X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=2272503c682ac2f026766eea21a970f952d4cd32;hb=dff521a8dde15542be1f65c634a628ee17b6fba3;hp=3b23a4871f15f8e926fa981b97de47119ab6bda3;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html index 3b23a48..2272503 100755 --- a/help/html/colourSchemes/annotationColouring.html +++ b/help/html/colourSchemes/annotationColouring.html @@ -24,73 +24,77 @@ -

- 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.
If the Per-sequence - only tick box is not greyed out, then ticking it will limit the - available annotation rows to just those that are sequence associated - (e.g. T-COFFEE scores and protein disorder - predictions), which will colour each sequence according to its own - per-residue scores.
- Per-sequence associated annotation colouring was introduced - in Jalview 2.8 -
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 -
-

+ Annotation Colouring +

Jalview allows the columns of an alignment to be coloured using + any numerical annotation rows added to that alignment.

→

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.

- -

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.

+ +