apollo.analysis.filter
Class AnalysisFilter

java.lang.Object
  apollo.analysis.filter.AnalysisFilter

All Implemented Interfaces:

AnalysisFilterI

public class AnalysisFilter
extends java.lang.Object
implements AnalysisFilterI

Field Summary

protected static int	CHIMERA_GAP
protected static java.lang.String	default_3prime
protected AnalysisInput	filter_input
protected static org.apache.log4j.Logger	logger
protected java.lang.String	suffix_3prime

Constructor Summary

AnalysisFilter()

Method Summary

void	cleanUp(CurationSet curation, java.lang.String analysis_type, AnalysisInput filter_input) All filters on computed results must support this interface.
protected void	cleanupByType(FeatureSetI fs, java.lang.String type) Experimental--not currently being used.
void	debugFeature(SeqFeatureI sf, SeqFeatureI sf2, java.lang.String prefix, boolean force)
void	debugFeature(SeqFeatureI sf, java.lang.String prefix)
void	debugFeature(SeqFeatureI sf, java.lang.String prefix, boolean force)
java.lang.String	debugName(SeqFeatureI sf)
double	identity(SeqFeatureI span)
protected boolean	lowIdentity(FeatureSetI hit, int min_identity)
protected void	removeFragmented(FeatureSetI analysis, int max_exons)
protected void	removeGappedAlign(FeatureSetI analysis, int max_missing)
protected void	removeLowContent(FeatureSetI analysis, int wordsize, int max_ratio)
protected void	removeShorties(FeatureSetI analysis, int min_length, boolean is_percentage)
protected void	splitTandemHits(FeatureSetI analysis, AnalysisInput filter_input)
protected boolean	tooShort(FeatureSetI hit, int min_length, boolean is_percentage)

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

CHIMERA_GAP

protected static int CHIMERA_GAP

default_3prime

protected static java.lang.String default_3prime

filter_input

protected AnalysisInput filter_input

suffix_3prime

protected java.lang.String suffix_3prime

Constructor Detail

AnalysisFilter

public AnalysisFilter()

Method Detail

cleanUp

public void cleanUp(CurationSet curation,
                    java.lang.String analysis_type,
                    AnalysisInput filter_input)

Description copied from interface: AnalysisFilterI

All filters on computed results must support this interface.
It applies the filtering options contained in the hashtable to the analysis. It deletes all spans and hits that do not meet the criteria given. If a hit is left with zero spans then that hit is deleted. An analysis is of a given type and thus different analyses may have been computed with the same program, but will be filtered independently.

Specified by:

cleanUp in interface AnalysisFilterI

cleanupByType

protected void cleanupByType(FeatureSetI fs,
                             java.lang.String type)

Experimental--not currently being used.

removeShorties

protected void removeShorties(FeatureSetI analysis,
                              int min_length,
                              boolean is_percentage)

tooShort

protected boolean tooShort(FeatureSetI hit,
                           int min_length,
                           boolean is_percentage)

removeGappedAlign

protected void removeGappedAlign(FeatureSetI analysis,
                                 int max_missing)

removeFragmented

protected void removeFragmented(FeatureSetI analysis,
                                int max_exons)

removeLowContent

protected void removeLowContent(FeatureSetI analysis,
                                int wordsize,
                                int max_ratio)

splitTandemHits

protected void splitTandemHits(FeatureSetI analysis,
                               AnalysisInput filter_input)

debugName

public java.lang.String debugName(SeqFeatureI sf)

debugFeature

public void debugFeature(SeqFeatureI sf,
                         SeqFeatureI sf2,
                         java.lang.String prefix,
                         boolean force)

debugFeature

public void debugFeature(SeqFeatureI sf,
                         java.lang.String prefix)

debugFeature

public void debugFeature(SeqFeatureI sf,
                         java.lang.String prefix,
                         boolean force)

identity

public double identity(SeqFeatureI span)

lowIdentity

protected boolean lowIdentity(FeatureSetI hit,
                              int min_identity)