CodonUsage

java.lang.Object

bacnet.datamodel.annotation.CodonUsage

public class CodonUsage extends Object

Tools for calculating codon Usage of amino acid sequences
Codon Usage tables came from : http://www.kazusa.or.jp/codon/

Author:: UIBC

Constructor Summary

Constructors

Constructor

Description

CodonUsage(String codonTableName)

Providing the name of codon Table, it loads the Table and create CodonUsage
Method Summary

Modifier and Type

Method

Description

double

calculate(String sequence)

Calculate Codon usage of a sequence
Providing codonTable has been loaded first

StringColor

colorizeSequence(String sequence)

org.eclipse.swt.graphics.Color

getCodonColor(double value)

double[][]

getValues(String sequence)

static void

verifyCodonUsage()

To verify the codon prediction on EGD-e genome we look at all the genome and count the number of AAA, ATG and CCC codons

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- CodonUsage
  
  public CodonUsage(String codonTableName)
  
  Providing the name of codon Table, it loads the Table and create CodonUsage
  
  Parameters:
  
  codonTableName -
Method Details
- calculate
  
  public double calculate(String sequence)
  
  Calculate Codon usage of a sequence
  Providing codonTable has been loaded first
  Parameters:
  
  sequence -
  
  Returns:
  
  See Also:
  
  CodonUsage
- colorizeSequence
  
  public StringColor colorizeSequence(String sequence)
- getCodonColor
  
  public org.eclipse.swt.graphics.Color getCodonColor(double value)
- getValues
  
  public double[][] getValues(String sequence)
- verifyCodonUsage
  
  public static void verifyCodonUsage()
  
  To verify the codon prediction on EGD-e genome we look at all the genome and count the number of AAA, ATG and CCC codons