X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=8156e9347b7d7918ccca1735eb72f09462602eda;hb=cb4b4b590add93fb0fb5c5ecd1d0532f1456ecc2;hp=d2ca48190c5e066a94100e4e009f8f34e7896cfc;hpb=c554d41a4effc6719895bda6b3abc04c032715a8;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index d2ca481..8156e93 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,4 +1,21 @@ + Alignment Window Menus @@ -193,6 +210,12 @@
  • Undefine Groups (Control U)
    The alignment will be reset with no defined groups.
    WARNING: This cannot be undone.
    • +
  • Make Groups
     + The currently selected groups of the alignment will be + subdivided according to the contents of the currently selected region. +
    Use this to subdivide an alignment based on the + different combinations of residues observed at specific + positions. (new in jalview 2.5)
  • View @@ -205,22 +228,58 @@
  • Gather Views (G)
    Each view associated with the alignment will be displayed within its own tab on the current alignment window.
    • -
  • Show→(all Columns / Sequences)
    - All hidden Columns / Sequences will be revealed.
    • -
  • Hide→(all Columns / Sequences)
    - Hides the all the currently selected Columns / Sequences
    • +
  • Show→(all Columns / Sequences / Sequences and Columns)
    + All hidden Columns / Sequences / Sequences and Columns will be revealed.
    • +
  • Hide→(all Columns / Sequences / Selected Region / All but Selected Region )
    + Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.
    • +
  • Automatic Scrolling
    +     When selected, the view will automatically scroll to display the + highlighted sequence position corresponding to the position under the mouse + pointer in a linked alignment or structure view. +
  • Show Annotations
    If this is selected the "Annotation Panel" will be displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
    • -
  • Show Sequence Features
    +
  • Autocalculated Annotation
    Settings for the display of autocalculated annotation. + +
    • +
  • Show Sequence Features
    Show or hide sequence features on this alignment.
  • Seqence Feature Settings...
    Opens the Sequence Feature Settings dialog box to control the colour and display of sequence features on the alignment, and configure and retrieve features from DAS annotation servers.
    • +
  • Sequence ID Tooltip (application only) +
    This submenu's options allow the inclusion or exclusion of + non-positional sequence features or database cross references + from the tooltip shown when the mouse hovers over the sequence ID panel.
    • +
  • Alignment Properties...
    +     Displays some simple statistics computed for the + current alignment view and any named properties defined on the + whole alignment.
  • Overview Window
    A scaled version of the alignment will be displayed in a @@ -283,6 +342,10 @@
  • Centre Annotation Labels
    Select this to center labels along an annotation row relative to their associated column (default is off, i.e. left-justified).
    • +
  • Show Unconserved
    +     When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments. +
    • +
  • Colour
      @@ -333,7 +396,10 @@
    • 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 Group
      +
    • 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.