-<html>\r
-\r
-<head><title>Annotations File Format</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Annotations File Format<br>\r
- </strong><br>\r
- A precalculated annotations fiile can read onto an alignment from the command \r
- line ("-annotations"), by drag and dropping the the annotations file \r
- onto an alignment or by selecting from the File menu "Load Features / Annotations".</p>\r
-<p>The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION \r
- as an identifier. Then a block of annotations are added in the form GRAPH_TYPE \r
- Label Values</p>\r
-<p>GRAPH_TYPE can be either BAR_GRAPH, LINE_GRAPH or NO_GRAPH. The values are \r
- per alignment column, separated by "|". Multiple content per column \r
- can be separated with commas, Jalview will display the content if it interprates \r
- the content as a text label, or secondary structure character (H or E)</p>\r
-<p>You can optionally associate an annotation with a sequence by adding a line \r
- SEQUENCE_REFseq_namestartIndex All Annotations after a SEQUENCE_REF will be \r
- associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.</p>\r
-<p>The visual graphs can be coloured or combined with other graphs, or have an \r
- arbitrary line drawn at a certain value using the following lines.</p>\r
-<p><font size="2" face="Courier New, Courier, mono">COLOUR<tab>graph name<tab>colour<br>\r
- COMBINE<tab>graph 1 name<tab>graph 2 name<br>\r
- GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour</font></p>\r
-<p>An example Annotation file may look like this:</p>\r
-<p><font size="2" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>\r
- JALVIEW_ANNOTATION<br>\r
- SEQUENCE_REF FER1_MESCR 5<br>\r
- BAR_GRAPH<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\r
- LINE_GRAPH<tab>Green Values<tab>1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2<br>\r
- LINE_GRAPH<tab>Red Values<tab>2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2<br>\r
- BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
- NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
- NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="2" face="Courier New, Courier, mono">COLOUR<tab>Bar Graph 2<tab>blue<br>\r
- COLOUR<tab>Red Values<tab>255,0,0<br>\r
- COLOUR<tab>Green Values<tab>green<br>\r
- COLOUR<tab>Purple Letters<tab>151,52,228<br>\r
- COMBINE<tab>Green Values<tab>Red Values</font></p>\r
-<p><font size="2" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black \r
- </font><br>\r
-</p>\r
-<p><br>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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>
+ -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><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>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><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>
+
+<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>
+<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
+(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>
+<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>
+<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>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
+</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,
+ 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:
+<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