--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Filter Columns by Annotation</title>
+</head>
+
+<body>
+ <p>
+ <strong> Filter Columns by Annotation </strong>
+ </p>
+ <p>Jalview allows the columns of an alignment to be filtered using
+ any annotation rows added to that alignment.</p>
+ From "Select" menu
+ <strong>→</strong> "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.
+ <br>
+ <br>
+
+ <div style="width: 48%; float: left; margin-left: 4%">
+ <img src="annotationColumnSelectionWithoutSM.gif">
+ </div>
+ <div style="width: 48%; float: right">
+ <img src="annotationColumnSelectionWithSM.gif">
+ </div>
+ <div> </div>
+
+ <ul>
+ <li>Select which annotation to base the filtering on using the
+ top-most selection box.</li>
+
+ <li><strong>Search Filter</strong>
+ <ul>
+ <li>When a text is entered in the textfield on the search
+ filter section, the "Display Label" and "Description"
+ checkboxes becomes selectable.</li>
+ <li>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.</li>
+ </ul>
+ <li><strong>Structure Filter</strong>
+ <ul>
+ <li>Alignment columns can also be filtered by the type of
+ secondary structure present in a choosen 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 the filtering when clicked.
+ </ul></li>
+ </ul>
+
+</body>
+</html>
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