JAL-1667 JAL-1668 JAL-1553 help docs update

[jalview.git] / help / html / calculations / columnFilterByAnnotation.html

diff --git a/help/html/calculations/columnFilterByAnnotation.html b/help/html/calculations/columnFilterByAnnotation.html
index a69e234..1ece1cc 100644 (file)
--- a/help/html/calculations/columnFilterByAnnotation.html
+++ b/help/html/calculations/columnFilterByAnnotation.html
@@ -27,24 +27,22 @@
        <p>
                <strong> Select/Hide Columns by Annotation </strong>
        </p>
-       <p>From Jalview-2.9 columns of an alignment can be filtered using
-               any annotation rows added to that alignment.</p>
-       To carry out this operation, navigate to &quot;Select&quot; menu
-       <strong>&#8594;</strong> &quot;Select/Hide Columns by Annotation...&quot; to bring
-       up the Select/Hide 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 &quot;<b>Select</b><strong><b>&#8594;</b></strong><b>Select/Hide Columns by Annotation...</b>&quot; 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> 
+       <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>&nbsp</div>
 
        <ul>
                <li>The target annotation row can be selected using the drop-down option menu in the top-most part of the window.</li>
@@ -52,7 +50,7 @@
                <li><strong>Search Filter</strong>
                        <ul>
                                <li>When a text is entered in the text box within the Search
-                                       Filter section, the &quot;Display Label&quot; and &quot;Description&quot;
+                                       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
@@ -78,15 +76,15 @@
                        </ul>
                <li><strong>Actions</strong>
                        <ul>
-                               <li>The &quot;Select&quot; and &quot;Hide&quot; 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 &quot;Select&quot; and this simply
+                               <li>The default option is 'Select' and this simply
                                        enables column selection on the matching alignment column.</li>
-                               <li>While the &quot;Hide&quot; 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 &quot;Ok&quot; button applies the filter when clicked.</li>
-                               <li>And finally, the &quot;Cancel&quot; button restores the alignment to its previous state before any filtering was applied. 
+                               <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>