- <li>Dragging an annotations file onto an alignment window</li>
- <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
- menu of an alignment window.</li>
-</ul>
-</p>
-<p>
- <strong>Exporting annotation files</strong><br /> An annotation file
- can be created for any alignment view from the "Export
- Annotations ..." entry in the <strong>File</strong> menu of an
- alignment window.
-</p>
-<p><strong>THE ANNOTATION FILE FORMAT</strong>
-<br/>An annotation file consists of lines containing an instruction followed by
-tab delimited fields. Any lines starting with "#" are considered comments, and
-ignored. The sections below describe the structure of an annotation file.
-</p><ul>
-<li><a href="#annheader">JALVIEW_ANNOTATION</a> mandatory header</li>
-<li><a href="#annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a> to create annotation rows</li>
-<li><a href="#combine">COMBINE, COLOUR and GRAPHLINE</a> for thresholds and complex line graphs</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="#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>
- </ul>
- <p>
- At the end of this document, you can also find notes on <a
- href="#compatibility">compatibility</a> of annotation files across
- different versions of Jalview. An <a href="#exampleann">example
- annotation file</a> is also provided along with instructions on how to
- import it to Jalview.
- </p>
- <hr/>
-<p><strong><em><a name="annheader">Header line</a></em></strong><br/>The first non-commented out line of a valid Annotations file
-must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
-<hr/>
-<p><strong><em><a name="annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a></em></strong><br/>
-Labels, secondary structure, histograms and line graphs are added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Description</em> (optional)	<em>Values</em></pre></strong></p>
- <p>
- Here, the <em>GRAPH_TYPE</em> field in the first column defines the
- appearance of the annotation row when rendered by Jalview. The next
- field is the row <em>label</em> for the annotation. This may be
- followed by a <em>description</em> for the row, which is shown in a
- tooltip when the user mouses over the annotation row's label. Since
- Jalview 2.7, the description field may also contain HTML tags (in the same
- way as a <a href="featuresFile.html">sequence feature's</a> label),
- providing the text is enclosed in an <html/> tag.
-
- <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 "|" 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>
- <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. "(|(||)|)" or "|A|A|A|(|a|a|a|)")</li>
- </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>
-<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><strong><a name="combine">COMBINE, COLOUR and GRAPHLINE</a> for line graphs</font></strong><br/>
-<em>LINE_GRAPH</em> type annotations can be given a colour
-(specified as 24 bit RGB triplet in hexadecimal or comma separated
-values), combined onto the same vertical axis, and have ordinate lines
-(horizontal lines at a particular vertical axis value) using the
-following commands (respectively):
-<pre>COLOUR	<em>graph_name</em>	<em>colour</em>
+ <li>Dragging an annotations file onto an alignment window</li>
+ <li>Via the "Load Features / Annotations" entry in
+ the <strong>File</strong> menu of an alignment window.
+ </li>
+ </ul>
+ </p>
+ <p>
+ <strong>Exporting annotation files</strong><br /> An annotation
+ file can be created for any alignment view from the "Export
+ Annotations ..." entry in the <strong>File</strong> menu of an
+ alignment window.
+ </p>
+ <p>
+ <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation
+ file consists of lines containing an instruction followed by tab
+ delimited fields. Any lines starting with "#" are
+ considered comments, and ignored. The sections below describe the
+ structure of an annotation file.
+ </p>
+ <ul>
+ <li><a href="#annheader">JALVIEW_ANNOTATION</a> mandatory
+ header</li>
+ <li><a href="#annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a>
+ to create annotation rows</li>
+ <li><a href="#combine">COMBINE, COLOUR and GRAPHLINE</a> for
+ thresholds and complex line graphs</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
+ 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> 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
+ href="#compatibility">compatibility</a> of annotation files
+ across different versions of Jalview. An <a href="#exampleann">example
+ annotation file</a> is also provided along with instructions on how to
+ import it to Jalview.
+ </p>
+ <hr />
+ <p>
+ <strong><em><a name="annheader">Header line</a></em></strong><br />The
+ first non-commented out line of a valid Annotations file must begin
+ with :<strong><pre>JALVIEW_ANNOTATION</pre></strong>
+ </p>
+ <hr />
+ <p>
+ <strong><em><a name="annrows">LINE_GRAPH,
+ BAR_GRAPH and NO_GRAPH</a></em></strong><br /> Labels, secondary structure,
+ histograms and line graphs are added with a line like <strong><pre>
+ <em>GRAPH_TYPE</em>	<em>Label</em>	<em>Description</em> (optional)	<em>Values</em>
+ </pre></strong>
+ </p>
+ <p>
+ Here, the <em>GRAPH_TYPE</em> field in the first column defines the
+ appearance of the annotation row when rendered by Jalview. The next
+ field is the row <em>label</em> for the annotation. This may be
+ followed by a <em>description</em> for the row, which is shown in a
+ tooltip when the user mouses over the annotation row's label. Since
+ Jalview 2.7, the description field may also contain HTML tags (in
+ the same way as a <a href="featuresFormat.html">sequence
+ feature's</a> label), providing the text is enclosed in an
+ <html/> tag.
+ <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 "|"
+ 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>
+ <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. "(|(||)|)" or
+ "|A|A|A|(|a|a|a|)")
+ </ul></li>
+ </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>
+ <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>
+ <strong><a name="combine">COMBINE, COLOUR and GRAPHLINE</a>
+ for line graphs</font></strong><br /> <em>LINE_GRAPH</em> type annotations can be
+ given a colour (specified as 24 bit RGB triplet in hexadecimal or
+ comma separated values), combined onto the same vertical axis, and
+ have ordinate lines (horizontal lines at a particular vertical axis
+ value) using the following commands (respectively):
+ <pre>COLOUR	<em>graph_name</em>	<em>colour</em>