org.biojava3.aaproperties.profeat.convertor
Class Convertor

java.lang.Object
  extended by org.biojava3.aaproperties.profeat.convertor.Convertor
Direct Known Subclasses:
Convert2Charge, Convert2Hydrophobicity, Convert2NormalizedVanDerWaalsVolume, Convert2Polarity, Convert2Polarizability, Convert2SecondaryStructure, Convert2SolventAccessibility

public abstract class Convertor
extends Object


Field Summary
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.
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)

static char group2
           
static char group3
           
static char unknownGroup
           
 
Constructor Summary
Convertor()
           
 
Method Summary
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