-<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>
+
+<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:
+<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>
+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
+</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
+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 / commitdiff