com.pacbio.secondary.vis.data.variableresolution.model.gff

Class VariableResolutionDataSetValues

java.lang.Object

com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues

All Implemented Interfaces:

java.io.Serializable

public class VariableResolutionDataSetValues
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	VariableResolutionDataSetValues.VariableResolutionDataSetValue

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.ArrayList<java.lang.String>	basemods
protected VariableResolutionDataSetValues.VariableResolutionDataSetValue[]	data
protected boolean	hasBaseMods
protected boolean	hasCoverage
protected boolean	hasVariants
protected java.util.ArrayList<java.lang.String>	motifs

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	VariableResolutionDataSetValues()
	VariableResolutionDataSetValues(int num_contigs)
	VariableResolutionDataSetValues(int num_contigs, int num_ipds)

Method Summary

Methods

Modifier and Type	Method and Description
double	getAbsMaxIPD(int contig)
double	getAbsMaxValue()
java.util.ArrayList<java.lang.String>	getBaseMods()
boolean	getHasBaseMods()
boolean	getHasCoverage()
boolean	getHasMotifs()
boolean	getHasVariants()
double	getMaxCoverage(int contig)
double	getMaxNormIPDFwd(int contig, int ipd_idx)
double	getMaxNormIPDRev(int contig, int ipd_idx)
int	getMaxVariants(int contig)
java.util.ArrayList<java.lang.String>	getMotifs()
VariableResolutionDataSetValues.VariableResolutionDataSetValue	getValue(int contig)
void	initValues(int ipd_values)
void	setHasBaseMods(boolean b)
void	setHasBaseMods(java.util.TreeMap<java.lang.String,java.lang.Integer> map) copy motifs to string array, index is motif id
void	setHasCoverage(boolean b)
void	setHasMotifs(java.util.ArrayList<java.lang.String> motifs)
void	setHasMotifs(java.util.TreeMap<java.lang.String,java.lang.Integer> map) copy motifs to string array, index is motif id
void	setHasVariants(boolean b)
void	setMaxCoverage(int contig, double max_coverage)
void	setMaxNormIPDFwd(int contig, int ipd_idx, double d)
void	setMaxNormIPDRev(int contig, int ipd_idx, double d)
void	setMaxVariants(int contig, int max_variants)

Methods inherited from class java.lang.Object

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

Field Detail

data

protected VariableResolutionDataSetValues.VariableResolutionDataSetValue[] data

hasCoverage

protected boolean hasCoverage

hasVariants

protected boolean hasVariants

hasBaseMods

protected boolean hasBaseMods

motifs

protected java.util.ArrayList<java.lang.String> motifs

basemods

protected java.util.ArrayList<java.lang.String> basemods

Constructor Detail

VariableResolutionDataSetValues

protected VariableResolutionDataSetValues()

VariableResolutionDataSetValues

public VariableResolutionDataSetValues(int num_contigs)

Parameters:

num_contigs -

VariableResolutionDataSetValues

public VariableResolutionDataSetValues(int num_contigs,
                               int num_ipds)

Method Detail

initValues

public void initValues(int ipd_values)

getValue

public VariableResolutionDataSetValues.VariableResolutionDataSetValue getValue(int contig)

getHasCoverage

public boolean getHasCoverage()

getHasVariants

public boolean getHasVariants()

getHasBaseMods

public boolean getHasBaseMods()

getHasMotifs

public boolean getHasMotifs()

getMotifs

public java.util.ArrayList<java.lang.String> getMotifs()

getBaseMods

public java.util.ArrayList<java.lang.String> getBaseMods()

setHasCoverage

public void setHasCoverage(boolean b)

setHasVariants

public void setHasVariants(boolean b)

setHasBaseMods

public void setHasBaseMods(boolean b)

setHasMotifs

public void setHasMotifs(java.util.TreeMap<java.lang.String,java.lang.Integer> map)

copy motifs to string array, index is motif id

Parameters:

map -

setHasMotifs

public void setHasMotifs(java.util.ArrayList<java.lang.String> motifs)

setHasBaseMods

public void setHasBaseMods(java.util.TreeMap<java.lang.String,java.lang.Integer> map)

copy motifs to string array, index is motif id

Parameters:

map -

getAbsMaxValue

public double getAbsMaxValue()

getMaxCoverage

public double getMaxCoverage(int contig)

setMaxCoverage

public void setMaxCoverage(int contig,
                  double max_coverage)

getMaxVariants

public int getMaxVariants(int contig)

setMaxVariants

public void setMaxVariants(int contig,
                  int max_variants)

getMaxNormIPDFwd

public double getMaxNormIPDFwd(int contig,
                      int ipd_idx)

setMaxNormIPDFwd

public void setMaxNormIPDFwd(int contig,
                    int ipd_idx,
                    double d)

getMaxNormIPDRev

public double getMaxNormIPDRev(int contig,
                      int ipd_idx)

setMaxNormIPDRev

public void setMaxNormIPDRev(int contig,
                    int ipd_idx,
                    double d)

getAbsMaxIPD

public double getAbsMaxIPD(int contig)