X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2FfeaturesFormat.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2FfeaturesFormat.html;h=02261753cce122e069cafae463055bae0191b7f7;hb=e086b0c30bee5fe084186c65ef1ded42c58560f9;hp=4d13dcdaa32499ba471eee15868e84b87c097ade;hpb=e51f922b88b1f316e27cf4c19eef437ff592d74d;p=jalview.git
diff --git a/help/help/html/features/featuresFormat.html b/help/help/html/features/featuresFormat.html
index 4d13dcd..0226175 100755
--- a/help/help/html/features/featuresFormat.html
+++ b/help/help/html/features/featuresFormat.html
@@ -26,17 +26,20 @@
Sequence Features File
+
-
The Sequence features file (which used to be known as the
- "Groups file" prior to version 2.08) is a simple way of getting your
- own sequence annotations into Jalview. It was introduced to allow
- sequence features to be rendered in the Jalview applet, and so is
- intentionally lightweight and minimal because the applet is often
- used in situations where data file size must be kept to a minimum,
- and no XML parser is available.
+
+ The Sequence features File provides a simple way of getting
+ your own sequence features into Jalview. It also allows feature
+ display styles and filters to be saved and imported to another
+ alignment. Users familiar with the earliest versions of Jalview will
+ know that features files were originally termed 'groups' files, and
+ that the format was was designed as a space efficient format to
+ allow sequence features to be rendered in the Jalview applet.
Features files are imported into Jalview in the following ways:
+
-
-
Sequence Features File Format
A features file is a simple ASCII text file, where each line
contains tab separated text fields. No comments are
- allowed.
+ allowed. Its structure consists of three blocks:
+
+
- Feature Colours
+ Feature Colours
The first set of lines contain feature type definitions and their colours:
-Feature label Feature Colour
+<Feature Type> <Feature Style>
- A feature type has a text label, and a colour specification. This can
- be either:
-
-
- - A single colour specified as either a red,green,blue 24 bit
+ Each feature type definition assigns a style to features of the given type. <Feature Style> can be either a simple colour, or a more complex Graduated Colour Scheme that shades features according to their description, score, or other attributes.
+
+ Assigning a colour for a <Feature Type>
A single colour specified as either a red,green,blue 24 bit
triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
(ranging from 0 to 255))
- (For help with colour values, see https://www.w3schools.com/colors/colors_converter.asp.)
-
- - A graduated colourscheme
- specified as a "|" separated list of fields:
-[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
-
The fields are as follows:
-
-
- - 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 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,
- but remember to specify the remaining fields)
-
- - absolute
An optional switch
- indicating that the minvalue and maxvalue
- parameters should be left as is, rather than rescaled
- according to the range of scores for this feature type.
-
- - minvalue and maxvalue
- Minimum and maximum values defining the range of scores for
- 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
- value which is used to control the display of features with
- a score either below or above the value.
-
-
+ (For help with colour values, see https://www.w3schools.com/colors/colors_converter.asp.)
+ Specifying a Graduated Colourscheme
+ Data dependent feature colourschemes are defined by a series of "|" separated fields:
+[label or score or attribute|<attName>|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
+
The fields are interpreted follows:
+
+
+ - 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
+ 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, but
+ remember to specify the remaining fields)
+
+ - absolute
An optional switch indicating
+ that the minvalue and maxvalue parameters should
+ be left as is, rather than rescaled according to the range of
+ scores for this feature type.
This also enables
+ the 'Threshold is Min/Max' option for this type's feature
+ shading style dialog.
+
+ - minvalue and maxvalue
Minimum
+ and maximum values defining the range of scores for 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 value which is used to
+ control the display of features with a score either below or above
+ the value.
-
- Feature Filters
+ 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.
@@ -168,30 +178,33 @@
- Feature Instances
+ Feature Definitions
- 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 may also be used to generate
- a colour for the feature).
+ The remaining lines in the file are sequence feature data.
+ Features are either non-positional - attached to a whole sequence
+ (as specified by its ID), or positional, so attached to a specific
+ range on a sequence. In addition to a type, features can also
+ include descriptive text and a score, and depending on the format
+ used, many additional attributes.
+ Importing Generalised Feature Format (GFF) feature data
- If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or
- GFF3
- (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format,
- then you can leave it as is, after first adding a line containing only
- 'GFF' after any Jalview feature colour definitions (this
- mixed format capability was added in Jalview 2.6). Alternately,
- you can use Jalview's own sequence feature annotation format, which
- additionally allows HTML and URLs to be directly attached to each
- piece of annotation.
+ Jalview has its own tabular format (described below) for describing
+ sequence features, which allows HTML descriptions (including URLs)
+ to be defined for each feature. However, sequence feature
+ definitions can also be provided in GFF2
+ (http://gmod.org/wiki/GFF2) or GFF3
+ (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
+ format. To do this, a line containing only 'GFF' should precede any
+ GFF data (this mixed format capability was added in Jalview
+ 2.6).
- Jalview's sequence feature annotation format
+ Jalview's sequence feature format
Each feature is specified as a tab-separated series of columns
as defined below: