From: jprocter Date: Thu, 15 Sep 2011 13:18:25 +0000 (+0100) Subject: documentation for JAL-234 X-Git-Tag: Release_2_7~41 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0e6634756268f473daa6dc76ddd21890baa88820;p=jalview.git documentation for JAL-234 --- diff --git a/help/html/colourSchemes/annotationColourSetting.jpg b/help/html/colourSchemes/annotationColourSetting.jpg old mode 100755 new mode 100644 index 7ca9acb..f3fbab6 Binary files a/help/html/colourSchemes/annotationColourSetting.jpg and b/help/html/colourSchemes/annotationColourSetting.jpg differ diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html index 3db00dd..e8c87e1 100755 --- a/help/html/colourSchemes/annotationColouring.html +++ b/help/html/colourSchemes/annotationColouring.html @@ -20,27 +20,42 @@

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.

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.
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 +
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 application's user + preferences.) +
+
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.

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.

+ +

diff --git a/help/html/colourSchemes/annotationColours.jpg b/help/html/colourSchemes/annotationColours.jpg old mode 100755 new mode 100644 index 36d100e..5fcfa49 Binary files a/help/html/colourSchemes/annotationColours.jpg and b/help/html/colourSchemes/annotationColours.jpg differ