Package org.biopax.paxtools.pattern.miner

Class ControlsStateChangeDetailedMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner

All Implemented Interfaces:

Miner

public class ControlsStateChangeDetailedMiner
extends MinerAdapter

Miner for the controls-state-change-detailed pattern. Different from the controls-state-change pattern, this miner also records the modifications of the controller, and gained and lost modifications of the changed gene.

Author:

Ozgun Babur

Field Summary

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

blacklist, description, idFetcher, idMap, name

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Pattern	constructPattern()	Constructs the pattern.
String	getHeader()	Gets the header of the result file.
String	getValue(Match m, int col)	Creates values for the result file columns.
void	writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the result as "A modifications-of-A B gains-of-B loss-of-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 Details

ControlsStateChangeDetailedMiner

public ControlsStateChangeDetailedMiner()

Constructor that sets name and description.

Method Details

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 modifications-of-A B gains-of-B loss-of-B", where A and B are gene symbols, and whitespace is tab. Modifications are comma separated.

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 the header of the result file.

Overrides:

getHeader in class MinerAdapter

Returns:

header

getValue

public String getValue(Match m,
 int col)

Creates values for the result file columns.

Overrides:

getValue in class MinerAdapter

Parameters:

m - current match

col - current column

Returns:

value of the given match at the given column