Release History

+ + +

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

+ 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 +

+ Calculations +

+ Fixed incorrect value in BLOSUM 62 score + matrix - C->R should be '-3'
Old matrix restored + with this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3 +
Fixed + Jalview's treatment of gaps in PCA and substitution matrix + based Tree calculations.

In earlier versions + of Jalview, gaps matching gaps were penalised, and gaps + matching non-gaps penalised even more. In the PCA + calculation, gaps were actually treated as non-gaps - so + different costs were applied, which meant Jalview's PCAs + were different to those produced by SeqSpace.
Jalview + now treats gaps in the same way as SeqSpace (ie it scores + them as 0).

Enter the following in the + Groovy console to restore pre-2.10.2 behaviour:
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true + // for 2.10.1 mode
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false + // to restore 2.10.2 mode

Note: + these settings will affect all subsequent tree and PCA + calculations (not recommended)

+ Fixed off-by-one bug that affected + scaling of branch lengths for trees computed using + Sequence Feature Similarity. +

+ PCA calculation could hang when + generating output report when working with highly + redundant alignments +

+ Sort by features includes features to + right of selected region when gaps present on right-hand + boundary +

+ User Interface +

+ Reopening Colour by annotation dialog + doesn't reselect a specific sequence's associated + annotation after it was used for colouring a view +
+ Current selection lost if popup menu + opened on a region of alignment without groups +
+ Popup menu not always shown for regions + of an alignment with overlapping groups +
+ Finder double counts if both a sequence's + name and description match +
+ Hiding column selection containing two + hidden regions results in incorrect hidden regions +
+ 'Apply to all groups' setting when + changing colour does not apply Conservation slider value + to all groups +
+ Percentage identity and conservation menu + items do not show a tick or allow shading to be disabled +
+ Conservation shading or PID threshold + lost when base colourscheme changed if slider not visible +
+ Sequence features shown in tooltip for + gaps before start of features +
+ Graduated feature colour threshold not + restored to UI when feature colour is edited +
+ Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode. +
+ Structure and alignment overview update + as graduate feature colour settings are modified via the + dialog box +
+ Overview window doesn't always update + when a group defined on the alignment is resized +
+ Mouseovers on left/right scale region in + wrapped view result in positional status updates +
+ Status bar doesn't show position for + ambiguous amino acid and nucleotide symbols +
+ Copy consensus sequence failed if + alignment included gapped columns +
+ Minimum size set for Jalview windows so + widgets don't permanently disappear +
+ Cannot select or filter quantitative + annotation that are shown only as column labels (e.g. + T-Coffee column reliability scores) +
+ Exception thrown if trying to create a + sequence feature on gaps only +
+ Features created with 'New feature' + button from a Find inherit previously defined feature type + rather than the Find query string +
+ incorrect title in output window when + exporting tree calculated in Jalview +
+ Hiding sequences at bottom of alignment + and then revealing them reorders sequences on the + alignment +
+ Group panel in sequence feature settings + doesn't update to reflect available set of groups after + interactively adding or modifying features +
+ Sequence Database chooser unusable on + Linux +
+ Hide insertions in PopUp->Selection menu + only excluded gaps in current sequence and ignored + selection. +

+ Rendering +

+ Overview window visible region moves + erratically when hidden rows or columns are present +
+ Per-residue colourschemes applied via the + Structure Viewer's colour menu don't correspond to + sequence colouring +
+ Protein specific colours only offered in + colour and group colour menu for protein alignments +
+ Colour threshold slider doesn't update to + reflect currently selected view or group's shading + thresholds +
+ Feature colour thresholds not respected + when rendered on overview and structures when opacity at + 100% +
+ User defined gap colour not shown in + overview when features overlaid on alignment +

+ Data import/export +

+ Very large alignments take a long time to + load +
+ Per-sequence RNA secondary structures + added after a sequence was imported are not written to + Stockholm File +
+ WUSS notation for simple pseudoknots lost + when importing RNA secondary structure via Stockholm +
+ Secondary structure arrows for [] and {} + not shown in correct direction for simple pseudoknots +
+ Cannot configure feature colours + with lightGray or darkGray via features file (but can + specify lightgray) +
+ Above PID colour threshold not recovered + when alignment view imported from project +
+ No mappings generated between + structure and sequences extracted from structure files + imported via URL and viewed in Jmol +
+ Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed +

+ Web Services +

+ EnsemblGenomes example failing after + release of Ensembl v.88 +
+ Proxy server address and port always + appear enabled in Preferences->Connections +
+ DAS registry not found exceptions + removed from console output +
+ Cannot retrieve protein products from + Ensembl by Peptide ID +
+ Incorrect PDB-Uniprot mappings + created from SIFTs, and spurious 'Couldn't open structure + in Chimera' errors raised after April 2017 update (problem + due to 'null' string rather than empty string used for + residues with no corresponding PDB mapping). +

+ Application UI +

+ User Defined Colours not added to Colour + menu +
+ Easier creation of colours for all 'Lower + case' residues (button in colourscheme editor debugged and + new documentation and tooltips added) +
+ Text colour threshold's 'Cancel' button + doesn't restore group-specific text colour thresholds +
+ Feature settings panel does not update as + new features are added to alignment +
+ Cancel in feature settings reverts + changes to feature colours via the Amend features dialog +
+ Null pointer exception when attempting to + edit graduated feature colour via amend features dialog + box +
+ Structure viewer's View -> Colour By view + selection menu changes colours of alignment views +
+ Spurious exceptions in console raised + from alignment calculation workers after alignment has + been closed +
+ Typo in selection popup menu - Create + groups now 'Create Group' +
+ CMD/CTRL and G or Shift G for + Create/Undefine group doesn't always work +
+ Tree Viewer's Print Dialog doesn't get + shown again after pressing 'Cancel' +
+ Trackpad horizontal scroll gesture + adjusts start position in wrap mode +
+ Status bar doesn't show positions for + ambiguous amino acids +
+ cDNA Consensus annotation not shown in + CDS/Protein view after CDS sequences added for aligned + proteins +
+ User defined colourschemes called 'User + Defined' don't appear in Colours menu +

+ Applet +

+ Switching between Nucleotide and Protein + score models doesn't always result in an updated PCA plot +
+ Features not rendered as transparent on + overview or linked structure view +
+ Colour group by conservation doesn't + work (since 2.8) +
+ Hitting Cancel after applying + user-defined colourscheme doesn't restore original + colourscheme +

+ Test Suite +

+ Unit test failure: + jalview.ws.jabaws.RNAStructExportImport setup fails +
+ Unit test failure: + jalview.ws.sifts.SiftsClientTest due to compatibility + problems with deep array comparison equality asserts in + successive versions of TestNG +
+ Relocated StructureChooserTest and + ParameterUtilsTest Unit tests to Network suite +

+ New Known Issues +

+ Protein/CDS view scrolling not always in + phase after a sequence motif find operation +
+ Importing annotation file with rows + containing just upper and lower case letters are + interpreted as WUSS RNA secondary structure symbols +
+ Cannot load and display Newick trees + reliably from eggnog Ortholog database +
+ Status bar shows 'Marked x columns + containing features of type Highlight' when 'B' is pressed + to mark columns containing highlighted regions. +
+ Dropping a PDB file onto a sequence + doesn't always add secondary structure annotation. +

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

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
+ 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

+ +

@@ -110,8 +1233,8 @@ General

- Updated Spanish translations. -
Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -400,6 +1523,10 @@ Quality and Conservation are now shown on load even when Consensus calculation is disabled
+ Remove right on penultimate column of + alignment does nothing +

Application

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 @@ -546,6 +1674,19 @@ Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+ Unable to read old Jalview projects that + contain non-XML data added after Jalvew wrote project. +
+ 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. +

@@ -614,6 +1755,12 @@

Applet

Split frame example added to applet examples page

Build and Deployment

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

@@ -1001,10 +2148,10 @@

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 @@ -1842,11 +2988,6 @@
- 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 @@ -2299,11 +3440,6 @@
- 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'
@@ -2318,11 +3454,6 @@
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 @@ -2334,11 +3465,6 @@
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -