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

Description

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

Builder(ProteinModification copyFrom)

Create a Builder from an existing ProteinModification.
Method Summary

Modifier and Type

Method

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 Details
- 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 Details
- 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.

Class ProteinModificationImpl.Builder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

Builder

Builder

Method Details

setCategory

setOccurrenceType

setCondition

setPdbccId

setPdbccName

setResidId

setResidName

setPsimodId

setPsimodName

setSystematicName

setDescription

addKeyword

addKeywords

setFormula

build