--- /dev/null
+<html>
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
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+ -->
+<head>
+<title>Select/Hide Columns by Annotation</title>
+</head>
+
+<body>
+ <p>
+ <strong>Select/Hide Columns by Annotation</strong>
+ </p>
+ <p>
+ The 'Select/Hide by Annotation' window allows columns to be selected
+ or hidden according to annotation rows on the alignment. The dialog
+ box is opened <em>via</em> "<strong>Select→Select/Hide
+ Columns by Annotation...</strong>", and different filters are then
+ presented for filtering data according to the selected annotation
+ row.
+ </p>
+ <table>
+ <tr>
+ <td><img src="AnnotationColumnSelectionWithSM.png"></td>
+ <td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
+ </tr>
+ </table>
+ <p>The drop down menu lists the annotation available on the
+ alignment. Sequence associated annotation rows will be shown with
+ the sequence ID appended to the annotation label. It is only
+ possible to select one row at a time.</p>
+ <p>
+ If an annotation with numeric values is selected, the threshold
+ filter option is activated. For other types of annotation, use the
+ text box and secondary structure check boxes (right). The radio
+ buttons at the bottom of the dialog specify the action applied to
+ columns matching the query.<br /> <em>Note: annotation
+ containing only numeric labels (e.g. T-COFFEE column confidence
+ scores) will not be treated as quantitative data. You will need to
+ enter search expressions to select columns in this case.</em>
+ </p>
+ <ul>
+ <li><strong>Search Filter</strong>
+ <ul>
+ <li>Enter text or regular expressions in the text box to
+ activate the 'Display Label' and 'Description' options.</li>
+ <li>Selecting the description or label options will
+ activate the filter, and any matching columns will be
+ highlighted or hidden.</li>
+ </ul>
+ <li><strong>Structure Filter</strong>
+ <ul>
+ <li>Select the checkboxes to filter by secondary structure
+ type.</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
+ the threshold.</li>
+ <li>Change the threshold value with the slider, or enter it
+ in the text box.
+ <li>The <em>As Percentage</em> checkbox allows thresholds to
+ be set as a percentage rather than absolute value.</li>
+ </ul>
+ <li><strong>Actions</strong>
+ <ul>
+ <li>'Select' (the default), selects columns matching the
+ query settings.</li>
+ <li>'Hide' causes matching columns to be hidden.</li>
+ </ul></li>
+ </ul>
+ <p>Hit 'Cancel' to restore the alignment view to its previous
+ state before any filtering was applied.</p>
+</body>
+</html>
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