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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
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- <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>
+ <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
+ presented dependent upon the data shown in the selected annotation row.
+ </p>
+ <table>
+ <tr>
+ <td><img src="annotationColumnSelectionWithSM.gif"></td>
+ <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ </tr>
+ </table>
+ <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.</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>
+ </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>
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