From: Jim Procter Date: Mon, 24 Jun 2019 12:59:59 +0000 (+0100) Subject: JAL-3111 JAL-2069 JAL-2808 documentation for feature filters and enhanced feature... X-Git-Tag: Release_2_11_0~4^2~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f52bfc916cbcc0f3c77707735d6a0fd63c2789c4;p=jalview.git JAL-3111 JAL-2069 JAL-2808 documentation for feature filters and enhanced feature colours. Revised feature settings documentation for legibility. --- diff --git a/help/help/html/features/featureDisplaySettings.png b/help/help/html/features/featureDisplaySettings.png new file mode 100644 index 0000000..775baad Binary files /dev/null and b/help/help/html/features/featureDisplaySettings.png differ diff --git a/help/help/html/features/featureSettings.gif b/help/help/html/features/featureSettings.gif deleted file mode 100755 index 31f245c..0000000 Binary files a/help/help/html/features/featureSettings.gif and /dev/null differ diff --git a/help/help/html/features/featureSettings.png b/help/help/html/features/featureSettings.png new file mode 100644 index 0000000..e55bb32 Binary files /dev/null and b/help/help/html/features/featureSettings.png differ diff --git a/help/help/html/features/featurecoloursettings.gif b/help/help/html/features/featurecoloursettings.gif deleted file mode 100644 index 1b889db..0000000 Binary files a/help/help/html/features/featurecoloursettings.gif and /dev/null differ diff --git a/help/help/html/features/featureschemes.html b/help/help/html/features/featureschemes.html index 37243d2..688e492 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.

+ 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
Graduated colour thresholded (greater than) by + feature Score
Colour by Feature Label (may also be thresholded)
The + current threshold and attribute is given 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. diff --git a/help/help/html/features/featuresettings.html b/help/help/html/features/featuresettings.html index a156a39..408cdc2 100755 --- a/help/help/html/features/featuresettings.html +++ b/help/help/html/features/featuresettings.html @@ -26,35 +26,86 @@

Sequence Feature Settings Dialog Box

+ Select View→Feature Settings... in an alignment + window to open the feature settings dialog box, which allows + precise control the visibility and appearance of sequence features for + an alignment view. +

+ Sequence Feature Settings for the Jalview Application (version 2.11) +

The top section of the dialog box lists all the sequence feature + groups, along with a tickbox for each that controls whether its + features are displayed. When many groups are present, their names may + be truncated, but the full name be shown in a tooltip when the mouse + hovers over their checkbox.

Feature colour schemes and filters +

+ The table in the middle lists all the feature types in the currently + selected groups, along with their display style, any configured + filters, and a tickbox indicating whether the type is enabled for + display.

Features may be highlighted with either a single colour or a feature colourscheme based on + either the scores associated with that feature or from the feature's + description (e.g. to distinguish different names associated with a + DOMAIN feature).The colour used for a feature can + be changed by clicking on its colour box. To configure the shading + style or filter for a feature, click its configuration box. +

+ Feature settings pop-up menu
Right-click + on a feature to open a pop-up menu that allows you to +

Hide, show and select columns containing that feature
Sort the alignment or current selection according to count or score for that feature + type (see below)

+ +

+ Transparency and Feature Ordering +

Sequence features represent a variety of different types of + positional annotation, and often overlap. For example, a metal binding + site feature may be attached to one position along a stretch of + sequence marked with a secondary structure feature.

+ The ordering of the sequence features in the dialog box list is the + order used by Jalview for rendering sequence features. A feature at + the bottom of the list is rendered below a feature higher + up in the list.
You can change + the order of a feature by dragging it up and down the list with + the mouse. +

+ Use the Optimise order button to adjust the + feature render ordering to place features that on average cover shorter regions + of sequence above features annotating longer regions. +

+ The transparency slider controls + the visibility of features rendered below other features. Reducing + the transparency will mean that features at the top of the list can + obscure features lower down, and increasing it allows the user to + 'see through' the upper layers of a set of features. +

- Select View→Feature Settings... menu entry in - an alignment window to open the feature settings dialog box, which - allows you to precisely control the presence and appearance of - sequence features for the current alignment. + You can save all features, with their + current colours and visibility in a Jalview format file.

- -

- Sequence Feature Settings for the Jalview Application -

- The top section of the dialog box lists all the sequence feature - groups, along with a tickbox for each that controls whether its - features are displayed. The table in the middle lists all the - features in the currently selected groups, along with their display - style and whether they are currently being displayed (only the - ticked features and groups are displayed). You - can change the colour or shading style used for a feature in the - associated alignment by clicking on its colour box. + Selecting alignment + columns by feature

- Selecting - alignment columns by feature
Double-clicking - a feature type in the Feature Settings dialog - allows you to select columns in the alignment that contain (or do - not contain) features of that type. If a region of the alignment is - currently selected, then only features in the current selection will - be searched. The following keys affect the way in which selections - are made: + Double-clicking a feature type in the Feature + Settings dialog allows you to select columns in the alignment that + contain (or do not contain) features of that type that are currently visible (e.g. not filtered out or excluded due to an applied colour scheme threshold). If a region of the + alignment is currently selected, then only features in the current + selection will be searched. The following keys affect the way in which + selections are made: +

Hold down Alt to select columns not containing features of a particular type. @@ -71,24 +122,8 @@ Select columns by feature was added in Jalview 2.8.1

- Feature settings pop-up menu
Right-click - on a feature to open a pop-up menu that allows you to -
- Hide, show and select columns containing that feature
- Sort the alignment or current selection using that feature - type (see below)
- Toggle the type of colouring used for the feature
-
- Features may be highlighted with either a single colour or a feature colourscheme based on - either the scores associated with that feature or from the feature's - description (e.g. to distinguish different names associated with a - DOMAIN feature). -
-
Ordering alignment by - features
The 'Seq Sort by Score' and 'Seq Sort by + features
The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the alignment based on the average score or total number of currently active features and groups on each sequence. To order the alignment using a specific feature type, use @@ -97,36 +132,5 @@ introduced in Jalview 2.5
-
- Transparency and Feature Ordering -
-
It is important to realise that sequence features are often not - distinct and often overlap (for example, a metal binding site - feature may be attached to one position along a stretch of sequence - marked with a secondary structure feature).
-
- The ordering of the sequence features in the dialog box list is the - order used by Jalview for rendering sequence features. A feature at - the bottom of the list is rendered below a feature higher - up in the list.
You can change - the order of a feature by dragging it up and down the list with - the mouse (not applet). -
-
- The Optimise order button (currently only - available in the application) will re-order the feature render - ordering based on the average length of each feature type. -
-
- The transparency slider setting controls - the visibility of features rendered below other features. Reducing - the transparency will mean that features at the top of the list can - obscure features lower down, and increasing it allows the user to - 'see through' the upper layers of a set of features. -
-
- You can save all features, with their - current colours and visibility in a Jalview format file. -