<html>\r
\r
-<head><title>The Alignment Annotations File</title></head>\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\r
- ASCII text file consisting of tab\r
- delimited records similar to the <a\r
- href="featuresFormat.html">Sequence Features File</a>, and\r
- introduced primarily for use with the Jalview applet.</p>\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
+ <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\r
-<strong>File</strong> menu of an alignment window.</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 must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>\r
-<p>A row of annotation is added with a line like\r
-<strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Values</em></pre></strong>\r
-<ul>\r
-<li><em>GRAPH_TYPE</em><br>This is can be either of "BAR_GRAPH",\r
- "LINE_GRAPH" or "NO_GRAPH", defining the type of\r
- annotation row that is being described.\r
- </li>\r
- <li><em>Values</em><br>This field is a series\r
- of symbols and/or quantities separated by the pipe symbol "|",\r
- mapped onto the columns of the alignment.<br>Some types of annotation\r
- can display both text, symbols and quantities at each column, and these are\r
- separated with commas within the pipe-delimited Value field. Jalview\r
- will display the content if it's values are appropriate for the type\r
- of the annotation being defined:<ul>\r
-<li>BAR_GRAPH<br><em>text\r
- character</em>,<em>number</em></li>\r
-<li>LINE_GRAPH<br><em>number</em></li>\r
-<li>NO_GRAPH<br><em>text label</em>,<em>H or E for helix or strand\r
- symbol</em></li></ul>\r
-</li></ul></p>\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
-<strong><pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre></strong>\r
-All Annotations defined after a SEQUENCE_REF command will then be \r
- associated with that sequence, and the first field in the Value\r
- field list will (optionally) be\r
- placed at the <em>startIndex</em>'th column.</p><p>Sequence associations\r
- are turned off for subsequent annotation definitions by:\r
-<strong><pre>SEQUENCE_REF	ALIGNMENT</pre></strong></p>\r
-<p><em>LINE_GRAPH</em> type annotations can be given a colour,\r
- combined onto the same vertical axis, and have abscissa (lines of\r
- constant value - <em>so they are horizontal</em>) at particular\r
- values using the following lines (respectively):<!--</p>\r
-<p><font size="3" face="Courier New, Courier, mono">-->\r
-<strong><pre>COLOUR	graph name	colour\r
-COMBINE	graph 1 name	graph 2 name\r
-GRAPHLINE	graph name	value	label	colour</pre></strong></p>\r
-<p>An example Annotation file is given below:</p>\r
-<p><font size="3" 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	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\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<br>\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<br>\r
- BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
- NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
- NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">COLOUR	Bar Graph 2	blue<br>\r
- COLOUR	Red Values	255,0,0<br>\r
- COLOUR	Green Values	green<br>\r
- COLOUR	Purple Letters	151,52,228<br>\r
- COMBINE	Green Values	Red Values</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">GRAPHLINE	Red Values	2.6	threshold	black \r
- </font><br>\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><br>\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