From: Jim Procter Date: Mon, 3 Oct 2016 13:11:32 +0000 (+0100) Subject: JAL-2189 release notes X-Git-Tag: Release_2_10_0~21^2~8 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=739e52dd5387687cce4831eaafa24116dcaddcb9;p=jalview.git JAL-2189 release notes --- diff --git a/help/html/releases.html b/help/html/releases.html index 0192c70..b8854f3 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -47,7 +47,7 @@
- 2.10.0
27/9/2016 + 2.10.0
04/10/2016
General @@ -64,8 +64,7 @@ Applet @@ -108,7 +111,10 @@
  • Extend selection with columns containing feature not working
  • Pfam format writer puts extra space at beginning of sequence
  • Incomplete sequence extracted from pdb entry 3a6s
    • -
  • Cannot create groups on an alignment from from a tree when t-coffee scores are shown
    • +
  • Cannot create groups on an alignment from from a tree when t-coffee scores are shown
    • +
  • Cannot import and view PDB structures with chains containing negative resnums (4q4h)
    • +
  • ArithmeticExceptions raised when parsing some structures
    • +
  • 'Empty' alignment blocks added to Clustal, PIR and PileUp output
    • Application @@ -124,7 +130,15 @@
  • Cannot save/restore representative sequence from project when only one sequence is represented
  • Disabled 'Best Uniprot Coverage' option in Structure Chooser
  • Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
    • -
  • View mapping in structure view shows mappings between sequence and all chains in a PDB file
    • +
  • View mapping in structure view shows mappings between sequence and all chains in a PDB file
    • +
  • PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
    • +
  • Export complete shown after destination file chooser is cancelled during an image export
    • +
  • Error when querying PDB Service with sequence name containing special characters
    • +
  • Manual PDB structure querying should be case insensitive
    • +
  • Large tooltips with broken HTML formatting don't wrap
    • +
  • Figures exported from wrapped view are truncated so L looks like I in consensus annotation
    • + + Applet diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index e1b00c4..1743f1c 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -37,16 +37,16 @@
  • Ensembl sequence fetcher. Annotated Genes, transcripts and proteins can be retrieved via Jalview's new Ensembl REST - client. Support for import of Ensembl data also allows: + client. Support for import of Ensembl data allows:
  • Working with structures.
    • -
  • UniProt Free Text Search. The new search +
  • UniProt Free Text Search. The new search dialog for UniProt allows you to browse and retrieve sequences from UniProt with free-text search and more structured queries
    • -
  • Reference sequence based alignment - visualisation.. When a reference sequence is defined for the - alignment, the alignment column ruler is now numbered according to - the reference sequence. The reference sequence for alignment views - can also be saved and restored from Jalview projects.
    • -
  • +
  • Reference sequence alignment view.. + Jalview 2.9 introduced support for reference sequences. In 2.10, + when a reference sequence is defined for the alignment, the + alignment column ruler is now numbered according to the reference + sequence. The reference sequence for alignment views can also be + saved and restored from Jalview projects.
    • +
  • Ensembl and ENA 'show cross-references' + support.The Calculations menu's 'Show cross-references' will now + offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein + mapping data is available for download or display.