public class WebDriverJr extends BeamDriver
BeamDriver
that has been modified so that WebDriver
can run it as a child process. Contains a main
method that calls Print.blockUnforcedPrints()
and runs super.runBeamPlus()
. Nothing is
ouotput to file-- instead, Print.forcePrintln()
is used to send the results of each stage of runBeamPlus()
to stdio. If an exception occurs, it is written to stderr.Modifier and Type | Field and Description |
---|---|
(package private) static org.apache.log4j.Logger |
logger |
AMBIGUIZER_NAME, BEAM_NAME, BIPARTITE_NAME, bpScorer, error, fileRoot, knownMotifs, MERGED_NAME, properties, scorer, subtestID, testID, verboseSave
Constructor and Description |
---|
WebDriverJr(java.lang.String threadID,
UberProperties properties,
int[] group)
|
WebDriverJr(java.lang.String threadID,
UberProperties properties,
java.lang.String[] group)
|
Modifier and Type | Method and Description |
---|---|
static void |
main(java.lang.String[] args)
Allows
WebDriver to do its dirty work in a child process. |
void |
printBestMotif(Motif m)
Need to override this to do nothing so that files don't get written.
|
protected void |
printResults(Motif[] motifs,
java.lang.String stageName)
Uses
Print.forcePrintln() to print the results for a stage to stdio. |
void |
saveFilterResults(Motif[] motifs,
java.lang.String section,
Stopwatch timer)
Uses
printResults(Motif[], String) to print to stdio the filtered results of only the stages that were actually run. |
void |
saveProperties()
Need to override this to do nothing so that files don't get written.
|
void |
saveResults(Motif[] motifs,
java.lang.String id,
Stopwatch timer,
MotifComparator comp)
Uses
printResults(Motif[], String) to print to stdio only the final merged results. |
void |
saveSpecialStats(Motif[] motifs,
Stopwatch timer)
Need to override this to do nothing so that files don't get written.
|
getScorer, refineBipartite, run, runAmbiguizerEtc, runBeamEtc, runBeamPlus, runBipartitesEtc, runFilterEtc, runMergeEtc, 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 WebDriverJr(java.lang.String threadID, UberProperties properties, int[] group) throws java.io.IOException, UnknownGeneException
java.io.IOException
UnknownGeneException
public WebDriverJr(java.lang.String threadID, UberProperties properties, java.lang.String[] group) throws java.io.IOException, UnknownGeneException
java.io.IOException
UnknownGeneException
public static void main(java.lang.String[] args)
WebDriver
to do its dirty work in a child process.
First, Print.blockUnforcedPrints()
is called so that only the output described below will get through to the parent process.
Then, we parse the command-line parameters, the first of which should be the toString()
representation of an UberProperties Object, and the second of which should be a semi-colon- or whitespace-separated list of gene names
to use as the group.
Finally, we instantiate a WebDriverJr and call runBeamPlus()
, which writes its results to stdio. These
results are formatted as follows, with stages listed in chronological order and results for each stage listed in descending order of
score:
>"stage name";"number results for stage" "motif score";"flagged motif sequence" "motif score";"flagged motif sequence" ... >"stage name";"number results for stage" ...If an exception occurs, it and it's cause chain are written to stderr as follows:
>"exception description";"number stack trace elements" "stack trace element" "stack trace element" ... >"exception description";"number stack trace elements" ... <pre>
public void printBestMotif(Motif m)
printBestMotif
in class BeamDriver
protected void printResults(Motif[] motifs, java.lang.String stageName)
Print.forcePrintln()
to print the results for a stage to stdio. Results are printed in the following format:
>"stage name";"number results for stage" "motif score";"flagged motif sequence" "motif score";"flagged motif sequence" ...
public void saveFilterResults(Motif[] motifs, java.lang.String section, Stopwatch timer) throws java.io.IOException
printResults(Motif[], String)
to print to stdio the filtered results of only the stages that were actually run.saveFilterResults
in class BeamDriver
java.io.IOException
public void saveProperties() throws java.io.IOException
saveProperties
in class BeamDriver
java.io.IOException
public void saveResults(Motif[] motifs, java.lang.String id, Stopwatch timer, MotifComparator comp) throws java.io.IOException
printResults(Motif[], String)
to print to stdio only the final merged results.saveResults
in class BeamDriver
java.io.IOException
public void saveSpecialStats(Motif[] motifs, Stopwatch timer)
saveSpecialStats
in class BeamDriver