public class FASTAdriver 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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FASTAdriver(java.lang.String threadID,
UberProperties properties)
Sets the file root, test ID, thread ID, properties, and scorer.
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FASTAdriver(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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void |
run()
Simply calls
writeFASTA(GroupScorer, String) on the internal scorer, using the name of this driver and the .FASTA extension. |
static void |
writeFASTA(GroupScorer groupScorer,
java.lang.String outputFileName)
Writes the genes of the group in group scorer to the given file.
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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 FASTAdriver(java.lang.String threadID, UberProperties properties) throws UnknownGeneException
UnknownGeneException
public FASTAdriver(java.lang.String threadID, UberProperties properties, int[] group)
public static void writeFASTA(GroupScorer groupScorer, java.lang.String outputFileName) throws java.io.IOException
java.io.IOException
public void run()
writeFASTA(GroupScorer, String)
on the internal scorer, using the name of this driver and the .FASTA extension.run
in interface java.lang.Runnable
run
in class BeamDriver