Lookup tables

Adrian

• October 31, 2016 09:54

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

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  Richard Moir

  • October 31, 2016 21:03

  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.

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  Adrian

  • October 31, 2016 23:38

  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

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  Adrian

  • October 31, 2016 23:56

  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

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  Richard Moir

  • November 01, 2016 01:37

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

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  Adrian

  • November 01, 2016 02:08

  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,

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  Richard Moir

  • November 01, 2016 19:13

  Try this: https://assets.geneious.com/developer/core-src/OpenColors.java

  We use a variable width font and center it ourselves to get the best result but that is a lot of work. More than you'd expect, thanks to the quirks of Java 2D. I would recommend sticking with a monospaced font.

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