+GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
+</em></strong>
+ </pre>
+ </p>
+ <hr />
+ <p>
+ <strong><a name="annrowprops">ROWPROPERTIES</a></strong><br /> 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. (<em>Not
+ available in Jalview applet due to AWT 1.1 limitations</em>)</li>
+ </ul>
+ </p>
+ <p>
+ <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br /> Groups
+ of sequences and column ranges can be defined using a tab delimited
+ statement like:
+ </p>
+ <pre>SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	<em>Sequences</em>
+ </pre>
+ <p>The sequences can be defined by alignment index and a range of
+ sequences can be defined in a comma delimited field such as</p>
+ <p>2-5,8-15,20,22</p>
+ <p>Enter * to select all groups.</p>
+ <p>
+ <strong>Note:</strong> If the alignment indices are not known, enter
+ -1, followed by a tab and then a tab delimited list of sequence IDs.
+ </p>
+ <p>
+ If a <a href="#seqgrprefs"><strong>SEQUENCE_REF</strong></a> has
+ been defined, then <em>group_start</em> and <em>group_end</em> will
+ be relative to the sequence residue numbering, otherwise the <em>group_start</em>
+ and <em>group_end</em> will be alignment column indices.
+ </p>
+ <hr />
+ <p>
+ <strong><a name="groupprops">PROPERTIES</a></strong><br />This
+ statement allows various visualisation properties to be assigned to
+ a named group. This takes a series of tab-delimited <em>key</em>=<em>value</em>
+ pairs:
+ </p>
+ <pre>PROPERTIES	Group_name	tab_delimited_key_value_pairs
+</pre>
+ <p>The currently supported set of sequence group key-value pairs
+ that can be provided here are :</p>
+ <table border="1">
+ <tbody>
+ <tr>
+ <td width="50%">Key</td>
+ <td>Value</td>
+ </tr>
+ <tr>
+ <td width="50%">description</td>
+ <td>Text - may include simple HTML tags</td>
+ </tr>
+ <tr>
+ <td width="50%">colour</td>
+ <td>A string resolving to a valid Jalview colourscheme
+ (e.g. Helix Propensity)</td>
+ </tr>
+ <tr>
+ <td width="50%">pidThreshold</td>
+ <td>A number from 0-100 specifying the Percent Identity
+ Threshold for colouring columns in the group or alignment</td>
+ </tr>
+ <tr>
+ <td width="50%">consThreshold</td>
+ <td>A number from 0-100 specifying the degree of bleaching
+ applied for conservation colouring</td>
+ </tr>
+ <tr>
+ <td width="50%">outlineColour</td>
+ <td>Line colour used for outlining the group (default is
+ red)</td>
+ </tr>
+ <tr>
+ <td width="50%">displayBoxes</td>
+ <td>Boolean (default true) controlling display of shaded
+ box for each alignment position</td>
+ </tr>
+ <tr>
+ <td width="50%">displayText</td>
+ <td>Boolean (default true) controlling display of text for
+ each alignment position</td>
+ </tr>
+ <tr>
+ <td width="50%">colourText</td>
+ <td>Boolean (default false) specifying whether text should
+ be shaded by applied colourscheme</td>
+ </tr>
+ <tr>
+ <td width="50%">textCol1</td>
+ <td>Colour for text when shown on a light background</td>
+ </tr>
+ <tr>
+ <td width="50%">textCol2</td>
+ <td>Colour for text when shown on a dark background</td>
+ </tr>
+ <tr>
+ <td width="50%">textColThreshold</td>
+ <td>Number from 0-100 specifying switching threshold
+ between light and dark background</td>
+ </tr>
+ <tr>
+ <td width="50%">idColour</td>
+ <td>Colour for highlighting the Sequence ID labels for this
+ group<br />If <em>idColour</em> is given but <em>colour</em>
+ is not, then idColor will also be used for the group
+ background colour.
+ </td>
+ </tr>
+ <tr>
+ <td width="50%">showunconserved</td>
+ <td>Boolean (default false) indicating whether residues
+ should only be shown that are different from current reference
+ or consensus sequence</td>
+ </tr>
+ <tr>
+ <td width="50%">hide</td>
+ <td>Boolean (default false) indicating whether the rows in
+ this group should be marked as hidden.<br />
+ <em>Note:</em> if the group is sequence associated (specified by
+ SEQUENCE_REF), then all members will be hidden and marked as
+ represented by the reference sequence.
+ </td>
+ </tr>
+ <!-- <tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr> -->
+ </tbody>
+ </table>
+
+ <p>
+ <strong>Specifying colours in PROPERTIES key-value pairs</strong><br />
+ 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.
+ </p>
+ <hr />
+ <p>
+ <strong><a name="seqgrprefs">SEQUENCE_REF and GROUP_REF</a></strong><br />
+ By default, annotation is associated with the alignment as a whole.
+ However, it is also possible to have an annotation row associated
+ with a specific sequence, or a sequence group. Clicking the
+ annotation label for sequence or group associated annotation will
+ highlight the associated rows in the alignment, and double clicking
+ will select those rows, allowing further analysis. While group
+ associated annotation remains associated with a particular
+ alignment, sequence associated annotation can move with a sequence -
+ so copying a sequence to another alignment will also copy its
+ associated annotation.
+ </p>
+ <p>You can associate an annotation with a sequence by preceding
+ its definition with the line:
+ <pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em>
+ </pre>
+ 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>
+
+ <p>Sequence associations are turned off for subsequent annotation
+ definitions by:
+ <pre>SEQUENCE_REF	ALIGNMENT</pre>
+ </p>
+ <p>Similarly, since Jalview 2.5, group associated annotation can
+ be defined by preceding the row definitions with the line:
+ <pre>GROUP_REF	<em>group_name</em>
+ </pre>
+ Group association is turned off for subsequent annotation rows by:
+ <pre>GROUP_REF	<em>ALIGNMENT</em>
+ </pre>
+ </p>
+ <hr />
+ <p>
+ <strong><a name="refsandviews">VIEW_SETREF,
+ VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br /> Since Jalview 2.9, the
+ Annotations file has also supported the definition of reference
+ sequences and hidden regions for an alignment view.
+ </p>
+ <!-- <p>
+ <em>VIEW_DEF</em> allows the current view to be named according to the
+ first argument after the tab character. If a second argument is
+ provided, then a new view is created with the given name, and
+ properties.
+ </p> -->
+ <p>
+ <em>VIEW_SETREF</em><br />Marks the first sequence in the
+ alignment, or alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, as the <a href="../calculations/referenceseq.html">reference
+ sequence</a> for the alignment.
+ </p>
+ <p>
+ <em>HIDE_INSERTIONS</em><br />This command hides all gapped
+ positions in the current target sequence. Any columns already hidden
+ will be re-displayed.<br /> <br>The current target sequence is
+ either the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, the alignment's reference sequence, or the first sequence
+ in the alignment.
+ </p>
+ <p>
+ <em>VIEW_HIDECOLS</em><br />Modifies the visibility of columns in
+ the view. The statement is followed by a single argument consisting
+ of a comma separated series of single integers or integer pairs
+ (like <em>3-4</em>). These define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ view.
+ </p>
+
+ <hr />
+ <p>
+ <strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br />
+ The interpretation of the COMBINE statement in <em>Version
+ 2.8.1</em> was refined so that only annotation line graphs with the
+ given names ands the same <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong>
+ scope are grouped.
+ </p>
+ <hr />
+
+ <p>
+ <strong><a name="exampleann">EXAMPLES</a></strong><br /> An example
+ Annotation file is given below. Copy and paste the contents into a
+ text file and load it onto the Jalview example protein alignment.
+ </p>
+ <pre>#Comment lines follow the hash symbol