procope.data.networks
Class NetworkWriter

java.lang.Object
  procope.data.networks.NetworkWriter

public class NetworkWriter
extends Object

Contains different methods to write ProteinNetwork objects to files or streams. Each line of the output contains one edge, a line looks as follows:

protein1[s]protein2[s]score[s]annotations

where [s] is the separator (TAB by default). If and edge has no score or no annotations that field is simply left empty. Annotations are stored as key/ value pairs in the form key1=value1;key2=value2;....

XGMML

This class also contains an XGMML export function for protein networks. These files are compatible with Cytoscape for instance.

Author:

Jan Krumsiek

Field Summary

static String

DEFAULT_SEPARATOR Default separator for the fields of each edge: TAB

Method Summary

static void	writeNetwork(ProteinNetwork network, File outfile) Writes a network to a specified file.
static void	writeNetwork(ProteinNetwork network, File outfile, String separator) Writes a network to a specified file.
static void	writeNetwork(ProteinNetwork network, OutputStream outstream) Writes a network to a specified outputstream.
static void	writeNetwork(ProteinNetwork network, OutputStream outstream, String separator) Writes a network to a specified outputstream.
static void	writeNetwork(ProteinNetwork network, String outfile) Writes a network to a specified file.
static void	writeNetwork(ProteinNetwork network, String outfile, String separator) Writes a network to a specified file.
static void	writeXGMML(ProteinNetwork network, File outfile) Creates a Cytoscape-compatible XGMML file.
static void	writeXGMML(ProteinNetwork network, OutputStream outstream) Creates a Cytoscape-compatible XGMML file, but writes to an output stream.
static void	writeXGMML(ProteinNetwork network, 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_SEPARATOR

public static final String DEFAULT_SEPARATOR

Default separator for the fields of each edge: TAB

See Also:

Constant Field Values

Method Detail

writeNetwork

public static void writeNetwork(ProteinNetwork network,
                                String outfile)
                         throws IOException

Writes a network to a specified file. TAB will be used as a separator between the fields of each edge.

Parameters:

network - the network to be written

outfile - path to the output file

Throws:

IOException - if the file could not be written

writeNetwork

public static void writeNetwork(ProteinNetwork network,
                                String outfile,
                                String separator)
                         throws IOException

Writes a network to a specified file.

Parameters:

network - the network to be written

outfile - path to the output file

separator - separator between the fields of each edge

Throws:

IOException - if the file could not be written

writeNetwork

public static void writeNetwork(ProteinNetwork network,
                                File outfile)
                         throws IOException

Writes a network to a specified file. TAB will be used as a separator between the fields of each edge.

Parameters:

network - the network to be written

outfile - path to the output file

Throws:

IOException - if the file could not be written

writeNetwork

public static void writeNetwork(ProteinNetwork network,
                                File outfile,
                                String separator)
                         throws IOException

Writes a network to a specified file.

Parameters:

network - the network to be written

outfile - path to the output file

separator - separator between the fields of each edge

Throws:

IOException - if the file could not be written

writeNetwork

public static void writeNetwork(ProteinNetwork network,
                                OutputStream outstream)

Writes a network to a specified outputstream. TAB will be used as a separator between the fields of each edge.

Parameters:

network - the network to be written

outstream - the stream to which the network will be written

Throws:

FileNotFoundException - if the file could not be opened

writeNetwork

public static void writeNetwork(ProteinNetwork network,
                                OutputStream outstream,
                                String separator)

Writes a network to a specified outputstream.

Parameters:

network - the network to be written

outstream - the stream to which the network will be written

separator - separator between the fields of each edge

Throws:

FileNotFoundException - if the file could not be opened

writeXGMML

public static void writeXGMML(ProteinNetwork network,
                              String outfile)
                       throws IOException

Creates a Cytoscape-compatible XGMML file. The edge weights will be annotated to the graph as an attribute called weight. All other annotations are written out using their respective key.

Parameters:

network - network to be stored as XGMML

outfile - path to output file

Throws:

IOException - if the file could not be written

writeXGMML

public static void writeXGMML(ProteinNetwork network,
                              File outfile)
                       throws IOException

Creates a Cytoscape-compatible XGMML file. The edge weights will be annotated to the graph as an attribute called weight. All other annotations are written out using their respective key.

Parameters:

network - network to be stored as XGMML

outfile - path to output file

Throws:

IOException - if the file could not be written

writeXGMML

public static void writeXGMML(ProteinNetwork network,
                              OutputStream outstream)

Creates a Cytoscape-compatible XGMML file, but writes to an output stream. The edge weights will be annotated to the graph as an attribute called confidence. All other annotations are written out using their respective key.

Parameters:

network - network to be stored as XGMML

outstream - to which the XGMML will be written to

Throws:

FileNotFoundException - if the output file could not be opened