de.bioforscher.singa.structure.parser.pdb.structures

Interface StructureParser.LocalSourceStep

Enclosing class:

StructureParser

public static interface StructureParser.LocalSourceStep

Select a local source to parse from.

Method Summary

Modifier and Type	Method and Description
StructureParser.SingleBranchStep	file(File file) The file to parse.
StructureParser.SingleBranchStep	fileLocation(String location) The location of a file as a sting.
StructureParser.MultiBranchStep	fileLocations(List<String> targetStructures) The location of files as strings.
StructureParser.MultiBranchStep	files(List<File> files) The files to parse.
StructureParser.SingleBranchStep	inputStream(InputStream inputStream) Parses a structure from an input stream of a pdb file.
StructureParser.AdditionalLocalSourceStep	localPDB(StructureParser.LocalPDB localPDB) The location of a local PDB installation.
StructureParser.MultiBranchStep	localPDB(StructureParser.LocalPDB localPDB, List<String> pdbIdentifiers) The location of a local PDB installation in addition to a list of structures, that are to be parsed.
StructureParser.SingleBranchStep	localPDB(StructureParser.LocalPDB localPDB, String pdbIdentifier) The location of a local PDB installation in addition to the structure, that is to be parsed.
StructureParser.SingleBranchStep	path(Path path) The path to parse.
StructureParser.MultiBranchStep	paths(List<Path> paths) The paths to parse.

Method Detail

file

StructureParser.SingleBranchStep file(File file)

The file to parse.

Parameters:

file - The file.

Returns:

Branch selection

files

StructureParser.MultiBranchStep files(List<File> files)

The files to parse.

Parameters:

files - The files.

Returns:

Branch selection

path

StructureParser.SingleBranchStep path(Path path)

The path to parse.

Parameters:

path - The path.

Returns:

Branch selection

paths

StructureParser.MultiBranchStep paths(List<Path> paths)

The paths to parse.

Parameters:

paths - The paths.

Returns:

Branch selection

localPDB

StructureParser.AdditionalLocalSourceStep localPDB(StructureParser.LocalPDB localPDB)

The location of a local PDB installation. This requires the input of a chin list in the following step.

Parameters:

localPDB - The local pdb.

Returns:

Additional local list file selection.

localPDB

StructureParser.SingleBranchStep localPDB(StructureParser.LocalPDB localPDB,
                                          String pdbIdentifier)

The location of a local PDB installation in addition to the structure, that is to be parsed.

Parameters:

localPDB - The local pdb.

pdbIdentifier - The PDB identifier.

Returns:

Branch selection

localPDB

StructureParser.MultiBranchStep localPDB(StructureParser.LocalPDB localPDB,
                                         List<String> pdbIdentifiers)

The location of a local PDB installation in addition to a list of structures, that are to be parsed.

Parameters:

localPDB - The local pdb.

pdbIdentifiers - The PDB identifiers.

Returns:

Branch selection

fileLocation

StructureParser.SingleBranchStep fileLocation(String location)

The location of a file as a sting.

Parameters:

location - The location.

Returns:

Branch selection

fileLocations

StructureParser.MultiBranchStep fileLocations(List<String> targetStructures)

The location of files as strings.

Parameters:

targetStructures - The locations

Returns:

Branch selection

inputStream

StructureParser.SingleBranchStep inputStream(InputStream inputStream)

Parses a structure from an input stream of a pdb file.

Parameters:

inputStream - The input stream of a pdb file.

Returns:

Branch selection