4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>24/02/2022</em></strong></td>
63 <td align="left" valign="top">
68 </ul> <em>JalviewJS</em>
69 <ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
71 </ul> <em>Development</em>
73 <li>Updated building instructions</li>
74 <li>First integrated JalviewJS and Jalview release</li>
81 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)
84 <!-- JAL-3761 -->Not all codon positions highlighted for
85 overlapping exon splice sites (e.g due to RNA slippage)
88 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
91 <li><!-- JAL-3583 -->Tooltip behaviour improved (slightly)</li>
92 <li><!-- JAL-3162 -->Can edit a feature so that start > end</li>
93 <li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
94 </ul> <em>Development</em>
96 <li>Fixed non-fatal gradle errors during build</li>
102 <td width="60" align="center" nowrap><strong><a
103 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
104 <em>18/01/2022</em></strong></td>
106 <td align="left" valign="top">
109 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
110 updated by Jalview or other applications (Windows, other non
113 </ul> <em>Security</em>
116 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
122 <td width="60" align="center" nowrap><strong><a
123 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
124 <em>6/01/2022</em></strong></td>
126 <td align="left" valign="top"><em>Security</em>
129 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
136 <td width="60" align="center" nowrap><strong><a
137 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
138 <em>20/12/2021</em></strong></td>
140 <td align="left" valign="top"><em>Security</em>
143 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
145 </ul> <em>Development</em>
147 <li>Updated building instructions</li>
152 <!-- JAL-3840 -->Occupancy calculation is incorrect for
153 alignment columns with over -1+2^32 gaps (breaking filtering
157 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
158 scale factors being set with buggy window-managers (linux
161 </ul> <em>Development</em>
163 <li>Fixed non-fatal gradle errors during build</li>
168 <td width="60" align="center" nowrap><strong><a
169 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
170 <em>09/03/2021</em></strong></td>
171 <td align="left" valign="top"><em>Improved control of
172 Jalview's use of network services via jalview_properties</em>
175 <!-- JAL-3814 -->New .jalview_properties token controlling
176 launch of the news browser (like -nonews argument)
179 <!-- JAL-3813 -->New .jalview_properties token controlling
180 download of linkout URLs from
181 www.jalview.org/services/identifiers
184 <!-- JAL-3812 -->New .jalview_properties token controlling
185 download of BIOJSHTML templates
188 <!-- JAL-3811 -->New 'Discover Web Services' option to
189 trigger a one off JABAWS discovery if autodiscovery was
193 <td align="left" valign="top">
196 <!-- JAL-3818 -->Intermittent deadlock opening structure in
199 </ul> <em>New Known defects</em>
202 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
203 always restored from project (since 2.10.3)
206 <!-- JAL-3806 -->Selections from tree built from CDS aren't
207 propagated to Protein alignment (since 2.11.1.3)
213 <td width="60" align="center" nowrap><strong><a
214 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
215 <em>29/10/2020</em></strong></td>
216 <td align="left" valign="top">
221 <td align="left" valign="top">
224 <!-- JAL-3765 -->Find doesn't always highlight all matching
225 positions in a sequence (bug introduced in 2.11.1.2)
228 <!-- JAL-3760 -->Alignments containing one or more protein
229 sequences can be classed as nucleotide
232 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
233 sequences after alignment of protein products (known defect
234 first reported for 2.11.1.0)
237 <!-- JAL-3725 -->No tooltip or popup menu for genomic
238 features outwith CDS shown overlaid on protein
241 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
242 correctly mapped by Jalview (e.g. affects viral CDS with
243 ribosomal slippage, since 2.9.0)
246 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
250 <!-- JAL-3700 -->Selections in CDS sequence panel don't
251 always select corresponding protein sequences
254 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
255 column selection doesn't always ignore hidden columns
257 </ul> <em>Installer</em>
260 <!-- JAL-3611 -->Space character in Jalview install path on
261 Windows prevents install4j launching getdown
263 </ul> <em>Development</em>
266 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
267 version numbers in doc/building.md
273 <td width="60" align="center" nowrap><strong><a
274 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
275 <em>25/09/2020</em></strong></td>
276 <td align="left" valign="top">
280 <td align="left" valign="top">
283 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
284 "Encountered problems opening
285 https://www.jalview.org/examples/exampleFile_2_7.jvp"
291 <td width="60" align="center" nowrap><strong><a
292 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
293 <em>17/09/2020</em></strong></td>
294 <td align="left" valign="top">
297 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
298 residue in cursor mode
301 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
302 HTSJDK from 2.12 to 2.23
305 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
306 optimisations and improvements suggested by Bob Hanson and
307 improved compatibility with JalviewJS
310 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
311 alignments from Pfam and Rfam
314 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
315 import (no longer based on .gz extension)
318 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
321 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
322 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
326 <!-- JAL-3667 -->Improved warning messages, debug logging
327 and fixed Retry action when Jalview encounters errors when
328 saving or making backup files.
331 <!-- JAL-3676 -->Enhanced Jalview Java Console:
333 <li>Jalview's logging level can be configured</li>
334 <li>Copy to Clipboard Buttion</li>
338 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
339 when running on Linux (Requires Java 11+)
341 </ul> <em>Launching Jalview</em>
344 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
345 through a system property
348 <!-- JAL-3477 -->Improved built-in documentation and command
349 line help for configuring Jalview's memory
353 <td align="left" valign="top">
356 <!-- JAL-3691 -->Conservation and Quality tracks are shown
357 but not calculated and no protein or DNA score models are
358 available for tree/PCA calculation when launched with
359 Turkish language locale
362 <!-- JAL-3493 -->Escape does not clear highlights on the
363 alignment (Since Jalview 2.10.3)
366 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
367 doesn't slide selected sequences, just sequence under cursor
370 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
371 sequence under the cursor
374 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
375 multiple EMBL gene products shown for a single contig
378 <!-- JAL-3696 -->Errors encountered when processing variants
379 from VCF files yield "Error processing VCF: Format specifier
383 <!-- JAL-3697 -->Count of features not shown can be wrong
384 when there are both local and complementary features mapped
385 to the position under the cursor
388 <!-- JAL-3673 -->Sequence ID for reference sequence is
389 clipped when Right align Sequence IDs enabled
392 <!-- JAL-2983 -->Slider with negative range values not
393 rendered correctly in VAqua4 (Since 2.10.4)
396 <!-- JAL-3685 -->Single quotes not displayed correctly in
397 internationalised text for some messages and log output
400 <!-- JAL-3490 -->Find doesn't report matches that span
401 hidden gapped columns
404 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
405 panels, Alignment viewport and annotation renderer.
408 <!-- JAL-3561 -->Jalview ignores file format parameter
409 specifying output format when exporting an alignment via the
413 <!-- JAL-3667 -->Windows 10: For a minority of users, if
414 backups are not enabled, Jalview sometimes fails to
415 overwrite an existing file and raises a warning dialog. (in
416 2.11.0, and 2.11.1.0, the workaround is to try to save the
417 file again, and if that fails, delete the original file and
421 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
425 <!-- JAL-3741 -->References to http://www.jalview.org in
426 program and documentation
428 </ul> <em>Launching Jalview</em>
431 <!-- JAL-3718 -->Jalview application fails when launched the
432 first time for a version that has different jars to the
433 previous launched version.
435 </ul> <em>Developing Jalview</em>
438 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
439 data, causing cloverReport gradle task to fail with an
443 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
444 monitor the release channel
446 </ul> <em>New Known defects</em>
449 <!-- JAL-3748 -->CDS shown in result of submitting proteins
450 in a CDS/Protein alignment to a web service is wrong when
451 proteins share a common transcript sequence (e.g.
452 genome of RNA viruses)
455 <!-- JAL-3576 -->Co-located features exported and re-imported
456 are ordered differently when shown on alignment and in
457 tooltips. (Also affects v2.11.1.0)
460 <!-- JAL-3702 -->Drag and drop of alignment file onto
461 alignment window when in a HiDPI scaled mode in Linux only
462 works for the top left quadrant of the alignment window
465 <!-- JAL-3701 -->Stale build data in jalview standalone jar
466 builds (only affects 2.11.1.1 branch)
469 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
470 when alignment view restored from project (since Jalview 2.11.0)
473 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
474 protein products for certain ENA records are repeatedly
475 shown via Calculate->Show Cross Refs
481 <td width="60" align="center" nowrap><strong><a
482 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
483 <em>22/04/2020</em></strong></td>
484 <td align="left" valign="top">
487 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
488 'virtual' codon features shown on protein (or vice versa)
489 for display in alignments, on structure views (including
490 transfer to UCSF chimera), in feature reports and for
494 <!-- JAL-3121 -->Feature attributes from VCF files can be
495 exported and re-imported as GFF3 files
498 <!-- JAL-3376 -->Capture VCF "fixed column" values
499 POS, ID, QUAL, FILTER as Feature Attributes
502 <!-- JAL-3375 -->More robust VCF numeric data field
503 validation while parsing
506 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
510 <!-- JAL-3535 -->Feature Settings dialog title includes name
514 <!-- JAL-3538 -->Font anti-aliasing in alignment views
518 <!-- JAL-3468 -->Very long feature descriptions truncated in
522 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
523 with no feature types visible
526 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
528 </ul><em>Jalview Installer</em>
531 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
532 in console (may be null when Jalview launched as executable jar or via conda)
535 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
538 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
541 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
543 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
544 </ul> <em>Release processes</em>
547 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
550 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
552 </ul> <em>Build System</em>
555 <!-- JAL-3510 -->Clover updated to 4.4.1
558 <!-- JAL-3513 -->Test code included in Clover coverage
562 <em>Groovy Scripts</em>
565 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
566 to stdout containing the consensus sequence for each
567 alignment in a Jalview session
570 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
571 genomic sequence_variant annotation from CDS as
572 missense_variant or synonymous_variant on protein products.
576 <td align="left" valign="top">
579 <!-- JAL-3581 -->Hidden sequence markers still visible when
580 'Show hidden markers' option is not ticked
583 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
584 PNG output when 'Automatically set ID width' is set in
585 jalview preferences or properties file
588 <!-- JAL-3571 -->Feature Editor dialog can be opened when
589 'Show Sequence Features' option is not ticked
592 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
593 buttons in Feature Settings dialog are clicked when no
597 <!-- JAL-3412 -->ID margins for CDS and Protein views not
598 equal when split frame is first opened
601 <!-- JAL-3296 -->Sequence position numbers in status bar not
602 correct after editing a sequence's start position
605 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
606 with annotation and exceptions thrown when only a few
607 columns shown in wrapped mode
610 <!-- JAL-3386 -->Sequence IDs missing in headless export of
611 wrapped alignment figure with annotations
614 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
615 ID fails with ClassCastException
618 <!-- JAL-3389 -->Chimera session not restored from Jalview
622 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
623 feature settings dialog also selects columns
626 <!-- JAL-3473 -->SpinnerNumberModel causes
627 IllegalArgumentException in some circumstances
630 <!-- JAL-3534 -->Multiple feature settings dialogs can be
634 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
635 alignment window is closed
638 <!-- JAL-3406 -->Credits missing some authors in Jalview
639 help documentation for 2.11.0 release
642 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
643 includes Pfam ID as sequence's accession rather than its
646 </ul> <em>Java 11 Compatibility issues</em>
649 <!-- JAL-2987 -->OSX - Can't view some search results in
650 PDB/Uniprot search panel
652 </ul> <em>Installer</em>
655 <!-- JAL-3447 -->Jalview should not create file associations
656 for 3D structure files (.pdb, .mmcif. .cif)
658 </ul> <em>Repository and Source Release</em>
661 <!-- JAL-3474 -->removed obsolete .cvsignore files from
665 <!-- JAL-3541 -->Clover report generation running out of
668 </ul> <em>New Known Issues</em>
671 <!-- JAL-3523 -->OSX - Current working directory not
672 preserved when Jalview.app launched with parameters from
676 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
677 clipped in headless figure export when Right Align option
681 <!-- JAL-3542 -->Jalview Installation type always reports
682 'Source' in console output
685 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
686 bamboo server but run fine locally.
692 <td width="60" align="center" nowrap>
693 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
694 <em>04/07/2019</em></strong>
696 <td align="left" valign="top">
699 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
700 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
701 source project) rather than InstallAnywhere
704 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
705 settings, receive over the air updates and launch specific
706 versions via (<a href="https://github.com/threerings/getdown">Three
710 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
711 formats supported by Jalview (including .jvp project files)
714 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
715 arguments and switch between different getdown channels
718 <!-- JAL-3141 -->Backup files created when saving Jalview project
723 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
724 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
726 <!-- JAL-2620 -->Alternative genetic code tables for
727 'Translate as cDNA'</li>
729 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
730 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
733 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
734 implementation that allows updates) used for Sequence Feature collections</li>
736 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
737 features can be filtered and shaded according to any
738 associated attributes (e.g. variant attributes from VCF
739 file, or key-value pairs imported from column 9 of GFF
743 <!-- JAL-2879 -->Feature Attributes and shading schemes
744 stored and restored from Jalview Projects
747 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
748 recognise variant features
751 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
752 sequences (also coloured red by default)
755 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
759 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
760 algorithm (Z-sort/transparency and filter aware)
763 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
769 <!-- JAL-3205 -->Symmetric score matrices for faster
770 tree and PCA calculations
772 <li><strong>Principal Components Analysis Viewer</strong>
775 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
776 and Viewer state saved in Jalview Project
778 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
781 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
785 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
790 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
792 <li><strong>Speed and Efficiency</strong>
795 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
796 multiple groups when working with large alignments
799 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
803 <li><strong>User Interface</strong>
806 <!-- JAL-2933 -->Finder panel remembers last position in each
810 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
811 what is shown)<br />Only visible regions of alignment are shown by
812 default (can be changed in user preferences)
815 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
816 to the Overwrite Dialog
819 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
823 <!-- JAL-1244 -->Status bar shows bounds when dragging a
824 selection region, and gap count when inserting or deleting gaps
827 <!-- JAL-3132 -->Status bar updates over sequence and annotation
831 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
835 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
839 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
842 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
846 <!-- JAL-3181 -->Consistent ordering of links in sequence id
850 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
852 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
856 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
857 <li><strong>Java 11 Support (not yet on general release)</strong>
860 <!-- -->OSX GUI integrations for App menu's 'About' entry and
865 <em>Deprecations</em>
867 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
868 capabilities removed from the Jalview Desktop
870 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
871 unmarshalling has been replaced by JAXB for Jalview projects
872 and XML based data retrieval clients</li>
873 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
874 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
875 </ul> <em>Documentation</em>
877 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
878 not supported in EPS figure export
880 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
881 </ul> <em>Development and Release Processes</em>
884 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
887 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
889 <!-- JAL-3225 -->Eclipse project configuration managed with
893 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
894 Bamboo continuous integration for unattended Test Suite
898 <!-- JAL-2864 -->Memory test suite to detect leaks in common
902 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
906 <!-- JAL-3248 -->Developer documentation migrated to
907 markdown (with HTML rendering)
910 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
913 <!-- JAL-3289 -->New URLs for publishing development
918 <td align="left" valign="top">
921 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
924 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
925 superposition in Jmol fail on Windows
928 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
929 structures for sequences with lots of PDB structures
932 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
936 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
937 project involving multiple views
940 <!-- JAL-3164 -->Overview for complementary view in a linked
941 CDS/Protein alignment is not updated when Hide Columns by
942 Annotation dialog hides columns
945 <!-- JAL-3158 -->Selection highlighting in the complement of a
946 CDS/Protein alignment stops working after making a selection in
947 one view, then making another selection in the other view
950 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
954 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
955 Settings and Jalview Preferences panels
958 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
959 overview with large alignments
962 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
963 region if columns were selected by dragging right-to-left and the
964 mouse moved to the left of the first column
967 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
968 hidden column marker via scale popup menu
971 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
972 doesn't tell users the invalid URL
975 <!-- JAL-2816 -->Tooltips displayed for features filtered by
979 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
980 show cross references or Fetch Database References are shown in
984 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
985 peptide sequence (computed variant shown as p.Res.null)
988 <!-- JAL-2060 -->'Graduated colour' option not offered for
989 manually created features (where feature score is Float.NaN)
992 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
993 when columns are hidden
996 <!-- JAL-3082 -->Regular expression error for '(' in Select
997 Columns by Annotation description
1000 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
1001 out of Scale or Annotation Panel
1004 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
1008 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1012 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
1016 <!-- JAL-3002 -->Column display is out by one after Page Down,
1017 Page Up in wrapped mode
1020 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1023 <!-- JAL-2932 -->Finder searches in minimised alignments
1026 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
1027 on opening an alignment
1030 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
1034 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
1035 different groups in the alignment are selected
1038 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1042 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1046 <!-- JAL-3125 -->Value input for graduated feature colour
1047 threshold gets 'unrounded'
1050 <!-- JAL-2982 -->PCA image export doesn't respect background
1054 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1057 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1060 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1064 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1068 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1069 shown in complementary view
1072 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1073 without normalisation
1076 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1080 <!-- JAL-914 -->Help page can be opened twice
1083 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1085 </ul> <em>Editing</em>
1088 <!-- JAL-2822 -->Start and End should be updated when sequence
1089 data at beginning or end of alignment added/removed via 'Edit'
1093 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1094 relocate sequence features correctly when start of sequence is
1095 removed (Known defect since 2.10)
1098 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1099 dialog corrupts dataset sequence
1102 <!-- JAL-868 -->Structure colours not updated when associated tree
1103 repartitions the alignment view (Regression in 2.10.5)
1105 </ul> <em>Datamodel</em>
1108 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1109 sequence's End is greater than its length
1111 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1112 general release)</em>
1115 <!-- JAL-3288 -->Menus work properly in split-screen
1117 </ul> <em>New Known Defects</em>
1120 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1123 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1124 regions of protein alignment.
1127 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1128 is restored from a Jalview 2.11 project
1131 <!-- JAL-3213 -->Alignment panel height can be too small after
1135 <!-- JAL-3240 -->Display is incorrect after removing gapped
1136 columns within hidden columns
1139 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1140 window after dragging left to select columns to left of visible
1144 <!-- JAL-2876 -->Features coloured according to their description
1145 string and thresholded by score in earlier versions of Jalview are
1146 not shown as thresholded features in 2.11. To workaround please
1147 create a Score filter instead.
1150 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1152 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1155 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1156 alignments with multiple views can close views unexpectedly
1159 <em>Java 11 Specific defects</em>
1162 <!-- JAL-3235 -->Jalview Properties file is not sorted
1163 alphabetically when saved
1169 <td width="60" nowrap>
1170 <div align="center">
1171 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1174 <td><div align="left">
1178 <!-- JAL-3101 -->Default memory for Jalview webstart and
1179 InstallAnywhere increased to 1G.
1182 <!-- JAL-247 -->Hidden sequence markers and representative
1183 sequence bolding included when exporting alignment as EPS,
1184 SVG, PNG or HTML. <em>Display is configured via the
1185 Format menu, or for command-line use via a Jalview
1186 properties file.</em>
1189 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1190 API and sequence data now imported as JSON.
1193 <!-- JAL-3065 -->Change in recommended way of starting
1194 Jalview via a Java command line: add jars in lib directory
1195 to CLASSPATH, rather than via the deprecated java.ext.dirs
1199 <em>Development</em>
1202 <!-- JAL-3047 -->Support added to execute test suite
1203 instrumented with <a href="http://openclover.org/">Open
1208 <td><div align="left">
1212 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1213 row shown in Feredoxin Structure alignment view of example
1217 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1218 annotation displayed.
1221 <!-- JAL-3107 -->Group conservation/consensus not shown
1222 for newly created group when 'Apply to all groups'
1226 <!-- JAL-3087 -->Corrupted display when switching to
1227 wrapped mode when sequence panel's vertical scrollbar is
1231 <!-- JAL-3003 -->Alignment is black in exported EPS file
1232 when sequences are selected in exported view.</em>
1235 <!-- JAL-3059 -->Groups with different coloured borders
1236 aren't rendered with correct colour.
1239 <!-- JAL-3092 -->Jalview could hang when importing certain
1240 types of knotted RNA secondary structure.
1243 <!-- JAL-3095 -->Sequence highlight and selection in
1244 trimmed VARNA 2D structure is incorrect for sequences that
1248 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1249 annotation when columns are inserted into an alignment,
1250 and when exporting as Stockholm flatfile.
1253 <!-- JAL-3053 -->Jalview annotation rows containing upper
1254 and lower-case 'E' and 'H' do not automatically get
1255 treated as RNA secondary structure.
1258 <!-- JAL-3106 -->.jvp should be used as default extension
1259 (not .jar) when saving a Jalview project file.
1262 <!-- JAL-3105 -->Mac Users: closing a window correctly
1263 transfers focus to previous window on OSX
1266 <em>Java 10 Issues Resolved</em>
1269 <!-- JAL-2988 -->OSX - Can't save new files via the File
1270 or export menus by typing in a name into the Save dialog
1274 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1275 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1276 'look and feel' which has improved compatibility with the
1277 latest version of OSX.
1284 <td width="60" nowrap>
1285 <div align="center">
1286 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1287 <em>7/06/2018</em></strong>
1290 <td><div align="left">
1294 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1295 annotation retrieved from Uniprot
1298 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1299 onto the Jalview Desktop
1303 <td><div align="left">
1307 <!-- JAL-3017 -->Cannot import features with multiple
1308 variant elements (blocks import of some Uniprot records)
1311 <!-- JAL-2997 -->Clustal files with sequence positions in
1312 right-hand column parsed correctly
1315 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1316 not alignment area in exported graphic
1319 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1320 window has input focus
1323 <!-- JAL-2992 -->Annotation panel set too high when
1324 annotation added to view (Windows)
1327 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1328 network connectivity is poor
1331 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1332 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1333 the currently open URL and links from a page viewed in
1334 Firefox or Chrome on Windows is now fully supported. If
1335 you are using Edge, only links in the page can be
1336 dragged, and with Internet Explorer, only the currently
1337 open URL in the browser can be dropped onto Jalview.</em>
1340 <em>New Known Defects</em>
1342 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1347 <td width="60" nowrap>
1348 <div align="center">
1349 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1352 <td><div align="left">
1356 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1357 for disabling automatic superposition of multiple
1358 structures and open structures in existing views
1361 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1362 ID and annotation area margins can be click-dragged to
1366 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1370 <!-- JAL-2759 -->Improved performance for large alignments
1371 and lots of hidden columns
1374 <!-- JAL-2593 -->Improved performance when rendering lots
1375 of features (particularly when transparency is disabled)
1378 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1379 exchange of Jalview features and Chimera attributes made
1385 <td><div align="left">
1388 <!-- JAL-2899 -->Structure and Overview aren't updated
1389 when Colour By Annotation threshold slider is adjusted
1392 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1393 overlapping alignment panel
1396 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1400 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1401 improved: CDS not handled correctly if transcript has no
1405 <!-- JAL-2321 -->Secondary structure and temperature
1406 factor annotation not added to sequence when local PDB
1407 file associated with it by drag'n'drop or structure
1411 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1412 dialog doesn't import PDB files dropped on an alignment
1415 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1416 scroll bar doesn't work for some CDS/Protein views
1419 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1420 Java 1.8u153 onwards and Java 1.9u4+.
1423 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1424 columns in annotation row
1427 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1428 honored in batch mode
1431 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1432 for structures added to existing Jmol view
1435 <!-- JAL-2223 -->'View Mappings' includes duplicate
1436 entries after importing project with multiple views
1439 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1440 protein sequences via SIFTS from associated PDB entries
1441 with negative residue numbers or missing residues fails
1444 <!-- JAL-2952 -->Exception when shading sequence with negative
1445 Temperature Factor values from annotated PDB files (e.g.
1446 as generated by CONSURF)
1449 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1450 tooltip doesn't include a text description of mutation
1453 <!-- JAL-2922 -->Invert displayed features very slow when
1454 structure and/or overview windows are also shown
1457 <!-- JAL-2954 -->Selecting columns from highlighted regions
1458 very slow for alignments with large numbers of sequences
1461 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1462 with 'StringIndexOutOfBounds'
1465 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1466 platforms running Java 10
1469 <!-- JAL-2960 -->Adding a structure to existing structure
1470 view appears to do nothing because the view is hidden behind the alignment view
1476 <!-- JAL-2926 -->Copy consensus sequence option in applet
1477 should copy the group consensus when popup is opened on it
1483 <!-- JAL-2913 -->Fixed ID width preference is not respected
1486 <em>New Known Defects</em>
1489 <!-- JAL-2973 --> Exceptions occasionally raised when
1490 editing a large alignment and overview is displayed
1493 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1494 repeatedly after a series of edits even when the overview
1495 is no longer reflecting updates
1498 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1499 structures for protein subsequence (if 'Trim Retrieved
1500 Sequences' enabled) or Ensembl isoforms (Workaround in
1501 2.10.4 is to fail back to N&W mapping)
1504 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1505 option gives blank output
1512 <td width="60" nowrap>
1513 <div align="center">
1514 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1517 <td><div align="left">
1518 <ul><li>Updated Certum Codesigning Certificate
1519 (Valid till 30th November 2018)</li></ul></div></td>
1520 <td><div align="left">
1521 <em>Desktop</em><ul>
1523 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1524 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1525 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1526 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1527 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1528 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1529 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1535 <td width="60" nowrap>
1536 <div align="center">
1537 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1540 <td><div align="left">
1544 <!-- JAL-2446 -->Faster and more efficient management and
1545 rendering of sequence features
1548 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1549 429 rate limit request hander
1552 <!-- JAL-2773 -->Structure views don't get updated unless
1553 their colours have changed
1556 <!-- JAL-2495 -->All linked sequences are highlighted for
1557 a structure mousover (Jmol) or selection (Chimera)
1560 <!-- JAL-2790 -->'Cancel' button in progress bar for
1561 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1564 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1565 view from Ensembl locus cross-references
1568 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1572 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1573 feature can be disabled
1576 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1577 PDB easier retrieval of sequences for lists of IDs
1580 <!-- JAL-2758 -->Short names for sequences retrieved from
1586 <li>Groovy interpreter updated to 2.4.12</li>
1587 <li>Example groovy script for generating a matrix of
1588 percent identity scores for current alignment.</li>
1590 <em>Testing and Deployment</em>
1593 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1597 <td><div align="left">
1601 <!-- JAL-2643 -->Pressing tab after updating the colour
1602 threshold text field doesn't trigger an update to the
1606 <!-- JAL-2682 -->Race condition when parsing sequence ID
1610 <!-- JAL-2608 -->Overview windows are also closed when
1611 alignment window is closed
1614 <!-- JAL-2548 -->Export of features doesn't always respect
1618 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1619 takes a long time in Cursor mode
1625 <!-- JAL-2777 -->Structures with whitespace chainCode
1626 cannot be viewed in Chimera
1629 <!-- JAL-2728 -->Protein annotation panel too high in
1633 <!-- JAL-2757 -->Can't edit the query after the server
1634 error warning icon is shown in Uniprot and PDB Free Text
1638 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1641 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1644 <!-- JAL-2739 -->Hidden column marker in last column not
1645 rendered when switching back from Wrapped to normal view
1648 <!-- JAL-2768 -->Annotation display corrupted when
1649 scrolling right in unwapped alignment view
1652 <!-- JAL-2542 -->Existing features on subsequence
1653 incorrectly relocated when full sequence retrieved from
1657 <!-- JAL-2733 -->Last reported memory still shown when
1658 Desktop->Show Memory is unticked (OSX only)
1661 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1662 features of same type and group to be selected for
1666 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1667 alignments when hidden columns are present
1670 <!-- JAL-2392 -->Jalview freezes when loading and
1671 displaying several structures
1674 <!-- JAL-2732 -->Black outlines left after resizing or
1678 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1679 within the Jalview desktop on OSX
1682 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1683 when in wrapped alignment mode
1686 <!-- JAL-2636 -->Scale mark not shown when close to right
1687 hand end of alignment
1690 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1691 each selected sequence do not have correct start/end
1695 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1696 after canceling the Alignment Window's Font dialog
1699 <!-- JAL-2036 -->Show cross-references not enabled after
1700 restoring project until a new view is created
1703 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1704 URL links appears when only default EMBL-EBI link is
1705 configured (since 2.10.2b2)
1708 <!-- JAL-2775 -->Overview redraws whole window when box
1709 position is adjusted
1712 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1713 in a multi-chain structure when viewing alignment
1714 involving more than one chain (since 2.10)
1717 <!-- JAL-2811 -->Double residue highlights in cursor mode
1718 if new selection moves alignment window
1721 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1722 arrow key in cursor mode to pass hidden column marker
1725 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1726 that produces correctly annotated transcripts and products
1729 <!-- JAL-2776 -->Toggling a feature group after first time
1730 doesn't update associated structure view
1733 <em>Applet</em><br />
1736 <!-- JAL-2687 -->Concurrent modification exception when
1737 closing alignment panel
1740 <em>BioJSON</em><br />
1743 <!-- JAL-2546 -->BioJSON export does not preserve
1744 non-positional features
1747 <em>New Known Issues</em>
1750 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1751 sequence features correctly (for many previous versions of
1755 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1756 using cursor in wrapped panel other than top
1759 <!-- JAL-2791 -->Select columns containing feature ignores
1760 graduated colour threshold
1763 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1764 always preserve numbering and sequence features
1767 <em>Known Java 9 Issues</em>
1770 <!-- JAL-2902 -->Groovy Console very slow to open and is
1771 not responsive when entering characters (Webstart, Java
1778 <td width="60" nowrap>
1779 <div align="center">
1780 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1781 <em>2/10/2017</em></strong>
1784 <td><div align="left">
1785 <em>New features in Jalview Desktop</em>
1788 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1790 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1794 <td><div align="left">
1798 <td width="60" nowrap>
1799 <div align="center">
1800 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1801 <em>7/9/2017</em></strong>
1804 <td><div align="left">
1808 <!-- JAL-2588 -->Show gaps in overview window by colouring
1809 in grey (sequences used to be coloured grey, and gaps were
1813 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1817 <!-- JAL-2587 -->Overview updates immediately on increase
1818 in size and progress bar shown as higher resolution
1819 overview is recalculated
1824 <td><div align="left">
1828 <!-- JAL-2664 -->Overview window redraws every hidden
1829 column region row by row
1832 <!-- JAL-2681 -->duplicate protein sequences shown after
1833 retrieving Ensembl crossrefs for sequences from Uniprot
1836 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1837 format setting is unticked
1840 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1841 if group has show boxes format setting unticked
1844 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1845 autoscrolling whilst dragging current selection group to
1846 include sequences and columns not currently displayed
1849 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1850 assemblies are imported via CIF file
1853 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1854 displayed when threshold or conservation colouring is also
1858 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1862 <!-- JAL-2673 -->Jalview continues to scroll after
1863 dragging a selected region off the visible region of the
1867 <!-- JAL-2724 -->Cannot apply annotation based
1868 colourscheme to all groups in a view
1871 <!-- JAL-2511 -->IDs don't line up with sequences
1872 initially after font size change using the Font chooser or
1879 <td width="60" nowrap>
1880 <div align="center">
1881 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1884 <td><div align="left">
1885 <em>Calculations</em>
1889 <!-- JAL-1933 -->Occupancy annotation row shows number of
1890 ungapped positions in each column of the alignment.
1893 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1894 a calculation dialog box
1897 <!-- JAL-2379 -->Revised implementation of PCA for speed
1898 and memory efficiency (~30x faster)
1901 <!-- JAL-2403 -->Revised implementation of sequence
1902 similarity scores as used by Tree, PCA, Shading Consensus
1903 and other calculations
1906 <!-- JAL-2416 -->Score matrices are stored as resource
1907 files within the Jalview codebase
1910 <!-- JAL-2500 -->Trees computed on Sequence Feature
1911 Similarity may have different topology due to increased
1918 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1919 model for alignments and groups
1922 <!-- JAL-384 -->Custom shading schemes created via groovy
1929 <!-- JAL-2526 -->Efficiency improvements for interacting
1930 with alignment and overview windows
1933 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1937 <!-- JAL-2388 -->Hidden columns and sequences can be
1941 <!-- JAL-2611 -->Click-drag in visible area allows fine
1942 adjustment of visible position
1946 <em>Data import/export</em>
1949 <!-- JAL-2535 -->Posterior probability annotation from
1950 Stockholm files imported as sequence associated annotation
1953 <!-- JAL-2507 -->More robust per-sequence positional
1954 annotation input/output via stockholm flatfile
1957 <!-- JAL-2533 -->Sequence names don't include file
1958 extension when importing structure files without embedded
1959 names or PDB accessions
1962 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1963 format sequence substitution matrices
1966 <em>User Interface</em>
1969 <!-- JAL-2447 --> Experimental Features Checkbox in
1970 Desktop's Tools menu to hide or show untested features in
1974 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1975 via Overview or sequence motif search operations
1978 <!-- JAL-2547 -->Amend sequence features dialog box can be
1979 opened by double clicking gaps within sequence feature
1983 <!-- JAL-1476 -->Status bar message shown when not enough
1984 aligned positions were available to create a 3D structure
1988 <em>3D Structure</em>
1991 <!-- JAL-2430 -->Hidden regions in alignment views are not
1992 coloured in linked structure views
1995 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1996 file-based command exchange
1999 <!-- JAL-2375 -->Structure chooser automatically shows
2000 Cached Structures rather than querying the PDBe if
2001 structures are already available for sequences
2004 <!-- JAL-2520 -->Structures imported via URL are cached in
2005 the Jalview project rather than downloaded again when the
2006 project is reopened.
2009 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2010 to transfer Chimera's structure attributes as Jalview
2011 features, and vice-versa (<strong>Experimental
2015 <em>Web Services</em>
2018 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2021 <!-- JAL-2335 -->Filter non-standard amino acids and
2022 nucleotides when submitting to AACon and other MSA
2026 <!-- JAL-2316, -->URLs for viewing database
2027 cross-references provided by identifiers.org and the
2028 EMBL-EBI's MIRIAM DB
2035 <!-- JAL-2344 -->FileFormatI interface for describing and
2036 identifying file formats (instead of String constants)
2039 <!-- JAL-2228 -->FeatureCounter script refactored for
2040 efficiency when counting all displayed features (not
2041 backwards compatible with 2.10.1)
2044 <em>Example files</em>
2047 <!-- JAL-2631 -->Graduated feature colour style example
2048 included in the example feature file
2051 <em>Documentation</em>
2054 <!-- JAL-2339 -->Release notes reformatted for readability
2055 with the built-in Java help viewer
2058 <!-- JAL-1644 -->Find documentation updated with 'search
2059 sequence description' option
2065 <!-- JAL-2485, -->External service integration tests for
2066 Uniprot REST Free Text Search Client
2069 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2072 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2077 <td><div align="left">
2078 <em>Calculations</em>
2081 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2082 matrix - C->R should be '-3'<br />Old matrix restored
2083 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2085 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2086 Jalview's treatment of gaps in PCA and substitution matrix
2087 based Tree calculations.<br /> <br />In earlier versions
2088 of Jalview, gaps matching gaps were penalised, and gaps
2089 matching non-gaps penalised even more. In the PCA
2090 calculation, gaps were actually treated as non-gaps - so
2091 different costs were applied, which meant Jalview's PCAs
2092 were different to those produced by SeqSpace.<br />Jalview
2093 now treats gaps in the same way as SeqSpace (ie it scores
2094 them as 0). <br /> <br />Enter the following in the
2095 Groovy console to restore pre-2.10.2 behaviour:<br />
2096 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2097 // for 2.10.1 mode <br />
2098 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2099 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2100 these settings will affect all subsequent tree and PCA
2101 calculations (not recommended)</em></li>
2103 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2104 scaling of branch lengths for trees computed using
2105 Sequence Feature Similarity.
2108 <!-- JAL-2377 -->PCA calculation could hang when
2109 generating output report when working with highly
2110 redundant alignments
2113 <!-- JAL-2544 --> Sort by features includes features to
2114 right of selected region when gaps present on right-hand
2118 <em>User Interface</em>
2121 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2122 doesn't reselect a specific sequence's associated
2123 annotation after it was used for colouring a view
2126 <!-- JAL-2419 -->Current selection lost if popup menu
2127 opened on a region of alignment without groups
2130 <!-- JAL-2374 -->Popup menu not always shown for regions
2131 of an alignment with overlapping groups
2134 <!-- JAL-2310 -->Finder double counts if both a sequence's
2135 name and description match
2138 <!-- JAL-2370 -->Hiding column selection containing two
2139 hidden regions results in incorrect hidden regions
2142 <!-- JAL-2386 -->'Apply to all groups' setting when
2143 changing colour does not apply Conservation slider value
2147 <!-- JAL-2373 -->Percentage identity and conservation menu
2148 items do not show a tick or allow shading to be disabled
2151 <!-- JAL-2385 -->Conservation shading or PID threshold
2152 lost when base colourscheme changed if slider not visible
2155 <!-- JAL-2547 -->Sequence features shown in tooltip for
2156 gaps before start of features
2159 <!-- JAL-2623 -->Graduated feature colour threshold not
2160 restored to UI when feature colour is edited
2163 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2164 a time when scrolling vertically in wrapped mode.
2167 <!-- JAL-2630 -->Structure and alignment overview update
2168 as graduate feature colour settings are modified via the
2172 <!-- JAL-2034 -->Overview window doesn't always update
2173 when a group defined on the alignment is resized
2176 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2177 wrapped view result in positional status updates
2181 <!-- JAL-2563 -->Status bar doesn't show position for
2182 ambiguous amino acid and nucleotide symbols
2185 <!-- JAL-2602 -->Copy consensus sequence failed if
2186 alignment included gapped columns
2189 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2190 widgets don't permanently disappear
2193 <!-- JAL-2503 -->Cannot select or filter quantitative
2194 annotation that are shown only as column labels (e.g.
2195 T-Coffee column reliability scores)
2198 <!-- JAL-2594 -->Exception thrown if trying to create a
2199 sequence feature on gaps only
2202 <!-- JAL-2504 -->Features created with 'New feature'
2203 button from a Find inherit previously defined feature type
2204 rather than the Find query string
2207 <!-- JAL-2423 -->incorrect title in output window when
2208 exporting tree calculated in Jalview
2211 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2212 and then revealing them reorders sequences on the
2216 <!-- JAL-964 -->Group panel in sequence feature settings
2217 doesn't update to reflect available set of groups after
2218 interactively adding or modifying features
2221 <!-- JAL-2225 -->Sequence Database chooser unusable on
2225 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2226 only excluded gaps in current sequence and ignored
2233 <!-- JAL-2421 -->Overview window visible region moves
2234 erratically when hidden rows or columns are present
2237 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2238 Structure Viewer's colour menu don't correspond to
2242 <!-- JAL-2405 -->Protein specific colours only offered in
2243 colour and group colour menu for protein alignments
2246 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2247 reflect currently selected view or group's shading
2251 <!-- JAL-2624 -->Feature colour thresholds not respected
2252 when rendered on overview and structures when opacity at
2256 <!-- JAL-2589 -->User defined gap colour not shown in
2257 overview when features overlaid on alignment
2260 <!-- JAL-2567 -->Feature settings for different views not
2261 recovered correctly from Jalview project file
2264 <!-- JAL-2256 -->Feature colours in overview when first opened
2265 (automatically via preferences) are different to the main
2269 <em>Data import/export</em>
2272 <!-- JAL-2576 -->Very large alignments take a long time to
2276 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2277 added after a sequence was imported are not written to
2281 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2282 when importing RNA secondary structure via Stockholm
2285 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2286 not shown in correct direction for simple pseudoknots
2289 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2290 with lightGray or darkGray via features file (but can
2294 <!-- JAL-2383 -->Above PID colour threshold not recovered
2295 when alignment view imported from project
2298 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2299 structure and sequences extracted from structure files
2300 imported via URL and viewed in Jmol
2303 <!-- JAL-2520 -->Structures loaded via URL are saved in
2304 Jalview Projects rather than fetched via URL again when
2305 the project is loaded and the structure viewed
2308 <em>Web Services</em>
2311 <!-- JAL-2519 -->EnsemblGenomes example failing after
2312 release of Ensembl v.88
2315 <!-- JAL-2366 -->Proxy server address and port always
2316 appear enabled in Preferences->Connections
2319 <!-- JAL-2461 -->DAS registry not found exceptions
2320 removed from console output
2323 <!-- JAL-2582 -->Cannot retrieve protein products from
2324 Ensembl by Peptide ID
2327 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2328 created from SIFTs, and spurious 'Couldn't open structure
2329 in Chimera' errors raised after April 2017 update (problem
2330 due to 'null' string rather than empty string used for
2331 residues with no corresponding PDB mapping).
2334 <em>Application UI</em>
2337 <!-- JAL-2361 -->User Defined Colours not added to Colour
2341 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2342 case' residues (button in colourscheme editor debugged and
2343 new documentation and tooltips added)
2346 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2347 doesn't restore group-specific text colour thresholds
2350 <!-- JAL-2243 -->Feature settings panel does not update as
2351 new features are added to alignment
2354 <!-- JAL-2532 -->Cancel in feature settings reverts
2355 changes to feature colours via the Amend features dialog
2358 <!-- JAL-2506 -->Null pointer exception when attempting to
2359 edit graduated feature colour via amend features dialog
2363 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2364 selection menu changes colours of alignment views
2367 <!-- JAL-2426 -->Spurious exceptions in console raised
2368 from alignment calculation workers after alignment has
2372 <!-- JAL-1608 -->Typo in selection popup menu - Create
2373 groups now 'Create Group'
2376 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2377 Create/Undefine group doesn't always work
2380 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2381 shown again after pressing 'Cancel'
2384 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2385 adjusts start position in wrap mode
2388 <!-- JAL-2563 -->Status bar doesn't show positions for
2389 ambiguous amino acids
2392 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2393 CDS/Protein view after CDS sequences added for aligned
2397 <!-- JAL-2592 -->User defined colourschemes called 'User
2398 Defined' don't appear in Colours menu
2404 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2405 score models doesn't always result in an updated PCA plot
2408 <!-- JAL-2442 -->Features not rendered as transparent on
2409 overview or linked structure view
2412 <!-- JAL-2372 -->Colour group by conservation doesn't
2416 <!-- JAL-2517 -->Hitting Cancel after applying
2417 user-defined colourscheme doesn't restore original
2424 <!-- JAL-2314 -->Unit test failure:
2425 jalview.ws.jabaws.RNAStructExportImport setup fails
2428 <!-- JAL-2307 -->Unit test failure:
2429 jalview.ws.sifts.SiftsClientTest due to compatibility
2430 problems with deep array comparison equality asserts in
2431 successive versions of TestNG
2434 <!-- JAL-2479 -->Relocated StructureChooserTest and
2435 ParameterUtilsTest Unit tests to Network suite
2438 <em>New Known Issues</em>
2441 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2442 phase after a sequence motif find operation
2445 <!-- JAL-2550 -->Importing annotation file with rows
2446 containing just upper and lower case letters are
2447 interpreted as WUSS RNA secondary structure symbols
2450 <!-- JAL-2590 -->Cannot load and display Newick trees
2451 reliably from eggnog Ortholog database
2454 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2455 containing features of type Highlight' when 'B' is pressed
2456 to mark columns containing highlighted regions.
2459 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2460 doesn't always add secondary structure annotation.
2465 <td width="60" nowrap>
2466 <div align="center">
2467 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2470 <td><div align="left">
2474 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2475 for all consensus calculations
2478 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2481 <li>Updated Jalview's Certum code signing certificate
2484 <em>Application</em>
2487 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2488 set of database cross-references, sorted alphabetically
2491 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2492 from database cross references. Users with custom links
2493 will receive a <a href="webServices/urllinks.html#warning">warning
2494 dialog</a> asking them to update their preferences.
2497 <!-- JAL-2287-->Cancel button and escape listener on
2498 dialog warning user about disconnecting Jalview from a
2502 <!-- JAL-2320-->Jalview's Chimera control window closes if
2503 the Chimera it is connected to is shut down
2506 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2507 columns menu item to mark columns containing highlighted
2508 regions (e.g. from structure selections or results of a
2512 <!-- JAL-2284-->Command line option for batch-generation
2513 of HTML pages rendering alignment data with the BioJS
2523 <!-- JAL-2286 -->Columns with more than one modal residue
2524 are not coloured or thresholded according to percent
2525 identity (first observed in Jalview 2.8.2)
2528 <!-- JAL-2301 -->Threonine incorrectly reported as not
2532 <!-- JAL-2318 -->Updates to documentation pages (above PID
2533 threshold, amino acid properties)
2536 <!-- JAL-2292 -->Lower case residues in sequences are not
2537 reported as mapped to residues in a structure file in the
2541 <!--JAL-2324 -->Identical features with non-numeric scores
2542 could be added multiple times to a sequence
2545 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2546 bond features shown as two highlighted residues rather
2547 than a range in linked structure views, and treated
2548 correctly when selecting and computing trees from features
2551 <!-- JAL-2281-->Custom URL links for database
2552 cross-references are matched to database name regardless
2557 <em>Application</em>
2560 <!-- JAL-2282-->Custom URL links for specific database
2561 names without regular expressions also offer links from
2565 <!-- JAL-2315-->Removing a single configured link in the
2566 URL links pane in Connections preferences doesn't actually
2567 update Jalview configuration
2570 <!-- JAL-2272-->CTRL-Click on a selected region to open
2571 the alignment area popup menu doesn't work on El-Capitan
2574 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2575 files with similarly named sequences if dropped onto the
2579 <!-- JAL-2312 -->Additional mappings are shown for PDB
2580 entries where more chains exist in the PDB accession than
2581 are reported in the SIFTS file
2584 <!-- JAL-2317-->Certain structures do not get mapped to
2585 the structure view when displayed with Chimera
2588 <!-- JAL-2317-->No chains shown in the Chimera view
2589 panel's View->Show Chains submenu
2592 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2593 work for wrapped alignment views
2596 <!--JAL-2197 -->Rename UI components for running JPred
2597 predictions from 'JNet' to 'JPred'
2600 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2601 corrupted when annotation panel vertical scroll is not at
2602 first annotation row
2605 <!--JAL-2332 -->Attempting to view structure for Hen
2606 lysozyme results in a PDB Client error dialog box
2609 <!-- JAL-2319 -->Structure View's mapping report switched
2610 ranges for PDB and sequence for SIFTS
2613 SIFTS 'Not_Observed' residues mapped to non-existant
2617 <!-- <em>New Known Issues</em>
2624 <td width="60" nowrap>
2625 <div align="center">
2626 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2627 <em>25/10/2016</em></strong>
2630 <td><em>Application</em>
2632 <li>3D Structure chooser opens with 'Cached structures'
2633 view if structures already loaded</li>
2634 <li>Progress bar reports models as they are loaded to
2635 structure views</li>
2641 <li>Colour by conservation always enabled and no tick
2642 shown in menu when BLOSUM or PID shading applied</li>
2643 <li>FER1_ARATH and FER2_ARATH labels were switched in
2644 example sequences/projects/trees</li>
2646 <em>Application</em>
2648 <li>Jalview projects with views of local PDB structure
2649 files saved on Windows cannot be opened on OSX</li>
2650 <li>Multiple structure views can be opened and superposed
2651 without timeout for structures with multiple models or
2652 multiple sequences in alignment</li>
2653 <li>Cannot import or associated local PDB files without a
2654 PDB ID HEADER line</li>
2655 <li>RMSD is not output in Jmol console when superposition
2657 <li>Drag and drop of URL from Browser fails for Linux and
2658 OSX versions earlier than El Capitan</li>
2659 <li>ENA client ignores invalid content from ENA server</li>
2660 <li>Exceptions are not raised in console when ENA client
2661 attempts to fetch non-existent IDs via Fetch DB Refs UI
2663 <li>Exceptions are not raised in console when a new view
2664 is created on the alignment</li>
2665 <li>OSX right-click fixed for group selections: CMD-click
2666 to insert/remove gaps in groups and CTRL-click to open group
2669 <em>Build and deployment</em>
2671 <li>URL link checker now copes with multi-line anchor
2674 <em>New Known Issues</em>
2676 <li>Drag and drop from URL links in browsers do not work
2683 <td width="60" nowrap>
2684 <div align="center">
2685 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2688 <td><em>General</em>
2691 <!-- JAL-2124 -->Updated Spanish translations.
2694 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2695 for importing structure data to Jalview. Enables mmCIF and
2699 <!-- JAL-192 --->Alignment ruler shows positions relative to
2703 <!-- JAL-2202 -->Position/residue shown in status bar when
2704 mousing over sequence associated annotation
2707 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2711 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2712 '()', canonical '[]' and invalid '{}' base pair populations
2716 <!-- JAL-2092 -->Feature settings popup menu options for
2717 showing or hiding columns containing a feature
2720 <!-- JAL-1557 -->Edit selected group by double clicking on
2721 group and sequence associated annotation labels
2724 <!-- JAL-2236 -->Sequence name added to annotation label in
2725 select/hide columns by annotation and colour by annotation
2729 </ul> <em>Application</em>
2732 <!-- JAL-2050-->Automatically hide introns when opening a
2733 gene/transcript view
2736 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2740 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2741 structure mappings with the EMBL-EBI PDBe SIFTS database
2744 <!-- JAL-2079 -->Updated download sites used for Rfam and
2745 Pfam sources to xfam.org
2748 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2751 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2752 over sequences in Jalview
2755 <!-- JAL-2027-->Support for reverse-complement coding
2756 regions in ENA and EMBL
2759 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2760 for record retrieval via ENA rest API
2763 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2767 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2768 groovy script execution
2771 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2772 alignment window's Calculate menu
2775 <!-- JAL-1812 -->Allow groovy scripts that call
2776 Jalview.getAlignFrames() to run in headless mode
2779 <!-- JAL-2068 -->Support for creating new alignment
2780 calculation workers from groovy scripts
2783 <!-- JAL-1369 --->Store/restore reference sequence in
2787 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2788 associations are now saved/restored from project
2791 <!-- JAL-1993 -->Database selection dialog always shown
2792 before sequence fetcher is opened
2795 <!-- JAL-2183 -->Double click on an entry in Jalview's
2796 database chooser opens a sequence fetcher
2799 <!-- JAL-1563 -->Free-text search client for UniProt using
2800 the UniProt REST API
2803 <!-- JAL-2168 -->-nonews command line parameter to prevent
2804 the news reader opening
2807 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2808 querying stored in preferences
2811 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2815 <!-- JAL-1977-->Tooltips shown on database chooser
2818 <!-- JAL-391 -->Reverse complement function in calculate
2819 menu for nucleotide sequences
2822 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2823 and feature counts preserves alignment ordering (and
2824 debugged for complex feature sets).
2827 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2828 viewing structures with Jalview 2.10
2831 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2832 genome, transcript CCDS and gene ids via the Ensembl and
2833 Ensembl Genomes REST API
2836 <!-- JAL-2049 -->Protein sequence variant annotation
2837 computed for 'sequence_variant' annotation on CDS regions
2841 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2845 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2846 Ref Fetcher fails to match, or otherwise updates sequence
2847 data from external database records.
2850 <!-- JAL-2154 -->Revised Jalview Project format for
2851 efficient recovery of sequence coding and alignment
2852 annotation relationships.
2854 </ul> <!-- <em>Applet</em>
2865 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2869 <!-- JAL-2018-->Export features in Jalview format (again)
2870 includes graduated colourschemes
2873 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2874 working with big alignments and lots of hidden columns
2877 <!-- JAL-2053-->Hidden column markers not always rendered
2878 at right of alignment window
2881 <!-- JAL-2067 -->Tidied up links in help file table of
2885 <!-- JAL-2072 -->Feature based tree calculation not shown
2889 <!-- JAL-2075 -->Hidden columns ignored during feature
2890 based tree calculation
2893 <!-- JAL-2065 -->Alignment view stops updating when show
2894 unconserved enabled for group on alignment
2897 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2901 <!-- JAL-2146 -->Alignment column in status incorrectly
2902 shown as "Sequence position" when mousing over
2906 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2907 hidden columns present
2910 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2911 user created annotation added to alignment
2914 <!-- JAL-1841 -->RNA Structure consensus only computed for
2915 '()' base pair annotation
2918 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2919 in zero scores for all base pairs in RNA Structure
2923 <!-- JAL-2174-->Extend selection with columns containing
2927 <!-- JAL-2275 -->Pfam format writer puts extra space at
2928 beginning of sequence
2931 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2935 <!-- JAL-2238 -->Cannot create groups on an alignment from
2936 from a tree when t-coffee scores are shown
2939 <!-- JAL-1836,1967 -->Cannot import and view PDB
2940 structures with chains containing negative resnums (4q4h)
2943 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2947 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2948 to Clustal, PIR and PileUp output
2951 <!-- JAL-2008 -->Reordering sequence features that are
2952 not visible causes alignment window to repaint
2955 <!-- JAL-2006 -->Threshold sliders don't work in
2956 graduated colour and colour by annotation row for e-value
2957 scores associated with features and annotation rows
2960 <!-- JAL-1797 -->amino acid physicochemical conservation
2961 calculation should be case independent
2964 <!-- JAL-2173 -->Remove annotation also updates hidden
2968 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2969 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2970 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2973 <!-- JAL-2065 -->Null pointer exceptions and redraw
2974 problems when reference sequence defined and 'show
2975 non-conserved' enabled
2978 <!-- JAL-1306 -->Quality and Conservation are now shown on
2979 load even when Consensus calculation is disabled
2982 <!-- JAL-1932 -->Remove right on penultimate column of
2983 alignment does nothing
2986 <em>Application</em>
2989 <!-- JAL-1552-->URLs and links can't be imported by
2990 drag'n'drop on OSX when launched via webstart (note - not
2991 yet fixed for El Capitan)
2994 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2995 output when running on non-gb/us i18n platforms
2998 <!-- JAL-1944 -->Error thrown when exporting a view with
2999 hidden sequences as flat-file alignment
3002 <!-- JAL-2030-->InstallAnywhere distribution fails when
3006 <!-- JAL-2080-->Jalview very slow to launch via webstart
3007 (also hotfix for 2.9.0b2)
3010 <!-- JAL-2085 -->Cannot save project when view has a
3011 reference sequence defined
3014 <!-- JAL-1011 -->Columns are suddenly selected in other
3015 alignments and views when revealing hidden columns
3018 <!-- JAL-1989 -->Hide columns not mirrored in complement
3019 view in a cDNA/Protein splitframe
3022 <!-- JAL-1369 -->Cannot save/restore representative
3023 sequence from project when only one sequence is
3027 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3028 in Structure Chooser
3031 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3032 structure consensus didn't refresh annotation panel
3035 <!-- JAL-1962 -->View mapping in structure view shows
3036 mappings between sequence and all chains in a PDB file
3039 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3040 dialogs format columns correctly, don't display array
3041 data, sort columns according to type
3044 <!-- JAL-1975 -->Export complete shown after destination
3045 file chooser is cancelled during an image export
3048 <!-- JAL-2025 -->Error when querying PDB Service with
3049 sequence name containing special characters
3052 <!-- JAL-2024 -->Manual PDB structure querying should be
3056 <!-- JAL-2104 -->Large tooltips with broken HTML
3057 formatting don't wrap
3060 <!-- JAL-1128 -->Figures exported from wrapped view are
3061 truncated so L looks like I in consensus annotation
3064 <!-- JAL-2003 -->Export features should only export the
3065 currently displayed features for the current selection or
3069 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3070 after fetching cross-references, and restoring from
3074 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3075 followed in the structure viewer
3078 <!-- JAL-2163 -->Titles for individual alignments in
3079 splitframe not restored from project
3082 <!-- JAL-2145 -->missing autocalculated annotation at
3083 trailing end of protein alignment in transcript/product
3084 splitview when pad-gaps not enabled by default
3087 <!-- JAL-1797 -->amino acid physicochemical conservation
3091 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3092 article has been read (reopened issue due to
3093 internationalisation problems)
3096 <!-- JAL-1960 -->Only offer PDB structures in structure
3097 viewer based on sequence name, PDB and UniProt
3102 <!-- JAL-1976 -->No progress bar shown during export of
3106 <!-- JAL-2213 -->Structures not always superimposed after
3107 multiple structures are shown for one or more sequences.
3110 <!-- JAL-1370 -->Reference sequence characters should not
3111 be replaced with '.' when 'Show unconserved' format option
3115 <!-- JAL-1823 -->Cannot specify chain code when entering
3116 specific PDB id for sequence
3119 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3120 'Export hidden sequences' is enabled, but 'export hidden
3121 columns' is disabled.
3124 <!--JAL-2026-->Best Quality option in structure chooser
3125 selects lowest rather than highest resolution structures
3129 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3130 to sequence mapping in 'View Mappings' report
3133 <!-- JAL-2284 -->Unable to read old Jalview projects that
3134 contain non-XML data added after Jalvew wrote project.
3137 <!-- JAL-2118 -->Newly created annotation row reorders
3138 after clicking on it to create new annotation for a
3142 <!-- JAL-1980 -->Null Pointer Exception raised when
3143 pressing Add on an orphaned cut'n'paste window.
3145 <!-- may exclude, this is an external service stability issue JAL-1941
3146 -- > RNA 3D structure not added via DSSR service</li> -->
3151 <!-- JAL-2151 -->Incorrect columns are selected when
3152 hidden columns present before start of sequence
3155 <!-- JAL-1986 -->Missing dependencies on applet pages
3159 <!-- JAL-1947 -->Overview pixel size changes when
3160 sequences are hidden in applet
3163 <!-- JAL-1996 -->Updated instructions for applet
3164 deployment on examples pages.
3171 <td width="60" nowrap>
3172 <div align="center">
3173 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3174 <em>16/10/2015</em></strong>
3177 <td><em>General</em>
3179 <li>Time stamps for signed Jalview application and applet
3184 <em>Application</em>
3186 <li>Duplicate group consensus and conservation rows
3187 shown when tree is partitioned</li>
3188 <li>Erratic behaviour when tree partitions made with
3189 multiple cDNA/Protein split views</li>
3195 <td width="60" nowrap>
3196 <div align="center">
3197 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3198 <em>8/10/2015</em></strong>
3201 <td><em>General</em>
3203 <li>Updated Spanish translations of localized text for
3205 </ul> <em>Application</em>
3207 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3208 <li>Signed OSX InstallAnywhere installer<br></li>
3209 <li>Support for per-sequence based annotations in BioJSON</li>
3210 </ul> <em>Applet</em>
3212 <li>Split frame example added to applet examples page</li>
3213 </ul> <em>Build and Deployment</em>
3216 <!-- JAL-1888 -->New ant target for running Jalview's test
3224 <li>Mapping of cDNA to protein in split frames
3225 incorrect when sequence start > 1</li>
3226 <li>Broken images in filter column by annotation dialog
3228 <li>Feature colours not parsed from features file</li>
3229 <li>Exceptions and incomplete link URLs recovered when
3230 loading a features file containing HTML tags in feature
3234 <em>Application</em>
3236 <li>Annotations corrupted after BioJS export and
3238 <li>Incorrect sequence limits after Fetch DB References
3239 with 'trim retrieved sequences'</li>
3240 <li>Incorrect warning about deleting all data when
3241 deleting selected columns</li>
3242 <li>Patch to build system for shipping properly signed
3243 JNLP templates for webstart launch</li>
3244 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3245 unreleased structures for download or viewing</li>
3246 <li>Tab/space/return keystroke operation of EMBL-PDBe
3247 fetcher/viewer dialogs works correctly</li>
3248 <li>Disabled 'minimise' button on Jalview windows
3249 running on OSX to workaround redraw hang bug</li>
3250 <li>Split cDNA/Protein view position and geometry not
3251 recovered from jalview project</li>
3252 <li>Initial enabled/disabled state of annotation menu
3253 sorter 'show autocalculated first/last' corresponds to
3255 <li>Restoring of Clustal, RNA Helices and T-Coffee
3256 color schemes from BioJSON</li>
3260 <li>Reorder sequences mirrored in cDNA/Protein split
3262 <li>Applet with Jmol examples not loading correctly</li>
3268 <td><div align="center">
3269 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3271 <td><em>General</em>
3273 <li>Linked visualisation and analysis of DNA and Protein
3276 <li>Translated cDNA alignments shown as split protein
3277 and DNA alignment views</li>
3278 <li>Codon consensus annotation for linked protein and
3279 cDNA alignment views</li>
3280 <li>Link cDNA or Protein product sequences by loading
3281 them onto Protein or cDNA alignments</li>
3282 <li>Reconstruct linked cDNA alignment from aligned
3283 protein sequences</li>
3286 <li>Jmol integration updated to Jmol v14.2.14</li>
3287 <li>Import and export of Jalview alignment views as <a
3288 href="features/bioJsonFormat.html">BioJSON</a></li>
3289 <li>New alignment annotation file statements for
3290 reference sequences and marking hidden columns</li>
3291 <li>Reference sequence based alignment shading to
3292 highlight variation</li>
3293 <li>Select or hide columns according to alignment
3295 <li>Find option for locating sequences by description</li>
3296 <li>Conserved physicochemical properties shown in amino
3297 acid conservation row</li>
3298 <li>Alignments can be sorted by number of RNA helices</li>
3299 </ul> <em>Application</em>
3301 <li>New cDNA/Protein analysis capabilities
3303 <li>Get Cross-References should open a Split Frame
3304 view with cDNA/Protein</li>
3305 <li>Detect when nucleotide sequences and protein
3306 sequences are placed in the same alignment</li>
3307 <li>Split cDNA/Protein views are saved in Jalview
3312 <li>Use REST API to talk to Chimera</li>
3313 <li>Selected regions in Chimera are highlighted in linked
3314 Jalview windows</li>
3316 <li>VARNA RNA viewer updated to v3.93</li>
3317 <li>VARNA views are saved in Jalview Projects</li>
3318 <li>Pseudoknots displayed as Jalview RNA annotation can
3319 be shown in VARNA</li>
3321 <li>Make groups for selection uses marked columns as well
3322 as the active selected region</li>
3324 <li>Calculate UPGMA and NJ trees using sequence feature
3326 <li>New Export options
3328 <li>New Export Settings dialog to control hidden
3329 region export in flat file generation</li>
3331 <li>Export alignment views for display with the <a
3332 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3334 <li>Export scrollable SVG in HTML page</li>
3335 <li>Optional embedding of BioJSON data when exporting
3336 alignment figures to HTML</li>
3338 <li>3D structure retrieval and display
3340 <li>Free text and structured queries with the PDBe
3342 <li>PDBe Search API based discovery and selection of
3343 PDB structures for a sequence set</li>
3347 <li>JPred4 employed for protein secondary structure
3349 <li>Hide Insertions menu option to hide unaligned columns
3350 for one or a group of sequences</li>
3351 <li>Automatically hide insertions in alignments imported
3352 from the JPred4 web server</li>
3353 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3354 system on OSX<br />LGPL libraries courtesy of <a
3355 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3357 <li>changed 'View nucleotide structure' submenu to 'View
3358 VARNA 2D Structure'</li>
3359 <li>change "View protein structure" menu option to "3D
3362 </ul> <em>Applet</em>
3364 <li>New layout for applet example pages</li>
3365 <li>New parameters to enable SplitFrame view
3366 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3367 <li>New example demonstrating linked viewing of cDNA and
3368 Protein alignments</li>
3369 </ul> <em>Development and deployment</em>
3371 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3372 <li>Include installation type and git revision in build
3373 properties and console log output</li>
3374 <li>Jalview Github organisation, and new github site for
3375 storing BioJsMSA Templates</li>
3376 <li>Jalview's unit tests now managed with TestNG</li>
3379 <!-- <em>General</em>
3381 </ul> --> <!-- issues resolved --> <em>Application</em>
3383 <li>Escape should close any open find dialogs</li>
3384 <li>Typo in select-by-features status report</li>
3385 <li>Consensus RNA secondary secondary structure
3386 predictions are not highlighted in amber</li>
3387 <li>Missing gap character in v2.7 example file means
3388 alignment appears unaligned when pad-gaps is not enabled</li>
3389 <li>First switch to RNA Helices colouring doesn't colour
3390 associated structure views</li>
3391 <li>ID width preference option is greyed out when auto
3392 width checkbox not enabled</li>
3393 <li>Stopped a warning dialog from being shown when
3394 creating user defined colours</li>
3395 <li>'View Mapping' in structure viewer shows sequence
3396 mappings for just that viewer's sequences</li>
3397 <li>Workaround for superposing PDB files containing
3398 multiple models in Chimera</li>
3399 <li>Report sequence position in status bar when hovering
3400 over Jmol structure</li>
3401 <li>Cannot output gaps as '.' symbols with Selection ->
3402 output to text box</li>
3403 <li>Flat file exports of alignments with hidden columns
3404 have incorrect sequence start/end</li>
3405 <li>'Aligning' a second chain to a Chimera structure from
3407 <li>Colour schemes applied to structure viewers don't
3408 work for nucleotide</li>
3409 <li>Loading/cut'n'pasting an empty or invalid file leads
3410 to a grey/invisible alignment window</li>
3411 <li>Exported Jpred annotation from a sequence region
3412 imports to different position</li>
3413 <li>Space at beginning of sequence feature tooltips shown
3414 on some platforms</li>
3415 <li>Chimera viewer 'View | Show Chain' menu is not
3417 <li>'New View' fails with a Null Pointer Exception in
3418 console if Chimera has been opened</li>
3419 <li>Mouseover to Chimera not working</li>
3420 <li>Miscellaneous ENA XML feature qualifiers not
3422 <li>NPE in annotation renderer after 'Extract Scores'</li>
3423 <li>If two structures in one Chimera window, mouseover of
3424 either sequence shows on first structure</li>
3425 <li>'Show annotations' options should not make
3426 non-positional annotations visible</li>
3427 <li>Subsequence secondary structure annotation not shown
3428 in right place after 'view flanking regions'</li>
3429 <li>File Save As type unset when current file format is
3431 <li>Save as '.jar' option removed for saving Jalview
3433 <li>Colour by Sequence colouring in Chimera more
3435 <li>Cannot 'add reference annotation' for a sequence in
3436 several views on same alignment</li>
3437 <li>Cannot show linked products for EMBL / ENA records</li>
3438 <li>Jalview's tooltip wraps long texts containing no
3440 </ul> <em>Applet</em>
3442 <li>Jmol to JalviewLite mouseover/link not working</li>
3443 <li>JalviewLite can't import sequences with ID
3444 descriptions containing angle brackets</li>
3445 </ul> <em>General</em>
3447 <li>Cannot export and reimport RNA secondary structure
3448 via jalview annotation file</li>
3449 <li>Random helix colour palette for colour by annotation
3450 with RNA secondary structure</li>
3451 <li>Mouseover to cDNA from STOP residue in protein
3452 translation doesn't work.</li>
3453 <li>hints when using the select by annotation dialog box</li>
3454 <li>Jmol alignment incorrect if PDB file has alternate CA
3456 <li>FontChooser message dialog appears to hang after
3457 choosing 1pt font</li>
3458 <li>Peptide secondary structure incorrectly imported from
3459 annotation file when annotation display text includes 'e' or
3461 <li>Cannot set colour of new feature type whilst creating
3463 <li>cDNA translation alignment should not be sequence
3464 order dependent</li>
3465 <li>'Show unconserved' doesn't work for lower case
3467 <li>Nucleotide ambiguity codes involving R not recognised</li>
3468 </ul> <em>Deployment and Documentation</em>
3470 <li>Applet example pages appear different to the rest of
3471 www.jalview.org</li>
3472 </ul> <em>Application Known issues</em>
3474 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3475 <li>Misleading message appears after trying to delete
3477 <li>Jalview icon not shown in dock after InstallAnywhere
3478 version launches</li>
3479 <li>Fetching EMBL reference for an RNA sequence results
3480 fails with a sequence mismatch</li>
3481 <li>Corrupted or unreadable alignment display when
3482 scrolling alignment to right</li>
3483 <li>ArrayIndexOutOfBoundsException thrown when remove
3484 empty columns called on alignment with ragged gapped ends</li>
3485 <li>auto calculated alignment annotation rows do not get
3486 placed above or below non-autocalculated rows</li>
3487 <li>Jalview dekstop becomes sluggish at full screen in
3488 ultra-high resolution</li>
3489 <li>Cannot disable consensus calculation independently of
3490 quality and conservation</li>
3491 <li>Mouseover highlighting between cDNA and protein can
3492 become sluggish with more than one splitframe shown</li>
3493 </ul> <em>Applet Known Issues</em>
3495 <li>Core PDB parsing code requires Jmol</li>
3496 <li>Sequence canvas panel goes white when alignment
3497 window is being resized</li>
3503 <td><div align="center">
3504 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3506 <td><em>General</em>
3508 <li>Updated Java code signing certificate donated by
3510 <li>Features and annotation preserved when performing
3511 pairwise alignment</li>
3512 <li>RNA pseudoknot annotation can be
3513 imported/exported/displayed</li>
3514 <li>'colour by annotation' can colour by RNA and
3515 protein secondary structure</li>
3516 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3517 post-hoc with 2.9 release</em>)
3520 </ul> <em>Application</em>
3522 <li>Extract and display secondary structure for sequences
3523 with 3D structures</li>
3524 <li>Support for parsing RNAML</li>
3525 <li>Annotations menu for layout
3527 <li>sort sequence annotation rows by alignment</li>
3528 <li>place sequence annotation above/below alignment
3531 <li>Output in Stockholm format</li>
3532 <li>Internationalisation: improved Spanish (es)
3534 <li>Structure viewer preferences tab</li>
3535 <li>Disorder and Secondary Structure annotation tracks
3536 shared between alignments</li>
3537 <li>UCSF Chimera launch and linked highlighting from
3539 <li>Show/hide all sequence associated annotation rows for
3540 all or current selection</li>
3541 <li>disorder and secondary structure predictions
3542 available as dataset annotation</li>
3543 <li>Per-sequence rna helices colouring</li>
3546 <li>Sequence database accessions imported when fetching
3547 alignments from Rfam</li>
3548 <li>update VARNA version to 3.91</li>
3550 <li>New groovy scripts for exporting aligned positions,
3551 conservation values, and calculating sum of pairs scores.</li>
3552 <li>Command line argument to set default JABAWS server</li>
3553 <li>include installation type in build properties and
3554 console log output</li>
3555 <li>Updated Jalview project format to preserve dataset
3559 <!-- issues resolved --> <em>Application</em>
3561 <li>Distinguish alignment and sequence associated RNA
3562 structure in structure->view->VARNA</li>
3563 <li>Raise dialog box if user deletes all sequences in an
3565 <li>Pressing F1 results in documentation opening twice</li>
3566 <li>Sequence feature tooltip is wrapped</li>
3567 <li>Double click on sequence associated annotation
3568 selects only first column</li>
3569 <li>Redundancy removal doesn't result in unlinked
3570 leaves shown in tree</li>
3571 <li>Undos after several redundancy removals don't undo
3573 <li>Hide sequence doesn't hide associated annotation</li>
3574 <li>User defined colours dialog box too big to fit on
3575 screen and buttons not visible</li>
3576 <li>author list isn't updated if already written to
3577 Jalview properties</li>
3578 <li>Popup menu won't open after retrieving sequence
3580 <li>File open window for associate PDB doesn't open</li>
3581 <li>Left-then-right click on a sequence id opens a
3582 browser search window</li>
3583 <li>Cannot open sequence feature shading/sort popup menu
3584 in feature settings dialog</li>
3585 <li>better tooltip placement for some areas of Jalview
3587 <li>Allow addition of JABAWS Server which doesn't
3588 pass validation</li>
3589 <li>Web services parameters dialog box is too large to
3591 <li>Muscle nucleotide alignment preset obscured by
3593 <li>JABAWS preset submenus don't contain newly
3594 defined user preset</li>
3595 <li>MSA web services warns user if they were launched
3596 with invalid input</li>
3597 <li>Jalview cannot contact DAS Registy when running on
3600 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3601 'Superpose with' submenu not shown when new view
3605 </ul> <!-- <em>Applet</em>
3607 </ul> <em>General</em>
3609 </ul>--> <em>Deployment and Documentation</em>
3611 <li>2G and 1G options in launchApp have no effect on
3612 memory allocation</li>
3613 <li>launchApp service doesn't automatically open
3614 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3616 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3617 InstallAnywhere reports cannot find valid JVM when Java
3618 1.7_055 is available
3620 </ul> <em>Application Known issues</em>
3623 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3624 corrupted or unreadable alignment display when scrolling
3628 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3629 retrieval fails but progress bar continues for DAS retrieval
3630 with large number of ID
3633 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3634 flatfile output of visible region has incorrect sequence
3638 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3639 rna structure consensus doesn't update when secondary
3640 structure tracks are rearranged
3643 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3644 invalid rna structure positional highlighting does not
3645 highlight position of invalid base pairs
3648 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3649 out of memory errors are not raised when saving Jalview
3650 project from alignment window file menu
3653 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3654 Switching to RNA Helices colouring doesn't propagate to
3658 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3659 colour by RNA Helices not enabled when user created
3660 annotation added to alignment
3663 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3664 Jalview icon not shown on dock in Mountain Lion/Webstart
3666 </ul> <em>Applet Known Issues</em>
3669 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3670 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3673 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3674 Jalview and Jmol example not compatible with IE9
3677 <li>Sort by annotation score doesn't reverse order
3683 <td><div align="center">
3684 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3687 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3690 <li>Internationalisation of user interface (usually
3691 called i18n support) and translation for Spanish locale</li>
3692 <li>Define/Undefine group on current selection with
3693 Ctrl-G/Shift Ctrl-G</li>
3694 <li>Improved group creation/removal options in
3695 alignment/sequence Popup menu</li>
3696 <li>Sensible precision for symbol distribution
3697 percentages shown in logo tooltip.</li>
3698 <li>Annotation panel height set according to amount of
3699 annotation when alignment first opened</li>
3700 </ul> <em>Application</em>
3702 <li>Interactive consensus RNA secondary structure
3703 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3704 <li>Select columns containing particular features from
3705 Feature Settings dialog</li>
3706 <li>View all 'representative' PDB structures for selected
3708 <li>Update Jalview project format:
3710 <li>New file extension for Jalview projects '.jvp'</li>
3711 <li>Preserve sequence and annotation dataset (to
3712 store secondary structure annotation,etc)</li>
3713 <li>Per group and alignment annotation and RNA helix
3717 <li>New similarity measures for PCA and Tree calculation
3719 <li>Experimental support for retrieval and viewing of
3720 flanking regions for an alignment</li>
3724 <!-- issues resolved --> <em>Application</em>
3726 <li>logo keeps spinning and status remains at queued or
3727 running after job is cancelled</li>
3728 <li>cannot export features from alignments imported from
3729 Jalview/VAMSAS projects</li>
3730 <li>Buggy slider for web service parameters that take
3732 <li>Newly created RNA secondary structure line doesn't
3733 have 'display all symbols' flag set</li>
3734 <li>T-COFFEE alignment score shading scheme and other
3735 annotation shading not saved in Jalview project</li>
3736 <li>Local file cannot be loaded in freshly downloaded
3738 <li>Jalview icon not shown on dock in Mountain
3740 <li>Load file from desktop file browser fails</li>
3741 <li>Occasional NPE thrown when calculating large trees</li>
3742 <li>Cannot reorder or slide sequences after dragging an
3743 alignment onto desktop</li>
3744 <li>Colour by annotation dialog throws NPE after using
3745 'extract scores' function</li>
3746 <li>Loading/cut'n'pasting an empty file leads to a grey
3747 alignment window</li>
3748 <li>Disorder thresholds rendered incorrectly after
3749 performing IUPred disorder prediction</li>
3750 <li>Multiple group annotated consensus rows shown when
3751 changing 'normalise logo' display setting</li>
3752 <li>Find shows blank dialog after 'finished searching' if
3753 nothing matches query</li>
3754 <li>Null Pointer Exceptions raised when sorting by
3755 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3757 <li>Errors in Jmol console when structures in alignment
3758 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3760 <li>Not all working JABAWS services are shown in
3762 <li>JAVAWS version of Jalview fails to launch with
3763 'invalid literal/length code'</li>
3764 <li>Annotation/RNA Helix colourschemes cannot be applied
3765 to alignment with groups (actually fixed in 2.8.0b1)</li>
3766 <li>RNA Helices and T-Coffee Scores available as default
3769 </ul> <em>Applet</em>
3771 <li>Remove group option is shown even when selection is
3773 <li>Apply to all groups ticked but colourscheme changes
3774 don't affect groups</li>
3775 <li>Documented RNA Helices and T-Coffee Scores as valid
3776 colourscheme name</li>
3777 <li>Annotation labels drawn on sequence IDs when
3778 Annotation panel is not displayed</li>
3779 <li>Increased font size for dropdown menus on OSX and
3780 embedded windows</li>
3781 </ul> <em>Other</em>
3783 <li>Consensus sequence for alignments/groups with a
3784 single sequence were not calculated</li>
3785 <li>annotation files that contain only groups imported as
3786 annotation and junk sequences</li>
3787 <li>Fasta files with sequences containing '*' incorrectly
3788 recognised as PFAM or BLC</li>
3789 <li>conservation/PID slider apply all groups option
3790 doesn't affect background (2.8.0b1)
3792 <li>redundancy highlighting is erratic at 0% and 100%</li>
3793 <li>Remove gapped columns fails for sequences with ragged
3795 <li>AMSA annotation row with leading spaces is not
3796 registered correctly on import</li>
3797 <li>Jalview crashes when selecting PCA analysis for
3798 certain alignments</li>
3799 <li>Opening the colour by annotation dialog for an
3800 existing annotation based 'use original colours'
3801 colourscheme loses original colours setting</li>
3806 <td><div align="center">
3807 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3808 <em>30/1/2014</em></strong>
3812 <li>Trusted certificates for JalviewLite applet and
3813 Jalview Desktop application<br />Certificate was donated by
3814 <a href="https://www.certum.eu">Certum</a> to the Jalview
3815 open source project).
3817 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3818 <li>Output in Stockholm format</li>
3819 <li>Allow import of data from gzipped files</li>
3820 <li>Export/import group and sequence associated line
3821 graph thresholds</li>
3822 <li>Nucleotide substitution matrix that supports RNA and
3823 ambiguity codes</li>
3824 <li>Allow disorder predictions to be made on the current
3825 selection (or visible selection) in the same way that JPred
3827 <li>Groovy scripting for headless Jalview operation</li>
3828 </ul> <em>Other improvements</em>
3830 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3831 <li>COMBINE statement uses current SEQUENCE_REF and
3832 GROUP_REF scope to group annotation rows</li>
3833 <li>Support '' style escaping of quotes in Newick
3835 <li>Group options for JABAWS service by command line name</li>
3836 <li>Empty tooltip shown for JABA service options with a
3837 link but no description</li>
3838 <li>Select primary source when selecting authority in
3839 database fetcher GUI</li>
3840 <li>Add .mfa to FASTA file extensions recognised by
3842 <li>Annotation label tooltip text wrap</li>
3847 <li>Slow scrolling when lots of annotation rows are
3849 <li>Lots of NPE (and slowness) after creating RNA
3850 secondary structure annotation line</li>
3851 <li>Sequence database accessions not imported when
3852 fetching alignments from Rfam</li>
3853 <li>Incorrect SHMR submission for sequences with
3855 <li>View all structures does not always superpose
3857 <li>Option widgets in service parameters not updated to
3858 reflect user or preset settings</li>
3859 <li>Null pointer exceptions for some services without
3860 presets or adjustable parameters</li>
3861 <li>Discover PDB IDs entry in structure menu doesn't
3862 discover PDB xRefs</li>
3863 <li>Exception encountered while trying to retrieve
3864 features with DAS</li>
3865 <li>Lowest value in annotation row isn't coloured
3866 when colour by annotation (per sequence) is coloured</li>
3867 <li>Keyboard mode P jumps to start of gapped region when
3868 residue follows a gap</li>
3869 <li>Jalview appears to hang importing an alignment with
3870 Wrap as default or after enabling Wrap</li>
3871 <li>'Right click to add annotations' message
3872 shown in wrap mode when no annotations present</li>
3873 <li>Disorder predictions fail with NPE if no automatic
3874 annotation already exists on alignment</li>
3875 <li>oninit javascript function should be called after
3876 initialisation completes</li>
3877 <li>Remove redundancy after disorder prediction corrupts
3878 alignment window display</li>
3879 <li>Example annotation file in documentation is invalid</li>
3880 <li>Grouped line graph annotation rows are not exported
3881 to annotation file</li>
3882 <li>Multi-harmony analysis cannot be run when only two
3884 <li>Cannot create multiple groups of line graphs with
3885 several 'combine' statements in annotation file</li>
3886 <li>Pressing return several times causes Number Format
3887 exceptions in keyboard mode</li>
3888 <li>Multi-harmony (SHMMR) method doesn't submit
3889 correct partitions for input data</li>
3890 <li>Translation from DNA to Amino Acids fails</li>
3891 <li>Jalview fail to load newick tree with quoted label</li>
3892 <li>--headless flag isn't understood</li>
3893 <li>ClassCastException when generating EPS in headless
3895 <li>Adjusting sequence-associated shading threshold only
3896 changes one row's threshold</li>
3897 <li>Preferences and Feature settings panel panel
3898 doesn't open</li>
3899 <li>hide consensus histogram also hides conservation and
3900 quality histograms</li>
3905 <td><div align="center">
3906 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3908 <td><em>Application</em>
3910 <li>Support for JABAWS 2.0 Services (AACon alignment
3911 conservation, protein disorder and Clustal Omega)</li>
3912 <li>JABAWS server status indicator in Web Services
3914 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3915 in Jalview alignment window</li>
3916 <li>Updated Jalview build and deploy framework for OSX
3917 mountain lion, windows 7, and 8</li>
3918 <li>Nucleotide substitution matrix for PCA that supports
3919 RNA and ambiguity codes</li>
3921 <li>Improved sequence database retrieval GUI</li>
3922 <li>Support fetching and database reference look up
3923 against multiple DAS sources (Fetch all from in 'fetch db
3925 <li>Jalview project improvements
3927 <li>Store and retrieve the 'belowAlignment'
3928 flag for annotation</li>
3929 <li>calcId attribute to group annotation rows on the
3931 <li>Store AACon calculation settings for a view in
3932 Jalview project</li>
3936 <li>horizontal scrolling gesture support</li>
3937 <li>Visual progress indicator when PCA calculation is
3939 <li>Simpler JABA web services menus</li>
3940 <li>visual indication that web service results are still
3941 being retrieved from server</li>
3942 <li>Serialise the dialogs that are shown when Jalview
3943 starts up for first time</li>
3944 <li>Jalview user agent string for interacting with HTTP
3946 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3948 <li>Examples directory and Groovy library included in
3949 InstallAnywhere distribution</li>
3950 </ul> <em>Applet</em>
3952 <li>RNA alignment and secondary structure annotation
3953 visualization applet example</li>
3954 </ul> <em>General</em>
3956 <li>Normalise option for consensus sequence logo</li>
3957 <li>Reset button in PCA window to return dimensions to
3959 <li>Allow seqspace or Jalview variant of alignment PCA
3961 <li>PCA with either nucleic acid and protein substitution
3963 <li>Allow windows containing HTML reports to be exported
3965 <li>Interactive display and editing of RNA secondary
3966 structure contacts</li>
3967 <li>RNA Helix Alignment Colouring</li>
3968 <li>RNA base pair logo consensus</li>
3969 <li>Parse sequence associated secondary structure
3970 information in Stockholm files</li>
3971 <li>HTML Export database accessions and annotation
3972 information presented in tooltip for sequences</li>
3973 <li>Import secondary structure from LOCARNA clustalw
3974 style RNA alignment files</li>
3975 <li>import and visualise T-COFFEE quality scores for an
3977 <li>'colour by annotation' per sequence option to
3978 shade each sequence according to its associated alignment
3980 <li>New Jalview Logo</li>
3981 </ul> <em>Documentation and Development</em>
3983 <li>documentation for score matrices used in Jalview</li>
3984 <li>New Website!</li>
3986 <td><em>Application</em>
3988 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3989 wsdbfetch REST service</li>
3990 <li>Stop windows being moved outside desktop on OSX</li>
3991 <li>Filetype associations not installed for webstart
3993 <li>Jalview does not always retrieve progress of a JABAWS
3994 job execution in full once it is complete</li>
3995 <li>revise SHMR RSBS definition to ensure alignment is
3996 uploaded via ali_file parameter</li>
3997 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3998 <li>View all structures superposed fails with exception</li>
3999 <li>Jnet job queues forever if a very short sequence is
4000 submitted for prediction</li>
4001 <li>Cut and paste menu not opened when mouse clicked on
4003 <li>Putting fractional value into integer text box in
4004 alignment parameter dialog causes Jalview to hang</li>
4005 <li>Structure view highlighting doesn't work on
4007 <li>View all structures fails with exception shown in
4009 <li>Characters in filename associated with PDBEntry not
4010 escaped in a platform independent way</li>
4011 <li>Jalview desktop fails to launch with exception when
4013 <li>Tree calculation reports 'you must have 2 or more
4014 sequences selected' when selection is empty</li>
4015 <li>Jalview desktop fails to launch with jar signature
4016 failure when java web start temporary file caching is
4018 <li>DAS Sequence retrieval with range qualification
4019 results in sequence xref which includes range qualification</li>
4020 <li>Errors during processing of command line arguments
4021 cause progress bar (JAL-898) to be removed</li>
4022 <li>Replace comma for semi-colon option not disabled for
4023 DAS sources in sequence fetcher</li>
4024 <li>Cannot close news reader when JABAWS server warning
4025 dialog is shown</li>
4026 <li>Option widgets not updated to reflect user settings</li>
4027 <li>Edited sequence not submitted to web service</li>
4028 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4029 <li>InstallAnywhere installer doesn't unpack and run
4030 on OSX Mountain Lion</li>
4031 <li>Annotation panel not given a scroll bar when
4032 sequences with alignment annotation are pasted into the
4034 <li>Sequence associated annotation rows not associated
4035 when loaded from Jalview project</li>
4036 <li>Browser launch fails with NPE on java 1.7</li>
4037 <li>JABAWS alignment marked as finished when job was
4038 cancelled or job failed due to invalid input</li>
4039 <li>NPE with v2.7 example when clicking on Tree
4040 associated with all views</li>
4041 <li>Exceptions when copy/paste sequences with grouped
4042 annotation rows to new window</li>
4043 </ul> <em>Applet</em>
4045 <li>Sequence features are momentarily displayed before
4046 they are hidden using hidefeaturegroups applet parameter</li>
4047 <li>loading features via javascript API automatically
4048 enables feature display</li>
4049 <li>scrollToColumnIn javascript API method doesn't
4051 </ul> <em>General</em>
4053 <li>Redundancy removal fails for rna alignment</li>
4054 <li>PCA calculation fails when sequence has been selected
4055 and then deselected</li>
4056 <li>PCA window shows grey box when first opened on OSX</li>
4057 <li>Letters coloured pink in sequence logo when alignment
4058 coloured with clustalx</li>
4059 <li>Choosing fonts without letter symbols defined causes
4060 exceptions and redraw errors</li>
4061 <li>Initial PCA plot view is not same as manually
4062 reconfigured view</li>
4063 <li>Grouped annotation graph label has incorrect line
4065 <li>Grouped annotation graph label display is corrupted
4066 for lots of labels</li>
4071 <div align="center">
4072 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4075 <td><em>Application</em>
4077 <li>Jalview Desktop News Reader</li>
4078 <li>Tweaked default layout of web services menu</li>
4079 <li>View/alignment association menu to enable user to
4080 easily specify which alignment a multi-structure view takes
4081 its colours/correspondences from</li>
4082 <li>Allow properties file location to be specified as URL</li>
4083 <li>Extend Jalview project to preserve associations
4084 between many alignment views and a single Jmol display</li>
4085 <li>Store annotation row height in Jalview project file</li>
4086 <li>Annotation row column label formatting attributes
4087 stored in project file</li>
4088 <li>Annotation row order for auto-calculated annotation
4089 rows preserved in Jalview project file</li>
4090 <li>Visual progress indication when Jalview state is
4091 saved using Desktop window menu</li>
4092 <li>Visual indication that command line arguments are
4093 still being processed</li>
4094 <li>Groovy script execution from URL</li>
4095 <li>Colour by annotation default min and max colours in
4097 <li>Automatically associate PDB files dragged onto an
4098 alignment with sequences that have high similarity and
4100 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4101 <li>'view structures' option to open many
4102 structures in same window</li>
4103 <li>Sort associated views menu option for tree panel</li>
4104 <li>Group all JABA and non-JABA services for a particular
4105 analysis function in its own submenu</li>
4106 </ul> <em>Applet</em>
4108 <li>Userdefined and autogenerated annotation rows for
4110 <li>Adjustment of alignment annotation pane height</li>
4111 <li>Annotation scrollbar for annotation panel</li>
4112 <li>Drag to reorder annotation rows in annotation panel</li>
4113 <li>'automaticScrolling' parameter</li>
4114 <li>Allow sequences with partial ID string matches to be
4115 annotated from GFF/Jalview features files</li>
4116 <li>Sequence logo annotation row in applet</li>
4117 <li>Absolute paths relative to host server in applet
4118 parameters are treated as such</li>
4119 <li>New in the JalviewLite javascript API:
4121 <li>JalviewLite.js javascript library</li>
4122 <li>Javascript callbacks for
4124 <li>Applet initialisation</li>
4125 <li>Sequence/alignment mouse-overs and selections</li>
4128 <li>scrollTo row and column alignment scrolling
4130 <li>Select sequence/alignment regions from javascript</li>
4131 <li>javascript structure viewer harness to pass
4132 messages between Jmol and Jalview when running as
4133 distinct applets</li>
4134 <li>sortBy method</li>
4135 <li>Set of applet and application examples shipped
4136 with documentation</li>
4137 <li>New example to demonstrate JalviewLite and Jmol
4138 javascript message exchange</li>
4140 </ul> <em>General</em>
4142 <li>Enable Jmol displays to be associated with multiple
4143 multiple alignments</li>
4144 <li>Option to automatically sort alignment with new tree</li>
4145 <li>User configurable link to enable redirects to a
4146 www.Jalview.org mirror</li>
4147 <li>Jmol colours option for Jmol displays</li>
4148 <li>Configurable newline string when writing alignment
4149 and other flat files</li>
4150 <li>Allow alignment annotation description lines to
4151 contain html tags</li>
4152 </ul> <em>Documentation and Development</em>
4154 <li>Add groovy test harness for bulk load testing to
4156 <li>Groovy script to load and align a set of sequences
4157 using a web service before displaying the result in the
4158 Jalview desktop</li>
4159 <li>Restructured javascript and applet api documentation</li>
4160 <li>Ant target to publish example html files with applet
4162 <li>Netbeans project for building Jalview from source</li>
4163 <li>ant task to create online javadoc for Jalview source</li>
4165 <td><em>Application</em>
4167 <li>User defined colourscheme throws exception when
4168 current built in colourscheme is saved as new scheme</li>
4169 <li>AlignFrame->Save in application pops up save
4170 dialog for valid filename/format</li>
4171 <li>Cannot view associated structure for UniProt sequence</li>
4172 <li>PDB file association breaks for UniProt sequence
4174 <li>Associate PDB from file dialog does not tell you
4175 which sequence is to be associated with the file</li>
4176 <li>Find All raises null pointer exception when query
4177 only matches sequence IDs</li>
4178 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4179 <li>Jalview project with Jmol views created with Jalview
4180 2.4 cannot be loaded</li>
4181 <li>Filetype associations not installed for webstart
4183 <li>Two or more chains in a single PDB file associated
4184 with sequences in different alignments do not get coloured
4185 by their associated sequence</li>
4186 <li>Visibility status of autocalculated annotation row
4187 not preserved when project is loaded</li>
4188 <li>Annotation row height and visibility attributes not
4189 stored in Jalview project</li>
4190 <li>Tree bootstraps are not preserved when saved as a
4191 Jalview project</li>
4192 <li>Envision2 workflow tooltips are corrupted</li>
4193 <li>Enabling show group conservation also enables colour
4194 by conservation</li>
4195 <li>Duplicate group associated conservation or consensus
4196 created on new view</li>
4197 <li>Annotation scrollbar not displayed after 'show
4198 all hidden annotation rows' option selected</li>
4199 <li>Alignment quality not updated after alignment
4200 annotation row is hidden then shown</li>
4201 <li>Preserve colouring of structures coloured by
4202 sequences in pre Jalview 2.7 projects</li>
4203 <li>Web service job parameter dialog is not laid out
4205 <li>Web services menu not refreshed after 'reset
4206 services' button is pressed in preferences</li>
4207 <li>Annotation off by one in Jalview v2_3 example project</li>
4208 <li>Structures imported from file and saved in project
4209 get name like jalview_pdb1234.txt when reloaded</li>
4210 <li>Jalview does not always retrieve progress of a JABAWS
4211 job execution in full once it is complete</li>
4212 </ul> <em>Applet</em>
4214 <li>Alignment height set incorrectly when lots of
4215 annotation rows are displayed</li>
4216 <li>Relative URLs in feature HTML text not resolved to
4218 <li>View follows highlighting does not work for positions
4220 <li><= shown as = in tooltip</li>
4221 <li>Export features raises exception when no features
4223 <li>Separator string used for serialising lists of IDs
4224 for javascript api is modified when separator string
4225 provided as parameter</li>
4226 <li>Null pointer exception when selecting tree leaves for
4227 alignment with no existing selection</li>
4228 <li>Relative URLs for datasources assumed to be relative
4229 to applet's codebase</li>
4230 <li>Status bar not updated after finished searching and
4231 search wraps around to first result</li>
4232 <li>StructureSelectionManager instance shared between
4233 several Jalview applets causes race conditions and memory
4235 <li>Hover tooltip and mouseover of position on structure
4236 not sent from Jmol in applet</li>
4237 <li>Certain sequences of javascript method calls to
4238 applet API fatally hang browser</li>
4239 </ul> <em>General</em>
4241 <li>View follows structure mouseover scrolls beyond
4242 position with wrapped view and hidden regions</li>
4243 <li>Find sequence position moves to wrong residue
4244 with/without hidden columns</li>
4245 <li>Sequence length given in alignment properties window
4247 <li>InvalidNumberFormat exceptions thrown when trying to
4248 import PDB like structure files</li>
4249 <li>Positional search results are only highlighted
4250 between user-supplied sequence start/end bounds</li>
4251 <li>End attribute of sequence is not validated</li>
4252 <li>Find dialog only finds first sequence containing a
4253 given sequence position</li>
4254 <li>Sequence numbering not preserved in MSF alignment
4256 <li>Jalview PDB file reader does not extract sequence
4257 from nucleotide chains correctly</li>
4258 <li>Structure colours not updated when tree partition
4259 changed in alignment</li>
4260 <li>Sequence associated secondary structure not correctly
4261 parsed in interleaved stockholm</li>
4262 <li>Colour by annotation dialog does not restore current
4264 <li>Hiding (nearly) all sequences doesn't work
4266 <li>Sequences containing lowercase letters are not
4267 properly associated with their pdb files</li>
4268 </ul> <em>Documentation and Development</em>
4270 <li>schemas/JalviewWsParamSet.xsd corrupted by
4271 ApplyCopyright tool</li>
4276 <div align="center">
4277 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4280 <td><em>Application</em>
4282 <li>New warning dialog when the Jalview Desktop cannot
4283 contact web services</li>
4284 <li>JABA service parameters for a preset are shown in
4285 service job window</li>
4286 <li>JABA Service menu entries reworded</li>
4290 <li>Modeller PIR IO broken - cannot correctly import a
4291 pir file emitted by Jalview</li>
4292 <li>Existing feature settings transferred to new
4293 alignment view created from cut'n'paste</li>
4294 <li>Improved test for mixed amino/nucleotide chains when
4295 parsing PDB files</li>
4296 <li>Consensus and conservation annotation rows
4297 occasionally become blank for all new windows</li>
4298 <li>Exception raised when right clicking above sequences
4299 in wrapped view mode</li>
4300 </ul> <em>Application</em>
4302 <li>multiple multiply aligned structure views cause cpu
4303 usage to hit 100% and computer to hang</li>
4304 <li>Web Service parameter layout breaks for long user
4305 parameter names</li>
4306 <li>Jaba service discovery hangs desktop if Jaba server
4313 <div align="center">
4314 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4317 <td><em>Application</em>
4319 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4320 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4323 <li>Web Services preference tab</li>
4324 <li>Analysis parameters dialog box and user defined
4326 <li>Improved speed and layout of Envision2 service menu</li>
4327 <li>Superpose structures using associated sequence
4329 <li>Export coordinates and projection as CSV from PCA
4331 </ul> <em>Applet</em>
4333 <li>enable javascript: execution by the applet via the
4334 link out mechanism</li>
4335 </ul> <em>Other</em>
4337 <li>Updated the Jmol Jalview interface to work with Jmol
4339 <li>The Jalview Desktop and JalviewLite applet now
4340 require Java 1.5</li>
4341 <li>Allow Jalview feature colour specification for GFF
4342 sequence annotation files</li>
4343 <li>New 'colour by label' keword in Jalview feature file
4344 type colour specification</li>
4345 <li>New Jalview Desktop Groovy API method that allows a
4346 script to check if it being run in an interactive session or
4347 in a batch operation from the Jalview command line</li>
4351 <li>clustalx colourscheme colours Ds preferentially when
4352 both D+E are present in over 50% of the column</li>
4353 </ul> <em>Application</em>
4355 <li>typo in AlignmentFrame->View->Hide->all but
4356 selected Regions menu item</li>
4357 <li>sequence fetcher replaces ',' for ';' when the ',' is
4358 part of a valid accession ID</li>
4359 <li>fatal OOM if object retrieved by sequence fetcher
4360 runs out of memory</li>
4361 <li>unhandled Out of Memory Error when viewing pca
4362 analysis results</li>
4363 <li>InstallAnywhere builds fail to launch on OS X java
4364 10.5 update 4 (due to apple Java 1.6 update)</li>
4365 <li>Installanywhere Jalview silently fails to launch</li>
4366 </ul> <em>Applet</em>
4368 <li>Jalview.getFeatureGroups() raises an
4369 ArrayIndexOutOfBoundsException if no feature groups are
4376 <div align="center">
4377 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4383 <li>Alignment prettyprinter doesn't cope with long
4385 <li>clustalx colourscheme colours Ds preferentially when
4386 both D+E are present in over 50% of the column</li>
4387 <li>nucleic acid structures retrieved from PDB do not
4388 import correctly</li>
4389 <li>More columns get selected than were clicked on when a
4390 number of columns are hidden</li>
4391 <li>annotation label popup menu not providing correct
4392 add/hide/show options when rows are hidden or none are
4394 <li>Stockholm format shown in list of readable formats,
4395 and parser copes better with alignments from RFAM.</li>
4396 <li>CSV output of consensus only includes the percentage
4397 of all symbols if sequence logo display is enabled</li>
4399 </ul> <em>Applet</em>
4401 <li>annotation panel disappears when annotation is
4403 </ul> <em>Application</em>
4405 <li>Alignment view not redrawn properly when new
4406 alignment opened where annotation panel is visible but no
4407 annotations are present on alignment</li>
4408 <li>pasted region containing hidden columns is
4409 incorrectly displayed in new alignment window</li>
4410 <li>Jalview slow to complete operations when stdout is
4411 flooded (fix is to close the Jalview console)</li>
4412 <li>typo in AlignmentFrame->View->Hide->all but
4413 selected Rregions menu item.</li>
4414 <li>inconsistent group submenu and Format submenu entry
4415 'Un' or 'Non'conserved</li>
4416 <li>Sequence feature settings are being shared by
4417 multiple distinct alignments</li>
4418 <li>group annotation not recreated when tree partition is
4420 <li>double click on group annotation to select sequences
4421 does not propagate to associated trees</li>
4422 <li>Mac OSX specific issues:
4424 <li>exception raised when mouse clicked on desktop
4425 window background</li>
4426 <li>Desktop menu placed on menu bar and application
4427 name set correctly</li>
4428 <li>sequence feature settings not wide enough for the
4429 save feature colourscheme button</li>
4438 <div align="center">
4439 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4442 <td><em>New Capabilities</em>
4444 <li>URL links generated from description line for
4445 regular-expression based URL links (applet and application)
4447 <li>Non-positional feature URL links are shown in link
4449 <li>Linked viewing of nucleic acid sequences and
4451 <li>Automatic Scrolling option in View menu to display
4452 the currently highlighted region of an alignment.</li>
4453 <li>Order an alignment by sequence length, or using the
4454 average score or total feature count for each sequence.</li>
4455 <li>Shading features by score or associated description</li>
4456 <li>Subdivide alignment and groups based on identity of
4457 selected subsequence (Make Groups from Selection).</li>
4458 <li>New hide/show options including Shift+Control+H to
4459 hide everything but the currently selected region.</li>
4460 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4461 </ul> <em>Application</em>
4463 <li>Fetch DB References capabilities and UI expanded to
4464 support retrieval from DAS sequence sources</li>
4465 <li>Local DAS Sequence sources can be added via the
4466 command line or via the Add local source dialog box.</li>
4467 <li>DAS Dbref and DbxRef feature types are parsed as
4468 database references and protein_name is parsed as
4469 description line (BioSapiens terms).</li>
4470 <li>Enable or disable non-positional feature and database
4471 references in sequence ID tooltip from View menu in
4473 <!-- <li>New hidden columns and rows and representatives capabilities
4474 in annotations file (in progress - not yet fully implemented)</li> -->
4475 <li>Group-associated consensus, sequence logos and
4476 conservation plots</li>
4477 <li>Symbol distributions for each column can be exported
4478 and visualized as sequence logos</li>
4479 <li>Optionally scale multi-character column labels to fit
4480 within each column of annotation row<!-- todo for applet -->
4482 <li>Optional automatic sort of associated alignment view
4483 when a new tree is opened.</li>
4484 <li>Jalview Java Console</li>
4485 <li>Better placement of desktop window when moving
4486 between different screens.</li>
4487 <li>New preference items for sequence ID tooltip and
4488 consensus annotation</li>
4489 <li>Client to submit sequences and IDs to Envision2
4491 <li><em>Vamsas Capabilities</em>
4493 <li>Improved VAMSAS synchronization (Jalview archive
4494 used to preserve views, structures, and tree display
4496 <li>Import of vamsas documents from disk or URL via
4498 <li>Sharing of selected regions between views and
4499 with other VAMSAS applications (Experimental feature!)</li>
4500 <li>Updated API to VAMSAS version 0.2</li>
4502 </ul> <em>Applet</em>
4504 <li>Middle button resizes annotation row height</li>
4507 <li>sortByTree (true/false) - automatically sort the
4508 associated alignment view by the tree when a new tree is
4510 <li>showTreeBootstraps (true/false) - show or hide
4511 branch bootstraps (default is to show them if available)</li>
4512 <li>showTreeDistances (true/false) - show or hide
4513 branch lengths (default is to show them if available)</li>
4514 <li>showUnlinkedTreeNodes (true/false) - indicate if
4515 unassociated nodes should be highlighted in the tree
4517 <li>heightScale and widthScale (1.0 or more) -
4518 increase the height or width of a cell in the alignment
4519 grid relative to the current font size.</li>
4522 <li>Non-positional features displayed in sequence ID
4524 </ul> <em>Other</em>
4526 <li>Features format: graduated colour definitions and
4527 specification of feature scores</li>
4528 <li>Alignment Annotations format: new keywords for group
4529 associated annotation (GROUP_REF) and annotation row display
4530 properties (ROW_PROPERTIES)</li>
4531 <li>XML formats extended to support graduated feature
4532 colourschemes, group associated annotation, and profile
4533 visualization settings.</li></td>
4536 <li>Source field in GFF files parsed as feature source
4537 rather than description</li>
4538 <li>Non-positional features are now included in sequence
4539 feature and gff files (controlled via non-positional feature
4540 visibility in tooltip).</li>
4541 <li>URL links generated for all feature links (bugfix)</li>
4542 <li>Added URL embedding instructions to features file
4544 <li>Codons containing ambiguous nucleotides translated as
4545 'X' in peptide product</li>
4546 <li>Match case switch in find dialog box works for both
4547 sequence ID and sequence string and query strings do not
4548 have to be in upper case to match case-insensitively.</li>
4549 <li>AMSA files only contain first column of
4550 multi-character column annotation labels</li>
4551 <li>Jalview Annotation File generation/parsing consistent
4552 with documentation (e.g. Stockholm annotation can be
4553 exported and re-imported)</li>
4554 <li>PDB files without embedded PDB IDs given a friendly
4556 <li>Find incrementally searches ID string matches as well
4557 as subsequence matches, and correctly reports total number
4561 <li>Better handling of exceptions during sequence
4563 <li>Dasobert generated non-positional feature URL
4564 link text excludes the start_end suffix</li>
4565 <li>DAS feature and source retrieval buttons disabled
4566 when fetch or registry operations in progress.</li>
4567 <li>PDB files retrieved from URLs are cached properly</li>
4568 <li>Sequence description lines properly shared via
4570 <li>Sequence fetcher fetches multiple records for all
4572 <li>Ensured that command line das feature retrieval
4573 completes before alignment figures are generated.</li>
4574 <li>Reduced time taken when opening file browser for
4576 <li>isAligned check prior to calculating tree, PCA or
4577 submitting an MSA to JNet now excludes hidden sequences.</li>
4578 <li>User defined group colours properly recovered
4579 from Jalview projects.</li>
4588 <div align="center">
4589 <strong>2.4.0.b2</strong><br> 28/10/2009
4594 <li>Experimental support for google analytics usage
4596 <li>Jalview privacy settings (user preferences and docs).</li>
4601 <li>Race condition in applet preventing startup in
4603 <li>Exception when feature created from selection beyond
4604 length of sequence.</li>
4605 <li>Allow synthetic PDB files to be imported gracefully</li>
4606 <li>Sequence associated annotation rows associate with
4607 all sequences with a given id</li>
4608 <li>Find function matches case-insensitively for sequence
4609 ID string searches</li>
4610 <li>Non-standard characters do not cause pairwise
4611 alignment to fail with exception</li>
4612 </ul> <em>Application Issues</em>
4614 <li>Sequences are now validated against EMBL database</li>
4615 <li>Sequence fetcher fetches multiple records for all
4617 </ul> <em>InstallAnywhere Issues</em>
4619 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4620 issue with installAnywhere mechanism)</li>
4621 <li>Command line launching of JARs from InstallAnywhere
4622 version (java class versioning error fixed)</li>
4629 <div align="center">
4630 <strong>2.4</strong><br> 27/8/2008
4633 <td><em>User Interface</em>
4635 <li>Linked highlighting of codon and amino acid from
4636 translation and protein products</li>
4637 <li>Linked highlighting of structure associated with
4638 residue mapping to codon position</li>
4639 <li>Sequence Fetcher provides example accession numbers
4640 and 'clear' button</li>
4641 <li>MemoryMonitor added as an option under Desktop's
4643 <li>Extract score function to parse whitespace separated
4644 numeric data in description line</li>
4645 <li>Column labels in alignment annotation can be centred.</li>
4646 <li>Tooltip for sequence associated annotation give name
4648 </ul> <em>Web Services and URL fetching</em>
4650 <li>JPred3 web service</li>
4651 <li>Prototype sequence search client (no public services
4653 <li>Fetch either seed alignment or full alignment from
4655 <li>URL Links created for matching database cross
4656 references as well as sequence ID</li>
4657 <li>URL Links can be created using regular-expressions</li>
4658 </ul> <em>Sequence Database Connectivity</em>
4660 <li>Retrieval of cross-referenced sequences from other
4662 <li>Generalised database reference retrieval and
4663 validation to all fetchable databases</li>
4664 <li>Fetch sequences from DAS sources supporting the
4665 sequence command</li>
4666 </ul> <em>Import and Export</em>
4667 <li>export annotation rows as CSV for spreadsheet import</li>
4668 <li>Jalview projects record alignment dataset associations,
4669 EMBL products, and cDNA sequence mappings</li>
4670 <li>Sequence Group colour can be specified in Annotation
4672 <li>Ad-hoc colouring of group in Annotation File using RGB
4673 triplet as name of colourscheme</li>
4674 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4676 <li>treenode binding for VAMSAS tree exchange</li>
4677 <li>local editing and update of sequences in VAMSAS
4678 alignments (experimental)</li>
4679 <li>Create new or select existing session to join</li>
4680 <li>load and save of vamsas documents</li>
4681 </ul> <em>Application command line</em>
4683 <li>-tree parameter to open trees (introduced for passing
4685 <li>-fetchfrom command line argument to specify nicknames
4686 of DAS servers to query for alignment features</li>
4687 <li>-dasserver command line argument to add new servers
4688 that are also automatically queried for features</li>
4689 <li>-groovy command line argument executes a given groovy
4690 script after all input data has been loaded and parsed</li>
4691 </ul> <em>Applet-Application data exchange</em>
4693 <li>Trees passed as applet parameters can be passed to
4694 application (when using "View in full
4695 application")</li>
4696 </ul> <em>Applet Parameters</em>
4698 <li>feature group display control parameter</li>
4699 <li>debug parameter</li>
4700 <li>showbutton parameter</li>
4701 </ul> <em>Applet API methods</em>
4703 <li>newView public method</li>
4704 <li>Window (current view) specific get/set public methods</li>
4705 <li>Feature display control methods</li>
4706 <li>get list of currently selected sequences</li>
4707 </ul> <em>New Jalview distribution features</em>
4709 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4710 <li>RELEASE file gives build properties for the latest
4711 Jalview release.</li>
4712 <li>Java 1.1 Applet build made easier and donotobfuscate
4713 property controls execution of obfuscator</li>
4714 <li>Build target for generating source distribution</li>
4715 <li>Debug flag for javacc</li>
4716 <li>.jalview_properties file is documented (slightly) in
4717 jalview.bin.Cache</li>
4718 <li>Continuous Build Integration for stable and
4719 development version of Application, Applet and source
4724 <li>selected region output includes visible annotations
4725 (for certain formats)</li>
4726 <li>edit label/displaychar contains existing label/char
4728 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4729 <li>shorter peptide product names from EMBL records</li>
4730 <li>Newick string generator makes compact representations</li>
4731 <li>bootstrap values parsed correctly for tree files with
4733 <li>pathological filechooser bug avoided by not allowing
4734 filenames containing a ':'</li>
4735 <li>Fixed exception when parsing GFF files containing
4736 global sequence features</li>
4737 <li>Alignment datasets are finalized only when number of
4738 references from alignment sequences goes to zero</li>
4739 <li>Close of tree branch colour box without colour
4740 selection causes cascading exceptions</li>
4741 <li>occasional negative imgwidth exceptions</li>
4742 <li>better reporting of non-fatal warnings to user when
4743 file parsing fails.</li>
4744 <li>Save works when Jalview project is default format</li>
4745 <li>Save as dialog opened if current alignment format is
4746 not a valid output format</li>
4747 <li>UniProt canonical names introduced for both das and
4749 <li>Histidine should be midblue (not pink!) in Zappo</li>
4750 <li>error messages passed up and output when data read
4752 <li>edit undo recovers previous dataset sequence when
4753 sequence is edited</li>
4754 <li>allow PDB files without pdb ID HEADER lines (like
4755 those generated by MODELLER) to be read in properly</li>
4756 <li>allow reading of JPred concise files as a normal
4758 <li>Stockholm annotation parsing and alignment properties
4759 import fixed for PFAM records</li>
4760 <li>Structure view windows have correct name in Desktop
4762 <li>annotation consisting of sequence associated scores
4763 can be read and written correctly to annotation file</li>
4764 <li>Aligned cDNA translation to aligned peptide works
4766 <li>Fixed display of hidden sequence markers and
4767 non-italic font for representatives in Applet</li>
4768 <li>Applet Menus are always embedded in applet window on
4770 <li>Newly shown features appear at top of stack (in
4772 <li>Annotations added via parameter not drawn properly
4773 due to null pointer exceptions</li>
4774 <li>Secondary structure lines are drawn starting from
4775 first column of alignment</li>
4776 <li>UniProt XML import updated for new schema release in
4778 <li>Sequence feature to sequence ID match for Features
4779 file is case-insensitive</li>
4780 <li>Sequence features read from Features file appended to
4781 all sequences with matching IDs</li>
4782 <li>PDB structure coloured correctly for associated views
4783 containing a sub-sequence</li>
4784 <li>PDB files can be retrieved by applet from Jar files</li>
4785 <li>feature and annotation file applet parameters
4786 referring to different directories are retrieved correctly</li>
4787 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4788 <li>Fixed application hang whilst waiting for
4789 splash-screen version check to complete</li>
4790 <li>Applet properly URLencodes input parameter values
4791 when passing them to the launchApp service</li>
4792 <li>display name and local features preserved in results
4793 retrieved from web service</li>
4794 <li>Visual delay indication for sequence retrieval and
4795 sequence fetcher initialisation</li>
4796 <li>updated Application to use DAS 1.53e version of
4797 dasobert DAS client</li>
4798 <li>Re-instated Full AMSA support and .amsa file
4800 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4808 <div align="center">
4809 <strong>2.3</strong><br> 9/5/07
4814 <li>Jmol 11.0.2 integration</li>
4815 <li>PDB views stored in Jalview XML files</li>
4816 <li>Slide sequences</li>
4817 <li>Edit sequence in place</li>
4818 <li>EMBL CDS features</li>
4819 <li>DAS Feature mapping</li>
4820 <li>Feature ordering</li>
4821 <li>Alignment Properties</li>
4822 <li>Annotation Scores</li>
4823 <li>Sort by scores</li>
4824 <li>Feature/annotation editing in applet</li>
4829 <li>Headless state operation in 2.2.1</li>
4830 <li>Incorrect and unstable DNA pairwise alignment</li>
4831 <li>Cut and paste of sequences with annotation</li>
4832 <li>Feature group display state in XML</li>
4833 <li>Feature ordering in XML</li>
4834 <li>blc file iteration selection using filename # suffix</li>
4835 <li>Stockholm alignment properties</li>
4836 <li>Stockhom alignment secondary structure annotation</li>
4837 <li>2.2.1 applet had no feature transparency</li>
4838 <li>Number pad keys can be used in cursor mode</li>
4839 <li>Structure Viewer mirror image resolved</li>
4846 <div align="center">
4847 <strong>2.2.1</strong><br> 12/2/07
4852 <li>Non standard characters can be read and displayed
4853 <li>Annotations/Features can be imported/exported to the
4855 <li>Applet allows editing of sequence/annotation/group
4856 name & description
4857 <li>Preference setting to display sequence name in
4859 <li>Annotation file format extended to allow
4860 Sequence_groups to be defined
4861 <li>Default opening of alignment overview panel can be
4862 specified in preferences
4863 <li>PDB residue numbering annotation added to associated
4869 <li>Applet crash under certain Linux OS with Java 1.6
4871 <li>Annotation file export / import bugs fixed
4872 <li>PNG / EPS image output bugs fixed
4878 <div align="center">
4879 <strong>2.2</strong><br> 27/11/06
4884 <li>Multiple views on alignment
4885 <li>Sequence feature editing
4886 <li>"Reload" alignment
4887 <li>"Save" to current filename
4888 <li>Background dependent text colour
4889 <li>Right align sequence ids
4890 <li>User-defined lower case residue colours
4893 <li>Menu item accelerator keys
4894 <li>Control-V pastes to current alignment
4895 <li>Cancel button for DAS Feature Fetching
4896 <li>PCA and PDB Viewers zoom via mouse roller
4897 <li>User-defined sub-tree colours and sub-tree selection
4899 <li>'New Window' button on the 'Output to Text box'
4904 <li>New memory efficient Undo/Redo System
4905 <li>Optimised symbol lookups and conservation/consensus
4907 <li>Region Conservation/Consensus recalculated after
4909 <li>Fixed Remove Empty Columns Bug (empty columns at end
4911 <li>Slowed DAS Feature Fetching for increased robustness.
4913 <li>Made angle brackets in ASCII feature descriptions
4915 <li>Re-instated Zoom function for PCA
4916 <li>Sequence descriptions conserved in web service
4918 <li>UniProt ID discoverer uses any word separated by
4920 <li>WsDbFetch query/result association resolved
4921 <li>Tree leaf to sequence mapping improved
4922 <li>Smooth fonts switch moved to FontChooser dialog box.
4929 <div align="center">
4930 <strong>2.1.1</strong><br> 12/9/06
4935 <li>Copy consensus sequence to clipboard</li>
4940 <li>Image output - rightmost residues are rendered if
4941 sequence id panel has been resized</li>
4942 <li>Image output - all offscreen group boundaries are
4944 <li>Annotation files with sequence references - all
4945 elements in file are relative to sequence position</li>
4946 <li>Mac Applet users can use Alt key for group editing</li>
4952 <div align="center">
4953 <strong>2.1</strong><br> 22/8/06
4958 <li>MAFFT Multiple Alignment in default Web Service list</li>
4959 <li>DAS Feature fetching</li>
4960 <li>Hide sequences and columns</li>
4961 <li>Export Annotations and Features</li>
4962 <li>GFF file reading / writing</li>
4963 <li>Associate structures with sequences from local PDB
4965 <li>Add sequences to exisiting alignment</li>
4966 <li>Recently opened files / URL lists</li>
4967 <li>Applet can launch the full application</li>
4968 <li>Applet has transparency for features (Java 1.2
4970 <li>Applet has user defined colours parameter</li>
4971 <li>Applet can load sequences from parameter
4972 "sequence<em>x</em>"
4978 <li>Redundancy Panel reinstalled in the Applet</li>
4979 <li>Monospaced font - EPS / rescaling bug fixed</li>
4980 <li>Annotation files with sequence references bug fixed</li>
4986 <div align="center">
4987 <strong>2.08.1</strong><br> 2/5/06
4992 <li>Change case of selected region from Popup menu</li>
4993 <li>Choose to match case when searching</li>
4994 <li>Middle mouse button and mouse movement can compress /
4995 expand the visible width and height of the alignment</li>
5000 <li>Annotation Panel displays complete JNet results</li>
5006 <div align="center">
5007 <strong>2.08b</strong><br> 18/4/06
5013 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5014 <li>Righthand label on wrapped alignments shows correct
5021 <div align="center">
5022 <strong>2.08</strong><br> 10/4/06
5027 <li>Editing can be locked to the selection area</li>
5028 <li>Keyboard editing</li>
5029 <li>Create sequence features from searches</li>
5030 <li>Precalculated annotations can be loaded onto
5032 <li>Features file allows grouping of features</li>
5033 <li>Annotation Colouring scheme added</li>
5034 <li>Smooth fonts off by default - Faster rendering</li>
5035 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5040 <li>Drag & Drop fixed on Linux</li>
5041 <li>Jalview Archive file faster to load/save, sequence
5042 descriptions saved.</li>
5048 <div align="center">
5049 <strong>2.07</strong><br> 12/12/05
5054 <li>PDB Structure Viewer enhanced</li>
5055 <li>Sequence Feature retrieval and display enhanced</li>
5056 <li>Choose to output sequence start-end after sequence
5057 name for file output</li>
5058 <li>Sequence Fetcher WSDBFetch@EBI</li>
5059 <li>Applet can read feature files, PDB files and can be
5060 used for HTML form input</li>
5065 <li>HTML output writes groups and features</li>
5066 <li>Group editing is Control and mouse click</li>
5067 <li>File IO bugs</li>
5073 <div align="center">
5074 <strong>2.06</strong><br> 28/9/05
5079 <li>View annotations in wrapped mode</li>
5080 <li>More options for PCA viewer</li>
5085 <li>GUI bugs resolved</li>
5086 <li>Runs with -nodisplay from command line</li>
5092 <div align="center">
5093 <strong>2.05b</strong><br> 15/9/05
5098 <li>Choose EPS export as lineart or text</li>
5099 <li>Jar files are executable</li>
5100 <li>Can read in Uracil - maps to unknown residue</li>
5105 <li>Known OutOfMemory errors give warning message</li>
5106 <li>Overview window calculated more efficiently</li>
5107 <li>Several GUI bugs resolved</li>
5113 <div align="center">
5114 <strong>2.05</strong><br> 30/8/05
5119 <li>Edit and annotate in "Wrapped" view</li>
5124 <li>Several GUI bugs resolved</li>
5130 <div align="center">
5131 <strong>2.04</strong><br> 24/8/05
5136 <li>Hold down mouse wheel & scroll to change font
5142 <li>Improved JPred client reliability</li>
5143 <li>Improved loading of Jalview files</li>
5149 <div align="center">
5150 <strong>2.03</strong><br> 18/8/05
5155 <li>Set Proxy server name and port in preferences</li>
5156 <li>Multiple URL links from sequence ids</li>
5157 <li>User Defined Colours can have a scheme name and added
5159 <li>Choose to ignore gaps in consensus calculation</li>
5160 <li>Unix users can set default web browser</li>
5161 <li>Runs without GUI for batch processing</li>
5162 <li>Dynamically generated Web Service Menus</li>
5167 <li>InstallAnywhere download for Sparc Solaris</li>
5173 <div align="center">
5174 <strong>2.02</strong><br> 18/7/05
5180 <li>Copy & Paste order of sequences maintains
5181 alignment order.</li>
5187 <div align="center">
5188 <strong>2.01</strong><br> 12/7/05
5193 <li>Use delete key for deleting selection.</li>
5194 <li>Use Mouse wheel to scroll sequences.</li>
5195 <li>Help file updated to describe how to add alignment
5197 <li>Version and build date written to build properties
5199 <li>InstallAnywhere installation will check for updates
5200 at launch of Jalview.</li>
5205 <li>Delete gaps bug fixed.</li>
5206 <li>FileChooser sorts columns.</li>
5207 <li>Can remove groups one by one.</li>
5208 <li>Filechooser icons installed.</li>
5209 <li>Finder ignores return character when searching.
5210 Return key will initiate a search.<br>
5217 <div align="center">
5218 <strong>2.0</strong><br> 20/6/05
5223 <li>New codebase</li>