X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=141379f3e4c9c5711f02edfd2285b147ce2049af;hb=b4b901505310c3bdd1809f122abed6799c2fa664;hp=fa6d3ddc96d6e79572d8474e3aab5062be1d999f;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index fa6d3dd..141379f 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
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. +
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