public class LinearityTesterDriver extends BeamDriver
AMBIGUIZER_NAME, BEAM_NAME, BIPARTITE_NAME, bpScorer, error, fileRoot, knownMotifs, MERGED_NAME, properties, scorer, scorerInfoMap, subtestID, testID, verboseSave
Constructor and Description |
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LinearityTesterDriver(java.lang.String threadID,
UberProperties properties)
Sets the file root, test ID, thread ID, properties, and scorer.
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LinearityTesterDriver(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.
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Modifier and Type | Method and Description |
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private void |
prismISMB_table2(MotifList ml)
Generates a table of Regulon, regSize, average sig of binding sites, max delta sig, average staring phi, and max delta phi.
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void |
run()
Calls scoreFile on each file in the root directory that passes
PhiScoreDriver.SuffixFilter . |
getScorer, printBestMotif, refineBipartite, runAmbiguizerEtc, runBeamEtc, runBeamPlus, runBipartitesEtc, runFilterEtc, 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
public LinearityTesterDriver(java.lang.String threadID, UberProperties properties) throws UnknownGeneException
UnknownGeneException
public LinearityTesterDriver(java.lang.String threadID, UberProperties properties, int[] group)
private void prismISMB_table2(MotifList ml)
public void run()
PhiScoreDriver.SuffixFilter
. Throws IllegalArgumentExceptions if
the root is not a directory.run
in interface java.lang.Runnable
run
in class BeamDriver