+++ /dev/null
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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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- * Jalview is free software: you can redistribute it and/or
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-<head>
-<title>Alignment Window Menus</title>
-</head>
-
-<body>
- <p>
- <strong>Alignment Window Colour Menu</strong>
- </p>
- <ul>
- <li><strong>Apply Colour To All Groups<br>
- </strong><em>If this is selected, any changes made to the background
- colour will be applied to all currently defined groups.<br>
- </em></li>
- <li><strong><a href="../colourSchemes/textcolour.html">Colour
- Text ...</a></strong><em><br> Opens the Colour Text dialog box to
- set a different text colour for light and dark background, and
- the intensity threshold for transition between them. </em></li>
- <li>Colour Scheme options: <strong>None, ClustalX,
- Blosum62 Score, Percentage Identity, Zappo, Taylor,
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
- Defined<br>
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
- a description of all colour schemes.
- </em><br>
- </li>
- <li><strong>Sequence ID<br></strong><em>Shades
- sequences using their Sequence ID colour. Useful when performing
- <a href="../calculations/treeviewer.html#partitioning">tree
- based subfamily analysis</a>.
- </em></li>
- <li><strong>By Conservation<br>
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
- by Conservation</a>.
- </em><br></li>
- <li><strong>Modify Conservation Threshold<br>
- </strong><em>Use this to display the conservation threshold slider
- window. Useful if the window has been closed, or if the 'by
- conservation' option appears to be doing nothing!</em><br></li>
- <li><strong>Above Identity Threshold<br>
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above
- Percentage Identity</a></em><strong>.<br>
- </strong></li>
- <li><strong>Modify Identity Threshold<br>
- </strong><em>Use this to set the threshold value for colouring above
- Identity. Useful if the window has been closed.<br>
- </em></li>
- <li><strong>By Annotation</strong><br> <em>Colours
- the alignment on a per-column value from a specified annotation.
- See <a href="../colourSchemes/annotationColouring.html">Annotation
- Colouring</a>.
- </em><br></li>
- <li><strong>By RNA Helices</strong><br> <em>Colours
- the helices of an RNA alignment loaded from a Stockholm file.
- See <a href="../colourSchemes/rnahelicesColouring.html">RNA
- Helices Colouring</a>.
- </em><br></li>
- </ul>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff