3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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23 <title>Select/Hide Columns by Annotation</title>
28 <strong> Select/Hide Columns by Annotation </strong>
30 <p>From Jalview-2.9 columns of an alignment can be filtered using
31 any annotation rows added to that alignment.</p>
32 To carry out this operation, navigate to "Select" menu
33 <strong>→</strong> "Select/Hide Columns by Annotation..." to bring
34 up the Select/Hide by Annotation window. The filter options vary depending
35 on the type of annotation selected. If an annotation that has a numeric
36 values is selected, the threshold filter option is activated as seen in the
37 figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
41 <div style="width: 48%; float: left; margin-left: 4%">
42 <img src="annotationColumnSelectionWithoutSM.gif">
44 <div style="width: 48%; float: right">
45 <img src="annotationColumnSelectionWithSM.gif">
50 <li>The target annotation row can be selected using the drop-down option menu in the top-most part of the window.</li>
52 <li><strong>Search Filter</strong>
54 <li>When a text is entered in the text box within the Search
55 Filter section, the "Display Label" and "Description"
56 options becomes enabled for selection. </li>
57 <li>On selecting any of the options, a regular expression
58 search (RegEx) is executed on the specified field of the current
59 annotation row selected, and the matching columns will be highlighted
60 in the alignment.</li>
62 <li><strong>Structure Filter</strong>
64 <li>Alignment columns can also be filtered by the type of
65 secondary structure present in a target annotation row.</li>
66 <li>This can be achieved by ticking the type of structure you
67 wish to filter by under the structures filter section.</li>
69 <li><strong>Threshold Filter</strong>
71 <li>This filter is only activated for annotation which contain
73 <li>Select whether to filter the alignment above or below an
74 adjustable threshold with the selection box within the threshold
76 <li>Change the threshold value with the slider, or enter the
77 exact value in the text box.</li>
79 <li><strong>Actions</strong>
81 <li>The "Select" and "Hide" radio buttons
82 determines the action that will be carried out on the matching
83 columns in the alignment during the filtering process.</li>
84 <li>The default option is "Select" and this simply
85 enables column selection on the matching alignment column.</li>
86 <li>While the "Hide" option enables the matching columns to
87 be hidden automatically during the filtering process.</li>
88 <li>The "Ok" button applies the filter when clicked.</li>
89 <li>And finally, the "Cancel" button restores the alignment to its previous state before any filtering was applied.