public class BeamDriver
extends java.lang.Thread
Modifier and Type | Field and Description |
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static java.lang.String |
AMBIGUIZER_NAME |
static java.lang.String |
BEAM_NAME |
private static java.lang.String |
beamDriverScoreDataSuffix |
static java.lang.String |
BIPARTITE_NAME |
protected Scorer |
bpScorer |
protected java.lang.Throwable |
error |
protected java.lang.String |
fileRoot |
protected Motif[] |
knownMotifs |
static java.lang.String |
MERGED_NAME |
protected UberProperties |
properties |
protected Scorer |
scorer |
(package private) static java.util.Map<java.lang.String,java.lang.String> |
scorerInfoMap |
protected java.lang.String |
subtestID |
protected java.lang.String |
testID |
protected boolean |
verboseSave |
Modifier | Constructor and Description |
---|---|
protected |
BeamDriver(java.lang.String threadID)
Makes a beam driver, setting the thread ID and leaving the rest of initialization up to subclasses who want to be creative.
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BeamDriver(java.lang.String threadID,
UberProperties properties)
Makes a beam driver.
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BeamDriver(java.lang.String threadID,
UberProperties properties,
int[] group)
Makes a beam driver using the specified group instead of pulling the group ID from the properties; the group doesn't need to be sorted.
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BeamDriver(java.lang.String threadID,
UberProperties properties,
MotifFinder groupMF,
MotifFinder mf) |
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BeamDriver(java.lang.String threadID,
UberProperties properties,
java.lang.String[] group)
Makes a beam driver using the specified group instead of pulling the group ID from the properties; the group doesn't need to be sorted.
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Modifier and Type | Method and Description |
---|---|
Scorer |
getScorer() |
void |
printBestMotif(Motif m) |
Motif |
refineBipartite(Motif m)
Takes a (presumably) bipartite motif and runs it through the linear optimizer and the reconstructor.
|
void |
run()
Calls
runBeamPlus() . |
Motif[] |
runAmbiguizerEtc(Motif[] motifs)
Runs the ambiguizer and saves the output to *_ambiguizer.txt and *_ambiguizer.sum.
|
Motif[] |
runBeamEtc()
Runs beam and saves the output to *_beam.txt and *_beam.sum.
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Motif[] |
runBeamPlus()
This is the current Beam+ suite of programs.
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Motif[] |
runBipartitesEtc()
Runs bipartite beams and saves the output to *_beam.txt and *_beam.sum.
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Motif[] |
runFilterEtc(Motif[] motifs,
java.lang.String section,
double cutoff)
Runs the filter specified in properties and saves the output to *_filter.txt.
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protected Motif[] |
runMergeEtc(Motif[][] motifs)
Merges all the given results, and returns an array without duplicates, null values or motifs containing repetitive instantiations.
|
void |
saveFilterResults(Motif[] motifs,
java.lang.String section,
Stopwatch timer)
Saves the filter results to file.
|
void |
saveProperties()
Writes the properties to fileRoot + testID + subtestID with a param extention.
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void |
saveResults(Motif[] motifs,
java.lang.String id,
Stopwatch timer,
MotifComparator comp)
Saves the ambiguizer results and stats to file.
|
void |
saveSpecialStats(Motif[] motifs,
Stopwatch timer)
Saves the special stats to file.
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void |
setFastaMotifFinder(MotifFinder mf)
Makes mf the new motif finder.
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protected void |
setMostParams(UberProperties properties)
Sets all the member variables except scorer.
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void |
setVerboseSave(boolean b)
If true, then files will be saved after every module of execution.
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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 static final java.lang.String AMBIGUIZER_NAME
public static final java.lang.String BEAM_NAME
public static final java.lang.String BIPARTITE_NAME
public static final java.lang.String MERGED_NAME
protected java.lang.Throwable error
protected java.lang.String fileRoot
protected Motif[] knownMotifs
protected UberProperties properties
protected Scorer scorer
protected Scorer bpScorer
protected java.lang.String subtestID
protected java.lang.String testID
protected boolean verboseSave
private static final java.lang.String beamDriverScoreDataSuffix
static final java.util.Map<java.lang.String,java.lang.String> scorerInfoMap
protected BeamDriver(java.lang.String threadID)
public BeamDriver(java.lang.String threadID, UberProperties properties) throws UnknownGeneException
If you have an int[], use the other constructor;
If seq.group.key is defined, this will be used no matter what seq.group.id is set at.
If no seq.group.key is defined, then seq.group.id is used.
If seq.group.source is key or keyFile, then seq.group.key specifies that key or key file. If we're looking for a keyFile, look in the
seq.group.root directory. If seq.group.source is groupFile or fastaFile, then look in the current directory.
UnknownGeneException
public BeamDriver(java.lang.String threadID, UberProperties properties, int[] group)
public BeamDriver(java.lang.String threadID, UberProperties properties, MotifFinder groupMF, MotifFinder mf)
public BeamDriver(java.lang.String threadID, UberProperties properties, java.lang.String[] group) throws java.io.IOException, UnknownGeneException
java.io.IOException
UnknownGeneException
public Scorer getScorer()
public void printBestMotif(Motif m)
public Motif refineBipartite(Motif m)
public void run()
runBeamPlus()
.run
in interface java.lang.Runnable
run
in class java.lang.Thread
public Motif[] runAmbiguizerEtc(Motif[] motifs) throws java.io.IOException
java.io.IOException
public Motif[] runBeamEtc() throws java.io.IOException
java.io.IOException
public Motif[] runBeamPlus() throws java.io.IOException
java.io.IOException
public Motif[] runBipartitesEtc() throws java.io.IOException
java.io.IOException
public Motif[] runFilterEtc(Motif[] motifs, java.lang.String section, double cutoff) throws java.io.IOException
java.io.IOException
protected Motif[] runMergeEtc(Motif[][] motifs) throws java.io.IOException
java.io.IOException
public void saveFilterResults(Motif[] motifs, java.lang.String section, Stopwatch timer) throws java.io.IOException
java.io.IOException
public void saveProperties() throws java.io.IOException
java.io.IOException
public void saveResults(Motif[] motifs, java.lang.String id, Stopwatch timer, MotifComparator comp) throws java.io.IOException
java.io.IOException
public void saveSpecialStats(Motif[] motifs, Stopwatch timer)
public void setFastaMotifFinder(MotifFinder mf)
protected void setMostParams(UberProperties properties)
public void setVerboseSave(boolean b)