org.biojava.nbio.protmod

Class ProteinModificationImpl.Builder

java.lang.Object

org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Enclosing class:

ProteinModificationImpl

public static class ProteinModificationImpl.Builder
extends Object

Uses Builder pattern to build a ProteinModification.

Constructor Summary

Constructors

Constructor and Description
Builder(ProteinModification copyFrom) Create a Builder from an existing ProteinModification.
Builder(String id, ModificationCategory cat, ModificationOccurrenceType occType, ModificationCondition condition)

Method Summary

Modifier and Type	Method and Description
ProteinModificationImpl.Builder	addKeyword(String keyword) Add a keyword associate with the PTM.
ProteinModificationImpl.Builder	addKeywords(Collection<String> keywords)
ProteinModificationImpl	build()
ProteinModificationImpl.Builder	setCategory(ModificationCategory cat)
ProteinModificationImpl.Builder	setCondition(ModificationCondition condition)
ProteinModificationImpl.Builder	setDescription(String description)
ProteinModificationImpl.Builder	setFormula(String formula) Set the residue formula.
ProteinModificationImpl.Builder	setOccurrenceType(ModificationOccurrenceType occType)
ProteinModificationImpl.Builder	setPdbccId(String pdbccId) Set the Protein Data Bank Chemical Component ID.
ProteinModificationImpl.Builder	setPdbccName(String pdbccName) Set the Protein Data Bank Chemical Component name.
ProteinModificationImpl.Builder	setPsimodId(String psimodId) Set the PSI-MOD ID.
ProteinModificationImpl.Builder	setPsimodName(String psimodName) Set the PSI-MOD name.
ProteinModificationImpl.Builder	setResidId(String residId) Set the RESID ID.
ProteinModificationImpl.Builder	setResidName(String residName) Set the RESID name.
ProteinModificationImpl.Builder	setSystematicName(String sysName) Set the systematic name.

Methods inherited from class java.lang.Object

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

Constructor Detail

Builder

public Builder(String id,
               ModificationCategory cat,
               ModificationOccurrenceType occType,
               ModificationCondition condition)

Parameters:

id -

cat -

occType -

condition -

Builder

public Builder(ProteinModification copyFrom)

Create a Builder from an existing ProteinModification.

Parameters:

copyFrom - the ProteinModification to be copied from.

Method Detail

setCategory

public ProteinModificationImpl.Builder setCategory(ModificationCategory cat)

setOccurrenceType

public ProteinModificationImpl.Builder setOccurrenceType(ModificationOccurrenceType occType)

setCondition

public ProteinModificationImpl.Builder setCondition(ModificationCondition condition)

setPdbccId

public ProteinModificationImpl.Builder setPdbccId(String pdbccId)

Set the Protein Data Bank Chemical Component ID.

Parameters:

pdbccId - Protein Data Bank Chemical Component ID.

Returns:

the same Builder object so you can chain setters.

setPdbccName

public ProteinModificationImpl.Builder setPdbccName(String pdbccName)

Set the Protein Data Bank Chemical Component name.

Parameters:

pdbccName - Protein Data Bank Chemical Component name.

Returns:

the same Builder object so you can chain setters.

setResidId

public ProteinModificationImpl.Builder setResidId(String residId)

Set the RESID ID.

Parameters:

residId - RESID ID.

Returns:

the same Builder object so you can chain setters.

setResidName

public ProteinModificationImpl.Builder setResidName(String residName)

Set the RESID name.

Parameters:

residName - RESID name.

Returns:

the same Builder object so you can chain setters.

setPsimodId

public ProteinModificationImpl.Builder setPsimodId(String psimodId)

Set the PSI-MOD ID.

Parameters:

psimodId - PSI-MOD ID.

Returns:

the same Builder object so you can chain setters.

setPsimodName

public ProteinModificationImpl.Builder setPsimodName(String psimodName)

Set the PSI-MOD name.

Parameters:

psimodName - PSI-MOD name.

Returns:

the same Builder object so you can chain setters.

setSystematicName

public ProteinModificationImpl.Builder setSystematicName(String sysName)

Set the systematic name.

Parameters:

sysName - systematic name.

Returns:

the same Builder object so you can chain setters.

setDescription

public ProteinModificationImpl.Builder setDescription(String description)

Parameters:

description - description of the modification.

Returns:

the same Builder object so you can chain setters.

addKeyword

public ProteinModificationImpl.Builder addKeyword(String keyword)

Add a keyword associate with the PTM.

Parameters:

keyword - a keyword.

Returns:

the same Builder object so you can chain setters.

Throws:

IllegalArgumentException - if the keyword is null.

addKeywords

public ProteinModificationImpl.Builder addKeywords(Collection<String> keywords)

setFormula

public ProteinModificationImpl.Builder setFormula(String formula)

Set the residue formula.

Parameters:

formula - residue formula.

Returns:

the same Builder object so you can chain setters.

build

public ProteinModificationImpl build()

Returns:

build ProteinModification.