X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=41d2b69825c9f6b3f29010f13f58104b1c1d491b;hb=e1cd94839128776e14e51ded3f3be2dcc7e72273;hp=682edfd6cda3cd8b1b2ceabf8dcec15b18cf3d52;hpb=96433cd123131e1a572be3bce03be00d61367876;p=jalview.git diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 682edfd..41d2b69 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: @@ -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