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

URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
+ 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

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 for April 2017 update due to 'null' strings in + RESNUM mapping field +

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 +

- -

+ General

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

- +

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

@@ -1233,10 +1768,10 @@ li:before { 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 @@ -2074,11 +2608,6 @@ li:before {
- 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 @@ -2531,11 +3060,6 @@ li:before {
- 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'
@@ -2550,11 +3074,6 @@ li:before {
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 @@ -2566,11 +3085,6 @@ li:before {
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -