org.biopax.paxtools.pattern.miner

Class ExtendedSIFWriter

java.lang.Object

org.biopax.paxtools.pattern.miner.ExtendedSIFWriter

public class ExtendedSIFWriter
extends Object

This class is used for writing the binary interactions to a text output stream in the so called Pathway Commons EXTENDED_BINARY_SIF format.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
ExtendedSIFWriter()

Method Summary

Modifier and Type	Method and Description
static boolean	write(Set<SIFInteraction> inters, OutputStream out) Writes down the given inferred binary interactions into the output stream using the Pathway Commons one-file EXTENDED_BINARY_SIF format, where edges (interactions) are written first, followed by a single blank line, followed by the nodes section (participant details and annotations).
static boolean	writeInteractions(Set<SIFInteraction> inters, OutputStream out) Writes down the given interactions into the given "edges" output stream.
static boolean	writeParticipants(Set<SIFInteraction> inters, OutputStream out) Writes down the interaction participants' (nodes) details to the given output stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtendedSIFWriter

public ExtendedSIFWriter()

Method Detail

write

public static boolean write(Set<SIFInteraction> inters,
                            OutputStream out)

Writes down the given inferred binary interactions into the output stream using the Pathway Commons one-file EXTENDED_BINARY_SIF format, where edges (interactions) are written first, followed by a single blank line, followed by the nodes section (participant details and annotations). Closes the output stream at the end.

Parameters:

inters - binary interactions

out - stream to write

Returns:

true if any output produced successfully

writeInteractions

public static boolean writeInteractions(Set<SIFInteraction> inters,
                                        OutputStream out)

Writes down the given interactions into the given "edges" output stream. Closes the stream at the end.

Parameters:

inters - binary interactions

out - stream to write

Returns:

true if any output produced successfully

writeParticipants

public static boolean writeParticipants(Set<SIFInteraction> inters,
                                        OutputStream out)

Writes down the interaction participants' (nodes) details to the given output stream. Closes the stream at the end.

Parameters:

inters - binary interactions

out - stream to write

Returns:

true if any output produced successfully