Release History

+ 2.10.5
6/09/2018 +

+ +

+ Default memory for Jalview webstart and + InstallAnywhere increased to 1G. +
+ Hidden sequence markers and representative + sequence bolding included when exporting alignment as EPS, + SVG, PNG or HTML. Display is configured via the + Format menu, or for command-line use via a jalview + properties file. +
+ Ensembl client updated to Version 7 REST + API and sequence data now imported as JSON. +
+ Change in recommended way of starting + Jalview via a Java command line: add jars in lib directory + to CLASSPATH, rather than via the deprecated java.ext.dirs + property. +

+ Development +

+ Support added to execute test suite + instrumented with Open + Clover +

+ +

+ Poorly scaled bar in quality annotation + row shown in Feredoxin Structure alignment view of example + alignment. +
+ Annotation obscures sequences if lots of + annotation displayed. +
+ Corrupted display when switching to + wrapped mode when sequence panel's vertical scrollbar is + visible. +
+ Alignment is black in exported EPS file + when sequences are selected in exported view. +
+ Groups with different coloured borders + aren't rendered with correct colour. +
+ Jalview could hang when importing certain + types of knotted RNA secondary structure. +
+ Sequence highlight and selection in + trimmed VARNA 2D structure is incorrect for sequences that + do not start at 1. +
+ '.' inserted into RNA secondary structure + annotation when columns are inserted into an alignment, + and when exporting as Stockholm flatfile. +
+ Jalview annotation rows containing upper + and lower-case 'E' and 'H' do not automatically get + treated as RNA secondary structure. +
+ .jvp should be used as default extension + (not .jar) when saving a jalview project file. +
+ Mac Users: closing a window correctly + transfers focus to previous window on OSX +

+ Java 10 Issues +

+ OSX - Can't save new files via the File + or export menus by typing in a name into the Save dialog + box. +

- 2.10.1
- 22/11/2016 + 2.10.4b1
+ 7/06/2018

- General -

Improved memory usage: sparse arrays used for all consensus calculations

+ Use HGVS nomenclature for variant + annotation retrieved from Uniprot +
+ Windows File Shortcuts can be dragged + onto the Jalview Desktop +

Application

Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets)
New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.
Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session
Custom URL links for database cross-references are matched to database name regardless of case
+ Cannot import features with multiple + variant elements (blocks import of some Uniprot records) +
+ Clustal files with sequence positions in + right-hand column parsed correctly +
+ Wrap view - export to SVG - IDs shown but + not alignment area in exported graphic +
+ F2/Keyboard mode edits work when Overview + window has input focus +
+ Annotation panel set too high when + annotation added to view (Windows) +
+ Jalview Desktop is slow to start up when + network connectivity is poor +
+ Drag URL from chrome, firefox, IE to + Jalview desktop on Windows doesn't open file
Dragging + the currently open URL and links from a page viewed in + Firefox or Chrome on Windows is now fully supported. If + you are using Edge, only links in the page can be + dragged, and with Internet Explorer, only the currently + open URL in the browser can be dropped onto Jalview. +

+ 2.10.4
10/05/2018 +

+ +

+ New Structure Chooser control + for disabling automatic superposition of multiple + structures and open structures in existing views +
+ Mouse cursor changes to indicate Sequence + ID and annotation area margins can be click-dragged to + adjust them. +
+ Jalview uses HTTPS for Uniprot, Xfam and + Ensembl services +
+ Improved performance for large alignments + and lots of hidden columns +
+ Improved performance when rendering lots + of features (particularly when transparency is disabled) +

+ Structure and Overview aren't updated + when Colour By Annotation threshold slider is adjusted +
+ Slow redraw when Overview panel shown + overlapping alignment panel +
+ Overview doesn't show end of unpadded + sequence as gaps +
+ Cross-reference handling + improved: CDS not handled correctly if transcript has no + UTR +
+ Secondary structure and temperature + factor annotation not added to sequence when local PDB + file associated with it by drag'n'drop or structure + chooser +
+ Answering 'No' to PDB Autoassociate + dialog doesn't import PDB files dropped on an alignment +
+ Linked scrolling via protein horizontal + scroll bar doesn't work for some CDS/Protein views +
+ Trackpad scrolling is broken on OSX on + Java 1.8u153 onwards and Java 1.9u4+. +
+ Tooltip shouldn't be displayed for empty + columns in annotation row +
+ Preferences panel's ID Width control is not + honored in batch mode +
+ Linked sequence highlighting doesn't work + for structures added to existing Jmol view +
+ 'View Mappings' includes duplicate + entries after importing project with multiple views +
+ Viewing or annotating Uniprot + protein sequences via SIFTS from associated PDB entries + with negative residue numbers or missing residues fails +
+ Exception when shading sequence with negative + Temperature Factor values from annotated PDB files (e.g. + as generated by CONSURF) +
+ Uniprot 'sequence variant' features + tooltip doesn't include a text description of mutation +
+ Invert displayed features very slow when + structure and/or overview windows are also shown +
+ Selecting columns from highlighted regions + very slow for alignments with large numbers of sequences +
+ Copy Consensus fails for group consensus + with 'StringIndexOutOfBounds' +
+ VAqua(4) provided as fallback Look and Feel for OSX + platforms running Java 10 +
+ Adding a structure to existing structure + view appears to do nothing because the view is hidden behind the alignment view +

+ Applet +

+ Copy consensus sequence option in applet + should copy the group consensus when popup is opened on it +

+ Batch Mode +

+ Fixed ID width preference is not respected +

+ New Known Defects +

+ Exceptions occasionally raised when + editing a large alignment and overview is displayed +
+ 'Overview updating' progress bar is shown + repeatedly after a series of edits even when the overview + is no longer reflecting updates +
+ 'SIFTS Mapping Error' when viewing + structures for protein subsequence (if 'Trim Retrieved + Sequences' enabled) or Ensembl isoforms (Workaround in + 2.10.4 is to fail back to N&W mapping) +

+ 2.10.3b1
24/1/2018 +

Updated Certum Codesigning Certificate + (Valid till 30th November 2018)

+ Desktop

Only one structure is loaded when several sequences and structures are selected for viewing/superposing
Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
Helix annotation has 'notches' when scrolled into view if columns are hidden
Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes

+ 2.10.3
17/11/2017 +

+ +

+ Faster and more efficient management and + rendering of sequence features +
+ More reliable Ensembl fetching with HTTP + 429 rate limit request hander +
+ Structure views don't get updated unless + their colours have changed +
+ All linked sequences are highlighted for + a structure mousover (Jmol) or selection (Chimera) +
+ 'Cancel' button in progress bar for + JABAWS AACon, RNAAliFold and Disorder prediction jobs +
+ Stop codons are excluded in CDS/Protein + view from Ensembl locus cross-references +
+ Start/End limits are shown in Pairwise + Alignment report +
+ Sequence fetcher's Free text 'autosearch' + feature can be disabled +
+ Retrieve IDs tab added for UniProt and + PDB easier retrieval of sequences for lists of IDs +
+ Short names for sequences retrieved from + Uniprot +

+ Scripting +

Groovy interpreter updated to 2.4.12
Example groovy script for generating a matrix of + percent identity scores for current alignment.

+ Testing and Deployment +

+ Test to catch memory leaks in Jalview UI +

+ General +

+ Pressing tab after updating the colour + threshold text field doesn't trigger an update to the + alignment view +
+ Race condition when parsing sequence ID + strings in parallel +
+ Overview windows are also closed when + alignment window is closed +
+ Export of features doesn't always respect + group visibility +
+ Jumping from column 1 to column 100,000 + takes a long time in Cursor mode +

+ Desktop +

+ Structures with whitespace chainCode + cannot be viewed in Chimera +
+ Protein annotation panel too high in + CDS/Protein view +
+ Can't edit the query after the server + error warning icon is shown in Uniprot and PDB Free Text + Search Dialogs +
+ Slow EnsemblGenome ID lookup +
+ Revised Ensembl REST API CDNA query +
+ Hidden column marker in last column not + rendered when switching back from Wrapped to normal view +
+ Annotation display corrupted when + scrolling right in unwapped alignment view +
+ Existing features on subsequence + incorrectly relocated when full sequence retrieved from + database +
+ Last reported memory still shown when + Desktop->Show Memory is unticked (OSX only) +
+ Amend Features dialog doesn't allow + features of same type and group to be selected for + amending +
+ Jalview becomes sluggish in wide + alignments when hidden columns are present +
+ Jalview freezes when loading and + displaying several structures +
+ Black outlines left after resizing or + moving a window +
+ Unable to minimise windows + within the Jalview desktop on OSX +
+ Mouse wheel doesn't scroll vertically + when in wrapped alignment mode +
+ Scale mark not shown when close to right + hand end of alignment +
+ Pairwise alignment of selected regions of + each selected sequence do not have correct start/end + positions +
+ Alignment ruler height set incorrectly + after canceling the Alignment Window's Font dialog +
+ Show cross-references not enabled after + restoring project until a new view is created +
+ Warning popup about use of SEQUENCE_ID in + URL links appears when only default EMBL-EBI link is + configured (since 2.10.2b2) +
+ Overview redraws whole window when box + position is adjusted +
+ Structure viewer doesn't map all chains + in a multi-chain structure when viewing alignment + involving more than one chain (since 2.10) +
+ Double residue highlights in cursor mode + if new selection moves alignment window +
+ Alignment vanishes when using + arrow key in cursor mode to pass hidden column marker +
+ Ensembl Genomes example ID changed to one + that produces correctly annotated transcripts and products +
+ Toggling a feature group after first time + doesn't update associated structure view +

+ Applet
+

+ Concurrent modification exception when + closing alignment panel +

+ BioJSON
+

+ BioJSON export does not preserve + non-positional features +

+ New Known Issues +

+ Delete/Cut selection doesn't relocate + sequence features correctly (for many previous versions of + Jalview) +
+ Cursor mode unexpectedly scrolls when + using cursor in wrapped panel other than top +
+ Select columns containing feature ignores + graduated colour threshold +
+ Edit sequence operation doesn't + always preserve numbering and sequence features +

+ Known Java 9 Issues +

+ Groovy Console very slow to open and is + not responsive when entering characters (Webstart, Java + 9.01, OSX 10.10) +

+ 2.10.2b2
+ 2/10/2017 +

+ New features in Jalview Desktop +

+ Uniprot Sequence Fetcher now uses web API at uniprot.org +
HTTPS used for all connections to ebi.ac.uk +

+ 2.10.2b1
+ 7/9/2017 +

+ +

+ Show gaps in overview window by colouring + in grey (sequences used to be coloured grey, and gaps were + white) +
+ Overview tab in Jalview Desktop + Preferences +
+ Overview updates immediately on increase + in size and progress bar shown as higher resolution + overview is recalculated +

+ +

+ Overview window redraws every hidden + column region row by row +
+ duplicate protein sequences shown after + retrieving Ensembl crossrefs for sequences from Uniprot +
+ Overview window throws NPE if show boxes + format setting is unticked +
+ Groups are coloured wrongly in overview + if group has show boxes format setting unticked +
+ Redraw problems when + autoscrolling whilst dragging current selection group to + include sequences and columns not currently displayed +
+ Not all chains are mapped when multimeric + assemblies are imported via CIF file +
+ Gap colour in custom colourscheme is not + displayed when threshold or conservation colouring is also + enabled. +
+ JABAWS 2.2 services report wrong JABAWS + server version +
+ Jalview continues to scroll after + dragging a selected region off the visible region of the + alignment +
+ Cannot apply annotation based + colourscheme to all groups in a view +
+ IDs don't line up with sequences + initially after font size change using the Font chooser or + middle-mouse zoom +

+ 2.10.2
17/8/2017 +

+ Calculations +

+ Occupancy annotation row shows number of + ungapped positions in each column of the alignment. +
+ Tree/PCA calculation menu items merged to + a calculation dialog box +
+ Revised implementation of PCA for speed + and memory efficiency (~30x faster) +
+ Revised implementation of sequence + similarity scores as used by Tree, PCA, Shading Consensus + and other calculations +
+ Score matrices are stored as resource + files within the Jalview codebase +
+ Trees computed on Sequence Feature + Similarity may have different topology due to increased + precision +

+ Rendering +

+ More robust colours and shader + model for alignments and groups +
+ Custom shading schemes created via groovy + scripts +

+ Overview +

+ Efficiency improvements for interacting + with alignment and overview windows +
+ Scrolling of wrapped alignment views via + overview +
+ Hidden columns and sequences can be + omitted in Overview +
+ Click-drag in visible area allows fine + adjustment of visible position +

+ + Data import/export +

+ Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
+ More robust per-sequence positional + annotation input/output via stockholm flatfile +
+ Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
+ Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +

+ User Interface +

+ Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application. +
+ Linked scrolling of CDS/Protein views + via Overview or sequence motif search operations +
+ Amend sequence features dialog box can be + opened by double clicking gaps within sequence feature + extent +
+ Status bar message shown when not enough + aligned positions were available to create a 3D structure + superposition. +

+ 3D Structure +

+ Hidden regions in alignment views are not + coloured in linked structure views +
+ Faster Chimera/Jalview communication by + file-based command exchange +
+ Structure chooser automatically shows + Cached Structures rather than querying the PDBe if + structures are already available for sequences +
+ Structures imported via URL are cached in + the Jalview project rather than downloaded again when the + project is reopened. +
+ New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa (Experimental + Feature) +

+ Web Services +

+ Updated JABAWS client to v2.2 +
+ Filter non-standard amino acids and + nucleotides when submitting to AACon and other MSA + Analysis services +
+ URLs for viewing database + cross-references provided by identifiers.org and the + EMBL-EBI's MIRIAM DB +

+ + Scripting +

+ FileFormatI interface for describing and + identifying file formats (instead of String constants) +
+ FeatureCounter script refactored for + efficiency when counting all displayed features (not + backwards compatible with 2.10.1) +

+ Example files +

+ Graduated feature colour style example + included in the example feature file +

+ Documentation +

+ Release notes reformatted for readability + with the built-in Java help viewer +
+ Find documentation updated with 'search + sequence description' option +

+ Test Suite +

+ External service integration tests for + Uniprot REST Free Text Search Client +
+ Added PrivilegedAccessor to test suite +
+ Prevent or clear modal dialogs raised + during tests +

- 2.10.0b1
- 25/10/2016 + 2.10.1
29/11/2016

General

Colour by conservation always enabled and no tick - shown in menu when BLOSUM or PID shading applied
FER1_ARATH and FER2_ARATH labels were switched in - example sequences/projects/trees
+ Improved memory usage: sparse arrays used + for all consensus calculations +
+ Jmol updated to version 14.6.4 (released + 3rd Oct 2016) +
Updated Jalview's Certum code signing certificate + for 2016-2017

Application

Jalview projects with views of local PDB structure - files saved on Windows cannot be opened on OSX
Multiple structure views can be opened and - superposed without timeout for structures with multiple - models or multiple sequences in alignment
Cannot import or associated local PDB files without - a PDB ID HEADER line
RMSD is not output in Jmol console when - superposition is performed
Drag and drop of URL from Browser fails for Linux - and OSX versions earlier than El Capitan
ENA client ignores invalid content from ENA server
Exceptions are not raised in console when ENA - client attempts to fetch non-existent IDs via Fetch DB - Refs UI option
Exceptions are not raised in console when a new - view is created on the alignment
OSX right-click fixed for group selections: - CMD-click to insert/remove gaps in groups and CTRL-click - to open group pop-up menu
+ Sequence ID tool tip presents abridged + set of database cross-references, sorted alphabetically +
+ New replacement token for creating URLs just + from database cross references. Users with custom links + will receive a warning + dialog asking them to update their preferences. +
+ Cancel button and escape listener on + dialog warning user about disconnecting Jalview from a + Chimera session +
+ Jalview's Chimera control window closes if + the Chimera it is connected to is shut down +
+ New keystroke (B) and Select highlighted + columns menu item to mark columns containing highlighted + regions (e.g. from structure selections or results of a + Find operation) +
+ Command line option for batch-generation + of HTML pages rendering alignment data with the BioJS + MSAviewer +

- Build and deployment +

+ +

+ General

URL link checker now copes with multi-line anchor - tags
+ Columns with more than one modal residue + are not coloured or thresholded according to percent + identity (first observed in Jalview 2.8.2) +
+ Threonine incorrectly reported as not + hydrophobic +
+ Updates to documentation pages (above PID + threshold, amino acid properties) +
+ Lower case residues in sequences are not + reported as mapped to residues in a structure file in the + View Mapping report +
+ Identical features with non-numeric scores + could be added multiple times to a sequence +
+ Disulphide + bond features shown as two highlighted residues rather + than a range in linked structure views, and treated + correctly when selecting and computing trees from features +
+ Custom URL links for database + cross-references are matched to database name regardless + of case +

- New Known Issues + Application

Drag and drop from URL links in browsers do not - work on Windows
+ Custom URL links for specific database + names without regular expressions also offer links from + Sequence ID +
+ Removing a single configured link in the + URL links pane in Connections preferences doesn't actually + update Jalview configuration +
+ CTRL-Click on a selected region to open + the alignment area popup menu doesn't work on El-Capitan +
+ Jalview doesn't offer to associate mmCIF + files with similarly named sequences if dropped onto the + alignment +
+ Additional mappings are shown for PDB + entries where more chains exist in the PDB accession than + are reported in the SIFTS file +
+ Certain structures do not get mapped to + the structure view when displayed with Chimera +
+ No chains shown in the Chimera view + panel's View->Show Chains submenu +
+ Export as HTML with embedded SVG doesn't + work for wrapped alignment views +
+ Rename UI components for running JPred + predictions from 'JNet' to 'JPred' +
+ Export as PNG or SVG is + corrupted when annotation panel vertical scroll is not at + first annotation row +
+ Attempting to view structure for Hen + lysozyme results in a PDB Client error dialog box +
+ Structure View's mapping report switched + ranges for PDB and sequence for SIFTS +

+ +

+ 2.10.0b1
+ 25/10/2016 +

+ + Application +

3D Structure chooser opens with 'Cached structures' + view if structures already loaded
Progress bar reports models as they are loaded to + structure views

+ +

+ General +

Colour by conservation always enabled and no tick + shown in menu when BLOSUM or PID shading applied
FER1_ARATH and FER2_ARATH labels were switched in + example sequences/projects/trees

+ Application +

Jalview projects with views of local PDB structure + files saved on Windows cannot be opened on OSX
Multiple structure views can be opened and superposed + without timeout for structures with multiple models or + multiple sequences in alignment
Cannot import or associated local PDB files without a + PDB ID HEADER line
RMSD is not output in Jmol console when superposition + is performed
Drag and drop of URL from Browser fails for Linux and + OSX versions earlier than El Capitan
ENA client ignores invalid content from ENA server
Exceptions are not raised in console when ENA client + attempts to fetch non-existent IDs via Fetch DB Refs UI + option
Exceptions are not raised in console when a new view + is created on the alignment
OSX right-click fixed for group selections: CMD-click + to insert/remove gaps in groups and CTRL-click to open group + pop-up menu

+ Build and deployment +

URL link checker now copes with multi-line anchor + tags

+ New Known Issues +

Drag and drop from URL links in browsers do not work + on Windows

+ +

@@ -179,8 +1557,8 @@ General

- Updated Spanish translations. -
Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -470,7 +1848,7 @@ load even when Consensus calculation is disabled
- Remove right on penultimate column of + Remove right on penultimate column of alignment does nothing

@@ -558,7 +1936,8 @@

Enable 'Get Cross-References' in menu - after fetching cross-references, and restoring from project + after fetching cross-references, and restoring from + project

Mouseover of a copy of a sequence is not @@ -623,10 +2002,15 @@ Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project.

Newly created annotation row reorders +

+ Newly created annotation row reorders after clicking on it to create new annotation for a column.

+ Null Pointer Exception raised when + pressing Add on an orphaned cut'n'paste window. +

@@ -695,9 +2079,12 @@ Applet

Split frame example added to applet examples page

Build and Deployment + Build and Deployment

New ant target for running Jalview's test suite
+ New ant target for running Jalview's test + suite +

@@ -1085,10 +2472,10 @@ Deployment and Documentation +

+ General +

+ --> Deployment and Documentation

2G and 1G options in launchApp have no effect on memory allocation

Certum

Jalview SRS links replaced by UniProt and EBI-search -
Jalview SRS links replaced by UniProt and EBI-search
Output in Stockholm format
Allow import of data from gzipped files
Export/import group and sequence associated line @@ -1926,11 +3312,6 @@
- URL links generated from description line for regular-expression based URL links (applet and application) - - - - -
- Non-positional feature URL links are shown in link menu
- Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
- Group-associated consensus, sequence logos and conservation plots
- Symbol distributions for each column can be exported @@ -2383,11 +3764,6 @@
- Cancel button for DAS Feature Fetching
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection - - - - -
- 'New Window' button on the 'Output to Text box'
@@ -2402,11 +3778,6 @@
Fixed Remove Empty Columns Bug (empty columns at end of alignment)
Slowed DAS Feature Fetching for increased robustness. - - - - -
Made angle brackets in ASCII feature descriptions display correctly @@ -2418,11 +3789,6 @@
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -