Package org.biojava.nbio.aaproperties.profeat.convertor

Class Convertor

java.lang.Object
org.biojava.nbio.aaproperties.profeat.convertor.Convertor
Direct Known Subclasses:
Convert2Charge, Convert2Hydrophobicity, Convert2NormalizedVanDerWaalsVolume, Convert2Polarity, Convert2Polarizability, Convert2SecondaryStructure, Convert2SolventAccessibility
public abstract class Convertor extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final char
    group1
    Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
    An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
    The seven different attributes are
    static final char
    group2
     
    static final char
    group3
     
    static final char
    unknownGroup
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    Convertor()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    abstract char
    convert(char aminoAcid)
    Returns the grouping of the amino acid character.
    String
    convert(ProteinSequence sequence)
    Returns the converted sequence.
    abstract String
    getAttribute()
    Return the attribute of the grouping
    abstract String[]
    getGrouping()
    Returns the groupings of the attribute

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • group1

      public static final char group1
      Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
      An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
      The seven different attributes are

      Hydrophobicity (Polar, Neutral, Hydrophobicity)
      Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
      Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
      Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)
      Charge (Positive, Neutral, Negative)
      Secondary structure (Helix, Strand, Coil)
      Solvent accessibility (Buried, Exposed, Intermediate)

      See Also:

    • group2

      public static final char group2
      See Also:

    • group3

      public static final char group3
      See Also:

    • unknownGroup

      public static final char unknownGroup
      See Also:

  • Constructor Details

  • Method Details

    • convert

      public abstract char convert(char aminoAcid)
      Returns the grouping of the amino acid character. The aminoAcid argument is preferably of non-ambiguous characters. Standard amino acids will be converted to '1', '2' or '3' depending on its grouping Non-standard amino acids are simply converted to '0'.
      Parameters:
      aminoAcid - an amino acid character preferably of non-ambiguous characters
      Returns:
      its grouping

    • getGrouping

      public abstract String[] getGrouping()
      Returns the groupings of the attribute
      Returns:
      the groupings of the attribute

    • getAttribute

      public abstract String getAttribute()
      Return the attribute of the grouping
      Returns:
      the attribute of the grouping

    • convert

      public String convert(ProteinSequence sequence)
      Returns the converted sequence. The sequence argument must be a protein sequence consisting of preferably non-ambiguous characters only. Standard amino acids will be converted to '1', '2' or '3' depending on its grouping Non-standard amino acids are simply converted to '0'.
      Parameters:
      sequence - a protein sequence consisting of preferably non-ambiguous characters only
      Returns:
      the converted sequence