X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=2272503c682ac2f026766eea21a970f952d4cd32;hb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;hp=9275a091077e2153fd7f0a707729e869882ee136;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 9275a09..2272503 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,46 +1,100 @@
-Annotation Colouring
+ * 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.
+ -->
+
+Annotation Colouring
+
- Annotation Colouring
-Jalview 2.08 allows an alignment to be coloured on a per-column basis based
- on any numerical annotation added to that alignment.
-Select "Colour" → "..
- by Annotation" to bring up the Colour by Annotation settings window.
-
-
- - Select which annotation to base the colouring scheme on using the top left
- selection box.
- - If the "Use Original Colours" box is selected, the colouring
- scheme will use the colouring scheme present on the alignment before the Annotation
- Colour Settings window was displayed.
- - The colour scheme can display a colour gradient from a colour representing
- the minimum value in the selected annotation to a colour representing the
- maximum value in the selected annotation. Use the "Min Colour" and
- "Max Colour" to set the colour gradient range.
- - Select whether to colour the alignment above or below an adjustable threshold
- with the selection box center left of the window.
- - Change the threshold value with the slider, or enter the exact value in
- the text box.
-
-
+
+ Annotation Colouring
+
+ Jalview allows the columns of an alignment to be coloured using
+ any numerical annotation rows added to that alignment.
+ Select "Colour"
+ → ".. by Annotation" to bring up the
+ Colour by Annotation settings window.
+
+
+
+
+
+ - Select which annotation to base the colouring scheme on
+ using the top left selection box. Sequence associated alignment
+ annotation are shown with the seuqence's name appended.
If
+ the Per-sequence only tick box is not greyed out,
+ then ticking it will limit the list of available annotation rows
+ to just the labels for those that are sequence associated.
+ Annotation rows on each sequence with the same label (e.g.
+ T-COFFEE scores and protein
+ disorder predictions) will then be used to colour its
+ corresponding positions in the alignment.
Per-sequence
+ associated annotation colouring is currently only available in
+ the Desktop.
+
+ - If the "Use Original Colours" box is selected,
+ the colouring scheme will use the colouring scheme present on the
+ alignment before the Annotation Colour Settings window was
+ displayed.
Please Note: If no
+ colour scheme was applied previously, then the colours for lines
+ and labels at each position in the annotation row will be used,
+ for secondary structure symbols and graphs, this may be black by
+ default, so your alignment will be coloured black.
+
+ - Secondary structure annotation colouring
By
+ default, Jalview will employ the helix or sheet colours to shade
+ sequences and columns by available secondary structure annotation
+ tracks. In the case of RNA, each structure is processed to
+ identify distinct RNA helices and rendered in the same way as the
+ RNA Helices shading scheme.
+ Structure based sequence shading was added in Jalview
+ 2.8.2
+ - The colour scheme can display a colour gradient from a
+ colour representing the minimum value in the selected annotation
+ to a colour representing the maximum value in the selected
+ annotation. Use the "Min Colour" and "Max
+ Colour" to set the colour gradient range.
+
+ - Press the "Defaults" button to reset the
+ minimum and maximum colours to their default settings (these
+ are configured in the applet's parameters or the application's
+ user preferences.).
Default min and max
+ colours were introduced in Jalview 2.7
+
+
+
+ - Select whether to colour the alignment above or below an
+ adjustable threshold with the selection box center left of the
+ window.
+ - Change the threshold value with the slider, or enter the
+ exact value in the text box.
+ - Select the "Threshold is Min/Max" checkbox to
+ assign colours using the thresholded range's minimum and maximum
+ values, otherwise the scale will be defined by the range of values
+ in the annotation row.
+
+
+ 
+