From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 May 2013 14:05:47 +0000 (+0100)
Subject: JAL-1296 reinstated tab characters so example annotation file can be copied and paste... 
X-Git-Tag: Jalview_2_9~249^2~20
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=79c99fe4555eca94840ab1d2571d3ebf27af50ee;p=jalview.git

JAL-1296 reinstated tab characters so example annotation file can be copied and pasted to a file and imported
---

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index fa6d3dd..17c2c8b 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -132,13 +132,13 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
 </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>
@@ -197,13 +197,14 @@ COLOUR&#9;Purple Letters&#9;151,52,228
 COMBINE&#9;Green Values&#9;Red Values
 GRAPHLINE&#9;Red Values&#9;2.6&#9;threshold&#9;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&#9;Group_A&#9;30&#9;50&#9;*
+SEQUENCE_GROUP&#9;Group_B&#9;1&#9;351&#9;2-5
+SEQUENCE_GROUP&#9;Group_C&#9;12&#9;14&#9;-1&#9;seq1&#9;seq2&#9;seq3
+PROPERTIES&#9;Group_A&#9;description=This is the description&#9;colour=Helix Propensity&#9;pidThreshold=0&#9;outlineColour=red&#9;displayBoxes=true&#9;displayText=false&#9;colourText=false&#9;textCol1=black&#9;textCol2=black&#9;textColThreshold=0
+PROPERTIES&#9;Group_B&#9;outlineColour=red
+PROPERTIES&#9;Group_C&#9;colour=Clustal
 </pre>
 </p>
+<p><em>Last updated for version 2.8.1</em></p>
 </body>
 </html>