From 79c99fe4555eca94840ab1d2571d3ebf27af50ee Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 21 May 2013 15:05:47 +0100 Subject: [PATCH] JAL-1296 reinstated tab characters so example annotation file can be copied and pasted to a file and imported --- help/html/features/annotationsFormat.html | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) 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 graph_name value label colo

(Since Jalview 2.2.1) SEQUENCE_GROUP

Groups of sequences can be defined using the tab delimited line

-
SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	Sequences
+
SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	Sequences

The sequences can be defined by alignment index and a range of sequences can be defined in a comma delimited field such as

2-5,8-15,20,22

Enter * to select all groups.

-

If the alignment indices are not known, enter -1 then a tab delimited list - of sequence ids.

+

Note: If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list +specifying the sequence ids.

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.

@@ -197,13 +197,14 @@ 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 +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

+

Last updated for version 2.8.1

-- 1.7.10.2