Annotation Colouring

From: jprocter Date: Tue, 4 Sep 2012 16:18:03 +0000 (+0100) Subject: JAL-1066 documentation for per-sequence annotation colouring X-Git-Tag: Jalview_2_9~340 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7bc3c614b6d38f11d3f804d5dab2df8dd2bf7204;p=jalview.git JAL-1066 documentation for per-sequence annotation colouring --- diff --git a/help/html/colourSchemes/annotationColourSetting.gif b/help/html/colourSchemes/annotationColourSetting.gif new file mode 100644 index 0000000..c4f719f Binary files /dev/null and b/help/html/colourSchemes/annotationColourSetting.gif differ diff --git a/help/html/colourSchemes/annotationColourSetting.jpg b/help/html/colourSchemes/annotationColourSetting.jpg deleted file mode 100644 index f3fbab6..0000000 Binary files a/help/html/colourSchemes/annotationColourSetting.jpg and /dev/null differ diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html index 9b8c95c..3d40a3e 100755 --- a/help/html/colourSchemes/annotationColouring.html +++ b/help/html/colourSchemes/annotationColouring.html @@ -16,46 +16,63 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> -Annotation Colouring + +Annotation Colouring + -

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 "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.

+ 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.
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 +
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.
- New in Jalview 2.7: 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 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.) + 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.
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.

+ +