X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=067363ab04dba6e84ebb2eeb7339dc6ddcfee12f;hb=5ef89ac7a5639c8de9769038285db42871cf6ec6;hp=3812056bb3ece1dfd26dc0fc2022be7fe44d0792;hpb=5dd170e1f8135791b8e5e2670b095bbd6009d3a6;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 3812056..067363a 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -51,32 +51,204 @@ li:before {

- + + + + + - -
-
- Release -
+ 		ReleaseNew FeaturesIssues Resolved
+ 2.11
+ 14/05/2019 (final due date !) 		-
- New Features -
+ 		+
    +
  • + Optional automatic backups when saving + Jalview project or alignment files
    • +
  • + Principal Components Analysis and + Viewer state is saved in Jalview Project
    The 'Change + parameters' option has also been removed from the PCA viewer
    • +
  • + New 'Colour by Sequence ID' (subgroup) option
    • +
  • + Alternative genetic code tables supported for + 'Translate as cDNA'
    • +
  • + Finder panel remembers last position in each view
    • +
  • + More efficient creation of selections and + multiple groups when working with large alignments
    • +
  • + Speedier import of annotation rows when + parsing stockholm files
    • +
  • + Update of Ensembl Rest Client to API v10.0
    • +
  • + Sequence features can be filtered and + shaded according to any associated attributes (e.g. variant + attributes from VCF file, or key-value pairs imported from + column 9 of GFF file)
    • +
  • + More efficient sequence feature render + algorithm (Z-sort/transparency and filter aware)
    • +
  • + Alignment Overview now by default shows + only visible region of alignment (this can be changed in + user preferences)
    • +
  • + File Chooser stays open after Cancel overwrite
    • +
  • + Better popup menu behaviour when + all sequences are hidden
    • +
  • + Status bar shows bounds when dragging a selection + region, and gap count when inserting or deleting gaps
    • +
  • + Status bar updates over sequence and annotation labels
    • +
  • + Show annotation tooltips and popup menus in wrapped mode
    • +
  • + Can select columns by dragging left/right in annotations
    • +
  • + Improved tooltips in Feature Settings dialog
    • +
  • + Help button on Uniprot and PDB search panels
    • +
  • + Cursor changes over draggable box in Overview panel
    • +
  • + Overview panel default changed to not show hidden regions
    • +
  • + Consistent ordering of links in sequence id popup menu
    • +
  • + Sequence Details report opens positioned to top of report
    • +
  • + Scale panel popup menu allows Hide selected columns adjacent + to a hidden column marker
    • +
+ Deprecations +
    +
  • + DAS sequence retrieval and annotation + capabilities removed from the Jalview Desktop +
    • +
+ Release Processes +
    +
  • + Atlassian Bamboo continuous integration server for + unattended Test Suite execution
    • +
  • + Memory test suite to detect leaks in common + operations
    • +
  • + IntervalStoreJ (new updatable NCList + implementation) used for Sequence Feature collections
    • +
  • + Castor library for XML marshalling and + unmarshalling has been replaced by JAXB for Jalview projects + and XML based data retrieval clients
    • +
-
- Issues Resolved -
+ 		+
    +
  • + Timeouts when retrieving data from Ensembl
    • +
  • + Warning of 'Duplicate entry' when saving + Jalview project involving multiple views
    • +
  • + Overview for complementary view in a linked + CDS/Protein alignment is not updated when Hide Columns by + Annotation dialog hides columns
    • +
  • + Selection highlighting in the complement of + a CDS/Protein alignment stops working after making a + selection in one view, then making another selection in the + other view
    • +
  • + Annotations tooltip changes beyond visible columns
    • +
  • + Table Columns could be re-ordered in + Feature Settings and Jalview Preferences panels
    • +
  • + Jalview hangs when closing windows + or the overview updates with large alignments
    • +
  • + Tree and PCA calculation fails for selected + region if columns were selected by dragging right-to-left + and the mouse moved to the left of the first column
    • +
  • + Error message for trying to load in invalid + URLs doesn't tell users the invalid URL
    • +
  • + Nonpositional features lose feature group + on export as Jalview features file
    • +
  • + Status bar updates beyond visible columns
    • +
  • + Blank extra columns drawn or + printed when columns are hidden
    • +
  • + Regular expression error in Select Columns by Annotation description
    • +
  • + Scroll doesn't stop on mouse up after + dragging out of Scale or Annotation Panel
    • +
  • + Display is incorrect after Page Down and Up in wrapped mode
    • +
  • + Help page can be opened twice
    • +
  • + Finder doesn't skip hidden regions
    • +
  • + Column selection incorrect after scrolling out of scale panel
    • +
  • + Tree calculation fails on a selection dragged to left of alignment
    • +
  • + 'Apply Colour to All Groups' not always selected on + opening an alignment
    • +
  • + 'Colour by Annotation' not marked selected in Colour menu
    • +
  • + Per-group Clustal colour scheme changes when + different groups in the alignment are selected
    • +
  • + Value input for graduated feature colour threshold gets 'unrounded'
    • +
+ Editing +
    +
  • + Start and End should be updated when + sequence data at beginning or end of alignment added/removed + via 'Edit' sequence
    • +
  • + Delete/Cut selection doesn't relocate + sequence features correctly when start of sequence is + removed (Known defect since 2.10)
    • +
+ New Known Defects +
    +
  • + Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
    • +
  • + Alignment panel height can be too small after 'New View'
    • +
- 2.10.5
4/09/2018 + 2.10.5
10/09/2018
  • + Default memory for Jalview webstart and + InstallAnywhere increased to 1G. +
    • +
  • Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. Display is configured via the @@ -85,7 +257,7 @@ li:before {
  • Ensembl client updated to Version 7 REST - API and sequence data now imported as JSON + API and sequence data now imported as JSON.
  • Change in recommended way of starting @@ -107,6 +279,20 @@ li:before {
    • + Poorly scaled bar in quality annotation + row shown in Feredoxin Structure alignment view of example + alignment. +
      • +
    • + Annotation obscures sequences if lots of + annotation displayed. +
      • +
    • + Group conservation/consensus not shown + for newly created group when 'Apply to all groups' + selected +
      • +
    • Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible. @@ -121,25 +307,47 @@ li:before {
    • Jalview could hang when importing certain - types of knotted RNA secondary structure + types of knotted RNA secondary structure.
    • Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that - do not start at 1 + do not start at 1.
    • '.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, - and when exporting as Stockolm flatfile. + and when exporting as Stockholm flatfile.
    • Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get - treated as RNA secondary structure + treated as RNA secondary structure. +
      • +
    • + .jvp should be used as default extension + (not .jar) when saving a jalview project file. +
      • +
    • + Mac Users: closing a window correctly + transfers focus to previous window on OSX
    -
+ Java 10 Issues Resolved +
    +
  • + OSX - Can't save new files via the File + or export menus by typing in a name into the Save dialog + box. +
    • +
  • + Jalview now uses patched version + of the VAqua5 + 'look and feel' which has improved compatibility with the + latest version of OSX. +
    • +
+