Package | Description |
---|---|
org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
|
Modifier and Type | Method and Description |
---|---|
Set<SIFInteraction> |
SIFMiner.createSIFInteraction(Match m,
IDFetcher fetcher)
Creates SIF interactions for the given match.
|
Set<SIFInteraction> |
MinerAdapter.createSIFInteraction(Match m,
IDFetcher fetcher)
Creates a SIF interaction for the given match.
|
Set<SIFInteraction> |
SIFSearcher.searchSIF(Model model)
Searches the given model with the contained miners.
|
Modifier and Type | Method and Description |
---|---|
String |
SIFToText.convert(SIFInteraction inter)
Creates the textual data corresponding to the given binary interaction.
|
String |
CustomFormat.convert(SIFInteraction inter)
Prepares the line in the output file for the given interaction.
|
String |
OutputColumn.getColumnValue(SIFInteraction inter)
Get the string to write in the output file.
|
void |
SIFInteraction.mergeWith(SIFInteraction equivalent)
Merges publications of the parameter equivalent sif with this one.
|
Modifier and Type | Method and Description |
---|---|
static boolean[][] |
SIFInteraction.convertToAdjacencyMatrix(Collection<SIFInteraction> sifInts,
SIFType... type)
Converts the given collection of interactions into an adjacency matrix.
|
static List<String> |
SIFInteraction.getSortedGeneNames(Collection<SIFInteraction> sifInts,
SIFType... type)
Collects and sorts sourceID and targetID of the given collection of sif interactions.
|
static boolean |
OldFormatWriter.write(Set<SIFInteraction> inters,
OutputStream out)
Writes down the given interactions into the given output stream in the old
EXTENDED_BINARY_SIF format.
|
Copyright © 2015 BioPAX. All rights reserved.