X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=c547ffb20c2cc361d7d803f656ff5ab0a366af7d;hb=344c86e8d9366e221c754771c373161d97d66183;hp=cf4bfedb857d44a3fff31c9159f70947b8706ab7;hpb=5079464ec6cdd401e4c114b09b21af31ab793587;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index cf4bfed..c547ffb 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -47,83 +47,469 @@
- 2.10.0
27/9/2016 + 2.10.0
06/10/2016
General Application Applet +
  • + Automatically hide introns when opening a + gene/transcript view +
    • +
  • + Uniprot Sequence fetcher Free Text Search + dialog +
    • +
  • + UniProt - PDB protein + structure mappings with the EMBL-EBI PDBe SIFTS database +
    • +
  • + Updated download sites used for Rfam and + Pfam sources to xfam.org +
    • +
  • + Disabled Rfam(Full) in the sequence fetcher +
    • +
  • + Show residue labels in Chimera when mousing + over sequences in Jalview +
    • +
  • + Support for reverse-complement coding + regions in ENA and EMBL +
    • +
  • + Upgrade to EMBL XML 1.2 + for record retrieval via ENA rest API +
    • +
  • + Support for ENA CDS records with reverse + complement operator +
    • +
  • + Update to groovy-2.4.6-indy - for faster + groovy script execution +
    • +
  • + New 'execute Groovy script' option in an + alignment window's Calculate menu +
    • +
  • + Allow groovy scripts that call + Jalview.getAlignFrames() to run in headless mode +
    • +
  • + Support for creating new alignment + calculation workers from groovy scripts +
    • +
  • + Store/restore reference sequence in + Jalview projects +
    • +
  • + Chain codes for a sequence's PDB + associations are now saved/restored from project +
    • +
  • + Database selection dialog always shown + before sequence fetcher is opened +
    • +
  • + Double click on an entry in Jalview's + database chooser opens a sequence fetcher +
    • +
  • + Free-text search client for UniProt using + the UniProt REST API +
    • +
  • + -nonews command line parameter to prevent + the news reader opening +
    • +
  • + Displayed columns for PDBe and Uniprot + querying stored in preferences +
    • +
  • + Pagination for displaying PDBe and Uniprot + search results +
    • +
  • + Tooltips shown on database chooser +
    • +
  • + Reverse complement function in calculate + menu for nucleotide sequences +
    • +
  • + Alignment sort by feature scores + and feature counts preserves alignment ordering (and + debugged for complex feature sets). +
    • +
  • + Chimera 1.11.1 minimum requirement for + viewing structures with Jalview 2.10 +
    • +
  • + Retrieve + genome, transcript CCDS and gene ids via the Ensembl and + Ensembl Genomes REST API +
    • +
  • + Protein sequence variant annotation + computed for 'sequence_variant' annotation on CDS regions + (Ensembl) +
    • +
  • + ENA CDS 'show cross references' for Uniprot + sequences +
    • +
  • + Improved warning messages when DB + Ref Fetcher fails to match, or otherwise updates sequence + data from external database records. +
    • +
  • + Revised Jalview Project format for + efficient recovery of sequence coding and alignment + annotation relationships. +
    • + - +
  • + -- JAL--- +
    • + -->
    General Application Applet
    @@ -164,7 +550,7 @@
  • Updated Spanish translations of localized text for 2.9
    • Application -