X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Findex.html;h=f7e2050bf12fcebbdeaa3f85fdd67727abbddc97;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hp=e5a9299d474b7151358bb250f19808ffe6a69e0b;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index e5a9299..f7e2050 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -1,21 +1,297 @@ - - - -

Colour schemes

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Jalview allows the user to set a background colour for the whole alignment - and also set the colour of defined groups within the alignment.

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To change the background colour, simply select the colour from the "Colour" - menu.

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To change the colour of a group, right click on any residue within a group - and use the popup menu to define the group colour.

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At the top of the "Colour" menu the tick box "Apply Background - Colour to all groups". This is automatically ticked as default and means - the chosen colour will be applied to all existing groups. If you wish to maintain - the colour scheme for defined groups, make sure you deselect this option before - changing the background colour.

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- - + + + +Colour Schemes + + + +

Colour schemes

+

Jalview allows the user to set a background colour for the whole +alignment view or for each group defined on regions within it.

+

To change the background colour, simply select the colour from +the "Colour" menu.

+

To change the colour of a group, right click on any residue +within a group and use the popup menu to define the group colour.

+

At the top of the "Colour" menu the tick box +"Apply Background Colour to all groups". This is ticked by +default so that a chosen colour scheme will be applied to all existing +groups. If you wish to maintain the colour scheme for defined groups, +make sure you deselect this option before changing the background +colour.

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The "Colour→Colour Text..." entry +opens a dialog box to set a different text colour for light and dark +background, and the intensity threshold for transition between them.

+

The default colour schemes are summarised in the table below: +

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+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ARNDCQEGHILKMFPSTWYVBXZ
Clustal
Zappo
Taylor
Hydrophobicity
Helix Propensity
Strand Propensity
Turn Propensity
Buried Index
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