Filter Columns by Annotation
Jalview allows the columns of an alignment to be filtered using
any annotation rows added to that alignment.
From "Select" menu
→ "Select by Annotation..." to bring
up the Select by Annotation window. The filter options vary depending
on the type of annotation selected. If an annotation that has a numeric
values is selected, the threshold filter option is activated as seen in the
figure on the right below.
- Select which annotation to base the filtering on using the
top-most selection box.
- Search Filter
- When a text is entered in the textfield on the search
filter section, the "Display Label" and "Description"
checkboxes becomes selectable.
- On selecting any of the checkboxes, a regular expresion
search (RegEx) is executed on the specified field of the current
annotation row selected, and the matching columns will be highlighted
in the alignment.
- Structure Filter
- Alignment columns can also be filtered by the type of
secondary structure present in a choosen annotation row.
- This can be achieved by ticking the type of structure you
wish to filter by under the structures filter section.
- Threshold Filter
- This filter is only activated for annotation which contain
numeric values
- Select whether to Filter the alignment above or below an
adjustable threshold with the selection box within the threshold
filter section.
- Change the threshold value with the slider, or enter the
exact value in the text box.
- Actions
- The "Select" and "Hide" radio buttons
determines the action that will be carried out on the matching
columns in the alignment during the filtering process.
- The default option is "Select" and this simply
enables column selection on the matching alignment column.
- While the "Hide" option enables the matching columns to
be hidden automatically during the filtering process.
- The "Ok" button applies the filter when clicked.
- And finally, The "Cancel" button restores the alignment to its previous state before the filtering when clicked.