4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>01/02/2022</em></strong></td>
63 <td align="left" valign="top">
68 </ul> <!-- <em>Development</em>
70 <li>Updated building instructions</li>
77 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
80 </ul> <em>Development</em>
82 <li>Fixed non-fatal gradle errors during build</li>
87 <td width="60" align="center" nowrap><strong><a
88 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
89 <em>18/01/2022</em></strong></td>
91 <td align="left" valign="top"><em>Security</em>
94 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
98 <!-- JAL-3702, JAL-3935 -->Files open in Jalview cannot be
99 updated by Jalview or other applications (Windows, other non
105 <td width="60" align="center" nowrap><strong><a
106 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
107 <em>6/01/2022</em></strong></td>
109 <td align="left" valign="top"><em>Security</em>
112 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
119 <td width="60" align="center" nowrap><strong><a
120 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
121 <em>20/12/2021</em></strong></td>
123 <td align="left" valign="top"><em>Security</em>
126 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
128 </ul> <em>Development</em>
130 <li>Updated building instructions</li>
135 <!-- JAL-3840 -->Occupancy calculation is incorrect for
136 alignment columns with over -1+2^32 gaps (breaking filtering
140 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
141 scale factors being set with buggy window-managers (linux
144 </ul> <em>Development</em>
146 <li>Fixed non-fatal gradle errors during build</li>
151 <td width="60" align="center" nowrap><strong><a
152 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
153 <em>09/03/2021</em></strong></td>
154 <td align="left" valign="top"><em>Improved control of
155 Jalview's use of network services via jalview_properties</em>
158 <!-- JAL-3814 -->New .jalview_properties token controlling
159 launch of the news browser (like -nonews argument)
162 <!-- JAL-3813 -->New .jalview_properties token controlling
163 download of linkout URLs from
164 www.jalview.org/services/identifiers
167 <!-- JAL-3812 -->New .jalview_properties token controlling
168 download of BIOJSHTML templates
171 <!-- JAL-3811 -->New 'Discover Web Services' option to
172 trigger a one off JABAWS discovery if autodiscovery was
176 <td align="left" valign="top">
179 <!-- JAL-3818 -->Intermittent deadlock opening structure in
182 </ul> <em>New Known defects</em>
185 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
186 always restored from project (since 2.10.3)
189 <!-- JAL-3806 -->Selections from tree built from CDS aren't
190 propagated to Protein alignment (since 2.11.1.3)
196 <td width="60" align="center" nowrap><strong><a
197 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
198 <em>29/10/2020</em></strong></td>
199 <td align="left" valign="top">
204 <td align="left" valign="top">
207 <!-- JAL-3765 -->Find doesn't always highlight all matching
208 positions in a sequence (bug introduced in 2.11.1.2)
211 <!-- JAL-3760 -->Alignments containing one or more protein
212 sequences can be classed as nucleotide
215 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
216 sequences after alignment of protein products (known defect
217 first reported for 2.11.1.0)
220 <!-- JAL-3725 -->No tooltip or popup menu for genomic
221 features outwith CDS shown overlaid on protein
224 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
225 correctly mapped by Jalview (e.g. affects viral CDS with
226 ribosomal slippage, since 2.9.0)
229 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
233 <!-- JAL-3700 -->Selections in CDS sequence panel don't
234 always select corresponding protein sequences
237 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
238 column selection doesn't always ignore hidden columns
240 </ul> <em>Installer</em>
243 <!-- JAL-3611 -->Space character in Jalview install path on
244 Windows prevents install4j launching getdown
246 </ul> <em>Development</em>
249 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
250 version numbers in doc/building.md
256 <td width="60" align="center" nowrap><strong><a
257 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
258 <em>25/09/2020</em></strong></td>
259 <td align="left" valign="top">
263 <td align="left" valign="top">
266 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
267 "Encountered problems opening
268 https://www.jalview.org/examples/exampleFile_2_7.jvp"
274 <td width="60" align="center" nowrap><strong><a
275 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
276 <em>17/09/2020</em></strong></td>
277 <td align="left" valign="top">
280 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
281 residue in cursor mode
284 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
285 HTSJDK from 2.12 to 2.23
288 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
289 optimisations and improvements suggested by Bob Hanson and
290 improved compatibility with JalviewJS
293 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
294 alignments from Pfam and Rfam
297 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
298 import (no longer based on .gz extension)
301 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
304 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
305 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
309 <!-- JAL-3667 -->Improved warning messages, debug logging
310 and fixed Retry action when Jalview encounters errors when
311 saving or making backup files.
314 <!-- JAL-3676 -->Enhanced Jalview Java Console:
316 <li>Jalview's logging level can be configured</li>
317 <li>Copy to Clipboard Buttion</li>
321 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
322 when running on Linux (Requires Java 11+)
324 </ul> <em>Launching Jalview</em>
327 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
328 through a system property
331 <!-- JAL-3477 -->Improved built-in documentation and command
332 line help for configuring Jalview's memory
336 <td align="left" valign="top">
339 <!-- JAL-3691 -->Conservation and Quality tracks are shown
340 but not calculated and no protein or DNA score models are
341 available for tree/PCA calculation when launched with
342 Turkish language locale
345 <!-- JAL-3493 -->Escape does not clear highlights on the
346 alignment (Since Jalview 2.10.3)
349 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
350 doesn't slide selected sequences, just sequence under cursor
353 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
354 sequence under the cursor
357 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
358 multiple EMBL gene products shown for a single contig
361 <!-- JAL-3696 -->Errors encountered when processing variants
362 from VCF files yield "Error processing VCF: Format specifier
366 <!-- JAL-3697 -->Count of features not shown can be wrong
367 when there are both local and complementary features mapped
368 to the position under the cursor
371 <!-- JAL-3673 -->Sequence ID for reference sequence is
372 clipped when Right align Sequence IDs enabled
375 <!-- JAL-2983 -->Slider with negative range values not
376 rendered correctly in VAqua4 (Since 2.10.4)
379 <!-- JAL-3685 -->Single quotes not displayed correctly in
380 internationalised text for some messages and log output
383 <!-- JAL-3490 -->Find doesn't report matches that span
384 hidden gapped columns
387 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
388 panels, Alignment viewport and annotation renderer.
391 <!-- JAL-3561 -->Jalview ignores file format parameter
392 specifying output format when exporting an alignment via the
396 <!-- JAL-3667 -->Windows 10: For a minority of users, if
397 backups are not enabled, Jalview sometimes fails to
398 overwrite an existing file and raises a warning dialog. (in
399 2.11.0, and 2.11.1.0, the workaround is to try to save the
400 file again, and if that fails, delete the original file and
404 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
408 <!-- JAL-3741 -->References to http://www.jalview.org in
409 program and documentation
411 </ul> <em>Launching Jalview</em>
414 <!-- JAL-3718 -->Jalview application fails when launched the
415 first time for a version that has different jars to the
416 previous launched version.
418 </ul> <em>Developing Jalview</em>
421 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
422 data, causing cloverReport gradle task to fail with an
426 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
427 monitor the release channel
429 </ul> <em>New Known defects</em>
432 <!-- JAL-3748 -->CDS shown in result of submitting proteins
433 in a CDS/Protein alignment to a web service is wrong when
434 proteins share a common transcript sequence (e.g.
435 genome of RNA viruses)
438 <!-- JAL-3576 -->Co-located features exported and re-imported
439 are ordered differently when shown on alignment and in
440 tooltips. (Also affects v2.11.1.0)
443 <!-- JAL-3702 -->Drag and drop of alignment file onto
444 alignment window when in a HiDPI scaled mode in Linux only
445 works for the top left quadrant of the alignment window
448 <!-- JAL-3701 -->Stale build data in jalview standalone jar
449 builds (only affects 2.11.1.1 branch)
452 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
453 when alignment view restored from project (since Jalview 2.11.0)
456 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
457 protein products for certain ENA records are repeatedly
458 shown via Calculate->Show Cross Refs
464 <td width="60" align="center" nowrap><strong><a
465 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
466 <em>22/04/2020</em></strong></td>
467 <td align="left" valign="top">
470 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
471 'virtual' codon features shown on protein (or vice versa)
472 for display in alignments, on structure views (including
473 transfer to UCSF chimera), in feature reports and for
477 <!-- JAL-3121 -->Feature attributes from VCF files can be
478 exported and re-imported as GFF3 files
481 <!-- JAL-3376 -->Capture VCF "fixed column" values
482 POS, ID, QUAL, FILTER as Feature Attributes
485 <!-- JAL-3375 -->More robust VCF numeric data field
486 validation while parsing
489 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
493 <!-- JAL-3535 -->Feature Settings dialog title includes name
497 <!-- JAL-3538 -->Font anti-aliasing in alignment views
501 <!-- JAL-3468 -->Very long feature descriptions truncated in
505 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
506 with no feature types visible
509 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
511 </ul><em>Jalview Installer</em>
514 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
515 in console (may be null when Jalview launched as executable jar or via conda)
518 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
521 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
524 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
526 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
527 </ul> <em>Release processes</em>
530 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
533 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
535 </ul> <em>Build System</em>
538 <!-- JAL-3510 -->Clover updated to 4.4.1
541 <!-- JAL-3513 -->Test code included in Clover coverage
545 <em>Groovy Scripts</em>
548 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
549 to stdout containing the consensus sequence for each
550 alignment in a Jalview session
553 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
554 genomic sequence_variant annotation from CDS as
555 missense_variant or synonymous_variant on protein products.
559 <td align="left" valign="top">
562 <!-- JAL-3581 -->Hidden sequence markers still visible when
563 'Show hidden markers' option is not ticked
566 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
567 PNG output when 'Automatically set ID width' is set in
568 jalview preferences or properties file
571 <!-- JAL-3571 -->Feature Editor dialog can be opened when
572 'Show Sequence Features' option is not ticked
575 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
576 buttons in Feature Settings dialog are clicked when no
580 <!-- JAL-3412 -->ID margins for CDS and Protein views not
581 equal when split frame is first opened
584 <!-- JAL-3296 -->Sequence position numbers in status bar not
585 correct after editing a sequence's start position
588 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
589 with annotation and exceptions thrown when only a few
590 columns shown in wrapped mode
593 <!-- JAL-3386 -->Sequence IDs missing in headless export of
594 wrapped alignment figure with annotations
597 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
598 ID fails with ClassCastException
601 <!-- JAL-3389 -->Chimera session not restored from Jalview
605 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
606 feature settings dialog also selects columns
609 <!-- JAL-3473 -->SpinnerNumberModel causes
610 IllegalArgumentException in some circumstances
613 <!-- JAL-3534 -->Multiple feature settings dialogs can be
617 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
618 alignment window is closed
621 <!-- JAL-3406 -->Credits missing some authors in Jalview
622 help documentation for 2.11.0 release
625 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
626 includes Pfam ID as sequence's accession rather than its
629 </ul> <em>Java 11 Compatibility issues</em>
632 <!-- JAL-2987 -->OSX - Can't view some search results in
633 PDB/Uniprot search panel
635 </ul> <em>Installer</em>
638 <!-- JAL-3447 -->Jalview should not create file associations
639 for 3D structure files (.pdb, .mmcif. .cif)
641 </ul> <em>Repository and Source Release</em>
644 <!-- JAL-3474 -->removed obsolete .cvsignore files from
648 <!-- JAL-3541 -->Clover report generation running out of
651 </ul> <em>New Known Issues</em>
654 <!-- JAL-3523 -->OSX - Current working directory not
655 preserved when Jalview.app launched with parameters from
659 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
660 clipped in headless figure export when Right Align option
664 <!-- JAL-3542 -->Jalview Installation type always reports
665 'Source' in console output
668 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
669 bamboo server but run fine locally.
675 <td width="60" align="center" nowrap>
676 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
677 <em>04/07/2019</em></strong>
679 <td align="left" valign="top">
682 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
683 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
684 source project) rather than InstallAnywhere
687 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
688 settings, receive over the air updates and launch specific
689 versions via (<a href="https://github.com/threerings/getdown">Three
693 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
694 formats supported by Jalview (including .jvp project files)
697 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
698 arguments and switch between different getdown channels
701 <!-- JAL-3141 -->Backup files created when saving Jalview project
706 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
707 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
709 <!-- JAL-2620 -->Alternative genetic code tables for
710 'Translate as cDNA'</li>
712 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
713 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
716 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
717 implementation that allows updates) used for Sequence Feature collections</li>
719 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
720 features can be filtered and shaded according to any
721 associated attributes (e.g. variant attributes from VCF
722 file, or key-value pairs imported from column 9 of GFF
726 <!-- JAL-2879 -->Feature Attributes and shading schemes
727 stored and restored from Jalview Projects
730 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
731 recognise variant features
734 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
735 sequences (also coloured red by default)
738 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
742 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
743 algorithm (Z-sort/transparency and filter aware)
746 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
752 <!-- JAL-3205 -->Symmetric score matrices for faster
753 tree and PCA calculations
755 <li><strong>Principal Components Analysis Viewer</strong>
758 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
759 and Viewer state saved in Jalview Project
761 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
764 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
768 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
773 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
775 <li><strong>Speed and Efficiency</strong>
778 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
779 multiple groups when working with large alignments
782 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
786 <li><strong>User Interface</strong>
789 <!-- JAL-2933 -->Finder panel remembers last position in each
793 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
794 what is shown)<br />Only visible regions of alignment are shown by
795 default (can be changed in user preferences)
798 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
799 to the Overwrite Dialog
802 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
806 <!-- JAL-1244 -->Status bar shows bounds when dragging a
807 selection region, and gap count when inserting or deleting gaps
810 <!-- JAL-3132 -->Status bar updates over sequence and annotation
814 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
818 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
822 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
825 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
829 <!-- JAL-3181 -->Consistent ordering of links in sequence id
833 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
835 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
839 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
840 <li><strong>Java 11 Support (not yet on general release)</strong>
843 <!-- -->OSX GUI integrations for App menu's 'About' entry and
848 <em>Deprecations</em>
850 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
851 capabilities removed from the Jalview Desktop
853 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
854 unmarshalling has been replaced by JAXB for Jalview projects
855 and XML based data retrieval clients</li>
856 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
857 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
858 </ul> <em>Documentation</em>
860 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
861 not supported in EPS figure export
863 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
864 </ul> <em>Development and Release Processes</em>
867 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
870 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
872 <!-- JAL-3225 -->Eclipse project configuration managed with
876 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
877 Bamboo continuous integration for unattended Test Suite
881 <!-- JAL-2864 -->Memory test suite to detect leaks in common
885 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
889 <!-- JAL-3248 -->Developer documentation migrated to
890 markdown (with HTML rendering)
893 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
896 <!-- JAL-3289 -->New URLs for publishing development
901 <td align="left" valign="top">
904 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
907 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
908 superposition in Jmol fail on Windows
911 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
912 structures for sequences with lots of PDB structures
915 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
919 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
920 project involving multiple views
923 <!-- JAL-3164 -->Overview for complementary view in a linked
924 CDS/Protein alignment is not updated when Hide Columns by
925 Annotation dialog hides columns
928 <!-- JAL-3158 -->Selection highlighting in the complement of a
929 CDS/Protein alignment stops working after making a selection in
930 one view, then making another selection in the other view
933 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
937 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
938 Settings and Jalview Preferences panels
941 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
942 overview with large alignments
945 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
946 region if columns were selected by dragging right-to-left and the
947 mouse moved to the left of the first column
950 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
951 hidden column marker via scale popup menu
954 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
955 doesn't tell users the invalid URL
958 <!-- JAL-2816 -->Tooltips displayed for features filtered by
962 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
963 show cross references or Fetch Database References are shown in
967 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
968 peptide sequence (computed variant shown as p.Res.null)
971 <!-- JAL-2060 -->'Graduated colour' option not offered for
972 manually created features (where feature score is Float.NaN)
975 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
976 when columns are hidden
979 <!-- JAL-3082 -->Regular expression error for '(' in Select
980 Columns by Annotation description
983 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
984 out of Scale or Annotation Panel
987 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
991 <!-- JAL-3074 -->Left/right drag in annotation can scroll
995 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
999 <!-- JAL-3002 -->Column display is out by one after Page Down,
1000 Page Up in wrapped mode
1003 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1006 <!-- JAL-2932 -->Finder searches in minimised alignments
1009 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
1010 on opening an alignment
1013 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
1017 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
1018 different groups in the alignment are selected
1021 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1025 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1029 <!-- JAL-3125 -->Value input for graduated feature colour
1030 threshold gets 'unrounded'
1033 <!-- JAL-2982 -->PCA image export doesn't respect background
1037 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1040 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1043 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1047 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1051 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1052 shown in complementary view
1055 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1056 without normalisation
1059 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1063 <!-- JAL-914 -->Help page can be opened twice
1066 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1068 </ul> <em>Editing</em>
1071 <!-- JAL-2822 -->Start and End should be updated when sequence
1072 data at beginning or end of alignment added/removed via 'Edit'
1076 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1077 relocate sequence features correctly when start of sequence is
1078 removed (Known defect since 2.10)
1081 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1082 dialog corrupts dataset sequence
1085 <!-- JAL-868 -->Structure colours not updated when associated tree
1086 repartitions the alignment view (Regression in 2.10.5)
1088 </ul> <em>Datamodel</em>
1091 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1092 sequence's End is greater than its length
1094 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1095 general release)</em>
1098 <!-- JAL-3288 -->Menus work properly in split-screen
1100 </ul> <em>New Known Defects</em>
1103 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1106 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1107 regions of protein alignment.
1110 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1111 is restored from a Jalview 2.11 project
1114 <!-- JAL-3213 -->Alignment panel height can be too small after
1118 <!-- JAL-3240 -->Display is incorrect after removing gapped
1119 columns within hidden columns
1122 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1123 window after dragging left to select columns to left of visible
1127 <!-- JAL-2876 -->Features coloured according to their description
1128 string and thresholded by score in earlier versions of Jalview are
1129 not shown as thresholded features in 2.11. To workaround please
1130 create a Score filter instead.
1133 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1135 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1138 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1139 alignments with multiple views can close views unexpectedly
1142 <em>Java 11 Specific defects</em>
1145 <!-- JAL-3235 -->Jalview Properties file is not sorted
1146 alphabetically when saved
1152 <td width="60" nowrap>
1153 <div align="center">
1154 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1157 <td><div align="left">
1161 <!-- JAL-3101 -->Default memory for Jalview webstart and
1162 InstallAnywhere increased to 1G.
1165 <!-- JAL-247 -->Hidden sequence markers and representative
1166 sequence bolding included when exporting alignment as EPS,
1167 SVG, PNG or HTML. <em>Display is configured via the
1168 Format menu, or for command-line use via a Jalview
1169 properties file.</em>
1172 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1173 API and sequence data now imported as JSON.
1176 <!-- JAL-3065 -->Change in recommended way of starting
1177 Jalview via a Java command line: add jars in lib directory
1178 to CLASSPATH, rather than via the deprecated java.ext.dirs
1182 <em>Development</em>
1185 <!-- JAL-3047 -->Support added to execute test suite
1186 instrumented with <a href="http://openclover.org/">Open
1191 <td><div align="left">
1195 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1196 row shown in Feredoxin Structure alignment view of example
1200 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1201 annotation displayed.
1204 <!-- JAL-3107 -->Group conservation/consensus not shown
1205 for newly created group when 'Apply to all groups'
1209 <!-- JAL-3087 -->Corrupted display when switching to
1210 wrapped mode when sequence panel's vertical scrollbar is
1214 <!-- JAL-3003 -->Alignment is black in exported EPS file
1215 when sequences are selected in exported view.</em>
1218 <!-- JAL-3059 -->Groups with different coloured borders
1219 aren't rendered with correct colour.
1222 <!-- JAL-3092 -->Jalview could hang when importing certain
1223 types of knotted RNA secondary structure.
1226 <!-- JAL-3095 -->Sequence highlight and selection in
1227 trimmed VARNA 2D structure is incorrect for sequences that
1231 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1232 annotation when columns are inserted into an alignment,
1233 and when exporting as Stockholm flatfile.
1236 <!-- JAL-3053 -->Jalview annotation rows containing upper
1237 and lower-case 'E' and 'H' do not automatically get
1238 treated as RNA secondary structure.
1241 <!-- JAL-3106 -->.jvp should be used as default extension
1242 (not .jar) when saving a Jalview project file.
1245 <!-- JAL-3105 -->Mac Users: closing a window correctly
1246 transfers focus to previous window on OSX
1249 <em>Java 10 Issues Resolved</em>
1252 <!-- JAL-2988 -->OSX - Can't save new files via the File
1253 or export menus by typing in a name into the Save dialog
1257 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1258 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1259 'look and feel' which has improved compatibility with the
1260 latest version of OSX.
1267 <td width="60" nowrap>
1268 <div align="center">
1269 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1270 <em>7/06/2018</em></strong>
1273 <td><div align="left">
1277 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1278 annotation retrieved from Uniprot
1281 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1282 onto the Jalview Desktop
1286 <td><div align="left">
1290 <!-- JAL-3017 -->Cannot import features with multiple
1291 variant elements (blocks import of some Uniprot records)
1294 <!-- JAL-2997 -->Clustal files with sequence positions in
1295 right-hand column parsed correctly
1298 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1299 not alignment area in exported graphic
1302 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1303 window has input focus
1306 <!-- JAL-2992 -->Annotation panel set too high when
1307 annotation added to view (Windows)
1310 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1311 network connectivity is poor
1314 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1315 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1316 the currently open URL and links from a page viewed in
1317 Firefox or Chrome on Windows is now fully supported. If
1318 you are using Edge, only links in the page can be
1319 dragged, and with Internet Explorer, only the currently
1320 open URL in the browser can be dropped onto Jalview.</em>
1323 <em>New Known Defects</em>
1325 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1330 <td width="60" nowrap>
1331 <div align="center">
1332 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1335 <td><div align="left">
1339 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1340 for disabling automatic superposition of multiple
1341 structures and open structures in existing views
1344 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1345 ID and annotation area margins can be click-dragged to
1349 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1353 <!-- JAL-2759 -->Improved performance for large alignments
1354 and lots of hidden columns
1357 <!-- JAL-2593 -->Improved performance when rendering lots
1358 of features (particularly when transparency is disabled)
1361 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1362 exchange of Jalview features and Chimera attributes made
1368 <td><div align="left">
1371 <!-- JAL-2899 -->Structure and Overview aren't updated
1372 when Colour By Annotation threshold slider is adjusted
1375 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1376 overlapping alignment panel
1379 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1383 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1384 improved: CDS not handled correctly if transcript has no
1388 <!-- JAL-2321 -->Secondary structure and temperature
1389 factor annotation not added to sequence when local PDB
1390 file associated with it by drag'n'drop or structure
1394 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1395 dialog doesn't import PDB files dropped on an alignment
1398 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1399 scroll bar doesn't work for some CDS/Protein views
1402 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1403 Java 1.8u153 onwards and Java 1.9u4+.
1406 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1407 columns in annotation row
1410 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1411 honored in batch mode
1414 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1415 for structures added to existing Jmol view
1418 <!-- JAL-2223 -->'View Mappings' includes duplicate
1419 entries after importing project with multiple views
1422 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1423 protein sequences via SIFTS from associated PDB entries
1424 with negative residue numbers or missing residues fails
1427 <!-- JAL-2952 -->Exception when shading sequence with negative
1428 Temperature Factor values from annotated PDB files (e.g.
1429 as generated by CONSURF)
1432 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1433 tooltip doesn't include a text description of mutation
1436 <!-- JAL-2922 -->Invert displayed features very slow when
1437 structure and/or overview windows are also shown
1440 <!-- JAL-2954 -->Selecting columns from highlighted regions
1441 very slow for alignments with large numbers of sequences
1444 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1445 with 'StringIndexOutOfBounds'
1448 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1449 platforms running Java 10
1452 <!-- JAL-2960 -->Adding a structure to existing structure
1453 view appears to do nothing because the view is hidden behind the alignment view
1459 <!-- JAL-2926 -->Copy consensus sequence option in applet
1460 should copy the group consensus when popup is opened on it
1466 <!-- JAL-2913 -->Fixed ID width preference is not respected
1469 <em>New Known Defects</em>
1472 <!-- JAL-2973 --> Exceptions occasionally raised when
1473 editing a large alignment and overview is displayed
1476 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1477 repeatedly after a series of edits even when the overview
1478 is no longer reflecting updates
1481 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1482 structures for protein subsequence (if 'Trim Retrieved
1483 Sequences' enabled) or Ensembl isoforms (Workaround in
1484 2.10.4 is to fail back to N&W mapping)
1487 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1488 option gives blank output
1495 <td width="60" nowrap>
1496 <div align="center">
1497 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1500 <td><div align="left">
1501 <ul><li>Updated Certum Codesigning Certificate
1502 (Valid till 30th November 2018)</li></ul></div></td>
1503 <td><div align="left">
1504 <em>Desktop</em><ul>
1506 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1507 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1508 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1509 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1510 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1511 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1512 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1518 <td width="60" nowrap>
1519 <div align="center">
1520 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1523 <td><div align="left">
1527 <!-- JAL-2446 -->Faster and more efficient management and
1528 rendering of sequence features
1531 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1532 429 rate limit request hander
1535 <!-- JAL-2773 -->Structure views don't get updated unless
1536 their colours have changed
1539 <!-- JAL-2495 -->All linked sequences are highlighted for
1540 a structure mousover (Jmol) or selection (Chimera)
1543 <!-- JAL-2790 -->'Cancel' button in progress bar for
1544 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1547 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1548 view from Ensembl locus cross-references
1551 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1555 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1556 feature can be disabled
1559 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1560 PDB easier retrieval of sequences for lists of IDs
1563 <!-- JAL-2758 -->Short names for sequences retrieved from
1569 <li>Groovy interpreter updated to 2.4.12</li>
1570 <li>Example groovy script for generating a matrix of
1571 percent identity scores for current alignment.</li>
1573 <em>Testing and Deployment</em>
1576 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1580 <td><div align="left">
1584 <!-- JAL-2643 -->Pressing tab after updating the colour
1585 threshold text field doesn't trigger an update to the
1589 <!-- JAL-2682 -->Race condition when parsing sequence ID
1593 <!-- JAL-2608 -->Overview windows are also closed when
1594 alignment window is closed
1597 <!-- JAL-2548 -->Export of features doesn't always respect
1601 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1602 takes a long time in Cursor mode
1608 <!-- JAL-2777 -->Structures with whitespace chainCode
1609 cannot be viewed in Chimera
1612 <!-- JAL-2728 -->Protein annotation panel too high in
1616 <!-- JAL-2757 -->Can't edit the query after the server
1617 error warning icon is shown in Uniprot and PDB Free Text
1621 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1624 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1627 <!-- JAL-2739 -->Hidden column marker in last column not
1628 rendered when switching back from Wrapped to normal view
1631 <!-- JAL-2768 -->Annotation display corrupted when
1632 scrolling right in unwapped alignment view
1635 <!-- JAL-2542 -->Existing features on subsequence
1636 incorrectly relocated when full sequence retrieved from
1640 <!-- JAL-2733 -->Last reported memory still shown when
1641 Desktop->Show Memory is unticked (OSX only)
1644 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1645 features of same type and group to be selected for
1649 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1650 alignments when hidden columns are present
1653 <!-- JAL-2392 -->Jalview freezes when loading and
1654 displaying several structures
1657 <!-- JAL-2732 -->Black outlines left after resizing or
1661 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1662 within the Jalview desktop on OSX
1665 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1666 when in wrapped alignment mode
1669 <!-- JAL-2636 -->Scale mark not shown when close to right
1670 hand end of alignment
1673 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1674 each selected sequence do not have correct start/end
1678 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1679 after canceling the Alignment Window's Font dialog
1682 <!-- JAL-2036 -->Show cross-references not enabled after
1683 restoring project until a new view is created
1686 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1687 URL links appears when only default EMBL-EBI link is
1688 configured (since 2.10.2b2)
1691 <!-- JAL-2775 -->Overview redraws whole window when box
1692 position is adjusted
1695 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1696 in a multi-chain structure when viewing alignment
1697 involving more than one chain (since 2.10)
1700 <!-- JAL-2811 -->Double residue highlights in cursor mode
1701 if new selection moves alignment window
1704 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1705 arrow key in cursor mode to pass hidden column marker
1708 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1709 that produces correctly annotated transcripts and products
1712 <!-- JAL-2776 -->Toggling a feature group after first time
1713 doesn't update associated structure view
1716 <em>Applet</em><br />
1719 <!-- JAL-2687 -->Concurrent modification exception when
1720 closing alignment panel
1723 <em>BioJSON</em><br />
1726 <!-- JAL-2546 -->BioJSON export does not preserve
1727 non-positional features
1730 <em>New Known Issues</em>
1733 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1734 sequence features correctly (for many previous versions of
1738 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1739 using cursor in wrapped panel other than top
1742 <!-- JAL-2791 -->Select columns containing feature ignores
1743 graduated colour threshold
1746 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1747 always preserve numbering and sequence features
1750 <em>Known Java 9 Issues</em>
1753 <!-- JAL-2902 -->Groovy Console very slow to open and is
1754 not responsive when entering characters (Webstart, Java
1761 <td width="60" nowrap>
1762 <div align="center">
1763 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1764 <em>2/10/2017</em></strong>
1767 <td><div align="left">
1768 <em>New features in Jalview Desktop</em>
1771 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1773 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1777 <td><div align="left">
1781 <td width="60" nowrap>
1782 <div align="center">
1783 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1784 <em>7/9/2017</em></strong>
1787 <td><div align="left">
1791 <!-- JAL-2588 -->Show gaps in overview window by colouring
1792 in grey (sequences used to be coloured grey, and gaps were
1796 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1800 <!-- JAL-2587 -->Overview updates immediately on increase
1801 in size and progress bar shown as higher resolution
1802 overview is recalculated
1807 <td><div align="left">
1811 <!-- JAL-2664 -->Overview window redraws every hidden
1812 column region row by row
1815 <!-- JAL-2681 -->duplicate protein sequences shown after
1816 retrieving Ensembl crossrefs for sequences from Uniprot
1819 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1820 format setting is unticked
1823 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1824 if group has show boxes format setting unticked
1827 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1828 autoscrolling whilst dragging current selection group to
1829 include sequences and columns not currently displayed
1832 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1833 assemblies are imported via CIF file
1836 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1837 displayed when threshold or conservation colouring is also
1841 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1845 <!-- JAL-2673 -->Jalview continues to scroll after
1846 dragging a selected region off the visible region of the
1850 <!-- JAL-2724 -->Cannot apply annotation based
1851 colourscheme to all groups in a view
1854 <!-- JAL-2511 -->IDs don't line up with sequences
1855 initially after font size change using the Font chooser or
1862 <td width="60" nowrap>
1863 <div align="center">
1864 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1867 <td><div align="left">
1868 <em>Calculations</em>
1872 <!-- JAL-1933 -->Occupancy annotation row shows number of
1873 ungapped positions in each column of the alignment.
1876 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1877 a calculation dialog box
1880 <!-- JAL-2379 -->Revised implementation of PCA for speed
1881 and memory efficiency (~30x faster)
1884 <!-- JAL-2403 -->Revised implementation of sequence
1885 similarity scores as used by Tree, PCA, Shading Consensus
1886 and other calculations
1889 <!-- JAL-2416 -->Score matrices are stored as resource
1890 files within the Jalview codebase
1893 <!-- JAL-2500 -->Trees computed on Sequence Feature
1894 Similarity may have different topology due to increased
1901 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1902 model for alignments and groups
1905 <!-- JAL-384 -->Custom shading schemes created via groovy
1912 <!-- JAL-2526 -->Efficiency improvements for interacting
1913 with alignment and overview windows
1916 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1920 <!-- JAL-2388 -->Hidden columns and sequences can be
1924 <!-- JAL-2611 -->Click-drag in visible area allows fine
1925 adjustment of visible position
1929 <em>Data import/export</em>
1932 <!-- JAL-2535 -->Posterior probability annotation from
1933 Stockholm files imported as sequence associated annotation
1936 <!-- JAL-2507 -->More robust per-sequence positional
1937 annotation input/output via stockholm flatfile
1940 <!-- JAL-2533 -->Sequence names don't include file
1941 extension when importing structure files without embedded
1942 names or PDB accessions
1945 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1946 format sequence substitution matrices
1949 <em>User Interface</em>
1952 <!-- JAL-2447 --> Experimental Features Checkbox in
1953 Desktop's Tools menu to hide or show untested features in
1957 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1958 via Overview or sequence motif search operations
1961 <!-- JAL-2547 -->Amend sequence features dialog box can be
1962 opened by double clicking gaps within sequence feature
1966 <!-- JAL-1476 -->Status bar message shown when not enough
1967 aligned positions were available to create a 3D structure
1971 <em>3D Structure</em>
1974 <!-- JAL-2430 -->Hidden regions in alignment views are not
1975 coloured in linked structure views
1978 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1979 file-based command exchange
1982 <!-- JAL-2375 -->Structure chooser automatically shows
1983 Cached Structures rather than querying the PDBe if
1984 structures are already available for sequences
1987 <!-- JAL-2520 -->Structures imported via URL are cached in
1988 the Jalview project rather than downloaded again when the
1989 project is reopened.
1992 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1993 to transfer Chimera's structure attributes as Jalview
1994 features, and vice-versa (<strong>Experimental
1998 <em>Web Services</em>
2001 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2004 <!-- JAL-2335 -->Filter non-standard amino acids and
2005 nucleotides when submitting to AACon and other MSA
2009 <!-- JAL-2316, -->URLs for viewing database
2010 cross-references provided by identifiers.org and the
2011 EMBL-EBI's MIRIAM DB
2018 <!-- JAL-2344 -->FileFormatI interface for describing and
2019 identifying file formats (instead of String constants)
2022 <!-- JAL-2228 -->FeatureCounter script refactored for
2023 efficiency when counting all displayed features (not
2024 backwards compatible with 2.10.1)
2027 <em>Example files</em>
2030 <!-- JAL-2631 -->Graduated feature colour style example
2031 included in the example feature file
2034 <em>Documentation</em>
2037 <!-- JAL-2339 -->Release notes reformatted for readability
2038 with the built-in Java help viewer
2041 <!-- JAL-1644 -->Find documentation updated with 'search
2042 sequence description' option
2048 <!-- JAL-2485, -->External service integration tests for
2049 Uniprot REST Free Text Search Client
2052 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2055 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2060 <td><div align="left">
2061 <em>Calculations</em>
2064 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2065 matrix - C->R should be '-3'<br />Old matrix restored
2066 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2068 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2069 Jalview's treatment of gaps in PCA and substitution matrix
2070 based Tree calculations.<br /> <br />In earlier versions
2071 of Jalview, gaps matching gaps were penalised, and gaps
2072 matching non-gaps penalised even more. In the PCA
2073 calculation, gaps were actually treated as non-gaps - so
2074 different costs were applied, which meant Jalview's PCAs
2075 were different to those produced by SeqSpace.<br />Jalview
2076 now treats gaps in the same way as SeqSpace (ie it scores
2077 them as 0). <br /> <br />Enter the following in the
2078 Groovy console to restore pre-2.10.2 behaviour:<br />
2079 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2080 // for 2.10.1 mode <br />
2081 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2082 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2083 these settings will affect all subsequent tree and PCA
2084 calculations (not recommended)</em></li>
2086 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2087 scaling of branch lengths for trees computed using
2088 Sequence Feature Similarity.
2091 <!-- JAL-2377 -->PCA calculation could hang when
2092 generating output report when working with highly
2093 redundant alignments
2096 <!-- JAL-2544 --> Sort by features includes features to
2097 right of selected region when gaps present on right-hand
2101 <em>User Interface</em>
2104 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2105 doesn't reselect a specific sequence's associated
2106 annotation after it was used for colouring a view
2109 <!-- JAL-2419 -->Current selection lost if popup menu
2110 opened on a region of alignment without groups
2113 <!-- JAL-2374 -->Popup menu not always shown for regions
2114 of an alignment with overlapping groups
2117 <!-- JAL-2310 -->Finder double counts if both a sequence's
2118 name and description match
2121 <!-- JAL-2370 -->Hiding column selection containing two
2122 hidden regions results in incorrect hidden regions
2125 <!-- JAL-2386 -->'Apply to all groups' setting when
2126 changing colour does not apply Conservation slider value
2130 <!-- JAL-2373 -->Percentage identity and conservation menu
2131 items do not show a tick or allow shading to be disabled
2134 <!-- JAL-2385 -->Conservation shading or PID threshold
2135 lost when base colourscheme changed if slider not visible
2138 <!-- JAL-2547 -->Sequence features shown in tooltip for
2139 gaps before start of features
2142 <!-- JAL-2623 -->Graduated feature colour threshold not
2143 restored to UI when feature colour is edited
2146 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2147 a time when scrolling vertically in wrapped mode.
2150 <!-- JAL-2630 -->Structure and alignment overview update
2151 as graduate feature colour settings are modified via the
2155 <!-- JAL-2034 -->Overview window doesn't always update
2156 when a group defined on the alignment is resized
2159 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2160 wrapped view result in positional status updates
2164 <!-- JAL-2563 -->Status bar doesn't show position for
2165 ambiguous amino acid and nucleotide symbols
2168 <!-- JAL-2602 -->Copy consensus sequence failed if
2169 alignment included gapped columns
2172 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2173 widgets don't permanently disappear
2176 <!-- JAL-2503 -->Cannot select or filter quantitative
2177 annotation that are shown only as column labels (e.g.
2178 T-Coffee column reliability scores)
2181 <!-- JAL-2594 -->Exception thrown if trying to create a
2182 sequence feature on gaps only
2185 <!-- JAL-2504 -->Features created with 'New feature'
2186 button from a Find inherit previously defined feature type
2187 rather than the Find query string
2190 <!-- JAL-2423 -->incorrect title in output window when
2191 exporting tree calculated in Jalview
2194 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2195 and then revealing them reorders sequences on the
2199 <!-- JAL-964 -->Group panel in sequence feature settings
2200 doesn't update to reflect available set of groups after
2201 interactively adding or modifying features
2204 <!-- JAL-2225 -->Sequence Database chooser unusable on
2208 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2209 only excluded gaps in current sequence and ignored
2216 <!-- JAL-2421 -->Overview window visible region moves
2217 erratically when hidden rows or columns are present
2220 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2221 Structure Viewer's colour menu don't correspond to
2225 <!-- JAL-2405 -->Protein specific colours only offered in
2226 colour and group colour menu for protein alignments
2229 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2230 reflect currently selected view or group's shading
2234 <!-- JAL-2624 -->Feature colour thresholds not respected
2235 when rendered on overview and structures when opacity at
2239 <!-- JAL-2589 -->User defined gap colour not shown in
2240 overview when features overlaid on alignment
2243 <!-- JAL-2567 -->Feature settings for different views not
2244 recovered correctly from Jalview project file
2247 <!-- JAL-2256 -->Feature colours in overview when first opened
2248 (automatically via preferences) are different to the main
2252 <em>Data import/export</em>
2255 <!-- JAL-2576 -->Very large alignments take a long time to
2259 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2260 added after a sequence was imported are not written to
2264 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2265 when importing RNA secondary structure via Stockholm
2268 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2269 not shown in correct direction for simple pseudoknots
2272 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2273 with lightGray or darkGray via features file (but can
2277 <!-- JAL-2383 -->Above PID colour threshold not recovered
2278 when alignment view imported from project
2281 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2282 structure and sequences extracted from structure files
2283 imported via URL and viewed in Jmol
2286 <!-- JAL-2520 -->Structures loaded via URL are saved in
2287 Jalview Projects rather than fetched via URL again when
2288 the project is loaded and the structure viewed
2291 <em>Web Services</em>
2294 <!-- JAL-2519 -->EnsemblGenomes example failing after
2295 release of Ensembl v.88
2298 <!-- JAL-2366 -->Proxy server address and port always
2299 appear enabled in Preferences->Connections
2302 <!-- JAL-2461 -->DAS registry not found exceptions
2303 removed from console output
2306 <!-- JAL-2582 -->Cannot retrieve protein products from
2307 Ensembl by Peptide ID
2310 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2311 created from SIFTs, and spurious 'Couldn't open structure
2312 in Chimera' errors raised after April 2017 update (problem
2313 due to 'null' string rather than empty string used for
2314 residues with no corresponding PDB mapping).
2317 <em>Application UI</em>
2320 <!-- JAL-2361 -->User Defined Colours not added to Colour
2324 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2325 case' residues (button in colourscheme editor debugged and
2326 new documentation and tooltips added)
2329 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2330 doesn't restore group-specific text colour thresholds
2333 <!-- JAL-2243 -->Feature settings panel does not update as
2334 new features are added to alignment
2337 <!-- JAL-2532 -->Cancel in feature settings reverts
2338 changes to feature colours via the Amend features dialog
2341 <!-- JAL-2506 -->Null pointer exception when attempting to
2342 edit graduated feature colour via amend features dialog
2346 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2347 selection menu changes colours of alignment views
2350 <!-- JAL-2426 -->Spurious exceptions in console raised
2351 from alignment calculation workers after alignment has
2355 <!-- JAL-1608 -->Typo in selection popup menu - Create
2356 groups now 'Create Group'
2359 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2360 Create/Undefine group doesn't always work
2363 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2364 shown again after pressing 'Cancel'
2367 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2368 adjusts start position in wrap mode
2371 <!-- JAL-2563 -->Status bar doesn't show positions for
2372 ambiguous amino acids
2375 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2376 CDS/Protein view after CDS sequences added for aligned
2380 <!-- JAL-2592 -->User defined colourschemes called 'User
2381 Defined' don't appear in Colours menu
2387 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2388 score models doesn't always result in an updated PCA plot
2391 <!-- JAL-2442 -->Features not rendered as transparent on
2392 overview or linked structure view
2395 <!-- JAL-2372 -->Colour group by conservation doesn't
2399 <!-- JAL-2517 -->Hitting Cancel after applying
2400 user-defined colourscheme doesn't restore original
2407 <!-- JAL-2314 -->Unit test failure:
2408 jalview.ws.jabaws.RNAStructExportImport setup fails
2411 <!-- JAL-2307 -->Unit test failure:
2412 jalview.ws.sifts.SiftsClientTest due to compatibility
2413 problems with deep array comparison equality asserts in
2414 successive versions of TestNG
2417 <!-- JAL-2479 -->Relocated StructureChooserTest and
2418 ParameterUtilsTest Unit tests to Network suite
2421 <em>New Known Issues</em>
2424 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2425 phase after a sequence motif find operation
2428 <!-- JAL-2550 -->Importing annotation file with rows
2429 containing just upper and lower case letters are
2430 interpreted as WUSS RNA secondary structure symbols
2433 <!-- JAL-2590 -->Cannot load and display Newick trees
2434 reliably from eggnog Ortholog database
2437 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2438 containing features of type Highlight' when 'B' is pressed
2439 to mark columns containing highlighted regions.
2442 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2443 doesn't always add secondary structure annotation.
2448 <td width="60" nowrap>
2449 <div align="center">
2450 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2453 <td><div align="left">
2457 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2458 for all consensus calculations
2461 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2464 <li>Updated Jalview's Certum code signing certificate
2467 <em>Application</em>
2470 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2471 set of database cross-references, sorted alphabetically
2474 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2475 from database cross references. Users with custom links
2476 will receive a <a href="webServices/urllinks.html#warning">warning
2477 dialog</a> asking them to update their preferences.
2480 <!-- JAL-2287-->Cancel button and escape listener on
2481 dialog warning user about disconnecting Jalview from a
2485 <!-- JAL-2320-->Jalview's Chimera control window closes if
2486 the Chimera it is connected to is shut down
2489 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2490 columns menu item to mark columns containing highlighted
2491 regions (e.g. from structure selections or results of a
2495 <!-- JAL-2284-->Command line option for batch-generation
2496 of HTML pages rendering alignment data with the BioJS
2506 <!-- JAL-2286 -->Columns with more than one modal residue
2507 are not coloured or thresholded according to percent
2508 identity (first observed in Jalview 2.8.2)
2511 <!-- JAL-2301 -->Threonine incorrectly reported as not
2515 <!-- JAL-2318 -->Updates to documentation pages (above PID
2516 threshold, amino acid properties)
2519 <!-- JAL-2292 -->Lower case residues in sequences are not
2520 reported as mapped to residues in a structure file in the
2524 <!--JAL-2324 -->Identical features with non-numeric scores
2525 could be added multiple times to a sequence
2528 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2529 bond features shown as two highlighted residues rather
2530 than a range in linked structure views, and treated
2531 correctly when selecting and computing trees from features
2534 <!-- JAL-2281-->Custom URL links for database
2535 cross-references are matched to database name regardless
2540 <em>Application</em>
2543 <!-- JAL-2282-->Custom URL links for specific database
2544 names without regular expressions also offer links from
2548 <!-- JAL-2315-->Removing a single configured link in the
2549 URL links pane in Connections preferences doesn't actually
2550 update Jalview configuration
2553 <!-- JAL-2272-->CTRL-Click on a selected region to open
2554 the alignment area popup menu doesn't work on El-Capitan
2557 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2558 files with similarly named sequences if dropped onto the
2562 <!-- JAL-2312 -->Additional mappings are shown for PDB
2563 entries where more chains exist in the PDB accession than
2564 are reported in the SIFTS file
2567 <!-- JAL-2317-->Certain structures do not get mapped to
2568 the structure view when displayed with Chimera
2571 <!-- JAL-2317-->No chains shown in the Chimera view
2572 panel's View->Show Chains submenu
2575 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2576 work for wrapped alignment views
2579 <!--JAL-2197 -->Rename UI components for running JPred
2580 predictions from 'JNet' to 'JPred'
2583 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2584 corrupted when annotation panel vertical scroll is not at
2585 first annotation row
2588 <!--JAL-2332 -->Attempting to view structure for Hen
2589 lysozyme results in a PDB Client error dialog box
2592 <!-- JAL-2319 -->Structure View's mapping report switched
2593 ranges for PDB and sequence for SIFTS
2596 SIFTS 'Not_Observed' residues mapped to non-existant
2600 <!-- <em>New Known Issues</em>
2607 <td width="60" nowrap>
2608 <div align="center">
2609 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2610 <em>25/10/2016</em></strong>
2613 <td><em>Application</em>
2615 <li>3D Structure chooser opens with 'Cached structures'
2616 view if structures already loaded</li>
2617 <li>Progress bar reports models as they are loaded to
2618 structure views</li>
2624 <li>Colour by conservation always enabled and no tick
2625 shown in menu when BLOSUM or PID shading applied</li>
2626 <li>FER1_ARATH and FER2_ARATH labels were switched in
2627 example sequences/projects/trees</li>
2629 <em>Application</em>
2631 <li>Jalview projects with views of local PDB structure
2632 files saved on Windows cannot be opened on OSX</li>
2633 <li>Multiple structure views can be opened and superposed
2634 without timeout for structures with multiple models or
2635 multiple sequences in alignment</li>
2636 <li>Cannot import or associated local PDB files without a
2637 PDB ID HEADER line</li>
2638 <li>RMSD is not output in Jmol console when superposition
2640 <li>Drag and drop of URL from Browser fails for Linux and
2641 OSX versions earlier than El Capitan</li>
2642 <li>ENA client ignores invalid content from ENA server</li>
2643 <li>Exceptions are not raised in console when ENA client
2644 attempts to fetch non-existent IDs via Fetch DB Refs UI
2646 <li>Exceptions are not raised in console when a new view
2647 is created on the alignment</li>
2648 <li>OSX right-click fixed for group selections: CMD-click
2649 to insert/remove gaps in groups and CTRL-click to open group
2652 <em>Build and deployment</em>
2654 <li>URL link checker now copes with multi-line anchor
2657 <em>New Known Issues</em>
2659 <li>Drag and drop from URL links in browsers do not work
2666 <td width="60" nowrap>
2667 <div align="center">
2668 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2671 <td><em>General</em>
2674 <!-- JAL-2124 -->Updated Spanish translations.
2677 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2678 for importing structure data to Jalview. Enables mmCIF and
2682 <!-- JAL-192 --->Alignment ruler shows positions relative to
2686 <!-- JAL-2202 -->Position/residue shown in status bar when
2687 mousing over sequence associated annotation
2690 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2694 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2695 '()', canonical '[]' and invalid '{}' base pair populations
2699 <!-- JAL-2092 -->Feature settings popup menu options for
2700 showing or hiding columns containing a feature
2703 <!-- JAL-1557 -->Edit selected group by double clicking on
2704 group and sequence associated annotation labels
2707 <!-- JAL-2236 -->Sequence name added to annotation label in
2708 select/hide columns by annotation and colour by annotation
2712 </ul> <em>Application</em>
2715 <!-- JAL-2050-->Automatically hide introns when opening a
2716 gene/transcript view
2719 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2723 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2724 structure mappings with the EMBL-EBI PDBe SIFTS database
2727 <!-- JAL-2079 -->Updated download sites used for Rfam and
2728 Pfam sources to xfam.org
2731 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2734 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2735 over sequences in Jalview
2738 <!-- JAL-2027-->Support for reverse-complement coding
2739 regions in ENA and EMBL
2742 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2743 for record retrieval via ENA rest API
2746 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2750 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2751 groovy script execution
2754 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2755 alignment window's Calculate menu
2758 <!-- JAL-1812 -->Allow groovy scripts that call
2759 Jalview.getAlignFrames() to run in headless mode
2762 <!-- JAL-2068 -->Support for creating new alignment
2763 calculation workers from groovy scripts
2766 <!-- JAL-1369 --->Store/restore reference sequence in
2770 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2771 associations are now saved/restored from project
2774 <!-- JAL-1993 -->Database selection dialog always shown
2775 before sequence fetcher is opened
2778 <!-- JAL-2183 -->Double click on an entry in Jalview's
2779 database chooser opens a sequence fetcher
2782 <!-- JAL-1563 -->Free-text search client for UniProt using
2783 the UniProt REST API
2786 <!-- JAL-2168 -->-nonews command line parameter to prevent
2787 the news reader opening
2790 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2791 querying stored in preferences
2794 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2798 <!-- JAL-1977-->Tooltips shown on database chooser
2801 <!-- JAL-391 -->Reverse complement function in calculate
2802 menu for nucleotide sequences
2805 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2806 and feature counts preserves alignment ordering (and
2807 debugged for complex feature sets).
2810 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2811 viewing structures with Jalview 2.10
2814 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2815 genome, transcript CCDS and gene ids via the Ensembl and
2816 Ensembl Genomes REST API
2819 <!-- JAL-2049 -->Protein sequence variant annotation
2820 computed for 'sequence_variant' annotation on CDS regions
2824 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2828 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2829 Ref Fetcher fails to match, or otherwise updates sequence
2830 data from external database records.
2833 <!-- JAL-2154 -->Revised Jalview Project format for
2834 efficient recovery of sequence coding and alignment
2835 annotation relationships.
2837 </ul> <!-- <em>Applet</em>
2848 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2852 <!-- JAL-2018-->Export features in Jalview format (again)
2853 includes graduated colourschemes
2856 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2857 working with big alignments and lots of hidden columns
2860 <!-- JAL-2053-->Hidden column markers not always rendered
2861 at right of alignment window
2864 <!-- JAL-2067 -->Tidied up links in help file table of
2868 <!-- JAL-2072 -->Feature based tree calculation not shown
2872 <!-- JAL-2075 -->Hidden columns ignored during feature
2873 based tree calculation
2876 <!-- JAL-2065 -->Alignment view stops updating when show
2877 unconserved enabled for group on alignment
2880 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2884 <!-- JAL-2146 -->Alignment column in status incorrectly
2885 shown as "Sequence position" when mousing over
2889 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2890 hidden columns present
2893 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2894 user created annotation added to alignment
2897 <!-- JAL-1841 -->RNA Structure consensus only computed for
2898 '()' base pair annotation
2901 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2902 in zero scores for all base pairs in RNA Structure
2906 <!-- JAL-2174-->Extend selection with columns containing
2910 <!-- JAL-2275 -->Pfam format writer puts extra space at
2911 beginning of sequence
2914 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2918 <!-- JAL-2238 -->Cannot create groups on an alignment from
2919 from a tree when t-coffee scores are shown
2922 <!-- JAL-1836,1967 -->Cannot import and view PDB
2923 structures with chains containing negative resnums (4q4h)
2926 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2930 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2931 to Clustal, PIR and PileUp output
2934 <!-- JAL-2008 -->Reordering sequence features that are
2935 not visible causes alignment window to repaint
2938 <!-- JAL-2006 -->Threshold sliders don't work in
2939 graduated colour and colour by annotation row for e-value
2940 scores associated with features and annotation rows
2943 <!-- JAL-1797 -->amino acid physicochemical conservation
2944 calculation should be case independent
2947 <!-- JAL-2173 -->Remove annotation also updates hidden
2951 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2952 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2953 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2956 <!-- JAL-2065 -->Null pointer exceptions and redraw
2957 problems when reference sequence defined and 'show
2958 non-conserved' enabled
2961 <!-- JAL-1306 -->Quality and Conservation are now shown on
2962 load even when Consensus calculation is disabled
2965 <!-- JAL-1932 -->Remove right on penultimate column of
2966 alignment does nothing
2969 <em>Application</em>
2972 <!-- JAL-1552-->URLs and links can't be imported by
2973 drag'n'drop on OSX when launched via webstart (note - not
2974 yet fixed for El Capitan)
2977 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2978 output when running on non-gb/us i18n platforms
2981 <!-- JAL-1944 -->Error thrown when exporting a view with
2982 hidden sequences as flat-file alignment
2985 <!-- JAL-2030-->InstallAnywhere distribution fails when
2989 <!-- JAL-2080-->Jalview very slow to launch via webstart
2990 (also hotfix for 2.9.0b2)
2993 <!-- JAL-2085 -->Cannot save project when view has a
2994 reference sequence defined
2997 <!-- JAL-1011 -->Columns are suddenly selected in other
2998 alignments and views when revealing hidden columns
3001 <!-- JAL-1989 -->Hide columns not mirrored in complement
3002 view in a cDNA/Protein splitframe
3005 <!-- JAL-1369 -->Cannot save/restore representative
3006 sequence from project when only one sequence is
3010 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3011 in Structure Chooser
3014 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3015 structure consensus didn't refresh annotation panel
3018 <!-- JAL-1962 -->View mapping in structure view shows
3019 mappings between sequence and all chains in a PDB file
3022 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3023 dialogs format columns correctly, don't display array
3024 data, sort columns according to type
3027 <!-- JAL-1975 -->Export complete shown after destination
3028 file chooser is cancelled during an image export
3031 <!-- JAL-2025 -->Error when querying PDB Service with
3032 sequence name containing special characters
3035 <!-- JAL-2024 -->Manual PDB structure querying should be
3039 <!-- JAL-2104 -->Large tooltips with broken HTML
3040 formatting don't wrap
3043 <!-- JAL-1128 -->Figures exported from wrapped view are
3044 truncated so L looks like I in consensus annotation
3047 <!-- JAL-2003 -->Export features should only export the
3048 currently displayed features for the current selection or
3052 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3053 after fetching cross-references, and restoring from
3057 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3058 followed in the structure viewer
3061 <!-- JAL-2163 -->Titles for individual alignments in
3062 splitframe not restored from project
3065 <!-- JAL-2145 -->missing autocalculated annotation at
3066 trailing end of protein alignment in transcript/product
3067 splitview when pad-gaps not enabled by default
3070 <!-- JAL-1797 -->amino acid physicochemical conservation
3074 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3075 article has been read (reopened issue due to
3076 internationalisation problems)
3079 <!-- JAL-1960 -->Only offer PDB structures in structure
3080 viewer based on sequence name, PDB and UniProt
3085 <!-- JAL-1976 -->No progress bar shown during export of
3089 <!-- JAL-2213 -->Structures not always superimposed after
3090 multiple structures are shown for one or more sequences.
3093 <!-- JAL-1370 -->Reference sequence characters should not
3094 be replaced with '.' when 'Show unconserved' format option
3098 <!-- JAL-1823 -->Cannot specify chain code when entering
3099 specific PDB id for sequence
3102 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3103 'Export hidden sequences' is enabled, but 'export hidden
3104 columns' is disabled.
3107 <!--JAL-2026-->Best Quality option in structure chooser
3108 selects lowest rather than highest resolution structures
3112 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3113 to sequence mapping in 'View Mappings' report
3116 <!-- JAL-2284 -->Unable to read old Jalview projects that
3117 contain non-XML data added after Jalvew wrote project.
3120 <!-- JAL-2118 -->Newly created annotation row reorders
3121 after clicking on it to create new annotation for a
3125 <!-- JAL-1980 -->Null Pointer Exception raised when
3126 pressing Add on an orphaned cut'n'paste window.
3128 <!-- may exclude, this is an external service stability issue JAL-1941
3129 -- > RNA 3D structure not added via DSSR service</li> -->
3134 <!-- JAL-2151 -->Incorrect columns are selected when
3135 hidden columns present before start of sequence
3138 <!-- JAL-1986 -->Missing dependencies on applet pages
3142 <!-- JAL-1947 -->Overview pixel size changes when
3143 sequences are hidden in applet
3146 <!-- JAL-1996 -->Updated instructions for applet
3147 deployment on examples pages.
3154 <td width="60" nowrap>
3155 <div align="center">
3156 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3157 <em>16/10/2015</em></strong>
3160 <td><em>General</em>
3162 <li>Time stamps for signed Jalview application and applet
3167 <em>Application</em>
3169 <li>Duplicate group consensus and conservation rows
3170 shown when tree is partitioned</li>
3171 <li>Erratic behaviour when tree partitions made with
3172 multiple cDNA/Protein split views</li>
3178 <td width="60" nowrap>
3179 <div align="center">
3180 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3181 <em>8/10/2015</em></strong>
3184 <td><em>General</em>
3186 <li>Updated Spanish translations of localized text for
3188 </ul> <em>Application</em>
3190 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3191 <li>Signed OSX InstallAnywhere installer<br></li>
3192 <li>Support for per-sequence based annotations in BioJSON</li>
3193 </ul> <em>Applet</em>
3195 <li>Split frame example added to applet examples page</li>
3196 </ul> <em>Build and Deployment</em>
3199 <!-- JAL-1888 -->New ant target for running Jalview's test
3207 <li>Mapping of cDNA to protein in split frames
3208 incorrect when sequence start > 1</li>
3209 <li>Broken images in filter column by annotation dialog
3211 <li>Feature colours not parsed from features file</li>
3212 <li>Exceptions and incomplete link URLs recovered when
3213 loading a features file containing HTML tags in feature
3217 <em>Application</em>
3219 <li>Annotations corrupted after BioJS export and
3221 <li>Incorrect sequence limits after Fetch DB References
3222 with 'trim retrieved sequences'</li>
3223 <li>Incorrect warning about deleting all data when
3224 deleting selected columns</li>
3225 <li>Patch to build system for shipping properly signed
3226 JNLP templates for webstart launch</li>
3227 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3228 unreleased structures for download or viewing</li>
3229 <li>Tab/space/return keystroke operation of EMBL-PDBe
3230 fetcher/viewer dialogs works correctly</li>
3231 <li>Disabled 'minimise' button on Jalview windows
3232 running on OSX to workaround redraw hang bug</li>
3233 <li>Split cDNA/Protein view position and geometry not
3234 recovered from jalview project</li>
3235 <li>Initial enabled/disabled state of annotation menu
3236 sorter 'show autocalculated first/last' corresponds to
3238 <li>Restoring of Clustal, RNA Helices and T-Coffee
3239 color schemes from BioJSON</li>
3243 <li>Reorder sequences mirrored in cDNA/Protein split
3245 <li>Applet with Jmol examples not loading correctly</li>
3251 <td><div align="center">
3252 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3254 <td><em>General</em>
3256 <li>Linked visualisation and analysis of DNA and Protein
3259 <li>Translated cDNA alignments shown as split protein
3260 and DNA alignment views</li>
3261 <li>Codon consensus annotation for linked protein and
3262 cDNA alignment views</li>
3263 <li>Link cDNA or Protein product sequences by loading
3264 them onto Protein or cDNA alignments</li>
3265 <li>Reconstruct linked cDNA alignment from aligned
3266 protein sequences</li>
3269 <li>Jmol integration updated to Jmol v14.2.14</li>
3270 <li>Import and export of Jalview alignment views as <a
3271 href="features/bioJsonFormat.html">BioJSON</a></li>
3272 <li>New alignment annotation file statements for
3273 reference sequences and marking hidden columns</li>
3274 <li>Reference sequence based alignment shading to
3275 highlight variation</li>
3276 <li>Select or hide columns according to alignment
3278 <li>Find option for locating sequences by description</li>
3279 <li>Conserved physicochemical properties shown in amino
3280 acid conservation row</li>
3281 <li>Alignments can be sorted by number of RNA helices</li>
3282 </ul> <em>Application</em>
3284 <li>New cDNA/Protein analysis capabilities
3286 <li>Get Cross-References should open a Split Frame
3287 view with cDNA/Protein</li>
3288 <li>Detect when nucleotide sequences and protein
3289 sequences are placed in the same alignment</li>
3290 <li>Split cDNA/Protein views are saved in Jalview
3295 <li>Use REST API to talk to Chimera</li>
3296 <li>Selected regions in Chimera are highlighted in linked
3297 Jalview windows</li>
3299 <li>VARNA RNA viewer updated to v3.93</li>
3300 <li>VARNA views are saved in Jalview Projects</li>
3301 <li>Pseudoknots displayed as Jalview RNA annotation can
3302 be shown in VARNA</li>
3304 <li>Make groups for selection uses marked columns as well
3305 as the active selected region</li>
3307 <li>Calculate UPGMA and NJ trees using sequence feature
3309 <li>New Export options
3311 <li>New Export Settings dialog to control hidden
3312 region export in flat file generation</li>
3314 <li>Export alignment views for display with the <a
3315 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3317 <li>Export scrollable SVG in HTML page</li>
3318 <li>Optional embedding of BioJSON data when exporting
3319 alignment figures to HTML</li>
3321 <li>3D structure retrieval and display
3323 <li>Free text and structured queries with the PDBe
3325 <li>PDBe Search API based discovery and selection of
3326 PDB structures for a sequence set</li>
3330 <li>JPred4 employed for protein secondary structure
3332 <li>Hide Insertions menu option to hide unaligned columns
3333 for one or a group of sequences</li>
3334 <li>Automatically hide insertions in alignments imported
3335 from the JPred4 web server</li>
3336 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3337 system on OSX<br />LGPL libraries courtesy of <a
3338 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3340 <li>changed 'View nucleotide structure' submenu to 'View
3341 VARNA 2D Structure'</li>
3342 <li>change "View protein structure" menu option to "3D
3345 </ul> <em>Applet</em>
3347 <li>New layout for applet example pages</li>
3348 <li>New parameters to enable SplitFrame view
3349 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3350 <li>New example demonstrating linked viewing of cDNA and
3351 Protein alignments</li>
3352 </ul> <em>Development and deployment</em>
3354 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3355 <li>Include installation type and git revision in build
3356 properties and console log output</li>
3357 <li>Jalview Github organisation, and new github site for
3358 storing BioJsMSA Templates</li>
3359 <li>Jalview's unit tests now managed with TestNG</li>
3362 <!-- <em>General</em>
3364 </ul> --> <!-- issues resolved --> <em>Application</em>
3366 <li>Escape should close any open find dialogs</li>
3367 <li>Typo in select-by-features status report</li>
3368 <li>Consensus RNA secondary secondary structure
3369 predictions are not highlighted in amber</li>
3370 <li>Missing gap character in v2.7 example file means
3371 alignment appears unaligned when pad-gaps is not enabled</li>
3372 <li>First switch to RNA Helices colouring doesn't colour
3373 associated structure views</li>
3374 <li>ID width preference option is greyed out when auto
3375 width checkbox not enabled</li>
3376 <li>Stopped a warning dialog from being shown when
3377 creating user defined colours</li>
3378 <li>'View Mapping' in structure viewer shows sequence
3379 mappings for just that viewer's sequences</li>
3380 <li>Workaround for superposing PDB files containing
3381 multiple models in Chimera</li>
3382 <li>Report sequence position in status bar when hovering
3383 over Jmol structure</li>
3384 <li>Cannot output gaps as '.' symbols with Selection ->
3385 output to text box</li>
3386 <li>Flat file exports of alignments with hidden columns
3387 have incorrect sequence start/end</li>
3388 <li>'Aligning' a second chain to a Chimera structure from
3390 <li>Colour schemes applied to structure viewers don't
3391 work for nucleotide</li>
3392 <li>Loading/cut'n'pasting an empty or invalid file leads
3393 to a grey/invisible alignment window</li>
3394 <li>Exported Jpred annotation from a sequence region
3395 imports to different position</li>
3396 <li>Space at beginning of sequence feature tooltips shown
3397 on some platforms</li>
3398 <li>Chimera viewer 'View | Show Chain' menu is not
3400 <li>'New View' fails with a Null Pointer Exception in
3401 console if Chimera has been opened</li>
3402 <li>Mouseover to Chimera not working</li>
3403 <li>Miscellaneous ENA XML feature qualifiers not
3405 <li>NPE in annotation renderer after 'Extract Scores'</li>
3406 <li>If two structures in one Chimera window, mouseover of
3407 either sequence shows on first structure</li>
3408 <li>'Show annotations' options should not make
3409 non-positional annotations visible</li>
3410 <li>Subsequence secondary structure annotation not shown
3411 in right place after 'view flanking regions'</li>
3412 <li>File Save As type unset when current file format is
3414 <li>Save as '.jar' option removed for saving Jalview
3416 <li>Colour by Sequence colouring in Chimera more
3418 <li>Cannot 'add reference annotation' for a sequence in
3419 several views on same alignment</li>
3420 <li>Cannot show linked products for EMBL / ENA records</li>
3421 <li>Jalview's tooltip wraps long texts containing no
3423 </ul> <em>Applet</em>
3425 <li>Jmol to JalviewLite mouseover/link not working</li>
3426 <li>JalviewLite can't import sequences with ID
3427 descriptions containing angle brackets</li>
3428 </ul> <em>General</em>
3430 <li>Cannot export and reimport RNA secondary structure
3431 via jalview annotation file</li>
3432 <li>Random helix colour palette for colour by annotation
3433 with RNA secondary structure</li>
3434 <li>Mouseover to cDNA from STOP residue in protein
3435 translation doesn't work.</li>
3436 <li>hints when using the select by annotation dialog box</li>
3437 <li>Jmol alignment incorrect if PDB file has alternate CA
3439 <li>FontChooser message dialog appears to hang after
3440 choosing 1pt font</li>
3441 <li>Peptide secondary structure incorrectly imported from
3442 annotation file when annotation display text includes 'e' or
3444 <li>Cannot set colour of new feature type whilst creating
3446 <li>cDNA translation alignment should not be sequence
3447 order dependent</li>
3448 <li>'Show unconserved' doesn't work for lower case
3450 <li>Nucleotide ambiguity codes involving R not recognised</li>
3451 </ul> <em>Deployment and Documentation</em>
3453 <li>Applet example pages appear different to the rest of
3454 www.jalview.org</li>
3455 </ul> <em>Application Known issues</em>
3457 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3458 <li>Misleading message appears after trying to delete
3460 <li>Jalview icon not shown in dock after InstallAnywhere
3461 version launches</li>
3462 <li>Fetching EMBL reference for an RNA sequence results
3463 fails with a sequence mismatch</li>
3464 <li>Corrupted or unreadable alignment display when
3465 scrolling alignment to right</li>
3466 <li>ArrayIndexOutOfBoundsException thrown when remove
3467 empty columns called on alignment with ragged gapped ends</li>
3468 <li>auto calculated alignment annotation rows do not get
3469 placed above or below non-autocalculated rows</li>
3470 <li>Jalview dekstop becomes sluggish at full screen in
3471 ultra-high resolution</li>
3472 <li>Cannot disable consensus calculation independently of
3473 quality and conservation</li>
3474 <li>Mouseover highlighting between cDNA and protein can
3475 become sluggish with more than one splitframe shown</li>
3476 </ul> <em>Applet Known Issues</em>
3478 <li>Core PDB parsing code requires Jmol</li>
3479 <li>Sequence canvas panel goes white when alignment
3480 window is being resized</li>
3486 <td><div align="center">
3487 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3489 <td><em>General</em>
3491 <li>Updated Java code signing certificate donated by
3493 <li>Features and annotation preserved when performing
3494 pairwise alignment</li>
3495 <li>RNA pseudoknot annotation can be
3496 imported/exported/displayed</li>
3497 <li>'colour by annotation' can colour by RNA and
3498 protein secondary structure</li>
3499 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3500 post-hoc with 2.9 release</em>)
3503 </ul> <em>Application</em>
3505 <li>Extract and display secondary structure for sequences
3506 with 3D structures</li>
3507 <li>Support for parsing RNAML</li>
3508 <li>Annotations menu for layout
3510 <li>sort sequence annotation rows by alignment</li>
3511 <li>place sequence annotation above/below alignment
3514 <li>Output in Stockholm format</li>
3515 <li>Internationalisation: improved Spanish (es)
3517 <li>Structure viewer preferences tab</li>
3518 <li>Disorder and Secondary Structure annotation tracks
3519 shared between alignments</li>
3520 <li>UCSF Chimera launch and linked highlighting from
3522 <li>Show/hide all sequence associated annotation rows for
3523 all or current selection</li>
3524 <li>disorder and secondary structure predictions
3525 available as dataset annotation</li>
3526 <li>Per-sequence rna helices colouring</li>
3529 <li>Sequence database accessions imported when fetching
3530 alignments from Rfam</li>
3531 <li>update VARNA version to 3.91</li>
3533 <li>New groovy scripts for exporting aligned positions,
3534 conservation values, and calculating sum of pairs scores.</li>
3535 <li>Command line argument to set default JABAWS server</li>
3536 <li>include installation type in build properties and
3537 console log output</li>
3538 <li>Updated Jalview project format to preserve dataset
3542 <!-- issues resolved --> <em>Application</em>
3544 <li>Distinguish alignment and sequence associated RNA
3545 structure in structure->view->VARNA</li>
3546 <li>Raise dialog box if user deletes all sequences in an
3548 <li>Pressing F1 results in documentation opening twice</li>
3549 <li>Sequence feature tooltip is wrapped</li>
3550 <li>Double click on sequence associated annotation
3551 selects only first column</li>
3552 <li>Redundancy removal doesn't result in unlinked
3553 leaves shown in tree</li>
3554 <li>Undos after several redundancy removals don't undo
3556 <li>Hide sequence doesn't hide associated annotation</li>
3557 <li>User defined colours dialog box too big to fit on
3558 screen and buttons not visible</li>
3559 <li>author list isn't updated if already written to
3560 Jalview properties</li>
3561 <li>Popup menu won't open after retrieving sequence
3563 <li>File open window for associate PDB doesn't open</li>
3564 <li>Left-then-right click on a sequence id opens a
3565 browser search window</li>
3566 <li>Cannot open sequence feature shading/sort popup menu
3567 in feature settings dialog</li>
3568 <li>better tooltip placement for some areas of Jalview
3570 <li>Allow addition of JABAWS Server which doesn't
3571 pass validation</li>
3572 <li>Web services parameters dialog box is too large to
3574 <li>Muscle nucleotide alignment preset obscured by
3576 <li>JABAWS preset submenus don't contain newly
3577 defined user preset</li>
3578 <li>MSA web services warns user if they were launched
3579 with invalid input</li>
3580 <li>Jalview cannot contact DAS Registy when running on
3583 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3584 'Superpose with' submenu not shown when new view
3588 </ul> <!-- <em>Applet</em>
3590 </ul> <em>General</em>
3592 </ul>--> <em>Deployment and Documentation</em>
3594 <li>2G and 1G options in launchApp have no effect on
3595 memory allocation</li>
3596 <li>launchApp service doesn't automatically open
3597 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3599 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3600 InstallAnywhere reports cannot find valid JVM when Java
3601 1.7_055 is available
3603 </ul> <em>Application Known issues</em>
3606 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3607 corrupted or unreadable alignment display when scrolling
3611 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3612 retrieval fails but progress bar continues for DAS retrieval
3613 with large number of ID
3616 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3617 flatfile output of visible region has incorrect sequence
3621 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3622 rna structure consensus doesn't update when secondary
3623 structure tracks are rearranged
3626 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3627 invalid rna structure positional highlighting does not
3628 highlight position of invalid base pairs
3631 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3632 out of memory errors are not raised when saving Jalview
3633 project from alignment window file menu
3636 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3637 Switching to RNA Helices colouring doesn't propagate to
3641 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3642 colour by RNA Helices not enabled when user created
3643 annotation added to alignment
3646 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3647 Jalview icon not shown on dock in Mountain Lion/Webstart
3649 </ul> <em>Applet Known Issues</em>
3652 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3653 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3656 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3657 Jalview and Jmol example not compatible with IE9
3660 <li>Sort by annotation score doesn't reverse order
3666 <td><div align="center">
3667 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3670 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3673 <li>Internationalisation of user interface (usually
3674 called i18n support) and translation for Spanish locale</li>
3675 <li>Define/Undefine group on current selection with
3676 Ctrl-G/Shift Ctrl-G</li>
3677 <li>Improved group creation/removal options in
3678 alignment/sequence Popup menu</li>
3679 <li>Sensible precision for symbol distribution
3680 percentages shown in logo tooltip.</li>
3681 <li>Annotation panel height set according to amount of
3682 annotation when alignment first opened</li>
3683 </ul> <em>Application</em>
3685 <li>Interactive consensus RNA secondary structure
3686 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3687 <li>Select columns containing particular features from
3688 Feature Settings dialog</li>
3689 <li>View all 'representative' PDB structures for selected
3691 <li>Update Jalview project format:
3693 <li>New file extension for Jalview projects '.jvp'</li>
3694 <li>Preserve sequence and annotation dataset (to
3695 store secondary structure annotation,etc)</li>
3696 <li>Per group and alignment annotation and RNA helix
3700 <li>New similarity measures for PCA and Tree calculation
3702 <li>Experimental support for retrieval and viewing of
3703 flanking regions for an alignment</li>
3707 <!-- issues resolved --> <em>Application</em>
3709 <li>logo keeps spinning and status remains at queued or
3710 running after job is cancelled</li>
3711 <li>cannot export features from alignments imported from
3712 Jalview/VAMSAS projects</li>
3713 <li>Buggy slider for web service parameters that take
3715 <li>Newly created RNA secondary structure line doesn't
3716 have 'display all symbols' flag set</li>
3717 <li>T-COFFEE alignment score shading scheme and other
3718 annotation shading not saved in Jalview project</li>
3719 <li>Local file cannot be loaded in freshly downloaded
3721 <li>Jalview icon not shown on dock in Mountain
3723 <li>Load file from desktop file browser fails</li>
3724 <li>Occasional NPE thrown when calculating large trees</li>
3725 <li>Cannot reorder or slide sequences after dragging an
3726 alignment onto desktop</li>
3727 <li>Colour by annotation dialog throws NPE after using
3728 'extract scores' function</li>
3729 <li>Loading/cut'n'pasting an empty file leads to a grey
3730 alignment window</li>
3731 <li>Disorder thresholds rendered incorrectly after
3732 performing IUPred disorder prediction</li>
3733 <li>Multiple group annotated consensus rows shown when
3734 changing 'normalise logo' display setting</li>
3735 <li>Find shows blank dialog after 'finished searching' if
3736 nothing matches query</li>
3737 <li>Null Pointer Exceptions raised when sorting by
3738 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3740 <li>Errors in Jmol console when structures in alignment
3741 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3743 <li>Not all working JABAWS services are shown in
3745 <li>JAVAWS version of Jalview fails to launch with
3746 'invalid literal/length code'</li>
3747 <li>Annotation/RNA Helix colourschemes cannot be applied
3748 to alignment with groups (actually fixed in 2.8.0b1)</li>
3749 <li>RNA Helices and T-Coffee Scores available as default
3752 </ul> <em>Applet</em>
3754 <li>Remove group option is shown even when selection is
3756 <li>Apply to all groups ticked but colourscheme changes
3757 don't affect groups</li>
3758 <li>Documented RNA Helices and T-Coffee Scores as valid
3759 colourscheme name</li>
3760 <li>Annotation labels drawn on sequence IDs when
3761 Annotation panel is not displayed</li>
3762 <li>Increased font size for dropdown menus on OSX and
3763 embedded windows</li>
3764 </ul> <em>Other</em>
3766 <li>Consensus sequence for alignments/groups with a
3767 single sequence were not calculated</li>
3768 <li>annotation files that contain only groups imported as
3769 annotation and junk sequences</li>
3770 <li>Fasta files with sequences containing '*' incorrectly
3771 recognised as PFAM or BLC</li>
3772 <li>conservation/PID slider apply all groups option
3773 doesn't affect background (2.8.0b1)
3775 <li>redundancy highlighting is erratic at 0% and 100%</li>
3776 <li>Remove gapped columns fails for sequences with ragged
3778 <li>AMSA annotation row with leading spaces is not
3779 registered correctly on import</li>
3780 <li>Jalview crashes when selecting PCA analysis for
3781 certain alignments</li>
3782 <li>Opening the colour by annotation dialog for an
3783 existing annotation based 'use original colours'
3784 colourscheme loses original colours setting</li>
3789 <td><div align="center">
3790 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3791 <em>30/1/2014</em></strong>
3795 <li>Trusted certificates for JalviewLite applet and
3796 Jalview Desktop application<br />Certificate was donated by
3797 <a href="https://www.certum.eu">Certum</a> to the Jalview
3798 open source project).
3800 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3801 <li>Output in Stockholm format</li>
3802 <li>Allow import of data from gzipped files</li>
3803 <li>Export/import group and sequence associated line
3804 graph thresholds</li>
3805 <li>Nucleotide substitution matrix that supports RNA and
3806 ambiguity codes</li>
3807 <li>Allow disorder predictions to be made on the current
3808 selection (or visible selection) in the same way that JPred
3810 <li>Groovy scripting for headless Jalview operation</li>
3811 </ul> <em>Other improvements</em>
3813 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3814 <li>COMBINE statement uses current SEQUENCE_REF and
3815 GROUP_REF scope to group annotation rows</li>
3816 <li>Support '' style escaping of quotes in Newick
3818 <li>Group options for JABAWS service by command line name</li>
3819 <li>Empty tooltip shown for JABA service options with a
3820 link but no description</li>
3821 <li>Select primary source when selecting authority in
3822 database fetcher GUI</li>
3823 <li>Add .mfa to FASTA file extensions recognised by
3825 <li>Annotation label tooltip text wrap</li>
3830 <li>Slow scrolling when lots of annotation rows are
3832 <li>Lots of NPE (and slowness) after creating RNA
3833 secondary structure annotation line</li>
3834 <li>Sequence database accessions not imported when
3835 fetching alignments from Rfam</li>
3836 <li>Incorrect SHMR submission for sequences with
3838 <li>View all structures does not always superpose
3840 <li>Option widgets in service parameters not updated to
3841 reflect user or preset settings</li>
3842 <li>Null pointer exceptions for some services without
3843 presets or adjustable parameters</li>
3844 <li>Discover PDB IDs entry in structure menu doesn't
3845 discover PDB xRefs</li>
3846 <li>Exception encountered while trying to retrieve
3847 features with DAS</li>
3848 <li>Lowest value in annotation row isn't coloured
3849 when colour by annotation (per sequence) is coloured</li>
3850 <li>Keyboard mode P jumps to start of gapped region when
3851 residue follows a gap</li>
3852 <li>Jalview appears to hang importing an alignment with
3853 Wrap as default or after enabling Wrap</li>
3854 <li>'Right click to add annotations' message
3855 shown in wrap mode when no annotations present</li>
3856 <li>Disorder predictions fail with NPE if no automatic
3857 annotation already exists on alignment</li>
3858 <li>oninit javascript function should be called after
3859 initialisation completes</li>
3860 <li>Remove redundancy after disorder prediction corrupts
3861 alignment window display</li>
3862 <li>Example annotation file in documentation is invalid</li>
3863 <li>Grouped line graph annotation rows are not exported
3864 to annotation file</li>
3865 <li>Multi-harmony analysis cannot be run when only two
3867 <li>Cannot create multiple groups of line graphs with
3868 several 'combine' statements in annotation file</li>
3869 <li>Pressing return several times causes Number Format
3870 exceptions in keyboard mode</li>
3871 <li>Multi-harmony (SHMMR) method doesn't submit
3872 correct partitions for input data</li>
3873 <li>Translation from DNA to Amino Acids fails</li>
3874 <li>Jalview fail to load newick tree with quoted label</li>
3875 <li>--headless flag isn't understood</li>
3876 <li>ClassCastException when generating EPS in headless
3878 <li>Adjusting sequence-associated shading threshold only
3879 changes one row's threshold</li>
3880 <li>Preferences and Feature settings panel panel
3881 doesn't open</li>
3882 <li>hide consensus histogram also hides conservation and
3883 quality histograms</li>
3888 <td><div align="center">
3889 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3891 <td><em>Application</em>
3893 <li>Support for JABAWS 2.0 Services (AACon alignment
3894 conservation, protein disorder and Clustal Omega)</li>
3895 <li>JABAWS server status indicator in Web Services
3897 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3898 in Jalview alignment window</li>
3899 <li>Updated Jalview build and deploy framework for OSX
3900 mountain lion, windows 7, and 8</li>
3901 <li>Nucleotide substitution matrix for PCA that supports
3902 RNA and ambiguity codes</li>
3904 <li>Improved sequence database retrieval GUI</li>
3905 <li>Support fetching and database reference look up
3906 against multiple DAS sources (Fetch all from in 'fetch db
3908 <li>Jalview project improvements
3910 <li>Store and retrieve the 'belowAlignment'
3911 flag for annotation</li>
3912 <li>calcId attribute to group annotation rows on the
3914 <li>Store AACon calculation settings for a view in
3915 Jalview project</li>
3919 <li>horizontal scrolling gesture support</li>
3920 <li>Visual progress indicator when PCA calculation is
3922 <li>Simpler JABA web services menus</li>
3923 <li>visual indication that web service results are still
3924 being retrieved from server</li>
3925 <li>Serialise the dialogs that are shown when Jalview
3926 starts up for first time</li>
3927 <li>Jalview user agent string for interacting with HTTP
3929 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3931 <li>Examples directory and Groovy library included in
3932 InstallAnywhere distribution</li>
3933 </ul> <em>Applet</em>
3935 <li>RNA alignment and secondary structure annotation
3936 visualization applet example</li>
3937 </ul> <em>General</em>
3939 <li>Normalise option for consensus sequence logo</li>
3940 <li>Reset button in PCA window to return dimensions to
3942 <li>Allow seqspace or Jalview variant of alignment PCA
3944 <li>PCA with either nucleic acid and protein substitution
3946 <li>Allow windows containing HTML reports to be exported
3948 <li>Interactive display and editing of RNA secondary
3949 structure contacts</li>
3950 <li>RNA Helix Alignment Colouring</li>
3951 <li>RNA base pair logo consensus</li>
3952 <li>Parse sequence associated secondary structure
3953 information in Stockholm files</li>
3954 <li>HTML Export database accessions and annotation
3955 information presented in tooltip for sequences</li>
3956 <li>Import secondary structure from LOCARNA clustalw
3957 style RNA alignment files</li>
3958 <li>import and visualise T-COFFEE quality scores for an
3960 <li>'colour by annotation' per sequence option to
3961 shade each sequence according to its associated alignment
3963 <li>New Jalview Logo</li>
3964 </ul> <em>Documentation and Development</em>
3966 <li>documentation for score matrices used in Jalview</li>
3967 <li>New Website!</li>
3969 <td><em>Application</em>
3971 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3972 wsdbfetch REST service</li>
3973 <li>Stop windows being moved outside desktop on OSX</li>
3974 <li>Filetype associations not installed for webstart
3976 <li>Jalview does not always retrieve progress of a JABAWS
3977 job execution in full once it is complete</li>
3978 <li>revise SHMR RSBS definition to ensure alignment is
3979 uploaded via ali_file parameter</li>
3980 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3981 <li>View all structures superposed fails with exception</li>
3982 <li>Jnet job queues forever if a very short sequence is
3983 submitted for prediction</li>
3984 <li>Cut and paste menu not opened when mouse clicked on
3986 <li>Putting fractional value into integer text box in
3987 alignment parameter dialog causes Jalview to hang</li>
3988 <li>Structure view highlighting doesn't work on
3990 <li>View all structures fails with exception shown in
3992 <li>Characters in filename associated with PDBEntry not
3993 escaped in a platform independent way</li>
3994 <li>Jalview desktop fails to launch with exception when
3996 <li>Tree calculation reports 'you must have 2 or more
3997 sequences selected' when selection is empty</li>
3998 <li>Jalview desktop fails to launch with jar signature
3999 failure when java web start temporary file caching is
4001 <li>DAS Sequence retrieval with range qualification
4002 results in sequence xref which includes range qualification</li>
4003 <li>Errors during processing of command line arguments
4004 cause progress bar (JAL-898) to be removed</li>
4005 <li>Replace comma for semi-colon option not disabled for
4006 DAS sources in sequence fetcher</li>
4007 <li>Cannot close news reader when JABAWS server warning
4008 dialog is shown</li>
4009 <li>Option widgets not updated to reflect user settings</li>
4010 <li>Edited sequence not submitted to web service</li>
4011 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4012 <li>InstallAnywhere installer doesn't unpack and run
4013 on OSX Mountain Lion</li>
4014 <li>Annotation panel not given a scroll bar when
4015 sequences with alignment annotation are pasted into the
4017 <li>Sequence associated annotation rows not associated
4018 when loaded from Jalview project</li>
4019 <li>Browser launch fails with NPE on java 1.7</li>
4020 <li>JABAWS alignment marked as finished when job was
4021 cancelled or job failed due to invalid input</li>
4022 <li>NPE with v2.7 example when clicking on Tree
4023 associated with all views</li>
4024 <li>Exceptions when copy/paste sequences with grouped
4025 annotation rows to new window</li>
4026 </ul> <em>Applet</em>
4028 <li>Sequence features are momentarily displayed before
4029 they are hidden using hidefeaturegroups applet parameter</li>
4030 <li>loading features via javascript API automatically
4031 enables feature display</li>
4032 <li>scrollToColumnIn javascript API method doesn't
4034 </ul> <em>General</em>
4036 <li>Redundancy removal fails for rna alignment</li>
4037 <li>PCA calculation fails when sequence has been selected
4038 and then deselected</li>
4039 <li>PCA window shows grey box when first opened on OSX</li>
4040 <li>Letters coloured pink in sequence logo when alignment
4041 coloured with clustalx</li>
4042 <li>Choosing fonts without letter symbols defined causes
4043 exceptions and redraw errors</li>
4044 <li>Initial PCA plot view is not same as manually
4045 reconfigured view</li>
4046 <li>Grouped annotation graph label has incorrect line
4048 <li>Grouped annotation graph label display is corrupted
4049 for lots of labels</li>
4054 <div align="center">
4055 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4058 <td><em>Application</em>
4060 <li>Jalview Desktop News Reader</li>
4061 <li>Tweaked default layout of web services menu</li>
4062 <li>View/alignment association menu to enable user to
4063 easily specify which alignment a multi-structure view takes
4064 its colours/correspondences from</li>
4065 <li>Allow properties file location to be specified as URL</li>
4066 <li>Extend Jalview project to preserve associations
4067 between many alignment views and a single Jmol display</li>
4068 <li>Store annotation row height in Jalview project file</li>
4069 <li>Annotation row column label formatting attributes
4070 stored in project file</li>
4071 <li>Annotation row order for auto-calculated annotation
4072 rows preserved in Jalview project file</li>
4073 <li>Visual progress indication when Jalview state is
4074 saved using Desktop window menu</li>
4075 <li>Visual indication that command line arguments are
4076 still being processed</li>
4077 <li>Groovy script execution from URL</li>
4078 <li>Colour by annotation default min and max colours in
4080 <li>Automatically associate PDB files dragged onto an
4081 alignment with sequences that have high similarity and
4083 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4084 <li>'view structures' option to open many
4085 structures in same window</li>
4086 <li>Sort associated views menu option for tree panel</li>
4087 <li>Group all JABA and non-JABA services for a particular
4088 analysis function in its own submenu</li>
4089 </ul> <em>Applet</em>
4091 <li>Userdefined and autogenerated annotation rows for
4093 <li>Adjustment of alignment annotation pane height</li>
4094 <li>Annotation scrollbar for annotation panel</li>
4095 <li>Drag to reorder annotation rows in annotation panel</li>
4096 <li>'automaticScrolling' parameter</li>
4097 <li>Allow sequences with partial ID string matches to be
4098 annotated from GFF/Jalview features files</li>
4099 <li>Sequence logo annotation row in applet</li>
4100 <li>Absolute paths relative to host server in applet
4101 parameters are treated as such</li>
4102 <li>New in the JalviewLite javascript API:
4104 <li>JalviewLite.js javascript library</li>
4105 <li>Javascript callbacks for
4107 <li>Applet initialisation</li>
4108 <li>Sequence/alignment mouse-overs and selections</li>
4111 <li>scrollTo row and column alignment scrolling
4113 <li>Select sequence/alignment regions from javascript</li>
4114 <li>javascript structure viewer harness to pass
4115 messages between Jmol and Jalview when running as
4116 distinct applets</li>
4117 <li>sortBy method</li>
4118 <li>Set of applet and application examples shipped
4119 with documentation</li>
4120 <li>New example to demonstrate JalviewLite and Jmol
4121 javascript message exchange</li>
4123 </ul> <em>General</em>
4125 <li>Enable Jmol displays to be associated with multiple
4126 multiple alignments</li>
4127 <li>Option to automatically sort alignment with new tree</li>
4128 <li>User configurable link to enable redirects to a
4129 www.Jalview.org mirror</li>
4130 <li>Jmol colours option for Jmol displays</li>
4131 <li>Configurable newline string when writing alignment
4132 and other flat files</li>
4133 <li>Allow alignment annotation description lines to
4134 contain html tags</li>
4135 </ul> <em>Documentation and Development</em>
4137 <li>Add groovy test harness for bulk load testing to
4139 <li>Groovy script to load and align a set of sequences
4140 using a web service before displaying the result in the
4141 Jalview desktop</li>
4142 <li>Restructured javascript and applet api documentation</li>
4143 <li>Ant target to publish example html files with applet
4145 <li>Netbeans project for building Jalview from source</li>
4146 <li>ant task to create online javadoc for Jalview source</li>
4148 <td><em>Application</em>
4150 <li>User defined colourscheme throws exception when
4151 current built in colourscheme is saved as new scheme</li>
4152 <li>AlignFrame->Save in application pops up save
4153 dialog for valid filename/format</li>
4154 <li>Cannot view associated structure for UniProt sequence</li>
4155 <li>PDB file association breaks for UniProt sequence
4157 <li>Associate PDB from file dialog does not tell you
4158 which sequence is to be associated with the file</li>
4159 <li>Find All raises null pointer exception when query
4160 only matches sequence IDs</li>
4161 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4162 <li>Jalview project with Jmol views created with Jalview
4163 2.4 cannot be loaded</li>
4164 <li>Filetype associations not installed for webstart
4166 <li>Two or more chains in a single PDB file associated
4167 with sequences in different alignments do not get coloured
4168 by their associated sequence</li>
4169 <li>Visibility status of autocalculated annotation row
4170 not preserved when project is loaded</li>
4171 <li>Annotation row height and visibility attributes not
4172 stored in Jalview project</li>
4173 <li>Tree bootstraps are not preserved when saved as a
4174 Jalview project</li>
4175 <li>Envision2 workflow tooltips are corrupted</li>
4176 <li>Enabling show group conservation also enables colour
4177 by conservation</li>
4178 <li>Duplicate group associated conservation or consensus
4179 created on new view</li>
4180 <li>Annotation scrollbar not displayed after 'show
4181 all hidden annotation rows' option selected</li>
4182 <li>Alignment quality not updated after alignment
4183 annotation row is hidden then shown</li>
4184 <li>Preserve colouring of structures coloured by
4185 sequences in pre Jalview 2.7 projects</li>
4186 <li>Web service job parameter dialog is not laid out
4188 <li>Web services menu not refreshed after 'reset
4189 services' button is pressed in preferences</li>
4190 <li>Annotation off by one in Jalview v2_3 example project</li>
4191 <li>Structures imported from file and saved in project
4192 get name like jalview_pdb1234.txt when reloaded</li>
4193 <li>Jalview does not always retrieve progress of a JABAWS
4194 job execution in full once it is complete</li>
4195 </ul> <em>Applet</em>
4197 <li>Alignment height set incorrectly when lots of
4198 annotation rows are displayed</li>
4199 <li>Relative URLs in feature HTML text not resolved to
4201 <li>View follows highlighting does not work for positions
4203 <li><= shown as = in tooltip</li>
4204 <li>Export features raises exception when no features
4206 <li>Separator string used for serialising lists of IDs
4207 for javascript api is modified when separator string
4208 provided as parameter</li>
4209 <li>Null pointer exception when selecting tree leaves for
4210 alignment with no existing selection</li>
4211 <li>Relative URLs for datasources assumed to be relative
4212 to applet's codebase</li>
4213 <li>Status bar not updated after finished searching and
4214 search wraps around to first result</li>
4215 <li>StructureSelectionManager instance shared between
4216 several Jalview applets causes race conditions and memory
4218 <li>Hover tooltip and mouseover of position on structure
4219 not sent from Jmol in applet</li>
4220 <li>Certain sequences of javascript method calls to
4221 applet API fatally hang browser</li>
4222 </ul> <em>General</em>
4224 <li>View follows structure mouseover scrolls beyond
4225 position with wrapped view and hidden regions</li>
4226 <li>Find sequence position moves to wrong residue
4227 with/without hidden columns</li>
4228 <li>Sequence length given in alignment properties window
4230 <li>InvalidNumberFormat exceptions thrown when trying to
4231 import PDB like structure files</li>
4232 <li>Positional search results are only highlighted
4233 between user-supplied sequence start/end bounds</li>
4234 <li>End attribute of sequence is not validated</li>
4235 <li>Find dialog only finds first sequence containing a
4236 given sequence position</li>
4237 <li>Sequence numbering not preserved in MSF alignment
4239 <li>Jalview PDB file reader does not extract sequence
4240 from nucleotide chains correctly</li>
4241 <li>Structure colours not updated when tree partition
4242 changed in alignment</li>
4243 <li>Sequence associated secondary structure not correctly
4244 parsed in interleaved stockholm</li>
4245 <li>Colour by annotation dialog does not restore current
4247 <li>Hiding (nearly) all sequences doesn't work
4249 <li>Sequences containing lowercase letters are not
4250 properly associated with their pdb files</li>
4251 </ul> <em>Documentation and Development</em>
4253 <li>schemas/JalviewWsParamSet.xsd corrupted by
4254 ApplyCopyright tool</li>
4259 <div align="center">
4260 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4263 <td><em>Application</em>
4265 <li>New warning dialog when the Jalview Desktop cannot
4266 contact web services</li>
4267 <li>JABA service parameters for a preset are shown in
4268 service job window</li>
4269 <li>JABA Service menu entries reworded</li>
4273 <li>Modeller PIR IO broken - cannot correctly import a
4274 pir file emitted by Jalview</li>
4275 <li>Existing feature settings transferred to new
4276 alignment view created from cut'n'paste</li>
4277 <li>Improved test for mixed amino/nucleotide chains when
4278 parsing PDB files</li>
4279 <li>Consensus and conservation annotation rows
4280 occasionally become blank for all new windows</li>
4281 <li>Exception raised when right clicking above sequences
4282 in wrapped view mode</li>
4283 </ul> <em>Application</em>
4285 <li>multiple multiply aligned structure views cause cpu
4286 usage to hit 100% and computer to hang</li>
4287 <li>Web Service parameter layout breaks for long user
4288 parameter names</li>
4289 <li>Jaba service discovery hangs desktop if Jaba server
4296 <div align="center">
4297 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4300 <td><em>Application</em>
4302 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4303 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4306 <li>Web Services preference tab</li>
4307 <li>Analysis parameters dialog box and user defined
4309 <li>Improved speed and layout of Envision2 service menu</li>
4310 <li>Superpose structures using associated sequence
4312 <li>Export coordinates and projection as CSV from PCA
4314 </ul> <em>Applet</em>
4316 <li>enable javascript: execution by the applet via the
4317 link out mechanism</li>
4318 </ul> <em>Other</em>
4320 <li>Updated the Jmol Jalview interface to work with Jmol
4322 <li>The Jalview Desktop and JalviewLite applet now
4323 require Java 1.5</li>
4324 <li>Allow Jalview feature colour specification for GFF
4325 sequence annotation files</li>
4326 <li>New 'colour by label' keword in Jalview feature file
4327 type colour specification</li>
4328 <li>New Jalview Desktop Groovy API method that allows a
4329 script to check if it being run in an interactive session or
4330 in a batch operation from the Jalview command line</li>
4334 <li>clustalx colourscheme colours Ds preferentially when
4335 both D+E are present in over 50% of the column</li>
4336 </ul> <em>Application</em>
4338 <li>typo in AlignmentFrame->View->Hide->all but
4339 selected Regions menu item</li>
4340 <li>sequence fetcher replaces ',' for ';' when the ',' is
4341 part of a valid accession ID</li>
4342 <li>fatal OOM if object retrieved by sequence fetcher
4343 runs out of memory</li>
4344 <li>unhandled Out of Memory Error when viewing pca
4345 analysis results</li>
4346 <li>InstallAnywhere builds fail to launch on OS X java
4347 10.5 update 4 (due to apple Java 1.6 update)</li>
4348 <li>Installanywhere Jalview silently fails to launch</li>
4349 </ul> <em>Applet</em>
4351 <li>Jalview.getFeatureGroups() raises an
4352 ArrayIndexOutOfBoundsException if no feature groups are
4359 <div align="center">
4360 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4366 <li>Alignment prettyprinter doesn't cope with long
4368 <li>clustalx colourscheme colours Ds preferentially when
4369 both D+E are present in over 50% of the column</li>
4370 <li>nucleic acid structures retrieved from PDB do not
4371 import correctly</li>
4372 <li>More columns get selected than were clicked on when a
4373 number of columns are hidden</li>
4374 <li>annotation label popup menu not providing correct
4375 add/hide/show options when rows are hidden or none are
4377 <li>Stockholm format shown in list of readable formats,
4378 and parser copes better with alignments from RFAM.</li>
4379 <li>CSV output of consensus only includes the percentage
4380 of all symbols if sequence logo display is enabled</li>
4382 </ul> <em>Applet</em>
4384 <li>annotation panel disappears when annotation is
4386 </ul> <em>Application</em>
4388 <li>Alignment view not redrawn properly when new
4389 alignment opened where annotation panel is visible but no
4390 annotations are present on alignment</li>
4391 <li>pasted region containing hidden columns is
4392 incorrectly displayed in new alignment window</li>
4393 <li>Jalview slow to complete operations when stdout is
4394 flooded (fix is to close the Jalview console)</li>
4395 <li>typo in AlignmentFrame->View->Hide->all but
4396 selected Rregions menu item.</li>
4397 <li>inconsistent group submenu and Format submenu entry
4398 'Un' or 'Non'conserved</li>
4399 <li>Sequence feature settings are being shared by
4400 multiple distinct alignments</li>
4401 <li>group annotation not recreated when tree partition is
4403 <li>double click on group annotation to select sequences
4404 does not propagate to associated trees</li>
4405 <li>Mac OSX specific issues:
4407 <li>exception raised when mouse clicked on desktop
4408 window background</li>
4409 <li>Desktop menu placed on menu bar and application
4410 name set correctly</li>
4411 <li>sequence feature settings not wide enough for the
4412 save feature colourscheme button</li>
4421 <div align="center">
4422 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4425 <td><em>New Capabilities</em>
4427 <li>URL links generated from description line for
4428 regular-expression based URL links (applet and application)
4430 <li>Non-positional feature URL links are shown in link
4432 <li>Linked viewing of nucleic acid sequences and
4434 <li>Automatic Scrolling option in View menu to display
4435 the currently highlighted region of an alignment.</li>
4436 <li>Order an alignment by sequence length, or using the
4437 average score or total feature count for each sequence.</li>
4438 <li>Shading features by score or associated description</li>
4439 <li>Subdivide alignment and groups based on identity of
4440 selected subsequence (Make Groups from Selection).</li>
4441 <li>New hide/show options including Shift+Control+H to
4442 hide everything but the currently selected region.</li>
4443 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4444 </ul> <em>Application</em>
4446 <li>Fetch DB References capabilities and UI expanded to
4447 support retrieval from DAS sequence sources</li>
4448 <li>Local DAS Sequence sources can be added via the
4449 command line or via the Add local source dialog box.</li>
4450 <li>DAS Dbref and DbxRef feature types are parsed as
4451 database references and protein_name is parsed as
4452 description line (BioSapiens terms).</li>
4453 <li>Enable or disable non-positional feature and database
4454 references in sequence ID tooltip from View menu in
4456 <!-- <li>New hidden columns and rows and representatives capabilities
4457 in annotations file (in progress - not yet fully implemented)</li> -->
4458 <li>Group-associated consensus, sequence logos and
4459 conservation plots</li>
4460 <li>Symbol distributions for each column can be exported
4461 and visualized as sequence logos</li>
4462 <li>Optionally scale multi-character column labels to fit
4463 within each column of annotation row<!-- todo for applet -->
4465 <li>Optional automatic sort of associated alignment view
4466 when a new tree is opened.</li>
4467 <li>Jalview Java Console</li>
4468 <li>Better placement of desktop window when moving
4469 between different screens.</li>
4470 <li>New preference items for sequence ID tooltip and
4471 consensus annotation</li>
4472 <li>Client to submit sequences and IDs to Envision2
4474 <li><em>Vamsas Capabilities</em>
4476 <li>Improved VAMSAS synchronization (Jalview archive
4477 used to preserve views, structures, and tree display
4479 <li>Import of vamsas documents from disk or URL via
4481 <li>Sharing of selected regions between views and
4482 with other VAMSAS applications (Experimental feature!)</li>
4483 <li>Updated API to VAMSAS version 0.2</li>
4485 </ul> <em>Applet</em>
4487 <li>Middle button resizes annotation row height</li>
4490 <li>sortByTree (true/false) - automatically sort the
4491 associated alignment view by the tree when a new tree is
4493 <li>showTreeBootstraps (true/false) - show or hide
4494 branch bootstraps (default is to show them if available)</li>
4495 <li>showTreeDistances (true/false) - show or hide
4496 branch lengths (default is to show them if available)</li>
4497 <li>showUnlinkedTreeNodes (true/false) - indicate if
4498 unassociated nodes should be highlighted in the tree
4500 <li>heightScale and widthScale (1.0 or more) -
4501 increase the height or width of a cell in the alignment
4502 grid relative to the current font size.</li>
4505 <li>Non-positional features displayed in sequence ID
4507 </ul> <em>Other</em>
4509 <li>Features format: graduated colour definitions and
4510 specification of feature scores</li>
4511 <li>Alignment Annotations format: new keywords for group
4512 associated annotation (GROUP_REF) and annotation row display
4513 properties (ROW_PROPERTIES)</li>
4514 <li>XML formats extended to support graduated feature
4515 colourschemes, group associated annotation, and profile
4516 visualization settings.</li></td>
4519 <li>Source field in GFF files parsed as feature source
4520 rather than description</li>
4521 <li>Non-positional features are now included in sequence
4522 feature and gff files (controlled via non-positional feature
4523 visibility in tooltip).</li>
4524 <li>URL links generated for all feature links (bugfix)</li>
4525 <li>Added URL embedding instructions to features file
4527 <li>Codons containing ambiguous nucleotides translated as
4528 'X' in peptide product</li>
4529 <li>Match case switch in find dialog box works for both
4530 sequence ID and sequence string and query strings do not
4531 have to be in upper case to match case-insensitively.</li>
4532 <li>AMSA files only contain first column of
4533 multi-character column annotation labels</li>
4534 <li>Jalview Annotation File generation/parsing consistent
4535 with documentation (e.g. Stockholm annotation can be
4536 exported and re-imported)</li>
4537 <li>PDB files without embedded PDB IDs given a friendly
4539 <li>Find incrementally searches ID string matches as well
4540 as subsequence matches, and correctly reports total number
4544 <li>Better handling of exceptions during sequence
4546 <li>Dasobert generated non-positional feature URL
4547 link text excludes the start_end suffix</li>
4548 <li>DAS feature and source retrieval buttons disabled
4549 when fetch or registry operations in progress.</li>
4550 <li>PDB files retrieved from URLs are cached properly</li>
4551 <li>Sequence description lines properly shared via
4553 <li>Sequence fetcher fetches multiple records for all
4555 <li>Ensured that command line das feature retrieval
4556 completes before alignment figures are generated.</li>
4557 <li>Reduced time taken when opening file browser for
4559 <li>isAligned check prior to calculating tree, PCA or
4560 submitting an MSA to JNet now excludes hidden sequences.</li>
4561 <li>User defined group colours properly recovered
4562 from Jalview projects.</li>
4571 <div align="center">
4572 <strong>2.4.0.b2</strong><br> 28/10/2009
4577 <li>Experimental support for google analytics usage
4579 <li>Jalview privacy settings (user preferences and docs).</li>
4584 <li>Race condition in applet preventing startup in
4586 <li>Exception when feature created from selection beyond
4587 length of sequence.</li>
4588 <li>Allow synthetic PDB files to be imported gracefully</li>
4589 <li>Sequence associated annotation rows associate with
4590 all sequences with a given id</li>
4591 <li>Find function matches case-insensitively for sequence
4592 ID string searches</li>
4593 <li>Non-standard characters do not cause pairwise
4594 alignment to fail with exception</li>
4595 </ul> <em>Application Issues</em>
4597 <li>Sequences are now validated against EMBL database</li>
4598 <li>Sequence fetcher fetches multiple records for all
4600 </ul> <em>InstallAnywhere Issues</em>
4602 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4603 issue with installAnywhere mechanism)</li>
4604 <li>Command line launching of JARs from InstallAnywhere
4605 version (java class versioning error fixed)</li>
4612 <div align="center">
4613 <strong>2.4</strong><br> 27/8/2008
4616 <td><em>User Interface</em>
4618 <li>Linked highlighting of codon and amino acid from
4619 translation and protein products</li>
4620 <li>Linked highlighting of structure associated with
4621 residue mapping to codon position</li>
4622 <li>Sequence Fetcher provides example accession numbers
4623 and 'clear' button</li>
4624 <li>MemoryMonitor added as an option under Desktop's
4626 <li>Extract score function to parse whitespace separated
4627 numeric data in description line</li>
4628 <li>Column labels in alignment annotation can be centred.</li>
4629 <li>Tooltip for sequence associated annotation give name
4631 </ul> <em>Web Services and URL fetching</em>
4633 <li>JPred3 web service</li>
4634 <li>Prototype sequence search client (no public services
4636 <li>Fetch either seed alignment or full alignment from
4638 <li>URL Links created for matching database cross
4639 references as well as sequence ID</li>
4640 <li>URL Links can be created using regular-expressions</li>
4641 </ul> <em>Sequence Database Connectivity</em>
4643 <li>Retrieval of cross-referenced sequences from other
4645 <li>Generalised database reference retrieval and
4646 validation to all fetchable databases</li>
4647 <li>Fetch sequences from DAS sources supporting the
4648 sequence command</li>
4649 </ul> <em>Import and Export</em>
4650 <li>export annotation rows as CSV for spreadsheet import</li>
4651 <li>Jalview projects record alignment dataset associations,
4652 EMBL products, and cDNA sequence mappings</li>
4653 <li>Sequence Group colour can be specified in Annotation
4655 <li>Ad-hoc colouring of group in Annotation File using RGB
4656 triplet as name of colourscheme</li>
4657 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4659 <li>treenode binding for VAMSAS tree exchange</li>
4660 <li>local editing and update of sequences in VAMSAS
4661 alignments (experimental)</li>
4662 <li>Create new or select existing session to join</li>
4663 <li>load and save of vamsas documents</li>
4664 </ul> <em>Application command line</em>
4666 <li>-tree parameter to open trees (introduced for passing
4668 <li>-fetchfrom command line argument to specify nicknames
4669 of DAS servers to query for alignment features</li>
4670 <li>-dasserver command line argument to add new servers
4671 that are also automatically queried for features</li>
4672 <li>-groovy command line argument executes a given groovy
4673 script after all input data has been loaded and parsed</li>
4674 </ul> <em>Applet-Application data exchange</em>
4676 <li>Trees passed as applet parameters can be passed to
4677 application (when using "View in full
4678 application")</li>
4679 </ul> <em>Applet Parameters</em>
4681 <li>feature group display control parameter</li>
4682 <li>debug parameter</li>
4683 <li>showbutton parameter</li>
4684 </ul> <em>Applet API methods</em>
4686 <li>newView public method</li>
4687 <li>Window (current view) specific get/set public methods</li>
4688 <li>Feature display control methods</li>
4689 <li>get list of currently selected sequences</li>
4690 </ul> <em>New Jalview distribution features</em>
4692 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4693 <li>RELEASE file gives build properties for the latest
4694 Jalview release.</li>
4695 <li>Java 1.1 Applet build made easier and donotobfuscate
4696 property controls execution of obfuscator</li>
4697 <li>Build target for generating source distribution</li>
4698 <li>Debug flag for javacc</li>
4699 <li>.jalview_properties file is documented (slightly) in
4700 jalview.bin.Cache</li>
4701 <li>Continuous Build Integration for stable and
4702 development version of Application, Applet and source
4707 <li>selected region output includes visible annotations
4708 (for certain formats)</li>
4709 <li>edit label/displaychar contains existing label/char
4711 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4712 <li>shorter peptide product names from EMBL records</li>
4713 <li>Newick string generator makes compact representations</li>
4714 <li>bootstrap values parsed correctly for tree files with
4716 <li>pathological filechooser bug avoided by not allowing
4717 filenames containing a ':'</li>
4718 <li>Fixed exception when parsing GFF files containing
4719 global sequence features</li>
4720 <li>Alignment datasets are finalized only when number of
4721 references from alignment sequences goes to zero</li>
4722 <li>Close of tree branch colour box without colour
4723 selection causes cascading exceptions</li>
4724 <li>occasional negative imgwidth exceptions</li>
4725 <li>better reporting of non-fatal warnings to user when
4726 file parsing fails.</li>
4727 <li>Save works when Jalview project is default format</li>
4728 <li>Save as dialog opened if current alignment format is
4729 not a valid output format</li>
4730 <li>UniProt canonical names introduced for both das and
4732 <li>Histidine should be midblue (not pink!) in Zappo</li>
4733 <li>error messages passed up and output when data read
4735 <li>edit undo recovers previous dataset sequence when
4736 sequence is edited</li>
4737 <li>allow PDB files without pdb ID HEADER lines (like
4738 those generated by MODELLER) to be read in properly</li>
4739 <li>allow reading of JPred concise files as a normal
4741 <li>Stockholm annotation parsing and alignment properties
4742 import fixed for PFAM records</li>
4743 <li>Structure view windows have correct name in Desktop
4745 <li>annotation consisting of sequence associated scores
4746 can be read and written correctly to annotation file</li>
4747 <li>Aligned cDNA translation to aligned peptide works
4749 <li>Fixed display of hidden sequence markers and
4750 non-italic font for representatives in Applet</li>
4751 <li>Applet Menus are always embedded in applet window on
4753 <li>Newly shown features appear at top of stack (in
4755 <li>Annotations added via parameter not drawn properly
4756 due to null pointer exceptions</li>
4757 <li>Secondary structure lines are drawn starting from
4758 first column of alignment</li>
4759 <li>UniProt XML import updated for new schema release in
4761 <li>Sequence feature to sequence ID match for Features
4762 file is case-insensitive</li>
4763 <li>Sequence features read from Features file appended to
4764 all sequences with matching IDs</li>
4765 <li>PDB structure coloured correctly for associated views
4766 containing a sub-sequence</li>
4767 <li>PDB files can be retrieved by applet from Jar files</li>
4768 <li>feature and annotation file applet parameters
4769 referring to different directories are retrieved correctly</li>
4770 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4771 <li>Fixed application hang whilst waiting for
4772 splash-screen version check to complete</li>
4773 <li>Applet properly URLencodes input parameter values
4774 when passing them to the launchApp service</li>
4775 <li>display name and local features preserved in results
4776 retrieved from web service</li>
4777 <li>Visual delay indication for sequence retrieval and
4778 sequence fetcher initialisation</li>
4779 <li>updated Application to use DAS 1.53e version of
4780 dasobert DAS client</li>
4781 <li>Re-instated Full AMSA support and .amsa file
4783 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4791 <div align="center">
4792 <strong>2.3</strong><br> 9/5/07
4797 <li>Jmol 11.0.2 integration</li>
4798 <li>PDB views stored in Jalview XML files</li>
4799 <li>Slide sequences</li>
4800 <li>Edit sequence in place</li>
4801 <li>EMBL CDS features</li>
4802 <li>DAS Feature mapping</li>
4803 <li>Feature ordering</li>
4804 <li>Alignment Properties</li>
4805 <li>Annotation Scores</li>
4806 <li>Sort by scores</li>
4807 <li>Feature/annotation editing in applet</li>
4812 <li>Headless state operation in 2.2.1</li>
4813 <li>Incorrect and unstable DNA pairwise alignment</li>
4814 <li>Cut and paste of sequences with annotation</li>
4815 <li>Feature group display state in XML</li>
4816 <li>Feature ordering in XML</li>
4817 <li>blc file iteration selection using filename # suffix</li>
4818 <li>Stockholm alignment properties</li>
4819 <li>Stockhom alignment secondary structure annotation</li>
4820 <li>2.2.1 applet had no feature transparency</li>
4821 <li>Number pad keys can be used in cursor mode</li>
4822 <li>Structure Viewer mirror image resolved</li>
4829 <div align="center">
4830 <strong>2.2.1</strong><br> 12/2/07
4835 <li>Non standard characters can be read and displayed
4836 <li>Annotations/Features can be imported/exported to the
4838 <li>Applet allows editing of sequence/annotation/group
4839 name & description
4840 <li>Preference setting to display sequence name in
4842 <li>Annotation file format extended to allow
4843 Sequence_groups to be defined
4844 <li>Default opening of alignment overview panel can be
4845 specified in preferences
4846 <li>PDB residue numbering annotation added to associated
4852 <li>Applet crash under certain Linux OS with Java 1.6
4854 <li>Annotation file export / import bugs fixed
4855 <li>PNG / EPS image output bugs fixed
4861 <div align="center">
4862 <strong>2.2</strong><br> 27/11/06
4867 <li>Multiple views on alignment
4868 <li>Sequence feature editing
4869 <li>"Reload" alignment
4870 <li>"Save" to current filename
4871 <li>Background dependent text colour
4872 <li>Right align sequence ids
4873 <li>User-defined lower case residue colours
4876 <li>Menu item accelerator keys
4877 <li>Control-V pastes to current alignment
4878 <li>Cancel button for DAS Feature Fetching
4879 <li>PCA and PDB Viewers zoom via mouse roller
4880 <li>User-defined sub-tree colours and sub-tree selection
4882 <li>'New Window' button on the 'Output to Text box'
4887 <li>New memory efficient Undo/Redo System
4888 <li>Optimised symbol lookups and conservation/consensus
4890 <li>Region Conservation/Consensus recalculated after
4892 <li>Fixed Remove Empty Columns Bug (empty columns at end
4894 <li>Slowed DAS Feature Fetching for increased robustness.
4896 <li>Made angle brackets in ASCII feature descriptions
4898 <li>Re-instated Zoom function for PCA
4899 <li>Sequence descriptions conserved in web service
4901 <li>UniProt ID discoverer uses any word separated by
4903 <li>WsDbFetch query/result association resolved
4904 <li>Tree leaf to sequence mapping improved
4905 <li>Smooth fonts switch moved to FontChooser dialog box.
4912 <div align="center">
4913 <strong>2.1.1</strong><br> 12/9/06
4918 <li>Copy consensus sequence to clipboard</li>
4923 <li>Image output - rightmost residues are rendered if
4924 sequence id panel has been resized</li>
4925 <li>Image output - all offscreen group boundaries are
4927 <li>Annotation files with sequence references - all
4928 elements in file are relative to sequence position</li>
4929 <li>Mac Applet users can use Alt key for group editing</li>
4935 <div align="center">
4936 <strong>2.1</strong><br> 22/8/06
4941 <li>MAFFT Multiple Alignment in default Web Service list</li>
4942 <li>DAS Feature fetching</li>
4943 <li>Hide sequences and columns</li>
4944 <li>Export Annotations and Features</li>
4945 <li>GFF file reading / writing</li>
4946 <li>Associate structures with sequences from local PDB
4948 <li>Add sequences to exisiting alignment</li>
4949 <li>Recently opened files / URL lists</li>
4950 <li>Applet can launch the full application</li>
4951 <li>Applet has transparency for features (Java 1.2
4953 <li>Applet has user defined colours parameter</li>
4954 <li>Applet can load sequences from parameter
4955 "sequence<em>x</em>"
4961 <li>Redundancy Panel reinstalled in the Applet</li>
4962 <li>Monospaced font - EPS / rescaling bug fixed</li>
4963 <li>Annotation files with sequence references bug fixed</li>
4969 <div align="center">
4970 <strong>2.08.1</strong><br> 2/5/06
4975 <li>Change case of selected region from Popup menu</li>
4976 <li>Choose to match case when searching</li>
4977 <li>Middle mouse button and mouse movement can compress /
4978 expand the visible width and height of the alignment</li>
4983 <li>Annotation Panel displays complete JNet results</li>
4989 <div align="center">
4990 <strong>2.08b</strong><br> 18/4/06
4996 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4997 <li>Righthand label on wrapped alignments shows correct
5004 <div align="center">
5005 <strong>2.08</strong><br> 10/4/06
5010 <li>Editing can be locked to the selection area</li>
5011 <li>Keyboard editing</li>
5012 <li>Create sequence features from searches</li>
5013 <li>Precalculated annotations can be loaded onto
5015 <li>Features file allows grouping of features</li>
5016 <li>Annotation Colouring scheme added</li>
5017 <li>Smooth fonts off by default - Faster rendering</li>
5018 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5023 <li>Drag & Drop fixed on Linux</li>
5024 <li>Jalview Archive file faster to load/save, sequence
5025 descriptions saved.</li>
5031 <div align="center">
5032 <strong>2.07</strong><br> 12/12/05
5037 <li>PDB Structure Viewer enhanced</li>
5038 <li>Sequence Feature retrieval and display enhanced</li>
5039 <li>Choose to output sequence start-end after sequence
5040 name for file output</li>
5041 <li>Sequence Fetcher WSDBFetch@EBI</li>
5042 <li>Applet can read feature files, PDB files and can be
5043 used for HTML form input</li>
5048 <li>HTML output writes groups and features</li>
5049 <li>Group editing is Control and mouse click</li>
5050 <li>File IO bugs</li>
5056 <div align="center">
5057 <strong>2.06</strong><br> 28/9/05
5062 <li>View annotations in wrapped mode</li>
5063 <li>More options for PCA viewer</li>
5068 <li>GUI bugs resolved</li>
5069 <li>Runs with -nodisplay from command line</li>
5075 <div align="center">
5076 <strong>2.05b</strong><br> 15/9/05
5081 <li>Choose EPS export as lineart or text</li>
5082 <li>Jar files are executable</li>
5083 <li>Can read in Uracil - maps to unknown residue</li>
5088 <li>Known OutOfMemory errors give warning message</li>
5089 <li>Overview window calculated more efficiently</li>
5090 <li>Several GUI bugs resolved</li>
5096 <div align="center">
5097 <strong>2.05</strong><br> 30/8/05
5102 <li>Edit and annotate in "Wrapped" view</li>
5107 <li>Several GUI bugs resolved</li>
5113 <div align="center">
5114 <strong>2.04</strong><br> 24/8/05
5119 <li>Hold down mouse wheel & scroll to change font
5125 <li>Improved JPred client reliability</li>
5126 <li>Improved loading of Jalview files</li>
5132 <div align="center">
5133 <strong>2.03</strong><br> 18/8/05
5138 <li>Set Proxy server name and port in preferences</li>
5139 <li>Multiple URL links from sequence ids</li>
5140 <li>User Defined Colours can have a scheme name and added
5142 <li>Choose to ignore gaps in consensus calculation</li>
5143 <li>Unix users can set default web browser</li>
5144 <li>Runs without GUI for batch processing</li>
5145 <li>Dynamically generated Web Service Menus</li>
5150 <li>InstallAnywhere download for Sparc Solaris</li>
5156 <div align="center">
5157 <strong>2.02</strong><br> 18/7/05
5163 <li>Copy & Paste order of sequences maintains
5164 alignment order.</li>
5170 <div align="center">
5171 <strong>2.01</strong><br> 12/7/05
5176 <li>Use delete key for deleting selection.</li>
5177 <li>Use Mouse wheel to scroll sequences.</li>
5178 <li>Help file updated to describe how to add alignment
5180 <li>Version and build date written to build properties
5182 <li>InstallAnywhere installation will check for updates
5183 at launch of Jalview.</li>
5188 <li>Delete gaps bug fixed.</li>
5189 <li>FileChooser sorts columns.</li>
5190 <li>Can remove groups one by one.</li>
5191 <li>Filechooser icons installed.</li>
5192 <li>Finder ignores return character when searching.
5193 Return key will initiate a search.<br>
5200 <div align="center">
5201 <strong>2.0</strong><br> 20/6/05
5206 <li>New codebase</li>