X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=59f3122ee65c088e9e7e75384cf790735b8f7c43;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=260443083ca7287cfd09c59822aa7cfc894204a3;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 2604430..59f3122 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -1,21 +1,24 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> The Alignment Annotations File @@ -132,13 +135,13 @@ 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.

@@ -178,6 +181,9 @@ property, then the idColour will also be used to colour the sequence. SEQUENCE_REF sequence reference statement, the sequence representative for the group will be set to the referenced sequence. +
  • The interpretation of the COMBINE statement in Version 2.8.1 was refined + so that only annotation line graphs with the given names ands the same + SEQUENCE_REF and GROUP_REF scope are grouped.

    • An example Annotation file is given below: @@ -187,7 +193,7 @@ SEQUENCE_REF FER1_MESCR 5 BAR_GRAPH Bar Graph 1 <html>an <em>html tooltip</em> for Bar graph 1.</html> ||-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 +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 @@ -197,13 +203,14 @@ 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