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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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+<head>
+<title>Select/Hide Columns by Annotation</title>
+</head>
+
+<body>
+ <p>
+ <strong> Select/Hide Columns by Annotation </strong>
+ </p>
+ <p>From Jalview 2.9 columns of an alignment can be filtered using
+ any annotation row added to that alignment.</p>
+ To carry out this operation, navigate to "<b>Select</b><strong><b>→</b></strong><b>Select/Hide Columns by Annotation...</b>" 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.
+ <br>
+ <br>
+ <table>
+ <tr>
+ <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ <td><img src="annotationColumnSelectionWithSM.gif"></td>
+ </tr>
+ </table>
+
+
+ <ul>
+ <li>The target annotation row can be selected using the drop-down option menu in the top-most part of the window.</li>
+
+ <li><strong>Search Filter</strong>
+ <ul>
+ <li>When a text is entered in the text box within the Search
+ Filter section, the 'Display Label' and 'Description'
+ options becomes enabled for selection. </li>
+ <li>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.</li>
+ </ul>
+ <li><strong>Structure Filter</strong>
+ <ul>
+ <li>Alignment columns can also be filtered by the type of
+ secondary structure present in a target annotation row.</li>
+ <li>This can be achieved by ticking the type of structure you
+ wish to filter by under the structures filter section.</li>
+ </ul>
+ <li><strong>Threshold Filter</strong>
+ <ul>
+ <li>This filter is only activated for annotation which contain
+ numeric values</li>
+ <li>Select whether to filter the alignment above or below an
+ adjustable threshold with the selection box within the threshold
+ filter section.</li>
+ <li>Change the threshold value with the slider, or enter the
+ exact value in the text box.</li>
+ </ul>
+ <li><strong>Actions</strong>
+ <ul>
+ <li>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.</li>
+ <li>The default option is 'Select' and this simply
+ enables column selection on the matching alignment column.</li>
+ <li>While the 'Hide' option enables the matching columns to
+ be hidden automatically during the filtering process.</li>
+ <li>The 'Ok' button applies the filter when clicked.</li>
+ <li>And finally, the 'Cancel' button restores the alignment to its previous state before any filtering was applied.
+ </ul></li>
+ </ul>
+
+</body>
+</html>
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