X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=451fb097b8a3e573201667aa2c7c3e8b47ce7ce3;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=6ee7ed8e20d80ed0b816316b299fdf38a492417f;hpb=1bd5b4d3aba2805e8c6b9ad5054ce317c6aa1d31;p=jalview.git diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 6ee7ed8..451fb09 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -1,4 +1,21 @@ + Alignment Window Menus @@ -9,6 +26,9 @@
  • by ID
    This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
    • +
  • by Length
    + This will sort the sequences according to their length (excluding gap characters). If the sort is + repeated, the order of the sorted sequences will be inverted.
  • by Group
    This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted. @@ -45,6 +65,12 @@ in the alignment. See Principal Component Analysis.
    • +
  • Extract Scores ... (optional)
    + This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
    + When selected, these numbers are parsed into sequence associated annotation which can + then be used to sort the alignment via the Sort by→Score menu.
    +
    • +
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations