Package pl.poznan.put.pdb.analysis

Class ImmutableDefaultCifModel.Builder

java.lang.Object

pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder

Enclosing class:

ImmutableDefaultCifModel

@NotThreadSafe
public static final class ImmutableDefaultCifModel.Builder
extends Object

Builds instances of type ImmutableDefaultCifModel. Initialize attributes and then invoke the build() method to create an immutable instance.

Builder is not thread-safe and generally should not be stored in a field or collection, but instead used immediately to create instances.

Method Summary

Modifier and Type	Method	Description
ImmutableDefaultCifModel.Builder	addAllAtoms(Iterable<? extends PdbAtomLine> elements)	Adds elements to atoms list.
ImmutableDefaultCifModel.Builder	addAllBasePairs(Iterable<? extends QuantifiedBasePair> elements)	Adds elements to basePairs list.
ImmutableDefaultCifModel.Builder	addAllChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Adds elements to chainTerminatedAfter set.
ImmutableDefaultCifModel.Builder	addAllMissingResidues(Iterable<? extends PdbRemark465Line> elements)	Adds elements to missingResidues list.
ImmutableDefaultCifModel.Builder	addAllModifiedResidues(Iterable<? extends PdbModresLine> elements)	Adds elements to modifiedResidues list.
ImmutableDefaultCifModel.Builder	addAtoms(PdbAtomLine element)	Adds one element to atoms list.
ImmutableDefaultCifModel.Builder	addAtoms(PdbAtomLine... elements)	Adds elements to atoms list.
ImmutableDefaultCifModel.Builder	addBasePairs(QuantifiedBasePair element)	Adds one element to basePairs list.
ImmutableDefaultCifModel.Builder	addBasePairs(QuantifiedBasePair... elements)	Adds elements to basePairs list.
ImmutableDefaultCifModel.Builder	addChainTerminatedAfter(PdbResidueIdentifier element)	Adds one element to chainTerminatedAfter set.
ImmutableDefaultCifModel.Builder	addChainTerminatedAfter(PdbResidueIdentifier... elements)	Adds elements to chainTerminatedAfter set.
ImmutableDefaultCifModel.Builder	addMissingResidues(PdbRemark465Line element)	Adds one element to missingResidues list.
ImmutableDefaultCifModel.Builder	addMissingResidues(PdbRemark465Line... elements)	Adds elements to missingResidues list.
ImmutableDefaultCifModel.Builder	addModifiedResidues(PdbModresLine element)	Adds one element to modifiedResidues list.
ImmutableDefaultCifModel.Builder	addModifiedResidues(PdbModresLine... elements)	Adds elements to modifiedResidues list.
ImmutableDefaultCifModel.Builder	atoms(Iterable<? extends PdbAtomLine> elements)	Sets or replaces all elements for atoms list.
ImmutableDefaultCifModel.Builder	basePairs(Iterable<? extends QuantifiedBasePair> elements)	Sets or replaces all elements for basePairs list.
ImmutableDefaultCifModel	build()	Builds a new ImmutableDefaultCifModel.
ImmutableDefaultCifModel.Builder	chainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Sets or replaces all elements for chainTerminatedAfter set.
ImmutableDefaultCifModel.Builder	experimentalData(PdbExpdtaLine experimentalData)	Initializes the value for the experimentalData attribute.
ImmutableDefaultCifModel.Builder	from(CifModel instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.CifModel instance.
ImmutableDefaultCifModel.Builder	from(DefaultCifModel instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.DefaultCifModel instance.
ImmutableDefaultCifModel.Builder	from(PdbModel instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbModel instance.
ImmutableDefaultCifModel.Builder	header(PdbHeaderLine header)	Initializes the value for the header attribute.
ImmutableDefaultCifModel.Builder	missingResidues(Iterable<? extends PdbRemark465Line> elements)	Sets or replaces all elements for missingResidues list.
ImmutableDefaultCifModel.Builder	modelNumber(int modelNumber)	Initializes the value for the modelNumber attribute.
ImmutableDefaultCifModel.Builder	modifiedResidues(Iterable<? extends PdbModresLine> elements)	Sets or replaces all elements for modifiedResidues list.
ImmutableDefaultCifModel.Builder	resolution(PdbRemark2Line resolution)	Initializes the value for the resolution attribute.
ImmutableDefaultCifModel.Builder	title(String title)	Initializes the value for the title attribute.

Methods inherited from class java.lang.Object

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

Method Detail

from

public final ImmutableDefaultCifModel.Builder from(PdbModel instance)

Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbModel instance.

Parameters:

instance - The instance from which to copy values

Returns:

this builder for use in a chained invocation

from

public final ImmutableDefaultCifModel.Builder from(CifModel instance)

Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.CifModel instance.

Parameters:

instance - The instance from which to copy values

Returns:

this builder for use in a chained invocation

from

public final ImmutableDefaultCifModel.Builder from(DefaultCifModel instance)

Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.DefaultCifModel instance.

Parameters:

instance - The instance from which to copy values

Returns:

this builder for use in a chained invocation

header

public final ImmutableDefaultCifModel.Builder header(PdbHeaderLine header)

Initializes the value for the header attribute.

Parameters:

header - The value for header

Returns:

this builder for use in a chained invocation

experimentalData

public final ImmutableDefaultCifModel.Builder experimentalData(PdbExpdtaLine experimentalData)

Initializes the value for the experimentalData attribute.

Parameters:

experimentalData - The value for experimentalData

Returns:

this builder for use in a chained invocation

resolution

public final ImmutableDefaultCifModel.Builder resolution(PdbRemark2Line resolution)

Initializes the value for the resolution attribute.

Parameters:

resolution - The value for resolution

Returns:

this builder for use in a chained invocation

modelNumber

public final ImmutableDefaultCifModel.Builder modelNumber(int modelNumber)

Initializes the value for the modelNumber attribute.

Parameters:

modelNumber - The value for modelNumber

Returns:

this builder for use in a chained invocation

addAtoms

public final ImmutableDefaultCifModel.Builder addAtoms(PdbAtomLine element)

Adds one element to atoms list.

Parameters:

element - A atoms element

Returns:

this builder for use in a chained invocation

addAtoms

public final ImmutableDefaultCifModel.Builder addAtoms(PdbAtomLine... elements)

Adds elements to atoms list.

Parameters:

elements - An array of atoms elements

Returns:

this builder for use in a chained invocation

atoms

public final ImmutableDefaultCifModel.Builder atoms(Iterable<? extends PdbAtomLine> elements)

Sets or replaces all elements for atoms list.

Parameters:

elements - An iterable of atoms elements

Returns:

this builder for use in a chained invocation

addAllAtoms

public final ImmutableDefaultCifModel.Builder addAllAtoms(Iterable<? extends PdbAtomLine> elements)

Adds elements to atoms list.

Parameters:

elements - An iterable of atoms elements

Returns:

this builder for use in a chained invocation

addModifiedResidues

public final ImmutableDefaultCifModel.Builder addModifiedResidues(PdbModresLine element)

Adds one element to modifiedResidues list.

Parameters:

element - A modifiedResidues element

Returns:

this builder for use in a chained invocation

addModifiedResidues

public final ImmutableDefaultCifModel.Builder addModifiedResidues(PdbModresLine... elements)

Adds elements to modifiedResidues list.

Parameters:

elements - An array of modifiedResidues elements

Returns:

this builder for use in a chained invocation

modifiedResidues

public final ImmutableDefaultCifModel.Builder modifiedResidues(Iterable<? extends PdbModresLine> elements)

Sets or replaces all elements for modifiedResidues list.

Parameters:

elements - An iterable of modifiedResidues elements

Returns:

this builder for use in a chained invocation

addAllModifiedResidues

public final ImmutableDefaultCifModel.Builder addAllModifiedResidues(Iterable<? extends PdbModresLine> elements)

Adds elements to modifiedResidues list.

Parameters:

elements - An iterable of modifiedResidues elements

Returns:

this builder for use in a chained invocation

addMissingResidues

public final ImmutableDefaultCifModel.Builder addMissingResidues(PdbRemark465Line element)

Adds one element to missingResidues list.

Parameters:

element - A missingResidues element

Returns:

this builder for use in a chained invocation

addMissingResidues

public final ImmutableDefaultCifModel.Builder addMissingResidues(PdbRemark465Line... elements)

Adds elements to missingResidues list.

Parameters:

elements - An array of missingResidues elements

Returns:

this builder for use in a chained invocation

missingResidues

public final ImmutableDefaultCifModel.Builder missingResidues(Iterable<? extends PdbRemark465Line> elements)

Sets or replaces all elements for missingResidues list.

Parameters:

elements - An iterable of missingResidues elements

Returns:

this builder for use in a chained invocation

addAllMissingResidues

public final ImmutableDefaultCifModel.Builder addAllMissingResidues(Iterable<? extends PdbRemark465Line> elements)

Adds elements to missingResidues list.

Parameters:

elements - An iterable of missingResidues elements

Returns:

this builder for use in a chained invocation

title

public final ImmutableDefaultCifModel.Builder title(String title)

Initializes the value for the title attribute.

Parameters:

title - The value for title

Returns:

this builder for use in a chained invocation

addChainTerminatedAfter

public final ImmutableDefaultCifModel.Builder addChainTerminatedAfter(PdbResidueIdentifier element)

Adds one element to chainTerminatedAfter set.

Parameters:

element - A chainTerminatedAfter element

Returns:

this builder for use in a chained invocation

addChainTerminatedAfter

public final ImmutableDefaultCifModel.Builder addChainTerminatedAfter(PdbResidueIdentifier... elements)

Adds elements to chainTerminatedAfter set.

Parameters:

elements - An array of chainTerminatedAfter elements

Returns:

this builder for use in a chained invocation

chainTerminatedAfter

public final ImmutableDefaultCifModel.Builder chainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)

Sets or replaces all elements for chainTerminatedAfter set.

Parameters:

elements - An iterable of chainTerminatedAfter elements

Returns:

this builder for use in a chained invocation

addAllChainTerminatedAfter

public final ImmutableDefaultCifModel.Builder addAllChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)

Adds elements to chainTerminatedAfter set.

Parameters:

elements - An iterable of chainTerminatedAfter elements

Returns:

this builder for use in a chained invocation

addBasePairs

public final ImmutableDefaultCifModel.Builder addBasePairs(QuantifiedBasePair element)

Adds one element to basePairs list.

Parameters:

element - A basePairs element

Returns:

this builder for use in a chained invocation

addBasePairs

public final ImmutableDefaultCifModel.Builder addBasePairs(QuantifiedBasePair... elements)

Adds elements to basePairs list.

Parameters:

elements - An array of basePairs elements

Returns:

this builder for use in a chained invocation

basePairs

public final ImmutableDefaultCifModel.Builder basePairs(Iterable<? extends QuantifiedBasePair> elements)

Sets or replaces all elements for basePairs list.

Parameters:

elements - An iterable of basePairs elements

Returns:

this builder for use in a chained invocation

addAllBasePairs

public final ImmutableDefaultCifModel.Builder addAllBasePairs(Iterable<? extends QuantifiedBasePair> elements)

Adds elements to basePairs list.

Parameters:

elements - An iterable of basePairs elements

Returns:

this builder for use in a chained invocation

build

public ImmutableDefaultCifModel build()

Builds a new ImmutableDefaultCifModel.

Returns:

An immutable instance of DefaultCifModel

Throws:

IllegalStateException - if any required attributes are missing