</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:
All Annotations defined after a SEQUENCE_REF command will then be
associated with that sequence, and the first field in the Value field
list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
+<ul><em>New in Jalview 2.4</em>: the tooltip displayed when the mouse is moved over the row
+label for sequence associated annotation gives the associated
+sequence's name followed by the annotation row's description.</ul>
<p>Sequence associations are turned off for subsequent annotation
definitions by:
<pre>SEQUENCE_REF	ALIGNMENT</pre>
COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<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	<em>Row label</em>	<em>centrelabs=true( or false)</em>	<em>showalllabs=true(default is false)</em>	<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>
textCol1=black<br>
textCol2=black<br>
textColThreshold=0<br>
- idColour=ff3322</p>
-<em>New Features in 2.4:</em><ul><li>if the <strong>idColour</strong> property
+ idColour=ff3322<br>
+ hide=false<br>
+ hidecols=false<br>
+ showunconserved=false</p>
+<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,
or a single colour specification (either a colour name like 'red' or an RGB
triplet like 'ff0066'). If a single colour is specified, then the group
will be coloured with that colour.</li>
+ <li><em>New Features in 2.4.1</em></li>
+ <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li>
+ <li>Sequence associated Groups<br>If a group is defined after a valid
+ <em>SEQUENCE_REF</em> sequence reference statement, the sequence representative
+ for the group will be set to the referenced sequence.<br><strong>Note:</strong> if the <em>hide</em>
+ property is set then only the representative sequence for the group will be shown in the alignment.</li>
</ul>
<p> </p>
<p>An example Annotation file is given below:
git://source.jalview.org / jalview.git / blobdiff