X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Ffeatureschemes.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Ffeatureschemes.html;h=63dd0e59ac54feb4a39f8909245f90152004023b;hb=6a05eb3f55d97e685f0c723822384633d5636778;hp=37243d2ed58626adc2345d29d41799527a16bc3e;hpb=d113749a183a3ea8f3f7e22c725511f59f1d833f;p=jalview.git diff --git a/help/help/html/features/featureschemes.html b/help/help/html/features/featureschemes.html index 37243d2..63dd0e5 100644 --- a/help/help/html/features/featureschemes.html +++ b/help/help/html/features/featureschemes.html @@ -25,82 +25,111 @@

- Sequence feature colour schemes -

- Jalview can visualize annotation present on parts of a sequence by - overlaying colours according to the annotation present at each - position. It allows features to be colored either according to type, - or for a particular type, according to an individual feature's - associated label or score. The Feature - Settings dialog box controls the order and display of each - sequence annotation type, and also allows the colour scheme used for - the the feature to be changed via the 'Graduated Colour' - option in the sequence feature pop-up menu (obtained by - right-clicking on a sequence feature). + Visualisation of Sequence Features

Jalview can visualize sequence features - the positional + annotation present on parts of a sequence, as colours overlaid on + corresponding positions in the alignment. Features may be coloured + either according to their type, or for a particular type, according to + each feature's associated label, score, or other attributes.

+ The Feature Settings dialog box + controls the order and display of each feature type, and + also allows filters and colour schemes to be configured. +

- -

Graduated feature - colour scheme settings dialog box - -

The Graduated Feature Colour dialog box has the following - controls: -

Colour by Label - when checked this derives a - colour for each feature based on the label text.
Min and Max Color boxes - Click on these boxes to - set the minimum and maximum colours used to shade features by - their associated score.
Threshold type combo box - Allows features to be - hidden features if their score is below or above a given - threshold.
Set the threshold using the slider or - type it in to the text box. The threshold cannot be set outside - the available range of feature scores.
Threshold is Min/Max - When checked, the threshold - will be used as the upper or lower limit when shading the features - according to their score using the Min and Max colour.

- Icon styles for graduated feature styles
-

- When a graduated colourscheme is applied to a feature, it is - indicated in the feature settings or amend feature dialog box by the - following types of icon:
-

- - - - - - - - - - - - - - - - - - - - - - - - -

Type of Colouring	Icon
Graduated colour by Feature Score
Graduated colour thresholded (less than) by - feature Score
Graduated colour thresholded (greater than) by - feature Score
Colour by Feature Label (may also be - thresholded)
The - current threshold is given in the icon's tooltip. -

- -

- Graduated feature colours were introduced in Jalview 2.5 + +

+ Feature Display Settings dialog for 'sequence_variant' + features imported from VCF +

The Feature Display Settings has the following controls: +

Colour

Simple Colour - select this to assign a given colour + to any features of this type. The assigned colour can be changed by + clicking on the colour box.
Colour by text - this option derives a colour for + each feature based on its label, or any other attributes presented via + the drop-down menu.
Graduated Colour - shade features according to + associated score, or other numeric attribute. +
- Min and Max Color boxes - Click on these boxes to + set the minimum and maximum colours for the shading scheme.
- Threshold type combo box - Specify an exclusion + threshold.
  Set the threshold using the slider or + type it in to the text box. The threshold cannot be set outside + the available range of values observed for the selected attribute.
- Threshold is Min/Max - When checked, the threshold + will be used as the upper or lower limit for shading using the Min + and Max colour.

+ Filters
Any number of filter + conditions may be specified to select features based on one or more + attributes. The join condition specifies whether all + filters must apply (And) or whether any one + filter must apply (Or) for a feature to be + selected. +

The filters available depend on the type of attribute:

Numeric - specify a threshold above, equal + to or below which a feature will be selected or ignored.
String - select or ignore features based on + presence, absence, equivalence, or containment of a string (not case sensitive).

+ The filters and colour schemes active for a particular feature type + are shown in the Colour and Configuration columns in + the feature settings dialog. Styles and filters can be saved as a + Jalview Feature Colours file, and are also exported and imported via Jalview Feature files. + +

+ Icon styles for feature rendering styles
+ +

+ When a graduated colour scheme is applied to a feature according to + the value of a particular attribute, it is indicated in the feature + settings or amend feature dialog box by the following types of icon:
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + +

Type of Colouring	Icon
Graduated colour by Feature Score
Graduated colour thresholded (less than) by + feature Score (or other attribute)
Graduated colour thresholded (greater than) by + feature Score (or other attribute)
Colour by Feature Label
The + current threshold and attribute is shown in the icon's tooltip. +

+ Graduated feature colours were introduced in Jalview 2.5. + Attribute based colouring and filters were added in Jalview 2.11.