X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Findex.html;h=450e1aae0921a13ffad9a38b7312ea7f59fbb1bb;hb=2fa2eead4ad3bd86197e691a6a86d9c0425a0174;hp=46a60d9c9bef9db2eb881e27768ae92f9d3a0ac7;hpb=ae78f920ed4f49b98c2af35a4ce2a48b8e3e495b;p=jalview.git diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index 46a60d9..450e1aa 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -1,247 +1,376 @@ - -
-Colour schemes
-Jalview allows the user to set a background colour for the whole alignment - and also set the colour of defined groups within the alignment.
-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 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
+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.
+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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Protein Colour Schemes
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Nucleotide Colour Schemes
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