documenting histogram colour spec

[jalview.git] / help / html / features / annotationsFormat.html

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index cc73162..fcec5c0 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -44,7 +44,8 @@ GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective
 </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.
+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>
 <p>You can associate an annotation with a sequence by preceding its
 definition with the line: 
@@ -68,6 +69,14 @@ following commands (respectively):
 COMBINE&#9;<em>graph_1_name</em>&#9;<em>graph_2_name</em>
 GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colour</em><strong><em>
 </em></strong></pre>
+<h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.4.1) ROWPROPERTIES</font></h3>
+<p>The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:</p>
+<pre>ROWPROPERTIES&#9;<em>Row label</em>&#9;<em>centrelabs=true( or false)</em>&#9;<em>showalllabs=true(default is false)</em>&#9;<em>scaletofit=true (default is false)</em></pre>
+<p>This sets the visual display properties according to the given values for all the annotation rows with labels matching <em>Row label</em>. The properties mostly affect the display of multi-character column labels, and are as follows:
+<ul><li><em>centrelabs</em> Centre each label on its column.</li>
+<li><em>showalllabs</em> Show every column label rather than only the first of a run of identical labels (setting this to true can have a drastic effect on secondary structure rows).</li>
+<li><em>scaletofit</em> Shrink each label's font size so that the label fits within the column. Useful when annotating an alignment with a specific column numbering system.</li>
+</ul></p>
 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
 <p>Groups of sequences can be defined using the tab delimited line</p>
 <pre>SEQUENCE_GROUP    Group_Name      Group_Start     Group_End       Sequences</pre>
@@ -102,7 +111,7 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
   hide=false<br>
   hidecols=false<br>
   showunconserved=false</p>
-<ul><li>if the <strong>idColour</strong> property
+<ul><li><em>New Features in 2.4:</em><br>if the <strong>idColour</strong> property
 is given without specifying a colour scheme with the <strong>colour</strong>
 property, then the idColour will also be used to colour the sequence.</li>
 <li>the <strong>colour</strong> property can take either a colour scheme name,