Release History

+ 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 +
+
+ Tree/PCA calculation menu items merged to + a calculation dialog box +
+ 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. +
+ File extension pruned from Sequence ID + for sequences derived from structure files without + embedded database accession +
+ Status bar message shown when not enough + aligned positions were available to create a 3D structure + superposition. +
+ More robust per-sequence positional + annotation input/output via stockholm flatfile +

+ Application +

+ 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 +
+ Structures imported via URL are cached in + the Jalview project rather than downloaded again when the + project is reopened. +

+ Experimental features +

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

+ Applet +

+ Test Suite +

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

+ General +

+ 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 +
+ Fixed off-by-one bug that affected + scaling of branch lengths for trees computed using + Sequence Feature Similarity. +
+ 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 +
+ 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) +
+ Gap colours in user-defined colourschemes + are not shown +
+ Exception thrown if trying to create a + sequence feature on gaps only +
+ Sort by features includes features to + right of selected region when gaps present on right-hand + boundary +
+ 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 +
+ 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 +
+ 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 +
+ +
+ +
+ +

+ Documentation +

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

+ Application +

+ Sequence Database chooser doesn't show + available databases panel on Linux +
+ EnsemblGenomes example failing after + release of Ensembl v.88 +
+ 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 +
+ 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 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 +
+ 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 +
+ 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). +

+ 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 +

+ 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 Newick trees 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. +

+ 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 +

+ 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 +
+ 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 +

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 +
+ 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 +

@@ -71,8 +864,8 @@ General

- Updated Spanish translations. -
Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -361,6 +1154,10 @@ 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 @@ -507,6 +1305,15 @@ 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. +

@@ -575,6 +1382,12 @@ Applet

Split frame example added to applet examples page

Build and Deployment +

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

@@ -962,10 +1775,10 @@ 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 @@ -1803,11 +2615,6 @@
- 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 @@ -2260,11 +3067,6 @@
- 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'
@@ -2279,11 +3081,6 @@
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 @@ -2295,11 +3092,6 @@
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -