de.bioforscher.singa.structure.parser.pfam

Class PfamParser.Builder

java.lang.Object

de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder

All Implemented Interfaces:

PfamParser.ChainStep, PfamParser.DomainStep, PfamParser.FamilyStep, PfamParser.VersionStep

Enclosing class:

PfamParser

public static class PfamParser.Builder
extends Object
implements PfamParser.VersionStep, PfamParser.FamilyStep, PfamParser.ChainStep, PfamParser.DomainStep

Field Summary

Fields

Modifier and Type	Field and Description
StructureParserOptions	structureParserOptions

Constructor Summary

Constructors

Constructor and Description
Builder()

Method Summary

Modifier and Type	Method and Description
PfamParser.DomainStep	all() Parse all chains annotated in Pfam.
PfamParser.DomainStep	chainList(Path chainListPath) Parse all chains annotated in Pfam and listed in the given chain list.
PfamParser.DomainStep	chainList(Path chainListPath, String chainListSeparator) Parse all chains annotated in Pfam and listed in the given chain list with the custom separator.
List<Chain>	chains() Parse all chains carrying one Pfam domain with the desired Pfam-ID.
List<List<LeafSubstructure<?>>>	domains() Parse only the domains.
PfamParser.ChainStep	pfamIdentifier(String pfamIdentifier) The Pfam-ID for which data should be fetched.
PfamParser.DomainStep	structureParserOptions(StructureParserOptions structureParserOptions) Specify StructureParserOptions used to parse the structures.
PfamParser.FamilyStep	version(PfamParser.PfamVersion version) The version of the Pfam database that should be used.

Methods inherited from class java.lang.Object

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

Field Detail

structureParserOptions

public StructureParserOptions structureParserOptions

Constructor Detail

Builder

public Builder()

Method Detail

version

public PfamParser.FamilyStep version(PfamParser.PfamVersion version)

Description copied from interface: PfamParser.VersionStep

The version of the Pfam database that should be used.

Specified by:

version in interface PfamParser.VersionStep

Parameters:

version - The PfamParser.PfamVersion.

Returns:

The PfamParser.FamilyStep to choose the Pfam-ID.

pfamIdentifier

public PfamParser.ChainStep pfamIdentifier(String pfamIdentifier)

Description copied from interface: PfamParser.FamilyStep

The Pfam-ID for which data should be fetched.

Specified by:

pfamIdentifier in interface PfamParser.FamilyStep

Parameters:

pfamIdentifier - The Pfam-ID.

Returns:

ChainStep to limit selection of chains.

all

public PfamParser.DomainStep all()

Description copied from interface: PfamParser.ChainStep

Parse all chains annotated in Pfam.

Specified by:

all in interface PfamParser.ChainStep

Returns:

The PfamParser.DomainStep to decide if domains or chains should be parsed.

chainList

public PfamParser.DomainStep chainList(Path chainListPath)

Description copied from interface: PfamParser.ChainStep

Parse all chains annotated in Pfam and listed in the given chain list. Default separator is "\t".

Specified by:

chainList in interface PfamParser.ChainStep

Parameters:

chainListPath - The Path to the given chain list.

Returns:

The PfamParser.DomainStep to decide if domains or chains should be parsed.

chainList

public PfamParser.DomainStep chainList(Path chainListPath,
                                       String chainListSeparator)

Description copied from interface: PfamParser.ChainStep

Parse all chains annotated in Pfam and listed in the given chain list with the custom separator.

Specified by:

chainList in interface PfamParser.ChainStep

Parameters:

chainListPath - The Path to the given chain list.

chainListSeparator - The separator used in the chain list.

Returns:

The PfamParser.DomainStep to decide if domains or chains should be parsed.

structureParserOptions

public PfamParser.DomainStep structureParserOptions(StructureParserOptions structureParserOptions)

Description copied from interface: PfamParser.DomainStep

Specify StructureParserOptions used to parse the structures.

Specified by:

structureParserOptions in interface PfamParser.DomainStep

Parameters:

structureParserOptions - The StructureParserOptions to be used

Returns:

The PfamParser.DomainStep to decide if domains or chains should be parsed.

domains

public List<List<LeafSubstructure<?>>> domains()

Description copied from interface: PfamParser.DomainStep

Parse only the domains.

Specified by:

domains in interface PfamParser.DomainStep

Returns:

Pfam domains.

chains

public List<Chain> chains()

Description copied from interface: PfamParser.DomainStep

Parse all chains carrying one Pfam domain with the desired Pfam-ID.

Specified by:

chains in interface PfamParser.DomainStep

Returns:

Chains with Pfam domains.