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).
- Edit Label/Description
This opens a dialog where you can change the name (displayed label), or the description
(as shown on the label tooltip) of the clicked annotation.
- Hide This Row
Hides the annotation row whose label was clicked in order to bring up
the menu.
- Hide All <label>
Hides all annotation rows whose label matches the one clicked.
(This option is only shown for annotations that relate to individual sequences,
not for whole alignment annotations. Since Jalview 2.8.2.)
- 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