public class UbiquitousIDMiner extends MinerAdapter
blacklist, description, idFetcher, idMap, name, pattern
Constructor and Description |
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UbiquitousIDMiner()
Constructor that sets name and description.
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Modifier and Type | Method and Description |
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Pattern |
constructPattern()
Constructs the pattern.
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String |
getHeader()
Gets header of the result file.
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String |
getValue(Match m,
int col)
Gets the ids of the small molecule reference and its physical entities.
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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.
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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
public UbiquitousIDMiner()
public Pattern constructPattern()
constructPattern
in class MinerAdapter
public void writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) throws IOException
matches
- pattern search resultout
- output streamIOException
- when there's a problem writing to the output streampublic String getHeader()
getHeader
in class MinerAdapter
public String getValue(Match m, int col)
getValue
in class MinerAdapter
m
- current matchcol
- current columnCopyright © 2015 BioPAX. All rights reserved.