 overview when features overlaid on alignment
2184 <!-- JAL-2567 -->Feature settings for different views not
2185 recovered correctly from Jalview project file
2188 <!-- JAL-2256 -->Feature colours in overview when first opened
2189 (automatically via preferences) are different to the main
2193 <em>Data import/export</em>
2196 <!-- JAL-2576 -->Very large alignments take a long time to
2200 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2201 added after a sequence was imported are not written to
2205 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2206 when importing RNA secondary structure via Stockholm
2209 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2210 not shown in correct direction for simple pseudoknots
2213 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2214 with lightGray or darkGray via features file (but can
2218 <!-- JAL-2383 -->Above PID colour threshold not recovered
2219 when alignment view imported from project
2222 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2223 structure and sequences extracted from structure files
2224 imported via URL and viewed in Jmol
2227 <!-- JAL-2520 -->Structures loaded via URL are saved in
2228 Jalview Projects rather than fetched via URL again when
2229 the project is loaded and the structure viewed
2232 <em>Web Services</em>
2235 <!-- JAL-2519 -->EnsemblGenomes example failing after
2236 release of Ensembl v.88
2239 <!-- JAL-2366 -->Proxy server address and port always
2240 appear enabled in Preferences->Connections
2243 <!-- JAL-2461 -->DAS registry not found exceptions
2244 removed from console output
2247 <!-- JAL-2582 -->Cannot retrieve protein products from
2248 Ensembl by Peptide ID
2251 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2252 created from SIFTs, and spurious 'Couldn't open structure
2253 in Chimera' errors raised after April 2017 update (problem
2254 due to 'null' string rather than empty string used for
2255 residues with no corresponding PDB mapping).
2258 <em>Application UI</em>
2261 <!-- JAL-2361 -->User Defined Colours not added to Colour
2265 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2266 case' residues (button in colourscheme editor debugged and
2267 new documentation and tooltips added)
2270 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2271 doesn't restore group-specific text colour thresholds
2274 <!-- JAL-2243 -->Feature settings panel does not update as
2275 new features are added to alignment
2278 <!-- JAL-2532 -->Cancel in feature settings reverts
2279 changes to feature colours via the Amend features dialog
2282 <!-- JAL-2506 -->Null pointer exception when attempting to
2283 edit graduated feature colour via amend features dialog
2287 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2288 selection menu changes colours of alignment views
2291 <!-- JAL-2426 -->Spurious exceptions in console raised
2292 from alignment calculation workers after alignment has
2296 <!-- JAL-1608 -->Typo in selection popup menu - Create
2297 groups now 'Create Group'
2300 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2301 Create/Undefine group doesn't always work
2304 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2305 shown again after pressing 'Cancel'
2308 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2309 adjusts start position in wrap mode
2312 <!-- JAL-2563 -->Status bar doesn't show positions for
2313 ambiguous amino acids
2316 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2317 CDS/Protein view after CDS sequences added for aligned
2321 <!-- JAL-2592 -->User defined colourschemes called 'User
2322 Defined' don't appear in Colours menu
2328 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2329 score models doesn't always result in an updated PCA plot
2332 <!-- JAL-2442 -->Features not rendered as transparent on
2333 overview or linked structure view
2336 <!-- JAL-2372 -->Colour group by conservation doesn't
2340 <!-- JAL-2517 -->Hitting Cancel after applying
2341 user-defined colourscheme doesn't restore original
2348 <!-- JAL-2314 -->Unit test failure:
2349 jalview.ws.jabaws.RNAStructExportImport setup fails
2352 <!-- JAL-2307 -->Unit test failure:
2353 jalview.ws.sifts.SiftsClientTest due to compatibility
2354 problems with deep array comparison equality asserts in
2355 successive versions of TestNG
2358 <!-- JAL-2479 -->Relocated StructureChooserTest and
2359 ParameterUtilsTest Unit tests to Network suite
2362 <em>New Known Issues</em>
2365 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2366 phase after a sequence motif find operation
2369 <!-- JAL-2550 -->Importing annotation file with rows
2370 containing just upper and lower case letters are
2371 interpreted as WUSS RNA secondary structure symbols
2374 <!-- JAL-2590 -->Cannot load and display Newick trees
2375 reliably from eggnog Ortholog database
2378 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2379 containing features of type Highlight' when 'B' is pressed
2380 to mark columns containing highlighted regions.
2383 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2384 doesn't always add secondary structure annotation.
2389 <td width="60" nowrap>
2390 <div align="center">
2391 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2394 <td><div align="left">
2398 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2399 for all consensus calculations
2402 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2405 <li>Updated Jalview's Certum code signing certificate
2408 <em>Application</em>
2411 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2412 set of database cross-references, sorted alphabetically
2415 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2416 from database cross references. Users with custom links
2417 will receive a <a href="webServices/urllinks.html#warning">warning
2418 dialog</a> asking them to update their preferences.
2421 <!-- JAL-2287-->Cancel button and escape listener on
2422 dialog warning user about disconnecting Jalview from a
2426 <!-- JAL-2320-->Jalview's Chimera control window closes if
2427 the Chimera it is connected to is shut down
2430 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2431 columns menu item to mark columns containing highlighted
2432 regions (e.g. from structure selections or results of a
2436 <!-- JAL-2284-->Command line option for batch-generation
2437 of HTML pages rendering alignment data with the BioJS
2447 <!-- JAL-2286 -->Columns with more than one modal residue
2448 are not coloured or thresholded according to percent
2449 identity (first observed in Jalview 2.8.2)
2452 <!-- JAL-2301 -->Threonine incorrectly reported as not
2456 <!-- JAL-2318 -->Updates to documentation pages (above PID
2457 threshold, amino acid properties)
2460 <!-- JAL-2292 -->Lower case residues in sequences are not
2461 reported as mapped to residues in a structure file in the
2465 <!--JAL-2324 -->Identical features with non-numeric scores
2466 could be added multiple times to a sequence
2469 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2470 bond features shown as two highlighted residues rather
2471 than a range in linked structure views, and treated
2472 correctly when selecting and computing trees from features
2475 <!-- JAL-2281-->Custom URL links for database
2476 cross-references are matched to database name regardless
2481 <em>Application</em>
2484 <!-- JAL-2282-->Custom URL links for specific database
2485 names without regular expressions also offer links from
2489 <!-- JAL-2315-->Removing a single configured link in the
2490 URL links pane in Connections preferences doesn't actually
2491 update Jalview configuration
2494 <!-- JAL-2272-->CTRL-Click on a selected region to open
2495 the alignment area popup menu doesn't work on El-Capitan
2498 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2499 files with similarly named sequences if dropped onto the
2503 <!-- JAL-2312 -->Additional mappings are shown for PDB
2504 entries where more chains exist in the PDB accession than
2505 are reported in the SIFTS file
2508 <!-- JAL-2317-->Certain structures do not get mapped to
2509 the structure view when displayed with Chimera
2512 <!-- JAL-2317-->No chains shown in the Chimera view
2513 panel's View->Show Chains submenu
2516 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2517 work for wrapped alignment views
2520 <!--JAL-2197 -->Rename UI components for running JPred
2521 predictions from 'JNet' to 'JPred'
2524 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2525 corrupted when annotation panel vertical scroll is not at
2526 first annotation row
2529 <!--JAL-2332 -->Attempting to view structure for Hen
2530 lysozyme results in a PDB Client error dialog box
2533 <!-- JAL-2319 -->Structure View's mapping report switched
2534 ranges for PDB and sequence for SIFTS
2537 SIFTS 'Not_Observed' residues mapped to non-existant
2541 <!-- <em>New Known Issues</em>
2548 <td width="60" nowrap>
2549 <div align="center">
2550 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2551 <em>25/10/2016</em></strong>
2554 <td><em>Application</em>
2556 <li>3D Structure chooser opens with 'Cached structures'
2557 view if structures already loaded</li>
2558 <li>Progress bar reports models as they are loaded to
2559 structure views</li>
2565 <li>Colour by conservation always enabled and no tick
2566 shown in menu when BLOSUM or PID shading applied</li>
2567 <li>FER1_ARATH and FER2_ARATH labels were switched in
2568 example sequences/projects/trees</li>
2570 <em>Application</em>
2572 <li>Jalview projects with views of local PDB structure
2573 files saved on Windows cannot be opened on OSX</li>
2574 <li>Multiple structure views can be opened and superposed
2575 without timeout for structures with multiple models or
2576 multiple sequences in alignment</li>
2577 <li>Cannot import or associated local PDB files without a
2578 PDB ID HEADER line</li>
2579 <li>RMSD is not output in Jmol console when superposition
2581 <li>Drag and drop of URL from Browser fails for Linux and
2582 OSX versions earlier than El Capitan</li>
2583 <li>ENA client ignores invalid content from ENA server</li>
2584 <li>Exceptions are not raised in console when ENA client
2585 attempts to fetch non-existent IDs via Fetch DB Refs UI
2587 <li>Exceptions are not raised in console when a new view
2588 is created on the alignment</li>
2589 <li>OSX right-click fixed for group selections: CMD-click
2590 to insert/remove gaps in groups and CTRL-click to open group
2593 <em>Build and deployment</em>
2595 <li>URL link checker now copes with multi-line anchor
2598 <em>New Known Issues</em>
2600 <li>Drag and drop from URL links in browsers do not work
2607 <td width="60" nowrap>
2608 <div align="center">
2609 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2612 <td><em>General</em>
2615 <!-- JAL-2124 -->Updated Spanish translations.
2618 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2619 for importing structure data to Jalview. Enables mmCIF and
2623 <!-- JAL-192 --->Alignment ruler shows positions relative to
2627 <!-- JAL-2202 -->Position/residue shown in status bar when
2628 mousing over sequence associated annotation
2631 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2635 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2636 '()', canonical '[]' and invalid '{}' base pair populations
2640 <!-- JAL-2092 -->Feature settings popup menu options for
2641 showing or hiding columns containing a feature
2644 <!-- JAL-1557 -->Edit selected group by double clicking on
2645 group and sequence associated annotation labels
2648 <!-- JAL-2236 -->Sequence name added to annotation label in
2649 select/hide columns by annotation and colour by annotation
2653 </ul> <em>Application</em>
2656 <!-- JAL-2050-->Automatically hide introns when opening a
2657 gene/transcript view
2660 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2664 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2665 structure mappings with the EMBL-EBI PDBe SIFTS database
2668 <!-- JAL-2079 -->Updated download sites used for Rfam and
2669 Pfam sources to xfam.org
2672 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2675 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2676 over sequences in Jalview
2679 <!-- JAL-2027-->Support for reverse-complement coding
2680 regions in ENA and EMBL
2683 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2684 for record retrieval via ENA rest API
2687 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2691 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2692 groovy script execution
2695 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2696 alignment window's Calculate menu
2699 <!-- JAL-1812 -->Allow groovy scripts that call
2700 Jalview.getAlignFrames() to run in headless mode
2703 <!-- JAL-2068 -->Support for creating new alignment
2704 calculation workers from groovy scripts
2707 <!-- JAL-1369 --->Store/restore reference sequence in
2711 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2712 associations are now saved/restored from project
2715 <!-- JAL-1993 -->Database selection dialog always shown
2716 before sequence fetcher is opened
2719 <!-- JAL-2183 -->Double click on an entry in Jalview's
2720 database chooser opens a sequence fetcher
2723 <!-- JAL-1563 -->Free-text search client for UniProt using
2724 the UniProt REST API
2727 <!-- JAL-2168 -->-nonews command line parameter to prevent
2728 the news reader opening
2731 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2732 querying stored in preferences
2735 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2739 <!-- JAL-1977-->Tooltips shown on database chooser
2742 <!-- JAL-391 -->Reverse complement function in calculate
2743 menu for nucleotide sequences
2746 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2747 and feature counts preserves alignment ordering (and
2748 debugged for complex feature sets).
2751 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2752 viewing structures with Jalview 2.10
2755 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2756 genome, transcript CCDS and gene ids via the Ensembl and
2757 Ensembl Genomes REST API
2760 <!-- JAL-2049 -->Protein sequence variant annotation
2761 computed for 'sequence_variant' annotation on CDS regions
2765 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2769 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2770 Ref Fetcher fails to match, or otherwise updates sequence
2771 data from external database records.
2774 <!-- JAL-2154 -->Revised Jalview Project format for
2775 efficient recovery of sequence coding and alignment
2776 annotation relationships.
2778 </ul> <!-- <em>Applet</em>
2789 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2793 <!-- JAL-2018-->Export features in Jalview format (again)
2794 includes graduated colourschemes
2797 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2798 working with big alignments and lots of hidden columns
2801 <!-- JAL-2053-->Hidden column markers not always rendered
2802 at right of alignment window
2805 <!-- JAL-2067 -->Tidied up links in help file table of
2809 <!-- JAL-2072 -->Feature based tree calculation not shown
2813 <!-- JAL-2075 -->Hidden columns ignored during feature
2814 based tree calculation
2817 <!-- JAL-2065 -->Alignment view stops updating when show
2818 unconserved enabled for group on alignment
2821 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2825 <!-- JAL-2146 -->Alignment column in status incorrectly
2826 shown as "Sequence position" when mousing over
2830 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2831 hidden columns present
2834 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2835 user created annotation added to alignment
2838 <!-- JAL-1841 -->RNA Structure consensus only computed for
2839 '()' base pair annotation
2842 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2843 in zero scores for all base pairs in RNA Structure
2847 <!-- JAL-2174-->Extend selection with columns containing
2851 <!-- JAL-2275 -->Pfam format writer puts extra space at
2852 beginning of sequence
2855 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2859 <!-- JAL-2238 -->Cannot create groups on an alignment from
2860 from a tree when t-coffee scores are shown
2863 <!-- JAL-1836,1967 -->Cannot import and view PDB
2864 structures with chains containing negative resnums (4q4h)
2867 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2871 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2872 to Clustal, PIR and PileUp output
2875 <!-- JAL-2008 -->Reordering sequence features that are
2876 not visible causes alignment window to repaint
2879 <!-- JAL-2006 -->Threshold sliders don't work in
2880 graduated colour and colour by annotation row for e-value
2881 scores associated with features and annotation rows
2884 <!-- JAL-1797 -->amino acid physicochemical conservation
2885 calculation should be case independent
2888 <!-- JAL-2173 -->Remove annotation also updates hidden
2892 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2893 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2894 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2897 <!-- JAL-2065 -->Null pointer exceptions and redraw
2898 problems when reference sequence defined and 'show
2899 non-conserved' enabled
2902 <!-- JAL-1306 -->Quality and Conservation are now shown on
2903 load even when Consensus calculation is disabled
2906 <!-- JAL-1932 -->Remove right on penultimate column of
2907 alignment does nothing
2910 <em>Application</em>
2913 <!-- JAL-1552-->URLs and links can't be imported by
2914 drag'n'drop on OSX when launched via webstart (note - not
2915 yet fixed for El Capitan)
2918 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2919 output when running on non-gb/us i18n platforms
2922 <!-- JAL-1944 -->Error thrown when exporting a view with
2923 hidden sequences as flat-file alignment
2926 <!-- JAL-2030-->InstallAnywhere distribution fails when
2930 <!-- JAL-2080-->Jalview very slow to launch via webstart
2931 (also hotfix for 2.9.0b2)
2934 <!-- JAL-2085 -->Cannot save project when view has a
2935 reference sequence defined
2938 <!-- JAL-1011 -->Columns are suddenly selected in other
2939 alignments and views when revealing hidden columns
2942 <!-- JAL-1989 -->Hide columns not mirrored in complement
2943 view in a cDNA/Protein splitframe
2946 <!-- JAL-1369 -->Cannot save/restore representative
2947 sequence from project when only one sequence is
2951 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2952 in Structure Chooser
2955 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2956 structure consensus didn't refresh annotation panel
2959 <!-- JAL-1962 -->View mapping in structure view shows
2960 mappings between sequence and all chains in a PDB file
2963 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2964 dialogs format columns correctly, don't display array
2965 data, sort columns according to type
2968 <!-- JAL-1975 -->Export complete shown after destination
2969 file chooser is cancelled during an image export
2972 <!-- JAL-2025 -->Error when querying PDB Service with
2973 sequence name containing special characters
2976 <!-- JAL-2024 -->Manual PDB structure querying should be
2980 <!-- JAL-2104 -->Large tooltips with broken HTML
2981 formatting don't wrap
2984 <!-- JAL-1128 -->Figures exported from wrapped view are
2985 truncated so L looks like I in consensus annotation
2988 <!-- JAL-2003 -->Export features should only export the
2989 currently displayed features for the current selection or
2993 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2994 after fetching cross-references, and restoring from
2998 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2999 followed in the structure viewer
3002 <!-- JAL-2163 -->Titles for individual alignments in
3003 splitframe not restored from project
3006 <!-- JAL-2145 -->missing autocalculated annotation at
3007 trailing end of protein alignment in transcript/product
3008 splitview when pad-gaps not enabled by default
3011 <!-- JAL-1797 -->amino acid physicochemical conservation
3015 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3016 article has been read (reopened issue due to
3017 internationalisation problems)
3020 <!-- JAL-1960 -->Only offer PDB structures in structure
3021 viewer based on sequence name, PDB and UniProt
3026 <!-- JAL-1976 -->No progress bar shown during export of
3030 <!-- JAL-2213 -->Structures not always superimposed after
3031 multiple structures are shown for one or more sequences.
3034 <!-- JAL-1370 -->Reference sequence characters should not
3035 be replaced with '.' when 'Show unconserved' format option
3039 <!-- JAL-1823 -->Cannot specify chain code when entering
3040 specific PDB id for sequence
3043 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3044 'Export hidden sequences' is enabled, but 'export hidden
3045 columns' is disabled.
3048 <!--JAL-2026-->Best Quality option in structure chooser
3049 selects lowest rather than highest resolution structures
3053 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3054 to sequence mapping in 'View Mappings' report
3057 <!-- JAL-2284 -->Unable to read old Jalview projects that
3058 contain non-XML data added after Jalvew wrote project.
3061 <!-- JAL-2118 -->Newly created annotation row reorders
3062 after clicking on it to create new annotation for a
3066 <!-- JAL-1980 -->Null Pointer Exception raised when
3067 pressing Add on an orphaned cut'n'paste window.
3069 <!-- may exclude, this is an external service stability issue JAL-1941
3070 -- > RNA 3D structure not added via DSSR service</li> -->
3075 <!-- JAL-2151 -->Incorrect columns are selected when
3076 hidden columns present before start of sequence
3079 <!-- JAL-1986 -->Missing dependencies on applet pages
3083 <!-- JAL-1947 -->Overview pixel size changes when
3084 sequences are hidden in applet
3087 <!-- JAL-1996 -->Updated instructions for applet
3088 deployment on examples pages.
3095 <td width="60" nowrap>
3096 <div align="center">
3097 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3098 <em>16/10/2015</em></strong>
3101 <td><em>General</em>
3103 <li>Time stamps for signed Jalview application and applet
3108 <em>Application</em>
3110 <li>Duplicate group consensus and conservation rows
3111 shown when tree is partitioned</li>
3112 <li>Erratic behaviour when tree partitions made with
3113 multiple cDNA/Protein split views</li>
3119 <td width="60" nowrap>
3120 <div align="center">
3121 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3122 <em>8/10/2015</em></strong>
3125 <td><em>General</em>
3127 <li>Updated Spanish translations of localized text for
3129 </ul> <em>Application</em>
3131 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3132 <li>Signed OSX InstallAnywhere installer<br></li>
3133 <li>Support for per-sequence based annotations in BioJSON</li>
3134 </ul> <em>Applet</em>
3136 <li>Split frame example added to applet examples page</li>
3137 </ul> <em>Build and Deployment</em>
3140 <!-- JAL-1888 -->New ant target for running Jalview's test
3148 <li>Mapping of cDNA to protein in split frames
3149 incorrect when sequence start > 1</li>
3150 <li>Broken images in filter column by annotation dialog
3152 <li>Feature colours not parsed from features file</li>
3153 <li>Exceptions and incomplete link URLs recovered when
3154 loading a features file containing HTML tags in feature
3158 <em>Application</em>
3160 <li>Annotations corrupted after BioJS export and
3162 <li>Incorrect sequence limits after Fetch DB References
3163 with 'trim retrieved sequences'</li>
3164 <li>Incorrect warning about deleting all data when
3165 deleting selected columns</li>
3166 <li>Patch to build system for shipping properly signed
3167 JNLP templates for webstart launch</li>
3168 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3169 unreleased structures for download or viewing</li>
3170 <li>Tab/space/return keystroke operation of EMBL-PDBe
3171 fetcher/viewer dialogs works correctly</li>
3172 <li>Disabled 'minimise' button on Jalview windows
3173 running on OSX to workaround redraw hang bug</li>
3174 <li>Split cDNA/Protein view position and geometry not
3175 recovered from jalview project</li>
3176 <li>Initial enabled/disabled state of annotation menu
3177 sorter 'show autocalculated first/last' corresponds to
3179 <li>Restoring of Clustal, RNA Helices and T-Coffee
3180 color schemes from BioJSON</li>
3184 <li>Reorder sequences mirrored in cDNA/Protein split
3186 <li>Applet with Jmol examples not loading correctly</li>
3192 <td><div align="center">
3193 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3195 <td><em>General</em>
3197 <li>Linked visualisation and analysis of DNA and Protein
3200 <li>Translated cDNA alignments shown as split protein
3201 and DNA alignment views</li>
3202 <li>Codon consensus annotation for linked protein and
3203 cDNA alignment views</li>
3204 <li>Link cDNA or Protein product sequences by loading
3205 them onto Protein or cDNA alignments</li>
3206 <li>Reconstruct linked cDNA alignment from aligned
3207 protein sequences</li>
3210 <li>Jmol integration updated to Jmol v14.2.14</li>
3211 <li>Import and export of Jalview alignment views as <a
3212 href="features/bioJsonFormat.html">BioJSON</a></li>
3213 <li>New alignment annotation file statements for
3214 reference sequences and marking hidden columns</li>
3215 <li>Reference sequence based alignment shading to
3216 highlight variation</li>
3217 <li>Select or hide columns according to alignment
3219 <li>Find option for locating sequences by description</li>
3220 <li>Conserved physicochemical properties shown in amino
3221 acid conservation row</li>
3222 <li>Alignments can be sorted by number of RNA helices</li>
3223 </ul> <em>Application</em>
3225 <li>New cDNA/Protein analysis capabilities
3227 <li>Get Cross-References should open a Split Frame
3228 view with cDNA/Protein</li>
3229 <li>Detect when nucleotide sequences and protein
3230 sequences are placed in the same alignment</li>
3231 <li>Split cDNA/Protein views are saved in Jalview
3236 <li>Use REST API to talk to Chimera</li>
3237 <li>Selected regions in Chimera are highlighted in linked
3238 Jalview windows</li>
3240 <li>VARNA RNA viewer updated to v3.93</li>
3241 <li>VARNA views are saved in Jalview Projects</li>
3242 <li>Pseudoknots displayed as Jalview RNA annotation can
3243 be shown in VARNA</li>
3245 <li>Make groups for selection uses marked columns as well
3246 as the active selected region</li>
3248 <li>Calculate UPGMA and NJ trees using sequence feature
3250 <li>New Export options
3252 <li>New Export Settings dialog to control hidden
3253 region export in flat file generation</li>
3255 <li>Export alignment views for display with the <a
3256 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3258 <li>Export scrollable SVG in HTML page</li>
3259 <li>Optional embedding of BioJSON data when exporting
3260 alignment figures to HTML</li>
3262 <li>3D structure retrieval and display
3264 <li>Free text and structured queries with the PDBe
3266 <li>PDBe Search API based discovery and selection of
3267 PDB structures for a sequence set</li>
3271 <li>JPred4 employed for protein secondary structure
3273 <li>Hide Insertions menu option to hide unaligned columns
3274 for one or a group of sequences</li>
3275 <li>Automatically hide insertions in alignments imported
3276 from the JPred4 web server</li>
3277 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3278 system on OSX<br />LGPL libraries courtesy of <a
3279 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3281 <li>changed 'View nucleotide structure' submenu to 'View
3282 VARNA 2D Structure'</li>
3283 <li>change "View protein structure" menu option to "3D
3286 </ul> <em>Applet</em>
3288 <li>New layout for applet example pages</li>
3289 <li>New parameters to enable SplitFrame view
3290 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3291 <li>New example demonstrating linked viewing of cDNA and
3292 Protein alignments</li>
3293 </ul> <em>Development and deployment</em>
3295 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3296 <li>Include installation type and git revision in build
3297 properties and console log output</li>
3298 <li>Jalview Github organisation, and new github site for
3299 storing BioJsMSA Templates</li>
3300 <li>Jalview's unit tests now managed with TestNG</li>
3303 <!-- <em>General</em>
3305 </ul> --> <!-- issues resolved --> <em>Application</em>
3307 <li>Escape should close any open find dialogs</li>
3308 <li>Typo in select-by-features status report</li>
3309 <li>Consensus RNA secondary secondary structure
3310 predictions are not highlighted in amber</li>
3311 <li>Missing gap character in v2.7 example file means
3312 alignment appears unaligned when pad-gaps is not enabled</li>
3313 <li>First switch to RNA Helices colouring doesn't colour
3314 associated structure views</li>
3315 <li>ID width preference option is greyed out when auto
3316 width checkbox not enabled</li>
3317 <li>Stopped a warning dialog from being shown when
3318 creating user defined colours</li>
3319 <li>'View Mapping' in structure viewer shows sequence
3320 mappings for just that viewer's sequences</li>
3321 <li>Workaround for superposing PDB files containing
3322 multiple models in Chimera</li>
3323 <li>Report sequence position in status bar when hovering
3324 over Jmol structure</li>
3325 <li>Cannot output gaps as '.' symbols with Selection ->
3326 output to text box</li>
3327 <li>Flat file exports of alignments with hidden columns
3328 have incorrect sequence start/end</li>
3329 <li>'Aligning' a second chain to a Chimera structure from
3331 <li>Colour schemes applied to structure viewers don't
3332 work for nucleotide</li>
3333 <li>Loading/cut'n'pasting an empty or invalid file leads
3334 to a grey/invisible alignment window</li>
3335 <li>Exported Jpred annotation from a sequence region
3336 imports to different position</li>
3337 <li>Space at beginning of sequence feature tooltips shown
3338 on some platforms</li>
3339 <li>Chimera viewer 'View | Show Chain' menu is not
3341 <li>'New View' fails with a Null Pointer Exception in
3342 console if Chimera has been opened</li>
3343 <li>Mouseover to Chimera not working</li>
3344 <li>Miscellaneous ENA XML feature qualifiers not
3346 <li>NPE in annotation renderer after 'Extract Scores'</li>
3347 <li>If two structures in one Chimera window, mouseover of
3348 either sequence shows on first structure</li>
3349 <li>'Show annotations' options should not make
3350 non-positional annotations visible</li>
3351 <li>Subsequence secondary structure annotation not shown
3352 in right place after 'view flanking regions'</li>
3353 <li>File Save As type unset when current file format is
3355 <li>Save as '.jar' option removed for saving Jalview
3357 <li>Colour by Sequence colouring in Chimera more
3359 <li>Cannot 'add reference annotation' for a sequence in
3360 several views on same alignment</li>
3361 <li>Cannot show linked products for EMBL / ENA records</li>
3362 <li>Jalview's tooltip wraps long texts containing no
3364 </ul> <em>Applet</em>
3366 <li>Jmol to JalviewLite mouseover/link not working</li>
3367 <li>JalviewLite can't import sequences with ID
3368 descriptions containing angle brackets</li>
3369 </ul> <em>General</em>
3371 <li>Cannot export and reimport RNA secondary structure
3372 via jalview annotation file</li>
3373 <li>Random helix colour palette for colour by annotation
3374 with RNA secondary structure</li>
3375 <li>Mouseover to cDNA from STOP residue in protein
3376 translation doesn't work.</li>
3377 <li>hints when using the select by annotation dialog box</li>
3378 <li>Jmol alignment incorrect if PDB file has alternate CA
3380 <li>FontChooser message dialog appears to hang after
3381 choosing 1pt font</li>
3382 <li>Peptide secondary structure incorrectly imported from
3383 annotation file when annotation display text includes 'e' or
3385 <li>Cannot set colour of new feature type whilst creating
3387 <li>cDNA translation alignment should not be sequence
3388 order dependent</li>
3389 <li>'Show unconserved' doesn't work for lower case
3391 <li>Nucleotide ambiguity codes involving R not recognised</li>
3392 </ul> <em>Deployment and Documentation</em>
3394 <li>Applet example pages appear different to the rest of
3395 www.jalview.org</li>
3396 </ul> <em>Application Known issues</em>
3398 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3399 <li>Misleading message appears after trying to delete
3401 <li>Jalview icon not shown in dock after InstallAnywhere
3402 version launches</li>
3403 <li>Fetching EMBL reference for an RNA sequence results
3404 fails with a sequence mismatch</li>
3405 <li>Corrupted or unreadable alignment display when
3406 scrolling alignment to right</li>
3407 <li>ArrayIndexOutOfBoundsException thrown when remove
3408 empty columns called on alignment with ragged gapped ends</li>
3409 <li>auto calculated alignment annotation rows do not get
3410 placed above or below non-autocalculated rows</li>
3411 <li>Jalview dekstop becomes sluggish at full screen in
3412 ultra-high resolution</li>
3413 <li>Cannot disable consensus calculation independently of
3414 quality and conservation</li>
3415 <li>Mouseover highlighting between cDNA and protein can
3416 become sluggish with more than one splitframe shown</li>
3417 </ul> <em>Applet Known Issues</em>
3419 <li>Core PDB parsing code requires Jmol</li>
3420 <li>Sequence canvas panel goes white when alignment
3421 window is being resized</li>
3427 <td><div align="center">
3428 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3430 <td><em>General</em>
3432 <li>Updated Java code signing certificate donated by
3434 <li>Features and annotation preserved when performing
3435 pairwise alignment</li>
3436 <li>RNA pseudoknot annotation can be
3437 imported/exported/displayed</li>
3438 <li>'colour by annotation' can colour by RNA and
3439 protein secondary structure</li>
3440 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3441 post-hoc with 2.9 release</em>)
3444 </ul> <em>Application</em>
3446 <li>Extract and display secondary structure for sequences
3447 with 3D structures</li>
3448 <li>Support for parsing RNAML</li>
3449 <li>Annotations menu for layout
3451 <li>sort sequence annotation rows by alignment</li>
3452 <li>place sequence annotation above/below alignment
3455 <li>Output in Stockholm format</li>
3456 <li>Internationalisation: improved Spanish (es)
3458 <li>Structure viewer preferences tab</li>
3459 <li>Disorder and Secondary Structure annotation tracks
3460 shared between alignments</li>
3461 <li>UCSF Chimera launch and linked highlighting from
3463 <li>Show/hide all sequence associated annotation rows for
3464 all or current selection</li>
3465 <li>disorder and secondary structure predictions
3466 available as dataset annotation</li>
3467 <li>Per-sequence rna helices colouring</li>
3470 <li>Sequence database accessions imported when fetching
3471 alignments from Rfam</li>
3472 <li>update VARNA version to 3.91</li>
3474 <li>New groovy scripts for exporting aligned positions,
3475 conservation values, and calculating sum of pairs scores.</li>
3476 <li>Command line argument to set default JABAWS server</li>
3477 <li>include installation type in build properties and
3478 console log output</li>
3479 <li>Updated Jalview project format to preserve dataset
3483 <!-- issues resolved --> <em>Application</em>
3485 <li>Distinguish alignment and sequence associated RNA
3486 structure in structure->view->VARNA</li>
3487 <li>Raise dialog box if user deletes all sequences in an
3489 <li>Pressing F1 results in documentation opening twice</li>
3490 <li>Sequence feature tooltip is wrapped</li>
3491 <li>Double click on sequence associated annotation
3492 selects only first column</li>
3493 <li>Redundancy removal doesn't result in unlinked
3494 leaves shown in tree</li>
3495 <li>Undos after several redundancy removals don't undo
3497 <li>Hide sequence doesn't hide associated annotation</li>
3498 <li>User defined colours dialog box too big to fit on
3499 screen and buttons not visible</li>
3500 <li>author list isn't updated if already written to
3501 Jalview properties</li>
3502 <li>Popup menu won't open after retrieving sequence
3504 <li>File open window for associate PDB doesn't open</li>
3505 <li>Left-then-right click on a sequence id opens a
3506 browser search window</li>
3507 <li>Cannot open sequence feature shading/sort popup menu
3508 in feature settings dialog</li>
3509 <li>better tooltip placement for some areas of Jalview
3511 <li>Allow addition of JABAWS Server which doesn't
3512 pass validation</li>
3513 <li>Web services parameters dialog box is too large to
3515 <li>Muscle nucleotide alignment preset obscured by
3517 <li>JABAWS preset submenus don't contain newly
3518 defined user preset</li>
3519 <li>MSA web services warns user if they were launched
3520 with invalid input</li>
3521 <li>Jalview cannot contact DAS Registy when running on
3524 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3525 'Superpose with' submenu not shown when new view
3529 </ul> <!-- <em>Applet</em>
3531 </ul> <em>General</em>
3533 </ul>--> <em>Deployment and Documentation</em>
3535 <li>2G and 1G options in launchApp have no effect on
3536 memory allocation</li>
3537 <li>launchApp service doesn't automatically open
3538 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3540 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3541 InstallAnywhere reports cannot find valid JVM when Java
3542 1.7_055 is available
3544 </ul> <em>Application Known issues</em>
3547 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3548 corrupted or unreadable alignment display when scrolling
3552 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3553 retrieval fails but progress bar continues for DAS retrieval
3554 with large number of ID
3557 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3558 flatfile output of visible region has incorrect sequence
3562 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3563 rna structure consensus doesn't update when secondary
3564 structure tracks are rearranged
3567 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3568 invalid rna structure positional highlighting does not
3569 highlight position of invalid base pairs
3572 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3573 out of memory errors are not raised when saving Jalview
3574 project from alignment window file menu
3577 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3578 Switching to RNA Helices colouring doesn't propagate to
3582 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3583 colour by RNA Helices not enabled when user created
3584 annotation added to alignment
3587 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3588 Jalview icon not shown on dock in Mountain Lion/Webstart
3590 </ul> <em>Applet Known Issues</em>
3593 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3594 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3597 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3598 Jalview and Jmol example not compatible with IE9
3601 <li>Sort by annotation score doesn't reverse order
3607 <td><div align="center">
3608 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3611 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3614 <li>Internationalisation of user interface (usually
3615 called i18n support) and translation for Spanish locale</li>
3616 <li>Define/Undefine group on current selection with
3617 Ctrl-G/Shift Ctrl-G</li>
3618 <li>Improved group creation/removal options in
3619 alignment/sequence Popup menu</li>
3620 <li>Sensible precision for symbol distribution
3621 percentages shown in logo tooltip.</li>
3622 <li>Annotation panel height set according to amount of
3623 annotation when alignment first opened</li>
3624 </ul> <em>Application</em>
3626 <li>Interactive consensus RNA secondary structure
3627 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3628 <li>Select columns containing particular features from
3629 Feature Settings dialog</li>
3630 <li>View all 'representative' PDB structures for selected
3632 <li>Update Jalview project format:
3634 <li>New file extension for Jalview projects '.jvp'</li>
3635 <li>Preserve sequence and annotation dataset (to
3636 store secondary structure annotation,etc)</li>
3637 <li>Per group and alignment annotation and RNA helix
3641 <li>New similarity measures for PCA and Tree calculation
3643 <li>Experimental support for retrieval and viewing of
3644 flanking regions for an alignment</li>
3648 <!-- issues resolved --> <em>Application</em>
3650 <li>logo keeps spinning and status remains at queued or
3651 running after job is cancelled</li>
3652 <li>cannot export features from alignments imported from
3653 Jalview/VAMSAS projects</li>
3654 <li>Buggy slider for web service parameters that take
3656 <li>Newly created RNA secondary structure line doesn't
3657 have 'display all symbols' flag set</li>
3658 <li>T-COFFEE alignment score shading scheme and other
3659 annotation shading not saved in Jalview project</li>
3660 <li>Local file cannot be loaded in freshly downloaded
3662 <li>Jalview icon not shown on dock in Mountain
3664 <li>Load file from desktop file browser fails</li>
3665 <li>Occasional NPE thrown when calculating large trees</li>
3666 <li>Cannot reorder or slide sequences after dragging an
3667 alignment onto desktop</li>
3668 <li>Colour by annotation dialog throws NPE after using
3669 'extract scores' function</li>
3670 <li>Loading/cut'n'pasting an empty file leads to a grey
3671 alignment window</li>
3672 <li>Disorder thresholds rendered incorrectly after
3673 performing IUPred disorder prediction</li>
3674 <li>Multiple group annotated consensus rows shown when
3675 changing 'normalise logo' display setting</li>
3676 <li>Find shows blank dialog after 'finished searching' if
3677 nothing matches query</li>
3678 <li>Null Pointer Exceptions raised when sorting by
3679 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3681 <li>Errors in Jmol console when structures in alignment
3682 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3684 <li>Not all working JABAWS services are shown in
3686 <li>JAVAWS version of Jalview fails to launch with
3687 'invalid literal/length code'</li>
3688 <li>Annotation/RNA Helix colourschemes cannot be applied
3689 to alignment with groups (actually fixed in 2.8.0b1)</li>
3690 <li>RNA Helices and T-Coffee Scores available as default
3693 </ul> <em>Applet</em>
3695 <li>Remove group option is shown even when selection is
3697 <li>Apply to all groups ticked but colourscheme changes
3698 don't affect groups</li>
3699 <li>Documented RNA Helices and T-Coffee Scores as valid
3700 colourscheme name</li>
3701 <li>Annotation labels drawn on sequence IDs when
3702 Annotation panel is not displayed</li>
3703 <li>Increased font size for dropdown menus on OSX and
3704 embedded windows</li>
3705 </ul> <em>Other</em>
3707 <li>Consensus sequence for alignments/groups with a
3708 single sequence were not calculated</li>
3709 <li>annotation files that contain only groups imported as
3710 annotation and junk sequences</li>
3711 <li>Fasta files with sequences containing '*' incorrectly
3712 recognised as PFAM or BLC</li>
3713 <li>conservation/PID slider apply all groups option
3714 doesn't affect background (2.8.0b1)
3716 <li>redundancy highlighting is erratic at 0% and 100%</li>
3717 <li>Remove gapped columns fails for sequences with ragged
3719 <li>AMSA annotation row with leading spaces is not
3720 registered correctly on import</li>
3721 <li>Jalview crashes when selecting PCA analysis for
3722 certain alignments</li>
3723 <li>Opening the colour by annotation dialog for an
3724 existing annotation based 'use original colours'
3725 colourscheme loses original colours setting</li>
3730 <td><div align="center">
3731 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3732 <em>30/1/2014</em></strong>
3736 <li>Trusted certificates for JalviewLite applet and
3737 Jalview Desktop application<br />Certificate was donated by
3738 <a href="https://www.certum.eu">Certum</a> to the Jalview
3739 open source project).
3741 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3742 <li>Output in Stockholm format</li>
3743 <li>Allow import of data from gzipped files</li>
3744 <li>Export/import group and sequence associated line
3745 graph thresholds</li>
3746 <li>Nucleotide substitution matrix that supports RNA and
3747 ambiguity codes</li>
3748 <li>Allow disorder predictions to be made on the current
3749 selection (or visible selection) in the same way that JPred
3751 <li>Groovy scripting for headless Jalview operation</li>
3752 </ul> <em>Other improvements</em>
3754 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3755 <li>COMBINE statement uses current SEQUENCE_REF and
3756 GROUP_REF scope to group annotation rows</li>
3757 <li>Support '' style escaping of quotes in Newick
3759 <li>Group options for JABAWS service by command line name</li>
3760 <li>Empty tooltip shown for JABA service options with a
3761 link but no description</li>
3762 <li>Select primary source when selecting authority in
3763 database fetcher GUI</li>
3764 <li>Add .mfa to FASTA file extensions recognised by
3766 <li>Annotation label tooltip text wrap</li>
3771 <li>Slow scrolling when lots of annotation rows are
3773 <li>Lots of NPE (and slowness) after creating RNA
3774 secondary structure annotation line</li>
3775 <li>Sequence database accessions not imported when
3776 fetching alignments from Rfam</li>
3777 <li>Incorrect SHMR submission for sequences with
3779 <li>View all structures does not always superpose
3781 <li>Option widgets in service parameters not updated to
3782 reflect user or preset settings</li>
3783 <li>Null pointer exceptions for some services without
3784 presets or adjustable parameters</li>
3785 <li>Discover PDB IDs entry in structure menu doesn't
3786 discover PDB xRefs</li>
3787 <li>Exception encountered while trying to retrieve
3788 features with DAS</li>
3789 <li>Lowest value in annotation row isn't coloured
3790 when colour by annotation (per sequence) is coloured</li>
3791 <li>Keyboard mode P jumps to start of gapped region when
3792 residue follows a gap</li>
3793 <li>Jalview appears to hang importing an alignment with
3794 Wrap as default or after enabling Wrap</li>
3795 <li>'Right click to add annotations' message
3796 shown in wrap mode when no annotations present</li>
3797 <li>Disorder predictions fail with NPE if no automatic
3798 annotation already exists on alignment</li>
3799 <li>oninit javascript function should be called after
3800 initialisation completes</li>
3801 <li>Remove redundancy after disorder prediction corrupts
3802 alignment window display</li>
3803 <li>Example annotation file in documentation is invalid</li>
3804 <li>Grouped line graph annotation rows are not exported
3805 to annotation file</li>
3806 <li>Multi-harmony analysis cannot be run when only two
3808 <li>Cannot create multiple groups of line graphs with
3809 several 'combine' statements in annotation file</li>
3810 <li>Pressing return several times causes Number Format
3811 exceptions in keyboard mode</li>
3812 <li>Multi-harmony (SHMMR) method doesn't submit
3813 correct partitions for input data</li>
3814 <li>Translation from DNA to Amino Acids fails</li>
3815 <li>Jalview fail to load newick tree with quoted label</li>
3816 <li>--headless flag isn't understood</li>
3817 <li>ClassCastException when generating EPS in headless
3819 <li>Adjusting sequence-associated shading threshold only
3820 changes one row's threshold</li>
3821 <li>Preferences and Feature settings panel panel
3822 doesn't open</li>
3823 <li>hide consensus histogram also hides conservation and
3824 quality histograms</li>
3829 <td><div align="center">
3830 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3832 <td><em>Application</em>
3834 <li>Support for JABAWS 2.0 Services (AACon alignment
3835 conservation, protein disorder and Clustal Omega)</li>
3836 <li>JABAWS server status indicator in Web Services
3838 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3839 in Jalview alignment window</li>
3840 <li>Updated Jalview build and deploy framework for OSX
3841 mountain lion, windows 7, and 8</li>
3842 <li>Nucleotide substitution matrix for PCA that supports
3843 RNA and ambiguity codes</li>
3845 <li>Improved sequence database retrieval GUI</li>
3846 <li>Support fetching and database reference look up
3847 against multiple DAS sources (Fetch all from in 'fetch db
3849 <li>Jalview project improvements
3851 <li>Store and retrieve the 'belowAlignment'
3852 flag for annotation</li>
3853 <li>calcId attribute to group annotation rows on the
3855 <li>Store AACon calculation settings for a view in
3856 Jalview project</li>
3860 <li>horizontal scrolling gesture support</li>
3861 <li>Visual progress indicator when PCA calculation is
3863 <li>Simpler JABA web services menus</li>
3864 <li>visual indication that web service results are still
3865 being retrieved from server</li>
3866 <li>Serialise the dialogs that are shown when Jalview
3867 starts up for first time</li>
3868 <li>Jalview user agent string for interacting with HTTP
3870 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3872 <li>Examples directory and Groovy library included in
3873 InstallAnywhere distribution</li>
3874 </ul> <em>Applet</em>
3876 <li>RNA alignment and secondary structure annotation
3877 visualization applet example</li>
3878 </ul> <em>General</em>
3880 <li>Normalise option for consensus sequence logo</li>
3881 <li>Reset button in PCA window to return dimensions to
3883 <li>Allow seqspace or Jalview variant of alignment PCA
3885 <li>PCA with either nucleic acid and protein substitution
3887 <li>Allow windows containing HTML reports to be exported
3889 <li>Interactive display and editing of RNA secondary
3890 structure contacts</li>
3891 <li>RNA Helix Alignment Colouring</li>
3892 <li>RNA base pair logo consensus</li>
3893 <li>Parse sequence associated secondary structure
3894 information in Stockholm files</li>
3895 <li>HTML Export database accessions and annotation
3896 information presented in tooltip for sequences</li>
3897 <li>Import secondary structure from LOCARNA clustalw
3898 style RNA alignment files</li>
3899 <li>import and visualise T-COFFEE quality scores for an
3901 <li>'colour by annotation' per sequence option to
3902 shade each sequence according to its associated alignment
3904 <li>New Jalview Logo</li>
3905 </ul> <em>Documentation and Development</em>
3907 <li>documentation for score matrices used in Jalview</li>
3908 <li>New Website!</li>
3910 <td><em>Application</em>
3912 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3913 wsdbfetch REST service</li>
3914 <li>Stop windows being moved outside desktop on OSX</li>
3915 <li>Filetype associations not installed for webstart
3917 <li>Jalview does not always retrieve progress of a JABAWS
3918 job execution in full once it is complete</li>
3919 <li>revise SHMR RSBS definition to ensure alignment is
3920 uploaded via ali_file parameter</li>
3921 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3922 <li>View all structures superposed fails with exception</li>
3923 <li>Jnet job queues forever if a very short sequence is
3924 submitted for prediction</li>
3925 <li>Cut and paste menu not opened when mouse clicked on
3927 <li>Putting fractional value into integer text box in
3928 alignment parameter dialog causes Jalview to hang</li>
3929 <li>Structure view highlighting doesn't work on
3931 <li>View all structures fails with exception shown in
3933 <li>Characters in filename associated with PDBEntry not
3934 escaped in a platform independent way</li>
3935 <li>Jalview desktop fails to launch with exception when
3937 <li>Tree calculation reports 'you must have 2 or more
3938 sequences selected' when selection is empty</li>
3939 <li>Jalview desktop fails to launch with jar signature
3940 failure when java web start temporary file caching is
3942 <li>DAS Sequence retrieval with range qualification
3943 results in sequence xref which includes range qualification</li>
3944 <li>Errors during processing of command line arguments
3945 cause progress bar (JAL-898) to be removed</li>
3946 <li>Replace comma for semi-colon option not disabled for
3947 DAS sources in sequence fetcher</li>
3948 <li>Cannot close news reader when JABAWS server warning
3949 dialog is shown</li>
3950 <li>Option widgets not updated to reflect user settings</li>
3951 <li>Edited sequence not submitted to web service</li>
3952 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3953 <li>InstallAnywhere installer doesn't unpack and run
3954 on OSX Mountain Lion</li>
3955 <li>Annotation panel not given a scroll bar when
3956 sequences with alignment annotation are pasted into the
3958 <li>Sequence associated annotation rows not associated
3959 when loaded from Jalview project</li>
3960 <li>Browser launch fails with NPE on java 1.7</li>
3961 <li>JABAWS alignment marked as finished when job was
3962 cancelled or job failed due to invalid input</li>
3963 <li>NPE with v2.7 example when clicking on Tree
3964 associated with all views</li>
3965 <li>Exceptions when copy/paste sequences with grouped
3966 annotation rows to new window</li>
3967 </ul> <em>Applet</em>
3969 <li>Sequence features are momentarily displayed before
3970 they are hidden using hidefeaturegroups applet parameter</li>
3971 <li>loading features via javascript API automatically
3972 enables feature display</li>
3973 <li>scrollToColumnIn javascript API method doesn't
3975 </ul> <em>General</em>
3977 <li>Redundancy removal fails for rna alignment</li>
3978 <li>PCA calculation fails when sequence has been selected
3979 and then deselected</li>
3980 <li>PCA window shows grey box when first opened on OSX</li>
3981 <li>Letters coloured pink in sequence logo when alignment
3982 coloured with clustalx</li>
3983 <li>Choosing fonts without letter symbols defined causes
3984 exceptions and redraw errors</li>
3985 <li>Initial PCA plot view is not same as manually
3986 reconfigured view</li>
3987 <li>Grouped annotation graph label has incorrect line
3989 <li>Grouped annotation graph label display is corrupted
3990 for lots of labels</li>
3995 <div align="center">
3996 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3999 <td><em>Application</em>
4001 <li>Jalview Desktop News Reader</li>
4002 <li>Tweaked default layout of web services menu</li>
4003 <li>View/alignment association menu to enable user to
4004 easily specify which alignment a multi-structure view takes
4005 its colours/correspondences from</li>
4006 <li>Allow properties file location to be specified as URL</li>
4007 <li>Extend Jalview project to preserve associations
4008 between many alignment views and a single Jmol display</li>
4009 <li>Store annotation row height in Jalview project file</li>
4010 <li>Annotation row column label formatting attributes
4011 stored in project file</li>
4012 <li>Annotation row order for auto-calculated annotation
4013 rows preserved in Jalview project file</li>
4014 <li>Visual progress indication when Jalview state is
4015 saved using Desktop window menu</li>
4016 <li>Visual indication that command line arguments are
4017 still being processed</li>
4018 <li>Groovy script execution from URL</li>
4019 <li>Colour by annotation default min and max colours in
4021 <li>Automatically associate PDB files dragged onto an
4022 alignment with sequences that have high similarity and
4024 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4025 <li>'view structures' option to open many
4026 structures in same window</li>
4027 <li>Sort associated views menu option for tree panel</li>
4028 <li>Group all JABA and non-JABA services for a particular
4029 analysis function in its own submenu</li>
4030 </ul> <em>Applet</em>
4032 <li>Userdefined and autogenerated annotation rows for
4034 <li>Adjustment of alignment annotation pane height</li>
4035 <li>Annotation scrollbar for annotation panel</li>
4036 <li>Drag to reorder annotation rows in annotation panel</li>
4037 <li>'automaticScrolling' parameter</li>
4038 <li>Allow sequences with partial ID string matches to be
4039 annotated from GFF/Jalview features files</li>
4040 <li>Sequence logo annotation row in applet</li>
4041 <li>Absolute paths relative to host server in applet
4042 parameters are treated as such</li>
4043 <li>New in the JalviewLite javascript API:
4045 <li>JalviewLite.js javascript library</li>
4046 <li>Javascript callbacks for
4048 <li>Applet initialisation</li>
4049 <li>Sequence/alignment mouse-overs and selections</li>
4052 <li>scrollTo row and column alignment scrolling
4054 <li>Select sequence/alignment regions from javascript</li>
4055 <li>javascript structure viewer harness to pass
4056 messages between Jmol and Jalview when running as
4057 distinct applets</li>
4058 <li>sortBy method</li>
4059 <li>Set of applet and application examples shipped
4060 with documentation</li>
4061 <li>New example to demonstrate JalviewLite and Jmol
4062 javascript message exchange</li>
4064 </ul> <em>General</em>
4066 <li>Enable Jmol displays to be associated with multiple
4067 multiple alignments</li>
4068 <li>Option to automatically sort alignment with new tree</li>
4069 <li>User configurable link to enable redirects to a
4070 www.Jalview.org mirror</li>
4071 <li>Jmol colours option for Jmol displays</li>
4072 <li>Configurable newline string when writing alignment
4073 and other flat files</li>
4074 <li>Allow alignment annotation description lines to
4075 contain html tags</li>
4076 </ul> <em>Documentation and Development</em>
4078 <li>Add groovy test harness for bulk load testing to
4080 <li>Groovy script to load and align a set of sequences
4081 using a web service before displaying the result in the
4082 Jalview desktop</li>
4083 <li>Restructured javascript and applet api documentation</li>
4084 <li>Ant target to publish example html files with applet
4086 <li>Netbeans project for building Jalview from source</li>
4087 <li>ant task to create online javadoc for Jalview source</li>
4089 <td><em>Application</em>
4091 <li>User defined colourscheme throws exception when
4092 current built in colourscheme is saved as new scheme</li>
4093 <li>AlignFrame->Save in application pops up save
4094 dialog for valid filename/format</li>
4095 <li>Cannot view associated structure for UniProt sequence</li>
4096 <li>PDB file association breaks for UniProt sequence
4098 <li>Associate PDB from file dialog does not tell you
4099 which sequence is to be associated with the file</li>
4100 <li>Find All raises null pointer exception when query
4101 only matches sequence IDs</li>
4102 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4103 <li>Jalview project with Jmol views created with Jalview
4104 2.4 cannot be loaded</li>
4105 <li>Filetype associations not installed for webstart
4107 <li>Two or more chains in a single PDB file associated
4108 with sequences in different alignments do not get coloured
4109 by their associated sequence</li>
4110 <li>Visibility status of autocalculated annotation row
4111 not preserved when project is loaded</li>
4112 <li>Annotation row height and visibility attributes not
4113 stored in Jalview project</li>
4114 <li>Tree bootstraps are not preserved when saved as a
4115 Jalview project</li>
4116 <li>Envision2 workflow tooltips are corrupted</li>
4117 <li>Enabling show group conservation also enables colour
4118 by conservation</li>
4119 <li>Duplicate group associated conservation or consensus
4120 created on new view</li>
4121 <li>Annotation scrollbar not displayed after 'show
4122 all hidden annotation rows' option selected</li>
4123 <li>Alignment quality not updated after alignment
4124 annotation row is hidden then shown</li>
4125 <li>Preserve colouring of structures coloured by
4126 sequences in pre Jalview 2.7 projects</li>
4127 <li>Web service job parameter dialog is not laid out
4129 <li>Web services menu not refreshed after 'reset
4130 services' button is pressed in preferences</li>
4131 <li>Annotation off by one in Jalview v2_3 example project</li>
4132 <li>Structures imported from file and saved in project
4133 get name like jalview_pdb1234.txt when reloaded</li>
4134 <li>Jalview does not always retrieve progress of a JABAWS
4135 job execution in full once it is complete</li>
4136 </ul> <em>Applet</em>
4138 <li>Alignment height set incorrectly when lots of
4139 annotation rows are displayed</li>
4140 <li>Relative URLs in feature HTML text not resolved to
4142 <li>View follows highlighting does not work for positions
4144 <li><= shown as = in tooltip</li>
4145 <li>Export features raises exception when no features
4147 <li>Separator string used for serialising lists of IDs
4148 for javascript api is modified when separator string
4149 provided as parameter</li>
4150 <li>Null pointer exception when selecting tree leaves for
4151 alignment with no existing selection</li>
4152 <li>Relative URLs for datasources assumed to be relative
4153 to applet's codebase</li>
4154 <li>Status bar not updated after finished searching and
4155 search wraps around to first result</li>
4156 <li>StructureSelectionManager instance shared between
4157 several Jalview applets causes race conditions and memory
4159 <li>Hover tooltip and mouseover of position on structure
4160 not sent from Jmol in applet</li>
4161 <li>Certain sequences of javascript method calls to
4162 applet API fatally hang browser</li>
4163 </ul> <em>General</em>
4165 <li>View follows structure mouseover scrolls beyond
4166 position with wrapped view and hidden regions</li>
4167 <li>Find sequence position moves to wrong residue
4168 with/without hidden columns</li>
4169 <li>Sequence length given in alignment properties window
4171 <li>InvalidNumberFormat exceptions thrown when trying to
4172 import PDB like structure files</li>
4173 <li>Positional search results are only highlighted
4174 between user-supplied sequence start/end bounds</li>
4175 <li>End attribute of sequence is not validated</li>
4176 <li>Find dialog only finds first sequence containing a
4177 given sequence position</li>
4178 <li>Sequence numbering not preserved in MSF alignment
4180 <li>Jalview PDB file reader does not extract sequence
4181 from nucleotide chains correctly</li>
4182 <li>Structure colours not updated when tree partition
4183 changed in alignment</li>
4184 <li>Sequence associated secondary structure not correctly
4185 parsed in interleaved stockholm</li>
4186 <li>Colour by annotation dialog does not restore current
4188 <li>Hiding (nearly) all sequences doesn't work
4190 <li>Sequences containing lowercase letters are not
4191 properly associated with their pdb files</li>
4192 </ul> <em>Documentation and Development</em>
4194 <li>schemas/JalviewWsParamSet.xsd corrupted by
4195 ApplyCopyright tool</li>
4200 <div align="center">
4201 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4204 <td><em>Application</em>
4206 <li>New warning dialog when the Jalview Desktop cannot
4207 contact web services</li>
4208 <li>JABA service parameters for a preset are shown in
4209 service job window</li>
4210 <li>JABA Service menu entries reworded</li>
4214 <li>Modeller PIR IO broken - cannot correctly import a
4215 pir file emitted by Jalview</li>
4216 <li>Existing feature settings transferred to new
4217 alignment view created from cut'n'paste</li>
4218 <li>Improved test for mixed amino/nucleotide chains when
4219 parsing PDB files</li>
4220 <li>Consensus and conservation annotation rows
4221 occasionally become blank for all new windows</li>
4222 <li>Exception raised when right clicking above sequences
4223 in wrapped view mode</li>
4224 </ul> <em>Application</em>
4226 <li>multiple multiply aligned structure views cause cpu
4227 usage to hit 100% and computer to hang</li>
4228 <li>Web Service parameter layout breaks for long user
4229 parameter names</li>
4230 <li>Jaba service discovery hangs desktop if Jaba server
4237 <div align="center">
4238 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4241 <td><em>Application</em>
4243 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4244 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4247 <li>Web Services preference tab</li>
4248 <li>Analysis parameters dialog box and user defined
4250 <li>Improved speed and layout of Envision2 service menu</li>
4251 <li>Superpose structures using associated sequence
4253 <li>Export coordinates and projection as CSV from PCA
4255 </ul> <em>Applet</em>
4257 <li>enable javascript: execution by the applet via the
4258 link out mechanism</li>
4259 </ul> <em>Other</em>
4261 <li>Updated the Jmol Jalview interface to work with Jmol
4263 <li>The Jalview Desktop and JalviewLite applet now
4264 require Java 1.5</li>
4265 <li>Allow Jalview feature colour specification for GFF
4266 sequence annotation files</li>
4267 <li>New 'colour by label' keword in Jalview feature file
4268 type colour specification</li>
4269 <li>New Jalview Desktop Groovy API method that allows a
4270 script to check if it being run in an interactive session or
4271 in a batch operation from the Jalview command line</li>
4275 <li>clustalx colourscheme colours Ds preferentially when
4276 both D+E are present in over 50% of the column</li>
4277 </ul> <em>Application</em>
4279 <li>typo in AlignmentFrame->View->Hide->all but
4280 selected Regions menu item</li>
4281 <li>sequence fetcher replaces ',' for ';' when the ',' is
4282 part of a valid accession ID</li>
4283 <li>fatal OOM if object retrieved by sequence fetcher
4284 runs out of memory</li>
4285 <li>unhandled Out of Memory Error when viewing pca
4286 analysis results</li>
4287 <li>InstallAnywhere builds fail to launch on OS X java
4288 10.5 update 4 (due to apple Java 1.6 update)</li>
4289 <li>Installanywhere Jalview silently fails to launch</li>
4290 </ul> <em>Applet</em>
4292 <li>Jalview.getFeatureGroups() raises an
4293 ArrayIndexOutOfBoundsException if no feature groups are
4300 <div align="center">
4301 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4307 <li>Alignment prettyprinter doesn't cope with long
4309 <li>clustalx colourscheme colours Ds preferentially when
4310 both D+E are present in over 50% of the column</li>
4311 <li>nucleic acid structures retrieved from PDB do not
4312 import correctly</li>
4313 <li>More columns get selected than were clicked on when a
4314 number of columns are hidden</li>
4315 <li>annotation label popup menu not providing correct
4316 add/hide/show options when rows are hidden or none are
4318 <li>Stockholm format shown in list of readable formats,
4319 and parser copes better with alignments from RFAM.</li>
4320 <li>CSV output of consensus only includes the percentage
4321 of all symbols if sequence logo display is enabled</li>
4323 </ul> <em>Applet</em>
4325 <li>annotation panel disappears when annotation is
4327 </ul> <em>Application</em>
4329 <li>Alignment view not redrawn properly when new
4330 alignment opened where annotation panel is visible but no
4331 annotations are present on alignment</li>
4332 <li>pasted region containing hidden columns is
4333 incorrectly displayed in new alignment window</li>
4334 <li>Jalview slow to complete operations when stdout is
4335 flooded (fix is to close the Jalview console)</li>
4336 <li>typo in AlignmentFrame->View->Hide->all but
4337 selected Rregions menu item.</li>
4338 <li>inconsistent group submenu and Format submenu entry
4339 'Un' or 'Non'conserved</li>
4340 <li>Sequence feature settings are being shared by
4341 multiple distinct alignments</li>
4342 <li>group annotation not recreated when tree partition is
4344 <li>double click on group annotation to select sequences
4345 does not propagate to associated trees</li>
4346 <li>Mac OSX specific issues:
4348 <li>exception raised when mouse clicked on desktop
4349 window background</li>
4350 <li>Desktop menu placed on menu bar and application
4351 name set correctly</li>
4352 <li>sequence feature settings not wide enough for the
4353 save feature colourscheme button</li>
4362 <div align="center">
4363 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4366 <td><em>New Capabilities</em>
4368 <li>URL links generated from description line for
4369 regular-expression based URL links (applet and application)
4371 <li>Non-positional feature URL links are shown in link
4373 <li>Linked viewing of nucleic acid sequences and
4375 <li>Automatic Scrolling option in View menu to display
4376 the currently highlighted region of an alignment.</li>
4377 <li>Order an alignment by sequence length, or using the
4378 average score or total feature count for each sequence.</li>
4379 <li>Shading features by score or associated description</li>
4380 <li>Subdivide alignment and groups based on identity of
4381 selected subsequence (Make Groups from Selection).</li>
4382 <li>New hide/show options including Shift+Control+H to
4383 hide everything but the currently selected region.</li>
4384 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4385 </ul> <em>Application</em>
4387 <li>Fetch DB References capabilities and UI expanded to
4388 support retrieval from DAS sequence sources</li>
4389 <li>Local DAS Sequence sources can be added via the
4390 command line or via the Add local source dialog box.</li>
4391 <li>DAS Dbref and DbxRef feature types are parsed as
4392 database references and protein_name is parsed as
4393 description line (BioSapiens terms).</li>
4394 <li>Enable or disable non-positional feature and database
4395 references in sequence ID tooltip from View menu in
4397 <!-- <li>New hidden columns and rows and representatives capabilities
4398 in annotations file (in progress - not yet fully implemented)</li> -->
4399 <li>Group-associated consensus, sequence logos and
4400 conservation plots</li>
4401 <li>Symbol distributions for each column can be exported
4402 and visualized as sequence logos</li>
4403 <li>Optionally scale multi-character column labels to fit
4404 within each column of annotation row<!-- todo for applet -->
4406 <li>Optional automatic sort of associated alignment view
4407 when a new tree is opened.</li>
4408 <li>Jalview Java Console</li>
4409 <li>Better placement of desktop window when moving
4410 between different screens.</li>
4411 <li>New preference items for sequence ID tooltip and
4412 consensus annotation</li>
4413 <li>Client to submit sequences and IDs to Envision2
4415 <li><em>Vamsas Capabilities</em>
4417 <li>Improved VAMSAS synchronization (Jalview archive
4418 used to preserve views, structures, and tree display
4420 <li>Import of vamsas documents from disk or URL via
4422 <li>Sharing of selected regions between views and
4423 with other VAMSAS applications (Experimental feature!)</li>
4424 <li>Updated API to VAMSAS version 0.2</li>
4426 </ul> <em>Applet</em>
4428 <li>Middle button resizes annotation row height</li>
4431 <li>sortByTree (true/false) - automatically sort the
4432 associated alignment view by the tree when a new tree is
4434 <li>showTreeBootstraps (true/false) - show or hide
4435 branch bootstraps (default is to show them if available)</li>
4436 <li>showTreeDistances (true/false) - show or hide
4437 branch lengths (default is to show them if available)</li>
4438 <li>showUnlinkedTreeNodes (true/false) - indicate if
4439 unassociated nodes should be highlighted in the tree
4441 <li>heightScale and widthScale (1.0 or more) -
4442 increase the height or width of a cell in the alignment
4443 grid relative to the current font size.</li>
4446 <li>Non-positional features displayed in sequence ID
4448 </ul> <em>Other</em>
4450 <li>Features format: graduated colour definitions and
4451 specification of feature scores</li>
4452 <li>Alignment Annotations format: new keywords for group
4453 associated annotation (GROUP_REF) and annotation row display
4454 properties (ROW_PROPERTIES)</li>
4455 <li>XML formats extended to support graduated feature
4456 colourschemes, group associated annotation, and profile
4457 visualization settings.</li></td>
4460 <li>Source field in GFF files parsed as feature source
4461 rather than description</li>
4462 <li>Non-positional features are now included in sequence
4463 feature and gff files (controlled via non-positional feature
4464 visibility in tooltip).</li>
4465 <li>URL links generated for all feature links (bugfix)</li>
4466 <li>Added URL embedding instructions to features file
4468 <li>Codons containing ambiguous nucleotides translated as
4469 'X' in peptide product</li>
4470 <li>Match case switch in find dialog box works for both
4471 sequence ID and sequence string and query strings do not
4472 have to be in upper case to match case-insensitively.</li>
4473 <li>AMSA files only contain first column of
4474 multi-character column annotation labels</li>
4475 <li>Jalview Annotation File generation/parsing consistent
4476 with documentation (e.g. Stockholm annotation can be
4477 exported and re-imported)</li>
4478 <li>PDB files without embedded PDB IDs given a friendly
4480 <li>Find incrementally searches ID string matches as well
4481 as subsequence matches, and correctly reports total number
4485 <li>Better handling of exceptions during sequence
4487 <li>Dasobert generated non-positional feature URL
4488 link text excludes the start_end suffix</li>
4489 <li>DAS feature and source retrieval buttons disabled
4490 when fetch or registry operations in progress.</li>
4491 <li>PDB files retrieved from URLs are cached properly</li>
4492 <li>Sequence description lines properly shared via
4494 <li>Sequence fetcher fetches multiple records for all
4496 <li>Ensured that command line das feature retrieval
4497 completes before alignment figures are generated.</li>
4498 <li>Reduced time taken when opening file browser for
4500 <li>isAligned check prior to calculating tree, PCA or
4501 submitting an MSA to JNet now excludes hidden sequences.</li>
4502 <li>User defined group colours properly recovered
4503 from Jalview projects.</li>
4512 <div align="center">
4513 <strong>2.4.0.b2</strong><br> 28/10/2009
4518 <li>Experimental support for google analytics usage
4520 <li>Jalview privacy settings (user preferences and docs).</li>
4525 <li>Race condition in applet preventing startup in
4527 <li>Exception when feature created from selection beyond
4528 length of sequence.</li>
4529 <li>Allow synthetic PDB files to be imported gracefully</li>
4530 <li>Sequence associated annotation rows associate with
4531 all sequences with a given id</li>
4532 <li>Find function matches case-insensitively for sequence
4533 ID string searches</li>
4534 <li>Non-standard characters do not cause pairwise
4535 alignment to fail with exception</li>
4536 </ul> <em>Application Issues</em>
4538 <li>Sequences are now validated against EMBL database</li>
4539 <li>Sequence fetcher fetches multiple records for all
4541 </ul> <em>InstallAnywhere Issues</em>
4543 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4544 issue with installAnywhere mechanism)</li>
4545 <li>Command line launching of JARs from InstallAnywhere
4546 version (java class versioning error fixed)</li>
4553 <div align="center">
4554 <strong>2.4</strong><br> 27/8/2008
4557 <td><em>User Interface</em>
4559 <li>Linked highlighting of codon and amino acid from
4560 translation and protein products</li>
4561 <li>Linked highlighting of structure associated with
4562 residue mapping to codon position</li>
4563 <li>Sequence Fetcher provides example accession numbers
4564 and 'clear' button</li>
4565 <li>MemoryMonitor added as an option under Desktop's
4567 <li>Extract score function to parse whitespace separated
4568 numeric data in description line</li>
4569 <li>Column labels in alignment annotation can be centred.</li>
4570 <li>Tooltip for sequence associated annotation give name
4572 </ul> <em>Web Services and URL fetching</em>
4574 <li>JPred3 web service</li>
4575 <li>Prototype sequence search client (no public services
4577 <li>Fetch either seed alignment or full alignment from
4579 <li>URL Links created for matching database cross
4580 references as well as sequence ID</li>
4581 <li>URL Links can be created using regular-expressions</li>
4582 </ul> <em>Sequence Database Connectivity</em>
4584 <li>Retrieval of cross-referenced sequences from other
4586 <li>Generalised database reference retrieval and
4587 validation to all fetchable databases</li>
4588 <li>Fetch sequences from DAS sources supporting the
4589 sequence command</li>
4590 </ul> <em>Import and Export</em>
4591 <li>export annotation rows as CSV for spreadsheet import</li>
4592 <li>Jalview projects record alignment dataset associations,
4593 EMBL products, and cDNA sequence mappings</li>
4594 <li>Sequence Group colour can be specified in Annotation
4596 <li>Ad-hoc colouring of group in Annotation File using RGB
4597 triplet as name of colourscheme</li>
4598 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4600 <li>treenode binding for VAMSAS tree exchange</li>
4601 <li>local editing and update of sequences in VAMSAS
4602 alignments (experimental)</li>
4603 <li>Create new or select existing session to join</li>
4604 <li>load and save of vamsas documents</li>
4605 </ul> <em>Application command line</em>
4607 <li>-tree parameter to open trees (introduced for passing
4609 <li>-fetchfrom command line argument to specify nicknames
4610 of DAS servers to query for alignment features</li>
4611 <li>-dasserver command line argument to add new servers
4612 that are also automatically queried for features</li>
4613 <li>-groovy command line argument executes a given groovy
4614 script after all input data has been loaded and parsed</li>
4615 </ul> <em>Applet-Application data exchange</em>
4617 <li>Trees passed as applet parameters can be passed to
4618 application (when using "View in full
4619 application")</li>
4620 </ul> <em>Applet Parameters</em>
4622 <li>feature group display control parameter</li>
4623 <li>debug parameter</li>
4624 <li>showbutton parameter</li>
4625 </ul> <em>Applet API methods</em>
4627 <li>newView public method</li>
4628 <li>Window (current view) specific get/set public methods</li>
4629 <li>Feature display control methods</li>
4630 <li>get list of currently selected sequences</li>
4631 </ul> <em>New Jalview distribution features</em>
4633 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4634 <li>RELEASE file gives build properties for the latest
4635 Jalview release.</li>
4636 <li>Java 1.1 Applet build made easier and donotobfuscate
4637 property controls execution of obfuscator</li>
4638 <li>Build target for generating source distribution</li>
4639 <li>Debug flag for javacc</li>
4640 <li>.jalview_properties file is documented (slightly) in
4641 jalview.bin.Cache</li>
4642 <li>Continuous Build Integration for stable and
4643 development version of Application, Applet and source
4648 <li>selected region output includes visible annotations
4649 (for certain formats)</li>
4650 <li>edit label/displaychar contains existing label/char
4652 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4653 <li>shorter peptide product names from EMBL records</li>
4654 <li>Newick string generator makes compact representations</li>
4655 <li>bootstrap values parsed correctly for tree files with
4657 <li>pathological filechooser bug avoided by not allowing
4658 filenames containing a ':'</li>
4659 <li>Fixed exception when parsing GFF files containing
4660 global sequence features</li>
4661 <li>Alignment datasets are finalized only when number of
4662 references from alignment sequences goes to zero</li>
4663 <li>Close of tree branch colour box without colour
4664 selection causes cascading exceptions</li>
4665 <li>occasional negative imgwidth exceptions</li>
4666 <li>better reporting of non-fatal warnings to user when
4667 file parsing fails.</li>
4668 <li>Save works when Jalview project is default format</li>
4669 <li>Save as dialog opened if current alignment format is
4670 not a valid output format</li>
4671 <li>UniProt canonical names introduced for both das and
4673 <li>Histidine should be midblue (not pink!) in Zappo</li>
4674 <li>error messages passed up and output when data read
4676 <li>edit undo recovers previous dataset sequence when
4677 sequence is edited</li>
4678 <li>allow PDB files without pdb ID HEADER lines (like
4679 those generated by MODELLER) to be read in properly</li>
4680 <li>allow reading of JPred concise files as a normal
4682 <li>Stockholm annotation parsing and alignment properties
4683 import fixed for PFAM records</li>
4684 <li>Structure view windows have correct name in Desktop
4686 <li>annotation consisting of sequence associated scores
4687 can be read and written correctly to annotation file</li>
4688 <li>Aligned cDNA translation to aligned peptide works
4690 <li>Fixed display of hidden sequence markers and
4691 non-italic font for representatives in Applet</li>
4692 <li>Applet Menus are always embedded in applet window on
4694 <li>Newly shown features appear at top of stack (in
4696 <li>Annotations added via parameter not drawn properly
4697 due to null pointer exceptions</li>
4698 <li>Secondary structure lines are drawn starting from
4699 first column of alignment</li>
4700 <li>UniProt XML import updated for new schema release in
4702 <li>Sequence feature to sequence ID match for Features
4703 file is case-insensitive</li>
4704 <li>Sequence features read from Features file appended to
4705 all sequences with matching IDs</li>
4706 <li>PDB structure coloured correctly for associated views
4707 containing a sub-sequence</li>
4708 <li>PDB files can be retrieved by applet from Jar files</li>
4709 <li>feature and annotation file applet parameters
4710 referring to different directories are retrieved correctly</li>
4711 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4712 <li>Fixed application hang whilst waiting for
4713 splash-screen version check to complete</li>
4714 <li>Applet properly URLencodes input parameter values
4715 when passing them to the launchApp service</li>
4716 <li>display name and local features preserved in results
4717 retrieved from web service</li>
4718 <li>Visual delay indication for sequence retrieval and
4719 sequence fetcher initialisation</li>
4720 <li>updated Application to use DAS 1.53e version of
4721 dasobert DAS client</li>
4722 <li>Re-instated Full AMSA support and .amsa file
4724 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4732 <div align="center">
4733 <strong>2.3</strong><br> 9/5/07
4738 <li>Jmol 11.0.2 integration</li>
4739 <li>PDB views stored in Jalview XML files</li>
4740 <li>Slide sequences</li>
4741 <li>Edit sequence in place</li>
4742 <li>EMBL CDS features</li>
4743 <li>DAS Feature mapping</li>
4744 <li>Feature ordering</li>
4745 <li>Alignment Properties</li>
4746 <li>Annotation Scores</li>
4747 <li>Sort by scores</li>
4748 <li>Feature/annotation editing in applet</li>
4753 <li>Headless state operation in 2.2.1</li>
4754 <li>Incorrect and unstable DNA pairwise alignment</li>
4755 <li>Cut and paste of sequences with annotation</li>
4756 <li>Feature group display state in XML</li>
4757 <li>Feature ordering in XML</li>
4758 <li>blc file iteration selection using filename # suffix</li>
4759 <li>Stockholm alignment properties</li>
4760 <li>Stockhom alignment secondary structure annotation</li>
4761 <li>2.2.1 applet had no feature transparency</li>
4762 <li>Number pad keys can be used in cursor mode</li>
4763 <li>Structure Viewer mirror image resolved</li>
4770 <div align="center">
4771 <strong>2.2.1</strong><br> 12/2/07
4776 <li>Non standard characters can be read and displayed
4777 <li>Annotations/Features can be imported/exported to the
4779 <li>Applet allows editing of sequence/annotation/group
4780 name & description
4781 <li>Preference setting to display sequence name in
4783 <li>Annotation file format extended to allow
4784 Sequence_groups to be defined
4785 <li>Default opening of alignment overview panel can be
4786 specified in preferences
4787 <li>PDB residue numbering annotation added to associated
4793 <li>Applet crash under certain Linux OS with Java 1.6
4795 <li>Annotation file export / import bugs fixed
4796 <li>PNG / EPS image output bugs fixed
4802 <div align="center">
4803 <strong>2.2</strong><br> 27/11/06
4808 <li>Multiple views on alignment
4809 <li>Sequence feature editing
4810 <li>"Reload" alignment
4811 <li>"Save" to current filename
4812 <li>Background dependent text colour
4813 <li>Right align sequence ids
4814 <li>User-defined lower case residue colours
4817 <li>Menu item accelerator keys
4818 <li>Control-V pastes to current alignment
4819 <li>Cancel button for DAS Feature Fetching
4820 <li>PCA and PDB Viewers zoom via mouse roller
4821 <li>User-defined sub-tree colours and sub-tree selection
4823 <li>'New Window' button on the 'Output to Text box'
4828 <li>New memory efficient Undo/Redo System
4829 <li>Optimised symbol lookups and conservation/consensus
4831 <li>Region Conservation/Consensus recalculated after
4833 <li>Fixed Remove Empty Columns Bug (empty columns at end
4835 <li>Slowed DAS Feature Fetching for increased robustness.
4837 <li>Made angle brackets in ASCII feature descriptions
4839 <li>Re-instated Zoom function for PCA
4840 <li>Sequence descriptions conserved in web service
4842 <li>UniProt ID discoverer uses any word separated by
4844 <li>WsDbFetch query/result association resolved
4845 <li>Tree leaf to sequence mapping improved
4846 <li>Smooth fonts switch moved to FontChooser dialog box.
4853 <div align="center">
4854 <strong>2.1.1</strong><br> 12/9/06
4859 <li>Copy consensus sequence to clipboard</li>
4864 <li>Image output - rightmost residues are rendered if
4865 sequence id panel has been resized</li>
4866 <li>Image output - all offscreen group boundaries are
4868 <li>Annotation files with sequence references - all
4869 elements in file are relative to sequence position</li>
4870 <li>Mac Applet users can use Alt key for group editing</li>
4876 <div align="center">
4877 <strong>2.1</strong><br> 22/8/06
4882 <li>MAFFT Multiple Alignment in default Web Service list</li>
4883 <li>DAS Feature fetching</li>
4884 <li>Hide sequences and columns</li>
4885 <li>Export Annotations and Features</li>
4886 <li>GFF file reading / writing</li>
4887 <li>Associate structures with sequences from local PDB
4889 <li>Add sequences to exisiting alignment</li>
4890 <li>Recently opened files / URL lists</li>
4891 <li>Applet can launch the full application</li>
4892 <li>Applet has transparency for features (Java 1.2
4894 <li>Applet has user defined colours parameter</li>
4895 <li>Applet can load sequences from parameter
4896 "sequence<em>x</em>"
4902 <li>Redundancy Panel reinstalled in the Applet</li>
4903 <li>Monospaced font - EPS / rescaling bug fixed</li>
4904 <li>Annotation files with sequence references bug fixed</li>
4910 <div align="center">
4911 <strong>2.08.1</strong><br> 2/5/06
4916 <li>Change case of selected region from Popup menu</li>
4917 <li>Choose to match case when searching</li>
4918 <li>Middle mouse button and mouse movement can compress /
4919 expand the visible width and height of the alignment</li>
4924 <li>Annotation Panel displays complete JNet results</li>
4930 <div align="center">
4931 <strong>2.08b</strong><br> 18/4/06
4937 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4938 <li>Righthand label on wrapped alignments shows correct
4945 <div align="center">
4946 <strong>2.08</strong><br> 10/4/06
4951 <li>Editing can be locked to the selection area</li>
4952 <li>Keyboard editing</li>
4953 <li>Create sequence features from searches</li>
4954 <li>Precalculated annotations can be loaded onto
4956 <li>Features file allows grouping of features</li>
4957 <li>Annotation Colouring scheme added</li>
4958 <li>Smooth fonts off by default - Faster rendering</li>
4959 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4964 <li>Drag & Drop fixed on Linux</li>
4965 <li>Jalview Archive file faster to load/save, sequence
4966 descriptions saved.</li>
4972 <div align="center">
4973 <strong>2.07</strong><br> 12/12/05
4978 <li>PDB Structure Viewer enhanced</li>
4979 <li>Sequence Feature retrieval and display enhanced</li>
4980 <li>Choose to output sequence start-end after sequence
4981 name for file output</li>
4982 <li>Sequence Fetcher WSDBFetch@EBI</li>
4983 <li>Applet can read feature files, PDB files and can be
4984 used for HTML form input</li>
4989 <li>HTML output writes groups and features</li>
4990 <li>Group editing is Control and mouse click</li>
4991 <li>File IO bugs</li>
4997 <div align="center">
4998 <strong>2.06</strong><br> 28/9/05
5003 <li>View annotations in wrapped mode</li>
5004 <li>More options for PCA viewer</li>
5009 <li>GUI bugs resolved</li>
5010 <li>Runs with -nodisplay from command line</li>
5016 <div align="center">
5017 <strong>2.05b</strong><br> 15/9/05
5022 <li>Choose EPS export as lineart or text</li>
5023 <li>Jar files are executable</li>
5024 <li>Can read in Uracil - maps to unknown residue</li>
5029 <li>Known OutOfMemory errors give warning message</li>
5030 <li>Overview window calculated more efficiently</li>
5031 <li>Several GUI bugs resolved</li>
5037 <div align="center">
5038 <strong>2.05</strong><br> 30/8/05
5043 <li>Edit and annotate in "Wrapped" view</li>
5048 <li>Several GUI bugs resolved</li>
5054 <div align="center">
5055 <strong>2.04</strong><br> 24/8/05
5060 <li>Hold down mouse wheel & scroll to change font
5066 <li>Improved JPred client reliability</li>
5067 <li>Improved loading of Jalview files</li>
5073 <div align="center">
5074 <strong>2.03</strong><br> 18/8/05
5079 <li>Set Proxy server name and port in preferences</li>
5080 <li>Multiple URL links from sequence ids</li>
5081 <li>User Defined Colours can have a scheme name and added
5083 <li>Choose to ignore gaps in consensus calculation</li>
5084 <li>Unix users can set default web browser</li>
5085 <li>Runs without GUI for batch processing</li>
5086 <li>Dynamically generated Web Service Menus</li>
5091 <li>InstallAnywhere download for Sparc Solaris</li>
5097 <div align="center">
5098 <strong>2.02</strong><br> 18/7/05
5104 <li>Copy & Paste order of sequences maintains
5105 alignment order.</li>
5111 <div align="center">
5112 <strong>2.01</strong><br> 12/7/05
5117 <li>Use delete key for deleting selection.</li>
5118 <li>Use Mouse wheel to scroll sequences.</li>
5119 <li>Help file updated to describe how to add alignment
5121 <li>Version and build date written to build properties
5123 <li>InstallAnywhere installation will check for updates
5124 at launch of Jalview.</li>
5129 <li>Delete gaps bug fixed.</li>
5130 <li>FileChooser sorts columns.</li>
5131 <li>Can remove groups one by one.</li>
5132 <li>Filechooser icons installed.</li>
5133 <li>Finder ignores return character when searching.
5134 Return key will initiate a search.<br>
5141 <div align="center">
5142 <strong>2.0</strong><br> 20/6/05
5147 <li>New codebase</li>
git://source.jalview.org / jalview.git / blob