Annotation Panel Menus

• Annotation Label Popup Menu
  This menu is opened by clicking anywhere on the annotation row labels area (below the sequence ID area).
  • Add New Row
    Adds a new, named annotation row (a dialog box will pop up for you to enter the label for the new row).
  • Hide Row
    Hides the annotation row whose label was clicked in order to bring up the menu.
  • Delete Row
    Deletes the annotation row whose label was clicked in order to bring up the menu.
  • Show All Hidden Rows
    Shows all hidden annotation rows.
  • Show Values in Text Box
    Opens a text box with a list of comma-separated values corresponding to the annotation (numerical or otherwise) at each position in the row. This is useful to export alignment quality measurements for further analysis.
  • Ignore Gaps in Consensus
    If this checkbox is selected, all consensus calculations performed in the current Alignment window will be done without counting gaps as a consensus character.
• Annotation Popup Menu
  This menu is opened when right-clicking on the selected positions of an annotation.
  • Helix
    Mark selected positions with a helix glyph (a red oval), and optional text label (see below). Consecutive ovals will be rendered as an unbroken red line.
  • Sheet
    Mark selected positions with a sheet glyph (a green arrow oriented from left to right), and optional text label (see below). Consecutive arrows will be joined together to form a single green arrow.
  • Label
    Sets the text label at the selected positions. If more that one consecutive position is marked with the same label, only the first position's label will be rendered.
  • Colour
    Changes the colour of the annotation text label.
  • Remove Annotation
    Blanks any annotation at the selected positions on the row. Note: This cannot be undone