3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
61 <em>27/10/2020</em></strong></td>
62 <td align="left" valign="top">
67 <td align="left" valign="top">
70 <!-- JAL-3765 -->Find doesn't always highlight all matching
71 positions in a sequence
74 <!-- JAL-3611 -->Space character in Jalview install path on
75 Windows prevents install4j launching getdown
81 <td width="60" align="center" nowrap><strong><a
82 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
83 <em>25/09/2020</em></strong></td>
84 <td align="left" valign="top">
88 <td align="left" valign="top">
91 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
92 "Encountered problems opening
93 https://www.jalview.org/examples/exampleFile_2_7.jvp"
99 <td width="60" align="center" nowrap><strong><a
100 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
101 <em>17/09/2020</em></strong></td>
102 <td align="left" valign="top">
105 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
106 residue in cursor mode
109 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
110 HTSJDK from 2.12 to 2.23
113 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
114 optimisations and improvements suggested by Bob Hanson and
115 improved compatibility with JalviewJS
118 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
119 alignments from Pfam and Rfam
122 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
123 import (no longer based on .gz extension)
126 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
129 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
130 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
134 <!-- JAL-3667 -->Improved warning messages, debug logging
135 and fixed Retry action when Jalview encounters errors when
136 saving or making backup files.
139 <!-- JAL-3676 -->Enhanced Jalview Java Console:
141 <li>Jalview's logging level can be configured</li>
142 <li>Copy to Clipboard Buttion</li>
146 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
147 when running on Linux (Requires Java 11+)
149 </ul> <em>Launching Jalview</em>
152 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
153 through a system property
156 <!-- JAL-3477 -->Improved built-in documentation and command
157 line help for configuring Jalview's memory
161 <td align="left" valign="top">
164 <!-- JAL-3691 -->Conservation and Quality tracks are shown
165 but not calculated and no protein or DNA score models are
166 available for tree/PCA calculation when launched with
167 Turkish language locale
170 <!-- JAL-3493 -->Escape does not clear highlights on the
171 alignment (Since Jalview 2.10.3)
174 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
175 doesn't slide selected sequences, just sequence under cursor
178 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
179 sequence under the cursor
182 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
183 multiple EMBL gene products shown forĀ a single contig
186 <!-- JAL-3696 -->Errors encountered when processing variants
187 from VCF files yield "Error processing VCF: Format specifier
191 <!-- JAL-3697 -->Count of features not shown can be wrong
192 when there are both local and complementary features mapped
193 to the position under the cursor
196 <!-- JAL-3673 -->Sequence ID for reference sequence is
197 clipped when Right align Sequence IDs enabled
200 <!-- JAL-2983 -->Slider with negative range values not
201 rendered correctly in VAqua4 (Since 2.10.4)
204 <!-- JAL-3685 -->Single quotes not displayed correctly in
205 internationalised text for some messages and log output
208 <!-- JAL-3490 -->Find doesn't report matches that span
209 hidden gapped columns
212 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
213 panels, Alignment viewport and annotation renderer.
216 <!-- JAL-3561 -->Jalview ignores file format parameter
217 specifying output format when exporting an alignment via the
221 <!-- JAL-3667 -->Windows 10: For a minority of users, if
222 backups are not enabled, Jalview sometimes fails to
223 overwrite an existing file and raises a warning dialog. (in
224 2.11.0, and 2.11.1.0, the workaround is to try to save the
225 file again, and if that fails, delete the original file and
229 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
233 <!-- JAL-3741 -->References to http://www.jalview.org in
234 program and documentation
236 </ul> <em>Launching Jalview</em>
239 <!-- JAL-3718 -->Jalview application fails when launched the
240 first time for a version that has different jars to the
241 previous launched version.
243 </ul> <em>Developing Jalview</em>
246 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
247 data, causing cloverReport gradle task to fail with an
251 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
252 monitor the release channel
254 </ul> <em>New Known defects</em>
257 <!-- JAL-3748 -->CDS shown in result of submitting proteins
258 in a CDS/Protein alignment to a web service is wrong when
259 proteins share a common transcript sequence (e.g.
260 genome of RNA viruses)
263 <!-- JAL-3576 -->Co-located features exported and re-imported
264 are ordered differently when shown on alignment and in
265 tooltips. (Also affects v2.11.1.0)
268 <!-- JAL-3702 -->Drag and drop of alignment file onto
269 alignment window when in a HiDPI scaled mode in Linux only
270 works for the top left quadrant of the alignment window
273 <!-- JAL-3701 -->Stale build data in jalview standalone jar
274 builds (only affects 2.11.1.1 branch)
277 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
278 when alignment view restored from project (since Jalview 2.11.0)
284 <td width="60" align="center" nowrap><strong><a
285 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
286 <em>22/04/2020</em></strong></td>
287 <td align="left" valign="top">
290 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
291 'virtual' codon features shown on protein (or vice versa)
292 for display in alignments, on structure views (including
293 transfer to UCSF chimera), in feature reports and for
297 <!-- JAL-3121 -->Feature attributes from VCF files can be
298 exported and re-imported as GFF3 files
301 <!-- JAL-3376 -->Capture VCF "fixed column" values
302 POS, ID, QUAL, FILTER as Feature Attributes
305 <!-- JAL-3375 -->More robust VCF numeric data field
306 validation while parsing
309 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
313 <!-- JAL-3535 -->Feature Settings dialog title includes name
317 <!-- JAL-3538 -->Font anti-aliasing in alignment views
321 <!-- JAL-3468 -->Very long feature descriptions truncated in
325 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
326 with no feature types visible
329 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
331 </ul><em>Jalview Installer</em>
334 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
335 in console (may be null when Jalview launched as executable jar or via conda)
338 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
341 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
344 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
346 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
347 </ul> <em>Release processes</em>
350 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
353 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
355 </ul> <em>Build System</em>
358 <!-- JAL-3510 -->Clover updated to 4.4.1
361 <!-- JAL-3513 -->Test code included in Clover coverage
365 <em>Groovy Scripts</em>
368 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
369 to stdout containing the consensus sequence for each
370 alignment in a Jalview session
373 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
374 genomic sequence_variant annotation from CDS as
375 missense_variant or synonymous_variant on protein products.
379 <td align="left" valign="top">
382 <!-- JAL-3581 -->Hidden sequence markers still visible when
383 'Show hidden markers' option is not ticked
386 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
387 PNG output when 'Automatically set ID width' is set in
388 jalview preferences or properties file
391 <!-- JAL-3571 -->Feature Editor dialog can be opened when
392 'Show Sequence Features' option is not ticked
395 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
396 buttons in Feature Settings dialog are clicked when no
400 <!-- JAL-3412 -->ID margins for CDS and Protein views not
401 equal when split frame is first opened
404 <!-- JAL-3296 -->Sequence position numbers in status bar not
405 correct after editing a sequence's start position
408 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
409 with annotation and exceptions thrown when only a few
410 columns shown in wrapped mode
413 <!-- JAL-3386 -->Sequence IDs missing in headless export of
414 wrapped alignment figure with annotations
417 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
418 ID fails with ClassCastException
421 <!-- JAL-3389 -->Chimera session not restored from Jalview
425 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
426 feature settings dialog also selects columns
429 <!-- JAL-3473 -->SpinnerNumberModel causes
430 IllegalArgumentException in some circumstances
433 <!-- JAL-3534 -->Multiple feature settings dialogs can be
437 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
438 alignment window is closed
441 <!-- JAL-3406 -->Credits missing some authors in Jalview
442 help documentation for 2.11.0 release
445 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
446 includes Pfam ID as sequence's accession rather than its
449 </ul> <em>Java 11 Compatibility issues</em>
452 <!-- JAL-2987 -->OSX - Can't view some search results in
453 PDB/Uniprot search panel
455 </ul> <em>Installer</em>
458 <!-- JAL-3447 -->Jalview should not create file associations
459 for 3D structure files (.pdb, .mmcif. .cif)
461 </ul> <em>Repository and Source Release</em>
464 <!-- JAL-3474 -->removed obsolete .cvsignore files from
468 <!-- JAL-3541 -->Clover report generation running out of
471 </ul> <em>New Known Issues</em>
474 <!-- JAL-3523 -->OSX - Current working directory not
475 preserved when Jalview.app launched with parameters from
479 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
480 clipped in headless figure export when Right Align option
484 <!-- JAL-3542 -->Jalview Installation type always reports
485 'Source' in console output
488 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
489 bamboo server but run fine locally.
495 <td width="60" align="center" nowrap>
496 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
497 <em>04/07/2019</em></strong>
499 <td align="left" valign="top">
502 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
503 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
504 source project) rather than InstallAnywhere
507 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
508 settings, receive over the air updates and launch specific
509 versions via (<a href="https://github.com/threerings/getdown">Three
513 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
514 formats supported by Jalview (including .jvp project files)
517 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
518 arguments and switch between different getdown channels
521 <!-- JAL-3141 -->Backup files created when saving Jalview project
526 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
527 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
529 <!-- JAL-2620 -->Alternative genetic code tables for
530 'Translate as cDNA'</li>
532 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
533 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
536 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
537 implementation that allows updates) used for Sequence Feature collections</li>
539 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
540 features can be filtered and shaded according to any
541 associated attributes (e.g. variant attributes from VCF
542 file, or key-value pairs imported from column 9 of GFF
546 <!-- JAL-2879 -->Feature Attributes and shading schemes
547 stored and restored from Jalview Projects
550 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
551 recognise variant features
554 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
555 sequences (also coloured red by default)
558 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
562 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
563 algorithm (Z-sort/transparency and filter aware)
566 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
572 <!-- JAL-3205 -->Symmetric score matrices for faster
573 tree and PCA calculations
575 <li><strong>Principal Components Analysis Viewer</strong>
578 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
579 and Viewer state saved in Jalview Project
581 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
584 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
588 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
593 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
595 <li><strong>Speed and Efficiency</strong>
598 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
599 multiple groups when working with large alignments
602 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
606 <li><strong>User Interface</strong>
609 <!-- JAL-2933 -->Finder panel remembers last position in each
613 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
614 what is shown)<br />Only visible regions of alignment are shown by
615 default (can be changed in user preferences)
618 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
619 to the Overwrite Dialog
622 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
626 <!-- JAL-1244 -->Status bar shows bounds when dragging a
627 selection region, and gap count when inserting or deleting gaps
630 <!-- JAL-3132 -->Status bar updates over sequence and annotation
634 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
638 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
642 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
645 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
649 <!-- JAL-3181 -->Consistent ordering of links in sequence id
653 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
655 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
659 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
660 <li><strong>Java 11 Support (not yet on general release)</strong>
663 <!-- -->OSX GUI integrations for App menu's 'About' entry and
668 <em>Deprecations</em>
670 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
671 capabilities removed from the Jalview Desktop
673 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
674 unmarshalling has been replaced by JAXB for Jalview projects
675 and XML based data retrieval clients</li>
676 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
677 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
678 </ul> <em>Documentation</em>
680 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
681 not supported in EPS figure export
683 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
684 </ul> <em>Development and Release Processes</em>
687 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
690 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
692 <!-- JAL-3225 -->Eclipse project configuration managed with
696 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
697 Bamboo continuous integration for unattended Test Suite
701 <!-- JAL-2864 -->Memory test suite to detect leaks in common
705 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
709 <!-- JAL-3248 -->Developer documentation migrated to
710 markdown (with HTML rendering)
713 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
716 <!-- JAL-3289 -->New URLs for publishing development
721 <td align="left" valign="top">
724 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
727 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
728 superposition in Jmol fail on Windows
731 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
732 structures for sequences with lots of PDB structures
735 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
739 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
740 project involving multiple views
743 <!-- JAL-3164 -->Overview for complementary view in a linked
744 CDS/Protein alignment is not updated when Hide Columns by
745 Annotation dialog hides columns
748 <!-- JAL-3158 -->Selection highlighting in the complement of a
749 CDS/Protein alignment stops working after making a selection in
750 one view, then making another selection in the other view
753 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
757 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
758 Settings and Jalview Preferences panels
761 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
762 overview with large alignments
765 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
766 region if columns were selected by dragging right-to-left and the
767 mouse moved to the left of the first column
770 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
771 hidden column marker via scale popup menu
774 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
775 doesn't tell users the invalid URL
778 <!-- JAL-2816 -->Tooltips displayed for features filtered by
782 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
783 show cross references or Fetch Database References are shown in
787 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
788 peptide sequence (computed variant shown as p.Res.null)
791 <!-- JAL-2060 -->'Graduated colour' option not offered for
792 manually created features (where feature score is Float.NaN)
795 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
796 when columns are hidden
799 <!-- JAL-3082 -->Regular expression error for '(' in Select
800 Columns by Annotation description
803 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
804 out of Scale or Annotation Panel
807 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
811 <!-- JAL-3074 -->Left/right drag in annotation can scroll
815 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
819 <!-- JAL-3002 -->Column display is out by one after Page Down,
820 Page Up in wrapped mode
823 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
826 <!-- JAL-2932 -->Finder searches in minimised alignments
829 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
830 on opening an alignment
833 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
837 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
838 different groups in the alignment are selected
841 <!-- JAL-2717 -->Internationalised colour scheme names not shown
845 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
849 <!-- JAL-3125 -->Value input for graduated feature colour
850 threshold gets 'unrounded'
853 <!-- JAL-2982 -->PCA image export doesn't respect background
857 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
860 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
863 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
867 <!-- JAL-2964 -->Associate Tree with All Views not restored from
871 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
872 shown in complementary view
875 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
876 without normalisation
879 <!-- JAL-3021 -->Sequence Details report should open positioned at top
883 <!-- JAL-914 -->Help page can be opened twice
886 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
888 </ul> <em>Editing</em>
891 <!-- JAL-2822 -->Start and End should be updated when sequence
892 data at beginning or end of alignment added/removed via 'Edit'
896 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
897 relocate sequence features correctly when start of sequence is
898 removed (Known defect since 2.10)
901 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
902 dialog corrupts dataset sequence
905 <!-- JAL-868 -->Structure colours not updated when associated tree
906 repartitions the alignment view (Regression in 2.10.5)
908 </ul> <em>Datamodel</em>
911 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
912 sequence's End is greater than its length
914 </ul> <em>Bugs fixed for Java 11 Support (not yet on
915 general release)</em>
918 <!-- JAL-3288 -->Menus work properly in split-screen
920 </ul> <em>New Known Defects</em>
923 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
926 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
927 regions of protein alignment.
930 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
931 is restored from a Jalview 2.11 project
934 <!-- JAL-3213 -->Alignment panel height can be too small after
938 <!-- JAL-3240 -->Display is incorrect after removing gapped
939 columns within hidden columns
942 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
943 window after dragging left to select columns to left of visible
947 <!-- JAL-2876 -->Features coloured according to their description
948 string and thresholded by score in earlier versions of Jalview are
949 not shown as thresholded features in 2.11. To workaround please
950 create a Score filter instead.
953 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
955 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
958 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
959 alignments with multiple views can close views unexpectedly
962 <em>Java 11 Specific defects</em>
965 <!-- JAL-3235 -->Jalview Properties file is not sorted
966 alphabetically when saved
972 <td width="60" nowrap>
974 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
977 <td><div align="left">
981 <!-- JAL-3101 -->Default memory for Jalview webstart and
982 InstallAnywhere increased to 1G.
985 <!-- JAL-247 -->Hidden sequence markers and representative
986 sequence bolding included when exporting alignment as EPS,
987 SVG, PNG or HTML. <em>Display is configured via the
988 Format menu, or for command-line use via a Jalview
989 properties file.</em>
992 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
993 API and sequence data now imported as JSON.
996 <!-- JAL-3065 -->Change in recommended way of starting
997 Jalview via a Java command line: add jars in lib directory
998 to CLASSPATH, rather than via the deprecated java.ext.dirs
1002 <em>Development</em>
1005 <!-- JAL-3047 -->Support added to execute test suite
1006 instrumented with <a href="http://openclover.org/">Open
1011 <td><div align="left">
1015 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1016 row shown in Feredoxin Structure alignment view of example
1020 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1021 annotation displayed.
1024 <!-- JAL-3107 -->Group conservation/consensus not shown
1025 for newly created group when 'Apply to all groups'
1029 <!-- JAL-3087 -->Corrupted display when switching to
1030 wrapped mode when sequence panel's vertical scrollbar is
1034 <!-- JAL-3003 -->Alignment is black in exported EPS file
1035 when sequences are selected in exported view.</em>
1038 <!-- JAL-3059 -->Groups with different coloured borders
1039 aren't rendered with correct colour.
1042 <!-- JAL-3092 -->Jalview could hang when importing certain
1043 types of knotted RNA secondary structure.
1046 <!-- JAL-3095 -->Sequence highlight and selection in
1047 trimmed VARNA 2D structure is incorrect for sequences that
1051 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1052 annotation when columns are inserted into an alignment,
1053 and when exporting as Stockholm flatfile.
1056 <!-- JAL-3053 -->Jalview annotation rows containing upper
1057 and lower-case 'E' and 'H' do not automatically get
1058 treated as RNA secondary structure.
1061 <!-- JAL-3106 -->.jvp should be used as default extension
1062 (not .jar) when saving a Jalview project file.
1065 <!-- JAL-3105 -->Mac Users: closing a window correctly
1066 transfers focus to previous window on OSX
1069 <em>Java 10 Issues Resolved</em>
1072 <!-- JAL-2988 -->OSX - Can't save new files via the File
1073 or export menus by typing in a name into the Save dialog
1077 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1078 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1079 'look and feel' which has improved compatibility with the
1080 latest version of OSX.
1087 <td width="60" nowrap>
1088 <div align="center">
1089 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1090 <em>7/06/2018</em></strong>
1093 <td><div align="left">
1097 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1098 annotation retrieved from Uniprot
1101 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1102 onto the Jalview Desktop
1106 <td><div align="left">
1110 <!-- JAL-3017 -->Cannot import features with multiple
1111 variant elements (blocks import of some Uniprot records)
1114 <!-- JAL-2997 -->Clustal files with sequence positions in
1115 right-hand column parsed correctly
1118 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1119 not alignment area in exported graphic
1122 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1123 window has input focus
1126 <!-- JAL-2992 -->Annotation panel set too high when
1127 annotation added to view (Windows)
1130 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1131 network connectivity is poor
1134 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1135 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1136 the currently open URL and links from a page viewed in
1137 Firefox or Chrome on Windows is now fully supported. If
1138 you are using Edge, only links in the page can be
1139 dragged, and with Internet Explorer, only the currently
1140 open URL in the browser can be dropped onto Jalview.</em>
1143 <em>New Known Defects</em>
1145 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1150 <td width="60" nowrap>
1151 <div align="center">
1152 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1155 <td><div align="left">
1159 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1160 for disabling automatic superposition of multiple
1161 structures and open structures in existing views
1164 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1165 ID and annotation area margins can be click-dragged to
1169 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1173 <!-- JAL-2759 -->Improved performance for large alignments
1174 and lots of hidden columns
1177 <!-- JAL-2593 -->Improved performance when rendering lots
1178 of features (particularly when transparency is disabled)
1181 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1182 exchange of Jalview features and Chimera attributes made
1188 <td><div align="left">
1191 <!-- JAL-2899 -->Structure and Overview aren't updated
1192 when Colour By Annotation threshold slider is adjusted
1195 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1196 overlapping alignment panel
1199 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1203 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1204 improved: CDS not handled correctly if transcript has no
1208 <!-- JAL-2321 -->Secondary structure and temperature
1209 factor annotation not added to sequence when local PDB
1210 file associated with it by drag'n'drop or structure
1214 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1215 dialog doesn't import PDB files dropped on an alignment
1218 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1219 scroll bar doesn't work for some CDS/Protein views
1222 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1223 Java 1.8u153 onwards and Java 1.9u4+.
1226 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1227 columns in annotation row
1230 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1231 honored in batch mode
1234 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1235 for structures added to existing Jmol view
1238 <!-- JAL-2223 -->'View Mappings' includes duplicate
1239 entries after importing project with multiple views
1242 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1243 protein sequences via SIFTS from associated PDB entries
1244 with negative residue numbers or missing residues fails
1247 <!-- JAL-2952 -->Exception when shading sequence with negative
1248 Temperature Factor values from annotated PDB files (e.g.
1249 as generated by CONSURF)
1252 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1253 tooltip doesn't include a text description of mutation
1256 <!-- JAL-2922 -->Invert displayed features very slow when
1257 structure and/or overview windows are also shown
1260 <!-- JAL-2954 -->Selecting columns from highlighted regions
1261 very slow for alignments with large numbers of sequences
1264 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1265 with 'StringIndexOutOfBounds'
1268 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1269 platforms running Java 10
1272 <!-- JAL-2960 -->Adding a structure to existing structure
1273 view appears to do nothing because the view is hidden behind the alignment view
1279 <!-- JAL-2926 -->Copy consensus sequence option in applet
1280 should copy the group consensus when popup is opened on it
1286 <!-- JAL-2913 -->Fixed ID width preference is not respected
1289 <em>New Known Defects</em>
1292 <!-- JAL-2973 --> Exceptions occasionally raised when
1293 editing a large alignment and overview is displayed
1296 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1297 repeatedly after a series of edits even when the overview
1298 is no longer reflecting updates
1301 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1302 structures for protein subsequence (if 'Trim Retrieved
1303 Sequences' enabled) or Ensembl isoforms (Workaround in
1304 2.10.4 is to fail back to N&W mapping)
1307 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1308 option gives blank output
1315 <td width="60" nowrap>
1316 <div align="center">
1317 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1320 <td><div align="left">
1321 <ul><li>Updated Certum Codesigning Certificate
1322 (Valid till 30th November 2018)</li></ul></div></td>
1323 <td><div align="left">
1324 <em>Desktop</em><ul>
1326 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1327 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1328 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1329 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1330 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1331 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1332 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1338 <td width="60" nowrap>
1339 <div align="center">
1340 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1343 <td><div align="left">
1347 <!-- JAL-2446 -->Faster and more efficient management and
1348 rendering of sequence features
1351 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1352 429 rate limit request hander
1355 <!-- JAL-2773 -->Structure views don't get updated unless
1356 their colours have changed
1359 <!-- JAL-2495 -->All linked sequences are highlighted for
1360 a structure mousover (Jmol) or selection (Chimera)
1363 <!-- JAL-2790 -->'Cancel' button in progress bar for
1364 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1367 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1368 view from Ensembl locus cross-references
1371 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1375 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1376 feature can be disabled
1379 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1380 PDB easier retrieval of sequences for lists of IDs
1383 <!-- JAL-2758 -->Short names for sequences retrieved from
1389 <li>Groovy interpreter updated to 2.4.12</li>
1390 <li>Example groovy script for generating a matrix of
1391 percent identity scores for current alignment.</li>
1393 <em>Testing and Deployment</em>
1396 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1400 <td><div align="left">
1404 <!-- JAL-2643 -->Pressing tab after updating the colour
1405 threshold text field doesn't trigger an update to the
1409 <!-- JAL-2682 -->Race condition when parsing sequence ID
1413 <!-- JAL-2608 -->Overview windows are also closed when
1414 alignment window is closed
1417 <!-- JAL-2548 -->Export of features doesn't always respect
1421 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1422 takes a long time in Cursor mode
1428 <!-- JAL-2777 -->Structures with whitespace chainCode
1429 cannot be viewed in Chimera
1432 <!-- JAL-2728 -->Protein annotation panel too high in
1436 <!-- JAL-2757 -->Can't edit the query after the server
1437 error warning icon is shown in Uniprot and PDB Free Text
1441 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1444 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1447 <!-- JAL-2739 -->Hidden column marker in last column not
1448 rendered when switching back from Wrapped to normal view
1451 <!-- JAL-2768 -->Annotation display corrupted when
1452 scrolling right in unwapped alignment view
1455 <!-- JAL-2542 -->Existing features on subsequence
1456 incorrectly relocated when full sequence retrieved from
1460 <!-- JAL-2733 -->Last reported memory still shown when
1461 Desktop->Show Memory is unticked (OSX only)
1464 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1465 features of same type and group to be selected for
1469 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1470 alignments when hidden columns are present
1473 <!-- JAL-2392 -->Jalview freezes when loading and
1474 displaying several structures
1477 <!-- JAL-2732 -->Black outlines left after resizing or
1481 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1482 within the Jalview desktop on OSX
1485 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1486 when in wrapped alignment mode
1489 <!-- JAL-2636 -->Scale mark not shown when close to right
1490 hand end of alignment
1493 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1494 each selected sequence do not have correct start/end
1498 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1499 after canceling the Alignment Window's Font dialog
1502 <!-- JAL-2036 -->Show cross-references not enabled after
1503 restoring project until a new view is created
1506 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1507 URL links appears when only default EMBL-EBI link is
1508 configured (since 2.10.2b2)
1511 <!-- JAL-2775 -->Overview redraws whole window when box
1512 position is adjusted
1515 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1516 in a multi-chain structure when viewing alignment
1517 involving more than one chain (since 2.10)
1520 <!-- JAL-2811 -->Double residue highlights in cursor mode
1521 if new selection moves alignment window
1524 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1525 arrow key in cursor mode to pass hidden column marker
1528 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1529 that produces correctly annotated transcripts and products
1532 <!-- JAL-2776 -->Toggling a feature group after first time
1533 doesn't update associated structure view
1536 <em>Applet</em><br />
1539 <!-- JAL-2687 -->Concurrent modification exception when
1540 closing alignment panel
1543 <em>BioJSON</em><br />
1546 <!-- JAL-2546 -->BioJSON export does not preserve
1547 non-positional features
1550 <em>New Known Issues</em>
1553 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1554 sequence features correctly (for many previous versions of
1558 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1559 using cursor in wrapped panel other than top
1562 <!-- JAL-2791 -->Select columns containing feature ignores
1563 graduated colour threshold
1566 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1567 always preserve numbering and sequence features
1570 <em>Known Java 9 Issues</em>
1573 <!-- JAL-2902 -->Groovy Console very slow to open and is
1574 not responsive when entering characters (Webstart, Java
1581 <td width="60" nowrap>
1582 <div align="center">
1583 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1584 <em>2/10/2017</em></strong>
1587 <td><div align="left">
1588 <em>New features in Jalview Desktop</em>
1591 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1593 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1597 <td><div align="left">
1601 <td width="60" nowrap>
1602 <div align="center">
1603 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1604 <em>7/9/2017</em></strong>
1607 <td><div align="left">
1611 <!-- JAL-2588 -->Show gaps in overview window by colouring
1612 in grey (sequences used to be coloured grey, and gaps were
1616 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1620 <!-- JAL-2587 -->Overview updates immediately on increase
1621 in size and progress bar shown as higher resolution
1622 overview is recalculated
1627 <td><div align="left">
1631 <!-- JAL-2664 -->Overview window redraws every hidden
1632 column region row by row
1635 <!-- JAL-2681 -->duplicate protein sequences shown after
1636 retrieving Ensembl crossrefs for sequences from Uniprot
1639 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1640 format setting is unticked
1643 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1644 if group has show boxes format setting unticked
1647 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1648 autoscrolling whilst dragging current selection group to
1649 include sequences and columns not currently displayed
1652 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1653 assemblies are imported via CIF file
1656 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1657 displayed when threshold or conservation colouring is also
1661 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1665 <!-- JAL-2673 -->Jalview continues to scroll after
1666 dragging a selected region off the visible region of the
1670 <!-- JAL-2724 -->Cannot apply annotation based
1671 colourscheme to all groups in a view
1674 <!-- JAL-2511 -->IDs don't line up with sequences
1675 initially after font size change using the Font chooser or
1682 <td width="60" nowrap>
1683 <div align="center">
1684 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1687 <td><div align="left">
1688 <em>Calculations</em>
1692 <!-- JAL-1933 -->Occupancy annotation row shows number of
1693 ungapped positions in each column of the alignment.
1696 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1697 a calculation dialog box
1700 <!-- JAL-2379 -->Revised implementation of PCA for speed
1701 and memory efficiency (~30x faster)
1704 <!-- JAL-2403 -->Revised implementation of sequence
1705 similarity scores as used by Tree, PCA, Shading Consensus
1706 and other calculations
1709 <!-- JAL-2416 -->Score matrices are stored as resource
1710 files within the Jalview codebase
1713 <!-- JAL-2500 -->Trees computed on Sequence Feature
1714 Similarity may have different topology due to increased
1721 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1722 model for alignments and groups
1725 <!-- JAL-384 -->Custom shading schemes created via groovy
1732 <!-- JAL-2526 -->Efficiency improvements for interacting
1733 with alignment and overview windows
1736 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1740 <!-- JAL-2388 -->Hidden columns and sequences can be
1744 <!-- JAL-2611 -->Click-drag in visible area allows fine
1745 adjustment of visible position
1749 <em>Data import/export</em>
1752 <!-- JAL-2535 -->Posterior probability annotation from
1753 Stockholm files imported as sequence associated annotation
1756 <!-- JAL-2507 -->More robust per-sequence positional
1757 annotation input/output via stockholm flatfile
1760 <!-- JAL-2533 -->Sequence names don't include file
1761 extension when importing structure files without embedded
1762 names or PDB accessions
1765 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1766 format sequence substitution matrices
1769 <em>User Interface</em>
1772 <!-- JAL-2447 --> Experimental Features Checkbox in
1773 Desktop's Tools menu to hide or show untested features in
1777 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1778 via Overview or sequence motif search operations
1781 <!-- JAL-2547 -->Amend sequence features dialog box can be
1782 opened by double clicking gaps within sequence feature
1786 <!-- JAL-1476 -->Status bar message shown when not enough
1787 aligned positions were available to create a 3D structure
1791 <em>3D Structure</em>
1794 <!-- JAL-2430 -->Hidden regions in alignment views are not
1795 coloured in linked structure views
1798 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1799 file-based command exchange
1802 <!-- JAL-2375 -->Structure chooser automatically shows
1803 Cached Structures rather than querying the PDBe if
1804 structures are already available for sequences
1807 <!-- JAL-2520 -->Structures imported via URL are cached in
1808 the Jalview project rather than downloaded again when the
1809 project is reopened.
1812 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1813 to transfer Chimera's structure attributes as Jalview
1814 features, and vice-versa (<strong>Experimental
1818 <em>Web Services</em>
1821 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1824 <!-- JAL-2335 -->Filter non-standard amino acids and
1825 nucleotides when submitting to AACon and other MSA
1829 <!-- JAL-2316, -->URLs for viewing database
1830 cross-references provided by identifiers.org and the
1831 EMBL-EBI's MIRIAM DB
1838 <!-- JAL-2344 -->FileFormatI interface for describing and
1839 identifying file formats (instead of String constants)
1842 <!-- JAL-2228 -->FeatureCounter script refactored for
1843 efficiency when counting all displayed features (not
1844 backwards compatible with 2.10.1)
1847 <em>Example files</em>
1850 <!-- JAL-2631 -->Graduated feature colour style example
1851 included in the example feature file
1854 <em>Documentation</em>
1857 <!-- JAL-2339 -->Release notes reformatted for readability
1858 with the built-in Java help viewer
1861 <!-- JAL-1644 -->Find documentation updated with 'search
1862 sequence description' option
1868 <!-- JAL-2485, -->External service integration tests for
1869 Uniprot REST Free Text Search Client
1872 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1875 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1880 <td><div align="left">
1881 <em>Calculations</em>
1884 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1885 matrix - C->R should be '-3'<br />Old matrix restored
1886 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1888 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1889 Jalview's treatment of gaps in PCA and substitution matrix
1890 based Tree calculations.<br /> <br />In earlier versions
1891 of Jalview, gaps matching gaps were penalised, and gaps
1892 matching non-gaps penalised even more. In the PCA
1893 calculation, gaps were actually treated as non-gaps - so
1894 different costs were applied, which meant Jalview's PCAs
1895 were different to those produced by SeqSpace.<br />Jalview
1896 now treats gaps in the same way as SeqSpace (ie it scores
1897 them as 0). <br /> <br />Enter the following in the
1898 Groovy console to restore pre-2.10.2 behaviour:<br />
1899 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1900 // for 2.10.1 mode <br />
1901 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1902 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1903 these settings will affect all subsequent tree and PCA
1904 calculations (not recommended)</em></li>
1906 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1907 scaling of branch lengths for trees computed using
1908 Sequence Feature Similarity.
1911 <!-- JAL-2377 -->PCA calculation could hang when
1912 generating output report when working with highly
1913 redundant alignments
1916 <!-- JAL-2544 --> Sort by features includes features to
1917 right of selected region when gaps present on right-hand
1921 <em>User Interface</em>
1924 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1925 doesn't reselect a specific sequence's associated
1926 annotation after it was used for colouring a view
1929 <!-- JAL-2419 -->Current selection lost if popup menu
1930 opened on a region of alignment without groups
1933 <!-- JAL-2374 -->Popup menu not always shown for regions
1934 of an alignment with overlapping groups
1937 <!-- JAL-2310 -->Finder double counts if both a sequence's
1938 name and description match
1941 <!-- JAL-2370 -->Hiding column selection containing two
1942 hidden regions results in incorrect hidden regions
1945 <!-- JAL-2386 -->'Apply to all groups' setting when
1946 changing colour does not apply Conservation slider value
1950 <!-- JAL-2373 -->Percentage identity and conservation menu
1951 items do not show a tick or allow shading to be disabled
1954 <!-- JAL-2385 -->Conservation shading or PID threshold
1955 lost when base colourscheme changed if slider not visible
1958 <!-- JAL-2547 -->Sequence features shown in tooltip for
1959 gaps before start of features
1962 <!-- JAL-2623 -->Graduated feature colour threshold not
1963 restored to UI when feature colour is edited
1966 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1967 a time when scrolling vertically in wrapped mode.
1970 <!-- JAL-2630 -->Structure and alignment overview update
1971 as graduate feature colour settings are modified via the
1975 <!-- JAL-2034 -->Overview window doesn't always update
1976 when a group defined on the alignment is resized
1979 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1980 wrapped view result in positional status updates
1984 <!-- JAL-2563 -->Status bar doesn't show position for
1985 ambiguous amino acid and nucleotide symbols
1988 <!-- JAL-2602 -->Copy consensus sequence failed if
1989 alignment included gapped columns
1992 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1993 widgets don't permanently disappear
1996 <!-- JAL-2503 -->Cannot select or filter quantitative
1997 annotation that are shown only as column labels (e.g.
1998 T-Coffee column reliability scores)
2001 <!-- JAL-2594 -->Exception thrown if trying to create a
2002 sequence feature on gaps only
2005 <!-- JAL-2504 -->Features created with 'New feature'
2006 button from a Find inherit previously defined feature type
2007 rather than the Find query string
2010 <!-- JAL-2423 -->incorrect title in output window when
2011 exporting tree calculated in Jalview
2014 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2015 and then revealing them reorders sequences on the
2019 <!-- JAL-964 -->Group panel in sequence feature settings
2020 doesn't update to reflect available set of groups after
2021 interactively adding or modifying features
2024 <!-- JAL-2225 -->Sequence Database chooser unusable on
2028 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2029 only excluded gaps in current sequence and ignored
2036 <!-- JAL-2421 -->Overview window visible region moves
2037 erratically when hidden rows or columns are present
2040 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2041 Structure Viewer's colour menu don't correspond to
2045 <!-- JAL-2405 -->Protein specific colours only offered in
2046 colour and group colour menu for protein alignments
2049 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2050 reflect currently selected view or group's shading
2054 <!-- JAL-2624 -->Feature colour thresholds not respected
2055 when rendered on overview and structures when opacity at
2059 <!-- JAL-2589 -->User defined gap colour not shown in
2060 overview when features overlaid on alignment
2063 <!-- JAL-2567 -->Feature settings for different views not
2064 recovered correctly from Jalview project file
2067 <!-- JAL-2256 -->Feature colours in overview when first opened
2068 (automatically via preferences) are different to the main
2072 <em>Data import/export</em>
2075 <!-- JAL-2576 -->Very large alignments take a long time to
2079 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2080 added after a sequence was imported are not written to
2084 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2085 when importing RNA secondary structure via Stockholm
2088 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2089 not shown in correct direction for simple pseudoknots
2092 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2093 with lightGray or darkGray via features file (but can
2097 <!-- JAL-2383 -->Above PID colour threshold not recovered
2098 when alignment view imported from project
2101 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2102 structure and sequences extracted from structure files
2103 imported via URL and viewed in Jmol
2106 <!-- JAL-2520 -->Structures loaded via URL are saved in
2107 Jalview Projects rather than fetched via URL again when
2108 the project is loaded and the structure viewed
2111 <em>Web Services</em>
2114 <!-- JAL-2519 -->EnsemblGenomes example failing after
2115 release of Ensembl v.88
2118 <!-- JAL-2366 -->Proxy server address and port always
2119 appear enabled in Preferences->Connections
2122 <!-- JAL-2461 -->DAS registry not found exceptions
2123 removed from console output
2126 <!-- JAL-2582 -->Cannot retrieve protein products from
2127 Ensembl by Peptide ID
2130 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2131 created from SIFTs, and spurious 'Couldn't open structure
2132 in Chimera' errors raised after April 2017 update (problem
2133 due to 'null' string rather than empty string used for
2134 residues with no corresponding PDB mapping).
2137 <em>Application UI</em>
2140 <!-- JAL-2361 -->User Defined Colours not added to Colour
2144 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2145 case' residues (button in colourscheme editor debugged and
2146 new documentation and tooltips added)
2149 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2150 doesn't restore group-specific text colour thresholds
2153 <!-- JAL-2243 -->Feature settings panel does not update as
2154 new features are added to alignment
2157 <!-- JAL-2532 -->Cancel in feature settings reverts
2158 changes to feature colours via the Amend features dialog
2161 <!-- JAL-2506 -->Null pointer exception when attempting to
2162 edit graduated feature colour via amend features dialog
2166 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2167 selection menu changes colours of alignment views
2170 <!-- JAL-2426 -->Spurious exceptions in console raised
2171 from alignment calculation workers after alignment has
2175 <!-- JAL-1608 -->Typo in selection popup menu - Create
2176 groups now 'Create Group'
2179 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2180 Create/Undefine group doesn't always work
2183 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2184 shown again after pressing 'Cancel'
2187 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2188 adjusts start position in wrap mode
2191 <!-- JAL-2563 -->Status bar doesn't show positions for
2192 ambiguous amino acids
2195 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2196 CDS/Protein view after CDS sequences added for aligned
2200 <!-- JAL-2592 -->User defined colourschemes called 'User
2201 Defined' don't appear in Colours menu
2207 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2208 score models doesn't always result in an updated PCA plot
2211 <!-- JAL-2442 -->Features not rendered as transparent on
2212 overview or linked structure view
2215 <!-- JAL-2372 -->Colour group by conservation doesn't
2219 <!-- JAL-2517 -->Hitting Cancel after applying
2220 user-defined colourscheme doesn't restore original
2227 <!-- JAL-2314 -->Unit test failure:
2228 jalview.ws.jabaws.RNAStructExportImport setup fails
2231 <!-- JAL-2307 -->Unit test failure:
2232 jalview.ws.sifts.SiftsClientTest due to compatibility
2233 problems with deep array comparison equality asserts in
2234 successive versions of TestNG
2237 <!-- JAL-2479 -->Relocated StructureChooserTest and
2238 ParameterUtilsTest Unit tests to Network suite
2241 <em>New Known Issues</em>
2244 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2245 phase after a sequence motif find operation
2248 <!-- JAL-2550 -->Importing annotation file with rows
2249 containing just upper and lower case letters are
2250 interpreted as WUSS RNA secondary structure symbols
2253 <!-- JAL-2590 -->Cannot load and display Newick trees
2254 reliably from eggnog Ortholog database
2257 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2258 containing features of type Highlight' when 'B' is pressed
2259 to mark columns containing highlighted regions.
2262 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2263 doesn't always add secondary structure annotation.
2268 <td width="60" nowrap>
2269 <div align="center">
2270 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2273 <td><div align="left">
2277 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2278 for all consensus calculations
2281 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2284 <li>Updated Jalview's Certum code signing certificate
2287 <em>Application</em>
2290 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2291 set of database cross-references, sorted alphabetically
2294 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2295 from database cross references. Users with custom links
2296 will receive a <a href="webServices/urllinks.html#warning">warning
2297 dialog</a> asking them to update their preferences.
2300 <!-- JAL-2287-->Cancel button and escape listener on
2301 dialog warning user about disconnecting Jalview from a
2305 <!-- JAL-2320-->Jalview's Chimera control window closes if
2306 the Chimera it is connected to is shut down
2309 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2310 columns menu item to mark columns containing highlighted
2311 regions (e.g. from structure selections or results of a
2315 <!-- JAL-2284-->Command line option for batch-generation
2316 of HTML pages rendering alignment data with the BioJS
2326 <!-- JAL-2286 -->Columns with more than one modal residue
2327 are not coloured or thresholded according to percent
2328 identity (first observed in Jalview 2.8.2)
2331 <!-- JAL-2301 -->Threonine incorrectly reported as not
2335 <!-- JAL-2318 -->Updates to documentation pages (above PID
2336 threshold, amino acid properties)
2339 <!-- JAL-2292 -->Lower case residues in sequences are not
2340 reported as mapped to residues in a structure file in the
2344 <!--JAL-2324 -->Identical features with non-numeric scores
2345 could be added multiple times to a sequence
2348 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2349 bond features shown as two highlighted residues rather
2350 than a range in linked structure views, and treated
2351 correctly when selecting and computing trees from features
2354 <!-- JAL-2281-->Custom URL links for database
2355 cross-references are matched to database name regardless
2360 <em>Application</em>
2363 <!-- JAL-2282-->Custom URL links for specific database
2364 names without regular expressions also offer links from
2368 <!-- JAL-2315-->Removing a single configured link in the
2369 URL links pane in Connections preferences doesn't actually
2370 update Jalview configuration
2373 <!-- JAL-2272-->CTRL-Click on a selected region to open
2374 the alignment area popup menu doesn't work on El-Capitan
2377 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2378 files with similarly named sequences if dropped onto the
2382 <!-- JAL-2312 -->Additional mappings are shown for PDB
2383 entries where more chains exist in the PDB accession than
2384 are reported in the SIFTS file
2387 <!-- JAL-2317-->Certain structures do not get mapped to
2388 the structure view when displayed with Chimera
2391 <!-- JAL-2317-->No chains shown in the Chimera view
2392 panel's View->Show Chains submenu
2395 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2396 work for wrapped alignment views
2399 <!--JAL-2197 -->Rename UI components for running JPred
2400 predictions from 'JNet' to 'JPred'
2403 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2404 corrupted when annotation panel vertical scroll is not at
2405 first annotation row
2408 <!--JAL-2332 -->Attempting to view structure for Hen
2409 lysozyme results in a PDB Client error dialog box
2412 <!-- JAL-2319 -->Structure View's mapping report switched
2413 ranges for PDB and sequence for SIFTS
2416 SIFTS 'Not_Observed' residues mapped to non-existant
2420 <!-- <em>New Known Issues</em>
2427 <td width="60" nowrap>
2428 <div align="center">
2429 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2430 <em>25/10/2016</em></strong>
2433 <td><em>Application</em>
2435 <li>3D Structure chooser opens with 'Cached structures'
2436 view if structures already loaded</li>
2437 <li>Progress bar reports models as they are loaded to
2438 structure views</li>
2444 <li>Colour by conservation always enabled and no tick
2445 shown in menu when BLOSUM or PID shading applied</li>
2446 <li>FER1_ARATH and FER2_ARATH labels were switched in
2447 example sequences/projects/trees</li>
2449 <em>Application</em>
2451 <li>Jalview projects with views of local PDB structure
2452 files saved on Windows cannot be opened on OSX</li>
2453 <li>Multiple structure views can be opened and superposed
2454 without timeout for structures with multiple models or
2455 multiple sequences in alignment</li>
2456 <li>Cannot import or associated local PDB files without a
2457 PDB ID HEADER line</li>
2458 <li>RMSD is not output in Jmol console when superposition
2460 <li>Drag and drop of URL from Browser fails for Linux and
2461 OSX versions earlier than El Capitan</li>
2462 <li>ENA client ignores invalid content from ENA server</li>
2463 <li>Exceptions are not raised in console when ENA client
2464 attempts to fetch non-existent IDs via Fetch DB Refs UI
2466 <li>Exceptions are not raised in console when a new view
2467 is created on the alignment</li>
2468 <li>OSX right-click fixed for group selections: CMD-click
2469 to insert/remove gaps in groups and CTRL-click to open group
2472 <em>Build and deployment</em>
2474 <li>URL link checker now copes with multi-line anchor
2477 <em>New Known Issues</em>
2479 <li>Drag and drop from URL links in browsers do not work
2486 <td width="60" nowrap>
2487 <div align="center">
2488 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2491 <td><em>General</em>
2494 <!-- JAL-2124 -->Updated Spanish translations.
2497 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2498 for importing structure data to Jalview. Enables mmCIF and
2502 <!-- JAL-192 --->Alignment ruler shows positions relative to
2506 <!-- JAL-2202 -->Position/residue shown in status bar when
2507 mousing over sequence associated annotation
2510 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2514 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2515 '()', canonical '[]' and invalid '{}' base pair populations
2519 <!-- JAL-2092 -->Feature settings popup menu options for
2520 showing or hiding columns containing a feature
2523 <!-- JAL-1557 -->Edit selected group by double clicking on
2524 group and sequence associated annotation labels
2527 <!-- JAL-2236 -->Sequence name added to annotation label in
2528 select/hide columns by annotation and colour by annotation
2532 </ul> <em>Application</em>
2535 <!-- JAL-2050-->Automatically hide introns when opening a
2536 gene/transcript view
2539 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2543 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2544 structure mappings with the EMBL-EBI PDBe SIFTS database
2547 <!-- JAL-2079 -->Updated download sites used for Rfam and
2548 Pfam sources to xfam.org
2551 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2554 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2555 over sequences in Jalview
2558 <!-- JAL-2027-->Support for reverse-complement coding
2559 regions in ENA and EMBL
2562 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2563 for record retrieval via ENA rest API
2566 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2570 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2571 groovy script execution
2574 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2575 alignment window's Calculate menu
2578 <!-- JAL-1812 -->Allow groovy scripts that call
2579 Jalview.getAlignFrames() to run in headless mode
2582 <!-- JAL-2068 -->Support for creating new alignment
2583 calculation workers from groovy scripts
2586 <!-- JAL-1369 --->Store/restore reference sequence in
2590 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2591 associations are now saved/restored from project
2594 <!-- JAL-1993 -->Database selection dialog always shown
2595 before sequence fetcher is opened
2598 <!-- JAL-2183 -->Double click on an entry in Jalview's
2599 database chooser opens a sequence fetcher
2602 <!-- JAL-1563 -->Free-text search client for UniProt using
2603 the UniProt REST API
2606 <!-- JAL-2168 -->-nonews command line parameter to prevent
2607 the news reader opening
2610 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2611 querying stored in preferences
2614 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2618 <!-- JAL-1977-->Tooltips shown on database chooser
2621 <!-- JAL-391 -->Reverse complement function in calculate
2622 menu for nucleotide sequences
2625 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2626 and feature counts preserves alignment ordering (and
2627 debugged for complex feature sets).
2630 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2631 viewing structures with Jalview 2.10
2634 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2635 genome, transcript CCDS and gene ids via the Ensembl and
2636 Ensembl Genomes REST API
2639 <!-- JAL-2049 -->Protein sequence variant annotation
2640 computed for 'sequence_variant' annotation on CDS regions
2644 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2648 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2649 Ref Fetcher fails to match, or otherwise updates sequence
2650 data from external database records.
2653 <!-- JAL-2154 -->Revised Jalview Project format for
2654 efficient recovery of sequence coding and alignment
2655 annotation relationships.
2657 </ul> <!-- <em>Applet</em>
2668 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2672 <!-- JAL-2018-->Export features in Jalview format (again)
2673 includes graduated colourschemes
2676 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2677 working with big alignments and lots of hidden columns
2680 <!-- JAL-2053-->Hidden column markers not always rendered
2681 at right of alignment window
2684 <!-- JAL-2067 -->Tidied up links in help file table of
2688 <!-- JAL-2072 -->Feature based tree calculation not shown
2692 <!-- JAL-2075 -->Hidden columns ignored during feature
2693 based tree calculation
2696 <!-- JAL-2065 -->Alignment view stops updating when show
2697 unconserved enabled for group on alignment
2700 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2704 <!-- JAL-2146 -->Alignment column in status incorrectly
2705 shown as "Sequence position" when mousing over
2709 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2710 hidden columns present
2713 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2714 user created annotation added to alignment
2717 <!-- JAL-1841 -->RNA Structure consensus only computed for
2718 '()' base pair annotation
2721 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2722 in zero scores for all base pairs in RNA Structure
2726 <!-- JAL-2174-->Extend selection with columns containing
2730 <!-- JAL-2275 -->Pfam format writer puts extra space at
2731 beginning of sequence
2734 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2738 <!-- JAL-2238 -->Cannot create groups on an alignment from
2739 from a tree when t-coffee scores are shown
2742 <!-- JAL-1836,1967 -->Cannot import and view PDB
2743 structures with chains containing negative resnums (4q4h)
2746 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2750 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2751 to Clustal, PIR and PileUp output
2754 <!-- JAL-2008 -->Reordering sequence features that are
2755 not visible causes alignment window to repaint
2758 <!-- JAL-2006 -->Threshold sliders don't work in
2759 graduated colour and colour by annotation row for e-value
2760 scores associated with features and annotation rows
2763 <!-- JAL-1797 -->amino acid physicochemical conservation
2764 calculation should be case independent
2767 <!-- JAL-2173 -->Remove annotation also updates hidden
2771 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2772 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2773 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2776 <!-- JAL-2065 -->Null pointer exceptions and redraw
2777 problems when reference sequence defined and 'show
2778 non-conserved' enabled
2781 <!-- JAL-1306 -->Quality and Conservation are now shown on
2782 load even when Consensus calculation is disabled
2785 <!-- JAL-1932 -->Remove right on penultimate column of
2786 alignment does nothing
2789 <em>Application</em>
2792 <!-- JAL-1552-->URLs and links can't be imported by
2793 drag'n'drop on OSX when launched via webstart (note - not
2794 yet fixed for El Capitan)
2797 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2798 output when running on non-gb/us i18n platforms
2801 <!-- JAL-1944 -->Error thrown when exporting a view with
2802 hidden sequences as flat-file alignment
2805 <!-- JAL-2030-->InstallAnywhere distribution fails when
2809 <!-- JAL-2080-->Jalview very slow to launch via webstart
2810 (also hotfix for 2.9.0b2)
2813 <!-- JAL-2085 -->Cannot save project when view has a
2814 reference sequence defined
2817 <!-- JAL-1011 -->Columns are suddenly selected in other
2818 alignments and views when revealing hidden columns
2821 <!-- JAL-1989 -->Hide columns not mirrored in complement
2822 view in a cDNA/Protein splitframe
2825 <!-- JAL-1369 -->Cannot save/restore representative
2826 sequence from project when only one sequence is
2830 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2831 in Structure Chooser
2834 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2835 structure consensus didn't refresh annotation panel
2838 <!-- JAL-1962 -->View mapping in structure view shows
2839 mappings between sequence and all chains in a PDB file
2842 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2843 dialogs format columns correctly, don't display array
2844 data, sort columns according to type
2847 <!-- JAL-1975 -->Export complete shown after destination
2848 file chooser is cancelled during an image export
2851 <!-- JAL-2025 -->Error when querying PDB Service with
2852 sequence name containing special characters
2855 <!-- JAL-2024 -->Manual PDB structure querying should be
2859 <!-- JAL-2104 -->Large tooltips with broken HTML
2860 formatting don't wrap
2863 <!-- JAL-1128 -->Figures exported from wrapped view are
2864 truncated so L looks like I in consensus annotation
2867 <!-- JAL-2003 -->Export features should only export the
2868 currently displayed features for the current selection or
2872 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2873 after fetching cross-references, and restoring from
2877 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2878 followed in the structure viewer
2881 <!-- JAL-2163 -->Titles for individual alignments in
2882 splitframe not restored from project
2885 <!-- JAL-2145 -->missing autocalculated annotation at
2886 trailing end of protein alignment in transcript/product
2887 splitview when pad-gaps not enabled by default
2890 <!-- JAL-1797 -->amino acid physicochemical conservation
2894 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2895 article has been read (reopened issue due to
2896 internationalisation problems)
2899 <!-- JAL-1960 -->Only offer PDB structures in structure
2900 viewer based on sequence name, PDB and UniProt
2905 <!-- JAL-1976 -->No progress bar shown during export of
2909 <!-- JAL-2213 -->Structures not always superimposed after
2910 multiple structures are shown for one or more sequences.
2913 <!-- JAL-1370 -->Reference sequence characters should not
2914 be replaced with '.' when 'Show unconserved' format option
2918 <!-- JAL-1823 -->Cannot specify chain code when entering
2919 specific PDB id for sequence
2922 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2923 'Export hidden sequences' is enabled, but 'export hidden
2924 columns' is disabled.
2927 <!--JAL-2026-->Best Quality option in structure chooser
2928 selects lowest rather than highest resolution structures
2932 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2933 to sequence mapping in 'View Mappings' report
2936 <!-- JAL-2284 -->Unable to read old Jalview projects that
2937 contain non-XML data added after Jalvew wrote project.
2940 <!-- JAL-2118 -->Newly created annotation row reorders
2941 after clicking on it to create new annotation for a
2945 <!-- JAL-1980 -->Null Pointer Exception raised when
2946 pressing Add on an orphaned cut'n'paste window.
2948 <!-- may exclude, this is an external service stability issue JAL-1941
2949 -- > RNA 3D structure not added via DSSR service</li> -->
2954 <!-- JAL-2151 -->Incorrect columns are selected when
2955 hidden columns present before start of sequence
2958 <!-- JAL-1986 -->Missing dependencies on applet pages
2962 <!-- JAL-1947 -->Overview pixel size changes when
2963 sequences are hidden in applet
2966 <!-- JAL-1996 -->Updated instructions for applet
2967 deployment on examples pages.
2974 <td width="60" nowrap>
2975 <div align="center">
2976 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2977 <em>16/10/2015</em></strong>
2980 <td><em>General</em>
2982 <li>Time stamps for signed Jalview application and applet
2987 <em>Application</em>
2989 <li>Duplicate group consensus and conservation rows
2990 shown when tree is partitioned</li>
2991 <li>Erratic behaviour when tree partitions made with
2992 multiple cDNA/Protein split views</li>
2998 <td width="60" nowrap>
2999 <div align="center">
3000 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3001 <em>8/10/2015</em></strong>
3004 <td><em>General</em>
3006 <li>Updated Spanish translations of localized text for
3008 </ul> <em>Application</em>
3010 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3011 <li>Signed OSX InstallAnywhere installer<br></li>
3012 <li>Support for per-sequence based annotations in BioJSON</li>
3013 </ul> <em>Applet</em>
3015 <li>Split frame example added to applet examples page</li>
3016 </ul> <em>Build and Deployment</em>
3019 <!-- JAL-1888 -->New ant target for running Jalview's test
3027 <li>Mapping of cDNA to protein in split frames
3028 incorrect when sequence start > 1</li>
3029 <li>Broken images in filter column by annotation dialog
3031 <li>Feature colours not parsed from features file</li>
3032 <li>Exceptions and incomplete link URLs recovered when
3033 loading a features file containing HTML tags in feature
3037 <em>Application</em>
3039 <li>Annotations corrupted after BioJS export and
3041 <li>Incorrect sequence limits after Fetch DB References
3042 with 'trim retrieved sequences'</li>
3043 <li>Incorrect warning about deleting all data when
3044 deleting selected columns</li>
3045 <li>Patch to build system for shipping properly signed
3046 JNLP templates for webstart launch</li>
3047 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3048 unreleased structures for download or viewing</li>
3049 <li>Tab/space/return keystroke operation of EMBL-PDBe
3050 fetcher/viewer dialogs works correctly</li>
3051 <li>Disabled 'minimise' button on Jalview windows
3052 running on OSX to workaround redraw hang bug</li>
3053 <li>Split cDNA/Protein view position and geometry not
3054 recovered from jalview project</li>
3055 <li>Initial enabled/disabled state of annotation menu
3056 sorter 'show autocalculated first/last' corresponds to
3058 <li>Restoring of Clustal, RNA Helices and T-Coffee
3059 color schemes from BioJSON</li>
3063 <li>Reorder sequences mirrored in cDNA/Protein split
3065 <li>Applet with Jmol examples not loading correctly</li>
3071 <td><div align="center">
3072 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3074 <td><em>General</em>
3076 <li>Linked visualisation and analysis of DNA and Protein
3079 <li>Translated cDNA alignments shown as split protein
3080 and DNA alignment views</li>
3081 <li>Codon consensus annotation for linked protein and
3082 cDNA alignment views</li>
3083 <li>Link cDNA or Protein product sequences by loading
3084 them onto Protein or cDNA alignments</li>
3085 <li>Reconstruct linked cDNA alignment from aligned
3086 protein sequences</li>
3089 <li>Jmol integration updated to Jmol v14.2.14</li>
3090 <li>Import and export of Jalview alignment views as <a
3091 href="features/bioJsonFormat.html">BioJSON</a></li>
3092 <li>New alignment annotation file statements for
3093 reference sequences and marking hidden columns</li>
3094 <li>Reference sequence based alignment shading to
3095 highlight variation</li>
3096 <li>Select or hide columns according to alignment
3098 <li>Find option for locating sequences by description</li>
3099 <li>Conserved physicochemical properties shown in amino
3100 acid conservation row</li>
3101 <li>Alignments can be sorted by number of RNA helices</li>
3102 </ul> <em>Application</em>
3104 <li>New cDNA/Protein analysis capabilities
3106 <li>Get Cross-References should open a Split Frame
3107 view with cDNA/Protein</li>
3108 <li>Detect when nucleotide sequences and protein
3109 sequences are placed in the same alignment</li>
3110 <li>Split cDNA/Protein views are saved in Jalview
3115 <li>Use REST API to talk to Chimera</li>
3116 <li>Selected regions in Chimera are highlighted in linked
3117 Jalview windows</li>
3119 <li>VARNA RNA viewer updated to v3.93</li>
3120 <li>VARNA views are saved in Jalview Projects</li>
3121 <li>Pseudoknots displayed as Jalview RNA annotation can
3122 be shown in VARNA</li>
3124 <li>Make groups for selection uses marked columns as well
3125 as the active selected region</li>
3127 <li>Calculate UPGMA and NJ trees using sequence feature
3129 <li>New Export options
3131 <li>New Export Settings dialog to control hidden
3132 region export in flat file generation</li>
3134 <li>Export alignment views for display with the <a
3135 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3137 <li>Export scrollable SVG in HTML page</li>
3138 <li>Optional embedding of BioJSON data when exporting
3139 alignment figures to HTML</li>
3141 <li>3D structure retrieval and display
3143 <li>Free text and structured queries with the PDBe
3145 <li>PDBe Search API based discovery and selection of
3146 PDB structures for a sequence set</li>
3150 <li>JPred4 employed for protein secondary structure
3152 <li>Hide Insertions menu option to hide unaligned columns
3153 for one or a group of sequences</li>
3154 <li>Automatically hide insertions in alignments imported
3155 from the JPred4 web server</li>
3156 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3157 system on OSX<br />LGPL libraries courtesy of <a
3158 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3160 <li>changed 'View nucleotide structure' submenu to 'View
3161 VARNA 2D Structure'</li>
3162 <li>change "View protein structure" menu option to "3D
3165 </ul> <em>Applet</em>
3167 <li>New layout for applet example pages</li>
3168 <li>New parameters to enable SplitFrame view
3169 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3170 <li>New example demonstrating linked viewing of cDNA and
3171 Protein alignments</li>
3172 </ul> <em>Development and deployment</em>
3174 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3175 <li>Include installation type and git revision in build
3176 properties and console log output</li>
3177 <li>Jalview Github organisation, and new github site for
3178 storing BioJsMSA Templates</li>
3179 <li>Jalview's unit tests now managed with TestNG</li>
3182 <!-- <em>General</em>
3184 </ul> --> <!-- issues resolved --> <em>Application</em>
3186 <li>Escape should close any open find dialogs</li>
3187 <li>Typo in select-by-features status report</li>
3188 <li>Consensus RNA secondary secondary structure
3189 predictions are not highlighted in amber</li>
3190 <li>Missing gap character in v2.7 example file means
3191 alignment appears unaligned when pad-gaps is not enabled</li>
3192 <li>First switch to RNA Helices colouring doesn't colour
3193 associated structure views</li>
3194 <li>ID width preference option is greyed out when auto
3195 width checkbox not enabled</li>
3196 <li>Stopped a warning dialog from being shown when
3197 creating user defined colours</li>
3198 <li>'View Mapping' in structure viewer shows sequence
3199 mappings for just that viewer's sequences</li>
3200 <li>Workaround for superposing PDB files containing
3201 multiple models in Chimera</li>
3202 <li>Report sequence position in status bar when hovering
3203 over Jmol structure</li>
3204 <li>Cannot output gaps as '.' symbols with Selection ->
3205 output to text box</li>
3206 <li>Flat file exports of alignments with hidden columns
3207 have incorrect sequence start/end</li>
3208 <li>'Aligning' a second chain to a Chimera structure from
3210 <li>Colour schemes applied to structure viewers don't
3211 work for nucleotide</li>
3212 <li>Loading/cut'n'pasting an empty or invalid file leads
3213 to a grey/invisible alignment window</li>
3214 <li>Exported Jpred annotation from a sequence region
3215 imports to different position</li>
3216 <li>Space at beginning of sequence feature tooltips shown
3217 on some platforms</li>
3218 <li>Chimera viewer 'View | Show Chain' menu is not
3220 <li>'New View' fails with a Null Pointer Exception in
3221 console if Chimera has been opened</li>
3222 <li>Mouseover to Chimera not working</li>
3223 <li>Miscellaneous ENA XML feature qualifiers not
3225 <li>NPE in annotation renderer after 'Extract Scores'</li>
3226 <li>If two structures in one Chimera window, mouseover of
3227 either sequence shows on first structure</li>
3228 <li>'Show annotations' options should not make
3229 non-positional annotations visible</li>
3230 <li>Subsequence secondary structure annotation not shown
3231 in right place after 'view flanking regions'</li>
3232 <li>File Save As type unset when current file format is
3234 <li>Save as '.jar' option removed for saving Jalview
3236 <li>Colour by Sequence colouring in Chimera more
3238 <li>Cannot 'add reference annotation' for a sequence in
3239 several views on same alignment</li>
3240 <li>Cannot show linked products for EMBL / ENA records</li>
3241 <li>Jalview's tooltip wraps long texts containing no
3243 </ul> <em>Applet</em>
3245 <li>Jmol to JalviewLite mouseover/link not working</li>
3246 <li>JalviewLite can't import sequences with ID
3247 descriptions containing angle brackets</li>
3248 </ul> <em>General</em>
3250 <li>Cannot export and reimport RNA secondary structure
3251 via jalview annotation file</li>
3252 <li>Random helix colour palette for colour by annotation
3253 with RNA secondary structure</li>
3254 <li>Mouseover to cDNA from STOP residue in protein
3255 translation doesn't work.</li>
3256 <li>hints when using the select by annotation dialog box</li>
3257 <li>Jmol alignment incorrect if PDB file has alternate CA
3259 <li>FontChooser message dialog appears to hang after
3260 choosing 1pt font</li>
3261 <li>Peptide secondary structure incorrectly imported from
3262 annotation file when annotation display text includes 'e' or
3264 <li>Cannot set colour of new feature type whilst creating
3266 <li>cDNA translation alignment should not be sequence
3267 order dependent</li>
3268 <li>'Show unconserved' doesn't work for lower case
3270 <li>Nucleotide ambiguity codes involving R not recognised</li>
3271 </ul> <em>Deployment and Documentation</em>
3273 <li>Applet example pages appear different to the rest of
3274 www.jalview.org</li>
3275 </ul> <em>Application Known issues</em>
3277 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3278 <li>Misleading message appears after trying to delete
3280 <li>Jalview icon not shown in dock after InstallAnywhere
3281 version launches</li>
3282 <li>Fetching EMBL reference for an RNA sequence results
3283 fails with a sequence mismatch</li>
3284 <li>Corrupted or unreadable alignment display when
3285 scrolling alignment to right</li>
3286 <li>ArrayIndexOutOfBoundsException thrown when remove
3287 empty columns called on alignment with ragged gapped ends</li>
3288 <li>auto calculated alignment annotation rows do not get
3289 placed above or below non-autocalculated rows</li>
3290 <li>Jalview dekstop becomes sluggish at full screen in
3291 ultra-high resolution</li>
3292 <li>Cannot disable consensus calculation independently of
3293 quality and conservation</li>
3294 <li>Mouseover highlighting between cDNA and protein can
3295 become sluggish with more than one splitframe shown</li>
3296 </ul> <em>Applet Known Issues</em>
3298 <li>Core PDB parsing code requires Jmol</li>
3299 <li>Sequence canvas panel goes white when alignment
3300 window is being resized</li>
3306 <td><div align="center">
3307 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3309 <td><em>General</em>
3311 <li>Updated Java code signing certificate donated by
3313 <li>Features and annotation preserved when performing
3314 pairwise alignment</li>
3315 <li>RNA pseudoknot annotation can be
3316 imported/exported/displayed</li>
3317 <li>'colour by annotation' can colour by RNA and
3318 protein secondary structure</li>
3319 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3320 post-hoc with 2.9 release</em>)
3323 </ul> <em>Application</em>
3325 <li>Extract and display secondary structure for sequences
3326 with 3D structures</li>
3327 <li>Support for parsing RNAML</li>
3328 <li>Annotations menu for layout
3330 <li>sort sequence annotation rows by alignment</li>
3331 <li>place sequence annotation above/below alignment
3334 <li>Output in Stockholm format</li>
3335 <li>Internationalisation: improved Spanish (es)
3337 <li>Structure viewer preferences tab</li>
3338 <li>Disorder and Secondary Structure annotation tracks
3339 shared between alignments</li>
3340 <li>UCSF Chimera launch and linked highlighting from
3342 <li>Show/hide all sequence associated annotation rows for
3343 all or current selection</li>
3344 <li>disorder and secondary structure predictions
3345 available as dataset annotation</li>
3346 <li>Per-sequence rna helices colouring</li>
3349 <li>Sequence database accessions imported when fetching
3350 alignments from Rfam</li>
3351 <li>update VARNA version to 3.91</li>
3353 <li>New groovy scripts for exporting aligned positions,
3354 conservation values, and calculating sum of pairs scores.</li>
3355 <li>Command line argument to set default JABAWS server</li>
3356 <li>include installation type in build properties and
3357 console log output</li>
3358 <li>Updated Jalview project format to preserve dataset
3362 <!-- issues resolved --> <em>Application</em>
3364 <li>Distinguish alignment and sequence associated RNA
3365 structure in structure->view->VARNA</li>
3366 <li>Raise dialog box if user deletes all sequences in an
3368 <li>Pressing F1 results in documentation opening twice</li>
3369 <li>Sequence feature tooltip is wrapped</li>
3370 <li>Double click on sequence associated annotation
3371 selects only first column</li>
3372 <li>Redundancy removal doesn't result in unlinked
3373 leaves shown in tree</li>
3374 <li>Undos after several redundancy removals don't undo
3376 <li>Hide sequence doesn't hide associated annotation</li>
3377 <li>User defined colours dialog box too big to fit on
3378 screen and buttons not visible</li>
3379 <li>author list isn't updated if already written to
3380 Jalview properties</li>
3381 <li>Popup menu won't open after retrieving sequence
3383 <li>File open window for associate PDB doesn't open</li>
3384 <li>Left-then-right click on a sequence id opens a
3385 browser search window</li>
3386 <li>Cannot open sequence feature shading/sort popup menu
3387 in feature settings dialog</li>
3388 <li>better tooltip placement for some areas of Jalview
3390 <li>Allow addition of JABAWS Server which doesn't
3391 pass validation</li>
3392 <li>Web services parameters dialog box is too large to
3394 <li>Muscle nucleotide alignment preset obscured by
3396 <li>JABAWS preset submenus don't contain newly
3397 defined user preset</li>
3398 <li>MSA web services warns user if they were launched
3399 with invalid input</li>
3400 <li>Jalview cannot contact DAS Registy when running on
3403 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3404 'Superpose with' submenu not shown when new view
3408 </ul> <!-- <em>Applet</em>
3410 </ul> <em>General</em>
3412 </ul>--> <em>Deployment and Documentation</em>
3414 <li>2G and 1G options in launchApp have no effect on
3415 memory allocation</li>
3416 <li>launchApp service doesn't automatically open
3417 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3419 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3420 InstallAnywhere reports cannot find valid JVM when Java
3421 1.7_055 is available
3423 </ul> <em>Application Known issues</em>
3426 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3427 corrupted or unreadable alignment display when scrolling
3431 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3432 retrieval fails but progress bar continues for DAS retrieval
3433 with large number of ID
3436 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3437 flatfile output of visible region has incorrect sequence
3441 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3442 rna structure consensus doesn't update when secondary
3443 structure tracks are rearranged
3446 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3447 invalid rna structure positional highlighting does not
3448 highlight position of invalid base pairs
3451 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3452 out of memory errors are not raised when saving Jalview
3453 project from alignment window file menu
3456 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3457 Switching to RNA Helices colouring doesn't propagate to
3461 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3462 colour by RNA Helices not enabled when user created
3463 annotation added to alignment
3466 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3467 Jalview icon not shown on dock in Mountain Lion/Webstart
3469 </ul> <em>Applet Known Issues</em>
3472 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3473 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3476 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3477 Jalview and Jmol example not compatible with IE9
3480 <li>Sort by annotation score doesn't reverse order
3486 <td><div align="center">
3487 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3490 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3493 <li>Internationalisation of user interface (usually
3494 called i18n support) and translation for Spanish locale</li>
3495 <li>Define/Undefine group on current selection with
3496 Ctrl-G/Shift Ctrl-G</li>
3497 <li>Improved group creation/removal options in
3498 alignment/sequence Popup menu</li>
3499 <li>Sensible precision for symbol distribution
3500 percentages shown in logo tooltip.</li>
3501 <li>Annotation panel height set according to amount of
3502 annotation when alignment first opened</li>
3503 </ul> <em>Application</em>
3505 <li>Interactive consensus RNA secondary structure
3506 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3507 <li>Select columns containing particular features from
3508 Feature Settings dialog</li>
3509 <li>View all 'representative' PDB structures for selected
3511 <li>Update Jalview project format:
3513 <li>New file extension for Jalview projects '.jvp'</li>
3514 <li>Preserve sequence and annotation dataset (to
3515 store secondary structure annotation,etc)</li>
3516 <li>Per group and alignment annotation and RNA helix
3520 <li>New similarity measures for PCA and Tree calculation
3522 <li>Experimental support for retrieval and viewing of
3523 flanking regions for an alignment</li>
3527 <!-- issues resolved --> <em>Application</em>
3529 <li>logo keeps spinning and status remains at queued or
3530 running after job is cancelled</li>
3531 <li>cannot export features from alignments imported from
3532 Jalview/VAMSAS projects</li>
3533 <li>Buggy slider for web service parameters that take
3535 <li>Newly created RNA secondary structure line doesn't
3536 have 'display all symbols' flag set</li>
3537 <li>T-COFFEE alignment score shading scheme and other
3538 annotation shading not saved in Jalview project</li>
3539 <li>Local file cannot be loaded in freshly downloaded
3541 <li>Jalview icon not shown on dock in Mountain
3543 <li>Load file from desktop file browser fails</li>
3544 <li>Occasional NPE thrown when calculating large trees</li>
3545 <li>Cannot reorder or slide sequences after dragging an
3546 alignment onto desktop</li>
3547 <li>Colour by annotation dialog throws NPE after using
3548 'extract scores' function</li>
3549 <li>Loading/cut'n'pasting an empty file leads to a grey
3550 alignment window</li>
3551 <li>Disorder thresholds rendered incorrectly after
3552 performing IUPred disorder prediction</li>
3553 <li>Multiple group annotated consensus rows shown when
3554 changing 'normalise logo' display setting</li>
3555 <li>Find shows blank dialog after 'finished searching' if
3556 nothing matches query</li>
3557 <li>Null Pointer Exceptions raised when sorting by
3558 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3560 <li>Errors in Jmol console when structures in alignment
3561 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3563 <li>Not all working JABAWS services are shown in
3565 <li>JAVAWS version of Jalview fails to launch with
3566 'invalid literal/length code'</li>
3567 <li>Annotation/RNA Helix colourschemes cannot be applied
3568 to alignment with groups (actually fixed in 2.8.0b1)</li>
3569 <li>RNA Helices and T-Coffee Scores available as default
3572 </ul> <em>Applet</em>
3574 <li>Remove group option is shown even when selection is
3576 <li>Apply to all groups ticked but colourscheme changes
3577 don't affect groups</li>
3578 <li>Documented RNA Helices and T-Coffee Scores as valid
3579 colourscheme name</li>
3580 <li>Annotation labels drawn on sequence IDs when
3581 Annotation panel is not displayed</li>
3582 <li>Increased font size for dropdown menus on OSX and
3583 embedded windows</li>
3584 </ul> <em>Other</em>
3586 <li>Consensus sequence for alignments/groups with a
3587 single sequence were not calculated</li>
3588 <li>annotation files that contain only groups imported as
3589 annotation and junk sequences</li>
3590 <li>Fasta files with sequences containing '*' incorrectly
3591 recognised as PFAM or BLC</li>
3592 <li>conservation/PID slider apply all groups option
3593 doesn't affect background (2.8.0b1)
3595 <li>redundancy highlighting is erratic at 0% and 100%</li>
3596 <li>Remove gapped columns fails for sequences with ragged
3598 <li>AMSA annotation row with leading spaces is not
3599 registered correctly on import</li>
3600 <li>Jalview crashes when selecting PCA analysis for
3601 certain alignments</li>
3602 <li>Opening the colour by annotation dialog for an
3603 existing annotation based 'use original colours'
3604 colourscheme loses original colours setting</li>
3609 <td><div align="center">
3610 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3611 <em>30/1/2014</em></strong>
3615 <li>Trusted certificates for JalviewLite applet and
3616 Jalview Desktop application<br />Certificate was donated by
3617 <a href="https://www.certum.eu">Certum</a> to the Jalview
3618 open source project).
3620 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3621 <li>Output in Stockholm format</li>
3622 <li>Allow import of data from gzipped files</li>
3623 <li>Export/import group and sequence associated line
3624 graph thresholds</li>
3625 <li>Nucleotide substitution matrix that supports RNA and
3626 ambiguity codes</li>
3627 <li>Allow disorder predictions to be made on the current
3628 selection (or visible selection) in the same way that JPred
3630 <li>Groovy scripting for headless Jalview operation</li>
3631 </ul> <em>Other improvements</em>
3633 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3634 <li>COMBINE statement uses current SEQUENCE_REF and
3635 GROUP_REF scope to group annotation rows</li>
3636 <li>Support '' style escaping of quotes in Newick
3638 <li>Group options for JABAWS service by command line name</li>
3639 <li>Empty tooltip shown for JABA service options with a
3640 link but no description</li>
3641 <li>Select primary source when selecting authority in
3642 database fetcher GUI</li>
3643 <li>Add .mfa to FASTA file extensions recognised by
3645 <li>Annotation label tooltip text wrap</li>
3650 <li>Slow scrolling when lots of annotation rows are
3652 <li>Lots of NPE (and slowness) after creating RNA
3653 secondary structure annotation line</li>
3654 <li>Sequence database accessions not imported when
3655 fetching alignments from Rfam</li>
3656 <li>Incorrect SHMR submission for sequences with
3658 <li>View all structures does not always superpose
3660 <li>Option widgets in service parameters not updated to
3661 reflect user or preset settings</li>
3662 <li>Null pointer exceptions for some services without
3663 presets or adjustable parameters</li>
3664 <li>Discover PDB IDs entry in structure menu doesn't
3665 discover PDB xRefs</li>
3666 <li>Exception encountered while trying to retrieve
3667 features with DAS</li>
3668 <li>Lowest value in annotation row isn't coloured
3669 when colour by annotation (per sequence) is coloured</li>
3670 <li>Keyboard mode P jumps to start of gapped region when
3671 residue follows a gap</li>
3672 <li>Jalview appears to hang importing an alignment with
3673 Wrap as default or after enabling Wrap</li>
3674 <li>'Right click to add annotations' message
3675 shown in wrap mode when no annotations present</li>
3676 <li>Disorder predictions fail with NPE if no automatic
3677 annotation already exists on alignment</li>
3678 <li>oninit javascript function should be called after
3679 initialisation completes</li>
3680 <li>Remove redundancy after disorder prediction corrupts
3681 alignment window display</li>
3682 <li>Example annotation file in documentation is invalid</li>
3683 <li>Grouped line graph annotation rows are not exported
3684 to annotation file</li>
3685 <li>Multi-harmony analysis cannot be run when only two
3687 <li>Cannot create multiple groups of line graphs with
3688 several 'combine' statements in annotation file</li>
3689 <li>Pressing return several times causes Number Format
3690 exceptions in keyboard mode</li>
3691 <li>Multi-harmony (SHMMR) method doesn't submit
3692 correct partitions for input data</li>
3693 <li>Translation from DNA to Amino Acids fails</li>
3694 <li>Jalview fail to load newick tree with quoted label</li>
3695 <li>--headless flag isn't understood</li>
3696 <li>ClassCastException when generating EPS in headless
3698 <li>Adjusting sequence-associated shading threshold only
3699 changes one row's threshold</li>
3700 <li>Preferences and Feature settings panel panel
3701 doesn't open</li>
3702 <li>hide consensus histogram also hides conservation and
3703 quality histograms</li>
3708 <td><div align="center">
3709 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3711 <td><em>Application</em>
3713 <li>Support for JABAWS 2.0 Services (AACon alignment
3714 conservation, protein disorder and Clustal Omega)</li>
3715 <li>JABAWS server status indicator in Web Services
3717 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3718 in Jalview alignment window</li>
3719 <li>Updated Jalview build and deploy framework for OSX
3720 mountain lion, windows 7, and 8</li>
3721 <li>Nucleotide substitution matrix for PCA that supports
3722 RNA and ambiguity codes</li>
3724 <li>Improved sequence database retrieval GUI</li>
3725 <li>Support fetching and database reference look up
3726 against multiple DAS sources (Fetch all from in 'fetch db
3728 <li>Jalview project improvements
3730 <li>Store and retrieve the 'belowAlignment'
3731 flag for annotation</li>
3732 <li>calcId attribute to group annotation rows on the
3734 <li>Store AACon calculation settings for a view in
3735 Jalview project</li>
3739 <li>horizontal scrolling gesture support</li>
3740 <li>Visual progress indicator when PCA calculation is
3742 <li>Simpler JABA web services menus</li>
3743 <li>visual indication that web service results are still
3744 being retrieved from server</li>
3745 <li>Serialise the dialogs that are shown when Jalview
3746 starts up for first time</li>
3747 <li>Jalview user agent string for interacting with HTTP
3749 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3751 <li>Examples directory and Groovy library included in
3752 InstallAnywhere distribution</li>
3753 </ul> <em>Applet</em>
3755 <li>RNA alignment and secondary structure annotation
3756 visualization applet example</li>
3757 </ul> <em>General</em>
3759 <li>Normalise option for consensus sequence logo</li>
3760 <li>Reset button in PCA window to return dimensions to
3762 <li>Allow seqspace or Jalview variant of alignment PCA
3764 <li>PCA with either nucleic acid and protein substitution
3766 <li>Allow windows containing HTML reports to be exported
3768 <li>Interactive display and editing of RNA secondary
3769 structure contacts</li>
3770 <li>RNA Helix Alignment Colouring</li>
3771 <li>RNA base pair logo consensus</li>
3772 <li>Parse sequence associated secondary structure
3773 information in Stockholm files</li>
3774 <li>HTML Export database accessions and annotation
3775 information presented in tooltip for sequences</li>
3776 <li>Import secondary structure from LOCARNA clustalw
3777 style RNA alignment files</li>
3778 <li>import and visualise T-COFFEE quality scores for an
3780 <li>'colour by annotation' per sequence option to
3781 shade each sequence according to its associated alignment
3783 <li>New Jalview Logo</li>
3784 </ul> <em>Documentation and Development</em>
3786 <li>documentation for score matrices used in Jalview</li>
3787 <li>New Website!</li>
3789 <td><em>Application</em>
3791 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3792 wsdbfetch REST service</li>
3793 <li>Stop windows being moved outside desktop on OSX</li>
3794 <li>Filetype associations not installed for webstart
3796 <li>Jalview does not always retrieve progress of a JABAWS
3797 job execution in full once it is complete</li>
3798 <li>revise SHMR RSBS definition to ensure alignment is
3799 uploaded via ali_file parameter</li>
3800 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3801 <li>View all structures superposed fails with exception</li>
3802 <li>Jnet job queues forever if a very short sequence is
3803 submitted for prediction</li>
3804 <li>Cut and paste menu not opened when mouse clicked on
3806 <li>Putting fractional value into integer text box in
3807 alignment parameter dialog causes Jalview to hang</li>
3808 <li>Structure view highlighting doesn't work on
3810 <li>View all structures fails with exception shown in
3812 <li>Characters in filename associated with PDBEntry not
3813 escaped in a platform independent way</li>
3814 <li>Jalview desktop fails to launch with exception when
3816 <li>Tree calculation reports 'you must have 2 or more
3817 sequences selected' when selection is empty</li>
3818 <li>Jalview desktop fails to launch with jar signature
3819 failure when java web start temporary file caching is
3821 <li>DAS Sequence retrieval with range qualification
3822 results in sequence xref which includes range qualification</li>
3823 <li>Errors during processing of command line arguments
3824 cause progress bar (JAL-898) to be removed</li>
3825 <li>Replace comma for semi-colon option not disabled for
3826 DAS sources in sequence fetcher</li>
3827 <li>Cannot close news reader when JABAWS server warning
3828 dialog is shown</li>
3829 <li>Option widgets not updated to reflect user settings</li>
3830 <li>Edited sequence not submitted to web service</li>
3831 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3832 <li>InstallAnywhere installer doesn't unpack and run
3833 on OSX Mountain Lion</li>
3834 <li>Annotation panel not given a scroll bar when
3835 sequences with alignment annotation are pasted into the
3837 <li>Sequence associated annotation rows not associated
3838 when loaded from Jalview project</li>
3839 <li>Browser launch fails with NPE on java 1.7</li>
3840 <li>JABAWS alignment marked as finished when job was
3841 cancelled or job failed due to invalid input</li>
3842 <li>NPE with v2.7 example when clicking on Tree
3843 associated with all views</li>
3844 <li>Exceptions when copy/paste sequences with grouped
3845 annotation rows to new window</li>
3846 </ul> <em>Applet</em>
3848 <li>Sequence features are momentarily displayed before
3849 they are hidden using hidefeaturegroups applet parameter</li>
3850 <li>loading features via javascript API automatically
3851 enables feature display</li>
3852 <li>scrollToColumnIn javascript API method doesn't
3854 </ul> <em>General</em>
3856 <li>Redundancy removal fails for rna alignment</li>
3857 <li>PCA calculation fails when sequence has been selected
3858 and then deselected</li>
3859 <li>PCA window shows grey box when first opened on OSX</li>
3860 <li>Letters coloured pink in sequence logo when alignment
3861 coloured with clustalx</li>
3862 <li>Choosing fonts without letter symbols defined causes
3863 exceptions and redraw errors</li>
3864 <li>Initial PCA plot view is not same as manually
3865 reconfigured view</li>
3866 <li>Grouped annotation graph label has incorrect line
3868 <li>Grouped annotation graph label display is corrupted
3869 for lots of labels</li>
3874 <div align="center">
3875 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3878 <td><em>Application</em>
3880 <li>Jalview Desktop News Reader</li>
3881 <li>Tweaked default layout of web services menu</li>
3882 <li>View/alignment association menu to enable user to
3883 easily specify which alignment a multi-structure view takes
3884 its colours/correspondences from</li>
3885 <li>Allow properties file location to be specified as URL</li>
3886 <li>Extend Jalview project to preserve associations
3887 between many alignment views and a single Jmol display</li>
3888 <li>Store annotation row height in Jalview project file</li>
3889 <li>Annotation row column label formatting attributes
3890 stored in project file</li>
3891 <li>Annotation row order for auto-calculated annotation
3892 rows preserved in Jalview project file</li>
3893 <li>Visual progress indication when Jalview state is
3894 saved using Desktop window menu</li>
3895 <li>Visual indication that command line arguments are
3896 still being processed</li>
3897 <li>Groovy script execution from URL</li>
3898 <li>Colour by annotation default min and max colours in
3900 <li>Automatically associate PDB files dragged onto an
3901 alignment with sequences that have high similarity and
3903 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3904 <li>'view structures' option to open many
3905 structures in same window</li>
3906 <li>Sort associated views menu option for tree panel</li>
3907 <li>Group all JABA and non-JABA services for a particular
3908 analysis function in its own submenu</li>
3909 </ul> <em>Applet</em>
3911 <li>Userdefined and autogenerated annotation rows for
3913 <li>Adjustment of alignment annotation pane height</li>
3914 <li>Annotation scrollbar for annotation panel</li>
3915 <li>Drag to reorder annotation rows in annotation panel</li>
3916 <li>'automaticScrolling' parameter</li>
3917 <li>Allow sequences with partial ID string matches to be
3918 annotated from GFF/Jalview features files</li>
3919 <li>Sequence logo annotation row in applet</li>
3920 <li>Absolute paths relative to host server in applet
3921 parameters are treated as such</li>
3922 <li>New in the JalviewLite javascript API:
3924 <li>JalviewLite.js javascript library</li>
3925 <li>Javascript callbacks for
3927 <li>Applet initialisation</li>
3928 <li>Sequence/alignment mouse-overs and selections</li>
3931 <li>scrollTo row and column alignment scrolling
3933 <li>Select sequence/alignment regions from javascript</li>
3934 <li>javascript structure viewer harness to pass
3935 messages between Jmol and Jalview when running as
3936 distinct applets</li>
3937 <li>sortBy method</li>
3938 <li>Set of applet and application examples shipped
3939 with documentation</li>
3940 <li>New example to demonstrate JalviewLite and Jmol
3941 javascript message exchange</li>
3943 </ul> <em>General</em>
3945 <li>Enable Jmol displays to be associated with multiple
3946 multiple alignments</li>
3947 <li>Option to automatically sort alignment with new tree</li>
3948 <li>User configurable link to enable redirects to a
3949 www.Jalview.org mirror</li>
3950 <li>Jmol colours option for Jmol displays</li>
3951 <li>Configurable newline string when writing alignment
3952 and other flat files</li>
3953 <li>Allow alignment annotation description lines to
3954 contain html tags</li>
3955 </ul> <em>Documentation and Development</em>
3957 <li>Add groovy test harness for bulk load testing to
3959 <li>Groovy script to load and align a set of sequences
3960 using a web service before displaying the result in the
3961 Jalview desktop</li>
3962 <li>Restructured javascript and applet api documentation</li>
3963 <li>Ant target to publish example html files with applet
3965 <li>Netbeans project for building Jalview from source</li>
3966 <li>ant task to create online javadoc for Jalview source</li>
3968 <td><em>Application</em>
3970 <li>User defined colourscheme throws exception when
3971 current built in colourscheme is saved as new scheme</li>
3972 <li>AlignFrame->Save in application pops up save
3973 dialog for valid filename/format</li>
3974 <li>Cannot view associated structure for UniProt sequence</li>
3975 <li>PDB file association breaks for UniProt sequence
3977 <li>Associate PDB from file dialog does not tell you
3978 which sequence is to be associated with the file</li>
3979 <li>Find All raises null pointer exception when query
3980 only matches sequence IDs</li>
3981 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3982 <li>Jalview project with Jmol views created with Jalview
3983 2.4 cannot be loaded</li>
3984 <li>Filetype associations not installed for webstart
3986 <li>Two or more chains in a single PDB file associated
3987 with sequences in different alignments do not get coloured
3988 by their associated sequence</li>
3989 <li>Visibility status of autocalculated annotation row
3990 not preserved when project is loaded</li>
3991 <li>Annotation row height and visibility attributes not
3992 stored in Jalview project</li>
3993 <li>Tree bootstraps are not preserved when saved as a
3994 Jalview project</li>
3995 <li>Envision2 workflow tooltips are corrupted</li>
3996 <li>Enabling show group conservation also enables colour
3997 by conservation</li>
3998 <li>Duplicate group associated conservation or consensus
3999 created on new view</li>
4000 <li>Annotation scrollbar not displayed after 'show
4001 all hidden annotation rows' option selected</li>
4002 <li>Alignment quality not updated after alignment
4003 annotation row is hidden then shown</li>
4004 <li>Preserve colouring of structures coloured by
4005 sequences in pre Jalview 2.7 projects</li>
4006 <li>Web service job parameter dialog is not laid out
4008 <li>Web services menu not refreshed after 'reset
4009 services' button is pressed in preferences</li>
4010 <li>Annotation off by one in Jalview v2_3 example project</li>
4011 <li>Structures imported from file and saved in project
4012 get name like jalview_pdb1234.txt when reloaded</li>
4013 <li>Jalview does not always retrieve progress of a JABAWS
4014 job execution in full once it is complete</li>
4015 </ul> <em>Applet</em>
4017 <li>Alignment height set incorrectly when lots of
4018 annotation rows are displayed</li>
4019 <li>Relative URLs in feature HTML text not resolved to
4021 <li>View follows highlighting does not work for positions
4023 <li><= shown as = in tooltip</li>
4024 <li>Export features raises exception when no features
4026 <li>Separator string used for serialising lists of IDs
4027 for javascript api is modified when separator string
4028 provided as parameter</li>
4029 <li>Null pointer exception when selecting tree leaves for
4030 alignment with no existing selection</li>
4031 <li>Relative URLs for datasources assumed to be relative
4032 to applet's codebase</li>
4033 <li>Status bar not updated after finished searching and
4034 search wraps around to first result</li>
4035 <li>StructureSelectionManager instance shared between
4036 several Jalview applets causes race conditions and memory
4038 <li>Hover tooltip and mouseover of position on structure
4039 not sent from Jmol in applet</li>
4040 <li>Certain sequences of javascript method calls to
4041 applet API fatally hang browser</li>
4042 </ul> <em>General</em>
4044 <li>View follows structure mouseover scrolls beyond
4045 position with wrapped view and hidden regions</li>
4046 <li>Find sequence position moves to wrong residue
4047 with/without hidden columns</li>
4048 <li>Sequence length given in alignment properties window
4050 <li>InvalidNumberFormat exceptions thrown when trying to
4051 import PDB like structure files</li>
4052 <li>Positional search results are only highlighted
4053 between user-supplied sequence start/end bounds</li>
4054 <li>End attribute of sequence is not validated</li>
4055 <li>Find dialog only finds first sequence containing a
4056 given sequence position</li>
4057 <li>Sequence numbering not preserved in MSF alignment
4059 <li>Jalview PDB file reader does not extract sequence
4060 from nucleotide chains correctly</li>
4061 <li>Structure colours not updated when tree partition
4062 changed in alignment</li>
4063 <li>Sequence associated secondary structure not correctly
4064 parsed in interleaved stockholm</li>
4065 <li>Colour by annotation dialog does not restore current
4067 <li>Hiding (nearly) all sequences doesn't work
4069 <li>Sequences containing lowercase letters are not
4070 properly associated with their pdb files</li>
4071 </ul> <em>Documentation and Development</em>
4073 <li>schemas/JalviewWsParamSet.xsd corrupted by
4074 ApplyCopyright tool</li>
4079 <div align="center">
4080 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4083 <td><em>Application</em>
4085 <li>New warning dialog when the Jalview Desktop cannot
4086 contact web services</li>
4087 <li>JABA service parameters for a preset are shown in
4088 service job window</li>
4089 <li>JABA Service menu entries reworded</li>
4093 <li>Modeller PIR IO broken - cannot correctly import a
4094 pir file emitted by Jalview</li>
4095 <li>Existing feature settings transferred to new
4096 alignment view created from cut'n'paste</li>
4097 <li>Improved test for mixed amino/nucleotide chains when
4098 parsing PDB files</li>
4099 <li>Consensus and conservation annotation rows
4100 occasionally become blank for all new windows</li>
4101 <li>Exception raised when right clicking above sequences
4102 in wrapped view mode</li>
4103 </ul> <em>Application</em>
4105 <li>multiple multiply aligned structure views cause cpu
4106 usage to hit 100% and computer to hang</li>
4107 <li>Web Service parameter layout breaks for long user
4108 parameter names</li>
4109 <li>Jaba service discovery hangs desktop if Jaba server
4116 <div align="center">
4117 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4120 <td><em>Application</em>
4122 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4123 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4126 <li>Web Services preference tab</li>
4127 <li>Analysis parameters dialog box and user defined
4129 <li>Improved speed and layout of Envision2 service menu</li>
4130 <li>Superpose structures using associated sequence
4132 <li>Export coordinates and projection as CSV from PCA
4134 </ul> <em>Applet</em>
4136 <li>enable javascript: execution by the applet via the
4137 link out mechanism</li>
4138 </ul> <em>Other</em>
4140 <li>Updated the Jmol Jalview interface to work with Jmol
4142 <li>The Jalview Desktop and JalviewLite applet now
4143 require Java 1.5</li>
4144 <li>Allow Jalview feature colour specification for GFF
4145 sequence annotation files</li>
4146 <li>New 'colour by label' keword in Jalview feature file
4147 type colour specification</li>
4148 <li>New Jalview Desktop Groovy API method that allows a
4149 script to check if it being run in an interactive session or
4150 in a batch operation from the Jalview command line</li>
4154 <li>clustalx colourscheme colours Ds preferentially when
4155 both D+E are present in over 50% of the column</li>
4156 </ul> <em>Application</em>
4158 <li>typo in AlignmentFrame->View->Hide->all but
4159 selected Regions menu item</li>
4160 <li>sequence fetcher replaces ',' for ';' when the ',' is
4161 part of a valid accession ID</li>
4162 <li>fatal OOM if object retrieved by sequence fetcher
4163 runs out of memory</li>
4164 <li>unhandled Out of Memory Error when viewing pca
4165 analysis results</li>
4166 <li>InstallAnywhere builds fail to launch on OS X java
4167 10.5 update 4 (due to apple Java 1.6 update)</li>
4168 <li>Installanywhere Jalview silently fails to launch</li>
4169 </ul> <em>Applet</em>
4171 <li>Jalview.getFeatureGroups() raises an
4172 ArrayIndexOutOfBoundsException if no feature groups are
4179 <div align="center">
4180 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4186 <li>Alignment prettyprinter doesn't cope with long
4188 <li>clustalx colourscheme colours Ds preferentially when
4189 both D+E are present in over 50% of the column</li>
4190 <li>nucleic acid structures retrieved from PDB do not
4191 import correctly</li>
4192 <li>More columns get selected than were clicked on when a
4193 number of columns are hidden</li>
4194 <li>annotation label popup menu not providing correct
4195 add/hide/show options when rows are hidden or none are
4197 <li>Stockholm format shown in list of readable formats,
4198 and parser copes better with alignments from RFAM.</li>
4199 <li>CSV output of consensus only includes the percentage
4200 of all symbols if sequence logo display is enabled</li>
4202 </ul> <em>Applet</em>
4204 <li>annotation panel disappears when annotation is
4206 </ul> <em>Application</em>
4208 <li>Alignment view not redrawn properly when new
4209 alignment opened where annotation panel is visible but no
4210 annotations are present on alignment</li>
4211 <li>pasted region containing hidden columns is
4212 incorrectly displayed in new alignment window</li>
4213 <li>Jalview slow to complete operations when stdout is
4214 flooded (fix is to close the Jalview console)</li>
4215 <li>typo in AlignmentFrame->View->Hide->all but
4216 selected Rregions menu item.</li>
4217 <li>inconsistent group submenu and Format submenu entry
4218 'Un' or 'Non'conserved</li>
4219 <li>Sequence feature settings are being shared by
4220 multiple distinct alignments</li>
4221 <li>group annotation not recreated when tree partition is
4223 <li>double click on group annotation to select sequences
4224 does not propagate to associated trees</li>
4225 <li>Mac OSX specific issues:
4227 <li>exception raised when mouse clicked on desktop
4228 window background</li>
4229 <li>Desktop menu placed on menu bar and application
4230 name set correctly</li>
4231 <li>sequence feature settings not wide enough for the
4232 save feature colourscheme button</li>
4241 <div align="center">
4242 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4245 <td><em>New Capabilities</em>
4247 <li>URL links generated from description line for
4248 regular-expression based URL links (applet and application)
4250 <li>Non-positional feature URL links are shown in link
4252 <li>Linked viewing of nucleic acid sequences and
4254 <li>Automatic Scrolling option in View menu to display
4255 the currently highlighted region of an alignment.</li>
4256 <li>Order an alignment by sequence length, or using the
4257 average score or total feature count for each sequence.</li>
4258 <li>Shading features by score or associated description</li>
4259 <li>Subdivide alignment and groups based on identity of
4260 selected subsequence (Make Groups from Selection).</li>
4261 <li>New hide/show options including Shift+Control+H to
4262 hide everything but the currently selected region.</li>
4263 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4264 </ul> <em>Application</em>
4266 <li>Fetch DB References capabilities and UI expanded to
4267 support retrieval from DAS sequence sources</li>
4268 <li>Local DAS Sequence sources can be added via the
4269 command line or via the Add local source dialog box.</li>
4270 <li>DAS Dbref and DbxRef feature types are parsed as
4271 database references and protein_name is parsed as
4272 description line (BioSapiens terms).</li>
4273 <li>Enable or disable non-positional feature and database
4274 references in sequence ID tooltip from View menu in
4276 <!-- <li>New hidden columns and rows and representatives capabilities
4277 in annotations file (in progress - not yet fully implemented)</li> -->
4278 <li>Group-associated consensus, sequence logos and
4279 conservation plots</li>
4280 <li>Symbol distributions for each column can be exported
4281 and visualized as sequence logos</li>
4282 <li>Optionally scale multi-character column labels to fit
4283 within each column of annotation row<!-- todo for applet -->
4285 <li>Optional automatic sort of associated alignment view
4286 when a new tree is opened.</li>
4287 <li>Jalview Java Console</li>
4288 <li>Better placement of desktop window when moving
4289 between different screens.</li>
4290 <li>New preference items for sequence ID tooltip and
4291 consensus annotation</li>
4292 <li>Client to submit sequences and IDs to Envision2
4294 <li><em>Vamsas Capabilities</em>
4296 <li>Improved VAMSAS synchronization (Jalview archive
4297 used to preserve views, structures, and tree display
4299 <li>Import of vamsas documents from disk or URL via
4301 <li>Sharing of selected regions between views and
4302 with other VAMSAS applications (Experimental feature!)</li>
4303 <li>Updated API to VAMSAS version 0.2</li>
4305 </ul> <em>Applet</em>
4307 <li>Middle button resizes annotation row height</li>
4310 <li>sortByTree (true/false) - automatically sort the
4311 associated alignment view by the tree when a new tree is
4313 <li>showTreeBootstraps (true/false) - show or hide
4314 branch bootstraps (default is to show them if available)</li>
4315 <li>showTreeDistances (true/false) - show or hide
4316 branch lengths (default is to show them if available)</li>
4317 <li>showUnlinkedTreeNodes (true/false) - indicate if
4318 unassociated nodes should be highlighted in the tree
4320 <li>heightScale and widthScale (1.0 or more) -
4321 increase the height or width of a cell in the alignment
4322 grid relative to the current font size.</li>
4325 <li>Non-positional features displayed in sequence ID
4327 </ul> <em>Other</em>
4329 <li>Features format: graduated colour definitions and
4330 specification of feature scores</li>
4331 <li>Alignment Annotations format: new keywords for group
4332 associated annotation (GROUP_REF) and annotation row display
4333 properties (ROW_PROPERTIES)</li>
4334 <li>XML formats extended to support graduated feature
4335 colourschemes, group associated annotation, and profile
4336 visualization settings.</li></td>
4339 <li>Source field in GFF files parsed as feature source
4340 rather than description</li>
4341 <li>Non-positional features are now included in sequence
4342 feature and gff files (controlled via non-positional feature
4343 visibility in tooltip).</li>
4344 <li>URL links generated for all feature links (bugfix)</li>
4345 <li>Added URL embedding instructions to features file
4347 <li>Codons containing ambiguous nucleotides translated as
4348 'X' in peptide product</li>
4349 <li>Match case switch in find dialog box works for both
4350 sequence ID and sequence string and query strings do not
4351 have to be in upper case to match case-insensitively.</li>
4352 <li>AMSA files only contain first column of
4353 multi-character column annotation labels</li>
4354 <li>Jalview Annotation File generation/parsing consistent
4355 with documentation (e.g. Stockholm annotation can be
4356 exported and re-imported)</li>
4357 <li>PDB files without embedded PDB IDs given a friendly
4359 <li>Find incrementally searches ID string matches as well
4360 as subsequence matches, and correctly reports total number
4364 <li>Better handling of exceptions during sequence
4366 <li>Dasobert generated non-positional feature URL
4367 link text excludes the start_end suffix</li>
4368 <li>DAS feature and source retrieval buttons disabled
4369 when fetch or registry operations in progress.</li>
4370 <li>PDB files retrieved from URLs are cached properly</li>
4371 <li>Sequence description lines properly shared via
4373 <li>Sequence fetcher fetches multiple records for all
4375 <li>Ensured that command line das feature retrieval
4376 completes before alignment figures are generated.</li>
4377 <li>Reduced time taken when opening file browser for
4379 <li>isAligned check prior to calculating tree, PCA or
4380 submitting an MSA to JNet now excludes hidden sequences.</li>
4381 <li>User defined group colours properly recovered
4382 from Jalview projects.</li>
4391 <div align="center">
4392 <strong>2.4.0.b2</strong><br> 28/10/2009
4397 <li>Experimental support for google analytics usage
4399 <li>Jalview privacy settings (user preferences and docs).</li>
4404 <li>Race condition in applet preventing startup in
4406 <li>Exception when feature created from selection beyond
4407 length of sequence.</li>
4408 <li>Allow synthetic PDB files to be imported gracefully</li>
4409 <li>Sequence associated annotation rows associate with
4410 all sequences with a given id</li>
4411 <li>Find function matches case-insensitively for sequence
4412 ID string searches</li>
4413 <li>Non-standard characters do not cause pairwise
4414 alignment to fail with exception</li>
4415 </ul> <em>Application Issues</em>
4417 <li>Sequences are now validated against EMBL database</li>
4418 <li>Sequence fetcher fetches multiple records for all
4420 </ul> <em>InstallAnywhere Issues</em>
4422 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4423 issue with installAnywhere mechanism)</li>
4424 <li>Command line launching of JARs from InstallAnywhere
4425 version (java class versioning error fixed)</li>
4432 <div align="center">
4433 <strong>2.4</strong><br> 27/8/2008
4436 <td><em>User Interface</em>
4438 <li>Linked highlighting of codon and amino acid from
4439 translation and protein products</li>
4440 <li>Linked highlighting of structure associated with
4441 residue mapping to codon position</li>
4442 <li>Sequence Fetcher provides example accession numbers
4443 and 'clear' button</li>
4444 <li>MemoryMonitor added as an option under Desktop's
4446 <li>Extract score function to parse whitespace separated
4447 numeric data in description line</li>
4448 <li>Column labels in alignment annotation can be centred.</li>
4449 <li>Tooltip for sequence associated annotation give name
4451 </ul> <em>Web Services and URL fetching</em>
4453 <li>JPred3 web service</li>
4454 <li>Prototype sequence search client (no public services
4456 <li>Fetch either seed alignment or full alignment from
4458 <li>URL Links created for matching database cross
4459 references as well as sequence ID</li>
4460 <li>URL Links can be created using regular-expressions</li>
4461 </ul> <em>Sequence Database Connectivity</em>
4463 <li>Retrieval of cross-referenced sequences from other
4465 <li>Generalised database reference retrieval and
4466 validation to all fetchable databases</li>
4467 <li>Fetch sequences from DAS sources supporting the
4468 sequence command</li>
4469 </ul> <em>Import and Export</em>
4470 <li>export annotation rows as CSV for spreadsheet import</li>
4471 <li>Jalview projects record alignment dataset associations,
4472 EMBL products, and cDNA sequence mappings</li>
4473 <li>Sequence Group colour can be specified in Annotation
4475 <li>Ad-hoc colouring of group in Annotation File using RGB
4476 triplet as name of colourscheme</li>
4477 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4479 <li>treenode binding for VAMSAS tree exchange</li>
4480 <li>local editing and update of sequences in VAMSAS
4481 alignments (experimental)</li>
4482 <li>Create new or select existing session to join</li>
4483 <li>load and save of vamsas documents</li>
4484 </ul> <em>Application command line</em>
4486 <li>-tree parameter to open trees (introduced for passing
4488 <li>-fetchfrom command line argument to specify nicknames
4489 of DAS servers to query for alignment features</li>
4490 <li>-dasserver command line argument to add new servers
4491 that are also automatically queried for features</li>
4492 <li>-groovy command line argument executes a given groovy
4493 script after all input data has been loaded and parsed</li>
4494 </ul> <em>Applet-Application data exchange</em>
4496 <li>Trees passed as applet parameters can be passed to
4497 application (when using "View in full
4498 application")</li>
4499 </ul> <em>Applet Parameters</em>
4501 <li>feature group display control parameter</li>
4502 <li>debug parameter</li>
4503 <li>showbutton parameter</li>
4504 </ul> <em>Applet API methods</em>
4506 <li>newView public method</li>
4507 <li>Window (current view) specific get/set public methods</li>
4508 <li>Feature display control methods</li>
4509 <li>get list of currently selected sequences</li>
4510 </ul> <em>New Jalview distribution features</em>
4512 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4513 <li>RELEASE file gives build properties for the latest
4514 Jalview release.</li>
4515 <li>Java 1.1 Applet build made easier and donotobfuscate
4516 property controls execution of obfuscator</li>
4517 <li>Build target for generating source distribution</li>
4518 <li>Debug flag for javacc</li>
4519 <li>.jalview_properties file is documented (slightly) in
4520 jalview.bin.Cache</li>
4521 <li>Continuous Build Integration for stable and
4522 development version of Application, Applet and source
4527 <li>selected region output includes visible annotations
4528 (for certain formats)</li>
4529 <li>edit label/displaychar contains existing label/char
4531 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4532 <li>shorter peptide product names from EMBL records</li>
4533 <li>Newick string generator makes compact representations</li>
4534 <li>bootstrap values parsed correctly for tree files with
4536 <li>pathological filechooser bug avoided by not allowing
4537 filenames containing a ':'</li>
4538 <li>Fixed exception when parsing GFF files containing
4539 global sequence features</li>
4540 <li>Alignment datasets are finalized only when number of
4541 references from alignment sequences goes to zero</li>
4542 <li>Close of tree branch colour box without colour
4543 selection causes cascading exceptions</li>
4544 <li>occasional negative imgwidth exceptions</li>
4545 <li>better reporting of non-fatal warnings to user when
4546 file parsing fails.</li>
4547 <li>Save works when Jalview project is default format</li>
4548 <li>Save as dialog opened if current alignment format is
4549 not a valid output format</li>
4550 <li>UniProt canonical names introduced for both das and
4552 <li>Histidine should be midblue (not pink!) in Zappo</li>
4553 <li>error messages passed up and output when data read
4555 <li>edit undo recovers previous dataset sequence when
4556 sequence is edited</li>
4557 <li>allow PDB files without pdb ID HEADER lines (like
4558 those generated by MODELLER) to be read in properly</li>
4559 <li>allow reading of JPred concise files as a normal
4561 <li>Stockholm annotation parsing and alignment properties
4562 import fixed for PFAM records</li>
4563 <li>Structure view windows have correct name in Desktop
4565 <li>annotation consisting of sequence associated scores
4566 can be read and written correctly to annotation file</li>
4567 <li>Aligned cDNA translation to aligned peptide works
4569 <li>Fixed display of hidden sequence markers and
4570 non-italic font for representatives in Applet</li>
4571 <li>Applet Menus are always embedded in applet window on
4573 <li>Newly shown features appear at top of stack (in
4575 <li>Annotations added via parameter not drawn properly
4576 due to null pointer exceptions</li>
4577 <li>Secondary structure lines are drawn starting from
4578 first column of alignment</li>
4579 <li>UniProt XML import updated for new schema release in
4581 <li>Sequence feature to sequence ID match for Features
4582 file is case-insensitive</li>
4583 <li>Sequence features read from Features file appended to
4584 all sequences with matching IDs</li>
4585 <li>PDB structure coloured correctly for associated views
4586 containing a sub-sequence</li>
4587 <li>PDB files can be retrieved by applet from Jar files</li>
4588 <li>feature and annotation file applet parameters
4589 referring to different directories are retrieved correctly</li>
4590 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4591 <li>Fixed application hang whilst waiting for
4592 splash-screen version check to complete</li>
4593 <li>Applet properly URLencodes input parameter values
4594 when passing them to the launchApp service</li>
4595 <li>display name and local features preserved in results
4596 retrieved from web service</li>
4597 <li>Visual delay indication for sequence retrieval and
4598 sequence fetcher initialisation</li>
4599 <li>updated Application to use DAS 1.53e version of
4600 dasobert DAS client</li>
4601 <li>Re-instated Full AMSA support and .amsa file
4603 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4611 <div align="center">
4612 <strong>2.3</strong><br> 9/5/07
4617 <li>Jmol 11.0.2 integration</li>
4618 <li>PDB views stored in Jalview XML files</li>
4619 <li>Slide sequences</li>
4620 <li>Edit sequence in place</li>
4621 <li>EMBL CDS features</li>
4622 <li>DAS Feature mapping</li>
4623 <li>Feature ordering</li>
4624 <li>Alignment Properties</li>
4625 <li>Annotation Scores</li>
4626 <li>Sort by scores</li>
4627 <li>Feature/annotation editing in applet</li>
4632 <li>Headless state operation in 2.2.1</li>
4633 <li>Incorrect and unstable DNA pairwise alignment</li>
4634 <li>Cut and paste of sequences with annotation</li>
4635 <li>Feature group display state in XML</li>
4636 <li>Feature ordering in XML</li>
4637 <li>blc file iteration selection using filename # suffix</li>
4638 <li>Stockholm alignment properties</li>
4639 <li>Stockhom alignment secondary structure annotation</li>
4640 <li>2.2.1 applet had no feature transparency</li>
4641 <li>Number pad keys can be used in cursor mode</li>
4642 <li>Structure Viewer mirror image resolved</li>
4649 <div align="center">
4650 <strong>2.2.1</strong><br> 12/2/07
4655 <li>Non standard characters can be read and displayed
4656 <li>Annotations/Features can be imported/exported to the
4658 <li>Applet allows editing of sequence/annotation/group
4659 name & description
4660 <li>Preference setting to display sequence name in
4662 <li>Annotation file format extended to allow
4663 Sequence_groups to be defined
4664 <li>Default opening of alignment overview panel can be
4665 specified in preferences
4666 <li>PDB residue numbering annotation added to associated
4672 <li>Applet crash under certain Linux OS with Java 1.6
4674 <li>Annotation file export / import bugs fixed
4675 <li>PNG / EPS image output bugs fixed
4681 <div align="center">
4682 <strong>2.2</strong><br> 27/11/06
4687 <li>Multiple views on alignment
4688 <li>Sequence feature editing
4689 <li>"Reload" alignment
4690 <li>"Save" to current filename
4691 <li>Background dependent text colour
4692 <li>Right align sequence ids
4693 <li>User-defined lower case residue colours
4696 <li>Menu item accelerator keys
4697 <li>Control-V pastes to current alignment
4698 <li>Cancel button for DAS Feature Fetching
4699 <li>PCA and PDB Viewers zoom via mouse roller
4700 <li>User-defined sub-tree colours and sub-tree selection
4702 <li>'New Window' button on the 'Output to Text box'
4707 <li>New memory efficient Undo/Redo System
4708 <li>Optimised symbol lookups and conservation/consensus
4710 <li>Region Conservation/Consensus recalculated after
4712 <li>Fixed Remove Empty Columns Bug (empty columns at end
4714 <li>Slowed DAS Feature Fetching for increased robustness.
4716 <li>Made angle brackets in ASCII feature descriptions
4718 <li>Re-instated Zoom function for PCA
4719 <li>Sequence descriptions conserved in web service
4721 <li>UniProt ID discoverer uses any word separated by
4723 <li>WsDbFetch query/result association resolved
4724 <li>Tree leaf to sequence mapping improved
4725 <li>Smooth fonts switch moved to FontChooser dialog box.
4732 <div align="center">
4733 <strong>2.1.1</strong><br> 12/9/06
4738 <li>Copy consensus sequence to clipboard</li>
4743 <li>Image output - rightmost residues are rendered if
4744 sequence id panel has been resized</li>
4745 <li>Image output - all offscreen group boundaries are
4747 <li>Annotation files with sequence references - all
4748 elements in file are relative to sequence position</li>
4749 <li>Mac Applet users can use Alt key for group editing</li>
4755 <div align="center">
4756 <strong>2.1</strong><br> 22/8/06
4761 <li>MAFFT Multiple Alignment in default Web Service list</li>
4762 <li>DAS Feature fetching</li>
4763 <li>Hide sequences and columns</li>
4764 <li>Export Annotations and Features</li>
4765 <li>GFF file reading / writing</li>
4766 <li>Associate structures with sequences from local PDB
4768 <li>Add sequences to exisiting alignment</li>
4769 <li>Recently opened files / URL lists</li>
4770 <li>Applet can launch the full application</li>
4771 <li>Applet has transparency for features (Java 1.2
4773 <li>Applet has user defined colours parameter</li>
4774 <li>Applet can load sequences from parameter
4775 "sequence<em>x</em>"
4781 <li>Redundancy Panel reinstalled in the Applet</li>
4782 <li>Monospaced font - EPS / rescaling bug fixed</li>
4783 <li>Annotation files with sequence references bug fixed</li>
4789 <div align="center">
4790 <strong>2.08.1</strong><br> 2/5/06
4795 <li>Change case of selected region from Popup menu</li>
4796 <li>Choose to match case when searching</li>
4797 <li>Middle mouse button and mouse movement can compress /
4798 expand the visible width and height of the alignment</li>
4803 <li>Annotation Panel displays complete JNet results</li>
4809 <div align="center">
4810 <strong>2.08b</strong><br> 18/4/06
4816 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4817 <li>Righthand label on wrapped alignments shows correct
4824 <div align="center">
4825 <strong>2.08</strong><br> 10/4/06
4830 <li>Editing can be locked to the selection area</li>
4831 <li>Keyboard editing</li>
4832 <li>Create sequence features from searches</li>
4833 <li>Precalculated annotations can be loaded onto
4835 <li>Features file allows grouping of features</li>
4836 <li>Annotation Colouring scheme added</li>
4837 <li>Smooth fonts off by default - Faster rendering</li>
4838 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4843 <li>Drag & Drop fixed on Linux</li>
4844 <li>Jalview Archive file faster to load/save, sequence
4845 descriptions saved.</li>
4851 <div align="center">
4852 <strong>2.07</strong><br> 12/12/05
4857 <li>PDB Structure Viewer enhanced</li>
4858 <li>Sequence Feature retrieval and display enhanced</li>
4859 <li>Choose to output sequence start-end after sequence
4860 name for file output</li>
4861 <li>Sequence Fetcher WSDBFetch@EBI</li>
4862 <li>Applet can read feature files, PDB files and can be
4863 used for HTML form input</li>
4868 <li>HTML output writes groups and features</li>
4869 <li>Group editing is Control and mouse click</li>
4870 <li>File IO bugs</li>
4876 <div align="center">
4877 <strong>2.06</strong><br> 28/9/05
4882 <li>View annotations in wrapped mode</li>
4883 <li>More options for PCA viewer</li>
4888 <li>GUI bugs resolved</li>
4889 <li>Runs with -nodisplay from command line</li>
4895 <div align="center">
4896 <strong>2.05b</strong><br> 15/9/05
4901 <li>Choose EPS export as lineart or text</li>
4902 <li>Jar files are executable</li>
4903 <li>Can read in Uracil - maps to unknown residue</li>
4908 <li>Known OutOfMemory errors give warning message</li>
4909 <li>Overview window calculated more efficiently</li>
4910 <li>Several GUI bugs resolved</li>
4916 <div align="center">
4917 <strong>2.05</strong><br> 30/8/05
4922 <li>Edit and annotate in "Wrapped" view</li>
4927 <li>Several GUI bugs resolved</li>
4933 <div align="center">
4934 <strong>2.04</strong><br> 24/8/05
4939 <li>Hold down mouse wheel & scroll to change font
4945 <li>Improved JPred client reliability</li>
4946 <li>Improved loading of Jalview files</li>
4952 <div align="center">
4953 <strong>2.03</strong><br> 18/8/05
4958 <li>Set Proxy server name and port in preferences</li>
4959 <li>Multiple URL links from sequence ids</li>
4960 <li>User Defined Colours can have a scheme name and added
4962 <li>Choose to ignore gaps in consensus calculation</li>
4963 <li>Unix users can set default web browser</li>
4964 <li>Runs without GUI for batch processing</li>
4965 <li>Dynamically generated Web Service Menus</li>
4970 <li>InstallAnywhere download for Sparc Solaris</li>
4976 <div align="center">
4977 <strong>2.02</strong><br> 18/7/05
4983 <li>Copy & Paste order of sequences maintains
4984 alignment order.</li>
4990 <div align="center">
4991 <strong>2.01</strong><br> 12/7/05
4996 <li>Use delete key for deleting selection.</li>
4997 <li>Use Mouse wheel to scroll sequences.</li>
4998 <li>Help file updated to describe how to add alignment
5000 <li>Version and build date written to build properties
5002 <li>InstallAnywhere installation will check for updates
5003 at launch of Jalview.</li>
5008 <li>Delete gaps bug fixed.</li>
5009 <li>FileChooser sorts columns.</li>
5010 <li>Can remove groups one by one.</li>
5011 <li>Filechooser icons installed.</li>
5012 <li>Finder ignores return character when searching.
5013 Return key will initiate a search.<br>
5020 <div align="center">
5021 <strong>2.0</strong><br> 20/6/05
5026 <li>New codebase</li>