* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>Filter Columns by Annotation</title>
+<title>Select/Hide Columns by Annotation</title>
</head>
<body>
<p>
- <strong> Filter Columns by Annotation </strong>
+ <strong> Select/Hide 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
+ <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.
+ figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
<br>
- <br>
+ <br>
+ <table>
+ <tr>
+ <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ <td><img src="annotationColumnSelectionWithSM.gif"></td>
+ </tr>
+ </table>
- <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>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 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
+ <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>
<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>
+ 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>
<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
+ <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
</ul>
<li><strong>Actions</strong>
<ul>
- <li>The "Select" and "Hide" radio buttons
+ <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
+ <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
+ <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.
+ <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>
git://source.jalview.org / jalview.git / blobdiff