procope.data.complexes
Class ComplexSetWriter

java.lang.Object
  procope.data.complexes.ComplexSetWriter

public class ComplexSetWriter
extends Object

This class contains static methods to write complex sets to files or streams. It is not instantiatable.

Complex sets are written out as one complex per line where the proteins of each complexes are seperated by a specified delimiter character (by default the TAB character).

Author:

Jan Krumsiek

See Also:

Complex, ComplexSet

Field Summary

static String

DEFAULT_DELIMITER Default delimiter which seperates the proteins of a complex: TAB

Constructor Summary

ComplexSetWriter()

Method Summary

static void	writeComplexes(ComplexSet set, File outfile) Writes a complex set to a specified file.
static void	writeComplexes(ComplexSet set, File outfile, String delimiter) Writes a complex set to a specified file.
static void	writeComplexes(ComplexSet set, OutputStream outstream) Writes a complex set to an OutputStream.
static void	writeComplexes(ComplexSet set, OutputStream outstream, String delimiter) Writes a complex set to an OutputStream.
static void	writeComplexes(ComplexSet set, String outfile) Writes a complex set to a specified file.
static void	writeComplexes(ComplexSet set, String outfile, String delimiter) Writes a complex set to a specified file.
static void	writeXGMML(ComplexSet set, ProteinNetwork net, File outfile) Creates a Cytoscape-compatible XGMML file.
static void	writeXGMML(ComplexSet set, ProteinNetwork net, OutputStream outstream) Creates a Cytoscape-compatible XGMML file, but writes to an output stream.
static void	writeXGMML(ComplexSet set, ProteinNetwork net, String outfile) Creates a Cytoscape-compatible XGMML file.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_DELIMITER

public static final String DEFAULT_DELIMITER

Default delimiter which seperates the proteins of a complex: TAB

See Also:

Constant Field Values

Constructor Detail

ComplexSetWriter

public ComplexSetWriter()

Method Detail

writeComplexes

public static void writeComplexes(ComplexSet set,
                                  String outfile)
                           throws IOException

Writes a complex set to a specified file.

Parameters:

set - the set to be written

outfile - path to the output file

Throws:

IOException - if the file could not be written

writeComplexes

public static void writeComplexes(ComplexSet set,
                                  String outfile,
                                  String delimiter)
                           throws IOException

Writes a complex set to a specified file. Accepts a custom delimiter string for the separation of proteins of a complex.

Parameters:

set - the set to be written

outfile - path to the output file

delimiter - custom delimiter character

Throws:

IOException - if the file could not be written

writeComplexes

public static void writeComplexes(ComplexSet set,
                                  File outfile)
                           throws IOException

Writes a complex set to a specified file.

Parameters:

set - the set to be written

outfile - path to the output file

Throws:

IOException - if the file could not be written

writeComplexes

public static void writeComplexes(ComplexSet set,
                                  File outfile,
                                  String delimiter)
                           throws IOException

Writes a complex set to a specified file. Accepts a custom delimiter string for the separation of proteins of a complex.

Parameters:

set - the set to be written

outfile - path to the output file

delimiter - custom delimiter character

Throws:

IOException - if the file could not be written

writeComplexes

public static void writeComplexes(ComplexSet set,
                                  OutputStream outstream)

Writes a complex set to an OutputStream.

Parameters:

set - the set to be written

outstream - output stream the complexes will be written to

writeComplexes

public static void writeComplexes(ComplexSet set,
                                  OutputStream outstream,
                                  String delimiter)

Writes a complex set to an OutputStream. Accepts a custom delimiter string for the separation of proteins of a complex.

Parameters:

set - the set to be written

outstream - output stream the complexes will be written to

delimiter - custom delimiter character

writeXGMML

public static void writeXGMML(ComplexSet set,
                              ProteinNetwork net,
                              String outfile)
                       throws IOException

Creates a Cytoscape-compatible XGMML file. Optionally, a network can be specified to annotate the inner-complex edges with given weights.

Parameters:

set - complex set to be stored as XGMML

net - network for edge weights, can be null

outfile - path to output file

Throws:

IOException - if the file could not be written

writeXGMML

public static void writeXGMML(ComplexSet set,
                              ProteinNetwork net,
                              File outfile)
                       throws IOException

Creates a Cytoscape-compatible XGMML file. Optionally, a network can be specified to annotate the inner-complex edges with given weights.

Parameters:

set - complex set to be stored as XGMML

net - network for edge weights, can be null

outfile - path to output file

Throws:

IOException - if the file could not be written

writeXGMML

public static void writeXGMML(ComplexSet set,
                              ProteinNetwork net,
                              OutputStream outstream)

Creates a Cytoscape-compatible XGMML file, but writes to an output stream. Optionally, a network can be specified to annotate the inner-complex edges with given weights.

Parameters:

set - complex set to be stored as XGMML

net - network for edge weights, can be null

outstream - outstream to which the XGMML will be written to

Throws:

FileNotFoundException - if the output file could not be opened