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Lookup tables

Where do we find documentation on how to access the lookup tables:

Some that are needed:

lookup from DNA RNA and protein

Ambiguity codes for a given set of nucleotides

Default Colors for protein.

I could copy them in an open source project but that sounds like redoing the work.

 

Thank you

Adrian

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Most of this is in jebl which is included with the development kit.

It sounds like you need the classes Nucleotides, AminoAcids and GeneticCode in package jebl.evolution.sequences.

The color schemes aren't in the public API unfortunately. If you want, I'll be happy to send you java files for any color schemes you need.

Richard Moir 0 votes
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Hi Richard,

Thank you for the info. I hope those will do. I would appreciate the java files for color schemes as it would be tedious to retype those from scratch.

 

Cheers

Adrian 0 votes
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Hi Richard,

Thank you for the info. I hope those will do. I would appreciate the java files for color schemes as it would be tedious to retype those from scratch.

 

Cheers

Adrian 0 votes
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From the Colors dropdown in the sequence view, which color scheme(s) would you like the code for?

Richard Moir 0 votes
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for translation ARND (default colors for for Translation), ARND Hydrophobicity and Polarity
for nucleotides default acgt (i guess that includes the ambiguity codes.

 

 

Also I'm wondering if you use Monospaced fonts or just little rectangles with centered non-monospaced letters. My sequence letters  are monospaced to keep the alignment but the rendering is not so nice,

Adrian 0 votes
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