JAL-1368 JAL-1863 JAL-1304 reformatting and revision of wording, clarify RNA secondar...

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index ce29e82..60c9e23 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -59,10 +59,9 @@ ignored. The sections below describe the structure of an annotation file.
 <li><a href="#annrowprops">ROWPROPERTIES</a> control the display of individual annotation rows</li>
 <li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
 <li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
 <li><a href="#annrowprops">ROWPROPERTIES</a> control the display of individual annotation rows</li>
 <li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
 <li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>

-<li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for attaching annotation to sequences and groups</li>
+<li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for specifying target sequences and groups for annotation, reference sequence and column visibilty commands.</li>

                <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>
                <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>

-                       for defining a reference sequence on the alignment and hiding regions
-                       based on gaps in a reference sequence</li>
+                       for assigning the reference sequence on the alignment and hiding columns.</li>

        </ul>
        <p>
                At the end of this document, you can also find notes on <a
        </ul>
        <p>
                At the end of this document, you can also find notes on <a

@@ -90,28 +89,34 @@ Labels, secondary structure, histograms and line graphs are added with a line li
        <ul><em>Please note: URL links embedded in HTML descriptions are not yet supported.</em>
        </ul>
        </p>
        <ul><em>Please note: URL links embedded in HTML descriptions are not yet supported.</em>
        </ul>
        </p>

-               <p>The final <em>Values</em>
-               field contains a series of &quot;|&quot; separated value fields. Each
-               value field is itself a comma separated list of fields of a particular
-               type defined by the annotation row's <em>GRAPH_TYPE</em>. The allowed values of
-               <em>GRAPH_TYPE</em> and corresponding interpretation of each <em>Value</em> are shown below:
+       <p>
+               The final <em>Values</em> field contains a series of &quot;|&quot;
+               separated value fields. Each value field is itself a comma separated
+               list of fields of a particular type defined by the annotation row's <em>GRAPH_TYPE</em>.
+               The allowed values of <em>GRAPH_TYPE</em> and corresponding
+               interpretation of each <em>Value</em> are shown below:

        
        <ul>
        
        <ul>

-               <li><strong>BAR_GRAPH</strong><br> Plots a histogram with labels below each
-                       bar.<br> <em>number</em>,<em>text character</em>,<em>Tooltip
-                               text</em>
-               </li>
-               <li><strong>LINE_GRAPH</strong><br> Draws a line between values on the
-                       annotation row.<br> <em>number</em>
-               </li>
-               <li><strong>NO_GRAPH</strong><br>For a row consisting of text labels and/or
-                       secondary structure symbols.<br><em>{Secondary Structure
-                               Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br/><br/>The type of secondary structure symbol depends on the alignment being annotated being either Protein or RNA. <br/>For proteins, structure symbols are <em>H</em> (for
-                       helix) and <em>E</em> (for strand)<br/><br/>For RNA, VIENNA, WUSS or extended notation can be used to specify positions that are paired (e.g. &quot;(|(||)|)&quot; or &quot;|A|A|A|(|a|a|a|)&quot;)</li>
+               <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
+                       labels below each bar.<br> <em>number</em>,<em>text
+                               character</em>,<em>Tooltip text</em></li>
+               <li><strong>LINE_GRAPH</strong><br> Draws a line between
+                       values on the annotation row.<br> <em>number</em></li>
+               <li><strong>NO_GRAPH</strong><br>For a row consisting of
+                       text labels and/or secondary structure symbols.<br> <em>{Secondary
+                               Structure Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br /> <br />The
+                       type of secondary structure symbol depends on the alignment being
+                       annotated being either Protein or RNA. <br />For proteins, structure
+                       symbols are <em>H</em> (for helix) and <em>E</em> (for strand)<br />
+                       <br />For RNA structures, VIENNA, WUSS, and extended notations can
+                       be used to specify paired positions.
+                       <ul>e.g. &quot;(|(||)|)&quot; or &quot;|A|A|A|(|a|a|a|)&quot;)
+                       </ul></li>

        </ul>
        Any or all value fields may be left empty, as well as the BAR_GRAPH's
        </ul>
        Any or all value fields may be left empty, as well as the BAR_GRAPH's

-text character field, and either or both of the text-label and secondary
-structure symbol fields of the NO_GRAPH type annotation rows.</p>
+       text character field, and either or both of the text-label and
+       secondary structure symbol fields of the NO_GRAPH type annotation rows.
+       </p>

 <p>Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.  
 </p>
 <hr/>
 <p>Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.  
 </p>
 <hr/>