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<head>
<title>The Alignment Annotations File</title>
</head>
menu of an alignment window.</li>
</ul>
</p>
-<p><strong>Annotations File Format</strong></p>
-<p>The File consists of lines containing an instruction followed by
+<p><h3><font face="Arial, Helvetica, sans-serif">Format of an Annotations File</font></h3>
+<p>The file consists of lines containing an instruction followed by
tab delimited fields, and any lines starting with "#" are
ignored. The first non-commented out line of a valid Annotations file
must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
-<p>A row of annotation is added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Values</em></pre></strong></p>
-<p>The <em>GRAPH_TYPE</em> field, which appears first, defines the
-appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. 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
-GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "<strong>|</strong>" symbol) are shown below:<ul>
- <li>BAR_GRAPH<br>
- Plots a histogram with labels below each bar.<br>
- <em>number</em>,<em>text character</em>,<em>Tooltip text</em></li>
- <li>LINE_GRAPH<br>
- Draws a line between values on the annotation row.<br>
- <em>number</em></li>
- <li>NO_GRAPH<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>
- Currently supported secondary structure structure symbols are <em>H</em> (for helix) and <em>E</em> (for strand)</li>
-</ul>
-Any or all value fields may be left empty, as well as the BAR_GRAPH's
+<p>A row of annotation is 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>
+ The <em>GRAPH_TYPE</em> field, which appears first, 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 in the same
+ way as a <a href="featuresFile.html">sequence feature's</a> label,
+ providing the html is enclosed in an <html/> tag.
+
+ <ul><em>Please note: URL links embedded in HTML descriptions will
+ be supported in a future release of Jalview</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 GRAPH_TYPE. The allowed values of
+ GRAPH_TYPE and the format of their respective value fields (with the
+ trailing "<strong>|</strong>" symbol) are shown below:
+
+ <ul>
+ <li>BAR_GRAPH<br> Plots a histogram with labels below each
+ bar.<br> <em>number</em>,<em>text character</em>,<em>Tooltip
+ text</em>
+ </li>
+ <li>LINE_GRAPH<br> Draws a line between values on the
+ annotation row.<br> <em>number</em>
+ </li>
+ <li>NO_GRAPH<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> Currently
+ supported secondary structure structure symbols are <em>H</em> (for
+ helix) and <em>E</em> (for strand)</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>
-<p>You can associate an annotation with a sequence by preceding its
+<p><h3><font face="Arial, Helvetica, sans-serif">SEQUENCE_REF and GROUP_REF</font></h3>
+ 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>
-<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.<br/>
-<em>New in Jalview 2.5 Desktop</em>: Clicking on a sequence or group associated annotation row's label will highlight the sequence or sequence group in the alignment, and double clicking the annotation row label will select the associated sequence or group.</ul>
+
<p>Sequence associations are turned off for subsequent annotation
definitions by:
<pre>SEQUENCE_REF	ALIGNMENT</pre>
</p>
-<p>Since version 2.5, Jalview allows annotation rows to be associated with a group defined on the alignment, by preceding the annotation row with the line:
+<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
+Group association is turned off for subsequent annotation rows by:
<pre>GROUP_REF	<em>ALIGNMENT</em></pre>
-Annotations may be associated with both a sequence and a group, however - group annotations are still experimental and unexpected behaviour may be observed when editing alignments containing both group and sequence associated annotation rows.</p>
+</p>
+<h3><font face="Arial, Helvetica, sans-serif">LINE_GRAPH Grouping</font></h3>
<p><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
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>
+</p>
<h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.5) 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>
</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>
+<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>If the alignment indices are not known, enter -1 then a tab delimited list
- of sequence ids. </p>
+<p><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list
+specifying the sequence ids. </p>
<p>If the SEQUENCE_REF has been defined, the group_start and group_end will be
relative to the sequence residue numbering, otherwise the group_start and group_end
will be the alignment column indices. </p>
<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>
+ <li>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.</li>
</ul>
<p> </p>
<p>An example Annotation file is given below:
<pre>#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF	FER1_MESCR	5
-BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+BAR_GRAPH	Bar Graph 1	<html>an <em>html tooltip</em> for Bar graph 1.</html>	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
-BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+BAR_GRAPH	Bar Graph 2	1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
COLOUR	Bar Graph 2	blue
COMBINE	Green Values	Red Values
GRAPHLINE	Red Values	2.6	threshold	black
-SEQUENCE_GROUP Group_A 30 50 *
-SEQUENCE_GROUP Group_B 1 351 2-5
-SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
-PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red
-PROPERTIES Group_C colour=Clustal
+SEQUENCE_GROUP	Group_A	30	50	*
+SEQUENCE_GROUP	Group_B	1	351	2-5
+SEQUENCE_GROUP	Group_C	12	14	-1	seq1	seq2	seq3
+PROPERTIES	Group_A	description=This is the description	colour=Helix Propensity	pidThreshold=0	outlineColour=red	displayBoxes=true	displayText=false	colourText=false	textCol1=black	textCol2=black	textColThreshold=0
+PROPERTIES	Group_B	outlineColour=red
+PROPERTIES	Group_C	colour=Clustal
</pre>
</p>
+<p><em>Last updated for version 2.8.1</em></p>
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