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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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<head>
<title>The Alignment Annotations File</title>
</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>
+<pre>SEQUENCE_GROUP Group_Name Group_Start Group_End <em>Sequences</em></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><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list
+specifying the 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>
<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>
+ <li>The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
+ so that only annotation line graphs with the given names ands the same
+ <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</li>
</ul>
<p> </p>
<p>An example Annotation file is given below:
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
+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>
+<p><em>Last updated for version 2.8.1</em></p>
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