Release History

- General -

Improved memory usage: sparse arrays used for all consensus calculations
Updated Jmol shipped with applet and desktop to 14.6.4

General

+ 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 +
+
+ More robust colours and shader + model for alignments and groups +
+ Custom shading schemes created via groovy + scripts +
+ linked scrolling of CDS/Protein views + via Overview or sequence motif search operations +
+ Efficiency improvements for interacting + with alignment and overview windows +
+ Hidden columns and sequences can be + omitted in Overview +
+ Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
+ Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
+ Amend sequence features dialog box can be + opened by double clicking gaps within sequence feature + extent +
+ Graduated feature colour style example + included in the example feature file +
+ Occupancy annotation row shows number of + ungapped positions in each column of the alignment. +

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
Jalview's chimera control window closes if the Chimera it is connected to is shut down
Custom URL links for database cross-references are matched to database name regardless of case
Select highlighted columns menu item and keystroke (B) to mark columns containing highlighted regions 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
+ Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application. +
+ Warning in alignment status bar when + there are not enough columns to superimpose structures in + Chimera +
+ Faster Chimera/Jalview communication by + file-based command exchange +
+ URLs for viewing database + cross-references provided by identifiers.org and the + EMBL-EBI's MIRIAM DB +
+ Updated JABAWS client to v2.2 +
+ Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +
+ Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences +

Experimental features

+ New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa. +

Applet

Build and deployment

Test Suite

Updated Jalview's Certum code signing certificate for 2016-2017
+ Added PrivilegedAccessor to test suite +
+ Prevent or clear modal dialogs raised + during tests +
+ Scripting +
- + FileFormatI interface for describing + and identifying file formats (instead of String + constants) +
- + +

General

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
+ 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). To restore pre-2.10.2 + behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for + 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to + restore 2.10.2 mode +
+ Reopening Colour by annotation dialog + doesn't reselect a specific sequence's associated + annotation after it was used for colouring a view +
+ Hidden regions in alignment views are not + coloured in linked structure views +
+ 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 +
+ PCA calculation could hang when + generating output report when working with highly + redundant alignments +
+ Cannot configure feature colours with + lightGray or darkGray via features file +
+ 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 +
+ 'Apply to all groups' setting when + changing colour does not apply Conservation slider value + to all groups +
+ Colour threshold slider doesn't update to + reflect currently selected view or group's shading + thresholds +
+ 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 +
+ Very large alignments take a long time to + load +
+ Graduated feature colour threshold not + restored to UI when feature colour is edited +
+ Feature colour thresholds not respected + when rendered on overview and structures when opacity at + 100% +
+ Structure and alignment overview update + as graduate feature colour settings are modified via the + dialog box +
+ Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode. +
+ 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 shows position for ambiguous + amino acid and nucleotide symbols +
+ Copy consensus sequence failed if + alignment included gapped columns +
+ User defined gap colour not shown in + overview when features overlaid on alignment +
+ +
+ +
+ +
+ +

+ Documentation +

+ Release notes reformatted for readibility + with the built-in Java help viewer +

Application

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
- 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 -
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
+ 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 +
+ Structure viewer's View -> Colour By view + selection menu changes colours of alignment views +
+ Proxy server address and port always + appear enabled in Preferences->Connections +
+ 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' +
+ DAS registry not found exceptions + removed from console output +
+ 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 +
+ Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed +
+ Trackpad horizontal scroll gesture + adjusts start position in wrap mode +
+ Status bar doesn't show positions for + ambiguous amino acids +
+ Hide insertions in PopUp menu excludes + gaps in selection, current sequence and only within + selected columns +
+ Cannot retrieve protein products from + Ensembl by Peptide ID +
+ cDNA Consensus annotation not shown in + CDS/Protein view after CDS sequences added for aligned + proteins +
+ cDNA Consensus not shown +

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 +

- Build and deployment + New Known Issues

Failing/passing unit tests
+ 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 Newick trees from eggnog + ortholog database +

- New Known Issues + Test Suite

+ Unit test failure: + jalview.ws.jabaws.RNAStructExportImport setup fails +
+ +

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

+ +

@@ -192,8 +727,8 @@ General

- Updated Spanish translations. -
Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -483,7 +1018,7 @@ load even when Consensus calculation is disabled
- Remove right on penultimate column of + Remove right on penultimate column of alignment does nothing

@@ -571,7 +1106,8 @@

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 @@ -636,7 +1172,8 @@ 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.

@@ -708,9 +1245,12 @@ 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 +

@@ -1098,10 +1638,10 @@ 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 @@ -1939,11 +2478,6 @@
- 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 @@ -2396,11 +2930,6 @@
- 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'
@@ -2415,11 +2944,6 @@
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 @@ -2431,11 +2955,6 @@
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -