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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+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
+
+