org.biopax.paxtools.pattern.miner

Class UbiquitousIDMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.UbiquitousIDMiner

All Implemented Interfaces:

Miner

public class UbiquitousIDMiner
extends MinerAdapter

Miner for getting ubiquitous small molecules in a model.

Author:

Ozgun Babur

Field Summary

Fields inherited from class org.biopax.paxtools.pattern.miner.MinerAdapter

blacklist, description, idFetcher, idMap, name, pattern

Constructor Summary

Constructors

Constructor and Description
UbiquitousIDMiner() Constructor that sets name and description.

Method Summary

Modifier and Type	Method and Description
Pattern	constructPattern() Constructs the pattern.
String	getHeader() Gets header of the result file.
String	getValue(Match m, int col) Gets the ids of the small molecule reference and its physical entities.
void	writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.

Methods inherited from class org.biopax.paxtools.pattern.miner.MinerAdapter

concat, createSIFInteraction, fetchIDs, getCellularLocations, getChain, getCompoundName, getDeltaCompartments, getDeltaModifications, getDescription, getGeneSymbol, getGeneSymbol, getIdentifiers, getIdMap, getMediatorLabels, getModifications, getModifications, getModificationTerm, getName, getPattern, getPositionInString, getPositionStart, getRelationType, getSourcePELabels, getTargetPELabels, getUniprotNameForHuman, getUniprotNameForHuman, isInhibition, labeledInactive, removeCommon, setBlacklist, setDescription, setIDFetcher, setIdMap, setName, sign, sign, toString, toStringSet, writeResultAsSIF, writeResultDetailed, writeSIFsUsingSIFFramework

Methods inherited from class java.lang.Object

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

Constructor Detail

UbiquitousIDMiner

public UbiquitousIDMiner()

Constructor that sets name and description.

Method Detail

constructPattern

public Pattern constructPattern()

Constructs the pattern.

Specified by:

constructPattern in class MinerAdapter

Returns:

pattern

writeResult

public void writeResult(Map<BioPAXElement,List<Match>> matches,
                        OutputStream out)
                 throws IOException

Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.

Parameters:

matches - pattern search result

out - output stream

Throws:

IOException - when there's a problem writing to the output stream

getHeader

public String getHeader()

Gets header of the result file.

Overrides:

getHeader in class MinerAdapter

Returns:

header

getValue

public String getValue(Match m,
                       int col)

Gets the ids of the small molecule reference and its physical entities.

Overrides:

getValue in class MinerAdapter

Parameters:

m - current match

col - current column

Returns:

ubique IDs