-<html>
-
-<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></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: <strong><pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre></strong>
-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: <strong><pre>SEQUENCE_REF	ALIGNMENT</pre></strong></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): <strong><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></pre></strong>
-<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
-</pre>
-</p>
-</body>
-</html>
+<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
git://source.jalview.org / jalview.git / blobdiff