Package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic

Class AASequenceFeature

java.lang.Object

com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature

All Implemented Interfaces:

Ms2pipFeature, SingleAAPropertyFeature

Direct Known Subclasses:

ComplementaryIonAminoAcidFeature, ForwardIonAminoAcidFeature, PeptideAminoAcidFeature

public abstract class AASequenceFeature
extends Object
implements Ms2pipFeature, SingleAAPropertyFeature

Feature based on the amino acid properties of a sequence.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	AASequenceFeature.Function	The different functions implemented to compare the amino acid features.

Field Summary

Fields

Modifier and Type	Field	Description
protected AminoAcid.Property	aminoAcidProperty	The property of the amino acids to consider.
protected AASequenceFeature.Function	function	The function used to compare the amino acid properties.

Fields inherited from interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature

implementations

Constructor Summary

Constructors

Constructor	Description
AASequenceFeature()	Empty default constructor

Method Summary

Modifier and Type	Method	Description
AminoAcid.Property	getAminoAcidProperty()	Returns the amino acid property to consider.
AASequenceFeature.Function	getFunction()	Returns the function used to compare the amino acid properties.
void	setAminoAcidProperty(AminoAcid.Property aminoAcidProperty)	Sets the amino acid property to consider.
void	setFunction(AASequenceFeature.Function function)	Sets the function used to compare the amino acid properties.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature

getCategory, getDescription, getIndex

Field Details

function

protected AASequenceFeature.Function function

The function used to compare the amino acid properties.

aminoAcidProperty

protected AminoAcid.Property aminoAcidProperty

The property of the amino acids to consider.

Constructor Details

AASequenceFeature

public AASequenceFeature()

Empty default constructor

Method Details

getFunction

public AASequenceFeature.Function getFunction()

Returns the function used to compare the amino acid properties.

Returns:

the function used to compare the amino acid properties

setFunction

public void setFunction(AASequenceFeature.Function function)

Sets the function used to compare the amino acid properties.

Parameters:

function - the function used to compare the amino acid properties

getAminoAcidProperty

public AminoAcid.Property getAminoAcidProperty()

Description copied from interface: SingleAAPropertyFeature

Returns the amino acid property to consider.

Specified by:

getAminoAcidProperty in interface SingleAAPropertyFeature

Returns:

the amino acid property to consider

setAminoAcidProperty

public void setAminoAcidProperty(AminoAcid.Property aminoAcidProperty)

Description copied from interface: SingleAAPropertyFeature

Sets the amino acid property to consider.

Specified by:

setAminoAcidProperty in interface SingleAAPropertyFeature

Parameters:

aminoAcidProperty - the amino acid property to consider