X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Findex.html;h=76641019721fd56fa8a639f7d6468a280012c2f2;hb=281aa090976818b388374b7aae780a29a8864b96;hp=e5a9299d474b7151358bb250f19808ffe6a69e0b;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index e5a9299..7664101 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -1,21 +1,403 @@ - - -
-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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