public abstract class AbstractSIFMiner extends MinerAdapter implements SIFMiner
blacklist, description, idFetcher, idMap, name, pattern
Constructor and Description |
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AbstractSIFMiner(SIFType type)
Constructor with interaction type.
|
AbstractSIFMiner(SIFType type,
String supplName,
String supplDesc)
Constructor with interaction type, supplementary name, supplementary description, and ubiquitous IDs.
|
Modifier and Type | Method and Description |
---|---|
SIFType |
getSIFType()
Gets the type of the interaction.
|
void |
setType(SIFType type) |
void |
writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the result as "A used-for-production-of B", where A and B are small molecule names,
and whitespace is tab.
|
concat, constructPattern, createSIFInteraction, fetchIDs, getCellularLocations, getChain, getCompoundName, getDeltaCompartments, getDeltaModifications, getDescription, getGeneSymbol, getGeneSymbol, getHeader, getIdentifiers, getIdMap, getMediatorLabels, getModifications, getModifications, getModificationTerm, getName, getPattern, getPositionInString, getPositionStart, getRelationType, getSourcePELabels, getTargetPELabels, getUniprotNameForHuman, getUniprotNameForHuman, getValue, isInhibition, labeledInactive, removeCommon, setBlacklist, setDescription, setIDFetcher, setIdMap, setName, sign, sign, toString, toStringSet, writeResultAsSIF, writeResultDetailed, writeSIFsUsingSIFFramework
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
createSIFInteraction, getSourceLabel, getTargetLabel, setBlacklist, setIDFetcher
getDescription, getName, getPattern
public AbstractSIFMiner(SIFType type)
type
- SIF typepublic AbstractSIFMiner(SIFType type, String supplName, String supplDesc)
type
- SIF typesupplName
- supplementary namesupplDesc
- supplemantary descriptionpublic void writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) throws IOException
writeResult
in interface Miner
matches
- pattern search resultout
- output streamIOException
- when there's a problem writing to the output streampublic SIFType getSIFType()
SIFMiner
getSIFType
in interface SIFMiner
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