#-------------------------------------------------------------------------------
# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
#
# This file is part of Jalview.
#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see .
#-------------------------------------------------------------------------------
Sequence feature colour schemes
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).
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