public abstract class Convertor extends Object
Modifier and Type | Field and Description |
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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 and Description |
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Convertor() |
Modifier and Type | Method and Description |
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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
|
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 String[] getGrouping()
public abstract String getAttribute()
public String convert(ProteinSequence sequence)
sequence
- a protein sequence consisting of preferably non-ambiguous characters onlyCopyright © 2000–2016 BioJava. All rights reserved.