de.bioforscher.singa.structure.parser.pfam

Interface PfamParser.ChainStep

All Known Implementing Classes:

PfamParser.Builder

Enclosing class:

PfamParser

public static interface PfamParser.ChainStep

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.

Method Detail

all

PfamParser.DomainStep all()

Parse all chains annotated in Pfam.

Returns:

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

chainList

PfamParser.DomainStep chainList(Path chainListPath)

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

Parameters:

chainListPath - The Path to the given chain list.

Returns:

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

chainList

PfamParser.DomainStep chainList(Path chainListPath,
                                String chainListSeparator)

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

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.