*
* 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><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>,<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
+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
+(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 2.5) 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	||-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