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<head>
<title>The Alignment Annotations File</title>
</head>
text file consisting of tab delimited records similar to the <a
href="featuresFormat.html">Sequence Features File</a>, and introduced
primarily for use with the Jalview applet.</p>
-<p>Alignment annotations files are imported into Jalview in the
-following ways:<br>
+
+<p><strong>Importing annotation files</strong><br/>
+Alignment annotations files are imported into Jalview in the
+following ways:<br/>
<ul>
<li>from the command line<strong><pre>
-annotations <<em>Annotations filename</em>></pre></strong></li>
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
-tab delimited fields, and any lines starting with "#" are
-ignored. The first non-commented out line of a valid Annotations file
+<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>
-<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
+<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>
-<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:
-<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>
-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><em>LINE_GRAPH</em> type annotations can be given a colour
+<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
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 2.5) ROWPROPERTIES</font></h3>
-<p>The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:</p>
+</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>
-<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>
+<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>If the alignment indices are not known, enter -1 then a tab delimited list
- of 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>
-<p>The group can (optionally) be assigned various visualisation properties via
- another tab delimited line thus:</p>
-<pre>PROPERTIES Group_name tab_delimited_key_value_pairs
+<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 key_value_pairs allow you to define a description and to colour the group
- in various ways. All, none or some of the following values could be used for
- a group:</p>
-<p>description=Text <br>
- colour=Helix Propensity<br>
- pidThreshold=0<br>
- consThreshold=0<br>
- outlineColour=red <br>
- displayBoxes=true<br>
- displayText=false<br>
- colourText=false<br>
- textCol1=black<br>
- textCol2=black<br>
- textColThreshold=0<br>
- idColour=ff3322<br>
- <!-- Not yet implemented in 2.5 release
- 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,
+<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.</li>
- <!-- <li><em>New Features in 2.5</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:
+ 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 2.8.3, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</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> takes either a single sequence ID string, or a
+ numeric index (second argument), and attempts to assign a
+ corresponding sequence as the <a href="../features/refsequence.html">reference
+ sequence</a> for the alignment.
+ </p>
+ <em>VIEW_HIDECOLS</em> takes either a single argument consisting of a
+ comma separated series of integer pairs like
+ <em>3-4</em>. These integer pairs define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ view.
+ </p>
+ <p>
+ <em>HIDE_INSERTIONS</em> takes a either a single sequence ID or a
+ numeric index, or no arguments. This command marks all gapped
+ positions in a specified sequence (either the one located by the
+ arguments, the current SEQUENCE_REF, or the reference sequence for the
+ view).
+ <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
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>
</body>
git://source.jalview.org / jalview.git / blobdiff