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 and Description
static 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.
static char	group2
static char	group3
static char	unknownGroup

Constructor Summary

Constructors

Constructor and Description
Convertor()

Method Summary

Modifier and Type	Method and 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 Detail

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:

Constant Field Values

group2

public static final char group2

See Also:

Constant Field Values

group3

public static final char group3

See Also:

Constant Field Values

unknownGroup

public static final char unknownGroup

See Also:

Constant Field Values

Constructor Detail

Convertor

public Convertor()

Method Detail

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