X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=92af37720f38fd1b721cc6ef4b2609b8d68f0a50;hb=14193747f3831242bc7dfac12394eb20eb0ba480;hp=e1640fc4cab268f63aefde0b57df489ffc9bf67a;hpb=e8f34952c34c4e1ad0000ad67113a672a73bb5ba;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index e1640fc..92af377 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -21,6 +21,29 @@ --> Release History +

@@ -47,129 +70,978 @@

- 2.10.1
- 22/11/2016 + 2.10.3
+ 10/10/2017
- General -
+ +
+ General - Applet + Desktop + Applet
+ - Build and deployment + BioJSON
-
+ - -
- General + + + +
+ 2.10.2b2
+ 2/10/2017 +
+ +
+ New features in Jalview Desktop - Application +
+
+
+ + + +
+ 2.10.2b1
+ 7/9/2017 +
+ +
+ + +
+
+ + +
+ + + +
+ 2.10.2
17/8/2017 +
+ +
+ Calculations + + Rendering + + Overview + + + Data import/export + + User Interface + + 3D Structure + + Web Services + + + Scripting + + Example files + + Documentation + + Test Suite + +
+
+ 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 +
    • +
  • + 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 +
    • +
+ 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
    -
  • Custom URL links for specific database names without regular expressions also offer invalid 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
    • - -
    • -
    • +
  • + 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
    +
  • + 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 + Test Suite
    -
  • Failing/passing unit tests
    • +
  • + 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 +
    • +
  • + 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. +
- - +
- 2.10.0b1
- 25/10/2016 + 2.10.1
29/11/2016
- Application - - -
+
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 +
    • + + SIFTS 'Not_Observed' residues mapped to non-existant + coordindate data +
+
+ +
+ 2.10.0b1
+ 25/10/2016 +
+ + Application + + +
+ 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
    • +
+
+ +
@@ -179,8 +1051,8 @@ General
  • - Updated Spanish translations. -
    • + Updated Spanish translations. +
  • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -470,7 +1342,7 @@ load even when Consensus calculation is disabled
  • - Remove right on penultimate column of + Remove right on penultimate column of alignment does nothing
@@ -558,7 +1430,8 @@
  • 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 @@ -623,6 +1496,15 @@ 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. +
    • +
  • + Null Pointer Exception raised when + pressing Add on an orphaned cut'n'paste window. +
    • @@ -691,9 +1573,12 @@ 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 +
    @@ -1081,10 +1966,10 @@ Deployment and Documentation +
      +
    General +
      +
    --> Deployment and Documentation
    • 2G and 1G options in launchApp have no effect on memory allocation
      • @@ -1292,8 +2177,7 @@ Certum to the Jalview open source project). -
    • 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 @@ -1922,11 +2806,6 @@
      • 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
        • @@ -1954,8 +2833,8 @@
      • 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 @@ -2379,11 +3258,6 @@
      • 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'
      @@ -2398,11 +3272,6 @@
    • 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 @@ -2414,11 +3283,6 @@
    • WsDbFetch query/result association resolved
    • Tree leaf to sequence mapping improved
    • Smooth fonts switch moved to FontChooser dialog box. - - - - -