X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=b58cb31ab448eecead8fdb9f141e490fb3aae856;hb=4992ecae64d0c987c217e8c584161706188f9d52;hp=a861901b4d1c92ac56aeceff2bf0028d87bd6634;hpb=ff8355109626f28f23ee8ae00be9212b49a5253e;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index a861901..b58cb31 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -51,26 +51,222 @@ 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)
    • +
  • + Show synonymous codon variants on peptide sequences
    • +
  • + Popup report of a selected sequence feature's details
    • +
  • + 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
    • +
  • + Can use shift + arrow keys to rotate PCA image incrementally
    • +
  • + PCA depth queuing with graduated colours
    • +
+ 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
    • +
  • + Blank extra columns drawn or + printed when columns are hidden
    • +
  • + Regular expression error for '(' in Select Columns by Annotation description
    • +
  • + Scroll doesn't stop on mouse up after + dragging out of Scale or Annotation Panel
    • +
  • + Column selection incorrect after scrolling out of scale panel
    • +
  • + Left/right drag in annotation can scroll alignment down
    • +
  • + Error if mouse moved before clicking Reveal in scale panel
    • +
  • + Column display is out by one after Page Down, Page Up in wrapped mode
    • +
  • + Finder doesn't skip hidden regions
    • +
  • + Finder searches in minimised alignments
    • +
  • + '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
    • +
  • + Internationalised colour scheme names not shown correctly in menu
    • +
  • + Colour by Annotation can go black at min/max threshold limit
    • +
  • + Value input for graduated feature colour threshold gets 'unrounded'
    • +
  • + PCA image export doesn't respect background colour
    • +
  • + PCA points don't dim when rotated about y axis
    • +
  • + PCA Print dialog continues after Cancel
    • +
  • + Cancel in Tree Font dialog resets alignment, not Tree font
    • +
  • + Associate Tree with All Views not restored from project file
    • +
  • + Scrolling of split frame is sluggish if Overview shown in complementary view
    • +
  • + stop_gained variants not shown correctly on peptide sequence
    • +
  • + Help page can be opened twice
    • +
+ 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
6/09/2018 + 2.10.5
10/09/2018
@@ -120,6 +316,11 @@ li:before { 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. @@ -151,16 +352,30 @@ li:before { and lower-case 'E' and 'H' do not automatically get 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 + 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. +
    -
    +