public class BiologicalBeamDriver extends BeamDriver
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
FILTERED |
private java.util.HashMap<java.lang.String,Motif[]> |
moduleResults |
AMBIGUIZER_NAME, BEAM_NAME, BIPARTITE_NAME, bpScorer, error, fileRoot, knownMotifs, MERGED_NAME, properties, scorer, scorerInfoMap, subtestID, testID, verboseSave
Constructor and Description |
---|
BiologicalBeamDriver(java.lang.String threadID,
UberProperties properties)
Sets the file root, test ID, thread ID, properties, and scorer.
|
BiologicalBeamDriver(java.lang.String threadID,
UberProperties properties,
int[] group)
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the
properties.
|
Modifier and Type | Method and Description |
---|---|
protected static Motif[] |
mergeResults(Motif[][] motifs)
Merges all the given results, and returns an array without duplicates, null values or motifs containing repetitive instantiations.
|
Motif[] |
runBeamPlus()
Mirrors BeamDriver's runBeamPlus method, then reads in known motifs and evaluates how each run did.
|
Motif[] |
runFilterEtc(Motif[] motifs,
java.lang.String section,
double cutoff)
Overrides {link #super.saveResults(Motif[], String, Stopwatch, MotifComparator)} to save the results to moduleResults for later phi
scoring.
|
getScorer, printBestMotif, refineBipartite, run, runAmbiguizerEtc, runBeamEtc, runBipartitesEtc, runMergeEtc, saveFilterResults, saveProperties, saveResults, saveSpecialStats, setFastaMotifFinder, setMostParams, setVerboseSave
activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield
private static java.lang.String FILTERED
private final java.util.HashMap<java.lang.String,Motif[]> moduleResults
public BiologicalBeamDriver(java.lang.String threadID, UberProperties properties) throws UnknownGeneException
UnknownGeneException
public BiologicalBeamDriver(java.lang.String threadID, UberProperties properties, int[] group)
protected static Motif[] mergeResults(Motif[][] motifs)
public Motif[] runBeamPlus()
runBeamPlus
in class BeamDriver
public Motif[] runFilterEtc(Motif[] motifs, java.lang.String section, double cutoff) throws java.io.IOException
runFilterEtc
in class BeamDriver
java.io.IOException