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.
  • Export Annotation (Application only)
    Annotations can be saved to file or output to a text window in either the Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
  • Show Values in Text Box (applet only)
    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.
  The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:
  • 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.
  • Show Consensus Histogram
    Enable or disable the display of the histogram above the consensus sequence.
  • Show Consensus Logo
    Enable or disable the display of the sequence logo above the consensus sequence.
  • Normalise Consensus Logo
    When enabled, scales all logo stacks to the same height, making it easier to compare symbol diversity in highly variable regions.
  • Copy Consensus Sequence
    Copies the consensus sequence to the clipboard in Fasta format, to allow the consensus sequence to be added to an alignment. Note the copied sequence is not accessible to other programs if Jalview is running as an applet in a web page.
• 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