Convert2Charge
, Convert2Hydrophobicity
, Convert2NormalizedVanDerWaalsVolume
, Convert2Polarity
, Convert2Polarizability
, Convert2SecondaryStructure
, Convert2SolventAccessibility
public abstract class Convertor
extends java.lang.Object
Modifier and Type | Field | 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. The seven different attributes are |
static char |
group2 |
|
static char |
group3 |
|
static char |
unknownGroup |
Constructor | Description |
---|---|
Convertor() |
Modifier and Type | Method | Description |
---|---|---|
abstract char |
convert(char aminoAcid) |
Returns the grouping of the amino acid character.
|
java.lang.String |
convert(ProteinSequence sequence) |
Returns the converted sequence.
|
abstract java.lang.String |
getAttribute() |
Return the attribute of the grouping
|
abstract java.lang.String[] |
getGrouping() |
Returns the groupings of the attribute
|
public static final char group1
public static final char group2
public static final char group3
public static final char unknownGroup
public abstract char convert(char aminoAcid)
aminoAcid
- an amino acid character preferably of non-ambiguous characterspublic abstract java.lang.String[] getGrouping()
public abstract java.lang.String getAttribute()
public java.lang.String convert(ProteinSequence sequence)
sequence
- a protein sequence consisting of preferably non-ambiguous characters only