de.mpg.biochem.mars.kcp

Class SegmentDistributionBuilder

java.lang.Object

de.mpg.biochem.mars.kcp.SegmentDistributionBuilder

public class SegmentDistributionBuilder
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
SegmentDistributionBuilder(MoleculeArchive<Molecule,MarsMetadata,MoleculeArchiveProperties<Molecule,MarsMetadata>,MoleculeArchiveIndex<Molecule,MarsMetadata>> archive, java.util.ArrayList<java.lang.String> UIDs, java.lang.String yColumnName, java.lang.String xColumnName, double start, double end, int bins, org.scijava.log.LogService logService, org.scijava.app.StatusService statusService)

Method Summary

Modifier and Type	Method and Description
void	bootstrapMolecules(int bootstrap_cycles)
void	bootstrapSegments(int bootstrap_cycles)
void	buildBootstrapDurationColumns(MarsTable table, java.util.concurrent.ConcurrentMap<java.lang.Integer,double[]> boot_distributions)
void	buildBootstrapRateColumns(MarsTable table, java.util.concurrent.ConcurrentMap<java.lang.Integer,double[]> boot_distributions)
MarsTable	buildDurationHistogram(int nThreads)
MarsTable	buildProcessivityByMoleculeHistogram(int nThreads)
MarsTable	buildProcessivityByRegionHistogram(int nThreads)
MarsTable	buildRateGaussian(int nThreads)
MarsTable	buildRateHistogram(int nThreads)
void	noBootstrapping()
void	setFilter(double filter_region_start, double filter_region_stop)
void	unsetFilter()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SegmentDistributionBuilder

public SegmentDistributionBuilder(MoleculeArchive<Molecule,MarsMetadata,MoleculeArchiveProperties<Molecule,MarsMetadata>,MoleculeArchiveIndex<Molecule,MarsMetadata>> archive,
                                  java.util.ArrayList<java.lang.String> UIDs,
                                  java.lang.String yColumnName,
                                  java.lang.String xColumnName,
                                  double start,
                                  double end,
                                  int bins,
                                  org.scijava.log.LogService logService,
                                  org.scijava.app.StatusService statusService)

Method Detail

setFilter

public void setFilter(double filter_region_start,
                      double filter_region_stop)

unsetFilter

public void unsetFilter()

bootstrapMolecules

public void bootstrapMolecules(int bootstrap_cycles)

bootstrapSegments

public void bootstrapSegments(int bootstrap_cycles)

noBootstrapping

public void noBootstrapping()

buildRateGaussian

public MarsTable buildRateGaussian(int nThreads)

buildRateHistogram

public MarsTable buildRateHistogram(int nThreads)

buildDurationHistogram

public MarsTable buildDurationHistogram(int nThreads)

buildProcessivityByMoleculeHistogram

public MarsTable buildProcessivityByMoleculeHistogram(int nThreads)

buildProcessivityByRegionHistogram

public MarsTable buildProcessivityByRegionHistogram(int nThreads)

buildBootstrapRateColumns

public void buildBootstrapRateColumns(MarsTable table,
                                      java.util.concurrent.ConcurrentMap<java.lang.Integer,double[]> boot_distributions)

buildBootstrapDurationColumns

public void buildBootstrapDurationColumns(MarsTable table,
                                          java.util.concurrent.ConcurrentMap<java.lang.Integer,double[]> boot_distributions)