X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=8156e9347b7d7918ccca1735eb72f09462602eda;hb=cb4b4b590add93fb0fb5c5ecd1d0532f1456ecc2;hp=b3682357451635911f443402b2b211a6a03d6f1d;hpb=3e0eb5fe92f38828607594c7b70dfdf012e4d3dc;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index b368235..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 @@ -205,21 +228,44 @@
  • 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 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→(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 Sequence Features
    +
  • 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.
    • +
  • Autocalculated Annotation
    Settings for the display of autocalculated annotation. + +
    • +
  • Show Sequence Features
    Show or hide sequence features on this alignment.
  • Seqence Feature Settings...
    @@ -230,7 +276,10 @@
    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 @@ -293,6 +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