io.github.msdk.datamodel

Class SimpleIonAnnotation

java.lang.Object

io.github.msdk.datamodel.SimpleIonAnnotation

All Implemented Interfaces:

IonAnnotation

Direct Known Subclasses:

SiriusIonAnnotation

public class SimpleIonAnnotation
extends Object
implements IonAnnotation

Simple IonAnnotation implementation;

Constructor Summary

Constructors

Constructor and Description
SimpleIonAnnotation()

Method Summary

Modifier and Type	Method and Description
URL	getAccessionURL() getAccessionURL.
String	getAnnotationId() getAnnotationId.
org.openscience.cdk.interfaces.IAtomContainer	getChemicalStructure() getChemicalStructure.
String	getDatabase() getDatabase
String	getDescription() getDescription.
Double	getExpectedMz() getExpectedMz.
Float	getExpectedRetentionTime() getRetentionTime.
org.openscience.cdk.interfaces.IMolecularFormula	getFormula() Chemical formula annotation should include charge, e.g.
String	getIdentificationMethod() getIdentificationMethod.
String	getInchiKey() getInchiKey
IonType	getIonType() getIonType.
Integer	getReliability() Returns the reliability of the identification.
String	getSpectraRef() getSpectraRef
void	setAccessionURL(URL accessionURL)
void	setAnnotationId(String annotationId)
void	setChemicalStructure(org.openscience.cdk.interfaces.IAtomContainer chemicalStructure)
void	setDatabase(String database)
void	setDescription(String description)
void	setExpectedMz(Double expectedMz)
void	setExpectedRetentionTime(Float expectedRT)
void	setFormula(org.openscience.cdk.interfaces.IMolecularFormula formula)
void	setIdentificationMethod(String identificationMethod)
void	setInchiKey(String inchiKey)
void	setIonType(IonType ionType)
void	setReliability(Integer reliability)
void	setSpectraRef(String spectraRef)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleIonAnnotation

public SimpleIonAnnotation()

Method Detail

getChemicalStructure

@Nullable
public org.openscience.cdk.interfaces.IAtomContainer getChemicalStructure()

getChemicalStructure.

Specified by:

getChemicalStructure in interface IonAnnotation

Returns:

Chemical structure of this annotation.

setChemicalStructure

public void setChemicalStructure(@Nullable
                                 org.openscience.cdk.interfaces.IAtomContainer chemicalStructure)

Parameters:

chemicalStructure - a IAtomContainer object.

getFormula

@Nullable
public org.openscience.cdk.interfaces.IMolecularFormula getFormula()

Chemical formula annotation should include charge, e.g. C6H13O6+ or [C34H58N5O35P3]2-.

Specified by:

getFormula in interface IonAnnotation

Returns:

Chemical formula of this annotation.

setFormula

public void setFormula(@Nullable
                       org.openscience.cdk.interfaces.IMolecularFormula formula)

Parameters:

formula - a IMolecularFormula object.

getIonType

@Nullable
public IonType getIonType()

getIonType.

Specified by:

getIonType in interface IonAnnotation

Returns:

Ionization type for this annotation.

setIonType

public void setIonType(@Nullable
                       IonType ionType)

Parameters:

ionType - a IonType object.

getExpectedMz

@Nullable
public Double getExpectedMz()

getExpectedMz.

Specified by:

getExpectedMz in interface IonAnnotation

Returns:

Expected m/z value of this annotation.

setExpectedMz

public void setExpectedMz(@Nullable
                          Double expectedMz)

Parameters:

expectedMz - a Double object.

getDescription

@Nullable
public String getDescription()

getDescription.

Specified by:

getDescription in interface IonAnnotation

Returns:

Textual description of this annotation.

setDescription

public void setDescription(@Nullable
                           String description)

Parameters:

description - a String object.

getIdentificationMethod

@Nullable
public String getIdentificationMethod()

getIdentificationMethod.

Specified by:

getIdentificationMethod in interface IonAnnotation

Returns:

Identification method (e.g. database name) of this annotation.

setIdentificationMethod

public void setIdentificationMethod(@Nullable
                                    String identificationMethod)

Parameters:

identificationMethod - a String object.

getAnnotationId

@Nullable
public String getAnnotationId()

getAnnotationId.

Specified by:

getAnnotationId in interface IonAnnotation

Returns:

a String object.

setAnnotationId

public void setAnnotationId(@Nullable
                            String annotationId)

Parameters:

annotationId - a String object.

getAccessionURL

@Nullable
public URL getAccessionURL()

getAccessionURL.

Specified by:

getAccessionURL in interface IonAnnotation

Returns:

Accession URL for a database, if this annotation comes from a database.

setAccessionURL

public void setAccessionURL(@Nullable
                            URL accessionURL)

Parameters:

accessionURL - a URL object.

getExpectedRetentionTime

@Nullable
public Float getExpectedRetentionTime()

getRetentionTime.

Specified by:

getExpectedRetentionTime in interface IonAnnotation

Returns:

RT

setExpectedRetentionTime

public void setExpectedRetentionTime(@Nullable
                                     Float expectedRT)

Parameters:

expectedRT - a Float object.

getInchiKey

@Nullable
public String getInchiKey()

getInchiKey

Specified by:

getInchiKey in interface IonAnnotation

Returns:

InChI key of this annotation.

setInchiKey

public void setInchiKey(@Nullable
                        String inchiKey)

Parameters:

inchiKey - a String object.

getDatabase

@Nullable
public String getDatabase()

getDatabase

Specified by:

getDatabase in interface IonAnnotation

Returns:

Textual database description of this annotation.

setDatabase

public void setDatabase(@Nullable
                        String database)

Parameters:

database - a String object.

getSpectraRef

@Nullable
public String getSpectraRef()

getSpectraRef

Specified by:

getSpectraRef in interface IonAnnotation

Returns:

Textual reference to a spectrum in a spectrum file for this annotation.

setSpectraRef

public void setSpectraRef(@Nullable
                          String spectraRef)

Parameters:

spectraRef - a String object.

getReliability

@Nullable
public Integer getReliability()

Returns the reliability of the identification. This must be reported as an integer between 1-4: 1: Identified metabolites 2: Putatively annotated compounds 3: Putatively characterized compound classes 4: Unknown compounds

Specified by:

getReliability in interface IonAnnotation

Returns:

The reliability of the ion annotation identification.

setReliability

public void setReliability(@Nullable
                           Integer reliability)

Parameters:

reliability - a Integer object.

toString

public String toString()

Overrides:

toString in class Object