X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=38a18ec2a9af1f8f869eff109d73ce857b56a583;hb=c4a72d18f6a7b2cf3de4a46b7a35cbfd0d76438f;hp=0eb4bb67c3f4af65cfe2b5b0d417f5659518667a;hpb=bf3d98e3a6ef3365f490284ab0513742dacd5a3b;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 0eb4bb6..38a18ec 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -25,24 +25,24 @@ ul { /* remove bullets, narrower indent */ list-style-type: none; - margin:0; + margin: 0; padding-left: 10px; padding-bottom: 4px; } li { /* separate the items from eachother */ - margin-left: -3px; - padding-bottom: 3px; - padding-left: 6px; + margin-left: -3px; + padding-bottom: 3px; + padding-left: 6px; } + li:before { /* doesnt get processed in javahelp */ content: '\00b7 '; padding: 3px; margin-left: -14px; } - @@ -70,142 +70,719 @@ 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) +
    • +
  • + 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
    -
  • 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
  • + 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 +
- Application + User Interface
  • - - Experimental Features Checkbox in Desktop's Tools - menu to hide or show untested features in the application. + 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.
    • -
  • 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
- Experimental features + 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. + features, and vice-versa (Experimental + Feature)
- Applet + 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 -
  • Added PrivilegedAccessor to test suite
    • -
  • Prevent or clear modal dialogs raised during tests
    • -
  • +
      +
    • + External service integration tests for + Uniprot REST Free Text Search Client +
      • +
    • + Added PrivilegedAccessor to test suite +
      • +
    • + Prevent or clear modal dialogs raised + during tests +
    -
    • - General +
    +
    + Calculations - Application + User Interface
      -
    • 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
      • +
    • + 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
      • -
    • 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
      • +
    + 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
      -
    • 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
      • +
    • + 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
      • +
    • + 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. +
    - -
    +
    - 2.10.1
    - 29/11/2016     + 2.10.1
    29/11/2016
    @@ -216,7 +793,8 @@ li:before { for all consensus calculations
  • - Jmol updated to version 14.6.4 (released 3rd Oct 2016) + Jmol updated to version 14.6.4 (released + 3rd Oct 2016)
  • Updated Jalview's Certum code signing certificate for 2016-2017
    • @@ -244,9 +822,9 @@ li:before {
  • 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) + 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 @@ -346,73 +924,78 @@ li:before { lysozyme results in a PDB Client error dialog box
  • - Structure View's mapping report switched ranges for PDB and sequence for SIFTS
    • - SIFTS 'Not_Observed' residues mapped to non-existant coordindate data + Structure View's mapping report switched + ranges for PDB and sequence for SIFTS + + + SIFTS 'Not_Observed' residues mapped to non-existant + coordindate data + -
    - -
    - 2.10.0b1
    - 25/10/2016     -
    - - Application + +
    + 2.10.0b1
    + 25/10/2016     +
    + + Application + + +
    + General - -
    - 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 + + Build and deployment + + New Known Issues + +
    + @@ -423,8 +1006,8 @@ li:before { General @@ -802,7 +1385,8 @@ li:before {
  • 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 @@ -867,7 +1451,8 @@ li:before { 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.
    • @@ -939,9 +1524,12 @@ li:before { Applet Build and Deployment + Build and Deployment
    @@ -1329,10 +1917,10 @@ li:before { Deployment and Documentation + General + --> Deployment and Documentation