X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=38a18ec2a9af1f8f869eff109d73ce857b56a583;hb=c4a72d18f6a7b2cf3de4a46b7a35cbfd0d76438f;hp=351b05553586025ec9f856b6ef2b1735a3b7bfac;hpb=cc0b6158d11333a9ee0b5cf57fbe890d5309e510;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 351b055..38a18ec 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -70,13 +70,157 @@ li:before {
- 2.10.2
8/8/2017 + 2.10.3
+ 10/10/2017
- General + + + +
+ + + + + + +
+ 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)
    • @@ -84,22 +228,20 @@ li:before { 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 + 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
    • @@ -107,178 +249,207 @@ li:before { Custom shading schemes created via groovy scripts -
  • - linked scrolling of CDS/Protein views - via Overview or sequence motif search operations -
    • +
+ 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
  • - Amend sequence features dialog box can be - opened by double clicking gaps within sequence feature - extent + Drag and drop load of AAIndex and NCBI + format sequence substitution matrices
    • +
+ User Interface +
  • - Graduated feature colour style example - included in the example feature file + Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application.
  • - Occupancy annotation row shows number of - ungapped positions in each column of the alignment. + Linked scrolling of CDS/Protein views + via Overview or sequence motif search operations
  • - File extension pruned from Sequence ID - for sequences derived from structure files without - embedded database accession + 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.
    • -
  • - More robust per-sequence positional annotation input/output via stockholm flatfile -
    • -
- Application + 3D Structure
  • - 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 + Hidden regions in alignment views are not + coloured in linked structure views
  • 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 + Structure chooser automatically shows + Cached Structures rather than querying the PDBe if + structures are already available for sequences
  • - Updated JABAWS client to v2.2 + Structures imported via URL are cached in + the Jalview project rather than downloaded again when the + project is reopened.
  • - Drag and drop load of AAIndex and NCBI - format sequence substitution matrices + New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa (Experimental + Feature)
    • +
+ Web Services +
  • - Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences + Updated JABAWS client to v2.2
  • - Structures imported via URL are cached in - the Jalview project rather than downloaded again when the - project is reopened. + 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
    • -
- Experimental features + + Scripting
  • - New entries in the Chimera menu - to transfer Chimera's structure attributes as Jalview - features, and vice-versa. + 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)
- Applet + Example files
  • - + Graduated feature colour style example + included in the example feature file
- Test Suite + Documentation
  • - Added PrivilegedAccessor to test suite + Release notes reformatted for readability + with the built-in Java help viewer
  • - Prevent or clear modal dialogs raised - during tests + Find documentation updated with 'search + sequence description' option
    • +
+ Test Suite +
  • 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) -
      • -
    • - -
      • - - -
    + Added PrivilegedAccessor to test suite +
    • +
  • + Prevent or clear modal dialogs raised + during tests +
- General + Calculations + User Interface +
  • 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
    • @@ -295,38 +466,11 @@ li:before { 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
    • @@ -339,17 +483,12 @@ li:before { 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% + Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode.
  • Structure and alignment overview update @@ -357,10 +496,6 @@ li:before { 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
    • @@ -368,20 +503,18 @@ li:before { 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 + Status bar doesn't show 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 + Minimum size set for Jalview windows so + widgets don't permanently disappear
  • Cannot select or filter quantitative @@ -389,13 +522,8 @@ li:before { 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 + Exception thrown if trying to create a + sequence feature on gaps only
  • Features created with 'New feature' @@ -407,47 +535,126 @@ li:before { exporting tree calculated in Jalview
  • - Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File + 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
  • - WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm + Sequence Database chooser unusable on + Linux
  • - Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots + 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
  • - 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 + Per-residue colourschemes applied via the + Structure Viewer's colour menu don't correspond to + sequence colouring
  • - Sequence Database chooser unusable on Linux + 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
- Documentation + Data import/export
  • - Release notes reformatted for readibility - with the built-in Java help viewer + 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
    • -
  • Find documentation updated with 'search sequence description' option
- Application + 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
  • - Sequence Database chooser doesn't show available databases panel on Linux + User Defined Colours not added to Colour + menu
    • -
  • 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 @@ -462,16 +669,17 @@ li:before { new features are added to alignment
  • - Cancel in feature settings reverts changes to feature colours via the Amend features dialog + 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 + Null pointer exception when attempting to + edit graduated feature colour via amend features dialog + box
  • - Proxy server address and port always - appear enabled in Preferences->Connections + Structure viewer's View -> Colour By view + selection menu changes colours of alignment views
  • Spurious exceptions in console raised @@ -491,24 +699,6 @@ li:before { 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
    • @@ -517,31 +707,18 @@ li:before { 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
  • - SIFTs mappings not created for some structures + 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
    • @@ -559,22 +736,6 @@ li:before { 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 -
    • -
Test Suite
  • @@ -591,7 +752,31 @@ li:before { 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. +