|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava3.aaproperties.profeat.convertor.Convertor
public abstract class Convertor
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 |
---|
public static final char group1
public static final char group2
public static final char group3
public static final char unknownGroup
Constructor Detail |
---|
public Convertor()
Method Detail |
---|
public abstract char convert(char aminoAcid)
aminoAcid
- an amino acid character preferably of non-ambiguous characters
public abstract String[] getGrouping()
public abstract String getAttribute()
public String convert(ProteinSequence sequence)
sequence
- a protein sequence consisting of preferably non-ambiguous characters only
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |