Select/Hide Columns by Annotation
From Jalview 2.9 columns of an alignment can be filtered using
any annotation row added to that alignment.
To carry out this operation, navigate to "Select→Select/Hide Columns by Annotation..." to bring
up the 'Select/Hide 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, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
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- The target annotation row can be selected using the drop-down option menu in the top-most part of the window.
- Search Filter
- When a text is entered in the text box within the Search
Filter section, the 'Display Label' and 'Description'
options becomes enabled for selection.
- On selecting any of the options, a regular expression
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 target 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 any filtering was applied.