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<head>
<title>The Alignment Annotations File</title>
</head>
<body>
-<p><strong>The Alignment Annotations File</strong></p>
-<p>Alignment annotations can be imported onto an alignment since
-version 2.08 of Jalview, via an annotations file. It is a simple ASCII
-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>
-<ul>
- <li>from the command line<strong><pre>
+ <p>
+ <strong>The Alignment Annotations File</strong>
+ </p>
+ <p>
+ Alignment annotations can be imported onto an alignment since
+ version 2.08 of Jalview, via an annotations file. It is a simple
+ ASCII 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>
+ <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>
- <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>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
-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></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><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>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><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="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 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>
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 2.2.1) 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>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
+</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 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</p>
-<em>New Features in 2.4:</em><ul><li>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>
-</ul>
-<p> </p>
-<p>An example Annotation file is given below:
-<pre>#Comment lines follow the hash symbol
+ <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
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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff