X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeatureschemes.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=2cebf12a86bc3a96d7c8289465b1b6444f9b7e23;hpb=247b4f59aad27b654fb55268b55645dc6496f12e;p=jalview.git
diff --git a/help/html/features/featureschemes.html b/help/html/features/featureschemes.html
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@@ -15,59 +15,4 @@
* 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
-
-