apollo.analysis.filter
Class TwilightFilter

java.lang.Object
  apollo.analysis.filter.TwilightFilter

public class TwilightFilter
extends java.lang.Object

Field Summary

protected static int	certainly_bad
protected static int	certainly_good
protected static org.apache.log4j.Logger	logger
protected boolean	ref_nucleic
protected boolean	seq_nucleic

Constructor Summary

TwilightFilter()

Method Summary

FeaturePairI	cleanUpTwilightZone(FeaturePairI terminal_span, FeaturePairI internal_span, boolean both_terminal, boolean debug)
protected int	getCertainlyBad()
protected void	setCertainlyBad(int lower_bound)
protected void	setCertainlyGood(int upper_bound)
void	setRefNucleic(boolean nucleic)
void	setSeqNucleic(boolean nucleic)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

certainly_good

protected static int certainly_good

certainly_bad

protected static int certainly_bad

seq_nucleic

protected boolean seq_nucleic

ref_nucleic

protected boolean ref_nucleic

Constructor Detail

TwilightFilter

public TwilightFilter()

Method Detail

setSeqNucleic

public void setSeqNucleic(boolean nucleic)

setRefNucleic

public void setRefNucleic(boolean nucleic)

setCertainlyBad

protected void setCertainlyBad(int lower_bound)

setCertainlyGood

protected void setCertainlyGood(int upper_bound)

getCertainlyBad

protected int getCertainlyBad()

cleanUpTwilightZone

public FeaturePairI cleanUpTwilightZone(FeaturePairI terminal_span,
                                        FeaturePairI internal_span,
                                        boolean both_terminal,
                                        boolean debug)
                                 throws java.lang.Exception

Throws:

java.lang.Exception