-<html>\r
-\r
-<head>\r
-<title>The Alignment Annotations File</title>\r
-</head>\r
-\r
-<body>\r
-<p><strong>The Alignment Annotations File</strong></p>\r
-<p>Alignment annotations can be imported onto an alignment since\r
-version 2.08 of Jalview, via an annotations file. It is a simple ASCII\r
-text file consisting of tab delimited records similar to the <a\r
- href="featuresFormat.html">Sequence Features File</a>, and introduced\r
-primarily for use with the Jalview applet.</p>\r
-<p>Alignment annotations files are imported into Jalview in the\r
-following ways:<br>\r
-<ul>\r
- <li>from the command line<strong><pre>\r
- -annotations <<em>Annotations filename</em>></pre></strong></li>\r
- <li>Dragging an annotations file onto an alignment window</li>\r
- <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>\r
- menu of an alignment window.</li>\r
-</ul>\r
-</p>\r
-<p><strong>Annotations File Format</strong></p>\r
-<p>The File consists of lines containing an instruction followed by\r
-tab delimited fields, and any lines starting with "#" are\r
-ignored. The first non-commented out line of a valid Annotations file\r
-must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>\r
-<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>\r
-<p>The <em>GRAPH_TYPE</em> field, which appears first, defines the\r
-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 "|"\r
-separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's\r
-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>\r
- <li>BAR_GRAPH<br>\r
- Plots a histogram with labels below each bar.<br>\r
- <em>number</em>,<em>text character</em></li>\r
- <li>LINE_GRAPH<br>\r
- Draws a line between values on the annotation row.<br>\r
- <em>number</em></li>\r
- <li>NO_GRAPH<br>\r
- For a row consisting of text labels and/or secondary structure symbols.<br>\r
- <em>{Secondary Structure Symbol}</em>,<em>text label</em><br>\r
- Currently supported secondary structure structure symbols are <em>H</em> (for helix) and <em>E</em> (for strand)</li>\r
-</ul>\r
-Any or all value fields may be left empty, as well as the BAR_GRAPH's\r
-text character field, and either or both of the text-label and secondary\r
-structure symbol fields of the NO_GRAPH type annotation rows.\r
-</p>\r
-<p>You can associate an annotation with a sequence by preceding its\r
-definition with the line: \r
-<pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre>\r
-All Annotations defined after a SEQUENCE_REF command will then be\r
-associated with that sequence, and the first field in the Value field\r
-list will (optionally) be placed at the <em>startIndex</em>'th column.</p>\r
-<p>Sequence associations are turned off for subsequent annotation\r
-definitions by: \r
-<pre>SEQUENCE_REF	ALIGNMENT</pre>\r
-</p>\r
-<p><em>LINE_GRAPH</em> type annotations can be given a colour\r
-(specified as 24 bit RGB triplet in hexadecimal or comma separated\r
-values), combined onto the same vertical axis, and have ordinate lines\r
-(horizontal lines at a particular vertical axis value) using the\r
-following commands (respectively): \r
-<pre>COLOUR	<em>graph_name</em>	<em>colour</em>\r
-COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>\r
-GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>\r
-</em></strong></pre>\r
-<h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>\r
-<p>Groups of sequences can be defined using the tab delimited line</p>\r
-<pre>SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences</pre>\r
-<p>The sequences can be defined by alignment index and a range of sequences can \r
- be defined in a comma delimited field such as</p>\r
-<p>2-5,8-15,20,22</p>\r
-<p>Enter * to select all groups. </p>\r
-<p>If the alignment indices are not known, enter -1 then a tab delimited list \r
- of sequence ids. </p>\r
-<p>If the SEQUENCE_REF has been defined, the group_start and group_end will be \r
- relative to the sequence residue numbering, otherwise the group_start and group_end \r
- will be the alignment column indices. </p>\r
-<p>The group can (optionally) be assigned various visualisation properties via \r
- another tab delimited line thus:</p>\r
-<pre>PROPERTIES Group_name tab_delimited_key_value_pairs\r
-</pre>\r
-<p>The key_value_pairs allow you to define a description and to colour the group \r
- in various ways. All, none or some of the following values could be used for \r
- a group:</p>\r
-<p>description=Text <br>\r
- colour=Helix Propensity<br>\r
- pidThreshold=0<br>\r
- consThreshold=0<br>\r
- outlineColour=red <br>\r
- displayBoxes=true<br>\r
- displayText=false<br>\r
- colourText=false<br>\r
- textCol1=black<br>\r
- textCol2=black<br>\r
- textColThreshold=0</p>\r
-<p> </p>\r
-<p>An example Annotation file is given below:\r
-<pre>#Comment lines follow the hash symbol\r
-JALVIEW_ANNOTATION\r
-SEQUENCE_REF	FER1_MESCR	5\r
-BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+\r
-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\r
-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\r
-BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4\r
-NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||\r
-NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n\r
-COLOUR	Bar Graph 2	blue\r
-COLOUR	Red Values	255,0,0\r
-COLOUR	Green Values	green\r
-COLOUR	Purple Letters	151,52,228\r
-COMBINE	Green Values	Red Values\r
-GRAPHLINE	Red Values	2.6	threshold	black\r
-\r
-SEQUENCE_GROUP Group_A 30 50 *\r
-SEQUENCE_GROUP Group_B 1 351 2-5\r
-SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3\r
-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\r
-PROPERTIES Group_B outlineColour=red\r
-PROPERTIES Group_C colour=Clustal\r
-</pre>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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><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>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>
+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>
+<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 2.8.3, 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	<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
+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
+COLOUR	Red Values	255,0,0
+COLOUR	Green Values	green
+COLOUR	Purple Letters	151,52,228
+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
+</pre>
+</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff