A graduated colourscheme
specified as a "|" separated list of fields:
-[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
+[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
The fields are as follows:
- - label
Indicate that the feature
+ - label
Indicates that the feature
description should be used to create a colour for features of
this type.
Note: if no threshold value is
- needed then the final '|' may be omitted.
This
+ needed then only 'label' is required.
This
keyword was added in Jalview 2.6
+ - score
Indicates that the feature
+ score should be used to create a graduated colour for features of
+ this type, in conjunction with mincolor, maxcolor.
This keyword was added in Jalview 2.11.
+ It may be omitted (score is the default) if mincolor and maxcolor are specified.
+
+
+ - attribute|attName
Indicates that the value of feature
+ attribute 'attName' should be used to create a colour for features of
+ this type.
+
For example, attribute|clinical_significance to colour by clinical_significance.
+
To colour by range of a numeric attribute, include mincolor and maxcolor, or omit to colour by text (category).
+
(Note: the value of the attribute used for colouring will also be shown in the tooltip as you mouse over features.)
+
A sub-attribute should be written as, for example, CSQ:IMPACT.
+
This keyword was added in Jalview 2.11
+
- mincolor and maxcolor
Colour
triplets specified as hexadecimal or comma separated values
(may be left blank for a label style colourscheme,
@@ -99,10 +118,15 @@
- minvalue and maxvalue
Minimum and maximum values defining the range of scores for
- which the colour range will be defined over. If minvalue is
+ which the colour range will be defined over.
If minvalue is
greater than maxvalue then the linear mapping will have
negative gradient.
+ - novalue
+ Specifies the colour to use if colouring by attribute, when the attribute is absent.
+ Valid options are novaluemin, novaluemax, novaluenone, to use mincolor, maxcolor, or no colour.
+
If not specified this will default to novaluemin.
+
- thresholdtype
Either
"none", "below", or "above". below
and above require an additional threshold
@@ -113,12 +137,45 @@
+
+ Feature Filters
+
+ This section is optional, and allows one or more filters to be defined for each feature type.
+
Only features that satisfy the filter conditions will be displayed.
+
Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+
Each line has the format:
+
featureType <tab> (filtercondition1) [and|or] (filtercondition2) [and|or]...
+ The parentheses are not needed if there is only one condition.
+ Combine multiple conditions with either and or or (but not a mixture).
+
Each condition is written as:
+ Label|Score|AttributeName condition [value]
+ where condition is not case sensitive, and should be one of
+
+ - Contains - value should contain the given text (not case sensitive); example clinical_significance contains Pathogenic
+ - NotContains - value should not contain the given text
+ - Matches - value should match the given text (not case sensitive)
+ - NotMatches - value should not match the given text (not case sensitive)
+ - Present - specified attribute is present on the feature (no value required); example CSQ:SIFT present
+ - NotPresent - specified attribute is not present on the feature (no value required)
+ - EQ - feature score, or specified attribute, is equal to the (numeric) value
+ - NE, LT, LE, GT, GE - tests for not equal to / less than / less than or equal to / greater than / greater than or equal to the value
+
+ A non-numeric value always fails a numeric test.
If either attribute name, or value to compare, contains spaces, then enclose in single quotes:
+ 'mutagenesis site' contains 'decreased affinity'
+
Tip: to see examples of valid syntax, first configure colours and filters in Jalview, then File | Export Features to Textbox in Jalview Format.
+
Feature filters were added in Jalview 2.11
+
+
+
+ Feature Instances
+
+
The remaining lines in the file are the sequence annotation
definitions, where the now defined features are attached to regions
on particular sequences. Each feature can optionally include some
descriptive text which is displayed in a tooltip when the mouse is
- near the feature on that sequence (and can also be used to generate
- a colour the feature).
+ near the feature on that sequence (and may also be used to generate
+ a colour for the feature).
If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or
@@ -204,6 +261,13 @@ signal peptide 0,155,165
helix ff0000
strand 00ff00
coil cccccc
+kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0
+
+STARTFILTERS
+metal ion-binding site Label Contains sulfur
+kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8)
+ENDFILTERS
+
Your Own description here FER_CAPAA -1 3 93 domain
Your Own description here FER_CAPAN -1 48 144 chain
Your Own description here FER_CAPAN -1 50 140 domain
@@ -211,10 +275,16 @@ Your Own description here FER_CAPAN -1 136 136 modified residue
Your Own description here FER1_LYCES -1 1 47 transit peptide
Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide
Your Own description here Q93XJ9_SOLTU -1 49 144 chain
-startgroup secondarystucture
+
+STARTGROUP secondarystucture
PDB secondary structure annotation FER1_SPIOL -1 52 59 strand
PDB secondary structure annotation FER1_SPIOL -1 74 80 helix
-endgroup secondarystructure
+ENDGROUP secondarystructure
+
+STARTGROUP kd
+Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8
+ENDGROUP kd
+
GFF
FER_CAPAA GffGroup domain 3 93 . .